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Not all serotonergic neurons are alike

Posted in Innovations, Innovations in Neurophysiology & Neuropsychology, Neurohumoral Transmission, Neuroscience, tagged serotonin, serotoninergic neuron subtypes on November 12, 2015| Leave a Comment »

Not all serotonergic neurons are alike

Curator: Larry H Bernstein, MD, FCAP

Time for a New Definition

Researchers uncover diverse subtypes of serotonin-producing neurons

By STEPHANIE DUTCHEN Nov 5, 2015 http://hms.harvard.edu/news/time-new-definition

http://hms.harvard.edu/sites/default/files/uploads/news/Glasses_HMS.jpg

In this illustration, a pair of eyeglasses “resolves” distinct serotonin neuron subtypes (shown as brightly colored cells) on a simple map of a region called the raphe in the mouse brain. By viewing serotonin neurons through multiple “lenses”—such as single-neuron and population-scale global gene expression, developmental lineage and anatomy—researchers have revealed diverse subtypes and principles of subtype organization in the brain. Image: Mallory Rice

It used to be enough to call a serotonergic neuron a serotonergic neuron.

These brain cells make the neurotransmitter serotonin, which helps regulate mood, appetite, breathing rate, body temperature and more.

Recently, however, scientists have begun to learn that these neurons differ from one another—and that the differences likely matter in dysfunction and disease.

Last year, a team led by Harvard Medical School genetics professor Susan Dymecki defined a subgroup of serotonergic neurons in mice by showing that those cells specifically, among all serotonergic neurons, were responsible for increasing the breathing rate when too much carbon dioxide builds up in the body.

Now, Dymecki and colleagues have taken a first stab at systematically characterizing serotonergic neurons at the molecular level and defining a full set of subtypes, again in mice.

The researchers report in Neuron that serotonergic neurons come in at least six major molecular subtypes defined by distinct expression patterns of hundreds of genes. In many cases, the subtypes modulate different behaviors in the body.

By conducting a cross-disciplinary series of experiments, the researchers found that the subtypes also vary in their developmental lineage, anatomical distribution, combinations of receptors on the cell surface and electrical firing properties.

“This work reveals how diverse serotonin neurons are at the molecular level, which may help to explain how, collectively, they are able to perform so many distinct functions,” said Benjamin Okaty, a postdoctoral researcher in the Dymecki lab and co-first author of the paper.

“To have the list of molecular players that make each of these subtypes different from one another gives us an important handle on learning more about what that cell type does and how we can manipulate only that subtype,” said Dymecki. “It holds enormous therapeutic potential.”

“This is an ancient neurotransmitter system that’s implicated in many different diseases, and it’s starting to be cracked open,” said Morgan Freret, a graduate student in the Dymecki lab and co-first author of the paper. “We can now ask questions in a more systematic way about which serotonergic cells and molecules are important in, for example, pain, sleep apnea or anxiety.”

Crucially, the team also showed that a serotonergic neuron’s gene expression and function depend not only on its location in the adult brain stem, but also on its cellular ancestor in the developing brain.

“Earlier work had shown that you could explore the relationship between a mature neuronal system and the different developmental lineages that gave rise to it, but we had no idea whether it was meaningful,” said Dymecki. “We show that the molecular phenotypes of these neurons track quite tightly to their developmental origin, with anatomy making some interesting contributions as well.”

While the work was done in mice, Dymecki is optimistic that it will be replicated in humans because the serotonergic neuronal system is in a highly conserved region of the brain, meaning it tends to remain consistent across vertebrate species.

Because of this, researchers can look for the same molecular signatures in human tissue and begin to tease apart whether particular subtypes of serotonergic neurons are involved in conditions such as sudden infant death syndrome (SIDS) or autism.

Such research could ultimately reveal previously unknown contributions of the serotonergic neuronal system to disease, inform the development of biomarkers or lead to more targeted therapies.

The team’s findings could also inform stem cell research. “Which subtype of serotonergic neuron are we getting when we use current stem cell protocols?” asked Dymecki. “Can we drive the development of different subtypes? Can we watch how gene expression patterns change over time during development for each subtype?”

Finally, the study provides an example of a highly integrative approach to understanding brain function at multiple scales, “linking genes and gene networks to the properties of single neurons and populations of neuron subtypes, all the way up to the level of animal behaviors,” said Okaty. “I think it’s a useful template going forward. Imagine what we’d learn by applying this approach to all the neurotransmitter systems in the brain.”

This research was supported by funding from the National Institutes of Health (R01 DA034022, P01 HD036379, T32 GM007753, R21 MH083613, R21 DA023643), the American SIDS Institute, a Harvard Stem Cell Institute seed grant, a NARSAD Distinguished Investigator Grant from the Brain and Behavior Foundation, and Harvard’s Blavatnik Biomedical Accelerator, which provides resources to develop early-stage biomedical technologies toward clinical applications. Harvard’s Office of Technology Development has filed a patent application on the technology.

Multi-Scale Molecular Deconstruction of the Serotonin Neuron System

Benjamin W. Okaty⁴, Morgan E. Freret⁴, Benjamin D. Rood, Rachael D. Brust, Morgan L. Hennessy, Danielle deBairos, Jun Chul Kim, Melloni N. Cook, Susan M. Dymeck

http://www.cell.com/neuron/abstract/S0896-6273(15)00873-9DOI: http://dx.doi.org/10.1016/j.neuron.2015.10.007

Highlights

•5HT neuron RNA-seq across anatomy and sublineage at population and single-cell scales
•Unbiased analyses identify 5HT neuron subtypes and organizing principles
•Differential gene expression predicts subtype-specific functions and disease associations
•In vitro drug responses, sensorimotor gating, and behaviors map to distinct subtypes

Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity—from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance.

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Size Matters

Posted in Amino acids, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Clinical Diagnostics, Clinical Genomics, Curation, Developmental biology, Gene Regulation and Evolution, Genome Biology, Innovations, Innovations in Neurophysiology & Neuropsychology, Metabolism, Mutant Gene Expression, Population Health Management, Proteomics, RNA Biology, tagged alternative splicing, Dscam1, exons, isoforms, MinION, RNA sequencing, transcripts on November 11, 2015| Leave a Comment »

Size Matters

Larry H. Bernstein, MD, FCAP, Curator

LPBI

MinION Sequencing Untangles RNA Transcripts in a Difficult Gene

By Aaron Krol

http://www.bio-itworld.com/2015/11/3/minion-sequencing-untangles-rna-transcripts-difficult-gene.html

RNA isoforms are distinct versions of the same gene. Through a process called alternative splicing, the different subunits, or “exons,” that make up a gene can be reshuffled in new combinations. Many genes have two or more mutually exclusive exons, and which ones are actually expressed as RNA and protein can have big effects on cellular behavior ― in effect, expanding the protein arsenal of the genome.

November 3, 2015 | Brenton Graveley received his first MinION shipment in April 2014, at his lab at the University of Connecticut’s Institute of Systems Genomics. His lab was among the first to unwrap one of the candy bar-sized DNA sequencers made by Oxford Nanopore Technologies, and although its accuracy was shaky and its throughput low, right away Graveley and his colleagues could see it was producing real DNA data.

“I’m still amazed to this day that it works at all,” Graveley says. “It’s like Star Trek.”

A lot of buzz around the MinION has focused on its tiny size: early adopters have plotted to take MinIONs into outbreak zones and species-hunting tromps through the rainforest, working with bare-bones labs and laptop computers. But for Graveley, the size of the DNA strands the MinION reads is just as exciting as the size of the sequencer itself. That’s because most other sequencers rely on picking up chemical reactions that become more error-prone over time, meaning DNA can only be read in short fragments. The MinION, which reads genetic material by observing single molecules of DNA as they pass through extremely narrow “nanopores,” keeps producing data for as long as DNA is moving through the pore.

“You get the read length of whatever fragment you put into the MinION,” he says. “We’ve gotten reads that are over 100 kilobases,” hundreds or even thousands of times longer than researchers can expect with most other technologies.

Now, in a paper published in Genome Biology, Graveley and two of his lab members, post-doc Mohan Bolisetty and PhD student Gopinath Rajadinakaran, have shown how these read lengths can help explain the cellular behavior of Dscam1, one of the most difficult-to-study genes known to science. Related to a gene in humans that has been linked to Down syndrome ― the name stands for “Down Syndrome Cell Adhesion Molecule” ―Dscam1 plays a fundamental role in forming the architecture of insect brains. This single gene can produce thousands of subtly different proteins, an ability that makes it both a fascinating subject of research, and almost impossible to understand using standard sequencing technology.

Determining exon connectivity in complex mRNAs by nanopore sequencing

Mohan T. Bolisetty¹²^†, Gopinath Rajadinakaran¹^† and Brenton R. Graveley¹^{*

Genome Biology 2015, 16:204 http://dx.doi.org:/10.1186/s13059-015-0777-z http://genomebiology.com/2015/16/1/204}

Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length. Here, we use the Oxford Nanopore MinION sequencer to identify 7,899 ‘full-length’ isoforms expressed from four Drosophila genes, Dscam1, MRP, Mhc, and Rdl. These results demonstrate that nanopore sequencing can be used to deconvolute individual isoforms and that it has the potential to be a powerful method for comprehensive transcriptome characterization.

High throughput RNA sequencing has revolutionized genomics and our understanding of the transcriptomes of many organisms. Most eukaryotic genes encode pre-mRNAs that are alternatively spliced [1]. In many genes, alternative splicing occurs at multiple places in the transcribed pre-mRNAs that are often located farther apart than the read lengths of most current high throughput sequencing platforms. As a result, several transcript assembly and quantitation software tools have been developed to address this [2], [3]. While these computational approaches do well with many transcripts, they generally have difficulty assembling transcripts of genes that express many isoforms. In fact, we have been unable to successfully assemble transcripts of complex alternatively spliced genes such as Dscam1 or Mhc using any transcript assembly software (data not shown). These software tools also have difficulty quantitating transcripts that have many isoforms, and for genes with distantly located alternatively spliced regions, they can only infer, and not directly measure, which isoforms may have been present in the original RNA sample [4]. For example, consider a gene containing two alternatively spliced exons located 2 kbp away from one another in the mRNA. If each exon is observed to be included at a frequency of 50 % from short read sequence data, it is impossible to determine whether there are two equally abundant isoforms that each contain or lack both exons, or four equally abundant isoforms that contain both, neither, or only one or the other exon.

Pacific Bioscience sequencing can generate read lengths sufficient to sequence full length cDNA isoforms and several groups have recently reported the use of this approach to characterize the transcriptome [5]. However, the large capital expense of this platform can be a prohibitive barrier for some users. Thus, it remains difficult to accurately and directly determine the connectivity of exons within the same transcript. The MinION nanopore sequencer from Oxford Nanopore requires a small initial financial investment, can generate extremely long reads, and has the potential to revolutionize transcriptome characterization, as well as other areas of genomics.

Several eukaryotic genes can encode hundreds to thousands of isoforms. For example, inDrosophila, 47 genes encode over 1,000 isoforms each [6]. Of these, Dscam1 is the most extensively alternatively spliced gene known and contains 115 exons, 95 of which are alternatively spliced and organized into four clusters [7]. The exon 4, 6, 9, and 17 clusters contain 12, 48, 33, and 2 exons, respectively. The exons within each cluster are spliced in a mutually exclusive manner and Dscam1 therefore has the potential to generate 38,016 different mRNA and protein isoforms. The variable exon clusters are also located far from one another in the mRNA and the exons within each cluster are up to 80 % identical to one another at the nucleotide level. Together, these characteristics present numerous challenges to characterize exon connectivity within full-length Dscam1 transcripts for any sequencing platform. Furthermore, though no other gene is as complex as Dscam1, many other genes have similar issues that confound the determination of exon connectivity.

We are interested in developing methods to perform simple and robust long-read sequencing of individual isoforms of Dscam1 and other complex alternatively spliced genes. Here, we use the Oxford Nanopore MinION to sequence ‘full-length’ cDNAs from four Drosophila genes – Rdl, MRP,Mhc, and Dscam1 – and identify a total of 7,899 distinct isoforms expressed by these four genes.

Similarity between alternative exons

We were interested in determining the feasibility of using the MinION nanopore sequencer to characterize the connectivity of distantly located exons in the mRNAs expressed from genes with complex splicing patterns. For the purposes of these experiments, we have focused on fourDrosophila genes with increasingly complex patterns of alternative splicing (Fig. 1). Resistant to dieldrin (Rdl) contains two clusters, each containing two mutually exclusive exons and therefore has the potential to generate four different isoforms (Fig. 1a). Multidrug-Resistance like Protein 1(MRP) contains two mutually exclusive exons in cluster 1 and eight mutually exclusive exons in cluster 2, and can generate 16 possible isoforms (Fig. 1b). Myosin heavy chain (Mhc) can potentially generate 180 isoforms due to five clusters of mutually exclusive exons – clusters 1 and 5 contain two exons, clusters 2 and 3 each contain three exons, and cluster 4 contains five exons. Finally, Dscam1 contains 12 exon 4 variants, 48 exon 6 variants, 33 exon 9 variants (Fig. 1d), and two exon 17 variants (not shown) and can potentially express 38,016 isoforms. For this study, however, we have focused only on the exon 3 through exon 10 region of Dscam1, which encompasses the 93 exon 4, 6, and 9 variants, and 19,008 potential isoforms (Fig. 1d).

Fig. 1. Schematic of the exon-intron structures of the genes examined in this study. a The Rdl gene contains two clusters (cluster one and two) which each contain two mutually exclusive exons. b The MRP gene contains contains two and eight mutually exclusive exons in clusters 1 and 2, respectively. c Mhc contains two mutually exclusive exons in clusters 1 and 5, three mutually exclusive exons in clusters 2 and 3, and five mutually exclusive exons in cluster 4. d The Dscam1 gene contains 12, 48, and 33 mutually exclusive exons in the exon 4, 6, and 9 clusters, respectively. For each gene, the constitutive exons are colored blue, while the variable exons are colored yellow, red, orange, green, or light blue

Because our nanopore sequence analysis pipeline uses LAST to perform alignments [8], we aligned all of the Rdl, MRP, Mhc, and Dscam1 exons within each cluster to one another using LAST to determine the extent of discrimination needed to accurately assign nanopore reads to a specific exon variant. For Rdl, each variable exon was only aligned to itself, and not to the other exon in the same cluster (data not shown). For MRP, the two exons within cluster 1 only align to themselves, and though the eight variable exons in cluster 2 do align to other exons, there is sufficient specificity to accurately assign nanopore reads to individual exons (Fig. 2a). For Mhc, the variable exons in cluster 1 and cluster 5 do not align to other exons, and the variable exons in cluster 2, cluster 3, and cluster 4 again align with sufficient discrimination to identify the precise exon present in the nanopore reads (Fig. 2b). Finally, for Dscam1, the difference in the LAST alignment scores between the best alignment (each exon to itself) and the second, third, and fourth best alignments are sufficient to identify the Dscam1 exon variant (Fig. 2c). This analysis indicates that for each gene in this study, LAST alignment scores are sufficiently distinct to identify the variable exons present in each nanopore read.

Fig. 2. Similarity distance between the variable alternative exons of MRP,Mhc, and Dscam1. a Violin plots of the LAST alignment scores of each variable exon within MRP cluster 1 and MRP cluster 2 to themselves and the second (2nd) best alignments. b Violin plots of the LAST alignment scores of each variable exon within each Mhc cluster to themselves and the second (2nd) best alignments. c Violin plots of the LAST alignment scores of each variable exon within each Dscam1 cluster to themselves (1st), and to the exons with the second (2nd), third (3rd) and fourth (4th) best alignments

Optimizing template switching in Dscam1 cDNA libraries

Template switching can occur frequently when libraries are prepared by PCR and can confound the interpretation of results [9], [10]. For example, CAM-Seq [11] and a similar method we independently developed called Triple-Read sequencing [12] to characterize Dscam1 isoforms, were found to have excessive template switching due to amplification during the library prep protocols. To assess template switching in our current study, we generated a spike-in mixture of in vitro transcribed RNAs representing six unique Dscam1 isoforms – Dscam1 ^{4.2,6.32,9.31} , Dscam1^{4.1,6.46,9.30} , Dscam1 ^4.3,6.33,9.9 , Dscam1 ^{4.12,6.44,9.32} , Dscam1 ^4.7,6.8,9.15 , and Dscam1 ^4.5,6.4,9.4. We used 10 pg of this control spike-in mixture and prepared libraries for MinION sequencing by amplifying the exon 3 through exon 10 region for 20, 25, or 30 cycles of RT-PCR. We then end-repaired and dA-tailed the fragments, ligated adapters, and sequenced the samples on a MinION (7.3) for 12 h each. We obtained 33,736, 8,961, and 7,511 base-called reads from the 20, 25, and 30 cycle libraries, respectively. Consistent with the size of the exon 3 to 10 cDNA fragment being 1,806–1,860 bp in length, depending on the precise combination of exons it contains, most reads we observed were in this size range (Fig. 3a). We used Poretools [13] to convert the raw output files into fasta format and then used LAST to align the reads to a LAST database containing each variable exon. From these alignments, we identified reads that mapped to all three exon clusters, as well as the exon with the best alignment score within each cluster. When examining the alignments to each cluster independently, we found that for these spike-in libraries, all reads mapped uniquely to the exons present in the input isoforms. Therefore, any observed isoforms that were not present in the input pool were a result of template switching during the RT-PCR and library prep protocol and not due to false alignments or sequencing errors.

Fig. 3. Optimized RT-PCR minimizes template-switching for MinION sequencing. a Histogram of read lengths from MinION sequencing ofDscam1 spike-ins from the library generated using 25 cycles of PCR. bBar plot indicating the extent of template switching in Dscam1 spike-ins at different PCR cycles (left). The blue portions indicate the fraction of reads corresponding to input isoforms while the red portions correspond to the fraction of reads corresponding to template-switched isoforms. On the right, plots of the rank order versus number of reads (log10) for the 20, 25, and 30 cycle libraries. The blue dots indicate input isoforms while the red portions correspond to template-switched isoforms

When comparing the combinations of exons within each read to the input isoforms, we observed that 32 % of the reads from the 30 cycle library corresponded to isoforms generated by template switching (Fig. 3b). The template-switched isoforms observed by the greatest number of reads in the 30 cycle library were due to template switching between the two most frequently sequenced input isoforms. In most cases, template switching occurred somewhere within exon 7 or 8 and resulted in a change in exon 9. However, the extent of template switching was reduced to only 1 % in the libraries prepared using 25 cycles, and to 0.2 % in the libraries prepared using 20 cycles of PCR (Fig. 3b). Again, for these two libraries the most frequently sequenced template-switched isoforms involved the input isoforms that were also the most frequently sequenced. These experiments demonstrate that the MinION nanopore sequencer can be used to sequence ‘full length’ Dscam1 cDNAs with sufficient accuracy to identify isoforms and that the cDNA libraries can be prepared in a manner that results in a very small amount of template switching.

Dscam1 isoforms observed in adult heads

To explore the diversity of Dscam1 isoforms expressed in a biological sample, we prepared aDscam1 library from RNA isolated from D. melanogaster heads prepared from mixed male and female adults using 25 cycles of PCR and sequenced it for 12 h on the MinION nanopore sequencer obtaining a total of 159,948 reads of which 78,097 were template reads, 48,474 were complement reads, and 33,377 were 2D reads (Fig. 4a). We aligned the reads individually to the exon 4, 6, and 9 variants using LAST. A total of 28,971 reads could be uniquely or preferentially aligned to a single variant in all three clusters. For further analysis, we used all 16,419 2D read alignments and 31 1D reads when both template and complement aligned to same variant exons (not all reads with both a template and complement yield a 2D read). The remaining 12,521 aligned reads were 1D reads where there was either only a template or complement read, or when the template and complement reads disagreed with one another and were therefore not used further. We observed 92 of the 93 potential exon 4, 6, or 9 variants – only exon 6.11 was not observed in any read (Fig. 4f). To assess the accuracy of the results we performed RT-PCR using primers in the flanking constitutive exons that contained Illumina sequencing primers to separately amplify the Dscam1exon 4, 6, and 9 clusters from the same RNA used to prepare the MinION libraries, and sequenced the amplicons on an Illumina MiSeq. The frequency of variable exon use in each cluster was extremely consistent between the two methods (R ² = 0.95, Fig. 5a).

Fig. 4. MinION sequencing of Dscam1 identified 7,874 isoforms. aHistogram of read length distribution for Drosophila head samples. b The total number of Dscam1 isoforms identified from MinION sequencing. cCumulative distribution of Dscam1 isoforms with respect to expression. dViolin plot of the number of isoforms identified using 100 random pools of the indicated number of reads. e Plot of the estimated number of total isoforms present in the library using the capture-recapture method with two random pools of the indicated number of reads. The shaded blue area indicates the 95 % confidence interval. f Deconvoluted expression of Dscam1 exon cluster variants (top) and the isoform connectivity of two highly expressed Dscam1 isoforms (bottom)

Fig. 5. Accuracy of Dscam1 sequencing results. a Comparison of the frequency of variable exon inclusion for the Dscam1 exon 4 (yellow), 6 (red), and 9 (orange) clusters as determined by nanopore sequencing or by amplicon sequencing using an Illumina MiSeq. b Percent identities (left) or LAST alignment scores (right) of full-length template, complement, and two directions (sequencing both template and complements) nanopore read alignments

Over their entire lengths, the 2D reads that map specifically to one exon 4, 6, and 9 variants map with an average 90.37 % identity and an average LAST score of approximately 1,200 (Fig. 5b). The 16,450 full length reads correspond to 7,874 unique isoforms, or 42 % of the 18,612 possible isoforms given the exon 4, 6, and 9 variants observed. We note, however, that while 4,385 isoforms were represented by more than one read, 3,516 of isoforms were represented by only one read indicating that the depth of sequencing has not reached saturation (Fig. 4b and c). This was further confirmed by performing a bootstrapped subsampling analysis (Fig. 4d) and by using the capture-recapture method to attempt to assess the complexity of isoforms present in the library (Fig. 4e), which suggests that over 11,000 isoforms are likely to be present, though even this analysis has not yet reached saturation. The most frequently observed isoforms were Dscam1^{4.1,6.12,9.30} and Dscam1 ^4.1,6.1,9.30 which were observed with 30 and 25 reads, respectively (Fig. 4e). In conclusion, these results demonstrate the practical application of using the MinION nanopore sequencer to identify thousands of distinct Dscam1 isoforms in a single biological sample.

Nanopore sequencing of ‘full-length’ Rdl, MRP, and Mhc isoforms

To extend this approach to other genes with complex splicing patterns, we focused on Rdl, MRP, and Mhc which have the potential to generate four, 16, and 180 isoforms, respectively. We prepared libraries for each of these genes by RT-PCR using primers in the constitutive exons flanking the most distal alternative exons using 25 cycles of PCR, pooled the three libraries and sequenced them together on the MinION nanopore sequencer for 12 h obtaining a total of 22,962 reads. The input libraries for Rdl, MRP, and Mhc were 567 bp, 1,769-1,772 bp, and 3,824 bp, respectively. The raw reads were aligned independently to LAST indexes of each cluster of variable exons. The alignment results were then used to assign reads to their respective libraries, identify reads that mapped to all variable exon clusters for each gene, and the exon with the best alignment score within each cluster. In total, we obtained 301, 337, and 112 full length reads forRdl (Fig. 6), MRP (Fig. 7), and Mhc (Fig. 8), respectively. For Rdl, both variable exons in each cluster was observed, and accordingly all four possible isoforms were observed, though in each case the first exon was observed at a much higher frequency than the second exon (Fig. 6d). Interestingly, the ratio of isoforms containing the first versus second exon in the second cluster is similar for isoforms containing either the first exon or the second exon in the first cluster indicating that the splicing of these two clusters may be independent. For MRP, both exons in the first cluster were observed and all but one of the exons in the second cluster (exon B) were observed, though the frequency at which the exons in both clusters were used varied dramatically (Fig. 7d). For example, within the first cluster, exon B was observed 333 times while exon A was observed only four times. Similarly, in the second cluster, exon A was observed 157 times whereas exons B, E, F, and G were observed 0 times, thrice, once, and twice, respectively, and exons D, E, and H were observed between 40 and 76 times. As a result, we observed only nine MRP isoforms. For Mhc, we again observed strong biases in the exons observed in each of the five clusters (Fig. 8d). In the first cluster, exon B was observed more frequently than exon A. In the second cluster, 109 of the reads corresponded to exon A, while exons B and C were observed by only two and one read, respectively. In the third cluster, exon A was not observed at all while exons B and C were observed in roughly 80 % and 20 % of reads, respectively. In the fourth cluster, exon A was observed only once, exons B and C were not observed at all, exon E was observed 13 times while exon D was present in all of the remaining reads. Finally, in the fifth cluster, only exon B was observed. As with MRP, these strong biases and near or complete absences of exons in some of the clusters severely reduces the number of possible isoforms that can be observed. In fact, of the 180 potential isoforms encoded by Mhc, we observed only 12 isoforms. Various Mhc isoforms are known to be expressed in striking spatial and temporally restricted patterns [14] and thus it is likely that other Mhc isoforms that we did not observe, could be observed by sequencing other tissue samples.

Fig. 6. MinION sequencing of Rdl identified four isoforms. a Histogram of read lengths. b The number of reads per isoform. c Cumulative distribution of isoforms with respect to expression. d The number of reads per alternative exon (top) and per isoform (below)

Fig. 7. MinION sequencing of MRP identified nine isoforms. a Histogram of read lengths. b The number of reads per isoform. c Cumulative distribution of isoforms with respect to expression. d The number of reads per alternative exon (top) and per isoform (below)

Fig. 8. MinION sequencing of Mhc identified 12 isoforms. a Histogram of read lengths. b The number of reads per isoform. c Cumulative distribution of isoforms with respect to expression. d The number of reads per alternative exon (top) and per isoform (below)

Conclusions

Here we have demonstrated that nanopore sequencing with the Oxford Nanopore MinION can be used to easily determine the connectivity of exons in a single transcript, including Dscam1, the most complicated alternatively spliced gene known in nature. This is an important advance for several reasons. First, because short-read sequence data cannot be used to conclusively determine which exons are present in the same RNA molecule, especially for complex alternatively spliced genes, long-read sequence data are necessary to fully characterize the transcript structure and exon connectivity of eukaryotic transcriptomes. Second, although the Pacific Bioscience platform can perform long-read sequencing, there are several differences between it and the Oxford Nanopore MinION that could cause users to choose one platform over the other. In general, the quality of the sequence generated by the Pacific Bioscience is higher than that currently generated by the Oxford Nanopore MinION. This is largely due to the fact that each molecule is sequenced multiple times on the Pacific Bioscience platform yielding a high quality consensus sequence whereas on the Oxford Nanopore MinION, each molecule is sequenced at most twice (in the template and complement). We have previously used the Pacific Bioscience platform to characterize Dscam1 isoforms and found that it works well, though due to the large amount of cDNA needed to generate the libraries, many cycles of PCR are necessary and we observed an extensive amount of template switching, making it impractical to use for these experiments (BRG, unpublished data). However, over the past year that we have been involved in the MAP, the quality of sequence has steadily increased. As this trend is likely to continue, the difference in sequence quality between these two platforms is almost certain to shrink. Nonetheless, as we demonstrate, the current quality of the data is more than sufficient to allow us to accurately distinguish between highly similar alternatively spliced isoforms of the most complex gene in nature. Third, the ability to accurately characterize alternatively spliced transcripts with the Oxford Nanopore MinION makes this technology accessible to a much broader range of researchers than was previously possible. This is in part due to the fact that, in contrast to all other sequencing platforms, very little capital expense is needed to acquire the sequencer. Moreover, the MinION is truly a portable sequencer that could literally be used in the field (provided one has access to an Internet connection), and due to its size, almost no laboratory space is required for its use.

Although nanopore sequencing has many exciting and potentially disruptive advantages, there are several areas in which improvement is needed. First, although we were able to accurately identify over 7,000 Dscam1 isoforms with an average identity of full-length alignments >90 %, there are several situations in which this level of accuracy will be insufficient to determine transcript structure. For instance, there are many micro-exons in the human genome [15], and these exons would be difficult to identify if they overlapped a portion of a read that contained errors. Additionally, small unannotated exons could be difficult to identify for similar reasons. Second, the current number of usable reads is lower than that which will be required to perform whole transcriptome analysis. One issue that plagues transcriptome studies is that the majority of the sequence generated comes from the most abundant transcripts. Thus, with the current throughput, numerous runs would be needed to generate a sufficient number of reads necessary to sample transcripts expressed at a low level. In fact, this is one reason that we chose in this study, to begin by targeting specific genes rather than attempting to sequence the entire transcriptome. We do note, however, that over the past year of our participation in the MAP, the throughput of the Oxford Nanopore MinION has increased, and it is reasonable to expect additional improvements in throughput that should make it possible to generate a sufficient number of long reads to deeply interrogate even the most complex transcriptome.

In conclusion, we anticipate that nanopore sequencing of whole transcriptomes, rather than targeted genes as we have performed here, will be a rapid and powerful approach for characterizing isoforms, especially with improvements in the throughput and accuracy of the technology, and the simplification and/or elimination of the time-consuming library preparations.

The Tangled Transcriptome

Graveley’s lab studies the transcriptome, the mass of RNA molecules in living cells whose job is to translate DNA into proteins. The transcriptome is a sort of snapshot of which parts of the genome are active at a given time and place. Which genes are transcribed into RNA, and in what quantities, changes from organ to organ and even cell to cell, and can vary over an organism’s lifetime or in response to environmental changes.

Of particular interest to Graveley are those RNA molecules than can take different shapes, or “isoforms,” depending on random chance or what the cell needs at a particular time. RNA isoforms are distinct versions of the same isoforms quote gene. Through a process called alternative splicing, the different subunits, or “exons,” that make up a gene can be reshuffled in new combinations. Many genes have two or more mutually exclusive exons, and which ones are actually expressed as RNA and protein can have big effects on cellular behavior ― in effect, expanding the protein arsenal of the genome.

“For the entire field of transcriptomics and gene function, knowing what isoforms are expressed is critical,” says Graveley. “Most genes are complicated, especially in humans, and have alternative splicing that occurs at multiple places.”

That brings us to the challenge of Dscam1, the world record holder for alternative splicing. In fruit flies, a particularly well-studied model organism, Dscam1 is made up of 115 exons, only 20 of which are always transcribed into RNA. The other 95 exist in four “clusters” of mutually exclusive exons, and as a result, over 38,000 possible isoforms of Dscam1 have been predicted.

“This is by far, an order of magnitude, more than any other gene,” Graveley explains. This flexibility makes sense in light of Dscam1’s function. The protein it makes helps to “identify” single neurons in the insect brain, making them distinct enough from their neighbors for these cells to assemble a neural circuit on principles of like avoiding like. In experiments where Dscam1 has been altered to make fewer RNA isoforms, the neural wiring breaks down during development, sometimes severely enough to kill the flies.

Dscam1 also plays a role in the insect immune system, another reason for it to produce a huge variety of isoforms. Each of these molecules might be more or less effective at fighting certain pathogens.

It’s frustratingly hard, however, to figure out exactly which isoforms are in a specific sample. Graveley has been working on Dscam1 in fruit flies for more than a decade, but very basic questions remain unanswered: are some isoforms more common, or more important, than others? Are all the theoretical isoforms expressed? Do the isoforms have different behaviors, or are they just arbitrary ways of tagging neurons?

Size Matters

The trouble is the current state of the art in sequencing technology, which reads just a couple of hundred DNA bases at a time. That works great for identifying which exons are present in the transcriptome, but it’s no good for saying which mix of exons any specific strand of RNA is carrying. Different exons can lie thousands of bases apart on the RNA molecule, and there’s no way to bridge the gap between reads.

Graveley has tried a lot of solutions. He’s used the outdated Sanger sequencing method, which is much slower and more labor-intensive than modern sequencers, but does span longer reads. His lab also worked out a roundabout way of reconstructing RNA transcripts with contemporary Illumina sequencers, through a combination of chemistry and computational approaches.

“It worked,” he says, “but it was complicated by a lot of library preparation artifacts, and you basically had to jury-rig a genome analyzer to do something it was not supposed to do.”

Graveley’s preferred method is to use a sequencer produced by Pacific Biosciences, which, like the MinION, is built on long-read, single-molecule technology. PacBio sequencing is much better established than nanopores, and its results are known to be reliable; it also has the high throughput typical of modern instruments. For researchers working on alternative splicing, it’s clearly the technology to beat.

Unfortunately, it’s also very expensive. So Graveley’s team set out to learn whether the MinION, a low-throughput but extremely cheap alternative, could be an adequate substitute.

For the Genome Biology paper, the team focused on a 1.8-kilobase region of Dscam1 RNA that covers 93 of the gene’s 95 alternatively spliced exons. To get their samples, they crushed fruit fly heads, isolated Dscam1 RNA from the sample using a polymerase, and reverse-transcribed it into cDNA for sequencing. They also sequenced transcripts of three other alternatively spliced genes, Rdl, MRP, and Mhc.

splicing quote

The biggest concern for new applications of the MinION is its shaky accuracy. While most sequencers can achieve comfortably over 99% consensus with reference sequences, Graveley’s group has seen only about 90% identity with the MinION. That’s actually a little better than most MinION users have managed, although the device’s accuracy has been steadily improving. Users have had to pick their projects carefully to account for this: the device is pretty reliable in resequencing studies that map DNA reads to known references, but it’s still a dubious choice for sequencing unknown genetic material from scratch (although it’s been tried).

To accurately pin down the exact isoforms in the transcriptome, the MinION didn’t have to read every RNA molecule perfectly, but it did have to come close enough to decisively tell one exon from another ― and inDscam1, those exons could be as much as 80% identical.

In fact, Graveley and his co-authors found that the MinION was very capable of this. Out of around 33,000 high-quality Dscam1 reads pulled off the sequencer, almost 29,000 were a strong match for one and only one combination of exons. To further check their accuracy, the team also sequenced the same sample on Illumina technology. While the Illumina sequencer could not give whole isoforms, it did show the same proportions of different exons, suggesting that the MinION gave a complete and unbiased picture of the sample.

“Alternative splicing, it turns out, is probably one of the ideal applications for this platform,” Graveley says. “Even with a gene as complicated as this one, we’re able to accurately distinguish the isoforms from one another. Unless you have very, very small exons, or two exons that are almost identical to each other, the accuracy is good enough.”

Make Way for PromethION

The results are good news for researchers studying the transcriptome, but the MinION probably won’t push out other methods for dealing with alternative splicing just yet. Its low throughput means that at best it can cover a very small portion of the transcriptome with each run ― and that means isolating targeted RNA transcripts, a process that can introduce new biases into the data.

“You need a lot of reads to get the whole transcriptome, and what happens is you end up sequencing boring genes like actin and tubulin, the really abundantly expressed things,” Graveley explains. Still, his data from this experiment was good enough to replicate a few earlier findings: for instance, that Dscam1 does appear to make every predicted isoform. In this experiment, his lab observed almost half the possible isoforms, containing 92 of 93 possible exons.

Meanwhile, Oxford Nanopore Technologies is working on a new instrument, the PromethION, which will contain 48 MinION-style flow cells in a battery. Graveley has already signed on to be one of the first recipients, in an access program that is likely to start in the winter.

Judging by studies like this one, the PromethION stands a good chance of becoming the instrument of choice for large-scale RNA sequencing. With Dscam1, Graveley hopes to reach high enough throughput to do functional studies, seeking to learn whether different combinations of isoforms give rise to physical or behavioral differences. He also wants to look at human genes with high levels of alternative splicing, and to test whether the MinION can accurately count total numbers of RNA isoforms.

“The fact that you can use this technology to characterize whole isoforms is very exciting,” Graveley says. “It’s going to help us start characterizing the transcriptome in ways that have been very difficult.”

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Accessing the Blood Brain Barrier for Chemotherapy

Posted in Cancer and Current Therapeutics, Clinical & Translational, Curation, Innovations in Neurophysiology & Neuropsychology, Neurodegenerative Diseases, tagged blood brain barrier, Neurology, therapeutics on November 9, 2015| Leave a Comment »

Accessing the Blood Brain Barrier for Chemotherapy

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Blood-Brain Barrier Opened Noninvasively with Focused Ultrasound for the First Time

Mon, 11/09/2015 – 9:26amby Focused Ultrasound Foundation
http://www.mdtmag.com/news/2015/11/blood-brain-barrier-opened-noninvasively-focused-ultrasound-first-time

The blood-brain barrier has been non-invasively opened in a patient for the first time. A team at Sunnybrook Health Sciences Centre in Toronto used focused ultrasound to enable temporary and targeted opening of the blood-brain barrier (BBB), allowing the more effective delivery of chemotherapy into a patient’s malignant brain tumor.

The team, led by neurosurgeon Todd Mainprize, MD, and physicist Kullervo Hynynen, PhD, infused the chemotherapy agent doxorubicin, along with tiny gas-filled bubbles, into the bloodstream of a patient with a brain tumor. They then applied focused ultrasound to areas in the tumor and surrounding brain, causing the bubbles to vibrate, loosening the tight junctions of the cells comprising the blood-brain barrier and allowing high concentrations of the chemotherapy to enter targeted tissues.

“The blood-brain barrier has been a persistent impediment to delivering valuable therapies to treat tumors,” said Dr. Mainprize. “We are encouraged that we were able to open this barrier to deliver chemotherapy directly into the brain, and we look forward to more opportunities to apply this revolutionary approach.”

This patient treatment is part of a pilot study of up to 10 patients to establish the feasibility, safety and preliminary efficacy of focused ultrasound to temporarily open the blood-brain barrier to deliver chemotherapy to brain tumors. The Focused Ultrasound Foundation is currently funding this trial through their Cornelia Flagg Keller Memorial Fund for Brain Research.

“Breaching this barrier opens up a new frontier in treating brain disorders,” said Neal Kassell, MD, Chairman of the Focused Ultrasound Foundation. “We are encouraged by the momentum building for the use of focused ultrasound to non-invasively deliver therapies for a number of brain disorders.”

Opening the blood-brain barrier in a localized region to deliver chemotherapy to a tumor is a predicate for utilizing focused ultrasound for the delivery of other drugs, DNA-loaded nanoparticles, viral vectors, and antibodies to the brain to treat a range of neurological conditions, including various types of brain tumors, Parkinson’s, Alzheimer’s and some psychiatric diseases.

The procedure was conducted using Insightec’s ExAblate Neuro system. “This first patient treatment is a technological breakthrough that may lead to many clinical applications,” said Eyal Zadicario, Vice President for R&D and Director of Neuro Programs, Insightec.

While the current trial is a first-in-human achievement, Dr. Kullervo Hynynen, senior scientist at the Sunnybrook Research Institute, has been performing similar pre-clinical studies for about a decade. His research has shown that the combination of focused ultrasound and microbubbles may not only enable drug delivery, but might also stimulate the brain’s natural responses to fight disease. For example, the temporary opening of the blood-brain barrier appears to facilitate the brain’s clearance of a key pathologic protein related to Alzheimer’s and improves cognitive function.

A recent study by Gerhard Leinenga and Jürgen Götz from the Queensland Brain Institute in Australia further corroborated Hynynen’s research, demonstrating opening the blood-brain barrier with focused ultrasound reduced brain plaques and improved memory in a mouse model of Alzheimer’s disease.

Based on these two pre-clinical studies, a pilot clinical trial using focused ultrasound to treat Alzheimer’s is being organized.

Blood-brain Barrier Opened Non-invasively for the First Time

http://www.biosciencetechnology.com/news/2015/11/blood-brain-barrier-opened-non-invasively-first-time

Scientists, for the first time, have non-invasively opened the blood-brain barrier (BBB) in a patient.

A team at Sunnybrook Health Sciences Centre in Toronto, led by neurosurgeon Todd Mainprize, M.D., used focused ultrasound technology to more effectively introduce chemotherapy drugs into a patient’s malignant brain tumor. The results were verified with a post procedure MRI scan, Mainprize said at a press conference Tuesday.

The blood-brain barrier is a protective layer that keeps harmful substances such as toxins from entering from the blood vessels into the brain. Unfortunately, it also prevents many drugs from reaching the brain in adequate doses.

At the press conference, Mainprize stressed that this is a phase one safety and concept study to show that they could pass through the BBB. He noted the operation went smoothly and the patient, a 56-year-old women, who is the first of 10 to undergo the procedure for the study, is doing well.

To breach the BBB, doctors infused a chemotherapy drug, along with tiny gas-filled bubbles, into the blood stream. Then focused ultrasound was applied to the tumor and surrounding brain, causing the bubbles to vibrate, and open the BBB so high concentrations of the chemotherapy could enter targeted tissues.

The team is actively analyzing brain tissue samples to see how much of the drug was able to enter. The findings have not been published yet, but were presented at the Focused Ultrasound Surgery Foundation meeting, according to Mainprize.

Mainprize described the device: It has 1,024 transducers that are arranged in a helmet shape that goes around the head and the forehead, and corrects for aberrations in the skull.

While the BBB has been non-invasively opened in animals, this was the first instance in humans.

“There have been hundreds and hundreds of animal models opening the blood-brain barrier, in mice, dogs, pigs, and primates, all of which have shown a very good safety profile with no changes in function behavior or hemorrhage,” Mainprize said at the press conference.

He noted that this is a reversible procedure, and the barrier is restored back to its normal function in 24 hours.

Nathan McDannold, Ph.D., associate professor of radiology at Brigham and Women’s Hospital said, “If you compare this to alternative methods, whatever risks there are, there much less than if you were invasively injecting drugs.”

The scientists believe the technology has applications beyond brain tumors, such as in Alzheimer’s and Parkinson’s diseases.

McDannold said that groups are in the process of planning a protocol that would deliver antibodies to clear amyloid proteins, associated with Alzheimer’s, and for Parkinson’s they are looking at neuroprotectives and potential gene therapies.

The trial is being funded by the Focused Ultrasound Foundation.

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Keeping Stem Cells in Check

Posted in Cell Biology, Curation, Developmental biology, Innovations, Innovations in Neurophysiology & Neuropsychology, Intellectual Property, Investment in Technological Breakthrough, Neurological Diseases, Neuroscience, Regenerative Biology and Medicine, tagged Broad Institute, regenerative medicine, stem cell biology, USC on November 5, 2015| Leave a Comment »

Keeping Stem Cells in Check

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Researchers track gene that keeps stem cells in check

“Prkci” influences whether stem cells self-renew or differentiate into more specialized cell types

http://news.usc.edu/88168/researchers-probe-a-gene-that-keeps-stem-cells-in-check/

Prkci gene

http://news.usc.edu/files/2015/10/nestin_tuj_ratreated_escells_WEB-824×549.jpg

When it comes to stem cells, too much of a good thing isn’t wonderful: Producing too many new stem cells may lead to cancer; producing too few inhibits the repair and maintenance of the body.

In a paper published in Stem Cell Reports, USC researcher In Kyoung Mah, who works in the lab of Francesca Mariani, and colleagues at the University of California, San Diego, describe a key gene that maintains this critical balance. Called Prkci, the gene influences whether stem cells self-renew to produce more stem cells or differentiate into more specialized cell types, such as blood or nerves.

In their experiments, the team grew mouse embryonic stem cells, which lacked Prkci, into embryo-like structures in the lab. Without Prkci, the stem cells favored self-renewal, generating large numbers of stem cells and, subsequently, an abundance of secondary structures.

Upon closer inspection, the stem cells lacking Prkci had many activated genes typical of stem cells, and some activated genes typical of neural, cardiac and blood-forming cells. Therefore, the loss of Prkci can also encourage stem cells to differentiate into the progenitor cells that form neurons, heart muscle and blood.

Follow the pathway

Prkci achieves these effects by activating or deactivating a well-known group of interacting genes that are part of the “Notch signaling pathway.” In the absence of Prkci, the Notch pathway produces a protein that signals to stem cells to make more stem cells. In the presence of Prkci, the Notch pathway remains silent, and stem cells differentiate into specific cell types.

These findings have implications for developing patient therapies. Even though Prkci can be active in certain skin cancers, inhibiting it might lead to unintended consequences, such as tumor overgrowth. However, for patients with certain injuries or diseases, it could be therapeutic to use small molecule inhibitors to block the activity of Prkci, thus boosting stem cell production.

“We expect that our findings will be applicable in diverse contexts and make it possible to easily generate stem cells that have typically been difficult to generate,” said Mariani, principal investigator at the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC.

Additional co-authors on the study include Rachel Soloff and Stephen Hedrick from UCSD. The research was supported by USC and the Robert E. and May R. Wright Foundation.

PRKCI protein kinase C, iota [ Homo sapiens (human) ]

http://www.ncbi.nlm.nih.gov/gene/5584

Official Symbol PRKCIprovided by HGNCOfficial
Full Name protein kinase C, iota , provided by HGNC

Primary source HGNC:HGNC:9404
See relatedEnsembl:ENSG00000163558; HPRD:02105; MIM:600539; Vega:OTTHUMG00000150214
Gene type protein coding RefSeq status

REVIEWED

Organism Homo sapiens
Lineage – Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known asPKCI; DXS1179E; nPKC-iota
Summary: This gene encodes a member of the protein kinase C (PKC) family of serine/threonine protein kinases. The PKC family comprises at least eight members, which are differentially expressed and are involved in a wide variety of cellular processes. This protein kinase is calcium-independent and phospholipid-dependent. It is not activated by phorbolesters or diacylglycerol. This kinase can be recruited to vesicle tubular clusters (VTCs) by direct interaction with the small GTPase RAB2, where this kinase phosphorylates glyceraldehyde-3-phosphate dehydrogenase (GAPD/GAPDH) and plays a role in microtubule dynamics in the early secretory pathway. This kinase is found to be necessary for BCL-ABL-mediated resistance to drug-induced apoptosis and therefore protects leukemia cells against drug-induced apoptosis. There is a single exon pseudogene mapped on chromosome X. [provided by RefSeq, Jul 2008]

A Prkci gene keeps stem cells in check

Date:: October 30, 2015
Source:: University of Southern California – Health Sciences
Summary:: When it comes to stem cells, too much of a good thing isn’t wonderful: producing too many new stem cells may lead to cancer; producing too few inhibits the repair and maintenance of the body. Medical researchers now describe a key gene in maintaining this critical balance between producing too many and too few stem cells.

Newly-discovered gene controls stem cell production

November 3, 2015 | Genetic Engineering & Biotechnology News

A scientific team from the University of Southern California (USC) and the University of California, San Diego have described an important gene that maintains a critical balance between producing too many and too few stem cells. Called Prkci, the gene influences whether stem cells self-renew to produce more stem cells, or differentiate into more specialized cell types, such as blood or nerves.

When it comes to stem cells, too much of a good thing isn’t necessarily a benefit: producing too many new stem cells may lead to cancer; making too few inhibits the repair and maintenance of the body.

In their experiments, the researchers grew mouse embryonic stem cells, which lacked Prkci, into embryo-like structures in the laboratory. Without Prkci, the stem cells favored self-renewal, generating large numbers of stem cells and, subsequently, an abundance of secondary structures.

Upon closer inspection, the stem cells lacking Prkci had many activated genes typical of stem cells, and some activated genes typical of neural, cardiac, and blood-forming cells. Therefore, the loss of Prkci can also encourage stem cells to differentiate into the progenitor cells that form neurons, heart muscle, and blood.

Prkci achieves these effects by activating or deactivating a well-known group of interacting genes that are part of the Notch signaling pathway. In the absence of Prkci, the Notch pathway produces a protein that signals to stem cells to make more stem cells. In the presence of Prkci, the Notch pathway remains silent, and stem cells differentiate into specific cell types.

“We expect that our findings will be applicable in diverse contexts and make it possible to easily generate stem cells that have typically been difficult to generate,” said Francesca Mariani, Ph.D., principal investigator at the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC.

Their study (“Atypical PKC-iota Controls Stem Cell Expansion via Regulation of the Notch Pathway”) was published in a Stem Cell Reports.

Atypical PKC-iota Controls Stem Cell Expansion via Regulation of the Notch Pathway
In Kyoung Mah,1 Rachel Soloff,2,3 Stephen M. Hedrick,2 and Francesca V. Mariani1, *
*Correspondence: fmariani@usc.edu http://dx.doi.org/10.1016/j.stemcr.2015.09.021

Mah et al., Atypical PKC-iota Controls Stem Cell Expansion via Regulation of the Notch Pathway, Stem Cell Reports (2015), http://dx.doi.org/10.1016/j.stemcr.2015.09.021

The number of stem/progenitor cells available can profoundly impact tissue homeostasis and the response to injury or disease. Here, we propose that an atypical PKC, Prkci, is a key player in regulating the switch from an expansion to a differentiation/maintenance phase via regulation of Notch, thus linking the polarity pathway with the control of stem cell self-renewal. Prkci is known to influence symmetric cell division in invertebrates; however a definitive role in mammals has not yet emerged. Using a genetic approach, we find that loss of Prkci results in a marked increase in the number of various stem/progenitor cells. The mechanism used likely involves inactivation and symmetric localization of NUMB, leading to the activation of NOTCH1 and its downstream effectors. Inhibition of atypical PKCs may be useful for boosting the production of pluripotent stem cells, multipotent stem cells, or possibly even primordial germ cells by promoting the stem cell/progenitor fate.

The control of asymmetric versus symmetric cell division in stem and progenitor cells balances self-renewal and differentiation to mediate tissue homeostasis and repair and involves key proteins that control cell polarity. In the case of excess symmetric division, too many stem-cell-like daughter cells are generated that can lead to tumor initiation and growth. Conversely, excess asymmetric cell division can severely limit the number of cells available for homeostasis and repair (Go´mez-Lo´pez et al., 2014; Inaba and Yamashita, 2012). The Notch pathway has been implicated in controlling stem cell self-renewal in a number of different contexts (Hori et al., 2013). However, how cell polarity, asymmetric cell division, and the activation of determinants ultimately impinges upon the control of stem cell expansion and maintenance is not fully understood. In this study, we examine the role of an atypical protein kinase C (aPKC), PRKCi, in stem cell self-renewal and, in particular, determine whether PRKCi acts via the Notch pathway.

PKCs are serine-threonine kinases that control many basic cellular processes and are typically classified into three subgroups—conventional, novel, and the aPKCs iota and zeta, which, in contrast to the others, are not activated by diacylglyceride or calcium. The aPKC proteins are best known for being central components of an evolutionarily conserved Par3-Par6-aPKC trimeric complex that controls cell polarity in C. elegans, Drosophila, Xenopus, zebrafish, and mammalian cells (Suzuki and Ohno, 2006).

Before Notch influences stem cell self-renewal, the regulation of cell polarity, asymmetric versus symmetric cell division, and the segregation of cell fate determinants such as NUMB may first be required (Knoblich, 2008). For example, mutational analysis in Drosophila has demonstrated that the aPKC-containing trimeric complex is required for maintaining polarity and for mediating asymmetric cell division during neurogenesis via activation and segregation of NUMB (Wirtz-Peitz et al., 2008). NUMB then functions as a cell fate determinant by inhibiting Notch signaling and preventing self-renewal (Wang et al., 2006). In mammals, the PAR3-PAR6-aPKC complex also can bind and phosphorylate NUMB in epithelial cells and can regulate the unequal distribution of Numb during asymmetric cell division (Smith et al., 2007). During mammalian neurogenesis, asymmetric division is also thought to involve the PAR3-PAR6-aPKC complex, NUMB segregation, and NOTCH activation (Bultje et al., 2009).

Mice deficient in Prkcz are grossly normal, with mild defects in secondary lymphoid organs (Leitges et al., 2001). In contrast, deficiency of the Prkci isozyme results in early embryonic lethality at embryonic day (E)9.5 (Seidl et al., 2013; Soloff et al., 2004). A few studies have investigated the conditional inactivation of Prkci; however, no dramatic changes in progenitor generation were detected in hematopoietic stem cells (HSCs) or the brain (Imai et al., 2006; Sengupta et al., 2011), although one study found evidence of a role for Prkci in controlling asymmetric cell division in the skin (Niessen et al., 2013). Analysis may be complicated by functional redundancy between the iota and zeta isoforms and/or because further studies perturbing aPKCs in specific cell lineages and/or at specific developmental stages are needed. Therefore, a complete picture for the requirement of aPKCs at different stages of mammalian development has not yet emerged.

Here, we investigate the requirement of Prkci in mouse cells using an in vitro system that bypasses early embryonic lethality. Embryonic stem (ES) cells are used to make embryoid bodies (EBs) that develop like the early post-implantation embryo in terms of lineage specification and morphology and can also be maintained in culture long enough to observe advanced stages of cellular differentiation (Desbaillets et al., 2000). Using this approach, we provide genetic evidence that inactivation of Prkci signaling leads to enhanced generation of pluripotent cells and some types of multipotent stem cells, including cells with primordial germ cell (PGC) characteristics. In addition, we provide evidence that aPKCs ultimately regulate stem cell fate via the Notch pathway

Figure 1. Prkci/ EBs Contain Cells with Pluripotency Characteristics (A and A0 ) Day (d) 12 heterozygous EBs have few OCT4/E-CAD+ cells, while null EBs contain many in clusters at the EB periphery. Inset: OCT4 (nucleus)/E-CAD (cytoplasm) double-positive cells. (B and B0 ) Adjacent sections in a null EB show that OCT4+ cells are likely also SSEA1+. (C) Dissociated day-12 Prkci/ EBs contain five to six times more OCT4+ and approximately three times more SSEA1+ cells than heterozygous EBs (three independent experiments). (D and D0 ) After 2 days in ES cell culture, no colonies are visible in null SSEA1 cultures while present in null SSEA1+ cultures (red arrows). (E–E00) SSEA1+ sorted cells can be maintained for many passages, 27+. (E) Prkci+/ sorted cells make colonies with differentiated cells at the outer edges (n = 27/35). (E0 ) Null cells form colonies with distinct edges (n = 39/45). (E00) The percentage of undifferentiated colonies is shown. ***p < 0.001.
(F) Sorted null cells express stem cell and differentiation markers at similar levels to normal ES cells (versus heterozygous EBs) (three independent experiments). (G) EBs made from null SSEA1+ sorted cells express germ layer marker genes at the indicated days. Error bars indicate mean ± SEM, three independent experiments. Scale bars, 100 mm in (A, D, and E); 25 mm in (B). See also Figure S1.

Prkci/ Cultures Have More Pluripotent Cells Even under Differentiation Conditions First, we compared Prkci null EB development to that of Prkci/ embryos. Consistent with another null allele (Seidl et al., 2013), both null embryos and EBs fail to properly cavitate (Figures S1A and S1B). The failure to cavitate is unlikely to be due to the inability to form one of the three germ layers, as null EBs express germ-layer-specific genes (Figure S1E). A failure of cavitation could alternatively be caused by an accumulation of pluripotent cells. For example, EBs generated from Timeless knockdown cells do not cavitate and contain large numbers of OCT4-expressing cells (O’Reilly et al., 2011). In addition, EBs generated with Prkcz isoform knockdown cells contain OCT4+ cells under differentiation conditions (Dutta et al., 2011; Rajendran et al., 2013). Thus, we first evaluated ES colony differentiation by alkaline phosphatase (AP) staining. After 4 days without leukemia inhibitory factor (LIF), Prkci/ ES cell colonies retained crisp boundaries and strong AP staining. In contrast, Prkci+/ colonies had uneven colony boundaries with diffuse AP staining (Figures S1F–S1F00). To definitively detect pluripotent cells, day-12 EBs were assayed for OCT4 and E-CADHERIN (E-CAD) protein expression. Prkci+/ EBs had very few OCT4/E-CAD double-positive cells (Figure 1A); however, null EBs contained large clusters of OCT4/E-CAD double-positive cells, concentrated in a peripheral zone (Figure 1A0 ). By examining adjacent sections, we found that OCT4+ cells could also be positive for stage-specific embryonic antigen 1 (SSEA1) (Figures 1B and 1B0 ). Quantification by fluorescence-activated cell sorting (FACS) analysis showed that day-12 Prkci/ EBs had more OCT4+ and SSEA1+ cells than Prkci+/ EBs (Figure 1C). We did not find any difference between heterozygous and wild-type cells with respect to the number of OCT4+ or SSEA1+ cells or in their levels of expression for Oct4, Nanog, and Sox2 (Figures S1I, S1I0 and S1J). However, we did find that Oct4, Nanog, and Sox2 were highly upregulated in OCT4+ null cells (Figure S1G). Thus, together, these data indicate that Prkci/ EBs contain large numbers of pluripotent stem cells, despite being cultured under differentiation conditions.

Functional Pluripotency Tests If primary EBs have a pluripotent population with the capacity to undergo self-renewal, they can easily form secondary EBs (O’Reilly et al., 2011). Using this assay, we found that more secondary EBs could be generated from Prkci/ versus Prkci+/ EBs, especially at days 6, 10, and 16; even when plated at a low density to control for aggregation (Figure S1H). To test whether SSEA1+ cells could maintain pluripotency long term, FACS-sorted Prkci/ SSEA1+ and SSEA1 cells were plated at a low density and maintained under ES cell culture conditions. SSEA1 cells were never able to form identifiable colonies and could not be maintained in culture (Figure 1D). SSEA1+ cells, however, formed many distinct colonies after 2 days of culture, and these cells could be maintained for over 27 passages (Figures 1D0 , 1E0 , and 1E00). Prkci+/ SSEA1+ cells formed colonies that easily differentiated at the outer edge, even in the presence of LIF (Figure 1E). In contrast Prkci/ SSEA1+ cells maintained distinct round colonies (Figure 1E0 ). Next, we determined whether null SSEA1+ cells expressed pluripotency and differentiation markers similarly to normal ES cells. Indeed, we found that Oct4, Nanog, and Sox2 were upregulated in both null SSEA1+ EB cells and heterozygous ES cells. In addition, differentiated markers (Fgf5, T, Wnt3, and Afp) and tissue stem/progenitor cell markers (neural: Nestin, Sox1, and NeuroD; cardiac: Nkx2-5 and Isl1; and hematopoietic: Gata1 and Hba-x) were downregulated in both SSEA1+ cells and heterozygous ES cells (Figure 1F). SSEA1+ cells likely have a wide range of potential, since EBs generated from these cells expressed markers for all three germ layers (Figure 1G). In addition, as expected, EBs made from null SSEA1+ cells were (F) Sorted null cells morphologically abnormal, similar to the EBs made from unsorted Prkci/ ES cells (Figure S1G0 ). Thus, taken together, several assays indicate that the OCT4 and SSEA1+ populations enriched in null EBs represent pluripotent stem cells that can self-renew and have broad differentiation capacity.

ERK1/2 Signaling during EB Development Stem cell self-renewal has been shown to require the activation of the JAK/STAT3 and PI3K/AKT pathways and the inhibition of ERK1/2 and GSK3 pathways (Kunath et al., 2007; Niwa et al., 1998; Sato et al., 2004; Watanabe et al., 2006). We found that both STAT3 and phosphorylated STAT3 levels were not grossly altered and that the p-STAT3/STAT3 ratio was similar between heterozygous and null ES cells and EBs (Figures S2A and S2B). In addition we did not see any difference in AKT, pAKT, or b-CATENIN levels when comparing heterozygous to null ES cells or EBs (Figures S2A and S2C). Thus, the effects observed by the loss of Prkci are unlikely to be due to a significant alteration in the JAK/STAT3, PI3K/AKT, or GSK3 pathways.

Next, we investigated ERK1/2 expression and activation. Consistent with other studies showing ERK1/2 activation to be downstream of Prkci in some mammalian cell types (Boeckeler et al., 2010; Litherland et al., 2010), pERK1/2 was markedly inactivated in Prkci null versus heterozygous ES cells. In addition, during differentiation, null EBs displayed strong pERK1/2 inhibition early (until day 6). Later, pERK1/2 was activated strongly, as the EB began differentiating (Figures 2A and 2B). By immunofluorescence, pERK1/2 was strongly enriched in the columnar epithelium of control EBs, while overall levels were much lower in Prkci/ EBs (Figure 2C). In addition, high OCT4 expression correlated with a marked inactivation of pERK1/2 (Figure 2C). Next, we examined Prkci/ SSEA1+ cells by western blot. We found that SSEA1+ cells isolated from day-12 null EBs had pSTAT3 expression levels similar to whole EBs, while pERK1/2 levels were low (Figure 2D). Thus, these experiments indicate that the higher numbers of pluripotent cells in null EBs correlate with a strong inactivation of ERK1/2.

Figure 2. Prkci and Pluripotency Pathways (A) ERK1/2 phosphorylation (Y202/Y204) is reduced in null ES cells and early day (d)-6 null EBs compared to heterozygous EBs and strongly increased at later stages. The first lane shows ES cells activated (A) by serum treatment 1 day after serum depletion. (B) Quantification of pERK1/2 normalized to non-phosphorylated ERK1/2 (three independent experiments; mean ± SEM; **p < 0.01). (C) pERK1/2 Y202/Y204 is strongly expressed in the columnar epithelium of heterozygous EBs that have just cavitated. Null EBs have lower expression. OCT4 and pERK1/2 expression do not co-localize. Scale bar, 100 mm. (D) pERK1/2Y202/Y204 levels are lower in null SSEA1+ sorted cells than in heterozygous or in null day-12 EBs that have undergone further differentiation. pSTAT3 and STAT levels are unchanged. See also Figure S2.

Neural Stem Cell Fate Is Favored in Prkci/ EBs It is well known that ERK/MEK inhibition is not sufficient for pluripotent stem cell maintenance (Ying et al., 2008); thus, other pathways are likely involved. Therefore, we used a TaqMan Mouse Stem Cell Pluripotency Panel (#4385363) on an OpenArray platform to investigate the mechanism of Prkci action. Day 13 and day 20 Prkci/ EBs expressed high levels of pluripotency and stemness markers versus heterozygous EBs, including Oct4, Utf1, Nodal, Xist, Fgf4, Gal, Lefty1, and Lefty2. However, interestingly, EBs also expressed markers for differentiated cell types and tissue stem cells, including Sst, Syp, and Sycp3 (neural-related genes), Isl1 (cardiac progenitor marker), Hba-x, and Cd34 (hematopoietic markers). Based on this first-pass test, we sought to determine whether loss of Prkci might favor the generation of neural, cardiac, and hematopoietic cell types and/or their progenitors.

First, we found that null EBs contained many more NESTIN- and PAX6-positive cells than heterozygous EBs (Figures 3A and 3B; Figures S3A and S3B) (neural stem A and progenitor markers) (Sansom et al., 2009; Tohyama et al., 1992). In addition, quantification of PAX6 immuno- fluorescence (easier to quantify because of its nuclear localization) using a pixel count method (Fogel et al., 2012) revealed more abundant PAX6+ cells in null EBs versus heterozygous EBs. This difference was no longer evident at day 16, presumably because most of the new neural progenitors had differentiated (Figure 3D). Indeed, differentiated neuronal markers MAP2 and TUJ1 could be expressed in null cell cultures (Figures 3C and 3C0 ). Retinoic acid (RA) treatment both in EBs and ES cells promotes neurogenesis (Xu et al., 2012). We found that, even under RA induction, null cultures contained a larger population of NESTIN+ and a smaller population of TUJ1+ cells when compared to heterozygous cultures (Figures 3E and 3F). Again, null neural progenitors were capable of undergoing some differentiation, since we could find cells expressing NEUROD, NEUN, and MAP2 (Figures 3F0 –3F000). We also assessed neurogenesis in monolayer culture, using media that promotes neural stem cell generation supplemented with a low concentration of RA (Xu et al., 2012). Similar to the EB assay, we found that null ES cells generated a larger NESTIN+ and smaller TUJ1+ population compared to heterozygous ES cells (Figures S3C and S3D). Like in EBs, MAP2- and TUJ1-positive cells could still be found in the null cultures (Figure S3D0 ). Thus, using several different neural-induction assays, we found that the absence of Prkci correlates with the production of more neural progenitors and that, although these cells may favor self-renewal, they are still capable of progressing toward differentiation.

Figure 3. Neural Stem Cell Populations Are Increased in Null EBs (A–C0 ) Prkci/ EBs (B) have more NESTINpositive cells than Prkci+/ EBs (A). (C and C0 ) MAP2 and TUJ1 are expressed in null EBs, similarly to heterozygous EBs (data not shown). (D) EBs were assessed for PAX6 expression, and the images were used for quantification (Figures S3A and S3B). The pixel count ratio of PAX6+ cells in null EBs (green) is substantially higher than that found in heterozygous EBs (black) (three independent experiments; mean ± SEM; *p < 0.05). (E–F000) Day 4 after RA treatment, Prkci/ EBs have more NESTIN- than TUJ1-positive neurons (E and F). However, null cells can still terminally differentiate into NEUROD-, NEUN-, and MAP2-positive cells (F0 –F000). Scale bars, 25 mm in (A and C) and 50 mm in (E). See also Figure S3.

The Generation of Cardiomyocyte and Erythrocyte Progenitors Is Also Favored Next, we examined ISL1 expression (a cardiac stem cell marker) by immunofluorescence and found that Prkci/ EBs contained larger ISL1 clusters compared with Prkci+/ EBs; this was confirmed using an image quantification assay (Figures 4A, 4A0 , and 4C). Differentiated cardiac cells and ventral spinal neurons can also express ISL1 (Ericson et al., 1992); therefore, we also examined Nkx2-5 expression, a better stem cell marker and regulator of cardiac progenitor determination (Brown et al., 2004), by RT-PCR and immunofluorescence. In null EBs, Nkx2-5 was upregulated (Figure 4D). In addition, in response to RA, which can promote cardiac fates in vitro (Niebruegge et al., 2008), cells expressing NKX2-5 were more prevalent in null versus heterozygous EBs (Figures 4B and 4B0 ).The abundant cardiac progenitors found in null EBs were still capable of undergoing differentiation (Figures 4E–4F0 ). Indeed, more cells exhibited the striated pattern characteristic of a-ACTININ in null versus heterozygous EBs with RA induction (Figures 4F and 4F0 ). In addition, many more Prkci/ EBs were beating after days 6 and 12 of culture (Figure 4G).

Figure 4. Cardiomyocyte and Erythrocyte Progenitors Are Increased in Prkci/ EBs (A–F0 ) In (A, A0 , E, and E0 ), Prkci/ EBs cultured without LIF have more ISL1 (cardiac progenitor marker) and a-ACTININ-positive cells compared to heterozygous EBs. (C) At day (d) 9, the pixel count ratio for ISL1 expression indicates that null EBs (green) have larger ISL1 populations than heterozygous EBs (black) (three independent experiments, n = 20 heterozygous EBs, 21 null EBs total; mean ± SEM; *p < 0.05). In (B, B0 , D, F, and F0 ), RA treatment induces more NKX2-5 (both nuclear and cytoplasmic) and a-ACTININ expression in null EBs. Arrows point to fibers in (F0 ). (G) Null EBs (green) generate more beating EBs with RA treatment compared to heterozygous EBs (black) (four independent experiments; mean ± SEM; *p < 0.05, ***p < 0.001). (H) Dissociated null EBs of different stages (green) generate more erythrocytes in a colony-forming assay (CFU-E) (four independent experiments; mean ± SEM; **p < 0.01). (I) Examples of red colonies. (J) Gene expression for primitive HSC markers is upregulated in null EBs (relative to heterozygous EBs) (three independent experiments; mean ± SEM). Scale bars, 50 mm in (A, B, and E); 100 mm in (F), and 25 mm in (I). See also Figure S4.

Hba-x expression is restricted to yolk sac blood islands and primitive erythrocyte populations (Lux et al., 2008; Trimborn et al., 1999). Cd34 is also a primitive HSC marker (Sutherland et al., 1992). Next, we determined whether the elevated expression of these markers observed with OpenArray might represent higher numbers of primitive hematopoietic progenitors. Using a colony-forming assay (Baum et al., 1992), we found that red colonies (indicative of erythrocyte differentiation; examples in Figure 4I) were produced significantly earlier and more readily from cells isolated from null versus heterozygous EBs (Figure 4H). By quantitative real-time PCR, upregulation of Hba-x and Cd34 genes confirmed the OpenArray results (Figure 4J). In addition, we found Gata1, an erythropoiesis-specific factor, and Epor, an erythropoietin receptor that mediates erythroid cell proliferation and differentiation (Chiba et al., 1991), to be highly upregulated in null versus heterozygous EBs (Figure 4J). These data suggest that the loss of Prkci promotes the generation of primitive erythroid progenitors that can differentiate into erythrocytes.

To determine whether the aforementioned tissue stem cells identified were represented in the OCT4+ population that we described earlier, we examined the expression of PAX6, ISL1, and OCT4 in adjacent EB sections. We found that cells expressing OCT4 appeared to represent a distinct population from those expressing PAX6 and ISL1 (although some cells were PAX6 and ISL1 double-positive) (Figures S4A–S4C).

Prkci/ Cells Are More Likely to Inherit NUMB/aNOTCH1 Symmetrically The enhanced production of both pluripotent and tissue stem cells suggests that the mechanism underlying the action of Prkci in these different contexts is fundamentally similar. Because the Notch pathway controls stem cell self-renewal in many contexts (Hori et al., 2013), and because previous studies implicated a connection between PRKCi function and the Notch pathway (Bultje et al., 2009; Smith et al., 2007), we examined the localization and activation of a key player in the Notch pathway, NUMB, (Inaba and Yamashita, 2012). Differences in NUMB expression were first evident in whole EBs, where polarized expression was evident in the ectodermal and endodermal epithelia of heterozygous EBs, while Prkci/ EBs exhibited a more even distribution (Figures 5A–5B0 ). To more definitively determine the inheritance of NUMB during cell division, doublets undergoing telophase or cytokinesis were scored for symmetric (evenly distributed in both cells) or asymmetric (unequally distributed) NUMB localization (examples: Figures 5C and 5C0 ). In dissociated day-10 EBs, Prkci+/ doublets displayed somewhat less symmetric versus asymmetric inheritance, while Prkci/ doublets exhibited nearly four times more symmetric versus asymmetric inheritance (Figure 5D). Although individual cells from null EBs that were OCT4+ or PAX6+ more likely to exhibit non-polarized NUMB distribution (Figures S5A and S5B), we decided to use an assay that allowed for FACS purifi- cation, followed by the more stringent doublet assay. Therefore, we chose CD24 (heat-stable antigen; BA-1), a cell-surface marker that is highly expressed in pre-differentiated neurons and neuroblasts (Pruszak et al., 2009), and tested this marker as a method to enrich for cells destined to differentiate into neurons (see Supplemental Experimental Procedures). To assess NUMB localization, FACSsorted CD24 cells isolated from the RA-treated EBs were then put in culture for 24 hr, and doublets were scored. Both Prkci/ CD24high and CD24low doublets exhibited more symmetric versus asymmetric NUMB localization when compared to Prkci+/ doublets (Figure 5E) (>23 more was observed for CD24low doublets; 1.5 ± 0.25 [null] versus 0.67 ± 0.2 [heterozygous]). Thus, in summary, loss of Prkci favors the generation of cells with symmetric NUMB distribution, even during EB differentiation. In addition, in situations where neurogenesis is stimulated (RA treatment), loss of Prkci favors symmetric NUMB distribution in both the CD24high/low subpopulations.

Because NUMB can be directly phosphorylated by aPKCs (both PRKCi and PRKCz) (Smith et al., 2007; Zhou et al., 2011), loss of Prkci might be expected to lead to decreased NUMB phosphorylation. Three NUMB phosphorylation sites—Ser7, Ser276, and Ser295—could be aPKC mediated (Smith et al., 2007). By immunofluorescence, we found that one of the most well-characterized sites (Ser276), was strongly inactivated in null versus heterozygous EBs, especially in the core (Figures 5F and 5G). Western analysis also confirmed that the levels of pNUMB (Ser276) were decreased in null versus heterozygous EBs (Figure S5F). Thus, genetic inactivation of Prkci leads to a marked decrease in the phosphorylation status of NUMB. Notch pathway inhibition by NUMB has been observed in flies and mammals (Berdnik et al., 2002; French et al., 2002). Therefore, we investigated whether reduced Numb activity in Prkci/ EBs might lead to enhanced NOTCH1 activity and the upregulation of the downstream transcriptional readouts (Meier-Stiegen et al., 2010). An overall increase in NOTCH1 activation was supported by western blot analysis showing that the level of activated NOTCH1 (aNOTCH1) was strongly increased in day 6 and day 10 null versus heterozygous EBs (Figure S5G). This was supported by immunofluorescence in EBs, where widespread strong expression of aNOTCH1 was seen in most null cells (Figures 5I and 5I0 ), while in heterozygous EBs, this pattern was observed only in the OCT4+ cells (Figures 5H and 5H0 ).

Figure 5. Prkci/ Cells Preferentially Inherit Symmetric Localization of NUMB and aNOTCH1 and Notch Signaling Is Required for Stem Cell Self-Renewal in Null Cells (A–B0 ) In (A and B), day (d)-7 heterozygous EBs have polarized NUMB localization within epithelia and strong expression in the endoderm, while null EBs have a more even distribution. (A0 and B0 ) Enlarged views. (C and C0 ) Asymmetric and symmetric NUMB expression examples. (D) Doublets from day-10 null EBs have more symmetric inheritance when compared to day-10 heterozygous doublets (three independent experiments; mean ± SEM; **p < 0.01). A red line indicates a ratio of 1 (equal percent symmetric and asymmetric). (E) CD24 high null doublets exhibited more symmetric NUMB inheritance than CD24 high heterozygous doublets (three independent experiments; mean ± SEM; *p < 0.05). A red line indicates where the ratio is 1. (F and G) Decreased pNUMB (Ser276) is evident in the core of null versus heterozygous EBs (n = 10 of each genotype). (H–I0 ) In (H and I), aNOTCH1 is strongly expressed in heterozygous EBs, including both OCT4+ and OCT4 cells, while strong aNOTCH1 expression is predominant in OCT4+ cells of null EBs (n = 10 of each genotype)). (H0 and I0 ) Enlarged views of boxed regions. OCT4+ cells are demarcated with dotted lines. (J and J0 ) OCT4+ cells express HES5 strongly in the nucleus (three independent experiments). (K) Null doublets from dissociated EBs have more symmetric aNOTCH1 inheritance compared to heterozygous doublets (three independent experiments; mean ± SEM; **p < 0.01). A red line indicates where the ratio is 1. (L) CD24high Prkci/ doublets exhibit more symmetric aNOTCH1 than CD24high heterozygous doublets (three independent experiments; mean ± SEM; *p < 0.05). A red line indicates where the ratio is 1. (M and M0 ) Examples of asymmetric and symmetric aNOTCH1 localization. (N and O) Day-3 DMSO-treated null ES colonies show strong AP staining all the way to the colony edge in (N). Treatment with 3 mM DAPT led to more differentiation in (O). (P–R) OCT4 is strongly expressed in day-4 DMSO-treated null ES cultures (P). With DAPT (Q,R), OCT4 expression is decreased. (S) Working model: In daughter cells that undergo differentiation, PRKCi can associate with PAR3 and PAR6. NUMB is recruited and directly phosphorylated. The activation of NUMB then leads to an inhibition in NOTCH1 activation and stimulation of a differentiation/maintenance program. In the absence of Prkci, the PAR3/PAR6 complex cannot assemble (although it may do so minimally with Prkcz). NUMB asymmetric localization and phosphorylation is reduced. Low levels of pNUMB are not sufficient to block NOTCH1 activation, and activated NOTCH1 preserves the stem cell self-renewal program. We suggest that PRKCi functions to drive differentiation by pushing the switch from an expansion phase that is symmetric to a differentiation and/or maintenance phase that is predominantly asymmetric. In situations of low or absent PRKCi, we propose that the expansion phase is prolonged. Scale bars, 50 mm in (A, B, F, G, H, I, J, J0 , P–R); 200 mm in (A0 and B0 ); 25 mm in (C, C0 , M, and M0 ); and 100 mm in (H0 , I0 , N, and O). See also Figure S5.

To examine the localization of aNOTCH1 and to better quantify the results seen in Figures 5H and 5I, doublets from dissociated EBs were scored. As seen with NUMB localization, null doublets were more likely to have symmetric localization of aNOTCH1 in comparison to heterozygous doublets (Figure 5K; examples in Figures 5M and 5M0 ). In addition, both CD24high and CD24low doublets from RA-treated null EBs were more likely to exhibit symmetric aNOTCH1 distribution versus doublets from RA-treated heterozygous EBs (Figure 5L; 3.46 ± 0.8 [null] versus 0.59 ± 0.06 [heterozygous] in CD24low doublets). In addition, by RT-PCR, the expression of Notch downstream genes Hes1, Hes5, Hey1, and Hey2 was increased in null versus heterozygous EBs (Figure S5I). Furthermore, HES5 by immunofluorescence was broadly expressed at similar levels in both null and heterozygous cells (Figures 5J and 5J0 ; Figures S5H and S5H0 ) but more strongly expressed in null OCT4+ cells (Figures 5J and 5J0 ). Thus, loss of Prkci is associated with NOTCH1 activation, aNOTCH1 symmetric localization, and the upregulation of Hes/Hey downstream genes in several assays.

To determine whether Notch pathway activation is required in the absence of Prkci, we examined AP activity and OCT4 expression while blocking the Notch pathway using DAPT to inhibit g-secretase (Sastre et al., 2001). DMSO-treated null ES cells stayed undifferentiated (sharp-edged colonies, strong AP staining); however, treatment of null ES cells with 3 mM DAPT led to more differentiation (AP-negative cells with cellular extensions) (Figures 5N, 5O, and S5J). In addition, OCT4 is strongly expressed in day-4 control ES cell cultures; however, in the presence of DAPT, OCT4 expression is much decreased both in monolayer culture (Figures 5P–5R) and in null EBs (48% lower OCT4+ signal versus DMSO controls, pixel counting on EB sections; data not shown). These results support the idea that activated Notch signaling is required in the absence of Prkci to see enhanced pluripotency.

Taken together, the combined effects of decreased NUMB activation, favored symmetric distribution of NUMB and aNOTCH1 and increased NOTCH1 activity support a model whereby loss of Prkci leads to sustained generation of pluripotent and some tissue stem cell populations (Figure 5S; and see Discussion).

Additional Loss of PRKCz Activity Boosts the Number of OCT4-, SSEA1-, and STELLA-Positive Cells The generation and maintenance of pluripotent stem cells from new sources or tissue stem cells for basic or translational research can be challenging, and there is need for new in vitro strategies. A PKC inhibitor (Go¨6983) that inhibits PKCa, -b, -g, -d, and -z has been used to help maintain mouse and rat ES cells in the absence of LIF (Dutta et al., 2011; Rajendran et al., 2013). Thus, we hypothesized that treating null cells with Go¨6983 might lead to better stem cell expansion compared to loss of just Prkci. In our hands, we found that, under differentiation conditions (no LIF), heterozygous ES cells treated with the inhibitor for 4 days still underwent differentiation (Figure 6A), while treated null ES cells largely stayed undifferentiated (Figure 6A0 ; Figure S6A). Drug treatment of heterozygous EBs boosted the generation of OCT4-expressing cells (Figure 6B), while treatment of null EBs resulted in an even larger OCT4+ population (Figure 6B0 ). NUMB localization was also moderately affected (Figure S6B). By cell sorting, we found that drug treatment significantly increased the percentage of OCT4+ cells in both Prkci+/ and Prkci/ EBs (Figures 6C and 6C0 ; Figures S6C and S6C0 ). Interestingly, Go¨6983 treatment also boosted the generation of SSEA1+ cells in both null and heterozygous EBs (Figures 6D and 6D0 ; Figures S6D and S6D0 ).

SSEA1 is expressed in BLIMP1-positive PGCs derived from mouse epiblast stem cells (Hayashi and Surani, 2009). Also, PGC-like cells can be derived from isolated SSEA1+/OCT4+ EB cells (Geijsen et al., 2004). Therefore, we speculated that the increase in SSEA1 and OCT4 due to Go¨6983 treatment could represent an increase in the generation of PGC-like cells instead of undifferentiated ES cells. Therefore, we examined the expression of STELLA (a PGC marker). As expected, heterozygous EBs contain small clusters of STELLA+ cells similar to EBs made of wild-type cells (Figure 6E) (Payer et al., 2006). The addition of Go¨6983 to Prkci+/ EBs induced a modest increase in the number of STELLA+ cells present in the clusters (Figure 6F). Without drug treatment, null EBs contained more clusters, and the clusters contained more STELLA+ cells when compared to heterozygous EBs (Figures 6E and 6G). Interestingly, when Prkci/ EBs were treated with Go¨6983, the generation of STELLA+ cells was strongly enhanced (Figure 6G versus Figure 6H). Because undifferentiated ES cells can still express STELLA (Payer et al., 2006), we co-stained Prkc EBs for VASA (a more differentiated PGC marker). We found many cells that were double positive (a little less than half) (Figure 6K) but also cells that expressed VASA only and STELLA only (23 more than VASA only) (Figures 6I–6K, red/green arrows). Therefore, the combined effect of loss of Prkci and PKC inhibition via Go¨6983 treatment leads to the production of STELLA and VASA+ PGC-like cells.

Figure 6. Additional Inhibition of PRKCz Results in an Even Higher Percentage of OCT4-, SSEA1-, and STELLA-Positive Cells (A and A0 ) After day 4 without LIF, heterozygous ES cells undergo differentiation in the presence of Go¨6983, while null ES cells stay as distinct colonies in (A0 ). (B and B0 ) Go¨6983 stimulates an increase in OCT4+ populations in heterozygous EBs and an even larger OCT4+ population in null EBs in (B0 , insets: green and red channels separately). (C–D0 ) An even higher percentage of cells are OCT4+ (C and C0 ) and SSEA1+ (D and D0 ) with Go¨6983 treatment (day 12, three independent experiments). (E and F) More STELLA+ clusters containing a larger number of cells are present in drugtreated heterozygous EBs. (G and H) Null EBs also have more STELLA+ clusters and cells. Drug-treated null EBs exhibit a dramatic increase in the number of STELLA+ cells. (I–K) Some cells are double positive for STELLA and VASA in drug-treated null EBs (yellow arrows). There are also VASAonly (green arrows) and STELLA-only cells (red arrows) (three independent experiments). (L–P) Treatment with ZIP results in an increase in OCT4+ and STELLA+ cells. ZIP treatment also results in more cells that are VASA+ (three independent experiments); n = 11 for Prkci+/, and n = 13 for Prkci+/ + ZIP; n = 14 for Prkci/, and n = 20 for Prkci/ + ZIP; eight EBs assayed for both STELLA and VASA expression). Scale bars, 100 mm in (A and A0 ); 50 mm in (B and B0 ); and 25 mm in (E, I, and L). See also Figure S6. 10 S.

Next, we examined whether the more specific aPKC inhibitor, ZIP, a myristolated aPKC pseudosubstrate with competitive binding to p62, had similar effects (Price and Ghosh, 2013; Tsai et al., 2015; Yao et al., 2013). We found that both heterozygous and null EBs treated with ZIP contained more OCT4+ cells compared to un-treated EBs (Figures 6L–6O). In addition, like Go¨6983, ZIP treatment resulted in a modest increase in the percentage of SSEA1+ cells found in heterozygous EBs and a strong increase in the percentage of SSEA1+ cells in null EBs (Figures S6E– S6F0 ). Furthermore, like Go¨6983, both STELLA+ and VASA+ populations were increased with ZIP treatment (Figure 6P). Thus, both pluripotent and PGC-like cells can be abundantly generated with Go¨6983 or ZIP treatment, suggesting that strategies that inhibit both PRKCi and/or PRKCz may be useful to maintain stem cell self-renewal and/or generate abundant PGC-like cells.

DISCUSSION In this report, we suggest that Prkci controls the balance between stem cell expansion and differentiation/maintenance by regulating the activation of NUMB, NOTCH1, and Hes /Hey downstream effector genes. In the absence of Prkci, the pluripotent cell fate is favored, even without LIF, yet cells still retain a broad capacity to differentiate. In addition, loss of Prkci results in enhanced generation of tissue progenitors such as neural stem cells and cardiomyocyte and erythrocyte progenitors. In contrast to recent findings on Prkcz (Dutta et al., 2011), loss of Prkci does not appear to influence STAT3, AKT, or GSK3 signaling but results in decreased ERK1/2 activation. We hypothesize that, in the absence of Prkci, although ERK1/2 inhibition may be involved, it is the decreased NUMB phosphorylation and increased NOTCH1 activation that promotes stem and progenitor cell fate. Thus, we conclude that PRKCi, a protein known to be required for cell polarity, also plays an essential role in controlling stem cell fate and generation via regulating NOTCH1 activation.

Notch Activation Drives the Decision to Self-Renew versus Differentiate Notch plays an important role in balancing stem cell selfrenewal and differentiation in a variety of stem cell types and may be one of the key downstream effectors of Prkci signaling. Sustained Notch1 activity in embryonic neural progenitors has been shown to maintain their undifferentiated state (Jadhav et al., 2006). Similarly, sustained constitutive activation of NOTCH1 stimulates the proliferation of immature cardiomyocytes in the rat myocardium (Collesi et al., 2008). In HSCs, overexpression of constitutively active NOTCH1 in hematopoietic progenitors and stem cells supports both primitive and definitive HSC selfrenewal (Stier et al., 2002). Together, these studies suggest that activation and/or sustained Notch signaling can lead to an increase in certain tissue stem cell populations. Thus, a working model for how tissue stem cell populations are favored in the absence of Prkci involves a sequence of events that ultimately leads to Notch activation. Recent studies have shown that aPKCs can be found in a complex with NUMB in both Drosophila and mammalian cells (Smith et al., 2007; Zhou et al., 2011); hence, in our working model (Figure 5S), we propose that the localization and phosphorylation of NUMB is highly dependent on the activity of PRKCi. When Prkci is downregulated or absent (as shown here), cell polarity is not promoted, leading to diffuse distribution and decreased phosphorylation of NUMB. Without active NUMB, NOTCH1 activation is enhanced, Hes/Hey genes are upregulated, and stem/progenitor fate generation is favored. To initiate differentiation, polarization could be stochastically determined but could also be dependent on external cues such as the presentation of certain ligands or extracellular matrix (ECM) proteins (Habib et al., 2013). When PRKCi is active and the cell becomes polarized, a trimeric complex is formed with PRKCi, PAR3, and PAR6. Numb is then recruited and phosphorylated, leading to Notch inactivation, the repression of downstream Hes/Hey genes, and differentiation is favored (see Figure 5S). Support for this working model comes from studies in Drosophila showing that the aPKC complex is essential for Numb activation and asymmetric localization (Knoblich, 2008; Smith et al., 2007; Wang et al., 2006). Additional studies on mouse neural progenitors show that regulating Numb localization and Notch activation is critical for maintaining the proper number of stem/progenitor cells in balance with differentiation (Bultje et al., 2009). Thus, an important function for PRKCi may be to regulate the switch between symmetric expansion of stem/progenitor cells to an asymmetric differentiation/maintenance phase. In situations of low or absent PRKCi, we propose that the expansion phase is favored. Thus, temporarily blocking either, or both, of the aPKC isozymes may be a powerful approach for expanding specific stem/progenitor populations for use in basic research or for therapeutic applications.

These studies, together with data presented here, provide genetic evidence that evolutionarily conserved polarity pathways may play a central role in NOTCH1 activation. and stem cell self-renewal in mammals. Further genetic studies using Cre transgenes that are specific for progenitors in the neural plate, primitive erythrocytes, cardiomyocytes, and other progenitors to ablate aPKC function will be needed to determine how generally this mechanism is used in diverse tissues.

Although we do not see changes in the activation status of the STAT3, AKT, or GSK3 pathway, loss of Prkci results in an inhibition of ERK1/2 (Figures 2A and 2B). This result is consistent with the findings that ERK1/2 inhibition is both correlated with and directly increases ES cell selfrenewal (Burdon et al., 1999). Modulation of ERK1/2 activity by Prkci has been observed in cancer cells and chondrocytes (Litherland et al., 2010; Murray et al., 2011). Although it is not clear whether a direct interaction exists between Prkci and ERK1/2, Prkcz directly interacts with ERK1/2 in the mouse liver and in hypoxia-exposed cells (Das et al., 2008; Peng et al., 2008). The Prkcz isozyme is still expressed in Prkci null cells but evidently cannot suf- ficiently compensate and activate the pathway normally. Furthermore, knocking down Prkcz function in ES cells does not result in ERK1/2 inhibition, suggesting that this isozyme does not impact ERK1/2 signaling in ES cells (Dutta et al., 2011). Therefore, although PRKCi may interact with ERK1/2 and be directly required for its activation, ERK1/2 inhibition could also be a readout for cells that are more stem-like. Further studies will be needed to address this question.

Utility of Inhibiting aPKC Function Loss of Prkci resulted in EBs that contained slightly more STELLA+ cells than EBs made from +/ cells. Furthermore, inhibition of both aPKC isozymes by treating Prkci null cells with the PKC inhibitor Go¨6983 or the more specific inhibitor, ZIP, strongly promoted the generation of large clusters of STELLA+ and VASA+ cells, suggesting that inhibition of both isozymes is important for PGC progenitor expansion (Figure 6). It is unclear what the mechanism for this might be; however, one possibility is that blocking both aPKCs is necessary to promote NOTCH1 activation in PGCs or in PGC progenitor cells that may ordinarily have strong inhibitions to expansion (Feng et al., 2014). Regardless of mechanism, the ability to generate PGC-like cells in culture is notoriously challenging, and our results provide a method for future studies on PGC specification and differentiation.

Expansion of stem/progenitor pools may not be desirable in the context of cancer. Prkci has been characterized as a human oncogene, a useful prognostic cancer marker, and a therapeutic target for cancer treatment. Overexpression of Prkci is found in epithelial cancers (Fields and Regala, 2007), and Prkci inhibitors are being evaluated as candidate cancer therapies (Atwood et al., 2013; Mansfield et al., 2013). However, because our results show that Prkci inhibition leads to enhanced stem cell production in vitro, Prkci inhibitor treatment as a cancer therapy might lead to unintended consequences (tumor overgrowth), depending on the context and treatment regimen. Thus, extending our findings to human stem and cancer stem cells is needed. In summary, here, we demonstrate that loss of Prkci leads to the generation of abundant pluripotent cells, even under differentiation conditions. In addition, we show that tissue stem cells such as neural stem cells, primitive erythrocytes, and cardiomyocyte progenitors can also be abundantly produced in the absence of Prkci. These increases in stem cell production correlate with decreased NUMB activation and symmetric NUMB localization and require Notch signaling. Further inhibition of Prkcz may have an additive effect and can enhance the production of PGC-like cells. Thus, Prkci (along with Prkcz) may play key roles in stem cell self-renewal and differentiation by regulating the Notch pathway. Furthermore, inhibition of Prkci and or Prkcz activity with specific small-molecule inhibitors might be a powerful method to boost stem cell production in the context of injury or disease.

SUPPLEMENTAL INFORMATION

Supplemental Information includes Supplemental Experimental Procedures, six figures, and two tables and can be found with this article online at http://dx.doi.org/10.1016/j.stemcr. 2015.09.021.

REFERENCES

Atwood, S.X., Li, M., Lee, A., Tang, J.Y., and Oro, A.E. (2013). GLI activation by atypical protein kinase C i/l regulates the growth of basal cell carcinomas. Nature 494, 484–488.

Baum, C.M., Weissman, I.L., Tsukamoto, A.S., Buckle, A.M., and Peault, B. (1992). Isolation of a candidate human hematopoietic stem-cell population. Proc. Natl. Acad. Sci. USA 89, 2804–2808.

Berdnik, D., To¨ro¨k, T., Gonza´lez-Gaita´n, M., and Knoblich, J.A. (2002). The endocytic protein alpha-Adaptin is required for numb-mediated asymmetric cell division in Drosophila.

Dev. Cell 3, 221–231. Boeckeler, K., Rosse, C., Howell, M., and Parker, P.J. (2010). Manipulating signal delivery – plasma-membrane ERK activation in aPKC-dependent migration. J. Cell Sci. 123, 2725–2732.

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USC offers a summer of stem cells for local high school students

The teens boost their scientific IQ by conducting research in USC labs

The goal of these unique programs is to educate bright young minds at the stage where they’re still formulating ideas and still open and receptive to new discoveries.

Andrew McMahon

Twenty-three local high school students spent their summer vacations in a very unusual place: the Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC.

The students celebrated their graduations this month from the USC Early Investigator High School (EiHS) and the USC CIRM Science, Technology and Research (STAR) programs. These are the only programs that offer comprehensive training in stem cell research to high school students.

“The goal of these unique programs is to educate bright young minds at the stage where they’re still formulating ideas and still open and receptive to new discoveries, and introduce them to the wonder and inspirational power of stem cell biology,” said Andrew McMahon, director of USC’s stem cell research center and the Department of Stem Cell Biology and Regenerative Medicine, and head of the university-wide USC Stem Cell initiative uniting more than 100 researchers from all disciplines.

Stem cells, ethics and public policy

Over the course of the summer, the high school students participated in either a 10-day training course or eight-week research internship, working with human stem cells in USC’s world-class laboratories.   Under the mentorship of USC faculty and graduate students, the students learned about the latest advances in regenerative medicine and explored stem cells, ethics and public policy.

Roberta Diaz Brinton, director of the CIRM STAR program, paid tribute to the accomplishments of the students.

“We’re very impressed by the caliber of science and more impressed by the caliber of young minds. These young scientists are generating the new knowledge from which stem cell biology and stem cell therapies will progress in the future,” said Brinton, professor at the USC School of Pharmacy, the USC Viterbi School of Engineering and the Keck School of Medicine of USC, and an executive committee member of USC Stem Cell.

True teamwork

Victoria Fox, director of the EiHS program, extended her thanks to everyone who contributed to the experience.

“The EiHS program was made possible by a team of very incredible people that starts with my laboratory staff and includes donors, the students, the administrators of the stem cell research center and the mentors who take the students in their laboratories,” she said. “I’m very grateful to all of these people.”

This year’s participants were selected from Harvard-Westlake School, Lifeline Education Charter School, Chadwick School and Bravo Medical Magnet High School, and many received scholarships.

“The program has motivated our students to be college-ready by giving them the opportunity to work in a university setting,” said Obed Nartey, principal of Lifeline Education Charter School. “Many of these students are the first generation to graduate from high school. For these students, college was seen as being out of reach until they met and worked with Dr. Fox and her team.”

On graduation day, the students shared their transformative summer experiences with their mentors, friends, parents and teachers by presenting scientific posters and by contributing articles to the program’s new EiHS Journal, which will publish its first issue in October.

“Being able to contribute to a scientific project that can play an important role in someone’s life is an amazing opportunity, and I would not trade it for the world,” said Marialuisa Flores, a student from Lifeline Education Charter School. “It was a very enjoyable learning experience, which has made a great impact on my life and future career.”

A retreat from everything but stem cells

BY Cristy Lytal

It wasn’t the pristine 27-hole course that drew more than 120 stem cell researchers from USC and beyond to the Desert Princess Golf Resort near Palm Springs, Calif. It was the sixth annual retreat for the Eli and Edy the Broad Center for Regenerative Medicine and Stem Cell Research at USC, which took place on Oct. 20-21.

The two-day, overnight retreat featured a plenary lecture by Clive Svendsen, director of the Regenerative Medicine Institute at Cedars-Sinai Medical Center, about the contribution of induced pluripotent stem (iPS) cells to regenerative medicine, particularly to studying and developing treatments for neurological disorders.

The retreat also included presentations by winners of the first Regenerative Medicine Initiative (RMI) Awards, which provide up to two years of seed funding for multi-investigator research collaborations that harness the full potential of USC-affiliated faculty members. The three winning teams are using various stem/progenitor cells that might lead to future therapies for certain forms of deafness, bone defects and pediatric leukemia.

Many other principal investigators, postdoctoral and graduate students shared innovative research advancing several key areas of regenerative medicine.

Rong Lu, who will leave Stanford University to join USC’s stem cell research center as a principal investigator in January, talked about her new cellular “tracking system” for hematopoietic, or blood-forming stem cells. The system allows for the more effective study of blood and other types of cancers.

Min Yu, who will leave Massachusetts General Hospital at Harvard Medical School to accept a joint appointment as a principal investigator at USC’s stem cell research center and the USC Norris Comprehensive Cancer Center in January, discussed how to filter out circulating cancer stem cells from billions of other blood cells to understand and stop cancer’s spread.

USC research associate Hu Zhao and research assistants Yichen Li and Yingxiao Shi gave presentations.

Postdoctoral students who presented research included Mohamed Hammad, Lori O’Brien, Sandeep Paul and Saaket Varma.

PhD student presenters included Wen-Hsuan Chang, Guanyi Huang, Sapna Jain, Erin Moran, Marie Rippen and Yuki Yamaguchi.

The retreat also showcased the USC stem cell research center’s core facilities for stem cell sorting, derivation, culture, iPS programming, imaging and therapeutic screening.

During the cocktail hour, guests exchanged new ideas while voting on their favorite posters, which introduced research opportunities related to the Development, Stem Cells, and Regenerative Medicine PhD program.

Retreat sponsors included the California Institute for Regenerative Medicine Amgen, Sanofi, Zeiss, Leica Microsystems, Fluidigm, Lonza and Novogenix Laboratories LLC.

“This year’s retreat was a great success,” said Andrew McMahon, who spearheads the USC Stem Cell initiative and directs the Broad Center. “It helped solidify USC Stem Cell as an interactive scientific community and build relationships with our colleagues at the university and beyond.”

$1.5M Goes to Stem Cell Research

$6.4M for Stem Cell Labs to USC, CHLA

$25 million Broad Foundation gift creates stem cell institute at USC

McMahon discusses central role of stem cell biology in medicine of the future

Andrew McMahon is a Provost Professor and inaugural holder of the W.M. Keck Professorship of Stem Cell Biology and Regenerative Medicine at USC. (Photo/Philip Channing)

McMahon installed as chair of stem cell biology

Army Research Laboratory selects USC institute as base for breakthroughs in science and technology

Brainpower applied to understanding of neural stem cells

BY Cristy Lytal OCTOBER 24, 2013

How do humans and other mammals get so brainy? USC researcher Wange Lu and his colleagues shed new light on this question in a paper published in the journal Cell Reports on Oct. 24.

The researchers donned their thinking caps to explain how neural stem and progenitor cells differentiate into neurons and related cells called glia. Neurons transmit information through electrical and chemical signals; glia surround, support and protect neurons in the brain and throughout the nervous system. Glia do everything from holding neurons in place to supplying them with nutrients and oxygen to protect them from pathogens.

By studying the embryo neural stem cells of mice in a petri dish, Lu and his colleagues discovered that a protein called SMEK1 promotes the differentiation of neural stem and progenitor cells. At the same time, SMEK1 keeps these cells in check by suppressing their uncontrolled proliferation.

The researchers also determined that SMEK1 doesn’t act alone: It works in concert with Protein Phosphatase 4 to suppress the activity of PAR3, a third protein that discourages neurogenesis — the birth of new neurons. With PAR3 out of the picture, neural stem cells and progenitors are free to differentiate into new neurons and glia.

“These studies reveal the mechanisms of how the brain keeps the balance of stem cells and neurons when the brain is formed,” said Wange Lu, associate professor of biochemistry and molecular biology at the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC. “If this process goes wrong, it leads to cancer or mental retardation or other neurological diseases.”

neural stem cells

Neural stem and progenitor cells offer tremendous promise as a future treatment for neurodegenerative disorders, and understanding their differentiation is the first step toward harnessing the cells’ therapeutic potential. This could offer new hope for patients with Alzheimer’s, Parkinson’s and many other currently incurable diseases.

Co-authors from the Broad Center included Vicky Yamamoto, Si Ho Choi and Zhong Wei. Co-authors Hee-Ryang Kim and Choun-Ki Joo work at the Catholic University of Korea in Seoul, and first author Jungmook Lyu is affiliated with both institutions.

Funding for the study came from the National Institutes of Health (grant number 5R01NS067213).

Protein phosphatase 4 and Smek complex negatively regulate Par3 and promote neuronal differentiation of neural stem/progenitor cells.

Lyu J¹, Kim HR, Yamamoto V, Choi SH, Wei Z, Joo CK, Lu W. Author information

Cell Rep. 2013 Nov 14;5(3):593-600. http://d.doi.org:/10.1016/j.celrep.2013.09.034. Epub 2013 Oct 24.

Neural progenitor cells (NPCs) are multipotent cells that can self-renew and differentiate into neurons and glial cells. However, mechanisms that control their fate decisions are poorly understood. Here, we show that Smek1, a regulatory subunit of the serine/threonine protein phosphatase PP4, promotes neuronal differentiation and suppresses the proliferative capacity of NPCs. We identify the cell polarity protein Par3, a negative regulator of neuronal differentiation, as a Smek1 substrate and demonstrate that Smek1 suppresses its activity. We also show that Smek1, which is predominantly nuclear in NPCs, is excluded from the nucleus during mitosis, allowing it to interact with cortical/cytoplasmic Par3 and mediate its dephosphorylation by the catalytic subunit PP4c. These results identify the PP4/Smek1 complex as a key regulator of neurogenesis.

Neural stem and progenitor cells located in the ventricular zone (VZ) of the embryonic neocortex are mitotically active, self-renewing cells with the potential to produce differentiated cell types (Temple, 2001). During cortical development, postmitotic neurons generated from NPCs migrate radially out of the VZ and form the cortical plate (CP) in an “inside-out pattern,” eventually establishing a six-layered cortex (Kriegstein et al., 2006). The timing of neuronal differentiation determines the size of the progenitor pool, the final number of neurons, and cortical thickness. However, the molecular mechanisms that control the switch from proliferation to neuronal differentiation of NPCs remain incompletely understood.

Studies of Drosophila neuroblasts show that the serine/threonine protein phosphatase 2A (PP2A) inhibits self-renewal and promotes neuronal differentiation by regulating the phosphorylation status of cell fate determinants, including Numb (Wang et al., 2009). Bazooka, a key component of the Par protein complex, is a well-characterized PP2A substrate in Drosophila neuroblasts (Krahn et al., 2009; Ogawa et al., 2009). PP2A antagonizes phosphorylation of Bazooka by Par1 kinase to control its subcellular localization. In mammals, a protein called Partitioning-defective 3 (Par3), the ortholog of Bazooka, accumulates at the tip of a growing axon in neurons and controls axon specification (Shi et al., 2003). Recently, it has been shown that Par3, which is enriched in the apical domain of NPCs of the VZ (Imai et al., 2006), critically regulates proliferation versus differentiation during cortical development (Bultje et al., 2009; Costa et al., 2008).

PP4, which belongs to the PP2A family, is a protein complex comprised of a catalytic subunit PP4c plus regulatory subunits (Gingras et al., 2005). Smek (also termed PP4R3) has been identified as a PP4 regulatory subunit and implicated in activities as diverse as regulation of MEK (Mendoza et al., 2005), insulin/IGF-1 signaling (Wolff et al., 2006), H2AX phosphorylation (Chowdhury et al., 2008), and histone H3 and H4 acetylation (Lyu et al., 2011). A recent study reported that Falafel (Flfl), the Drosophila homolog of Smek, mediates localization of the adaptor protein Miranda and the cell fate determinant Prospero in neuroblasts (Sousa-Nunes et al., 2009). However, the direct substrate of Smek remains unclear. Here we identify Par3 as a direct substrate of the PP4/Smek1 complex in NPCs and report a novel role for Smek1 in regulating neuronal differentiation.

Smek1 is required for neuronal differentiation of NPCs

During mouse cortical development, Smek1 is expressed in a distinct temporal and spatial pattern. At E11.5, we observed that Smek1 protein is expressed in most NPCs at the apical side of the forebrain VZ (Figure 1Aand S1A). At E14.5, Smek1 protein was detectable primarily in CP neurons (Figure 1B and S1B), while weak Smek1 expression was seen in some NPCs undergoing mitosis at the ventricle surface (Figure 1B, boxes). Interestingly, VZ neurons that migrate to the CP also expressed Smek1 protein (Figure 1B, arrows). In postnatal forebrain, Smek1 protein expression remained detectable in cortical layers I-IV (Figure S1C). Moreover, E14 cortices of Smek1-depleted mice (Smek1^gt/gt) exhibited an increase in the number of Pax6-positive cells (an NPC marker) and a decrease in the number of Tbr1-positive cells (a marker of cortical neurons) as compared to E14 cortices of wild-type (Smek1^+/+) mice (Figure 1C and S1D).

Figure 1

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Smek1 regulates neuronal differentiation in the early phase of NPC differentiation

To assess Smek1’ function in neurogenesis, we employed an in vitro culture system using NPCs isolated from the E11.5 mouse forebrain neocortex. NPCs transduced with lentivirus expressing shRNA againstSmek1 or control shRNA under control of a doxycycline-inducible promoter (Figure S1E) were cultured in medium containing doxycycline for 6 days under differentiating conditions and then assessed for neurogenesis using TUJ1 (a marker of immature neurons) or MAP2 (a marker of mature neurons). The number of TUJ1- or MAP2-positive cells significantly decreased in Smek1 knockdown cultures compared to cultures expressing control shRNA (Figure 1D), indicating a neuronal differentiation defect. A decrease in number of neurons can be caused by a defect in NPC proliferation or neuronal apoptotic cell death. While no significant difference in the number of apoptotic cell death (as determined by TUNEL staining) was observed between control and Smek1 knockdown cells cultured under differentiation condition (data not shown),Smek1 knockdown NPCs grown under proliferation conditions underwent hyperproliferation (Figure S1F and G). We then asked whether Smek1 regulated the transition of NPCs from proliferative to differentiation states by knocking down Smek1 in NPCs prior to placing them in differentiating culture conditions. Western blotting of cells expressing Smek1 shRNA showed decreased levels of TUJ1 protein relative to controls by day 1 of culture (Figure S1H). At this time point, we found that the percentage of undifferentiated NPCs expressing both Nestin (an NPC marker) and Ki67 (a marker of proliferation) or Pax6 increased in cultures expressing Smek1 shRNA compared to control cultures, while the percentage of TUJ1-positive cells significantly decreased (Figure 1E and F). These findings suggest that Smek1 is required for neuronal differentiation and suppression of NPC proliferative capacity at an early phase of differentiation.

Smek1 recruits PP4c to promote neuronal differentiation

To determine Smek1 as a regulatory subunit of PP4 in neurogenesis, we asked whether Smek1 binds to the catalytic subunit PP4c in NPCs using co-immunoprecipitation. Western blot analysis revealed PP4c in Smek1 but not control immunoprecipitates, indicating that Smek1 physically interacts with PP4c. Such interactions did not change during differentiation (Figure 2A). To examine whether PP4c functions in neurogenesis, NPCs were exposed to lentivirus expressing PP4c or control shRNA and cultured as described in Figure 1D. PP4c knockdown led to changes similar to those accompanying Smek1 knockdown: relative to control cultures TUJ1 expression and the number of TUJ1-positive neurons decreased while Pax6-positive NPCs increased (Figure 2B and S2A and B). We next mapped Smek1 domains required for PP4c interaction. Smek contains four conserved domains: an N-terminal Ran-binding domain (RanBD), a domain of unknown function 625 (DUF625), an armadillo (Arm) repeat region, and a C-terminal nuclear localization sequence (NLS). We constructed a series of Flag-tagged deletion mutants, including Smek1ΔRanBD (lacking amino acid (aa) 2–100), ΔDUF625 (lacking aa 162-355), ΔArm (lacking 350-653), and ΔNLS (lacking aa 809-820) (Figure 2C, top) and introduced them or a wild-type construct into NPCs. PP4c was not be detected in anti-Flag immunoprecipitates from NPCs expressing Flag-Smek1ΔArm (Figure 2C, bottom) but was detected in cells expressing wild-type or other deletion mutants, suggesting that PP4c/Smek1 complex formation requires the Arm repeats. We also found that, while expression of wild-type Smek1 or corresponding ΔNLS mutant in cultures lacking endogenous Smek1 rescued the neuronal differentiation defect, the other mutants did not (Figure 2D and S2C and D). These results indicate that Smek1 regulates neuronal differentiation via its Arm repeats region through PP4c and suggest that both RanBD and DUF625 domains also participate in neurogenesis.

Figure 2

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PP4c is required for neuronal differentiation

Smek1 binds to and mediates Par3 dephosphorylation

To identify PP4 substrates regulated by Smek1 in NPCs, we employed affinity purification to purify proteins interacting with Smek1. Mass spectrometry analysis identified potential Smek1-binding proteins, including Par3, Kinesin-like protein, coiled-coil domain-containing protein 30 (CCDC 30), heat shock protein 90 (HSP90), PKC lambda, and HDAC1 Figure S3A. Among these, Par3, an intrinsic regulator of neurogenesis, is a particularly attractive candidate (Bultje et al., 2009; Costa et al., 2008). Using an antibody that detects the major isoforms (180, 150, and 100 kDa) of Par3, Western blot analysis revealed the predominant expression of two isoforms, 180 and 100 kDa forms, in NPCs, and that only the 180 kDa Par3 was detectable in Smek1 immunoprecipitates (Figure 3A). To determine whether Smek1/Par3 binding was direct, we performed an in vitro pull-down assay using purified Flag-Smek1 and His-fused Par3 fragments, the latter containing the CR1 domain (aa 1-338), the PDZ domain (aa 343-733), the aPKC-BR domain (aa 711-1054), or the C-terminal coiled-coil region (aa 1055-1334) (Figure S3B). Western blot analysis revealed that Flag-Smek1 pulled down only the Par3 coiled-coil region (Figure 3B), indicating direct binding through that region. Moreover, Par3 was detected in Flag immunoprecipitates derived from NPCs transduced with lentivirus expressing Myc-Par3 plus lentivirus expressing Flag-Smek1 wild-type or Smek1ΔRanBD, Smek1ΔArm, or Smek1ΔNLS constructs but not from NPCs expressing Smek1ΔDUF625 (Figure 3C). This result indicates that Smek1 DUF625 domain is required for Smek1/Par3 interaction.

Figure 3

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Smek1 interacts with Par3 and inhibits its function in neuronal differentiation

To assess potential dephosphorylation of Par3 by Smek1, we phosphorylayed Myc-Par3 protein in vitro by incubating it with an NPC lysate and ³²P-ATP and then treated it with a complex containing Flag-Smek1 proteins (Figure 3D). ³²P-labeling of Par3 was significantly decreased when Par3 protein was incubated with a complex containing wild-type Flag-Smek1 protein and PP4c (Figure 3D). By contrast, treatment with a Flag-Smek1ΔArm protein complex lacking PP4c binding significantly reduced Par3 dephosphorylation. Moreover, Western blot analysis of Par3 immunoprecipitates with an anti-phospho-serine/threonine antibody confirmed that Smek1 and PP4c regulate Par3 phosphorylation through serine/threonine residues (Figure S3C). Since the DUF625 and Arm repeats regions of Smek1 are required for binding to Par3 and PP4c respectively, we examined the Par3 phosphorylation state in NPCs expressing Flag-tagged wild-type or mutant Smek1 together with Myc-tagged Par3. Western blot analysis of Myc-Par3 immunoprecipitates using anti-phospho-serine/threonine antibody showed that overexpression of wild-type Smek1 or Smek1ΔNLS significantly decreased Par3 phosphorylation levels compared to controls, whereas overexpression of Smek1ΔRanBD, ΔDUF625, or ΔArm did not (Figure 3E). These results suggest that, in addition to the DUF625 and Arm, the RanBD domain of Smek1 participates in regulation of Par3 phosphorylation at serine/threonine residues.

Smek1 negatively regulates Par3 in neurogenesis

Next we asked whether Par3 is required for Smek1-mediated neurogenesis. To this end, we assessed the effect of Smek1 loss-or gain-of function on neuronal differentiation in the presence or absence of Par3. NPCs expressing either Smek1 shRNA or wild-type Smek1 were transduced with lentivirus expressing Par3 or control shRNA (Figure S3D). At day 1 after differentiation, in the presence of Par3, knockdown of Smek1 led to a decrease in the number of TUJ1-positive neurons and an increase in the number of Nestin/Ki67 double-positive NPCs, while overexpression of Smek1 had the opposite effect (Figure 3F and S3E). In the absence of Par3 by using shRNA, the number of TUJ1-positve cell was increased and the number of Nestin/Ki67 double positive NPCs was decreased. However, in these cultures knockdown or overexpression of Smek1 did not significantly alter the number of neurons or undifferentiated NPCs. In addition, we also observed increased expression of mRNAs encoding the Notch targets Hes1 and Hes5 in cells expressing Smek1 shRNA compared to control cells (Figure S3F). Moreover, analysis of Notch reporter gene activity revealed that wild-type Smek1 inhibited Notch signaling activity induced by Par3 overexpression, while Smek1ΔDUF625 did not (Figure S3G). Given that Par3 activates Notch signaling (Bultje et al., 2009), these results suggest that Smek1 acts upstream of Par3 to negatively regulate its activity in neurogenesis.

Par3 loss of function promotes neuronal differentiation (Costa et al., 2008), consistent with the effect seen following Smek1 overexpression (Figure 3F). To confirm that Smek1 promotes neurogenesis by suppressing Par3 function, we transduced NPCs with lentiviruses expressing Par3 alone or Par3 together with wild-type Smek1 or Smek1ΔDUF625, cultured them under differentiation conditions, and then neuronal differentiation was quantified by determining the percentage of TUJ1-positive and Nestin/Ki67 double-positive cells one day later. Par3 overexpression decreased the number of TUJ1-positive neurons and increased the number of Nestin/Ki67-positive undifferentiated NPCs compared with control cells (Figure 3G and S3H). As expected, wild-type Smek1 negated the effect of Par3 overexpression, as determined by comparing the percentage of TUJ1-positive and Nestin/Ki67 double-positive cells in cultures expressing both Smek1 and Par3 to cultures expressing Par3 alone. In comparison with wild-type Smek1, no significant change was seen in cultures transduced with Smek1ΔDUF625, which cannot bind Par3. These experiments further confirm that Smek1 negatively regulates Par3 in NPC differentiation.

Dynamic changes in Smek1 subcellular localization facilitate targeting of PP4 to Par3

Par3 localizes to the apical cortex of NPCs (Bultje et al., 2009), while Smek1 is predominantly nuclear (Figure 1A and C). To determine if changes in Smek1 subcellular localization occur in NPCs during neurogenesis, coronal sections from E11.5 forebrain were immunostained with anti-Smek1 and -α-tubulin (a cytoplasmic marker) antibodies. Smek1 co-localized with α-tubulin in cells on the ventricular surface (Figure 4A, arrows), indicating a cytoplasmic/cortical localization in mitotic NPCs. In mitotic cells, Par3 showed a similar localization (Figure S4A and B). Moreover, immunostaining of NPC cultures with anti-Smek1 and -α-tubulin antibodies showed that Smek1 undergoes dynamic changes in subcellular localization during mitosis. While Smek1 was nuclear in interphase and prophase cells, it showed a cytoplasmic/cortical localization from prometaphase to anaphase (Figure 4B and S4C). Metaphase and anaphase cells also showed Smek1 enrichment at spindle microtubules.

Figure 4

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Smek1 regulates subcellular localization of PP4c but not Par3

The RanBD motif of the Dictyostelium discoideum Smek homolog is reportedly critical for its cytoplasmic/cortical localization (Mendoza et al., 2005). To test whether this was the case for mammalian Smek1, Smek1-depleted NPCs were transduced with constructs encoding Flag-tagged wild-type Smek1 or its deletion mutants and immunostained with anti-Flag and anti-phospho-histone H3 (a marker of mitosis and chromatin condensation). Consistent with results reported in Dictyostelium discoideum, the Smek1ΔRanBD mutant failed to localize to the cytoplasm/spindle during mitosis but rather localized in the nucleus and remained there in interphase (Figure 4C). The subcellular localization of other mutants tested resembled that of wild-type Smek1, with the exception of Smek1ΔNLS, which was expressed in both the nucleus and cytoplasm of interphase cells. Smek1ΔRanBD contains domains that can bind Par3 and PP4c, as shown by immunoprecipitation (Figure 2C and and3C).3C). We thus asked whether ectopic expression of Smek1ΔRanBD promoted mislocalization of Par3 and PP4c during mitosis. When we expressed Smek1ΔRanBD ectopically in Smek1-depleted NPCs, cytoplasmic/cortical Par3 remained unchanged while Smek1ΔRanBD was nuclear (Figure S4D). In addition, no difference in localization of Par3 between Smek1-depleted and wild-type Smek1 re-expressing cells was observed, suggesting that Smek1 does not alter Par3 localization. To evaluate PP4c subcellular localization, chromosome-associated and cytosolic protein fractions were isolated from M phase-synchronized NPCs and compared by Western analysis using indicated antibodies (Figure 4D). Interestingly, PP4c protein levels increased in the chromosomal fraction from cells expressing Flag-Smek1ΔRanBD compared to control cells or wild-type Flag-Smek1, while in the cytosolic fraction the level of PP4c protein decreased, indicating altered localization of cytoplasmic PP4c to the nucleus. Taken together, these results demonstrate that PP4c subcellular localization depends on Smek1 localization during mitosis and suggest that cytoplasmic/cortical localization of Smek1 targets PP4 to Par3.

DISCUSSION

Neural stem and progenitor cells have been suggested as potential therapeutics for neurodegenerative disorders. However, understanding molecular and cellular mechanisms underlying their differentiation is a prerequisite to manipulating stem cell behavior. We show that Smek1, an evolutionarily conserved regulatory subunit of PP4, regulates neuronal differentiation and reveal an unreported function of PP4 in mammalian neurogenesis. Moreover, identification of Par3 as a novel Smek1-interacting protein and characterization of its conserved domains reveals a molecular mechanism by which Smek1 targets PP4 to Par3 during mitosis and negatively regulates Par3 function in neurogenesis.

In this study we identify Par3 as a PP4 substrate. We propose that Smek1, through its DUF625 domain, binds directly to the Par3 C-terminus. In NPCs Par3 is primarily cytoplasmic in interphase and mitosis. Thus, nuclear export of Smek1 to the cytoplasm is required for its interaction with Par3. We show dynamic changes in Smek1 subcellular localization in NPCs. While Smek1 localizes exclusively to the nucleus in interphase, during mitosis it becomes cytoplasmic. The RanBD of several proteins reportedly recognizes GTP-bound Ran (RanGTP), which directs assembly of spindle microtubules allowing chromosomal segregation and cytokinesis in mitosis (Carazo-Salas et al., 2001). Smek1 enrichment at spindle microtubules in metaphase and anaphase cells suggests that its RanBD may function in a RanGTP-dependent pathway during mitosis. Notably, nuclear export of Smek1 to the cytoplasm was observed from prometaphase cells when microtubules invade the nuclear space, and deletion of the Smek1 RanBD abolished this effect, as seen by nuclear localization. Thus our data suggest that Smek1 subcellular localization is regulated through the RanBD and that this activity may depend on microtubule dynamics functioning in a Ran-dependent pathway.

Most Smek homologs physically interact with the catalytic subunit PP4c (Gingras et al., 2005; Chowdhury et al., 2008), suggesting that the PP4 complex is evolutionarily conserved. We show that PP4c recognizes the Arm repeats region of Smek1 and its subcellular localization depends on Smek1 localization. Thus, nuclear export of Smek1 during mitosis facilitates dephosphorylation of Par3. This idea is supported by our observation that, while expression of Smek1 induced Par3 dephosphorylation in NPCs, expression of Smek1 mutants lacking RanBD and Arm repeats region did not. Interestingly, studies of Drosophila neuroblasts previously revealed that cell fate specification is tightly linked with phosphorylation status of bazooka protein (Betschinger et al., 2003; Krahn et al., 2009). However, it is now yet clear whether Par3 dephosphorylation directly regulates NPC neurogenesis. Although we could not identify specific phosphorylation sites targeted by PP4, our data defines three conserved domains of Smek1, namely RanBD, DUF625, and Arm repeats, necessary to target PP4 to its substrate Par3 and provides insight into the molecular mechanism by Smek1 to regulate PP4 function in NPCs.

We here show that Smek1 suppresses Par3, a negative regulator of neuronal differentiation. Par3 acts upstream of Notch signaling (Bultje et al., 2009), which critically regulates cell fate decision of NPCs in cortical development (Gaiano and Fishell, 2002). Notch gain-of-function activity inhibits neuronal differentiation (Nye et al., 1994), an effect similar to Smek1 loss-of-function. Moreover, Smek1 inhibits Par3-induced Notch reporter gene activity. Although it remains unclear whether Smek1 inhibits Par3’s ability to activate Notch signaling during mitosis, ensuring a neuronal fate, our data demonstrate Smek1 as a negative regulator of Par3 in regulating neuronal differentiation and suggest a novel role for PP4 in mammalian neurogenesis.

Supplementary Material Click here to view.^{(13M, pdf)}

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855259/bin/NIHMS530096-supplement-01.pdf

Acknowledgments We thank the USC Transgenic Core Facility for generating mutant mice. This research is funded by a NIH grant to W.L (5R01NS067213) and an NRF grant (NRF-2011-35B-E00015) to J.L.

References

Betschinger J, Mechtler K, Knoblich JA. The Par complex directs asymmetric cell division by phosphorylating the cytoskeletal protein Lgl. Nature. 2003;422:326–330. [PubMed]
Bultje RS, Castaneda-Castellanos DR, Jan LY, Jan YN, Kriegstein AR, Shi SH. Mammalian Par3 regulates progenitor cell asymmetric division via notch signaling in the developing neocortex. Neuron.2009;63:189–202. [PMC free article] [PubMed]
Carazo-Salas RE, Gruss OJ, Mattaj IW, Karsenti E. Ran-GTP coordinates regulation of microtubule nucleation and dynamics during mitotic-spindle assembly. Nat Cell Biol. 2001;3:228–234. [PubMed]
Chowdhury D, Xu X, Zhong X, Ahmed F, Zhong J, Liao J, Dykxhoorn DM, Weinstock DM, Pfeifer GP, Lieberman J. A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication. Mol Cell. 2008;31:33–46. [PMC free article] [PubMed]
Costa MR, Wen G, Lepier A, Schroeder T, Gotz M. Par-complex proteins promote proliferative progenitor divisions in the developing mouse cerebral cortex. Development. 2008;135:11–22.[PubMed]
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Advances in acoustics and in learning

Posted in Behavior, Biological Networks, Cell Biology, Signaling & Cell Circuits, Cerebrovascular and Neurodegenerative Diseases, Clinical & Translational, Curation, Human Sensation and Cellular Transduction: Physiology and Therapeutics, Innovations, Innovations in Neurophysiology & Neuropsychology, Neurodegenerative Diseases, Neurological Diseases, Neuroscience, tagged acoustics, Aging, Cognition, mechanosensation, memory loss on October 31, 2015| Leave a Comment »

Advances in acoustics and in learning

Larry H. Brnstein, MD, FCAP, Curator

LPBI

Controlling acoustic properties with algorithms and computational methods

http://www.kurzweilai.net/controlling-acoustic-properties-with-algorithms-and-computational-methods

October 28, 2015

Computer scientists at Columbia Engineering, Harvard, and MIT have demonstrated that acoustic properties — both sound and vibration — can be controlled by 3D-printing specific shapes.

They designed an optimization algorithm and used computational methods and digital fabrication to alter the shape of 2D and 3D objects, creating what looks to be a simple children’s musical instrument — a xylophone with keys in the shape of zoo animals.

Practical uses

“Our discovery could lead to a wealth of possibilities that go well beyond musical instruments,” says Changxi Zheng, assistant professor of computer science at Columbia Engineering, who led the research team.

“Our algorithm could lead to ways to build less noisy computer fans and bridges that don’t amplify vibrations under stress, and advance the construction of micro-electro-mechanical resonators whose vibration modes are of great importance.”

Zheng, who works in the area of dynamic, physics-based computational sound for immersive environments, wanted to see if he could use computation and digital fabrication to actively control the acoustical property, or vibration, of an object.

Zheng’s team decided to focus on simplifying the slow, complicated, manual process of designing “idiophones” — musical instruments that produce sounds through vibrations in the instrument itself, not through strings or reeds.

The surface vibration and resulting sounds depend on the idiophone’s shape in a complex way, so designing the shapes to obtain desired sound characteristics is not straightforward, and their forms have so far been limited to well-understood designs such as bars that are tuned by careful drilling of dimples on the underside of the instrument.

Optimizing sound properties

To demonstrate their new technique, the team settled on building a “zoolophone,” a metallophone with playful animal shapes (a metallophone is an idiophone made of tuned metal bars that can be struck to make sound, such as a glockenspiel).

What happens in the brain when we learn

http://www.kurzweilai.net/what-happens-in-the-brain-when-we-learn

Findings could enhance teaching methods and lead to treatments for cognitive problems

October 28, 2015

A Johns Hopkins University-led research team has proven a working theory that explains what happens in the brain when we learn, as described in the current issue of the journal Neuron.

More than a century ago, Pavlov figured out that dogs fed after hearing a bell eventually began to salivate when they heard the bell ring. The team looked into the question of how Pavlov’s dogs (in “classical conditioning”) managed to associate an action with a delayed reward to create knowledge. For decades, scientists had a working theory of how it happened, but the team is now the first to prove it.

“If you’re trying to train a dog to sit, the initial neural stimuli, the command, is gone almost instantly — it lasts as long as the word sit,” said neuroscientist Alfredo Kirkwood, a professor with the university’s Zanvyl Krieger Mind/Brain Institute. “Before the reward comes, the dog’s brain has already turned to other things. The mystery was, ‘How does the brain link an action that’s over in a fraction of a second with a reward that doesn’t come until much later?’ ”

Eligibility traces

The working theory — which Kirkwood’s team has now validated experimentally — is that invisible “synaptic eligibility traces” effectively tag the synapses activated by the stimuli so that the learning can be cemented with the arrival of a reward. The reward is a neuromodulator* (neurochemical) that floods the dog’s brain with “good feelings.” Though the brain has long since processed the “sit” command, eligibility traces in the synapse respond to the neuromodulators, prompting a lasting synaptic change, a.k.a. “learning.”

The team was able to prove the eligibility-traces theory by isolating cells in the visual cortex of a mouse. When they stimulated the axon of one cell with an electrical impulse, they sparked a response in another cell. By doing this repeatedly, they mimicked the synaptic response between two cells as they process a stimulus and create an eligibility trace.

When the researchers later flooded the cells with neuromodulators, simulating the arrival of a delayed reward, the response between the cells strengthened (“long-term potentiation”) or weakened (“long-term depression”), showing that the cells had “learned” and were able to do so because of the eligibility trace.

“This is the basis of how we learn things through reward,” Kirkwood said, “a fundamental aspect of learning.”

In addition to a greater understanding of the mechanics of learning, these findings could enhance teaching methods and lead to treatments for cognitive problems, the researchers suggest.

Scientists at the University of Texas at Houston and the University of California, Davis were also involved in the research, which was supported by grants from JHU’s Science of Learning Institute and National Institutes of Health.

* The neuromodulators tested were norepinephrine, serotonin, dopamine, and acetylcholine, all of which have been implicated in cortical plasticity (ability to grow and form new connections to other neurons).

Abstract of Distinct Eligibility Traces for LTP and LTD in Cortical Synapses

In reward-based learning, synaptic modifications depend on a brief stimulus and a temporally delayed reward, which poses the question of how synaptic activity patterns associate with a delayed reward. A theoretical solution to this so-called distal reward problem has been the notion of activity-generated “synaptic eligibility traces,” silent and transient synaptic tags that can be converted into long-term changes in synaptic strength by reward-linked neuromodulators. Here we report the first experimental demonstration of eligibility traces in cortical synapses. We demonstrate the Hebbian induction of distinct traces for LTP and LTD and their subsequent timing-dependent transformation into lasting changes by specific monoaminergic receptors anchored to postsynaptic proteins. Notably, the temporal properties of these transient traces allow stable learning in a recurrent neural network that accurately predicts the timing of the reward, further validating the induction and transformation of eligibility traces for LTP and LTD as a plausible synaptic substrate for reward-based learning.

references:

Kaiwen He, Marco Huertas, Su Z. Hong, XiaoXiu Tie, Johannes W. Hell, Harel Shouval, Alfredo Kirkwood. Distinct Eligibility Traces for LTP and LTD in Cortical Synapses. Neuron (2015); DOI: 10.1016/j.neuron.2015.09.037

Holographic sonic tractor beam lifts and moves objects using soundwaves

Another science-fiction idea realized

October 27, 2015

British researchers have built a working Star-Trek-style “tractor beam” — a device that can attract or repel one object to another from a distance. It uses high-amplitude soundwaves to generate an acoustic hologram that can grasp and move small objects.

The technique, published in an open-access paper in Nature Communications October 27, has a wide range of potential applications, the researchers say. A sonic production line could transport delicate objects and assemble them, all without physical contact. Or a miniature version could grip and transport drug capsules or microsurgical instruments through living tissue.

The device was developed at the Universities of Sussex and Bristol in collaboration with Ultrahaptics.

https://youtu.be/wDzhlW-rKvM
University of Sussex | Levitation using sound waves

The researchers used an array of 64 miniature loudspeakers. The whole system consumes just 9 Watts of power, used to create high-pitched (40Khz), high-intensity sound waves to levitate a spherical bead 4mm in diameter made of expanded polystyrene.

The tractor beam works by surrounding the object with high-intensity sound to create a force field that keeps the objects in place. By carefully controlling the output of the loudspeakers, the object can be held in place, moved, or rotated.

Three different shapes of acoustic force fields work as tractor beams: an acoustic force field that resembles a pair of fingers or tweezers; an acoustic vortex, the objects becoming trapped at the core; and a high-intensity “cage” that surrounds the objects and holds them in place from all directions.

Previous attempts surrounded the object with loudspeakers, which limits the extent of movement and restricts many applications. Last year, the University of Dundee presented the concept of a tractor beam, but no objects were held in the ray.

The team is now designing different variations of this system. A bigger version aims at levitating a soccer ball from 10 meters away and a smaller version aims at manipulating particles inside the human body.

https://youtu.be/g_EM1y4MKSc
Asier Marzo, Matt Sutton, Bruce Drinkwater and Sriram Subramanian | Acoustic holograms are projected from a flat surface and contrary to traditional holograms, they exert considerable forces on the objects contained within. The acoustic holograms can be updated in real time to translate, rotate and combine levitated particles enabling unprecedented contactless manipulators such as tractor beams.

Abstract of Holographic acoustic elements for manipulation of levitated objects

Sound can levitate objects of different sizes and materials through air, water and tissue. This allows us to manipulate cells, liquids, compounds or living things without touching or contaminating them. However, acoustic levitation has required the targets to be enclosed with acoustic elements or had limited maneuverability. Here we optimize the phases used to drive an ultrasonic phased array and show that acoustic levitation can be employed to translate, rotate and manipulate particles using even a single-sided emitter. Furthermore, we introduce the holographic acoustic elements framework that permits the rapid generation of traps and provides a bridge between optical and acoustical trapping. Acoustic structures shaped as tweezers, twisters or bottles emerge as the optimum mechanisms for tractor beams or containerless transportation. Single-beam levitation could manipulate particles inside our body for applications in targeted drug delivery or acoustically controlled micro-machines that do not interfere with magnetic resonance imaging.

references:

Asier Marzo, Sue Ann Seah, Bruce W. Drinkwater, Deepak Ranjan Sahoo, Benjamin Long, Sriram Subramanian. Holographic acoustic elements for manipulation of levitated objects. Nature Communications, 2015; 6: 8661 DOI: 10.1038/ncomms9661 (open access)

A drug-delivery technique to bypass the blood-brain barrier

http://www.kurzweilai.net/a-drug-delivery-technique-to-bypass-the-blood-brain-barrier

Could benefit a large population of patients with neurodegenerative disorders

October 26, 2015

Researchers at Massachusetts Eye and Ear/Harvard Medical School and Boston University have developed a new technique to deliver drugs across the blood-brain barrier and have successfully tested it in a Parkinson’s mouse model (a line of mice that has been genetically modified to express the symptoms and pathological features of Parkinson’s to various extents).

Their findings, published in the journal Neurosurgery, lend hope to patients with neurological conditions that are difficult to treat due to a barrier mechanism that prevents approximately 98 percent of drugs from reaching the brain and central nervous system.

“Although we are currently looking at neurodegenerative disease, there is potential for the technology to be expanded to psychiatric diseases, chronic pain, seizure disorders, and many other conditions affecting the brain and nervous system down the road,” said senior author Benjamin S. Bleier, M.D., of the department of otolaryngology at Mass. Eye and Ear/Harvard Medical School.

The nasal mucosal grafting solution

Researchers delivered glial derived neurotrophic factor (GDNF), a therapeutic protein in testing for treating Parkinson’s disease, to the brains of mice. They showed that their delivery method was equivalent to direct injection of GDNF, which has been shown to delay and even reverse disease progression of Parkinson’s disease in pre-clinical models.

Once they have finished the treatment, they use adjacent nasal lining to rebuild the hole in a permanent and safe way. Nasal mucosal grafting is a technique regularly used in the ENT (ear, nose, and throat) field to reconstruct the barrier around the brain after surgery to the skull base. ENT surgeons commonly use endoscopic approaches to remove brain tumors through the nose by making a window through the blood-brain barrier to access the brain.

The safety and efficacy of these methods have been well established through long-term clinical outcomes studies in the field, with the nasal lining protecting the brain from infection just as the blood brain barrier has done.

By functionally replacing a section of the blood-brain barrier with nasal mucosa, which is more than 1,000 times more permeable than the native barrier, surgeons could create a “screen door” to allow for drug delivery to the brain and central nervous system.

The technique has the potential to benefit a large population of patients with neurodegenerative disorders, where there is still a specific unmet need for blood-brain-penetrating therapeutic delivery strategies.

The study was funded by The Michael J. Fox Foundation for Parkinson’s Research (MJFF).

Abstract of Heterotopic Mucosal Grafting Enables the Delivery of Therapeutic Neuropeptides Across the Blood Brain Barrier

BACKGROUND: The blood-brain barrier represents a fundamental limitation in treating neurological disease because it prevents all neuropeptides from reaching the central nervous system (CNS). Currently, there is no efficient method to permanently bypass the blood-brain barrier.

OBJECTIVE: To test the feasibility of using nasal mucosal graft reconstruction of arachnoid defects to deliver glial-derived neurotrophic factor (GDNF) for the treatment of Parkinson disease in a mouse model.

METHODS: The Institutional Animal Care and Use Committee approved this study in an established murine 6-hydroxydopamine Parkinson disease model. A parietal craniotomy and arachnoid defect was repaired with a heterotopic donor mucosal graft. The therapeutic efficacy of GDNF (2 [mu]g/mL) delivered through the mucosal graft was compared with direct intrastriatal GDNF injection (2 [mu]g/mL) and saline control through the use of 2 behavioral assays (rotarod and apomorphine rotation). An immunohistological analysis was further used to compare the relative preservation of substantia nigra cell bodies between treatment groups.

RESULTS: Transmucosal GDNF was equivalent to direct intrastriatal injection at preserving motor function at week 7 in both the rotarod and apomorphine rotation behavioral assays. Similarly, both transmucosal and intrastriatal GDNF demonstrated an equivalent ratio of preserved substantia nigra cell bodies (0.79 +/- 0.14 and 0.78 +/- 0.09, respectively, P = NS) compared with the contralateral control side, and both were significantly greater than saline control (0.53 +/- 0.21; P = .01 and P = .03, respectively).

CONCLUSION: Transmucosal delivery of GDNF is equivalent to direct intrastriatal injection at ameliorating the behavioral and immunohistological features of Parkinson disease in a murine model. Mucosal grafting of arachnoid defects is a technique commonly used for endoscopic skull base reconstruction and may represent a novel method to permanently bypass the blood-brain barrier.

references:

Bleier, Benjamin S. MD; Kohman, Richie E. PhD; Guerra, Kevin BS; Nocera, Angela L. MS; Ramanlal, Shreshtha BS; Kocharyan, Armine H. MD; Curry, William T. MD; Han, Xue PhD. Heterotopic Mucosal Grafting Enables the Delivery of Therapeutic Neuropeptides Across the Blood Brain Barrier. Neurosurgery, 2015; DOI: 10.1227/NEU.0000000000001016

Creating an artificial sense of touch by electrical stimulation of the brain

http://www.kurzweilai.net/creating-an-artificial-sense-of-touch-by-electrical-stimulation-of-the-brain

DARPA-funded study may lead to building prosthetic limbs for humans using a direct brain-electrode interface to recreate the sense of touch

October 26, 2015

Neuroscientists in a project headed by the University of Chicago have determined some of the specific characteristics of electrical stimuli that should be applied to the brain to produce different sensations in an artificial upper limb intended to restore natural motor control and sensation in amputees.

The research is part of Revolutionizing Prosthetics, a multi-year Defense Advanced Research Projects Agency (DARPA).

For this study, the researchers used monkeys, whose sensory systems closely resemble those of humans. They implanted electrodes into the primary somatosensory cortex, the area of the brain that processes touch information from the hand. The animals were trained to perform two perceptual tasks: one in which they detected the presence of an electrical stimulus, and a second task in which they indicated which of two successive stimuli was more intense.

The sense of touch is made up of a complex and nuanced set of sensations, from contact and pressure to texture, vibration and movement. The goal of the research is to document the range, composition and specific increments of signals that create sensations that feel different from each other.

To achieve that, the researchers manipulated various features of the electrical pulse train, such as its amplitude, frequency, and duration, and noted how the interaction of each of these factors affected the animals’ ability to detect the signal.

Of specific interest were the “just-noticeable differences” (JND),” — the incremental changes needed to produce a sensation that felt different. For instance, at a certain frequency, the signal may be detectable first at a strength of 20 microamps of electricity. If the signal has to be increased to 50 microamps to notice a difference, the JND in that case is 30 microamps.*

“When you grasp an object, for example, you can hold it with different grades of pressure. To recreate a realistic sense of touch, you need to know how many grades of pressure you can convey through electrical stimulation,” said Sliman Bensmaia, PhD, Associate Professor in the Department of Organismal Biology and Anatomy at the University of Chicago and senior author of the study, which was published today (Oct. 26) in the Proceedings of the National Academy of Sciences. “Ideally, you can have the same dynamic range for artificial touch as you do for natural touch.”

“This study gets us to the point where we can actually create real algorithms that work. It gives us the parameters as to what we can achieve with artificial touch, and brings us one step closer to having human-ready algorithms.”

Researchers from the University of Pittsburgh and Johns Hopkins University were also involved in the DARPA-supported study.

* The study also has important scientific implications beyond neuroprosthetics. In natural perception, a principle known as Weber’s Law states that the just-noticeable difference between two stimuli is proportional to the size of the stimulus. For example, with a 100-watt light bulb, you might be able to detect a difference in brightness by increasing its power to 110 watts. The JND in that case is 10 watts. According to Weber’s Law, if you double the power of the light bulb to 200 watts, the JND would also be doubled to 20 watts.

However, Bensmaia’s research shows that with electrical stimulation of the brain, Weber’s Law does not apply — the JND remains nearly constant, no matter the size of the stimulus. This means that the brain responds to electrical stimulation in a much more repeatable, consistent way than through natural stimulation.

“It shows that there is something fundamentally different about the way the brain responds to electrical stimulation than it does to natural stimulation,” Bensmaia said.

Abstract of Behavioral assessment of sensitivity to intracortical microstimulation of primate somatosensory cortex

Intracortical microstimulation (ICMS) is a powerful tool to investigate the functional role of neural circuits and may provide a means to restore sensation for patients for whom peripheral stimulation is not an option. In a series of psychophysical experiments with nonhuman primates, we investigate how stimulation parameters affect behavioral sensitivity to ICMS. Specifically, we deliver ICMS to primary somatosensory cortex through chronically implanted electrode arrays across a wide range of stimulation regimes. First, we investigate how the detectability of ICMS depends on stimulation parameters, including pulse width, frequency, amplitude, and pulse train duration. Then, we characterize the degree to which ICMS pulse trains that differ in amplitude lead to discriminable percepts across the range of perceptible and safe amplitudes. We also investigate how discriminability of pulse amplitude is modulated by other stimulation parameters—namely, frequency and duration. Perceptual judgments obtained across these various conditions will inform the design of stimulation regimes for neuroscience and neuroengineering applications.

references:

Sungshin Kim, Thierri Callier, Gregg A. Tabot, Robert A. Gaunt, Francesco V. Tenore, and Sliman J. Bensmaia. Behavioral assessment of sensitivity to intracortical microstimulation of primate somatosensory cortex. PNAS 2015; doi:10.1073/pnas.1509265112

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impairment of cognitive function and neurogenesis

Posted in Biological Networks, Cell Biology, Signaling & Cell Circuits, Cerebrovascular and Neurodegenerative Diseases, Curation, Disease Biology, Immunology, Innovations in Neurophysiology & Neuropsychology, tagged Aging, blood brain barrier, Cognition, cytochrome c, β2-microglobulin, neurogenesis on October 31, 2015| Leave a Comment »

impairment of cognitive function and neurogenesis

Larry H. Bernstein, MD, FCAP, Curator

LPBI

β2-microglobulin is a systemic pro-aging factor that impairs cognitive function and neurogenesis

Lucas K Smith, Yingbo He, Jeong-Soo Park, Gregor Bieri, Cedric E Snethlage, Karin Lin, Geraldine Gontier, Rafael Wabl, et al.
Nature Medicine 21,932–937(2015) http://dx.doi.org:/10.1038/nm.3898

Aging drives cognitive and regenerative impairments in the adult brain, increasing susceptibility to neurodegenerative disorders in healthy individuals^{1, 2, 3, 4}. Experiments using heterochronic parabiosis, in which the circulatory systems of young and old animals are joined, indicate that circulating pro-aging factors in old blood drive aging phenotypes in the brain^{5, 6}. Here we identify β2-microglobulin (B2M), a component of major histocompatibility complex class 1 (MHC I) molecules, as a circulating factor that negatively regulates cognitive and regenerative function in the adult hippocampus in an age-dependent manner. B2M is elevated in the blood of aging humans and mice, and it is increased within the hippocampus of aged mice and young heterochronic parabionts. Exogenous B2M injected systemically, or locally in the hippocampus, impairs hippocampal-dependent cognitive function and neurogenesis in young mice. The negative effects of B2M and heterochronic parabiosis are, in part, mitigated in the hippocampus of young transporter associated with antigen processing 1 (Tap1)-deficient mice with reduced cell surface expression of MHC I. The absence of endogenous B2M expression abrogates age-related cognitive decline and enhances neurogenesis in aged mice. Our data indicate that systemic B2M accumulation in aging blood promotes age-related cognitive dysfunction and impairs neurogenesis, in part via MHC I, suggesting that B2M may be targeted therapeutically in old age.

Figure 1: Systemic B2M increases with age and impairs hippocampal-dependent cognitive function and neurogenesis

Systemic B2M increases with age and impairs hippocampal-dependent cognitive function and neurogenesis.

http://www.nature.com/nm/journal/v21/n8/carousel/nm.3898-F1.jpg

(a,b) Schematics of unpaired young versus aged mice (a), and young isochronic versus heterochronic parabionts (b). (a,b) Changes in plasma concentration of B2M with age at 3, 6, 12, 18 and 24 months (a) and between young isochronic and…

Figure 2: B2M expression increases in the aging hippocampus and impairs hippocampal-dependent cognitive function and neurogenesis.close

http://www.nature.com/nm/journal/v21/n8/carousel/nm.3898-F2.jpg

(a,b) Western blot and quantification of hippocampal lysates probed with B2M- and actin-specific antibodies from young (3 months) and aged (18 months) unpaired animals (a), or young isochronic and young heterochronic parabionts five wee…

Figure 3: Reducing MHC I surface expression mitigates the negative effects of heterochronic parabiosis on neurogenesis.close

http://www.nature.com/nm/journal/v21/n8/carousel/nm.3898-F3.jpg

(a) Schematic of young (3 months) WT and Tap1^−/− isochronic parabionts and young WT and Tap1^−/− heterochronic parabionts. (b,c) Representative (of six sections per mouse) images of the DG (b) and quantification of DCX immunostaining (c)…

Figure 4: Absence of B2M enhances hippocampal-dependent cognitive function and neurogenesis in aged animals.

Absence of B2M enhances hippocampal-dependent cognitive function and neurogenesis in aged animals.

http://www.nature.com/nm/journal/v21/n8/carousel/nm.3898-F4.jpg

(a–d) Learning and memory in young (3 months) and aged (17 months) WT and B2m-knockout (B2m^−/−) mice by RAWM (a,c) and contextual fear conditioning (b,d). Data are from 10 young WT, 10 young B2m^−/−, 8 aged WT, and 12 aged B2m^−/− mice. (…

Neuroscience. 2015 Nov 12;308:75-94. doi: 10.1016/j.neuroscience.2015.09.012. Epub 2015 Sep 10.

Synergistic neuroprotection by epicatechin and quercetin: Activation of convergent mitochondrial signaling pathways.

Nichols M¹, Zhang J², Polster BM³, Elustondo PA⁴, Thirumaran A⁵, Pavlov EV⁶, Robertson GS⁷. Author information

In view of evidence that increased consumption of epicatechin (E) and quercetin (Q) may reduce the risk of stroke, we have measured the effects of combining E and Q on mitochondrial function and neuronal survival following oxygen-glucose deprivation (OGD). Relative to mouse cortical neuron cultures pretreated (24h) with either E or Q (0.1-10μM), E+Q synergistically attenuated OGD-induced neuronal cell death. E, Q and E+Q (0.3μM) increased spare respiratory capacity but only E+Q (0.3μM) preserved this crucial parameter of neuronal mitochondrial function after OGD. These improvements were accompanied by corresponding increases in cyclic AMP response element binding protein (CREB) phosphorylation and the expression of CREB-target genes that promote neuronal survival (Bcl-2) and mitochondrial biogenesis (PGC-1α). Consistent with these findings, E+Q (0.1 and 1.0μM) elevated mitochondrial gene expression (MT-ND2 and MT-ATP6) to a greater extent than E or Q after OGD. Q (0.3-3.0μM), but not E (3.0μM), elevated cytosolic calcium (Ca(2+)) spikes and the mitochondrial membrane potential. Conversely, E and E+Q (0.1 and 0.3μM), but not Q (0.1 and 0.3μM), activated protein kinase B (Akt). Nitric oxide synthase (NOS) inhibition with L-N(G)-nitroarginine methyl ester (1.0μM) blocked neuroprotection by E (0.3μM) or Q (1.0μM). Oral administration of E+Q (75mg/kg; once daily for 5days) reduced hypoxic-ischemic brain injury. These findings suggest E and Q activate Akt- and Ca(2+)-mediated signaling pathways that converge on NOS and CREB resulting in synergistic improvements in neuronal mitochondrial performance which confer profound protection against ischemic injury.

MiR-34a regulates blood–brain barrier permeability and mitochondrial function by targeting cytochrome c

Mimi Bukeirat1, Saumyendra N Sarkar1, Heng Hu1,2, Dominic D Quintana1, James W Simpkins1,2, Xuefang Ren1,2 ⇑
J Cereb Blood Flow Metab Sep 30, 2015 0271678X15606147
http://jcb.sagepub.com/content/early/2015/09/15/0271678X15606147.abstract http://dx.doi.org:/10.1177/0271678X15606147

The blood–brain barrier is composed of cerebrovascular endothelial cells and tight junctions, and maintaining its integrity is crucial for the homeostasis of the neuronal environment. Recently, we discovered that mitochondria play a critical role in maintaining blood–brain barrier integrity. We report for the first time a novel mechanism underlying blood–brain barrier integrity: miR-34a mediated regulation of blood–brain barrier through a mitochondrial mechanism. Bioinformatics analysis suggests miR-34a targets several mitochondria-associated gene candidates. We demonstrated that miR-34a triggers the breakdown of blood–brain barrier in cerebrovascular endothelial cell monolayer in vitro, paralleled by reduction of mitochondrial oxidative phosphorylation and adenosine triphosphate production, and decreased cytochrome c levels.

The blood–brain barrier (BBB) is composed of highly specialized cerebrovascular endothelial cells (CECs), separates brain tissue from the circulating blood, and maintains homeostasis of the neuronal environment.¹ The CECs are interconnected by tight junctions including cytoplasmic zonula occludens (ZO) proteins, and various transmembrane proteins such as occludin and claudins.² Disruption of BBB tight junctions has been well documented in cerebrovascular diseases and neurodegenerative disorders and is considered to be a pathological condition of the diseases and plays a key role in disease progression as well.²

A recent study demonstrates that the mitochondrial mechanisms regulate BBB integrity and permeability using oxygen–glucose deprivation and reoxygenation (OGD-R), anin vitro model of ischemic reperfusion injury.³ Our work demonstrates that compromised mitochondria lead to the disruption of tight junctions, opening of the BBB, and exacerbation of stroke outcomes.⁴ As such, regulation of mitochondrial function may affect BBB openings and could be critical in limiting the pathological progression of cerebrovascular diseases and neurodegenerative disorders.

MicroRNAs (miRNAs) are short non-coding functional RNAs that target certain messenger RNAs (mRNAs) through complementary base-pairing between the miRNAs and its mRNA targets, resulting in the inhibition of mRNA translation or degradation of mRNA.⁵ It has been documented that miRNAs are involved in mitochondrial structure and function, such as miR-181c which regulates mitochondrial morphology,⁶ miR-1 which affects mitochondrial mRNA translation,⁷ and miR-378 which targets mitochondrial enzymes involved in oxidative energy metabolism.⁸ Additionally, several miRNAs have recently been found to regulate BBB permeability. MiR-155, miR-181c, and miR-29c negatively affect BBB function by targeting tight junction protein genes directly or affecting related signal pathways.^9⇓–11 The miR-34 family members were discovered computationally and later verified experimentally as a part of the p53 tumor suppressor network. Recent work demonstrates that miR-34a modulates the expression of synaptic targets and neuronal morphology and function.¹² However, little is known regarding the role of miR-34a in mitochondrial function and BBB permeability.

In the present study, we report that the overexpression of miR-34a breaks down the BBB through inhibition of mitochondrial function. Furthermore, cytochrome c (CYC) is experimentally verified as a target of miR-34a in vitro.

Overexpression of miR-34a affects BBB permeability and disrupts tight junctions in CECs

To determine whether miR-34a functionally affected the BBB, we transfected CECs with miR34a plasmid versus vector control in 24-well plates, cultured the cells for 48 h, conducted a BBB permeability assay in a CEC monolayer transwell system in vitro with an additional culture of 48 h, and measured the fluorescent dye FD-4 permeability of each well (Figure 1(a)). As shown in Figure 1(a), FD-4 permeability was significantly increased in wells containing miR-34a overexpression CEC monolayer. Papp, the permeability coefficient, was also significantly higher in CECs overexpressed with miR-34a in comparison to vector controls (Figure 1(a)). Furthermore, immunohis-tochemistry staining of tight junction-related proteins revealed that ZO-1 was continuously distributed in the control, but a discontinuous distribution of ZO-1 was observed in miR-34a overexpressed CEC monolayer (Figure 1(b)). Disruption of tight junctions was not associated with cell viability in CECs transfected with plasmids for 48 h or 96 h (Supplementary Figure 2). Altogether, these data suggest that overexpression of miR-34a increases BBB permeability and compromises BBB tight junctions.

View larger version:

Figure 1.

Overexpression of miR-34a increases BBB permeability in vitro. (a) A schematic protocol using fluorescein isothiocyanate–dextran-4 (FD-4) to detect BBB permeability in vitro. FD-4 permeability in CECs that overexpressed miR-34a plasmid (0.017 ng) versus control was presented as real-time rate of FD-4 mean fluorescent intensity (2-way ANOVA followed by post hoc Dunnett’s test; n = 3; **, P < 0.01; ****, P < 0.0001). Calculated apparent permeability coefficient P_app(Student’s t-test; ****, P < 0.0001) is expressed as mean ± SD. (b) Confocal fluorescence images of CECs confluent monolayers confirmed microscopically after transfection with miR-34a plasmid versus control. Fluorescent staining: tight junctions ZO-1 (red), cell nuclei (DAPI, blue). Overexpression of miR-34a apparently disrupted tight junctions and resulted in gaps between cells (white arrows). Results are representative of three independent experiments.

MiR-34a affects mitochondrial function by targeting CYC in CECs

Our recent work demonstrated that mitochondria play a pivotal role in the maintenance of BBB integrity. BBB tight junctions are rapidly disrupted if oxidative phosphorylation is reduced by mitochondrial inhibitors.⁴ To investigate whether the miR-34a regulates BBB openings via affecting mitochondrial function in CECs, we examined cellular energetic OCRs in CECs transfected with miR-34a plasmid versus vector control. Interestingly, overexpression of miR-34a significantly impaired mitochondrial function in CECs (Figure 2(a) and Supplementary Figure 3). Basal respiration, ATP production, maximal respiration, and spare capacity were all significantly reduced in CECs overexpressing miR-34a for 48 and 72 h (Figure 2(a)). ATP level was also substantially reduced in CECs following overexpression of miR-34a in a dose dependent manner at 72 h (Figure 2(b)).

View larger version:

Figure 2.

Overexpression of mir-34a reduces mitochondrial function and decreases CYC level in cerebrovascular endothelial cells. (a) Basal respiration, ATP production, maximal respiration, and spare capacity were calculated from the bioenergetics functional assay at post-transfection 48 and 72 h (raw data in Supplementary Figure 3). Data are expressed as mean ± SD (n = 5). 1-way ANOVA followed by post hoc Tukey’s test. (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001). (b) ATP level was measured at 72 h post-transfection. Data are expressed as mean ± SD (n = 5). 1-way ANOVA followed by post hoc Tukey’s test. (****, P < 0.0001). (c) Bioinfomatic analysis of miR-34a-targeting candidates related to mitochondria. (d) Flow cytometry analysis of mitochondrial specific proteins for complex I proteins (NDUFAF1, NDUFC2 and NDUFS2), complex II protein (SDHC), complex III protein (CYB), complex IV protein (CYC oxidase, Cox IV), cytochrome c (CYCS), pyruvate dehydrogenase kinase (PDK), and voltage-dependent anion channel protein (VDAC) at 72 h post-transfection. CYC level was significantly lower in the cells that were transfected with the miR-34a plasmid. Data are presented as mean ± SD (n = 3) and analyzed by Student’s t-test, *, P < 0.05; ***, P < 0.001; ****, P < 0.0001. Results are representative of three independent experiments.

To further determine miR-34a targets and uncover the mechanism that is used to affect mitochondria, we performed a bioinformatics analysis of the miR-34a database (miRbase and TargetScan). MiR-34a potentially targets several mitochondria-associated gene candidates including succinate dehydrogenase subunit c (SDHC), cytochrome B reductase 1 (CYBRD1), cytochrome B5 reductase 3 (CYBRD5), cytochrome c (CYCS), pyruvate dehydrogenase kinase isozyme 1 and 2 (PDK1 and PDK2) (Figure 2(c). However, CECs transfected with the miR-34a plasmid had robustly decreased CYCS levels measured by flow cytometry, suggesting that CYCS is one of the miR-34a targets among the potential candidates (Figure 2(d)). Moreover, overexpression of miR-34a slightly increased potential target SDHC but did not change the protein level of CYB and PKD (Figure 2(d)). Off-target genes, NDUFAF1, and VDAC showed no significant change in protein level, but NDUFC2, NDUFS2, and Cox IV were all increased in parallel with overexpression of miR-34a (Figure 2(d)). Taken together, these results experimentally verified CYCS as a miR-34a target, which is associated with the reduction of mitochondrial oxidative phosphorylation in CECs.

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Discussion

In the present study, we demonstrated that the overexpression of miR-34a results in an increased BBB permeability and the disruption of tight junctions ZO-1 in CECs. Consistently, overexpression of miR-34a impaired mitochondrial oxidative phosphorylation and reduced ATP production in CECs. Bioinformatics analysis revealed series of potential miR-34a-targeting candidates related to mitochondrial function. We elucidated that CYCS is a miR-34a target, and the overexpression of miR-34a inhibited the CYCS expression and increased with the expression of other mitochondria-associated genes.

The overexpression of miR-34a disrupted tight junction protein ZO-1 (Figure 1). However, bioinformatics analysis indicated that miR-34a did not target the ZO-1 gene or other tight junction related genes, which suggests that the increased BBB permeability is not directly caused by the targeting of tight junction protein genes. The compromised mitochondrial function by overexpression of miR-34a may influence cellular metabolism in a way that is critical to maintain BBB tight junctions. Among several potential mitochondria-associated gene targets (Figure 2(c)), miR-34a initiated the reduction of CYCS level. Interestingly, potential target SDHC and other off-target gene proteins (NDUFC2, NDUFS2, and Cox IV) were concurrently upregulated (Figure 2(d)), which might be due to the compensation for the reduced target gene protein CYCS, or the disturbance of the coordinated gene translation in mitochondria. We therefore concluded that CYCS is a miR-34a target and is responsible for the miR-34a-induced reduction of mitochondrial oxidative phosphorylation.

Protein kinase C (PKC) signaling has also been shown to affect BBB or other endothelial barriers in vitro and in vivo. A recent study reported that miR-34a regulated blood–tumor barrier by targeting PKCɛ using glioma endothelial cells.¹³ In this study, we did not assess the PKC pathways that could contain additional targets of miR-34a. However, our data do support that miR-34a affects BBB via a mitochondrial mechanism, which is novel and may lead a new direction for designing BBB-related therapeutics.

We have noted several limitations in our study. First, we did not examine the effects of knockdown or knockout miR-34a on BBB function, which might fully establish the role of miR-34a in the BBB and mitochondria. Second, this work was conducted in cell culture models, which adequately address the mechanism of effect that miR-34a exerts on the BBB and mitochondria but do not provide evidence of its involvement in cerebrovascular or neurodegenerative conditions. Further studies in relevant experimental models are warranted.

Mitochondria play a pivotal role in cellular bioenergetics and cell survival, participating in a variety of cellular processes, including the generation of ATP, and the regulation of apoptotic signaling and other signaling pathways.¹⁴ MiR-34a targets and represses multiple genes involved in cell proliferation, apoptosis, cell cycle, migration, etc.,¹⁵ but it is not known if these effects are modulated by the observed mitochondrial effects as well. The present study provides the first description of miR-34a affecting mitochondrial activity, which could lead to a revision of current miR-34a targets and may lead to discovery of new mechanisms. The elucidation of the miR-34a’s role in mitochondrial oxidative phosphorylation and the BBB integrity offers a novel therapeutic strategy for targeting miR-34a to treat cerebrovascular and neurodegenerative diseases such as stroke and Alzheimer’s disease. These neuropathological diseases are known to involve a host of conditions that lead to mitochondrial impairment and BBB disruption. Finally, transient opening of the BBB could prove to be useful for CNS drug delivery.

Long-term aerobic exercise prevents age-related brain deterioration
http://www.kurzweilai.net/long-term-aerobic-exercise-prevents-age-related-brain-deterioration

October 30, 2015

A study of the brains of mice shows that structural deterioration associated with old age can be prevented by long-term aerobic exercise starting in mid-life, according to the authors of an open-access paper in the journal PLOS Biologyyesterday (October 29).

Old age is the major risk factor for Alzheimer’s disease, like many other diseases, as the authors at The Jackson Laboratory in Bar Harbor, Maine, note. Age-related cognitive deficits are due partly to changes in neuronal function, but also correlate with deficiencies in the blood supply to the brain and with low-level inflammation.

“Collectively, our data suggests that normal aging causes significant dysfunction to the cortical neurovascular unit, including basement membrane reduction and pericyte (cells that wrap around blood capillaries) loss. These changes correlate strongly with an increase in microglia/monocytes in the aged cortex,” said Ileana Soto, lead author on the study.*

Benefits of aerobic exercise

However, the researchers found that if they let the mice run freely, the structural changes that make the blood-brain barrier leaky and result in inflammation of brain tissues in old mice can be mitigated. That suggests that there are also beneficial effects of exercise on dementia in humans.**

Further work will be required to establish the mechanism(s): what is the role of the complement-producing microglia/macrophages, how does Apoe decline contribute to age-related neurovascular decline, does the leaky blood-brain barrier allow the passage of damaging factors from the circulation into the brain?

This work was funded in part by The Jackson Laboratory Nathan Shock Center, the Fraternal Order of the Eagle, the Jane B Cook Foundation and NIH.

* The authors investigated the changes in the brains of normal young and aged laboratory mice by comparing by their gene expression profiles using a technique called RNA sequencing, and by comparing their structures at high-resolution by using fluorescence microscopy and electron microscopy. The gene expression analysis indicated age-related changes in the expression of genes relevant to vascular function (including focal adhesion, vascular smooth muscle and ECM-receptor interactions), and inflammation (especially related to the complement system, which clears foreign particles) in the brain cortex.

These changes were accompanied by a decline in the function of astrocytes (key support cells in the brain) and loss of pericytes (the contractile cells that surround small capillaries and venules and maintain the blood-brain barrier). There were also effects on the basement membrane, which forms an integral part of the blood-brain barrier, as well as an increase in the density and functional activation of the immune cells known as microglia/monocytes, which scavenge the brain for infectious agents and damaged cells.

** To investigate the impact of long-term physical exercise on the brain changes seen in the aging mice, the researchers provided the animals with a running wheel from 12 months old (equivalent to middle aged in humans) and assessed their brains at 18 months (equivalent to ~60yrs old in humans, when the risk of Alzheimer’s disease is greatly increased). Young and old mice alike ran about two miles per night, and this physical activity improved the ability and motivation of the old mice to engage in the typical spontaneous behaviors that seem to be affected by aging.

This exercise significantly reduced age-related pericyte loss in the brain cortex and improved other indicators of dysfunction of the vascular system and blood-brain barrier. Exercise also decreased the numbers of microglia/monocytes expressing a crucial initiating component of the complement pathway that others have shown previously to play are role in age-related cognitive decline. Interestingly, these beneficial effects of exercise were not seen in mice deficient in a gene called Apoe, variants of which are a major genetic risk factor for Alzheimer’s disease. The authors also report that Apoe expression in the brain cortex declines in aged mice and this decline can also be prevented by exercise.

Abstract of APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction

Aging is the major risk factor for neurodegenerative diseases such as Alzheimer’s disease, but little is known about the processes that lead to age-related decline of brain structures and function. Here we use RNA-seq in combination with high resolution histological analyses to show that aging leads to a significant deterioration of neurovascular structures including basement membrane reduction, pericyte loss, and astrocyte dysfunction. Neurovascular decline was sufficient to cause vascular leakage and correlated strongly with an increase in neuroinflammation including up-regulation of complement component C1QA in microglia/monocytes. Importantly, long-term aerobic exercise from midlife to old age prevented this age-related neurovascular decline, reduced C1QA+ microglia/monocytes, and increased synaptic plasticity and overall behavioral capabilities of aged mice. Concomitant with age-related neurovascular decline and complement activation, astrocytic Apoe dramatically decreased in aged mice, a decrease that was prevented by exercise. Given the role of APOE in maintaining the neurovascular unit and as an anti-inflammatory molecule, this suggests a possible link between astrocytic Apoe, age-related neurovascular dysfunction and microglia/monocyte activation. To test this, Apoe-deficient mice were exercised from midlife to old age and in contrast to wild-type (Apoe-sufficient) mice, exercise had little to no effect on age-related neurovascular decline or microglia/monocyte activation in the absence of APOE. Collectively, our data shows that neurovascular structures decline with age, a process that we propose to be intimately linked to complement activation in microglia/monocytes. Exercise prevents these changes, but not in the absence of APOE, opening up new avenues for understanding the complex interactions between neurovascular and neuroinflammatory responses in aging and neurodegenerative diseases such as Alzheimer’s disease.

references:

Ileana Soto, Leah C. Graham, Hannah J. Richter, Stephen N. Simeone, Jake E. Radell, Weronika Grabowska, W. Keith Funkhouser, Megan C. Howell, Gareth R. Howell. APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction. PLOS Biology, October 29, 2015; DOI: 10.1371/journal.pbio.1002279 (open access)

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Current Advances in Medical Technology

Posted in Bio Instrumentation in Experimental Life Sciences Research, BioIT: BioInformatics, Biological Networks, Cell Biology, Cerebrovascular and Neurodegenerative Diseases, Clinical & Translational, Clinical Diagnostics, Curation, Drug Development using MultiOrgan Chip, Gastroenterology, Genetics & Pharmaceutical, Genome Biology, Image Processing/Computing, Infectious Disease Immunodiagnostics, Innovations, Innovations in Neurophysiology & Neuropsychology, Organ-on-a-Chip, Programmable Sensors (Carbon Nano Tubes), tagged biomedical imaging, gene editing, Influenza virus typing, Medical technology, organ on a chip on October 13, 2015| Leave a Comment »

Current Advances in Medical Technology

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Pumpkin-Shaped Molecule Enables 100-Fold Improved MRI Contrast

Tue, 10/13/2015 – 9:16amby Forschungsverbund Berlin e.V. (FVB)

http://www.mdtmag.com/news/2015/10/pumpkin-shaped-molecule-enables-100-fold-improved-mri-contrast

Assuming that we could visualize pathological processes such as cancer at a very early stage and additionally distinguish the various different cell types, this would represent a giant step for personalized medicine. Xenon magnetic resonance imaging has the potential to fulfil this promise – if suitable contrast media are found that react sensitively enough to the “exposure”. Researchers at the Leibniz-Institut für Molekulare Pharmakologie in Berlin have now found that a class of pumpkin-shaped molecules called cucurbiturils together with the inert gas xenon, enables particularly good image contrast – namely around 100 times better than has been possible up to now. This finding published in the November issue cover article of Chemical Science by the Royal Society of Chemistry points the way to the tailoring of new contrast agents to different cell types and has the potential to enable molecular diagnostics even without tissue samples in the future.

Personalized medicine instead of one treatment for all – especially in cancer medicine, this approach has led to a paradigm shift. Molecular diagnostics is the key that will give patients access to tailor-made therapy. However, if tumors are located in poorly accessible areas of the body or several tumor foci are already present, this often fails due to a lack of sufficient sensitivity of the diagnostic imaging. But such sensitivity is needed to determine the different cell types, which differ considerably even within a tumor. Although even the smallest of tumor foci and other pathological changes can be detected using the PET-CT, a differentiation according to cell type is usually not possible.

Scientists from the FMP are therefore focusing on xenon magnetic resonance imaging: The further development of standard magnetic resonance imaging makes use of the “illuminating power” of the inert gas xenon, which can provide a 10,000-fold enhanced signal in the MRI. To do this, it must be temporarily captured by so-called “cage molecules” in the diseased tissue. This has been more or less successful with the molecules used to date, but the experimental approach is still far from a medical application.

Cucurbituril Provides Stunning Image Contrasts
The research group led by Dr. Leif Schröder at the Leibniz-Institut für Molekulare Pharmakologie (FMP) has now discovered a molecule class for this purpose that eclipses all of the molecules used to date. Cucurbituril exchanges around 100 times more xenon per unit of time than its fellow molecules, which leads to a much better image contrast. “It very quickly became clear that cucurbituril might be suitable as a contrast medium,” reports Leif Schröder. “However, it was surprising that areas marked with it were imaged with a much better contrast than previously.” The explanation is to be found in the speed. Upon exposure, so to speak, cucurbituril generates contrast more rapidly than all molecules used to date, as it only binds the xenon very briefly and thus transmits the radio waves to detect the inert gas to very many xenon atoms within a fraction of a second. In this way, the inert gas is passed through the molecule much more efficiently.

In the study, which appeared in the specialist journal “Chemical Science”, the world’s first MRI images with cucurbituril have been achieved. With the aid of a powerful laser and a vaporized alkali metal, the researchers initially greatly strengthened the magnetic properties of normal xenon. The hyperpolarized gas was then introduced into a test solution with the cage molecules. A subsequent MRI image showed the distribution of the xenon in the object. In a second image, the curcurbituril together with radio waves destroyed the magnetization of the xenon, leading to dark spots on the images.

“Comparison of the two images demonstrates that only the xenon in the cages has the right resonance frequency to produce a dark area,” explains Schröder. “This blackening is possible to a much better degree with cucurbituril than with previous cage molecules, for it works like a very light-sensitive photographic paper. The contrast is around 100 times stronger.”

Time-of-Flight IC Revolutionizes Object Detection and Distance Measurement

Tue, 10/13/2015 – 9:07amby Intersil

New ISL29501 signal processing IC detects objects up to two meters

http://www.mdtmag.com/product-release/2015/10/time-flight-ic-revolutionizes-object-detection-and-distance-measurement
Intersil Corporation has introduced an innovative time-of-flight (ToF) signal processing IC that provides a complete object detection and distance measurement solution when combined with an external emitter (LED or laser) and photodiode. The ISL29501 ToF device offers one-of-a-kind functionality, including ultra-small size, low-power consumption and superior performance ideal for connected devices that make up the Internet of Things (IoT), as well as consumer mobile devices and the emerging commercial drone market.

The ISL29501 overcomes the shortcomings of traditional amplitude-based proximity sensors and other ToF solutions that perform poorly in lighting conditions above 2,000 lux, or cannot provide distance information unless the object is perpendicular to the sensor.

The ISL29501 applies Intersil’s power management expertise to save power and extend battery life through several innovations.

“Prior to Intersil’s time-of-flight technology breakthrough, there was no practical way to measure distance up to two meters in a small form factor,” said Andrew Cowell, senior vice president of Mobile Power Products at Intersil. “The innovative ISL29501 provides customers a cost-effective, small footprint solution that also gives them the flexibility to use multiple devices to increase the field of view to a full 360 degrees for enhanced object detection capabilities.”

Key Features and Specifications

On-chip DSP calculates ToF for accurate proximity detection and distance measurement up to two meters
Modulation frequency of 4.5MHz prevents interference with other consumer products such as IR TV remote controls that operate at 40kHzOn-chip emitter DAC with programmable current up to 255mA
Allows designers to choose the desired current level to optimize distance measurement and power budget
Operates in single shot mode for initial object detection and approximate distance measurement, while continuous mode improve distance accuracy
On-chip active ambient light rejection minimizes or eliminates the influence of ambient light during distance measurement
Programmable distance zones: allows the user to define three ToF distance zones for determining interrupt alerts
Interrupt controller generates interrupt alerts using distance measurements and user defined thresholds
Automatic gain control sets optimum analog signal levels to achieve best SNR response
Supply voltage range of 2.7V to 3.3V
I2C interface supports 1.8V and 3.3V bus

The ISL29501 can be combined with the ISL9120 buck-boost regulator to further reduce power consumption and extend battery life in consumer and home automation applications.

Optoelectronic Implantable Could Enable Two-Way Communication with Brain

Mon, 10/12/2015 – 4:04pmby Brown University

http://www.mdtmag.com/news/2015/10/optoelectronic-implantable-could-enable-two-way-communication-brain

Brown University researchers have created a new type of optoelectronic implantable device to access brain microcircuits, synergizing a technique that enables scientists to control the activity of brains cells using pulses of light. The invention, described in the journal Nature Methods, is a cortical microprobe that can stimulate multiple neuronal targets optically by specific patterns on micrometer scale while simultaneously recording the effects of that stimulation in the underlying neural microcircuits of interest with millisecond precision.

“We think this is a window-opener,” said Joonhee Lee, a senior research associate in Professor Arto Nurmikko’s lab in the School of Engineering at Brown and one of the lead authors of the new paper. “The ability to rapidly perturb neural circuits according specific spatial patterns and at the same time reconstruct how the circuits involved are perturbed, is in our view a substantial advance.”

First introduced around 2005, optogenetics has enriched ability of scientists seeking to understand brain function at the neuronal level. The technique involves genetically engineering neurons to express light-sensitive proteins on their membranes. With those proteins expressed, pulses of light can be used to either promote or suppress activity in those particular cells. The method gives researchers in principle unprecedented ability to control specific brain cells at specific times.

But until now, simultaneous optogenetic stimulation and recording of brain activity rapidly across multiple points within a brain microcircuit of interest has proven difficult. Doing it requires a device that can both generate a spatial pattern of light pulses and detect the dynamical patterns of electrical reverberations generated by excited cellular activity. Previous attempts to do this involved devices that cobbled together separate components for light emission and electrical sensing. Such probes were physically bulky, not ideal for insertion into a brain. And because the emitters and the sensors were necessarily a hundreds of micrometers apart, a sizable distance, the link between stimulation and recorded signal was ambiguous.

The new compact, integrated device developed by Nurmikko’s lab begins with the unique advantages endowed by a so-called wide bandgap semiconductor called zinc oxide. It is optically transparent yet able readily to conduct an electrical current.

“Very few materials have that pair of physical properties,” Lee said. “The combination makes it possible to both stimulate and detect with the same material.”

Joonhee Lee, with Assistant Research Professor Ilker Ozden and Professor Yoon-Kyu Song at Seoul National University in Korea, co-developed a novel microfabrication method with Nurmikko to shape the material into a monolithic chip just a few millimeters square with sixteen micrometer sized pin-like “optoelectrodes,” each capable of both delivering light pulses and sensing electrical current. The array of optoelectrodes enables the device to couple to neural microcircuits composed of many neurons rather than single neurons.

Such ability to stimulate and record at the network level on spatial and time scales at which they operate is key, Nurmikko says. Brain functions are driven by neural circuits rather than single neurons.

“For example, when I move my hand, that’s an example of action driven by specific network-level activity in the brain,” he said. “Our new device approach gives scientists and engineers a tool in applying the full power of optogenetics as a means of neural stimulation, while providing the means to read activity of perturbed networks at multiple points at high spatial precision and time resolution.”

Ozden led the initial testing of the device in rodent models. The researchers looked at the extent to which different light intensities could stimulate network activity. The tests showed that increasing optical power led to distinct recruitment of neuronal circuits revealing functional connectivity in the targeted network.

“We went over a range of optical power that was large–over three orders of magnitude–and in so doing we got a range of network-related responses, in particular we could replicate an activity pattern naturally occurring in the brain.” Ozden said. “It gave us a new insight into how optogenetics operates on the network level. This gives us encouragement to go ahead and extend the repertoire and application of the device technology.”

Nurmikko’s group together with the Song lab in Seoul plan to continue further development of the device, ultimately include an access via wireless means. Their next steps anticipate the use of the new device technology as chronic implant in non-human primates at potentially hundreds of points and, depending on progress in worldwide research on optogenetics ahead, perhaps even one day in humans.

“At least, the initial building blocks are here,” Nurmikko said, who conceived the idea with his Korean colleague Song.

Study Advances Possibility of Mind-Controlled Devices

Mon, 10/12/2015 – 10:50amby Ryan Bushey, Associate Editor, R&D

A study published in the journal Nature Medicine has shown a possible path to creating effective neural prosthetics.

http://www.mdtmag.com/blog/2015/10/study-advances-possibility-mind-controlled-devices

The study’s subjects, only listed as T6 and T7, have Amyotropic Lateral Sclerosis (ALS). The scientists performed surgery on them one year ago to place a “neural recording device” in the part of the brain in charge of controlling hand function, notes Bloomberg.

The test documented in the study required T6 and T7 to perform a variety of tasks, such as moving a cursor to hit different targets on a computer screen. The device receives electrical impulses from the brain and morphs them into a computer signal to operate the cursor.

Both test subjects had the highest published performance so far, and even doubled the results of the previous clinical trial participant, according to the study.

The hope is that these devices can improve quality of life for people suffering from paralysis.

You can watch how T6 performed in her test below.

https://youtu.be/9P-qsiIORVU

Removing 62 Barriers to Pig–to–Human Organ Transplant in One Fell Swoop

Mon, 10/12/2015 – 9:09amby Wyss Institute for Biologically Inspired Engineering

The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them

http://www.mdtmag.com/news/2015/10/removing-62-barriers-pig%E2%80%93%E2%80%93human-organ-transplant-one-fell-swoop

Never before have scientists been able to make scores of simultaneous genetic edits to an organism’s genome. But now in a landmark study by George Church, Ph.D., and his team at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Harvard Medical School, the gene editing system known as “CRISPR–Cas9” has been used to genetically engineer pig DNA in 62 locations – an explosive leap forward in CRISPR’s capability when compared to its previous record maximum of just six simultaneous edits. The 62 edits were executed by the team to inactivate retroviruses found natively in the pig genome that have so far inhibited pig organs from being suitable for transplant in human patients. With the retroviruses safely removed via genetic engineering, however, the road is now open toward the possibility that humans could one day receive life–saving organ transplants from pigs.

Church is a Wyss Core Faculty member, the Robert Winthrop Professor of Genetics at Harvard Medical School (HMS) and Professor of Health Sciences and Technology at Harvard and MIT. The advance, reported by Church and his team including the study’s lead author Luhan Yang, Ph.D., a Postdoctoral Fellow at HMS and the Wyss Institute, was published in the October 11 issue of Science.

The concept of xenotransplantation, which is the transplant of an organ from one species to another, is nothing new. Researchers and clinicians have long hoped that one of the major challenges facing patients suffering from organ failure – which is the lack of available organs in the United States and worldwide – could be alleviated through the availability of suitable animal organs for transplant. Pigs in particular have been especially promising candidates due to their similar size and physiology to humans. In fact, pig heart valves are already commonly sterilized and de–cellularized for use repairing or replacing human heart valves.

This artistic rendering shows pig chromosomes (background) which reside in the nucleus of pig cells and contain a single strand of RNA, and the Cas9 protein targeting DNA (foreground). The CRISPR–Cas9 gene editing system works like molecular scissors to precisely edit genes of interest. A new advance reported in Science by Wyss Core Faculty member George Church and his team used Cas9 to make 62 edits to the pig genome to remove latent retroviruses, presenting a solution to one of the largest safety concerns that has so far blocked progress in making pig organs compatible for xenotransplant in humans. (Credit: Wyss Institute at Harvard University)

But the transplant of whole, functional organs comprised of living cells and tissue constructs has presented a unique set of challenges for scientists. One of the primary problems has been the fact that most mammals including pigs contain repetitive, latent retrovirus fragments in their genomes – present in all their living cells – that are harmless to their native hosts but can cause disease in other species.

“The presence of this type of virus found in pigs – known as porcine endogenous retroviruses or PERVs – brought over a billion of dollars of pharmaceutical industry investments into developing xenotransplant methods to a standstill by the early 2000s,” said Church. “PERVs and the lack of ability to remove them from pig DNA was a real showstopper on what had been a promising stage set for xenotransplantation.”

Now – using CRISPR–Cas9 like a pair of molecular scissors – Church and his team have inactivated all 62 repetitive genes containing a PERV in pig DNA, surpassing a significant obstacle on the path to bringing xenotransplantation to clinical reality. With more than 120,000 patients currently in the United States awaiting transplant and less than 30,000 transplants on average occurring annually, xenotransplantation could give patients and clinicians an alternative in the future.

“Pig kidneys can already function experimentally for months in baboons, but concern about the potential risks of PERVs has posed a problem for the field of xenotransplantation for many years,” said David H. Sachs, M.D., Director of the TBRC Laboratories at Massachusetts General Hospital, Paul S. Russell Professor of Surgery Emeritus at Harvard Medical School, and Professor of Surgical Sciences at Columbia University’s Center for Translational Immunology. Sachs has been developing special pigs for xenotransplantation for more than 30 years and is currently collaborating with Church on further genetic modifications of his pigs. “If Church and his team are able to produce pigs from genetically engineered embryos lacking PERVs by the use of CRISPR-Cas9, they would eliminate an important potential safety concern facing this field.”

Yang says the team hopes eventually they can completely eliminate the risk that PERVs could cause disease in clinical xenotransplantation by using modified pig cells to clone a line of pigs that would have their PERV genes inactivated.

“This advance overcomes a major hurdle that has until now halted the progress of xenotransplantation research and development,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences. “The real value and potential impact is in the number of lives that could be saved if we can one day use xenotransplants to close the huge gap between the number of available functional organs and the number of people who desperately need them.”

The remarkable and newly demonstrated capability for CRISPR to edit tens of repetitive genes such as PERVs will also unlock new ways for scientists to study and understand repetitive regions in the genome, which has been estimated to comprise more than two–thirds of our own human genome.

Contributors to the work also included: co–lead authors Marc Güell of the Wyss Institute and Harvard Medical School Department of Genetics, Dong Niu of HMS Dept. of Genetics and Zhejiang University’s College of Animal Sciences, and Haydy George of HMS Dept. of Genetics; and co–authors Emal Lesha, Dennis Grishin, Jürgen Poci, Ellen Shrock, and Rebeca Cortazio of HMS Dept. of Genetics, Weihong Xu of Massachusetts General Hospital Department of Surgery, and Robert Wilkinson and Jay Fishman of MGH’s Transplant Infection Disease & Compromised Host Program.

Novel Gut-on-a-Chip Nearly Indistinguishable from Human GI Tract

Fri, 10/09/2015 – 1:17pmby University of North Carolina Healthcare

http://www.mdtmag.com/news/2015/10/novel-gut-chip-nearly-indistinguishable-human-gi-tract?et_cid=4876632&et_rid=535648082

A team of researchers from the University of North Carolina at Chapel Hill and NC State University has received a $5.3 million, five-year Transformative Research (R01) Award from the National Institutes of Health (NIH) to create fully functioning versions of the human gut that fit on a chip the size of a dime.

Such “organs-on-a-chip” have become vital for biomedical research, as researchers seek alternatives to animal models for drug discovery and testing. The new grant will fund a technology that represents a major step forward for the field, overcoming limitations that have mired other efforts.

The technology will use primary cells derived directly from human biopsies, which are known to provide more relevant results than the immortalized cell lines used in current approaches. In addition, the device will sculpt these cells into the sophisticated architecture of the gut, rather than the disorganized ball of cells that are created in other miniature organ systems.

This is a picture of a schematic of colonic epithelial tissue. Crypt units are pointed down, flat surface faces center of the gut tube. Stem cells are red, progenitor cells are pink, differentiated cells are grey, blue and green. Yellow cells are stem cell niche cells. Lumenal surface is above crypts. (Credit: Scott Magness, PhD, UNC School of Medicine)

“We are building a device that goes far beyond the organ-on-a-chip,” said Nancy L. Allbritton, MD, PhD, professor and chair of the UNC-NC State joint department of biomedical engineering and one of four principle investigators on the NIH grant. “We call it a ‘simulacrum,’ a term used in science fiction to describe a duplicate. The idea is to create something that is indistinguishable from your own gut.”

Allbritton is an expert at microfabrication and microengineering. Also on the team are intestinal stem cell expert Scott T. Magness, PhD, associate professor of medicine, biomedical engineering, and cell and molecular physiology in the UNC School of Medicine; microbiome expert Scott Bultman, PhD, associate professor of genetics in the UNC School of Medicine; and bioinformatics expert Shawn Gomez, associate professor of biomedical engineering at UNC-Chapel Hill and NC State.

The impetus for the “organ-on-chip” movement comes largely from the failings of the pharmaceutical industry. For just a single drug to go through the discovery, testing, and approval process can take as many as 15 years and as much as $5 billion dollars. Animal models are expensive to work with and often don’t respond to drugs and diseases the same way humans do. Human cells grown in flat sheets on Petri dishes are also a poor proxy. Three-dimensional “organoids” are an improvement, but these hollow balls are made of a mishmash of cells that doesn’t accurately mimic the structure and function of the real organ.

Basically, the human gut is a 30-foot long hollow tube made up of a continuous single-layer of specialized cells. Regenerative stem cells reside deep inside millions of small pits or “crypts” along the tube, and mature differentiated cells are linked to the pits and live further out toward the surface. The gut also contains trillions of microbes, which are estimated to outnumber human cells by ten to one. These diverse microbial communities — collectively known as the microbiota — process toxins and pharmaceuticals, stimulate immunity, and even release hormones to impact behavior.

These are fluorescent images of the side view of two synthetic crypts. Blue: nuclei of the cells. Red: proliferating stem cells in similar location to those in the human colon. (Credit: Scott Magness, PhD, UNC School of Medicine)

To create a dime-sized version of this complex microenvironment, the UNC-NC State team borrowed fabrication technologies from the electronics and microfluidics world. The device is composed of a polymer base containing an array of imprinted or shaped “hydrogels,” a mesh of molecules that can absorb water like a sponge. These hydrogels are specifically engineered to provide the structural support and biochemical cues for growing cells from the gut. Plugged into the device will be various kinds of plumbing that bring in chemicals, fluids, and gases to provide cues that tell the cells how and where to differentiate and grow. For example, the researchers will engineer a steep oxygen gradient into the device that will enable oxygen-loving human cells and anaerobic microbes to coexist in close proximity.

“The underlying concept — to simply grow a piece of human tissue in a dish — doesn’t seem that groundbreaking,” said Magness. “We have been doing that for a long time with cancer cells, but those efforts do not replicate human physiology. Using native stem cells from the small intestine or colon, we can now develop gut tissue layers in a dish that contains stem cells and all the differentiated cells of the gut. That is the thing stem cell biologists and engineers have been shooting for, to make real tissue behave properly in a dish to create better models for drug screening and cell-based therapies. With this work, we made a big leap toward that goal.”

Right now, the team has a working prototype that can physically and chemically guide mouse intestinal stem cells into the appropriate structure and function of the gut. For several years, Magness has been isolating and banking human stem cells from samples from patients undergoing routine colonoscopies at UNC Hospitals. As part of the grant, he will work with the rest of the team to apply these stem cells to the new device and create “simulacra” that are representative of each patient’s individual gut. The approach will enable researchers to explore in a personalized way how both the human and microbial cells of the gut behave during healthy and diseased states.

“Having a system like this will advance microbiota research tremendously,” said Bultman. “Right now microbiota studies involve taking samples, doing sequencing, and then compiling an inventory of all the microbes in the disease cases and healthy controls. These studies just draw associations, so it is difficult to glean cause and effect. This device will enable us to probe the microbiota, and gain a better understanding of whether changes in these microbial communities are the cause or the consequence of disease.”

On-Chip Optical Sensing Technique Detects Multiple Flu Strains

Tue, 10/06/2015 – 10:11amby University of California – Santa Cruz

http://www.mdtmag.com/news/2015/10/chip-optical-sensing-technique-detects-multiple-flu-strains?et_cid=4876632&et_rid=535648082

A schematic view shows the optical waveguide intersecting a fluidic microchannel containing target particles. Targets are optically excited as they flow past well-defined excitation spots created by multi-mode interference; fluorescence is collected by the liquid-core waveguide channel and routed into solid-core waveguides (red). (Credit: Ozcelik et al., PNAS 2015)

New chip-based optical sensing technologies developed by researchers at UC Santa Cruz and Brigham Young University enable the rapid detection and identification of multiple biomarkers. In a paper published October 5 in Proceedings of the National Academy of Sciences, researchers describe a novel method to perform diagnostic assays for multiple strains of flu virus on a small, dedicated chip.

“A standard flu test checks for about ten different flu strains, so it’s important to have an assay that can look at ten to 15 things at once. We showed a completely new way to do that on an optofluidic chip,” said senior author Holger Schmidt, the Kapany Professor of Optoelectronics in the Baskin School of Engineering at UC Santa Cruz.

Over the past decade, Schmidt and his collaborators at BYU have developed chip-based technology to optically detect single molecules without the need for high-end laboratory equipment. Diagnostic instruments based on their optofluidic chips could provide a rapid, low-cost, and portable option for identifying specific disease-related molecules or virus particles.

In the new study, Schmidt demonstrated a novel application of a principle called wavelength division multiplexing, which is widely used in fiber-optic communications. By superimposing multiple wavelengths of light in an optical waveguide on a chip, he was able to create wavelength-dependent spot patterns in an intersecting fluidic channel. Virus particles labeled with fluorescent markers give distinctive signals as they pass through the fluidic channel depending on which wavelength of light the markers absorb.

“Each color of light produces a different spot pattern in the channel, so if the virus particle is labeled to respond to blue light, for example, it will light up nine times as it goes through the channel, if it’s labeled for red it lights up seven times, and so on,” Schmidt explained.

The researchers tested the device using three different influenza subtypes labeled with different fluorescent markers. Initially, each strain of the virus was labeled with a single dye color, and three wavelengths of light were used to detect them in a mixed sample. In a second test, one strain was labeled with a combination of the colors used to label the other two strains. Again, the detector could distinguish among the viruses based on the distinctive signals from each combination of markers. This combinatorial approach is important because it increases the number of different targets that can be detected with a given number of wavelengths of light.

For these tests, each viral subtype was separately labeled with fluorescent dye. For an actual diagnostic assay, fluorescently labeled antibodies could be used to selectively attach distinctive fluorescent markers to different strains of the flu virus.

While previous studies have shown the sensitivity of Schmidt’s optofluidic chips for detection of single molecules or particles, the demonstration of multiplexing adds another important feature for on-chip bioanalysis. Compact instruments based on the chip could provide a versatile tool for diagnostic assays targeting a variety of biological particles and molecular markers.

The optofluidic chip was fabricated by Schmidt’s collaborators at Brigham Young University led by Aaron Hawkins. The joint first authors of the PNAS paper are Damla Ozcelik and Joshua Parks, both graduate students in Schmidt’s lab at UC Santa Cruz. Other coauthors include Hong Cai and Joseph Parks at UC Santa Cruz and Thomas Wall and Matthew Stott at BYU.

In another recent paper, published September 25 in Nature Scientific Reports, Schmidt’s team reported the development of a hybrid device that integrates an optofluidic chip for virus detection with a microfluidic chip for sample preparation.

“These two papers represent important milestones for us. Our goal has always been to use this technology to analyze clinically relevant samples, and now we are doing it,” Schmidt said.

Boom in Gene-Editing Studies amid Ethics Debate over Its Use

Mon, 10/12/2015 – 1:54pmby Lauran Neergaard, AP Medical Writer

http://www.mdtmag.com/news/2015/10/boom-gene-editing-studies-amid-ethics-debate-over-its-use-0

The hottest tool in biology has scientists using words like revolutionary as they describe the long-term potential: wiping out certain mosquitoes that carry malaria, treating genetic diseases like sickle cell, preventing babies from inheriting a life-threatening disorder.

It may sound like sci-fi, but research into genome editing is booming. So is a debate about its boundaries, what’s safe and what’s ethical to try in the quest to fight disease.

Does the promise warrant experimenting with human embryos? Researchers in China already have, and they’re poised to in Britain.

Should we change people’s genes in a way that passes traits to future generations? Beyond medicine, what about the environmental effects if, say, altered mosquitoes escape before we know how to use them?

“We need to try to get the balance right,” said Jennifer Doudna, a biochemist at the University of California, Berkeley. She helped develop new gene-editing technology and hears from desperate families, but urges caution in how it’s eventually used in people.

The U.S. National Academies of Science, Engineering and Medicine will bring international scientists, ethicists and regulators together in December to start determining that balance. The biggest debate is whether it ever will be appropriate to alter human heredity by editing an embryo’s genes.

“This isn’t a conversation on a cloud,” but something that families battling devastating rare diseases may want, Dr. George Daley of Boston Children’s Hospital told specialists meeting this week to plan the ethics summit. “There will be a drive to move this forward.”

Laboratories worldwide are embracing a technology to precisely edit genes inside living cells — turning them off or on, repairing or modifying them — like a biological version of cut-and-paste software. Researchers are building stronger immune cells, fighting muscular dystrophy in mice and growing human-like organs in pigs for possible transplant. Biotech companies have raised millions to develop therapies for sickle cell disease and other disorders.

The technique has a wonky name — CRISPR-Cas9 — and a humble beginning.

Doudna was studying how bacteria recognize and disable viral invaders, using a protein she calls “a genetic scalpel” to slice DNA. That system turned out to be programmable, she reported in 2012, letting scientists target virtually any gene in many species using a tailored CRISPR recipe.

There are older methods to edit genes, including one that led to an experimental treatment for the AIDS virus, but the CRISPR technique is faster and cheaper and allows altering of multiple genes simultaneously.

“It’s transforming almost every aspect of biology right now,” said National Institutes of Health genomics specialist Shawn Burgess.

In this photo provided by UC Berkeley Public Affairs, taken June 20, 2014 Jennifer Doudna, right, and her lab manager, Kai Hong, work in her laboratory in Berkeley, Calif. The hottest tool in biology has scientists using words like revolutionary as they describe the long-term potential: wiping out certain mosquitoes that carry malaria, treating genetic diseases like sickle-cell, preventing babies from inheriting a life-threatening disorder. “We need to try to get the balance right,” said Doudna. She helped develop new gene-editing technology and hears from desperate families, but urges caution in how it’s eventually used in people. (Cailey Cotner/UC Berkeley via AP)

CRISPR’s biggest use has nothing to do with human embryos. Scientists are engineering animals with human-like disorders more easily than ever before, to learn to fix genes gone awry and test potential drugs.

Engineering rodents to harbor autism-related genes once took a year. It takes weeks with CRISPR, said bioengineer Feng Zhang of the Broad Institute at MIT and Harvard, who also helped develop and patented the CRISPR technique. (Doudna’s university is challenging the patent.)

A peek inside an NIH lab shows how it works. Researchers inject a CRISPR-guided molecule into microscopic mouse embryos, to cause a gene mutation that a doctor suspects of causing a patient’s mysterious disorder. The embryos will be implanted into female mice that wake up from the procedure in warm blankets to a treat of fresh oranges. How the resulting mouse babies fare will help determine the gene defect’s role.

Experts predict the first attempt to treat people will be for blood-related diseases such as sickle cell, caused by a single gene defect that’s easy to reach. The idea is to use CRISPR in a way similar to a bone marrow transplant, but to correct someone’s own blood-producing cells rather than implanting donated ones.

“It’s like a race. Will the research provide a cure while we’re still alive?” asked Robert Rosen of Chicago, who has one of a group of rare bone marrow abnormalities that can lead to leukemia or other life-threatening conditions. He co-founded the MPN Research Foundation, which has begun funding some CRISPR-related studies.

So why the controversy? CRISPR made headlines last spring when Chinese scientists reported the first-known attempt to edit human embryos, working with unusable fertility clinic leftovers. They aimed to correct a deadly disease-causing gene but it worked in only a few embryos and others developed unintended mutations, raising fears of fixing one disease only to cause another.

If ever deemed safe enough to try in pregnancy, that type of gene change could be passed on to later generations. Then there are questions about designer babies, altered for other reasons than preventing disease.

In the U.S., the NIH has said it won’t fund such research in human embryos.

In Britain, regulators are considering researchers’ request to gene-edit human embryos — in lab dishes only — for a very different reason, to study early development.

Medicine aside, another issue is environmental: altering insects or plants in a way that ensures they pass genetic changes through wild populations as they reproduce. These engineered “gene drives” are in very early stage research, too, but one day might be used to eliminate invasive plants, make it harder for mosquitoes to carry malaria or even spread a defect that gradually kills off the main malaria-carrying species, said Kevin Esvelt of Harvard’s Wyss Institute for Biologically Inspired Engineering.

No one knows how that might also affect habitats, Esvelt said. His team is calling for the public to weigh in and for scientists to take special precautions. For example, Esvelt said colleagues are researching a tropical mosquito species unlikely to survive cold Boston even if one escaped locked labs.

“There is no societal precedent whatsoever for a widely accessible and inexpensive technology capable of altering the shared environment,” Esvelt told a recent National Academy of Sciences hearing.

Researchers Use ‘Avatar’ Experiments to Get Leg Up On Locomotion

Mon, 10/12/2015 – 5:09pmby North Carolina State University

North Carolina State University scientists take a giant leap closer to understanding locomotion from the leg up

http://www.mdtmag.com/news/2015/10/researchers-use-avatar-experiments-get-leg-locomotion

Simple mechanical descriptions of the way people and animals walk, run, jump and hop liken whole leg behavior to a spring or pogo stick.

But until now, no one has mapped the body’s complex physiology – which in locomotion includes multiple leg muscle-tendons crossing the hip, knee and ankle joints, the weight of a body, and control signals from the brain – with the rather simple physics of spring-like limb behavior.

Using an “Avatar”-like bio-robotic motor system that integrates a real muscle and tendon along with a computer controlled nerve stimulator acting as the avatar’s spinal cord, North Carolina State University researchers have taken a giant leap closer to understanding locomotion from the leg up. The findings could help create robotic devices that begin to merge human and machine in order to assist human locomotion.

Despite the complicated physiology involved, NC State biomedical engineer Greg Sawicki and Temple University post-doctoral researcher Ben Robertson show that if you know the mass, the stiffness and the leverage of the ankle’s primary muscle-tendon unit, you can predict neural control strategies that will result in spring-like behavior.

“We tried to build locomotion from the bottom up by starting with a single muscle-tendon unit, the basic power source for locomotion in all things that move,” said Greg Sawicki, associate professor in the NC State and UNC-Chapel Hill Joint Department of Biomedical Engineering and co-author of a paper published in Proceedings of the National Academy of Sciences that describes the work. “We connected that muscle-tendon unit to a motor inside a custom robotic interface designed to simulate what the muscle-tendon unit ‘feels’ inside the leg, and then electrically stimulated the muscle to get contractions going on the benchtop.”

The researchers showed that resonance tuning is a likely mechanism behind springy leg behavior during locomotion. That is, the electrical system – in this case the body’s nervous system – drives the mechanical system – the leg’s muscle-tendon unit – at a frequency which provides maximum ‘bang for the buck’ in terms of efficient power output.

Sawicki likened resonance tuning to interacting with a slinky toy. “When you get it oscillating well, you hardly have to move your hand – it’s the timing of the interaction forces that matters.

“In locomotion, resonance comes from tuning the interaction between the nervous system and the leg so they work together,” Sawicki said. “It turns out that if I know the mass, leverage and stiffness of a muscle-tendon unit, I can tell you exactly how often I should stimulate it to get resonance in the form of spring-like, elastic behavior.”

The findings have design implications relevant to designing exoskeletons for able-bodied individuals, as well as exoskeleton or prosthetic systems for people with mobility impairments.

“In the end, we found that the same simple underlying principles that govern resonance in simple mechanical systems also apply to these extraordinarily complicated physiological systems,” said Robertson, the corresponding author of the paper.

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Lonely Receptors: RXR – Jensen, Chambon, and Evans

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Clinical & Translational, CT, Discovery process, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Endocrine Diseases, Experimental validation, Explanatory, Gene Regulation, Genomic Endocrinology, Genomic Expression, Innovations in Neurophysiology & Neuropsychology, Metabolism, Molecular Genetics & Pharmaceutical, Neuroscience, Nutrition Disorders, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, tagged breast cancer, Estrogen receptor, nuclear receptor, progesterone receptor, retinoids, RXR, vitamin A and vitamin D metabolism on September 7, 2015| Leave a Comment »

Lonely Receptors: RXR – Jensen, Chambon, and Evans

Larry H. Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Series E. 2; 7.2

Nuclear receptors provoke RNA production in response to steroid hormones

Albert Lasker Basic Medical Research Award

Pierre Chambon, Ronald Evans and Elwood Jensen

For the discovery of the superfamily of nuclear hormone receptors and elucidation of a unifying mechanism that regulates embryonic development and diverse metabolic pathways.

Hormones control a vast array of biological processes, including embryonic development, growth rate, and body weight. Scientists had known since the early 1900s that tiny hormone doses dramatically alter physiology, but they had no idea that these signaling molecules did so by prodding genes. The 1950s, when Jensen began his work, was the great era of enzymology. Conventional wisdom held that estradiol—the female sex hormone that instigates growth of immature reproductive tissue such as the uterus—entered the cell and underwent a series of chemical reactions that produced a particular compound as a byproduct. This compound—NADPH—is essential for many enzymes’ operations but its small quantities normally limit their productivity. A spike in NADPH concentrations would stimulate growth or other activities by unleashing the enzymes, the reasoning went.

In 1956, Jensen (at the University of Chicago) decided to scrutinize what happened to estradiol within its target tissues, but he had a problem: The hormone is physiologically active in minute quantities, so he needed an extremely sensitive way to track it. He devised an apparatus that tagged it with tritium—a radioactive form of hydrogen—at an efficiency level that had not previously been achieved. This innovation allowed him to detect a trillionth of a gram of estradiol.

When he injected this radioactive substance into immature rats, he noticed that most tissues—skeletal muscle, kidneys and liver, for example—started expelling it within 15 minutes. In contrast, tissues known to respond to the hormone—those of the reproductive tract—held onto it tightly. Furthermore, the hormone showed up in the nuclei of cells, where genes reside. Something there was apparently grabbing the estradiol.

Jensen subsequently showed that his radioactive hormone remained chemically unchanged once inside the cell. Estrogen did not act by being metabolized and producing NADPH, but presumably by performing some job in the nucleus. Subsequent work by Jensen and Jack Gorski established that estradiol converts a protein in the cytoplasm, its receptor, into a form that can migrate to the nucleus, embrace DNA, and turn on specific genes.

From 1962 to 1980, molecular endocrinologists built on Jensen’s work to discover the receptors for the other major steroid hormones—testosterone, progesterone, glucocorticoids, aldosterone, and the steroid-like vitamin D. In addition to Jensen and Gorski, many scientists—notably Bert O’Malley, Jan-Ake Gustafsson, Keith Yamamoto, and the late Gordon Tompkins—made crucial observations during the early days of steroid receptor research.

Clinical Applications of Estrogen-Receptor Detection

Clinicians knew that removing the ovaries or adrenal glands of women with breast cancer would stop tumor growth in one out of three patients, but the molecular basis for this phenomenon was mysterious. Jensen showed that breast cancers with low estrogen-receptor content do not respond to surgical treatment. Receptor status could therefore indicate who would benefit from the procedure and who should skip an unnecessary operation. In the mid-1970s, Jensen and his colleague Craig Jordan found that women with cancers that contain large amounts of estrogen receptor are also likely to benefit from tamoxifen, an anti-estrogen compound that mimics the effect of removing the ovaries or adrenal glands. The other patients—those with small numbers of receptors—could immediately move on to chemotherapy that might combat their disease rather than waiting months to find out that the tumors were growing despite tamoxifen treatment. By 1980, Jensen’s test had become a standard part of care for breast cancer patients.

In the meantime, Jensen set about generating antibodies that bound the receptor—a tool that provided a more reliable way to measure receptor quantities in excised breast tumor specimens. His work has transformed the treatment of breast cancer patients and saves or prolongs more than 100,000 lives annually.

Long-Lost Relatives

By the early 1980s, interest in molecular endocrinology had shifted toward the rapidly developing area of gene control. Chambon and Evans had long wondered how genes turn on and off, and recognized nuclear hormone signaling as the best system for studying regulated gene transcription. They wanted to know exactly how nuclear receptors provoke RNA production in response to steroid hormones. To manipulate and analyze the receptors, they would need to isolate the genes for them.

By late 1985 and early 1986, Evans (at the Salk Institute in La Jolla) and Chambon (at the Institute of Genetics and Molecular and Cellular Biology in Strasbourg, France) had pieced together the glucocorticoid and estrogen receptor genes, respectively. They noticed that the sequences resembled that of v-erbA, a miscreant viral protein that fosters uncontrolled cell growth. This observation raised the possibility that v-erbA and its well-behaved cellular counterpart, c-erbA, would also bind DNA and control gene activity in response to some chemical activator, or ligand. In 1986, Evans and Björn Vennström simultaneously reported that c-erbA was a thyroid hormone receptor that was related to the steroid hormone receptors, thus uniting the fields of thyroid and steroid biology.

Chambon and Evans set to work deconstructing the glucocorticoid and estrogen receptors. By creating mutations at different spots and probing which activities the resulting proteins lost, they dissected the receptor into three domains: one bound hormone, one bound DNA, and one activated target genes. The structure of each domain strongly resembled the analogous one in the other receptor.

Chambon and Evans wanted to match other members of the growing receptor gene family with their chemical triggers. Because the DNA- and ligand-binding regions functioned independently, it was possible to hook the DNA-binding domain of, say, the glucocorticoid receptor to the ligand-binding domain of another receptor whose ligand was unknown. The ligand for that receptor would then activate a glucocorticoid-responsive test gene.

Evans would use this method to identify ligands for several novel members of the nuclear receptor family, and both he and Chambon exploited it to discover a physiologically crucial receptor. In the late 1970s, scientists had suggested that the physiologically active derivative of vitamin A, retinoic acid, could exert its effects by binding to a nuclear receptor. This nutrient is essential from fertilization through adulthood, and researchers were eager to understand its activities on a molecular level. During embryonic development, deficiency of retinoic acid impairs formation of most organs, and the compound can hinder cancer cell proliferation. So Chambon set out to find a receptor that responded to retinoic acid. He isolated a member of the nuclear receptor gene family whose production increased in breast cancer cells that slowed their growth upon exposure to the chemical. Simultaneously, Evans identified the same protein. He tested whether more than a dozen compounds activated an unknown receptor and one passed: retinoic acid.

Remarkably, in 1986, the two scientists had independently—and unbeknownst to each other—identified the same retinoic acid receptor, a molecule of tremendous significance. The discovery of this molecule provided an entry point for detailing vitamin A biology.

Rx for Lonely Receptors: RXR

The list of presumptive nuclear receptors was growing quickly as scientists realized that the common DNA sequences provided a handle with which to grab these molecules from the genome. Because their chemical activators weren’t known, they were called “orphan” receptors, and researchers were keen on “adopting” them to ligands. Some of these ligands, they reasoned, would represent previously unknown classes of gene activators. The test system that Chambon and Evans used to match up retinoic acid with its receptor, in which they stitched an unknown ligand-binding domain to a DNA-binding domain for a receptor with known target sequences, could be harnessed to accomplish this task.

Evans had identified some potential nuclear receptors from fruit flies. He decided to pursue a human orphan receptor that closely resembled one of these receptor genes, reasoning that a protein that functioned in both flies and mammals was likely to perform an important job.

This receptor responded to retinoic acid in intact cells but did not bind it in the test tube, so Evans called it the Retinoid X Receptor (RXR), thinking that its ligand was some retinoic acid derivative. In cells, enzymes convert retinoic acid to metabolites and it seemed possible that one of these compounds was RXR’s ligand. In 1992, Evans’s group and one at Hoffmann-La Roche discovered that 9-cis-retinoic acid, a stereoisomer of retinoic acid, could activate RXR, identifying the first new receptor ligand in 25 years. This finding launched the orphan receptor field because it provided strong evidence that the strategy could unearth previously unknown ligands.

In the meantime, Chambon had found that the purified retinoic acid receptor, in contrast to the estrogen receptor, did not bind efficiently to its target DNA. Other nuclear receptors, too, needed help grasping genes. In the test tube, the retinoic acid, thyroid hormone, and vitamin D3 receptors could attach well to their target DNA only when supplemented with cellular material, which presumably contained some crucial substance. Chambon and Michael Rosenfeld independently purified a single protein that performed this feat, and it turned out to be none other than RXR. This ability of RXR to pair with other receptors—forming so-called heterodimers—would turn out to be key for switching on many orphan receptors. These heterodimeric couplings yield large numbers of distinct gene-controlling entities.

Chambon revealed the power of mixing and matching in these molecular duos through his thorough and extensive genetic manipulations in mice. He has shown that vitamin A exerts its wide-ranging effects on organ development in the embryo through the action of eight different forms of the retinoic acid receptor and six different forms of RXR, interacting with each other in a multitude of combinations.

Clinical Applications of the Superfamily Work

The concept of RXR as a promiscuous heterodimeric partner for certain nuclear receptors led to the unexpected identification of a number of clinically relevant receptors. These proteins include the peroxisome proliferator-activated receptor (PPAR), which stimulates fat-cell maturation and sits at the center of Type 2 diabetes and a number of lipid-related disorders; the liver X receptors (LXRs) and bile acid receptor (FXR), which help manage cholesterol homeostasis; and the steroid and xenobiotic receptor (PXR), which turns on enzymes that dispose of chemicals that need to be detoxified, such as drugs.

Because the nuclear receptors wield such physiological power, they have provided excellent targets for disease treatment. The anti-diabetes compounds glitazones, for example, work by stimulating PPAR, and the clinically used lipid-lowering medications called fibrates work by binding a closely related receptor, PPAR. Retinoic acid therapy has dramatically altered the prognosis of people with acute promyelocytic leukemia by triggering specialization of the immature white blood cells that accumulate in these individuals. The three-dimensional structure of nuclear receptors with and without their ligands, which Chambon and his colleagues first solved, promises to accelerate drug discovery in the whole field.

Nuclear hormone receptors have touched on human health in other ways as well. Genetic perturbations in the genes for these proteins cause a variety of illnesses. For example, certain forms of rickets arise from mutations in the vitamin D receptor and several disorders of male sexual differentiation stem from defects in the androgen receptor.

The discoveries of Jensen, Chambon, and Evans revealed an unimagined superfamily of proteins. At the start of this work almost 50 years ago, no one would have anticipated that steroids, thyroid hormone, retinoids, vitamin D, fatty acids, bile acids, and many lipid-based drugs transmit their signal through similar pathways. Four dozen human nuclear receptors are now known, and scientists are working out the roles of these proteins in normal and aberrant physiology. These discoveries have revolutionized the fields of endocrinology and metabolism, and pointed toward new tactics for drug discovery.

by Evelyn Strauss, Ph.D.

The 2004 Lasker Award for Basic Medical Research will be presented to Elwood Jensen, Ph.D., the Charles B. Huggins Distinguished Service Professor Emeritus in the Ben May Institute for Cancer Research at the University of Chicago, one of three scientists whose discoveries “revolutionized the fields of endocrinology and metabolism,” according to the award citation. Jensen’s work had a rapid, direct and lasting impact on treatment and prevention of breast cancer.

The Lasker Awards are the nation’s most distinguished honor for outstanding contributions to basic and clinical medical research. Often called “America’s Nobels,” the Lasker Award has been awarded to 68 scientists who subsequently went on to receive the Nobel Prize, including 15 in the last 10 years.

Jensen will share the basic medical research award with two colleagues, Pierre Chambon, of the Institute of Genetics and Molecular and Cellular Biology (Strasbourg, France), and Ronald M. Evans of the Salk Institute for Biological Studies (La Jolla, California) and the Howard Hughes Medical Institute.

They were selected for their discovery of the “superfamily of nuclear hormone receptors and the elucidation of a unifying mechanism that regulates embryonic development and diverse metabolic pathways.” The implications of this research for understanding human disease and accelerating drug discovery “have been profound and hold much promise for the future,” notes the announcement from the Lasker Foundation.

Jensen is being honored for his pioneering research on how steroid hormones, such as estrogen, exert their influence. His discoveries explained how these hormones work, which has led to the development of drugs that can enhance or inhibit the process.

Hormones control a vast array of biological processes, including embryonic development, growth rate and body weight. Before Jensen, however, the way which hormones cause these effects was “a complete mystery,” recalled Gene DeSombre, Ph.D., professor emeritus at the University of Chicago, who worked with Jensen in the Ben May Institute as a post-doctoral fellow and then as a colleague.

In the 1950s, biochemists thought a hormone entered a cell, where a series of oxidation and reductions reactions with the estrogen provided needed energy for the growth stimulation and other specific actions shown by estrogens.

From the late 1950s to the 1970s Jensen entirely overturned that notion. Working with estrogen, he proved that hormones do not undergo chemical change. Instead, they bind to a receptor protein within the cell. This hormone-receptor complex then travels to the cell nucleus, where it regulates gene expression.

At the time, this idea was heresy. “That really got him into some hot water,” recalled DeSombre. “Jensen struggled quite a lot,” echoes Shutsung Liao, Ph.D., another Ben May colleague, who subsequently found a similar system for testosterone action. But for Jensen, just getting into hot water was a struggle. When he first presented preliminary data at a 1958 meeting in Vienna, only five people attended, three of whom were the other speakers. More than 1,000 attended a simultaneous symposium on the metabolic processing of estrogen.

In the next 20 years, Jensen convinced his colleagues by publishing a series of major and highly original discoveries in four related areas of hormone research:

Jensen discovered the estrogen receptor, the first receptor found for any hormone. In 1958, using a radioactive marker, he showed that only the tissues that respond to estrogen, such as those of the female reproductive tract, were able to concentrate injected estrogen from the blood. This specific uptake suggested that these cells must contain binding proteins, which he called “estrogen receptors.”
In 1967, Jensen and Jack Gorski of the University of Wisconsin showed that these putative receptors were macromolecules that could be extracted from these tissues. With this method, Jensen showed that when estrogen bound to this receptor, the compound then migrated to the nucleus where it bound avidly and activated specific genes, stimulating new RNA synthesis.
By 1968, Jensen had devised a reliable test for the presence of estrogen receptors in breast cancer cells. It had been known for decades that about one-third of premenopausal women who had advanced breast cancer would respond to estrogen blockade brought about by removing their ovaries, the source of estrogen, but there was no way to predict which women would respond. In 1971, Jensen showed that women with receptor-rich breast cancers often have remissions following removal of the sources of estrogen, but cancers that contain few or no estrogen receptors do not respond to estrogen-blocking therapy.
By 1977, Jensen and Geoffrey Greene, Ph.D., also in the University of Chicago’s Ben May Institute, had developed monoclonal antibodies directed against estrogen receptors, which enabled then to quickly and accurately detect and count estrogen receptors in breast and other tumors. By 1980, this test had become a standard part of care for breast cancer patients

This work “transformed the treatment of breast cancer patients,” notes the Lasker Foundation, “and saves or prolongs more than a 100,000 lives annually.”

”Jensen’s revolutionary discovery of estrogen receptors is beyond doubt one of the major achievements in biochemical endocrinology of our time,” said DeSombre. “His work is hallmarked by great technical ingenuity and conceptual novelty. His promulgation of simple yet profound ideas concerning the role of receptors in estrogen action have been of the greatest importance for research on the basic and clinical physiology not only of estrogens but also of all other categories of steroid hormones.”

By the early 1970s, Jensen was searching for chemical, rather than surgical, ways to shield estrogen-dependent tumors from circulating hormones. He and colleague Craig Jordan (then at the Worcester Foundation for Experimental Biology in Massachusetts) subsequently found that women with cancers that contain large amounts of estrogen receptor are also likely to benefit from tamoxifen, a compound that blocks some of the effects of estrogen. Patients with few or no receptors could immediately move on to chemotherapy rather than waiting months to find out that the tumors were growing despite tamoxifen treatment.

Following Jensen’s lead, researchers soon found that the receptors for the other major steroid hormones, such as testosterone, progesterone, and cortisone, worked essentially the same way.

In 1986, Pierre Chambon and Ronald Evans separately but simultaneously discovered that the steroid hormone receptors were merely the tip of the iceberg of what would turn out to be a large family of structurally related nuclear receptors, now known to consist of 48 members. Evans and Chambon unearthed a number of these receptors, which revealed new regulatory systems that control the body’s response to essential nutrients (such as Vitamin A), fat-soluble signaling molecules (such as fatty acids and bile acids), and drugs (such as the glitazones used to treat Type 2 diabetes and retinoic acid for certain forms of acute leukemia).

These three individuals “created the field of nuclear hormone receptor research, which now occupies a large area of biological and medical investigation,” said Dr. Joseph L. Goldstein, chairman of the international jury of researchers that selects recipients of the Lasker Awards, and recipient of the Lasker Award for Basic Medical Research and the Nobel Prize in Medicine in 1985.

They revealed the “unexpected and unifying mechanism by which many signaling molecules regulate a plethora of key physiological pathways that operate from embryonic development through adulthood. They discovered a family of proteins that allows chemicals as diverse as steroid hormones, Vitamin A, and thyroid hormone to perform in the body.”

Jensen, known for concluding his lectures in verse, neatly summed up what his extraordinary series of discoveries might mean to a woman who has been diagnosed with breast cancer:

“A lady with growth neoplastic
Thought surgical ablation too drastic.
She preferred that her ill
Could be cured with a pill,
Which today is no longer fantastic.”

JBC THEMATIC MINIREVIEW SERIES 2011

Nuclear Receptors in Biology and Diseases

Thematic Minireview Series on Nuclear Receptors in Biology and Diseases

Sohaib Khan and Jerry B Lingrel

Although a connection between breast cancer and the ovary was made by Sir George Beatson in 1896 and estrogen was purified in 1920, it remained puzzling as to how the hormone exerted its biological effects. In the late 1950s, when Elwood Jensen delved into this problem by asking, essentially, “What does tissue do with this hormone?” little did he know that his quest would lead to the establishment of the nuclear receptor field. The late 1950s was the era of intermediary metabolism and enzymology, when steroid hormones were considered likely substrates in the formation of metabolites that functioned as cofactors in an essential metabolic pathway. The biological responses to estrogens and other steroids were thought to be mediated by enzymes. Against this background and prevailing dogma, Jensen and colleagues defined the biochemical mechanisms by which steroid hormones exert their effects. While working at the University of Chicago’s Ben May Institute for Cancer Research, they synthesized tritium-labeled estradiol and concurrently developed a new method to measure its uptake in biological material. These tools enabled them to determine the biochemical fate of physiological amounts of hormone. They discovered that the reproductive tissues of the immature rat contain characteristic hormone-binding components with which estradiol reacts to induce uterine growth without itself being chemically changed. From the close correlation between the inhibition of binding and inhibition of growth response, Jensen established that the binding substances were receptors. Thus, we saw the birth of the first member of the nuclear receptor family (known as the estrogen receptor). These findings stimulated the search for other physiological receptors, and the pioneering works by Pierre Chambon, Ronald Evans, Jan-Åke Gustafsson, Bert W. O’Malley, and Keith Yamamoto led to the discoveries of the glucocorticoid receptor (GR),2 progesterone receptor, retinoic acid receptor, and orphan receptors. In a rather short span of time, the nuclear receptor family has grown into a 49-member-strong “superfamily.” This is a family whose members, functioning as sequence-specific transcription factors, have defined the many intricacies of the mechanism of transcription. These ligand-dependent transcription factors generally possess similar “domain organizations,” of which the DNA-binding domain and the ligand-binding domain are critical in amplifying the hormonal signals via the receptor target genes. The nuclear receptor family is divided into four groups: (i) Group 1 is composed of steroid hormone receptors that control target gene transcription by binding as homodimers to response element (RE) palindromes; (ii) in Group 2, the nuclear receptors heterodimerize with retinoid X receptor and generally bind to direct repeat REs; (iii) Group 3 consists of those orphan receptors that function as homodimers and bind to direct repeat REs; and (iv) orphan receptors in Group 4 function as monomers and bind to single REs.

Since the early demonstration by Jack Gorski and Jensen that the estrogen receptor (ER) activates transcription, the nuclear receptor field has come a long way. In addition to the first cloning of the polymerase II transcription factors (GR and ER cDNAs), of note is the discovery of steroid receptor coactivators (SRCs), a truly major piece of the transcriptional jigsaw puzzle, described by the laboratories of O’Malley and Myles Brown. The induction of coactivators and corepressors in the transcriptional machinery has expanded tremendously our understanding of this complex process. We now know that ligand binding to the respective receptors triggers a fascinating chain of events, including the translocation of the receptors to the nucleus, ligand-induced changes in the receptor conformations, receptor dimerization, interaction with the target gene promoter elements, recruitment of coactivators (or corepressors), chromatin remodeling, and subsequent interaction with the polymerase II complex to initiate transcription.

By virtue of their abilities to regulate a myriad of human developmental and physiological functions (reproduction, development, metabolism), nuclear receptors have been implicated in a wide range of diseases, such as cancer, diabetes, obesity, etc. Not surprisingly, drug companies are spending billions of dollars to develop medicines for cancer and metabolic disorders that involve nuclear receptors. More than 50 years after the discovery of the ER, the scientific community owes Jensen and other founding members of the nuclear receptor family much gratitude, for they have taken us through a remarkable expedition filled with eureka moments to understand how hormones and other ligands function!

This thematic minireview series will cover a range of topics in the nuclear receptor field. The minireviews include the current studies of identifying subtypes of the GR. Different receptors arise from alternative mRNA splicing and from the use of different promoter start sites and post-translational modifications, such as phosphorylation. The series covers the physiological roles of the different GRs. The field of orphan nuclear receptors and the search for possible ligands also are reviewed. One minireview concentrates largely on the following nuclear receptors: peroxisome proliferator-activated receptor (PPAR) α, PPARγ, Rev-erbα, and retinoic acid receptor-related orphan receptor α. ERα was the first identified and has been studied the most, whereas ERβ has not been studied in the same detail. ERβ is very important, and one of the minireviews provides a summary of the new biological functions that are being ascribed to it. Also, the development of small molecule inhibitors for the ER will be considered. An important aspect of nuclear receptor function is how these receptors function in transcription. The role of transcriptional coactivators in nuclear receptor gene regulation will be reviewed as well as how signal amplification and interaction are involved in transcription regulation by steroids. The SRC/p160 family of coregulators includes SRC-1, SRC-2, and SRC-3, and the latter has been shown to act as an oncogene, particularly in breast cancer. Molecular analysis of its role in breast cancer progression and metastasis will be the focus of one of the minireviews. In addition, interactions of nuclear receptors with the genome will be reviewed, as will the role of the homeodomain protein HoxB13 in specifying the cellular response to androgens. Mining nuclear receptor cistromes and how nuclear receptors reset metabolism also will be considered. The association of nuclear receptors (e.g. PPARδ) with physiological functions, such as circadian rhythm and muscle functions, will also be addressed. Finally, the role of nuclear receptors in disease using the retinoid X receptor α/β knock-out and transgenic mouse model skin syndromes and asthma will be reviewed. These are diverse and important topics that are critical in understanding the regulation of nuclear receptors and the biological roles they play in normal function and disease.

The Nuclear Receptor Superfamily: A Rosetta Stone for Physiology

Ronald M. Evans
Howard Hughes Medical Institute, Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
Molecular Endocrinology 19(6):1429–143 http://dx.doi.org:/10.1210/me.2005-0046

In the December 1985 issue of Nature, we described the cloning of the first nuclear receptor cDNA encoding the human glucocorticoid receptor (GR) (1). In the 20 yr since that event, our field has witnessed a quantum leap by the subsequent discovery and functional elaboration of the nuclear receptor superfamily (2)—a family whose history is linked to the evolution of the entire animal kingdom and whose actions, by decoding the genome, span the vast diversity of biological functions from development to physiology, pathology, and treatment. A messenger is an envoy or courier charged with transmitting a communication or message. In one sense, the cloning of that first messenger (the GR) represented the completion of a prediction that began with Elwood Jensen’s characterization of the first steroid receptor protein (3) and continued with the pioneering work of others in the steroid receptor field (including Gorski, O’Malley, Gustafsson, and Yamamoto). Yet, like the discovery of the Rosetta stone in 1799, the revelation of the GR sequence heralded a completely unpredictable demarcation in the field, helping to solve mysteries unearthed nearly 100 yr ago as well as opening a portal to the future. The beginnings of the adventure lie in disciplines such as medicine and nutrition, which gave rise to the emergent field of endocrinology in the first half of the last century. The purification of chemical messengers ultimately known as hormones from organs and vitamins from foods spurred the study of these compounds and their physiologic effects on the body. At about the same time, the field of molecular biology was emerging from the disciplines of chemistry, physics, and their application to biological problems such as the structure of DNA and the molecular events surrounding its replication and transcription. It would not be until the late 1960s and 1970s that endocrinology and molecular biology would begin to intersect as the link between receptors and transcriptional control were being laid down. During this time, the work of Jensen (4) and Gorski (5) identified a high-affinity estrogen receptor (ER) that suggested an action in the nucleus. Gordon Tomkins and his associates (J. Baxter, G. Ringold, E. B. Thompson, H. Samuels, H. Bourne, and others) were one of the most creative forces studying glucocorticoid action (6). Concurrent work by O’Malley, Gustafsson, and Yamamoto provided further, important evidence supporting a link between steroid receptor action and transcription (see accompanying perspective articles in this issue of Molecular Endocrinology). But whereas the steroid hormone field continued to evolve in this direction, it is of interest to note that the mechanism of action of thyroid hormone and retinoids remained clouded and controversial until the eventual cloning of their receptors in the late 1980s. Likewise, no one had foreseen the possibility that other lipophilic molecules (like oxysterols, bile acids, and fatty acids) would also function through a similar mechanism, or that other steroid receptor-like proteins existed that would play an important role in transcriptional regulation of so many diverse pathways. Thus, the GR isolation in 1985 led to the concept of a hidden superfamily of receptors that in a very real way provided the needed molecular code to unravel the puzzle of physiologic homeostasis.

Unconventional Gene-Ology

The study of RNA tumor viruses was ascendant, and the concept that they evolved by pirating key signaling pathways greatly influenced my future studies. With this training, I went on to work with Jim Darnell at the Rockefeller University on adenovirus transcription, a model brought to the lab by Lennart Philipson. At the time, adenovirus was one of the best tools to study programmed gene expression in an animal cell. My sole focus was to localize the elusive major late promoter, which provided my first Nature paper (7). Ed Ziff, a newly hired assistant professor from Cambridge, brought innovative unpublished DNA and RNA sequencing techniques that, after much technical angst, allowed us to sequence the major late promoter and derive the structure of the first eukaryotic polymerase II promoter (8). This thrilling result convinced me that the problem of gene control could be solved at the molecular level. Our next goal, which I shared with Michael Harpold in the Darnell lab, was to translate the concepts developed around adenovirus into cellular systems. My model was to analyze the glucocorticoid and thyroid hormone regulation of the GH gene. Under the strict federal guidelines for newly approved recombinant DNA research, we cloned the GH cDNA in 1977 and the first genomic clones in 1978 (9) after I moved on to The Salk Institute. However, to fully address the hormone signaling problem, I realized that it would be necessary to clone the GR and thyroid hormone receptors (TRs), which began in earnest in 1981. Up until that time, the purification and cloning of any polymerase II transcription factor had eluded researchers because of their low abundance. Four years later, the GR would be the first transcription factor for a defined response element to be cloned, sequenced, and functionally identified.

A Rock and A Hard Place

A key question was whether the GR protein encoded by the receptor was sufficient, when expressed in a heterologous cell, to convey the hormonal message. Before the publication, a new postdoc, Vincent Giguere, began tinkering with the isolated GR, trying to address this question. The rate of development of any field is limited by the existing techniques and depends on the development of new ones. Vincent devised a revolutionary technique—the cotransfection assay that required two plasmids to be taken up in the same cell, the expression vector to be transcribed, the encoded protein to be functional and an inducible promoter linked to a chloramphenicol acetyltransferase reporter in the nucleus ready to flicker on (10, 12). With so many variables and unknowns, I was stunned and expressionless when it worked the very first time. Cotransfection was an easy, fast, and quantitative technique. It would become (and still remains) the dominant assay to characterize receptor function. It would also become the mainstay for drug discovery in the pharmaceutical industry. The development of this technique proved a great advantage because existing technology involved creating stable cell lines, a tedious process prone to integration artifacts that ultimately could not match the explosive pace of the field. Indeed, within 4 months Stan and Vincent had fully characterized 27 insertional mutants delineating the DBD, LBD, and two activation domains (12). The route to understanding the signaling mechanism now had a solid structural foundation. A serendipitous gift to my retroviral origins was the homology of the GR sequence to the v-erbA oncogene product of the avian erythroblastosis virus genome (13). With this discovery, erbA advanced to a candidate nuclear transcription factor potentially involved in a signal transduction pathway. Thus, while Stan concentrated on the GR, Cary began to delve into the erbA discovery. Within months of the GR publication, the human c-erbA gene was in hand (14). Unbeknownst to us, Bjorn Vennstrom, one of the first to characterize the avian erythroblastosis virus genome, had also isolated c-erbA and was searching for a function. Based on the low homology of the LBD region to the GR and ER, both groups deduced that the imaginary erbA ligand would be nonsteroidal.

The work of our two groups (15, 16), published in December of 1986, broadened the principles of the signal transduction pathway by demonstrating that thyroid and steroid hormone receptor signaling had a common evolutionary origin and provided an entree to understand how mutations within a receptor could activate it to an oncogene. Although we did not know it at the time, this work would also lead us to the concept of the corepressor. In the meantime, my student, Catherine Thompson, zeroed in on an erb-A-related gene and soon identified a second TR expressed at high levels in the central nervous system (17). Thus came into existence the and forms of the TR. Jeff Arriza, the third graduate student in the lab, purified a genomic fragment that had weakly hybridized to the GR resulting in the isolation of the human mineralocorticoid receptor (MR) (18). MR proved to have an at least 10-fold higher affinity for glucocorticoids than the GR itself and was further distinguished by its ability to bind and be activated by aldosterone. This enabled the development of GR- and MR-selective drugs such as the recent MR antagonist eplerenone. Thus, in a 2-yr time span our lab had progressed on three distinct, albeit related, receptor systems, and in doing so molecular biology and endocrinology were irrevocably linked. The field of molecular endocrinology (and coincidentally the eponymous journal) was born.

Ligands From Stone

I have often been asked how we could handle so many divergent systems. Indeed, from a medical perspective, these systems seem widely unrelated. Studies of ER, progesterone receptor, and androgen receptor (AR) fall under reproductive physiology, vitamin D under bone and mineral metabolism, with vitamin A part of nutritional science. Medical fields are naturally idiosyncratic because of the specialized knowledge required to conduct experiments. With my training as a molecular biologist, physiology was the complex output of genes and thus control of gene expression was the overriding problem. This conceptual approach had a great unifying effect because all receptors transduce their signaling through the gene. As an “outsider,” my goal was to exploit multiple receptor systems to seek general principles. This philosophical approach afforded us a freedom to redefine the signaling problem from the nucleus outward and thus even poorly characterized, even unknown, physiologic systems fell into the crosshairs of our molecular gun.

Vincent, while screening a testes Fig. 1. Models of Nuclear Receptor Structure Top, Original hand-shaped wire model (circa 1992) of the nuclear receptor DBD. Bottom, Schematic representation of the GR DBD. Conserved residues in zinc fingers, P-box and D-box are indicated isolated what would become the vitamin A or retinoic acid receptor (RAR) (19). Initially, Vincent thought he had isolated the AR, although this later proved not to be the case. By that stage, the lab had perfected a new technique—the domain swap—by which the GR DBD could be introduced into any receptor and confers on the chimeric protein the ability to activate a mouse mammary tumor virus reporter. This clever technique, independently developed in the Chambon lab, would prove to be essential. Effectively, the domain swap would enable us to screen for ligands without any knowledge of their physiologic function. Activation of a target gene was all that was needed! By creating this GR chimera, Vincent was able to screen the new receptor against a ligand cocktail including androgens, steroids, thyroid hormone, cholesterol, and the vitamin A metabolite retinoic acid. From the first assay, it was clear that he had isolated a high-affinity selective RAR that had no response to any other test ligand. Thus, without knowing any true direct target gene for retinoic acid, we were nonetheless able to isolate and characterize its receptor. Remarkably, Martin Petkovich in the Chambon lab isolated the same gene. Once again, this is an example where a new technique offered an entirely new approach to a problem. Both papers were published in the December 1987 issue of Nature (19, 20). With the combination of steroids, thyroid hormones, and vitamin A, the three elemental components of the nuclear receptor superfamily were in hand. By the time the RAR papers were published, Vincent with Na Yang, had already isolated two estrogen-related receptors termed ERR1 and 2 that would represent the first true orphan receptors in the evolving superfamily (21). A third receptor (ERR3) would be isolated 10 yr later (22). The three ERRs are distinguished by their ability to activate through ER response elements, but required no ligand. However, of potential major medical relevance, estrogen antagonists such as 4-hydroxy-tamoxifen silences ERR constitutive activity (23). The superfamily was growing exponentially, transforming into a new field, driven by a new breed of exceptional students and fellows attracted by the mechanics of transcription and its emerging link to physiology. For example, the RAR and TR offered an unprecedented look at understanding the action of vitamin A as a morphogen and the role of thyroxin in setting the basal metabolic rate of the body. We were a relatively small group, and our decision to work on multiple different receptor systems created a unique environment. Because there was so little overlap between projects, postdocs and students readily discussed all results, exchanged reagents and freely collaborated, resulting in a tremendous acceleration of progress. The high level of camaraderie was powered by the joie de vivre of the exciting discoveries and the ability of our family of students and postdocs to each adopt their own receptors. We all felt we were in a golden age and even more was to come.

In 1989, Jan Sap in Vennstrom’s group and Klaus Damm in our group demonstrated that the TR becomes oncogenic by mutation in the LBD (24, 25). Although we expected ligand-independent activation, it was clearly a constituitive repressor becoming the first example of a dominant-negative oncogene. The concept of the dominant-negative oncogene had been proposed one year earlier by Ira Herskowitz (26). This discovery changed our thinking on hormone action, and repression soon would be shown to be a common feature of receptor antagonists. David Mangelsdorf, who had arrived in the lab the year before was captivated by the glow of weakly hybridizing DNA bands and, in 1989, had amassed his own collection of orphan receptors, among which was the future retinoid X receptor (RXR) (27). In search for biological activity, a candidate ligand was found in lipid extracts from outdated human blood. However, the key test came from demonstrating that addition of all-trans retinoic acid to cultured cells would lead to its rapid metabolism coupled with the release of an inducing activity for RXR, which we termed retinoid X. David and his benchmate, Rich Heyman, began working on the chemistry of this inducer along with Gregor Eichele and Christine Thaller, then at Baylor College of Medicine (Houston, TX). This work led to the identification of 9-cis retinoic acid by our lab and a group at Hoffman LaRoche (Nutley, NJ) (28, 29). Like the retinal molecule in rhodopsin, 9-cis-retinoic acid represents the exploitation of retinoid isomerization by nature to control a key signaling pathway. More importantly, in the 39 yr since the discovery of aldosterone in 1953, this revelation would reawaken and reinvent the single most defining but dormant tool of endocrinology—ligand discovery. Indeed, the discovery that new receptors could lead to new ligands opened up an entirely new avenue of research. Like the puzzle of the structure of the benzene ring, which was solved in 1890 when Fredrick Kekule dreamed of a snake biting its own tail, the physiologic head of the “endocrine snake” and the molecular biology tail had come full circle. The era of reverse endocrinology was now upon us.

Response Elements: Deciphering The Scripts

One problem in addressing the downstream effects of our newly discovered receptors was that their response elements and target genes were by definition unknown. Kaz Umesono delved into this mystery and would produce a paradigm shift that would both solve the problem and further unify the field. With the view that the DBD functioned as a molecular receptor for its cognate hormone response element, meticulous mutational studies revealed two key DBD sequences, termed the P-box and D-box, that controlled the process (30).

The D-box was shown to direct dimerization, a feature previously thought to be unique to the LBD. One perplexing point was that the P-boxes of the nonsteroidal receptors were conserved, leading to the improbable prediction that many different receptors would recognize the same target sequence. By manual compilation and comparison of all known response elements, Kaz proposed a core hexamer— AGGTCA—as the prototypic common target sequence. By requiring the half-site to be an obligate hexamer an underlying pattern—the direct repeat—emerged. In the direct repeat paradigm, we proposed that half-site spacing, not sequence difference, was the key ingredient to distinguishing the response elements. The metric was referred to as the 3-4-5 rule (31). According to the rule, direct repeats of AGGTCA spaced by three nucleotides, would be a vitamin D response element (DR-3), the same repeat spaced by four nucleotides a thyroid hormone response element (DR-4), and the same repeat spaced by five nucleotides a vitamin A response element (DR-5). Eventually, all steps from 0–5 on the DR ladder would be filled (Fig. 2). The validity of this paradigm was ensured by a crystal structure solved in collaboration with Paul Sigler’s group at Yale (32). Indeed, of the remaining 40 nonsteroidal receptors, all but three can be demonstrated to have a preferred binding site within some component of the direct repeat ladder. Exceptions include SHP and DAX, which lack DBDs, and farnesoid X receptor (FXR) that binds to the ecdysone response element as a palindrome with zero spacing. Kaz’s insight, by drawing commonality from diversity, came to solve a problem that impacted on virtually every receptor. Remarkably, each new receptor in the superfamily could immediately be assigned a place on the ladder. The ladder also provided a simple means to conduct a ligand screening assay in absence of any knowledge of an endogenous target gene. Kaz’s ladder was a turbo charge for the field. The next major advance in the field was the discovery of the RXR heterodimer. Although we knew that retinoid and thyroid receptors required a nuclear competence factor for DNA binding, its identity was unknown. We tested RXR, but our initial experiments were flawed. Of the first four papers describing the discovery, that from Chambon’s lab was most elegant because they simply purified an activity to homogeneity to find RXR (33)! Rosenfeld was first to publish, and Ozato, Pfahl and Kliewer all concurred (34–37). Tony Oro and Pang Yao in our lab soon published that the ecdysone receptor functions as a heterodimer with ultraspiracle, the insect homolog of RXR (38, 39), revealing that the ancient origins of the heterodimer which arose before the divergence of vertebrates and invertebrates.

Reverse Endocrinology: Decoding Physiology

The orphan receptors would transform our view of endocrine physiology with unexpected links to toxicology, nutrition, cholesterol, and triglyceride metabolism as well as to a myriad of diseases including atherosclerosis, diabetes, and cancer. The three RXR isoforms formed the core with 14 heterodimer partners including the vitamin D receptor (VDR), TR/, and RAR//. The initial adopters of orphan receptors included Giguere, Mangelsdorf, Weinberger, Bruce Blumberg, Steve Kliewer, and Barry Forman. Barry unlocked the first secret to for peroxisome proliferator-activated receptor (PPAR) by identifying prostaglandin J2 (PGJ2) as a high-affinity ligand (40). The second step, in collaboration with Peter Tontonoz in Bruce Spiegleman’s lab, revealed that PGJ2 was adipogenic in cell lines and perhaps more importantly that the synthetic antidiabetic drug Troglitazone was a potent PPAR agonist (41). Similar work was conducted and published by Kliewer, who had now moved to Glaxo (42). By acquiring a ligand, a physiologic response, and a drug, PPAR was suddenly transported to the center of a physiologic cyclone that would spin into its own specialty field. Since 1995, more than 1000 papers (see PubMed) have been published on PPAR and its natural and synthetic ligands. This early work illuminated the molecular strategy of reverse endocrinology and the emerging importance of the orphan receptors in human disease and drug discovery. Cary returned to the lab for a sabbatical and, with Barry, demonstrated that FXR was responsive to farnesoids and other molecules in the mevalonate pathway. The findings by Mangelsdorf that liver X receptors (LXRs) bound oxysterols (43) and by Kliewer, Mangelsdorf, and Forman that FXR is a bile acid receptor (44–46) provided a whole new conceptual approach to cholesterol and triglyceride homeostasis. The steroid and xenobiotic receptors (SXR)/pregnane X receptor (PXR) (47–49) and the constituitive androstane receptor (CAR) (50) respond to xenobiotics to activate genes for P450 Fig. 2. Examples of Receptor Heterodimer Combinations that Fill the Direct Repeat (DR) Response Element Ladder from DR1 to DR5 Evans enzymes, conjugation and transport systems that detoxify drugs, foreign chemicals, and endogenous steroids. RXR and its associated heterodimeric partners quickly established a new branch of physiology, shedding its dependence on endocrine glands and allowing the body to decode signals from environmental toxins, dietary nutrients, and common metabolites of intermediary metabolism.

Continued…

ROCK OF AGES

The human body is, after all a living machine, a complex device that consumes and uses energy to sustain itself, defend against predators, and ultimately reproduce. One might reasonably ask, “If the superfamily acts through a common molecular template, can the family as a whole be viewed as a functional entity?” In other words, is there yet some overarching principle that we have yet to grasp. . . and might this imaginary principle lie at the heart of systems physiology? Simply stated, what led to the evolution of integrated physiology as the functional output of the superfamily? One obvious speculation is survival. To survive, all organisms must be able to acquire, absorb, distribute, store, and use energy. The receptors are exquisitely evolved to manage fuel—everything from dietary and endogenous fats (PPARs), cholesterol (LXR, FXR), sugar mobilization (GR), salt (MR), and calcium (VDR) balance and maintenance of basal metabolic rate (TR). Because only a fraction of the material we voluntarily place in our bodies is nutritional, the xenobiotic receptors (PXR, CAR) are specialized to defend against the innumerable toxins in our environment. Survival also means reproduction, which is controlled by the gonadal steroid receptors (progesterone receptor, ER, AR). However, fertility is dependent on nutritional status, indicating the presumptive communication between these two branches of the family. The third key component managed by the nuclear receptor family is inflammation. During viral, bacterial, or fungal infection, the inflammatory response defends the body while suppressing appetite, conserving fuel, and encouraging sleep (associated with cytokine release). However, if needed, even an ill body is capable of defending itself by releasing adrenal steroids, mobilizing massive amounts of fuel, and transiently suppressing inflammation. In fact, clinically, (with the exception of hormone replacement) glucocorticoids are only used as antiinflammatory agents. Other receptors including the RARs, LXRs, PPAR and , and vitamin D receptor protect against inflammation. Thus, nature evolved within the structure of the receptor the combined ability to manage energy and inflammation, indicating the important duality between these two systems. In aggregate, this commonality between distinct physiologic branches suggests that the superfamily might be approached as an intact functional dynamic entity.

Historically, endocrinologists and geneticists rarely saw eye to eye. As I have indicated in this perspective article, the disciplines have now become united in a new subject—transcriptional physiology. With this in mind, we might expect the existence of larger organizational principles that establish how the various evolutionary branches of the superfamily integrate to form whole body physiology. The existence of molecular rules governing the function and evolution of a megagenetic entity like the nuclear receptor superfamily, if correct, may be useful in understanding complex human disease and provide a conceptual basis to create more effective pharmacology. With so much accomplished in the last 20 yr (see Fig. 3), there are glimpses of clarity—enough to see the enormity and wonder of the problem and enough to know there is still a long and challenging voyage ahead. But who knows, the next breakthrough may only be a stone’s throw away.

http://press.endocrine.org/doi/pdf/10.1210/me.2005-0046

Pierre Chambon MD

Recipient of the Canada Gairdner International Award, 2010

“For the elucidation of fundamental mechanisms of transcription in animal cells and to the discovery of the nuclear receptor superfamily.”

Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, France

Dr. Pierre Chambon is Honorary Professor at the College de France (Paris), and Emeritus Professor at the Faculté de Médecine of the Strasbourg University. He was the Founder and former Director of the IGBMC, and also the Founder and former Director of the Institut Clinique de la Souris (ICS/MCI), in Strasbourg.

Dr. Pierre Chambon is a world expert in the fields of gene structure, and transcriptional control of gene expression. During the last 25 years his studies on the structure and function of nuclear receptors has changed our concept of signal transduction and endocrinology. By cloning the estrogen and progesterone receptors, and discovering the retinoic acid receptor family, he markedly contributed to the discovery of the superfamily of nuclear receptors and to the elucidation of their universal mechanism of action that links transcription, physiology and pathology. Through extensive site-directed mutagenesis and genetic studies in the mouse, Pierre Chambon has unveiled the paramount importance of nuclear receptor signaling in embryonic development and homeostasis at the adult stage. The discoveries of Pierre Chambon have revolutionized the fields of development, endocrinology and metabolism, and their disorders, pointing to new tactics for drug discovery, and finding important applications in biotechnology and modern medicine.

These scientific achievements are logically inscribed in an uninterrupted series of discoveries made by Pierre Chambon over the last 45 years in the field of transcriptional control of gene expression in higher eukaryotes: discovery of PolyADPribose (1963), discovery of multiple RNA polymerases differently sensitive to a-amanitin (1969), contribution to elucidation of chromatin structure: the Nucleosome (1974), discovery of animal split genes (1977), discovery of enhancer elements (1981), discovery of multiple promoter elements and their cognate factors (1980-1993).

Pierre Chambon has received numerous international awards, including the 2004 Lasker Basic Medical Research Award for the discovery of the superfamily of nuclear hormone receptors and the elucidation of a unifying mechanism that regulates embryonic development and diverse metabolic pathways. He is a member of the French Académie des Sciences, and also a Foreign Member of the National Academy of Sciences (USA) and of the Royal Swedish Academy of Sciences. Pierre Chambon serves on a number of editorial boards, including Cell, and Molecular Cell. Pierre Chambon is author of more than 900 publications. He has been ranked fourth among most prominent life scientists for the 1983-2002 period.

An Interview with Pierre Chambon
2004 Albert Lasker Basic Medical Research Award
http://www.laskerfoundation.org/media/v_chambon.htm

Pierre Chambon, MD

Honorary Professor at the Collège-de-France and Professor of Molecular Biology and Genetics, Institute for Advanced Study, University of Strasbourg; Group Leader, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch-Graffenstaden, Strasburg, France

A pioneer in the fields of gene structure and transcriptional control of gene expression, Dr. Chambon has fundamentally changed our understanding of signal transduction, which has led to revolutionary new tactics for drug discovery. His work elucidated how molecules that promote gene transcription are organized and regulated in eukaryotic organisms and, independently of Dr. Ronald Evans, he discovered in 1987 the retinoid receptor families, which led to the discovery and characterization of the superfamily of nuclear hormone receptors, including steroid and retinoid receptors.

Dr. Chambon’s previous research led to the discovery of PolyADPribose, multiple RNA polymerases differentially sensitive to α-amaniti, and has markedly contributed to the elucidation of the nucleosome and chromatin structure, as well as to the discovery of animal split genes, DNA sequences called enhancer elements, and multiple promoter elements and their cognate factors. These discoveries have greatly enhanced understanding of embryonic development and cell differentiation. To further studies of various nuclear receptors, Dr. Chambon has developed a method that allows in the mouse the generation of somatic mutations of any gene, at any time, and in any specific cell type, a tool valuable in generating mouse models of cancer.

In 1994, Dr. Chambon took on the role of founding a major research institute in France. As the first director of IGBMC, he built the institute to encompass hundreds of top researchers and multiple research programs funded by public agencies and private industry. In 2002, he founded and was the first director of the Institut Clinique de la Souris in Strasbourg. In these positions, he has succeeded in supporting and influencing a generation of scientists.

Career Highlights

2010 Canada Gairdner International Award

2004 Albert Lasker Basic Medical Research Award

2003 Alfred P. Sloan, Jr., Prize, General Motors Cancer Foundation

1999 Louisa Gross Horwitz Prize, Columbia University

1998 Robert A. Welch Award in Chemistry

1991 Prix Louis-Jeantet de médecine, Fondation Louis-Jeantet

1990 Sir Hans Krebs Medal, Federation of European Biochemical Societies

1988 King Faisal International Prize for Science, King Faisal Foundation

1987 Harvey Prize, Technicon-Israel Institute of Technology

more…

Minireviews In This Series:

Thematic Minireview Series on Nuclear Receptors in Biology and Diseases

Sohaib Khan and Jerry B Lingrel

Steroid Receptor Coactivator (SRC) Family: Masters of Systems Biology

Brian York and Bert W. O’Malley

Estrogen Signaling via Estrogen Receptor β

Chunyan Zhao, Karin Dahlman-Wright, and Jan-Åke Gustafsson

Small Molecule Inhibitors as Probes for Estrogen and Androgen Receptor Action

David J. Shapiro, Chengjian Mao, and Milu T Cherian

Cellular Processing of the Glucocorticoid Receptor Gene and Protein: New Mechanisms for Generating Tissue Specific Actions of Glucocorticoids

Robert H Oakley and John A Cidlowski

Endogenous Ligands for Nuclear Receptors: Digging Deeper

Michael Schupp and Mitchell A. Lazar

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To reduce symptoms of mental illness and retrain the brain

Posted in Innovations in Neurophysiology & Neuropsychology, Molecular Genetics & Pharmaceutical, Neurological Diseases, Neuroscience, Pharmaceutical Analytics, Pharmaceutical Drug Discovery, Pharmacologic toxicities, Population Health Management, Schizophrenia, Signaling & Cell Circuits, Social Development, Stress Disorders, tagged brain retraining, medication, mental illness on September 7, 2015| Leave a Comment »

To reduce symptoms of mental illness and retrain the brain

Larry H. Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Series E. 2; 5.11

Researchers have found that by specifically targeting a central signaling pathway in the brain, they can improve the innate behavioral response to stress in mice. Stress-induced behaviors in rodents reflect many of the symptoms that affect people suffering from major depression and other clinical conditions associated with stress. The findings, published July 20th online in the journalNature Neuroscience, suggest a new strategy for treating depression and other stress-associated disorders.

The study was led by James A. Bibb, Ph.D., at The University of Texas Southwestern Medical Center, who received NARSAD Young Investigator grants in 2000 and 2003, and lead authorFlorian Plattner, Ph.D. The scientific team also included Paul Greengard, Ph.D., a member of BBRF’s Scientific Council and a 1992, 2002, and 2008 Distinguished Investigator; Eric J. Nestler, M.D., Ph.D., a Scientific Council Member and a 1996 Distinguished Investigator; 2006 Young Investigator Kanehiro Hayashi, Ph.D.; 2007 Young Investigator Eunice Y. Yuen, Ph.D.; 1999 and 2004 Young Investigator Zhen Yan, Ph.D.; and 1999 Independent Investigator and 2006 Distinguished Investigator Angus C. Nairn, Ph.D.

The team’s findings are a result of a detailed investigation into a “signaling cascade,” called the cAMP/PKA pathway, which regulates a wide range of processes in the central nervous system. Disruption of the pathway has been linked with several mental disorders, including depression. Some existing antidepressant medications are known to boost cAMP signaling, but better understanding how this signaling network works could help researchers develop treatments that are more effective or cause fewer side effects.

Two new small-molecule compounds tested in mice can alleviate some symptoms of schizophrenia-like behaviors, including movement abnormalities, social avoidance, and cognitive performance. As reported in the July 1st issue of Neuropsychopharmacology, these research results may point the way toward new kinds of medications that treat specific aspects ofschizophrenia behaviors.

Current antipsychotic drugs used to treat the disorder target the dopamine D2 receptor, an important communication port for some neurons in the brain. These drugs are used primarily to treat schizophrenia “positive” symptoms such as delusions and hallucinations. They are less effective in treating “negative” symptoms such as a lack of pleasure in everyday life, or concentration and memory problems (“cognitive symptoms”), according to Duke University Medical Center scientists William C. Wetsel, Ph.D., a 1998 NARSAD Independent Investigator grantee, and Marc G. Caron, Ph.D., a Foundation Scientific Council member and 2005 NARSAD Distinguished Investigator grantee.

Current antipsychotic drugs were developed to bind to and block one specific type of communication pathway through dopamine D2 receptors, but the receptors are involved in more than one type of signaling pathway. Dr. Wetsel and colleagues decided to look for drug candidates that would block other pathways related to the dopamine D2 receptor, in the hope that this might reveal novel ways to treat a wider variety of schizophrenia symptoms.

They tested two dopamine D2 receptor-targeting compounds called UNC9975 and UNC9994 (developed by Jian Jin, Ph.D., of the University of North Carolina) that influence the beta-arrestin communication pathway, a different pathway than the one typically affected by antipsychotic drugs. The researchers showed that the compounds could normalize schizophrenia-like symptoms in mice by reducing their hyperactive movements, improving their memory for novel stimuli, and making them more social around other mice, among other improvements.

The new compounds also produced a much lower level of catalepsy—the rigid muscle, “trance-like” state that is sometimes a side effect of schizophrenic treatment—than traditional antipsychotic drugs such as haloperidol. Targeting different pathways connected to the dopamine D2 receptors, the researchers say, may increase the possibilities for treating people with schizophrenia in more individualized, fine-tuned ways that match their exact symptoms and vulnerabilities to side effects.

Effects of β-Arrestin-Biased Dopamine D2 Receptor Ligands on Schizophrenia-Like Behavior in Hypoglutamatergic Mice

Su M Park¹, Meng Chen¹, Claire M Schmerberg¹, Russell S Dulman¹, Ramona M Rodriguiz¹^,², Marc G Caron³, Jian Jin⁴ and William C Wetsel¹^,²^,³^,⁵
Neuropsychopharmacology 2015; http://dx.doi.org:/10.1038/npp.2015.196

Current antipsychotic drugs (APDs) show efficacy with positive symptoms, but are limited in treating negative or cognitive features of schizophrenia. Whereas all currently FDA-approved medications target primarily the dopamine D2 receptor (D2R) to inhibit G_i/o-mediated adenylyl cyclase, a recent study has shown that many APDs affect not only G_i/o– but they can also influence β-arrestin- (βArr)-mediated signaling. The ability of ligands to differentially affect signaling through these pathways is termed functional selectivity. We have developed ligands that are devoid of D2R-mediated G_i/o protein signaling, but are simultaneously partial agonists for D2R/βArr interactions. The purpose of this study was to test the effectiveness of UNC9975 or UNC9994 on schizophrenia-like behaviors in phencyclidine-treated or NR1-knockdown hypoglutamatergic mice. We have found the UNC compounds reduce hyperlocomotion in the open field, restore PPI, improve novel object recognition memory, partially normalize social behavior, decrease conditioned avoidance responding, and elicit a much lower level of catalepsy than haloperidol. These preclinical results suggest that exploitation of functional selectivity may provide unique opportunities to develop drugs with fewer side effects, greater therapeutic selectivity, and enhanced efficacy for treating schizophrenia and related conditions than medications that are currently available.

The estrogen-related drug raloxifene can improve attention and memory in men and women with schizophrenia, according to a new study published in the journal Molecular Psychiatry.

University of New South Wales researcher Cynthia S. Weickert, Ph.D., a 1999 and 2001 NARSAD Young Investigator and 2004 Independent Investigator grantee, and her colleagues say their raloxifene findings could help improve some cognitive problems related to schizophrenia that have been the most difficult to treat with drugs. Dr. Weickert’s research team included NARSAD Young Investigator grantees Rhoshel K. Lenroot, M.D., (2003), and Ans Vercammen, Ph.D., (2010), along with Independent Investigator grantee Jayashri Kulkarni, Ph.D., (2000), and her husband and first author Tom Weickert, Ph.D.

A growing body of evidence suggests that estrogen plays a beneficial role in the brain, supporting growth and protecting neurons from damage. From work supported by her NARSAD Young Investigator awards, Dr. Weickert and her colleagues found that brain estrogen receptors are altered in some people with schizophrenia, blunting their ability to respond to estrogen’s beneficial effects. Raloxifene stimulates estrogen receptors and can help overcome a blunted estrogen response. Raloxifene is probably best known as a treatment for osteoporosis in women, where it mimics estrogen’s beneficial action in bones. The drug also stimulates estrogen receptors in the brain and may guard against memory loss in aging, making it potentially useful for cognitive problems in schizophrenia patients.

The research team examined the drug’s effect in 98 people diagnosed with schizophrenia or schizoaffective disorder (which combines symptoms of schizophrenia and depression). All of the patients received a daily dose of raloxifene along with their usual antipsychotic medications in one phase of the clinical trial and a placebo in another phase.

After the first six-week period, patients taking raloxifene had improved scores on memory and attention, compared to those taking placebo. When considering all the people in the study during both phases, raloxifene treatment significantly improved attention and thought processing speed. Raloxifene didn’t reduce the severity of schizophrenia symptoms more than the placebo did, but both groups showed less symptoms overall during the study, and none of the patients had severe side effects from the treatment.

Dr. Weickert and colleagues did detect some signs that the positive impact of raloxifene lasted more than one month after the treatment stopped. Although the researchers do not know the exact reasons for the lasting effects, they note that stimulating estrogen receptors might protect neurons, reduce inflammation, and increase connections between nerve cells in the brain over a longer time frame than drugs working on other neurotransmitter receptors. In light of their findings, they suggest future studies should replicate these results in a larger group of schizophrenia patients and also determine how long the cognitive benefits of a six-week treatment with raloxifene may last.

An injectable antipsychotic medication whose effects last for three months has successfully delayed the return of schizophrenia symptoms, researchers have found. Taking the drug in this form may help people with schizophrenia who struggle to stay on treatment by enabling them to take medication less frequently.

The research team, which included Adam J. Savitz, M.D., Ph.D., recipient of a NARSAD Young Investigator Grant in 2001, examined use of the long-acting antipsychotic medication paliperidone palmitate (Invega) in treating symptoms of schizophrenia such as hallucinations, delusions, and strong feelings of suspicion. The research was published online March 29th inJAMA Psychiatry.

When a person with schizophrenia cannot maintain a daily medication schedule, the drug level in his or her body can dip too low to combat symptoms, leading to relapse (return of symptoms) and an increased risk of being hospitalized. This study aimed to determine whether a dosage that would only have to be taken once every three months, rather than every day, would effectively hold off symptoms. After starting with a once-monthly dosage, patients took a three-month dosage to maintain symptom prevention and then were given randomly either placebo or the same three-month dosage every 12 weeks to see whether the medication’s positive effects would persist. (A placebo is a look-alike with inactive ingredients.)

Significantly fewer people who got the second three-month dosage experienced symptom relapse during the experimental phase of the study, compared to those taking a placebo. During this phase, the placebo group also reported more severe symptoms, while the paliperidone palmitate group’s symptoms remained constant.

The two groups also showed different patterns of side effects. The more serious side effects occurred in the placebo group: anxiety and return of other symptoms of schizophrenia. The paliperidone palmitate group more frequently experienced headaches, weight gain, common colds, as well as so-called extrapyramidal symptoms, which involve disruptions to movement.

This study did not include people with a history of substance dependence, major active medical problems, or other serious mental disorders. More research is needed to know whether less frequent dosage of long-acting injectable medication like paliperidone palmitate can help prevent relapse in these groups.

Efficacy and Safety of the 3-Month Formulation of Paliperidone Palmitate vs Placebo for Relapse Prevention of Schizophrenia – A Randomized Clinical Trial

Joris Berwaerts, MD1; Yanning Liu, MS2; Srihari Gopal, MD, MHS1; Isaac Nuamah, PhD1; Haiyan Xu, PhD1; Adam Savitz, MD, PhD1; Danielle Coppola, MD1; Alain Schotte, PhD3; Bart Remmerie, Chem Eng3; Nataliya Maruta, MD, PhD4; David W. Hough, MD1
JAMA Psychiatry. 2015; 72(8):830-839. http://dx.doi.org:/10.1001/jamapsychiatry.2015.0241.

Design, Setting, and Participants This randomized, multicenter trial conducted from April 26, 2012, through April 9, 2014, in 8 countries consisted of 4 phases: 3-week screening phase, flexible-dose 17-week open-label transition phase, 12-week open-label maintenance phase, and open-ended double-blind (DB) phase. Of the 506 patients enrolled (aged 18-70 years; DSM-IV-TR diagnosis of schizophrenia), 305 were randomized to 3-month paliperidone palmitate (n = 160) or placebo (n = 145) in the DB phase.

Interventions Patients received once-monthly doses of the 1-month formulation of paliperidone palmitate (50, 75, 100, or 150 mg eq) during the transition phase, followed by a single dose of the 3-month formulation (3.5 times the stabilized dose of once-monthly paliperidone palmitate) during the maintenance phase. Stabilized patients were randomized to receive either a fixed dose of 3-month paliperidone palmitate (175, 263, 350, or 525 mg eq) or placebo once every 3 months during the DB phase.

Main Outcomes and Measures Time from randomization to the first relapse event (time to relapse) in the DB phase.

Results In the interim analysis, time to first relapse was significantly different in favor of the paliperidone palmitate group vs the placebo group (hazard ratio = 3.45; 95% CI, 1.73-6.88; P < .001); median time to relapse was 274 days for placebo but not estimable for 3-month paliperidone palmitate. An independent data monitoring committee recommended early study termination due to efficacy. In the DB phase, 183 of 305 patients (62% with 3-month paliperidone palmitate; 58% with placebo) had at least 1 treatment-emergent adverse event; those noted more frequently in the group receiving paliperidone palmitate than in the placebo group were headache (9% vs 4%), weight increased (9% vs 3%), nasopharyngitis (6% vs 1%), and akathisia (4% vs 1%).

Conclusions and Relevance Compared with placebo, the 3-month formulation of paliperidone palmitate administered 4 times yearly significantly delayed time to relapse in patients with schizophrenia. The 3-month formulation was generally tolerable and has a safety profile consistent with other marketed paliperidone formulations.

Trial Registration clinicaltrials.gov Identifier:NCT01529515

Tracking Down the Causes of Alzheimer’s

University of Basel
http://www.biosciencetechnology.com/news/2015/09/tracking-down-causes-alzheimers?et_cid=4792750&et_rid=535648082&location=top

Researchers from the University of Basel were able to show that memory function (image shows the hippocampus highlighted) depends on calcium-regulating genes. (Source: MCN University of Basel

http://www.biosciencetechnology.com/sites/biosciencetechnology.com/files/bt1509_basel_brain.jpg

Genes are not only important for regular memory performance, but also for the development of Alzheimer’s disease. Researchers at the University of Basel now identified a specific group of genes that plays a central role in both processes. This group of molecules controls the concentration of calcium ions inside the cell. Their results appear in the current issue of the journal JAMA Psychiatry.

Intact memory capacity is crucial for everyday life. This fact becomes apparent once a memory disorder has developed. Alzheimer’s disease is the most common cause of age-associated memory disorders. Due to increasing life expectancy, the disease is on the rise in Switzerland and worldwide. Unfortunately, there is no effective treatment to cure or even slow down Alzheimer’s yet. Thus, understanding the origins of this neurodegenerative disorder is key to the development of much needed treatments.

Scientists have known for some years now, that genes do not only play a crucial role in normal memory performance, but also in the development of Alzheimer’s. However, it was so far unclear if specific genes are involved in both these processes.

Researchers at the transfaculty research platform at the Psychiatric University Clinics Basel and the Faculty of Psychology at the University of Basel were now able to show in a large scale study that a specific group of genes controls several processes that are central for regular brain functions as well as for the development of Alzheimer. First author Dr. Angela Heck collected and analyzed data of over 57,000 participants for this study.

Calcium is crucial

The study identified genes responsible for the concentration of calcium ions in the cell as central players of physiological and disease processes in the brain. Calcium genes stand in mutual relationship with memory performance of young and older healthy adults as well as with the function of the hippocampus, a brain region that is central to intact memory. Furthermore, calcium genes correlate with the risk for Alzheimer disease. The results contribute to the understanding of the complex processes that lead to memory disorders, such as Alzheimer’s.

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Outstanding Achievement in Schizophrenia Research

Posted in Innovations in Neurophysiology & Neuropsychology, Neurological Diseases, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Drug Discovery, Population Health Management, Genetics & Pharmaceutical, Schizophrenia, Social Development, Translational Science, tagged mood disorders, psychiatric research, Schizophrenia on September 6, 2015| Leave a Comment »

Outstanding Achievement in Schizophrenia Research

Larry H. Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Innovation

Series E. 2; 5.9

2014 Prizewinner:
David Braff, M.D. – University of California, San Diego School of Medicine – Watch Video

David Braff M.D. named Lieber Prize winner

David Braff MD, Distinguished Professor at UCSD’s Department of Psychiatry has been named this year’s Lieber Prize winner by the National Brain and Behavior Research Foundation (NBBRF) and the National Association for Research in Schizophrenia and Depression (NARSAD). This Prize is given to an outstanding neuropsychiatric researcher who has enhanced our fundamental understanding of schizophrenia, a devastating no fault heritable clinical brain disorder affecting 1% of the world’s population. Schizophrenia causes psychosis, cognitive dysfunction and profound disability in many patients. It also affects the families of the patients, since the disability-often strikes early in young adult life. Past Lieber Prize winners include two Nobel Laureates and many other world leading distinguished neuroscientists. The Award will be presented at a scientific meeting, ceremony and dinner in New York at the NBBRF-NARSAD Annual Gala at Lincoln Center in late October.

Dr. Braff has pursued and extended our understanding of schizophrenia via a number of major research projects. The Consortium on the Genomics of Schizophrenia (COGS) is a 30 million-dollar 10 year NIMH-funded consortium on the neurocognitive, neurophysiological, neural circuit and dysfunctional genomic architecture of schizophrenia. Dr Braff has been Principal Scientist and Director of this 7-site study: COGS 1 examined clinical features, neurocognitive and neurophysiological, and other familial endophenotypes or biomarkers in schizophrenia patients and their families as well as healthy control subjects. The follow up COGS 2 is studying 2500 schizophrenia patients and case-control subjects. Genomic and related methods include extensive behavioral, candidate gene, genome wide association, sequencing, methylation and stem cell projects from COGS and UCSD grants. This has led to an increased understanding of both the neural network and underlying genomic network bases of schizophrenia and has enhanced our understanding of risk and vulnerability markers which may provide targets for very early intervention and even, in the longer run, prevention. This neurodevelopmental psychotic process starts early in life but usually manifests itself in late teenagers and young adults. In addition, because of the underlying complex neural and genomic networks that have been identified by this work and the studies of other scientific projects, we have hope of finding novel therapeutic targets for pharmacological and sensory training- cognitive behavioral therapies for this devastating disorder.

Dr. Braff also has conducted longstanding translational (TRANS) and genomic studies over 30 years of continuously funded projects supported by NIMH, NARSAD and the Brain and Behavior Foundation. This research, conducted with many essential colleagues, including TRANS Co-PIs Mark Geyer, Ph.D. and Neal Swerdlow, M.D. Ph.D., has led to cross-species translational advances in understanding the neurobiology of schizophrenia and created powerful tools for screening candidate antipsychotic compounds to treat schizophrenia. Braff has also Directed the VA VISN 22 Mental Illness Research Center Clinical Neuroscience and Genomics Project, which provides crucial infrastructure and intellectual support for this work.

In recent years, Dr. Braff, a NARSAD Distinguished Investigator, has consistently been ranked by “ISI” in the top half of the top percent of all cited neuropsychiatric researchers based on the frequency with which his 300 publications are cited. He has also been awarded the Warren Award from the International Congress of Schizophrenia, the Inspiration Pioneer Research Award from NAMI, the Dean Award from the American College of Psychiatrists and the Marmor Award from the American Psychiatric Association, all given to honor an outstanding neuropsychiatric researcher. Dr. Braff’s colleagues at UCSD have included crucial contributions and context from TRANS Co-PIs, Mark Geyer Ph.D. and Neal Swerdlow MD Ph.D., Department Vice Chair (Also Deputy Director of COGS) as well as more recent faculty appointees Gregory Light, Ph.D (UCSD COGS Director and San Diego VA VISN 22 MIRECC Director) and Tiffany Greenwood, Ph.D. (Genetics And Statistical Genetics Lead Scientist) and many others.

Dr. Igor Grant, Chair of the Department commented, “Professor David Braff has been at the forefront of research into the neurobiology of schizophrenia. Beginning with observations on neurophysiologic biomarkers related to aberrant attentional and other cognitive mechanisms in those afflicted with schizophrenia, his work has progressed to linking such biomarkers to genetic underpinnings of this serious disorder, which affects 1% of our population, and causes great disruptions both for the person affected, and their families and loved ones. Professor Braff’s innovative work has opened better understanding of the interplay of genetic and neurodevelopmental factors in the evolution of schizophrenia, as well as promise of specific diagnostic markers that may help with early identification of people vulnerable to this disorder, at a time when preventive strategies may be most useful. As such his work will inform both improved treatment and prevention. Dr. Braff has also been a generative mentor to younger scientists, a fine educator, and helped the Department establish a modern inpatient psychiatric unit to care for people with severe mental disorders. The Department is very proud that Professor Braff was recognized with the Lieber Prize, reserved for the very finest psychiatrist scientists.”

https://youtu.be/c1_FtkMLJc4

“We are entering a new era of the neuropsychiatric and genomic revolutions, where advanced bioinformatics and other evolving technologies will help us to integrate brain, behavioral and genomic data about schizophrenia that we only imagined was possible in the past. Receiving this prize will serve to enhance all of our endeavors.”

Patrick F. Sullivan, M.D., Karolinska Institutet & University of North Carolina – Watch Video

Patrick F. Sullivan Awarded 2014 Lieber Prize for Outstanding Achievement in Schizophrenia Research

Patrick F. Sullivan, MD, FRANZCP, M. Hayworth & Family Distinguished Professor of Psychiatry and Professor of Genetics and Psychiatry at the University of North Carolina School of Medicine, is one of two researchers awarded the 2014 Lieber Prize for Outstanding Achievement in Schizophrenia Research.

The $50,000 cash award from the Brain & Behavior Research Foundation is given in recognition of a research scientist who has made distinguished contributions to the understanding of schizophrenia. It rewards past achievement and provides further incentive for an outstanding working scientist to continue to do exceptional research into the causes, prevention, and treatment of schizophrenia.

“The 2014 Outstanding Achievement Prize winners have dedicated their lives to solving some of the most intractable psychiatric problems in order to improve the lives of millions of people and their families,” said Jeffrey Borenstein, MD, CEO of the Brain & Behavior Research Foundation. “We applaud their past and future accomplishments.”

As a psychiatric geneticist, Dr. Sullivan works to decode the molecular and cellular consequences of genetic variations underlying schizophrenia. He heads large, multinational projects across a range of disorders, dividing his time between Sweden, where he is a Professor at the Karolinska Institutet, and UNC, where he is the Director of the Center for Psychiatric Genomics.

As founder and lead investigator of the Psychiatric Genomics Consortium (PGC), Dr. Sullivan directs 300 scientists from 70 institutions in 19 countries who are conducting mega-analyses, involving 90,000 participants, of genetic risk for schizophrenia, depression, autism, bipolar disorder and attention-deficit hyperactivity disorder. He is also the principal investigator for a Swedish genetic study of 10,000 patients with schizophrenia and bipolar disorder, one of the few projects looking into the impact of environmental factors in these disorders.

Patrick Sullivan: Why care about psychiatric genetics? – YouTube

http://www.youtube.com/watch%3Fv%3DPzoEgKv5yKQ Feb 5, 2015 …

A Stockholm Psychiatry Lecture held at Karolinska Institutet Feb 3 2015 by Prof. Patrick F Sullivan, UNC and KI.

Schizophrenia: Q&A with Patrick F. Sullivan – Dana Foundation

http://www.dana.org/Briefing_Papers/Schizophrenia__Q_A_with_Patrick_F__Sullivan/Jul 14, 2015 …

Baby steps may become giant steps in the next ten years for schizophrenia, an illness which impacts an estimated 2.4 million Americans

https://youtu.be/uJmA0gGTUnk

“It is my deep hope that the work that led to my selection of this prize will continue so that we can greatly expand our knowledge of the genetic basis of schizophrenia so that these new findings will, in turn, lead to advances that improve the lives of people living with schizophrenia and other serious mental disorders.”

SIDNEY R. BAER, JR. PRIZE FOR INNOVATIVE AND PROMISING SCHIZOPHRENIA RESEARCH

Gregory Light, Ph.D.
University of California, San Diego

https://youtu.be/XqtcBkyz7vE

“This award strengthens my resolve to continue to develop treatment strategies that will ameliorate, prevent, and perhaps even cure schizophrenia and related psychotic illnesses in the next stages of my career.”

Stephan Ripke, M.D.
Broad Institute

https://youtu.be/nMfKsWFdM-k

“As a result of the immense collaborative efforts of the PGC, I believe that we are now on the path towards making seminal discoveries into the biology of this devastating disease. New therapeutic targets are imminent and the support of this prize will have a great impact on realizing this goal.”

Colvin Prize for Outstanding Achievement in Mood Disorders Research:

Wayne C. Drevets, M.D.
Janssen Pharmaceutica

https://youtu.be/xs7c3u3_pjk

“This prize not only affirms the significance of our past work, it also inspires and invigorates our current and future research, which we hope will improve the lives of people affected by bipolar disorder by leading to the discovery and development of new treatments.”

Fritz A. Henn, M.D., Ph.D.
Cold Spring Harbor Laboratory

https://youtu.be/-HVF-Lxpx14

“That my peers feel our work merits recognition is the greatest reward after a lifetime of work aimed at understanding and better treating major mental illness.”

2013	Marc G. Caron, Ph.D. Video Clip	Duke University School of Medicine
2012	Michael J. Owen, M.D., Ph.D. Video Clip	Cardiff University
2012	Michael O’Donovan, M.D., Ph.D. Video Clip	Cardiff University
2011	Carol A. Tamminga, M.D. Video Clip	UT Southwestern Medical Center at Dallas
2011	Joel E. Kleinman, M.D., Ph.D. Video Clip	National Institute of Mental Health (NIMH)
2010	Ming T. Tsuang, M.D., Ph.D., D.Sc. Video Clip

Goldman-Rakic Prize for Outstanding Achievement in Cognitive Neuroscience

2014 Prizewinner:

Richard L. Huganir, Ph.D. – The Johns Hopkins University School of Medicine – Watch Video

Department Affiliation: Primary: Neuroscience; Secondary: Biological Chemistry; Howard Hughes Medical Institute
Degree: Ph.D., Cornell University
Rank: Professor/Director, Department of Neuroscience

Regulation of Neurotransmitter Receptors and Brain Function in Heath and Disease

Neurotransmitter receptors mediate signal transduction at the postsynaptic membrane of synaptic connections between neurons in the nervous system. We have been studying the molecular mechanisms in the regulation of neurotransmitter receptor function. Recently we have focused on glutamate receptors, the major excitatory receptors in the brain. Glutamate receptors can be divided into two major classes: AMPA and NMDA receptors. AMPA receptors mediate rapid excitatory synaptic transmission while NMDA receptors play important roles in neuronal plasticity and development. Studies in our laboratory have found that both AMPA and NMDA receptors are multiply phosphorylated by a variety of protein kinases. Phosphorylation regulates several functional properties of these receptors including conductance and membrane targeting. Recent studies in our lab have demonstrated that the phosphorylation of AMPA receptors is regulated during cellular models of learning and memory such as long-term potentiation (LTP) and long-term depression (LTD). Moreover, phosphorylation of the AMPA receptor GluR1 subunit is required for the expression of these forms of plasticity and for the retention of spatial memory and also regulates emotional memory formation and erasure.

We have also been examining the mechanisms of the subcellular targeting and clustering of glutamate receptors at synapses. We have recently identified a variety of proteins that directly or indirectly interact with AMPA and NMDA receptors. We have found a novel family of proteins that we call GRIPs (Glutamate Receptor Interacting Proteins) that directly bind to the C-termini of the GluR2/3 subunits of AMPA receptors. GRIPs contain seven PDZ domains, protein-protein interaction motifs, which crosslink AMPA receptors to each other or link them to other proteins. In addition, we have found that the C-termini of GluR2 also interacts with the PDZ domain of PICK1, a protein kinase C-binding protein that is found at excitatory synapses. The GluR2 subunit also interacts with the NSF protein, a protein involved in the regulation of membrane fusion events. These AMPA receptor interacting proteins are critical in the proper membrane trafficking and synaptic targeting of these receptors. We have shown that the binding of PICK1 and GRIP is required for a specific form of LTD in the cerebellum that is a cellular model for motor learning. Moreover, we have found that this receptor complex is critical for hippocampal LTP and LTD and spatial learning.

In addition to these studies on AMPA receptors, we have been characterizing a separate NMDA receptor associated protein complex that is important in synaptic targeting and downstream signaling of NMDA receptors. We have identified an excitatory synapse specific rasGAP, which we call synGAP that regulates synaptic Ras signaling and has profound effects on synaptic plasticity.

Importantly, recent evidence has implicated glutamate receptor associated complexes in several neurological and psychiatric disorders including Alzheimer’s disease, schizophrenia, autism, mental retardation as well as in chronic pain and drug addiction.

In summary, we have examined the molecular mechanisms underlying the regulation of neurotransmitter receptor function. Our studies have suggested that regulation of receptor function may be a major mechanism for the regulation of synaptic plasticity in the nervous system in health and disease and may be an important determinant of animal behavior.

Representative Publications:

Volk, L.J., Bachman, J.L., Johnson, R., Yu, Y., Huganir, R.L. (2013) PKM-Z is not required for hippocampal synaptic plasticity, learning and memory. Nature 493(7432): 420-3. Pub Med Reference
Thomas, G.M., Hayashi, T., Chiu, S.L., Chen, C.M., Huganir, R.L. (2012) Palmitoylation by DHHC5/8 targets GRIP1 to dendritic endosomes to regulate AMPA-R trafficking. Neuron73(3):482-96. Pub Med Reference
Makuch, L., Volk, L., Anggono, V., Johnson, R.C., Yu, Y., Duning, K., Kremerskothen, J., Xia, J., Takamiya, K., Huganir, R.L. (2011) Regulation of AMPA receptor function by the human memory-associated gene KIBRA. Neuron 71(6):1022-9. Pub Med Reference
Makino, Y., Johnson, R.C., Yu, Y., Takamiya, K., Huganir, R.L. (2011) Enhanced synaptic plasticity in mice with phosphomimetic mutation of the GluA1 AMPA receptor. Proc Natl Acad Sci USA. 108(20):8450-5. Epub 2011 May 2. Pub Med Reference
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GOLDMAN-RAKIC PRIZE FOR OUTSTANDING ACHIEVEMENT IN COGNITIVE NEUROSCIENCE

https://youtu.be/4alesBVcM3s

“This has been my life long career goal—to understand how memory is encoded in the brain and how these mechanisms are disrupted in cognitive disorders. I am honored to be associated with Dr. Goldman- Rakic’s legacy.”

2013	Karl Deisseroth, M.D., Ph.D. Video Clip	Stanford University
2012	Larry R. Squire, Ph.D. Video Clip	University of California, San Diego
2011	Michael E. Goldberg, M.D. Video Clip	Columbia University/NYSPI
2010	Robert Malenka, M.D., Ph.D. Video Clip	Stanford University

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Archive for the ‘Innovations in Neurophysiology & Neuropsychology’ Category

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$1.5M Goes to Stem Cell Research

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Long-term aerobic exercise prevents age-related brain deterioration http://www.kurzweilai.net/long-term-aerobic-exercise-prevents-age-related-brain-deterioration

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Thematic Minireview Series on Nuclear Receptors in Biology and Diseases

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Long-term aerobic exercise prevents age-related brain deterioration
http://www.kurzweilai.net/long-term-aerobic-exercise-prevents-age-related-brain-deterioration