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Printing Cancer Tumors in 3D for Identification of Response to Drugs – Teleconference by Prof. Satchi-Fainaro, TAU, Medical School, 4/5/2016 noon EST

Reporter: Aviva Lev-Ari, PhD, RN

NY-Satchi-Fainaro-Teleconference_r1

 

 

 

 

PATENT EXPIRY DATES

PATENT EXPIRY DATES

Reporter: Stephen J Williams, PhD

The global generic pharmaceuticals market is likely to witness strong growth in the next few years owing to the patent expiration of key blockbuster drugs and the judicious cost containment efforts…

Source: PATENT EXPIRY DATES

Next Generation Sequencing in Clinical Laboratory, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Next Generation Sequencing in Clinical Laboratory

Curator: Larry H. Bernstein, MD, FCAP

INSIGHTS on Next-Generation Sequencing

Next-generation (NGS) sequencing brings scalability and sensitivity to diagnostics in ways that traditional DNA analysis could not

Enabling Technology for Diagnosis, Prognosis, and Personalized Medicine

Significantly higher speed, lower cost, smaller sample size, and higher accuracy compared with conventional Sanger sequencing make next-generation sequencing (NGS) an attractive platform for medical diagnostics. By practically eliminating cost and time barriers, NGS allows testing of virtually any gene or genetic mutation associated with diseases.

Scalability and Sensitivity

NGS brings scalability and sensitivity to diagnostics in ways that traditional DNA analysis could not. “NGS analyzes hundreds of gene variants or biomarkers simultaneously. Traditional sequencing is better suited for analysis of single genes or fewer than 100 variants,” notes Joseph Bernardo, president of next-generation sequencing and oncology at Thermo Fisher Scientific (Waltham, MA).

Related Article: Computational Changes in Next-Generation Sequencing

Thermo Fisher’s Oncomine Focus Assay for NGS, for example, analyzes close to 1,000 biomarkers associated with the 52-gene panel. These biomarkers constitute about 1,000 different locations on the 52 genes that correlate with the efficacy of certain drugs. The assay allows single-workflow concurrent analysis of DNA and RNA, enabling sequencing of 35 hot-spot genes, 19 genes associated with copy number gain, and 23 fusion genes.

NGS is also better suited to detect lower levels of variants present in heterogeneous material, such as tumor samples. And while both NGS and Sanger sequencing are versatile, NGS can analyze both DNA and RNA, including RNA fusions, at a much more cost-efficient price point.

“When interrogating a limited number of analytes, Sanger sequencing is the standard for many laboratory- developed tests, offering fast turnaround times and lower cost than NGS,” Bernardo says. “We view the two methods as complementary.”

Diagnostic NGS is moving inexorably toward targeted sequencing, particularly for tumor analysis. The targets are specific regions within a tumor’s DNA or individual genes, or specific locations on single genes.

“Targeted sequencing lends itself to diagnostic testing, particularly in oncology, as the goal is to analyze multiple genes associated with cancer using a platform that offers high sensitivity, reliability, and rapid turnaround time,” Bernardo tells Lab Manager. “It is simply more cost-effective.”

That is why the National Cancer Institute (NCI) chose Thermo Fisher’s Ion Torrent sequencing system and the Oncomine reagents for NCI-MATCH, the most ambitious trial to date of NGS oncology diagnostics.

NCI-MATCH will use a 143-gene panel to test submitted tumor samples at four centers (NCI, MD Anderson Cancer Center, Massachusetts General Hospital, and Yale University). The centers then provide sequencing data that helps direct appropriate treatments.

The NCI test protocol ensures consistency across multiple instruments and sites.

Personalized Treatments

Another great opportunity for NGS-based diagnostics is in personalized or precision medicine for both new and existing drugs. Companion diagnostics—co-approved with the relevant drug—drive this entire business. “The only way personalized medicine can succeed commercially is if pharmaceutical companies incorporate a universal assay philosophy in their development programs instead of developing a unique assay for each new drug,” Bernardo explains. For example, in late 2015, Thermo Fisher partnered with Pfizer and Novartis to develop a universal companion diagnostic with the goal of identifying personalized therapy selection from a menu of drugs targeting non-small-cell lung cancer, which annually causes more deaths than breast, colon, and prostate cancer combined.

While advances in sequencing have been remarkable in recent years, the eventual success of NGS-based diagnostics will not depend on instrumentation alone. “What [ensures] ease of use and commonality of results is the cohesiveness of the entire workflow, from sample prep to rapid sequencing systems and bioinformatics,” Bernardo says. “Those components working together will drive NGS into a realizable solution for the clinical market.”

In addition to confirming a disease condition (diagnosis), NGS also provides valuable information on disease susceptibility, prognosis, and the potential effect of drugs on individual patients. The latter idea, known as precision medicine or personalized medicine, uses an individual’s molecular profile to guide treatment. The idea is to differentiate diseases into subtypes based on molecular (usually genetic) characteristics and tailor therapies accordingly.

Precision medicine is still in its infancy, but dozens of pharmaceutical, diagnostics, and genetics firms have bought into the idea.

“We are just at the beginning of connecting genomic and genetic information to target specific therapies for patients,” says T.J. Johnson, president and CEO of HTG Molecular Diagnostics (Tuscon, AZ). “Precision medicine will have a bright future as we gain better understanding of the root causes of disease.”

In 2013, HTG commercialized its HTG Edge instrument platform and a portfolio of RNA assays, which fully automate the company’s proprietary nuclease protection chemistry. This chemistry measures mRNA and miRNA gene expression levels from very small quantities of difficult-to-handle samples.

HTG entered the NGS market in 2014 with the launch of the first HTG EdgeSeq product, an assay that targets and digitally measures the expression of more than 2,000 microRNAs. The assay utilizes the HTG Edge for sample and library preparation, and it uses a suitable NGS instrument (from either Illumina or Thermo Fisher) for quantitation. The data is imported back into the HTG EdgeSeq instrument for analytics and reporting.

In 2015, the company launched four additional HTG EdgeSeq panels: immuno- oncology and pan-oncology biomarker panels, a lymphoma profiling panel, and a classifier for subtyping diffuse large B-cell lymphomas (DLBCL).

Eliminating Biopsies?

Traditional biopsies for tumor DNA analysis are invasive, risky, and often impossible to obtain, and they may not uncover the heterogeneity often present in tumors. It was recently discovered that dying tumor cells release small pieces of DNA into the bloodstream. This cell-free circulating tumor DNA (ctDNA) is detectable in samples through NGS.

In September 2015, Memorial Sloan Kettering Cancer Center (MSK) and NGS leader Illumina (San Diego, CA) entered a collaboration to study ctDNA for cancer diagnosis and monitoring. The aim is to establish ctDNA as a relevant cancer biomarker.

Heterogeneity as it pertains to cancer traditionally refers to multiple tissues located within a tumor, as determined histologically. A number of recent studies suggest that tumor heterogeneity occurs at the genetic level as well. “In particular, there appears to be a tremendous variety of sequence variants within the same tumor, even resulting in situations where one tumor can have multiple mutated genes that have been demonstrated to drive cancer,” says John Leite, PhD, vice president, oncology—market development and product marketing at Illumina.

Heterogeneity challenges the search for treatments that target a specific gene product or pathway. Once the patient is treated, biopsies tell very little about how that patient is responding. “Our hope is that ctDNA provides clinicians with a real-time measure of the abundance of those mutated genes and that a decrease in the relative abundance is synonymous with a lower tumor burden,” Leite adds.

Clinical trials are needed to demonstrate that patients whose therapy was selected using ctDNA versus traditional tissue biopsy testing had a significantly improved outcome or that the analysis might be informative for prognosis.

What about cancer cells that do not release DNA? “Studies show that tumors from different organs or tissues release more or less ctDNA into the peripheral blood,” Leite explains, “but in general the possibility that some cells might not release ctDNA is an open area of research.”

For the MSK-Illumina collaboration, the cancer center will collect samples, and Illumina will apply its sequencing technology to detect ctDNA in those samples. The big draw here is the potential to reduce the number of invasive, expensive diagnostic and monitoring procedures with a simple blood test. This would not be possible without deep next-generation sequencing—the genomics vernacular for sequencing at great depths of coverage.

“Whereas sequencing to identify germline variants can be performed at a nominal depth of coverage—for example, reading a DNA strand 30 times—sequencing rare variants such as in ctDNA requires a much higher level of sensitivity, which is driven by increasing depth of coverage [as much] as 25,000 times,” Leite tells Lab Manager.

In addition to the Illumina MSK collaboration and the work of Thermo Fisher Scientific described above, many more studies involving research consortia and pharmaceutical companies are under way.

“This is a really exciting time for oncology,” Leite says.

Reducing Sample Size

Similarly, in November 2015, Circulogene Theranostics (Birmingham, AL) launched its cfDNA (cell-free DNA) liquid biopsy products for testing ten tumor types, including breast, lung, and colon cancers. The company claims the ability to enrich circulating cfDNA from a single drop of blood.

“While all liquid biopsy companies are focusing on the downstream novel technologies to selectively enrich or amplify tumor-specific cfDNA from a dominantly normal population, the upstream 40 to 90 percent material loss during cfDNA extraction leads to potential false negative results of cancer mutation detection,” explains Chen Yeh, Circulogene’s chief scientific officer. “This is why 10 to 20 mL of blood [are] generally required for conventional cfDNA liquid biopsies.”

Related Article: Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens

Released cfDNA fragments often complex with proteins and lipids, which shift their densities to values much lower than those of pure DNA or protein while protecting the corresponding cfDNA from attack by circulating nucleases. Circulogene’s cfDNA breakthrough concentrates and enriches these genetic fragments through density fractionation followed by enzyme-based DNA modification and manipulation, eliminating extraction-associated loss. The technology ensures near-full recovery of both small-molecular-weight (apoptotic cell death) and high-molecular-weight (necrotic cell death) cell-free DNA species from droplet volumes of plasma, serum, or other body fluids.

“The 50-gene panel is our first offering,” says Yeh. “We will continue to develop and cover more comprehensive, informative, and actionable genes and tests.”

The current bottleneck in personalized and precision medicine is the severe shortage of anticancer drugs. Yeh provides perspective, saying, “We have about 60 FDA-approved drugs for cancer-targeted therapies on market, while there are approximately 150 cancer driver genes to aim for. If counting all mutations within these 150 genes, the numbers will be overwhelming.”

Circulogene’s cell-free DNA enrichment technology may be followed up with NGS, conventional Sanger sequencing, or any DNA assay based on PCR or mass spectrometry. However, the sensitivity of Sanger sequencing is insufficient for detecting variants with volumes below 15 percent. Moreover, the company’s multiplex NGS liquid biopsy test captures and monitors real-time, longitudinal tumor heterogeneity or tumor clonal dynamic evolution, which goes well beyond testing of a single mutation on a single sample in traditional sequencing.

 

Gene Editing Casts a Wide Net 

With CRISPR, Gene Editing Can Trawl the Murk, Catching Elusive Phenotypes amidst the Epigenetic Ebb and Flow

http://www.genengnews.com/gen-articles/gene-editing-casts-a-wide-net/5713/

  • Genome editing, a much-desired means of accomplishing gene knockout, gene activation, and other tasks, once seemed just beyond the reach of most research scientists and drug developers. But that was before the advent of CRISPR technology, an easy, versatile, and dependable means of implementing genetic modifications. It is in the process of democratizing genome editing.

    CRISPR stands for “clustered, regularly interspaced, short palindromic repeats,” segments of DNA that occur naturally in many types of bacteria. These segments function as part of an ancient immune system. Each segment precedes “spacer DNA,” a short base sequence that is derived from a fragment of foreign DNA. Spacers serve as reminders of past encounters with phages or plasmids.

    The CRISPR-based immune system encompasses several mechanisms, including one in which CRISPR loci are transcribed into small RNAs that may complex with a nuclease called CRISPR-associated protein (Cas). Then the RNA guides Cas, which cleaves invading DNA on the basis of sequence complementarity.

    In the laboratory, CRISPR sequences are combined with a short RNA complementary to a target gene site. The result is a complex in which the RNA guides Cas to a preselected target.

    Cas produces precise site-specific DNA breaks, which, with imperfect repair, cause gene mutagenesis. In more recent applications, Cas can serve as an anchor for other proteins, such as transcriptional factors and epigenetic enzymes. This system, it seems, has almost limitless versatility.

  • Edited Stem Cells

    The Sanger Institute Mouse Genetic Program, along with other academic institutions around the world, provides access to thousands of genetically modified mouse strains. “Genetic engineering of mouse embryonic stem (ES) cells by homologous recombination is a powerful technique that has been around since the 1980s,” says William Skarnes, Ph.D., senior group leader at the Wellcome Trust Sanger Institute.

    “A significant drawback of the ES technology is the time required to achieve a germline transmission of the modified genetic locus,” he continues. “While we have an exhaustive collection of modified ES cells, only about 5,000 knockout mice, or a quarter of mouse genome, were derived on the basis of this methodology.”

    The dominant position of the mouse ES cell engineering is now effectively challenged by the CRISPR technology. Compared with very low rates of homologous recombination in fertilized eggs, CRISPR generates high levels of mutations, and off-target effects may be so few as to be undetectable.

    “We used the whole-genome sequencing to thoroughly assess off-target mutations in the offspring of CRISPR-engineered founder animals,” informs Dr. Skarnes. “A mutated Cas9 nuclease was deployed to increase specificity, resulting in nearly perfect targeting.”

    Dr. Skarnes explains that the major mouse genome centers are now switching to CRISPR to complete the creation of the world-wide repository of mouse knockouts. His own research is now focused on genetically engineered induced pluripotent stem cells (iPSCs). These cells are adult cells that have been reprogrammed to an embryonic stem cell–like state, and are thus devoid of ethical issues associated with research on human embryonic stem cells. The ultimate goal is to establish a world-wide panel of reference iPSCs created by high-throughput genetic editing of every single human gene.

    “We are poised to begin a large-scale phenotypic analysis of human genes,” declares Dr. Skarnes. His lab is releasing the first set of functional data on 100 DNA repair genes. “By knocking out individual proteins involved in DNA repair and sequencing the genomes of mutant cells,” declares Dr. Skarnes, “we hope to better understand the mutational signatures that occur in cancer.”

  • Pooled CRISPR Libraries

    Researchers hope to gain a better understanding of the mutational signatures found in cancers by using CRISPR techniques to knock out individual proteins involved in DNA repair and then sequencing the genomes of mutant cells. [iStock/zmeel]

    Connecting a phenotype to the underlying genomics requires an unbiased screening of multiple genes at once. “Pooled CRISPR libraries provide an opportunity to cast a wide net at a reasonably low cost,” says Donato Tedesco, Ph.D., lead research scientist at Cellecta. “Screening one gene at a time on genome scale is a significant investment of time and money that not everyone can afford, especially when looking for common genetic drivers across many cell models.”

    Building on years of experience with shRNA libraries, Cellecta is uniquely positioned to prepare pooled CRISPR libraries for genome-wide or targeted screens of gene families. While shRNA interferes with gene translation, CRISPR disrupts a gene and the genomic level due to imperfections in the DNA repair mechanism.

    To determine if these different mechanisms for inactivating genes affect the results of genetic screens, the team conducted a side-by-side comparison of Cellecta’s Human Genome-Wide Module 1 shRNA Library, which expresses 50,000 shRNA targeting 6,300 human genes, with the library of 50,000 gRNA targeting the same gene set. The concordance between approaches was very high, suggesting that these technologies may be complementary and used for cross-confirmation of results.

    Also, a recently completed Phase I NIH SBIR Grant was used to create and test guiding strand RNA (sgRNA) structures to drastically improve efficiency of gene targeting. For this work, Cellecta used a pool library strategy to simultaneously test multiple sgRNA structures for their efficiency and specificity. An early customized Cellecta pooled gRNA library was successfully utilized for screening for epigenetic genes. This particular screen is highly dependent on a complete loss of function, and could not have been accomplished by shRNA inhibition.

    Scientists from Epizyme interrogated 600 genes in a panel of 100 cell lines and, in addition to finding many epigenetic genes required for proliferation in nearly all cell lines, were able to identify validate several essential epigenetic genes required only in subsets of cells with specific genetic lesions. In other words, pooled cell line screening was able to distinguish targets that are likely to produce toxic side effects in certain types of cancer cells from gene targets that are essential in most cells.

    “A more complicated application of CRISPR technology is to use it for gene activation,” adds Dr. Tedesco. “Cellecta plans to optimize this application to bring forth highly efficient, inexpensive, high-throughput genetic screens based on their pooled libraries.

  • Chemically Modified sgRNA

    Scientists based at Agilent Research Laboratories and Stanford University worked together to demonstrate that chemically modified single guide RNA can be used to enhance the genome editing of primary hepatopoietic stem cells and T cells. This image, which is from the Stanford laboratory of Matthew Porteus, M.D., Ph.D., shows CD34+ human hematopoietic stem cells that were edited to turn green. Editing involved inserting a construct for green fluorescent protein. About 1,000 cells are pictured here.

    Researchers at Agilent Technologies applied their considerable experience in DNA and RNA synthesis to develop a novel chemical synthesis method that can generate long RNAs of 100 nucleotides or more, such as single guide RNAs (sgRNAs) for CRISPR genome editing. “We have used this capability to design and test numerous chemical modifications at different positions of the RNA molecule,” said Laurakay Bruhn, Ph.D., section manager, biological chemistry, Agilent.

    Agilent Research Laboratories worked closely with the laboratory of Matthew Porteus, M.D., Ph.D., an associate professor of pediatrics and stem cell transplantation at Stanford University. The Agilent and Stanford researchers collaborated to further explore the benefits of chemically modified sgRNAs in genome editing of primary hematopoetic stem cells and T cells.

    Dr. Porteus’ lab chose three key target genes implicated in the development of severe combined immunodeficiency (SCID), sickle cell anemia, and HIV transmission. Editing these genes in the patient-derived cells offers an opportunity for novel precision therapies, as the edited cells can renew, expand, and colonize the donor’s bone marrow.

    Dr. Bruhn emphasized the importance of editing specificity, so that no other cellular function is affected by the change. The collaborators focused on three chemical modifications strategically placed at each end of sgRNAs that Agilent had previously tested to show they maintained sgRNA function. A number of other optimization strategies in cell culturing and transfection were explored to ensure high editing yields.

    “Primary cells are difficult to manipulate and edit in comparison with cell lines already adapted to cell culture,” maintains Dr. Bruhn. Widely varied cellular properties of primary cells may require experimental adaptation of editing techniques for each primary cell type.

    The resulting data showed that chemical modifications can greatly enhance efficiency of gene editing. The next step would translate these findings into animal models. Another advantage of chemical synthesis of RNA is that it can potentially be used to make large enough quantities for therapeutics.

    “We are working with Agilent’s Nucleic Acid Solution Division—a business focused on GMP manufacturing of oligonucleotides for therapeutics—to engage with customers interested in this capability and better understand how we might be able to help them accomplish their goals,” says Dr. Bruhn.

  • Customized Animal Models

    “Given their gene-knockout capabilities, zinc-finger-based technologies and CRISPR-based technologies opened the doors for creation of animal models that more closely resemble human disease than mouse models,” says Myung Shin, Ph.D., senior principal scientist, Merck & Co. Dr. Shin’s team supports Merck’s drug discovery and development program by creating animal models mimicking human genetics.

    For example, Dr. Shin’s team has worked with the Dahl salt-sensitive strain of rats, a widely studied model of hypertension. “We used zinc-finger nucleases to generate a homozygous knockout of a renal outer medullary potassium channel (ROMK) gene,” elaborates Dr. Shin. “The resulting model represents a major advance in elucidating the role of ROMK gene.”

    According to Dr. Shin, the model may also provide a bridge between genetics and physiology, particularly in studies of renal regulation and blood pressure. In one study, the model generated animal data that suggest ROMK plays a key role in kidney development and sodium absorption. Work along these lines may lead to a pharmacological strategy to manage hypertension.

    In another study, the team applied zinc-finger nuclease strategy to knockout the coagulation Factor XII, and thoroughly characterize them in thrombosis and hemostasis studies. Results confirmed and extended previous literature findings suggesting Factor XII as a potential target for antithrombotic therapies that carry minimal bleeding risk. The model can be further utilized to study safety profiles and off-target effects of such novel Factor XII inhibitors.

    “We use one-cell embryos to conduct genome editing with zinc-fingers and CRISPR,” continues Dr. Shin. “The ease of this genetic manipulation speeds up generation of animal models for testing of various hypotheses.”

    A zinc finger–generated knockout of the multidrug resistance protein MDR 1a P-glycoprotein became an invaluable tool for evaluating drug candidates for targets located in the central nervous system. For example, it demonstrated utility in pharmacological analyses.

    Dr. Shin’s future research is directed toward preclinical animal models that would contain specific nucleotide changes corresponding to those of humans. “CRISPR technology,” insists Dr. Shin, “brings an unprecedented power to manipulate genome at the level of a single nucleotide, to create gain- or loss-of-function genetic alterations, and to deeply understand the biology of a disease.”

  • Transcriptionally Active dCas9

    “Epigenome editing is important for several reasons,” says Charles Gersbach, Ph.D., an associate professor of biomedical engineering at Duke University. “It is a tool that helps us answer fundamental questions about biology. It advances disease modeling and drug screening. And it may, in the future, serve as mode of genetic therapy.”

    “One part of our research focuses on studying the function of epigenetic marks,” Dr. Gersback continues. “While many of these marks are catalogued, and some have been associated with the certain gene-expression states, the exact causal link between these marks and their effect on gene expression is not known. CRISPR technology can potentially allow for targeted direct manipulation of each epigenetic mark, one at a time.”

    Dr. Gersback’s team mutated the Cas9 nuclease to create deactivated Cas9 (dCas9), which is devoid of endonuclease activity. Although the dCas9 protein lacks catalytic activity, it may still serve as an anchor for a plethora of other important proteins, such as transcription factors and methyltransferases.

    In an elegant study, Dr. Gersbach and colleagues demonstrated that recruitment of a histone acetyltransferase by dCas9 to a genomic site activates nearby gene expression. Moreover, the activation occurred even when the acetyltransferase domain was targeted to a distal enhancer. Similarly, recruitment of KRAB repressor to a distant site silenced the target gene in a very specific manner. These findings support the important role of three-dimensional chromatin structures in gene activation.

    “Genome regulation by epigenetic markers is not static,” maintains Dr. Gersbach. “It responds to changes in the environment and other stimuli. It also changes during cell differentiation. We designed an inducible system providing us with an ability to execute dynamic control over the target genes.”

    In a light-activated CRISPR-Cas9 effector (LACE) system, blue light may be used to control the recruitment of the transcriptional factor VP64 to target DNA sequences. The system has been used to provide robust activation of four target genes with only minimal background activity. Selective illumination of culture plates created a pattern of gene expression in a population of cells, which could be used to mimic what is observed in natural tissues.

    Together with collaborators at Duke University, Dr. Gersbach intends to carry out the high-throughput analysis of all currently identified regulatory elements in the genome. “Our ultimate goal,” he declares, “is to assign function to all of these elements.”

Rice University researches develop new CRISPR-CAS9 strategy to reduce off-target gene editing effects

Reporter: Stephen J. Williams, PhD

Rice University researches develop new CRISPR-CAS9 strategy to reduce off-target gene editing effects, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

Series B, Volume 2:

Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS & BioInformatics, Simulations and the Genome Ontology

https://www.amazon.com/dp/B08385KF87

New strategies, tools offered for genome editing

 Reported from Science Daily at  https://www.sciencedaily.com/

Bioengineer Gang Bao and team explore CRISPR-Cas9 alternatives

Date:
February 8, 2016
Source:
Rice University
Summary:
Bioengineers have studied alternative CRISPR-Cas9 systems for precision genome editing, with a focus on improving its accuracy and limiting ‘off-target’ errors.
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FULL STORY

A Cas9 protein (light blue) with guide RNA (purple) and DNA (red) shows a DNA bulge, marking a sequence that would be considered off-target for CRISPR-Cas9 editing. The Rice University lab of bioengineer Gang Bao has developed Web-based tools to search for such off-targets.
Credit: Bao Lab/Rice University
 
 

Rice University bioengineers have found new techniques for precision genome editing that are more accurate and have fewer off-target errors.

The new strategies are shared in three papers in an upcoming special issue of the Nature journal Molecular Therapy on improving the revolutionary genome-editing technique called CRISPR-Cas9.

Bioengineering Professor Gang Bao and his colleagues present ideas for maximizing on-target gene editing with biological catalysts capable of cutting DNA called “engineered nucleases.” Several such systems have been studied for years, but for the past three, the promise of cut-and-paste editing via CRISPR-Cas9 has captured the attention of scientists worldwide.

CRISPR-Cas9, a naturally occurring defense system in bacteria, allows researchers to design a short sequence of RNA called “guide RNA” that targets a specific section of genetic code (DNA) in a cell. An associated Cas9 protein then cuts the section, disrupts it or replaces it with the desired code.

That’s how bacteria use CRISPR-Cas9 to immunize themselves from disease. Exposure to an invader causes the bacteria to adapt by adding the invader’s genetic signature to a CRISPR database. The bacteria then recognize future enemies and destroy them with an appropriate Cas9 protein.

About three years ago researchers discovered that bacterial CRISPR-Cas9 could be modified to edit DNA in human cells by, for instance, replacing mutant sequences with normal, or “wild-type,” sequences in much the same way a bacterium banks an invader’s DNA signature. The technique is seen as having great potential for disease modeling and treatment, synthetic biology and molecular pathway dissection.

But CRISPR-Cas9 is still vulnerable to snipping the wrong sequences — called “off-targets” — in addition to the right ones. In therapeutic applications, Bao said, off-target cutting by CRISPR-Cas9 could cause many detrimental effects, including cancer.

Bao, who moved to Rice’s BioScience Research Collaborative (BRC) in 2015 with a grant from the Cancer Prevention and Research Institute of Texas, is studying ways to refine CRISPR-Cas9, which he described as “nanoscissors for editing genes.”

One of his goals is to treat the hereditary disease sickle cell anemia, which he hopes CRISPR-Cas9 will eventually cure. But first the therapy must become much better at avoiding off-targets that can cause unwanted side effects.

In two of the papers, the researchers study different orthologs: Cas9 proteins from species with the same ancestors as the Streptococcus pyogenes (Spy)bacterium commonly used in CRISPR/Cas9.

“Our approach in these papers is to explore the possibility of using different Cas9 orthologs,” Bao said. “There are many possibilities.”

In the first paper, Bao and his group used experiments on mammalian cells to characterize a CRISPR-Cas9 system from the Neisseria meningitides (Nme) bacterium. It differs from Spy in a way that bioengineers can use to reduce the risk of off-target edits, he said.

That difference lies primarily in a sequence of code that is not part of the target, but close by. Known as a protospacer-adjacent motif (PAM), it’s a marker for target DNA sequences and necessary for Cas9 protein binding. InSpyCas9 editing, the PAM sequence is generally three nucleotides long. For Nme, the required PAM sequence is significantly longer — eight nucleotides. While Nme may find fewer targets, those targets are more likely to be the correct ones, according to the researchers. That, they argue, may make it a safer alternative for gene editing.

The second paper, a collaboration with colleagues at the University of Freiburg, Germany, addresses highly specific human-gene editing using yet another bacteria’s immune system. For this study, Cas9 proteins from Spy were replaced with Streptococcus thermophiles (Sth) proteins that also recognize longer PAMs. Tests carried out in human cells found Sth proteins with more stringent PAM requirements were significantly better than SpyCas9 proteins at avoiding off-targets.

Bao and company also looked at the effect of bulges in DNA and RNA that can influence targeting. Bulges appear when a sequence is one nucleotide longer or one nucleotide shorter than the expected DNA sequence targeted by guide RNA.

“We found that even with DNA or RNA bulges, the Cas9 protein can still cut,” he said. “That’s a unique contribution. Nobody saw that would be the case, but we demonstrated it. Consequently, we’ve developed a Web-based tool to search for three cases of potential off-target sites that contain base mismatches, RNA bulges and DNA bulges.”

Bao noted the Nme and Sth Cas9 proteins, unlike Spy, are small enough to be packaged within an adeno-associated virus for delivery to and treatment of specific cells in an animal. “That’s another advantage, and why we want to go on to explore these two systems,” he said.

The third paper is a review of current CRISPR-Cas9 techniques that focuses on genome-editing tools available for target selection, experimental methods and validation. Bao and his team also lay out a list of challenges yet to be solved to eliminate off-target effects.

He said there is a path forward, represented in part by his investigation of two new bacterial systems as well as the fact that CRISPR-Cas9 is a much easier technique to implement in the lab than other genome-editing systems such as TALEN and zinc finger nuclease.

Bao said that unlike those older genome-editing techniques, CRISPR-Cas9 is straightforward enough for students to learn and use in a short time.

Bao hopes to establish his lab as a focal point for genome editing in the Texas Medical Center. To that end, he brought the TMC genome-editing community together for a well-attended workshop at the BRC last December.

“We had a lot of good discussions,” he said. “One thing I would like to stimulate is the formation of a consortium among the many labs in TMC using CRISPR. They have needs to design CRISPR systems for different applications, but there are a lot of common issues. If we work together, it will be easier to address them.”

 

Story Source:

The above post is reprinted from materials provided by Rice University.Note: Materials may be edited for content and length.


Journal References:

  1. Ciaran M. Lee, Thomas J. Cradick, Gang Bao. The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells. Molecular Therapy, 2016; DOI:10.1038/mt.2016.8
  2. Maximilian Müller, Ciaran M Lee, Giedrius Gasiunas, Timothy H Davis, Thomas J Cradick, Virginijus Siksnys, Gang Bao, Toni Cathomen, Claudio Mussolino. Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome. Molecular Therapy, 2015; DOI: 10.1038/mt.2015.218
  3. Ciaran M. Lee, Thomas J. Cradick, Eli J Fine, Gang Bao. Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing. Molecular Therapy, 2016; DOI: 10.1038/mt.2016.1

Cite This Page:

Rice University. “New strategies, tools offered for genome editing: Bioengineer Gang Bao and team explore CRISPR-Cas9 alternatives.” ScienceDaily. ScienceDaily, 8 February 2016. <www.sciencedaily.com/releases/2016/02/160208135449.htm>.
 

Cardiovascular Medical Devices Cleared by FDA 2016

Reporter: Aviva Lev-Ari, PhD, RN

 

In other regulatory news:

SOURCE

http://www.medpagetoday.com/Cardiology/Prevention/56832?isalert=1&uun=g99985d4908R5099207u&xid=NL_breakingnews_2016-03-21

FDA approves 4th-gen MitraClip for TMVR 

Updated Issue with Delivery System Deployment Process: MitraClip Clip Recalled by Abbott Vascular

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 8/26/2024

TEER with Abbott’s MitraClip linked to low stroke risk, new study confirms

 

Abbott, the company behind the MitraClip technology, did help fund the GIOTTA registry. In addition, some authors had prior relationships with Abbott.

Treating mitral regurgitation with transcatheter mitral edge-to-edge repair (TEER) using the MitraClip device is associated with a low risk of cerebrovascular accidents (CVAs) such as stroke and transient ischemic attack (TIA), according to new data published in The American Journal of Cardiology.[1]

The authors noted that some studies have suggested TEER may increase a patient’s vulnerability to stroke and TIAs. To learn more, the group evaluated data from more than 2,200 patients with significant mitral regurgitation treated with TEER under transesophageal echocardiogram (TEE) guidance. All patients were treated with Abbott’s MitraClip device, arguably the world’s most well-known TEER device. Data came from the GIOTTA registry, which is sponsored by the Italian Society of Invasive Cardiology.

Overall, just 1.5% of patients experienced a CVA after a median follow-up period of 14 months. A majority of the reported incidents were ischemic strokes. The CVA risk increased when patients presented with atrial fibrillation (AFib), renal dysfunction, a higher EuroSCORE II or higher CHA2DS2-VASc score.

The authors did emphasize, however, that CHA2DS2-VASc score did not prove to be good predictors for when a patient may experience a post-TEER stroke or TIA. In addition, experiencing a CVA did not appear to significantly increase a patient’s short-term risk of adverse outcomes, but the data did suggest that CVA may increase a patient’s mid-term risk of death or other poor outcomes.

Giordano et al. also wrote that AFib was bound to increase a patient’s stroke risk, “both acutely and chronically.” Patients should be proactively treated with anticoagulant therapy—or even left atrial appendage occlusion (LAAO) when necessary—to help manage this risk, the group added.

Original Study

1. Arturo Giordano, MD, PhD Paolo Ferraro, MD Filippo Finizio, MD, et al. Incidence and Predictors of Cerebrovascular Accidents in Patients Undergoing Transcatheter Mitral Valve Repair with Mitraclip. The American Journal of Cardiology. August 1, 2024.

SOURCE

https://cardiovascularbusiness.com/topics/clinical/structural-heart-disease/mitral-valve/teer-abbotts-mitraclip-stroke-tia-tmvr

 

Related studies

 

 

 

UPDATED on 4/26/2022

VIDEO: MitraClip vs. surgical mitral valve replacement

Joanna Chikwe, MD, founding chair of the Department of Cardiac Surgery and the Irina and George Schaeffer Distinguished Chair in Cardiac Surgery, Cedars-Sinai Hospital, Los Angeles, led a panel discussion comparing transcatheter edge-to-edge repair (TEER) to mitral valve surgery for primary mitral regurgitation. At the American College of Cardiology (ACC) 2022 session, Chikwe steered the discussion on the latest evidence in valvular disease, surgical repair and structural heart repair for primary mitral regurgitation.

Related TEER and Mitral Valve Content:

New risk score predicts mortality after TEER

Both younger and elderly heart failure patients benefit from TEER

Cutting edge findings shine new light on mitral valve surgery after failed TEER

New risk calculator detects TEER patients who may need to be readmitted for HF

TEER associated with ‘important and significant’ reductions in hospitalization rates

In-hospital stroke rates higher after TAVR than MitraClip procedures
SOURCE

https://www.cardiovascularbusiness.com/topics/structural-heart-disease/video-mitraclip-vs-surgical-mitral-valve-replacement?utm_source=newsletter&utm_medium=cvb_tavr

UPDATED on 11/21/2019

MitraClip Cases Often Involve Risky Pulmonary HTN

Intervention should be earlier in the disease course, study suggests

by Nicole Lou, Reporter, MedPage Today/CRTonline.org

As in the case of mitral valve surgery, there is a graded association between pulmonary hypertension and increased mortality following the MitraClip procedure, a registry study showed.

Higher invasive mean pulmonary arterial pressure (mPAP) at baseline was associated with greater likelihood of death and heart failure readmission 1 year after transcatheter mitral valve repair (P<0.001):

  • No pulmonary hypertension (mPAP <25 mm Hg): 27.8%
  • Mild pulmonary hypertension (mPAP 25-34 mm Hg): 32.4%
  • Moderate pulmonary hypertension (mPAP 35-44 mm Hg): 36.0%
  • Severe pulmonary hypertension (mPAP 45 mm Hg or above): 45.2%

The overall incidence of the composite outcome was 33.6% in a U.S. registry that showed most people going into valve repair with at least mild pulmonary hypertension, according to the report by Sammy Elmariah, MD, MPH, of Massachusetts General Hospital in Boston, and colleagues, published online in JAMA Cardiology.

After multivariable adjustment, pulmonary hypertension remained significantly associated with mortality (HR 1.05 per 5-mm Hg increase in mPAP, 95% CI 1.01-1.09) and heart failure hospitalization (HR 1.04 per 5-mm Hg increase in mPAP, 95% CI 1.01-1.07) after MitraClip placement.

The findings have implications for patient management, according to Elmariah’s team.

Primary Source

JAMA Cardiology

Source Reference: Al-Bawardy R, et al “Association of pulmonary hypertension with clinical outcomes of transcatheter mitral valve repair” JAMA Cardiol 2019; DOI: 10.1001/jamacardio.2019.4428.

SOURCE

https://www.medpagetoday.com/cardiology/pci/83475?xid=nl_mpt_DHE_2019-11-21

UPDATED on 7/17/2019

FDA approves 4th-gen MitraClip for TMVR

SOURCE

https://www.cardiovascularbusiness.com/topics/structural-congenital-heart-disease/fda-approves-4th-gen-mitraclip-tmvr?utm_source=newsletter&utm_medium=cvb_news

UPDATED on 9/20/2018

TCT: Second Chance for MitraClip in Functional Mitral Regurgitation?

COAPT takes the spotlight in San Diego

by Nicole Lou, Contributing Writer, MedPage Today

This article is a collaboration between MedPage Today® and:

 Medpage Today

SAN DIEGO — The highly-anticipated COAPT trial — examining cardiovascular outcomes in certain heart failure patients treated with the MitraClip device — will be a highlight of the upcoming Transcatheter Cardiovascular Therapeutics (TCT) conference, which turns 30 years old this year.

COAPT will be the MitraClip’s shot at redemption and features a similar patient population as the MITRA-FR trial, which showed no improvement over medical therapy alone for preventing hard outcomes in heart failure patients with secondary mitral regurgitation. MITRA-FR was recently presented at the European Society of Cardiology meeting.

SOURCE

https://www.medpagetoday.com/meetingcoverage/tct/75181?xid=nl_mpt_ACC_Reporter_2018-09-20&eun=g5099207d2r

MitraClip

Photo of MitraClip Clip Delivery System®

http://www.fda.gov/MedicalDevices/Safety/ListofRecalls/ucm490774.htm

 

Device Use

The Abbott Vascular MitraClip Delivery System is intended to treat patients with degenerative mitral regurgitation (DMR) a condition involving a dysfunction of the heart’s mitral valve. The MitraClip Clip Delivery System is indicated for use in patients who have been determined to be at prohibitive risk for mitral valve surgery.

The delivery system has three parts: a delivery catheter; a steerable sleeve; and an implantable clip. The implantable clip is introduced into the left atrium of the heart through the steerable sleeve and the delivery catheter. The implantable clip is then positioned and closed between the leaflets that separate the left atrium and the left ventricle to reduce the reversed blood flow.

Reason for Recall

Abbott Vascular has received reports of cases where the Clip Delivery System could not be detached from the Clip due to a malfunction of the device. These cases resulted in open heart surgery to retrieve the delivery system. Abbott Vascular is therefore recalling the MitraClip Delivery System to provide updated instructions and training for health care providers who use the device.

The use of affected products may cause serious adverse health consequences, including serious patient injury or death. Currently there are 3,534 devices on the market, with nine reports of this malfunction. There has been 1 death.

Who May be Affected

  • Health care providers implanting the MitraClip Clip Delivery System
  • All patients undergoing a mitral regurgitation procedure using the MitraClip Clip Delivery System

What to Do

On February 4, 2016, Abbott Vascular issued a safety notice to all physicians using the device instructing them to:

  • Carefully read the revised deployment sequence instructions
  • Participate in training with an Abbott Vascular representative
  • Share the information with other pertinent staff

Contact Information:

Customers can contact Abbott Vascular Customer Support at 1-800-227-9902.

Date Recall Initiated:

February 4, 2016

How do I report a problem?

Health care professionals and consumers may report adverse reactions or quality problems they experienced using these devices to MedWatch: The FDA Safety Information and Adverse Event Reporting Program online, by regular mail or by FAX.

 

SOURCES

http://www.fda.gov/MedicalDevices/Safety/ListofRecalls/ucm490774.htm

Abbott Issues Voluntary Safety Notice on MitraClip® Delivery System Deployment Process

MitraClip Delivery System by Abbott: Safety Notice – Reinforcement of Proper Procedures to Operate and Deploy

Role of infectious agent in Alzheimer’s Disease?

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Role of Infection in Alzheimer’s Ignored, Experts Say

Nancy A. Melville   http://www.medscape.com/viewarticle/860615

The potentially critical role of infection in the etiology of Alzheimer’s disease is largely neglected, despite decades of robust evidence from hundreds of human studies, as well as the possible therapeutic implications, experts say.

“Despite all the supportive evidence, the topic [of linking infections to Alzheimer’s disease] is often dismissed as ‘controversial,’ ” the authors of an editorial, signed by an international group of 33 researchers and clinicians, write.

The editorial was published online March 8 in theJournal of Alzheimer’s Disease.

Antiviral Treatment

“One recalls the widespread opposition initially to data showing that viruses cause some types of cancer, and that a bacterium causes stomach ulcers,” the authors write.

The implications could be just as important with regard to Alzheimer’s disease, coauthor Ruth F. Itzhaki, PhD, of the Faculty of Life Sciences at the University of Manchester, United Kingdom, toldMedscape Medical News.

“The implications are that patients could be treated with antiviral agents. These would not cure them, but might slow or even stop the progression of the disease,” she said.

The evidence points to herpes simplex virus type 1 (HSV1), Chlamydia pneumoniae, and several types of spirochetes, which make their way into the central nervous system (CNS), where they can remain in latent form indefinitely, the authors note.

The link with HSV1 is supported by as many as 100 studies. Only two studies oppose the association; both were published more than a decade ago, the authors state.

Under the prevailing theory, agents such as HSV1 undergo reactivation in the brain during aging and with the decline of the immune system, as well as when persons are under stress.

“The consequent neuronal damage ― caused by direct viral action and by virus-induced inflammation ― occurs recurrently, leading to (or acting as a cofactor for) progressive synaptic dysfunction, neuronal loss, and ultimately AD [Alzheimer’s disease],” the authors write

Importantly, that damage includes the induction of amyloid-β (Aβ) peptide deposits, considered a hallmark of Alzheimer’s disease, which initially appears to be only a defense mechanism, the authors add.

Causative Role?

In outlining some of the strongest evidence behind the theory, the authors note that although viruses and other microbes are common in the elderly brain and are usually dormant, influences such as stress and immunosuppression can cause reactivation.

“For example, HSV1 DNA is amplified in the brain of immunosuppressed patients,” they write.

In addition, herpes simplex encephalitis is known to damage regions of the CNS linked to the limbic system, and therefore to memory as well as cognitive and affective processes, the same regions affected in Alzheimer’s disease.

HSV infection is known to be significantly associated with the development of Alzheimer’s, and the disease is known to have a strong inflammatory component that is characteristic of infection, the authors say.

On a genetic level, research has shown that polymorphisms in the apolipoprotein E gene (APOE) that are linked to the risk for Alzheimer’s also control immune function and susceptibility to infectious disease.

In terms of evidence of a causative role of infection in Alzheimer’s disease, the authors cite studies indicating that brain infection, such as HIV or herpes virus, is linked to pathology similar to Alzheimer’s.

Notably, infection with HSV1 or bacteria in mice and cell culture studies has been shown to result in Aβ deposition and tau abnormalities typical of Alzheimer’s disease.

In addition, the olfactory dysfunction that is an early symptom of Alzheimer’s disease is consonant with a role of infection: The olfactory nerve leads to the lateral entorhinal cortex, where Alzheimer’s pathology spreads through the brain, and it is the likely portal of entry of HSV1 and other viruses into the brain, the authors note.

“Further, brainstem areas that harbor latent HSV directly irrigate these brain regions: brainstem virus reactivation would thus disrupt the same tissues as those affected in Alzheimer’s disease,” they write.

In terms of mechanisms, the authors cite mounting evidence that virus infection selectively upregulates the gene encoding cholesterol 25-hydroxylase (CH25H), and innate antiviral immunity is induced by its enzymatic product 25-hydroxycholesterol (25OHC).

The human CH25H polymorphisms control susceptibility to Alzheimer’s as well as Aβ deposition.

Consequently, “Aβ induction is likely to be among the targets of 25OHC, providing a potential mechanistic link between infection and Aβ production,” the authors write.

Considering the devastating toll Alzheimer’s disease takes on individual lives and society, the need to reconsider the collective evidence of a role for infection is pressing, the authors note.

“Alzheimer’s disease causes great emotional and physical harm to sufferers and their carers, as well as having enormously damaging economic consequences,” they write.

“Given the failure of the 413 trials of other types of therapy for Alzheimer’s disease carried out in the period 2002-2012, antiviral/antimicrobial treatment of Alzheimer’s disease patients, notably those who areAPOE ɛ4 carriers, could rectify the ‘no drug works’ impasse.

“We propose that further research on the role of infectious agents in Alzheimer’s disease causation, including prospective trials of antimicrobial therapy, is now justified.”

Chicken or the Egg?

Commenting on the editorial for Medscape Medical News, Richard B. Lipton, MD, Edwin S. Lowe Professor, vice chair of neurology, and director of the Division of Cognitive Aging and Dementia at Albert Einstein College of Medicine in New York City, applauded the effort to raise awareness of the issue.

“The authors are to be commended for reminding us of the hypothesis that infection may contribute to Alzheimer’s disease,” he told Medscape Medical News.

He noted the variety of genetic and environmental factors that can influence onset and progression of complex disorders such as Alzheimer’s disease.

“For Alzheimer’s disease, most people would agree that cardiovascular risk factors, traumatic brain injury, and stress increase risk of disease,” he said.

“It is entirely plausible that infectious agents may be one of many factors that contribute to the development of Alzheimer’s disease. Infectious agents could operate through several mechanisms.”

The evidence does not necessarily prove a causative role, he added.

“Temporality means that infection precedes disease,” he said. “The studies showing infectious and inflammatory markers in the Alzheimer’s brain don’t tell us which came first. Alzheimer’s disease could be a state which predisposes to infection.”

The editorialists’ financial disclosures are available online. Dr Lipton has disclosed no relevant financial relationships.

Microbes and Alzheimer’s Disease

KEY POINTS

  • Herpes simplex virus 1 (HSV-1) encephalitis predominantly involves the orbital surface of the frontal lobes and medial surface of the temporal lobes, resulting in areas of increased T2 signal on MRI
  • Herpes simplex virus 2 (HSV-2) is the primary cause of recurrent meningitis
  • After varicella, the varicella zoster virus (VZV) becomes latent in ganglia along the entire neuraxis; its reactivation can lead to herpes zoster, vasculopathy, myelitis, necrotizing retinitis or zoster sine herpete
  • The neurological complications of Epstein–Barr virus are diverse, and include meningitis, encephalitis, myelitis, radiculoneuropathy, and even autonomic neuropathy
  • The most common neurological complication of cytomegalovirus (CMV) is poly-radiculoneuropathy in immunocompromised individuals
  • Virological confirmation of neurological disease relies on the detection of herpesvirus-specific DNA in bodily fluids or tissues, herpesvirus-specific IgM in blood, or herpesvirus-specific IgM or IgG antibody in cerebrospinal fluid
  • HSV-1, HSV-2, VZV and CMV are the most treatable herpesviruses

Most HHVs can cause serious neurological disease of the PNS and CNS through primary infection or following virus reactivation from latently infected human ganglia or lymphoid tissue. The neurological complications include meningitis, encephalitis, myelitis, vasculopathy, acute and chronic radiculoneuritis, and various inflammatory diseases of the eye. Disease can be monophasic, recurrent or chronic.

 

The researchers also add that a gene mutation – APOEe4 – which appears to makes some of the population more susceptible to Alzheimer’s disease, could also increase these people’s susceptibility to infectious diseases.

 As a counter view, Professor John Hardy, Teacher of Neuroscience, UCL, told the website Journal Focus he was doubtful about the claims: “This is a minority sight in Alzheimer research study. There had actually been no convincing evidence of infections triggering Alzheimer disease. We require constantly to maintain an open mind however this editorial does not show exactly what many scientists think of Alzheimer disease.”

However, another of the researchers, Resia Pretorius of the University of Pretoria, told Bioscience Technology: “The microbial presence in blood may also play a fundamental role as causative agent of systemic inflammation, which is a characteristic of Alzheimer’s disease. Furthermore, there is ample evidence that this can cause neuroinflammation and amyloid-β plaque formation.”

The possibility of transfer has been reported to the journal Nature. The paper is titled “Evidence for human transmission of amyloid-β pathology and cerebral amyloid angiopathy.”

The report explains that during the period from 1958 to 1985, 30,000 people worldwide — mainly children — were administered injections of human growth hormone. This was designed to treat short stature. The hormone was extracted from thousands of human pituitary glands, with the source material being recently deceased people.

It now appears, The Economist summarizes, that some of these hormonal extracts contained prions. Around one in 16 of the children developed the brain disorder Creutzfeldt-Jakob disease (CJD). The concern with CJD centered on prions.

Read more: http://www.digitaljournal.com/science/alzheimer-s-and-parkinson-s-diseases-may-be-transmissible/article/444338#ixzz43Y

Chain reaction

Evidence emerges that Alzheimer’s disease, and other neurodegenerative disorders such as Parkinson’s, may be transmissible

 

KAREN WEINTRAUB

Reporting from the frontiers of health and medicine

A rare disease killed her mother. Can this scientist save herself?

http://www.statnews.com/2016/01/20/prion-disease-genes/

CAMBRIDGE, Mass. — Five years ago, after watching her 51-year-old mother descend quickly into dementia, disability, and then death, Sonia Vallabh learned she was destined for the same fate. They both shared an extremely rare genetic mutation that leads a protein in the brain to turn toxic.

Vallabh, then a recent Harvard Law School graduate working as a consultant, decided to quit her job to spend time learning more about the mutation and nascent efforts to understand and treat it.

Now, she and her husband, Eric Minikel, a former transportation planner, are first authors on a paper about so-called prion diseases. Published Wednesday in Science Translational Medicine, the paper found that not all prion gene mutations are an early death sentence — though Vallabh’s variation is.

The husband-and-wife team, now both PhD students working in the same lab at the Broad Institute, also found that people can survive with only one copy of the prion gene, suggesting that a treatment to block the mutated version can be delivered safely.

Prion diseases were made famous by “mad cow disease,” outbreaks of which have led to mass killings of cattle. Eating sick cows can cause the fatal neurodegenerative illness known as Creutzfeldt-Jakob disease. But there are genetic versions of prion diseases that account for about 15 percent of cases. They come from mutations to the prion protein gene PRNP, which causes a protein in the brain to fold the wrong way, forming toxic clumps. Once these proteins get a foothold in the brain, they can cause extremely rapid damage.

Vallabh’s mother, who seemed completely normal at Christmastime in 2009, showed the first symptoms of disease in January 2010 and was demented and unable to speak clearly by March. She last recognized her daughter in May, Vallabh said, and died two days before Christmas that year, shortly after doctors finally identified the cause of her bizarre symptoms.

Vallabh, Minikel, and their coauthors compared a data set — painstakingly collected over decades — of gene sequences from 16,000 prion disease patients from all over the world, with two data sets of sequences from healthy people: more than 60,000 collected by the Broad-led Exome Aggregation Consortium and 530,000 from 23andMe, a consumer genetics company that invites clients to volunteer their gene sequences for research.

The size of the data sets allowed the researchers to draw conclusions even with a condition as rare as prion disease. Doctors had previously only known about 63 possible mutations in people with disease, so they had thought that all the mutations necessarily caused problems. But the researchers found 141 healthy people in the 23andMe dataset who had mutations to the PRNP gene — a rate far higher than the incidence of prion disease. That means some of the mutations must be harmless or at least not always cause disease, said J. Fah Sathirapongsasuti, a computational biologist at 23andMe and a study coauthor.

Out of 16 mutations for which there was evidence in the larger populations, they concluded that three were likely benign, three caused somewhat increased risk of disease, and four others, including Vallabh’s mutation, definitely do cause the fatal illness, they found.

They also discovered three older, healthy people who carried only one functional copy of the PRNP gene. That means that knocking out the mutated version of PRNP with gene therapy, or tamping down its activity with drugs, should be an effective way to eliminate the risk of disease without causing life-threatening problems.

Their paper has already helped at least one person, according to Dr. Robert Green, a medical geneticist at Brigham and Women’s Hospital, who cowrote an opinion piece published alongside the new study.

One of Green’s patients, whose mother died of prion disease, had been told her mom’s mutation — which she didn’t inherit, but her sister did — was always fatal. After seeing the new study, Green was able to inform the sister that her mutation was most likely harmless.

 

GT198 Mutation from common Progenitor Cells of different types of Stromal Cells in Breast Tissue function as Early Indicator of Breast Cancer

Reporter: Aviva Lev-Ari, PhD, RN

 

Cause to breast cancer found by

  • Nahid Mivechi, PhD, cell biologist & radiobiologist, a group leader at the Cancer Center and a study co-author;
  • Nita Maihle, PhD, an MCG cancer biologist, associate center director for education at the university’s Cancer Center and a study co-author;
  • Dr. Lan Ko, cancer biologist in the Department of Pathology at the Medical College of Georgia at Augusta University and at the Georgia Cancer Center at AU

 

Augusta

Image Credit: Phil Jones

  • About 4 percent of familial breast cancers would include inherited mutations of GT198, which is also considered a causative gene in sporadic cases, Ko said.
  • Ko first cloned the human GT198 gene while a postdoctoral fellow at Harvard Medical School, and subsequent studies by her and others have shown it has multiple roles that also include regulating stem cells, cell suicide and turning other genes off and on.

Their studies, published in the American Journal of Pathology, were done on an international sampling from 254 cases of breast cancer in pre- and postmenopausal women.

 

Story Source:

The above post is reprinted from materials provided by Medical College of Georgia at Augusta University. Note: Materials may be edited for content and length.


Journal Reference:

  1. Zheqiong Yang, Min Peng, Liang Cheng, Kimya Jones, Nita J. Maihle, Nahid F. Mivechi, Lan Ko. GT198 Expression Defines Mutant Tumor Stroma in Human Breast Cancer. The American Journal of Pathology, 2016; DOI: 10.1016/j.ajpath.2016.01.006

Abstract

Human breast cancer precursor cells remain to be elucidated. Using breast cancer gene product GT198 (PSMC3IP; alias TBPIP or Hop2) as a unique marker, we revealed the cellular identities of GT198 mutant cells in human breast tumor stroma. GT198 is a steroid hormone receptor coactivator and a crucial factor in DNA repair. Germline mutations in GT198 are present in breast and ovarian cancer families. Somatic mutations inGT198 are present in ovarian tumor stromal cells. Herein, we show that human breast tumor stromal cells carry GT198 somatic mutations and express cytoplasmic GT198 protein. GT198+ stromal cells share vascular smooth muscle cell origin, including myoepithelial cells, adipocytes, capillary pericytes, and stromal fibroblasts. Frequent GT198 mutations are associated with GT198+ tumor stroma but not with GT198 tumor cells. GT198+ progenitor cells are mostly capillary pericytes. When tested in cultured cells, mutant GT198 induces vascular endothelial growth factor promoter, and potentially promotes angiogenesis and adipogenesis. Our results suggest that multiple lineages of breast tumor stromal cells are mutated in GT198. These findings imply the presence of mutant progenitors, whereas their descendants, carrying the sameGT198 mutations, are collectively responsible for forming breast tumor microenvironment. GT198 expression is, therefore, a specific marker of mutant breast tumor stroma and has the potential to facilitate diagnosis and targeted treatment of human breast cancer.

SOURCE

http://ajp.amjpathol.org/article/S0002-9440(16)00087-0/abstract


Cite This Page:

http://www.sciencedaily.com/releases/2016/03/160318111445.htm

Medical College of Georgia at Augusta University. “New gene identified as cause, early indicator of breast cancer.” ScienceDaily. ScienceDaily, 18 March 2016. .

New Gene Found as Early Indicator of Breast Cancer?

Mon, 03/21/2016 – 10:13am
Medical College of Georgia at Augusta University

The gene GT198, whether mutated by genetics and/or environmental factors, has strong potential as both as a way to diagnose breast cancer early and as a new treatment target, said Dr. Lan Ko, cancer biologist in the Department of Pathology at the Medical College of Georgia at Augusta University and at the Georgia Cancer Center at Augusta University.

Mutations of the gene are known to be present in both early onset breast and ovarian cancer. Now scientists have shown that the stem, or progenitor cells, which should ultimately make healthy breast tissue, can also have GT198 mutations that prompt them to instead make a perfect bed for breast cancer.

Their studies, published in the American Journal of Pathology, were done on an international sampling from 254 cases of breast cancer in pre- and postmenopausal women.

“This gene mutation can be in both the blood and the tumor tissue of patients, and in the tissue, it’s in high percentages,” said Ko, the study’s corresponding author. “We believe that once this gene is mutated, it induces the tumor to grow.”

 

SOURCE

http://www.rdmag.com/news/2016/03/new-gene-found-early-indicator-breast-cancer?et_cid=5187994&et_rid=461755519&location=top&et_cid=5187994&et_rid=461755519&linkid=http%3a%2f%2fwww.rdmag.com%2fnews%2f2016%2f03%2fnew-gene-found-early-indicator-breast-cancer%3fet_cid%3d5187994%26et_rid%3d%%subscriberid%%%26location%3dtop

Philip Hemme,  Interviewing Anker Lundemose in Zurich @ 9th Annual Sachs conference for European Biotech CEOs

Reporter: Aviva Lev-Ari, PhD, RN

 

 

Philip Hemme, Co-Founder & CEO of Labiotech.eu

Anker Lundemose, CEO of Mission Therapeutics, from just outside of Cambridge (UK). Founded in 2011, Mission Therapeutics, a private drug discovery company which aims to commercialize highly expert research towards the treatment of cancer and other diseases via the ubiquitin cell signaling pathway.

9th Annual ELSCEO Forum & Exhibition, is being held on 15th-16th March 2016 at the Hilton Zurich Airport Hotel, Switzerland. This event will be highly transactional, bringing together an exciting cross-section of venture-funded and small-cap companies with leading investors, pharmas, and scientific thought leaders. We expect around350 delegates and 80 presenting companies. Event’s networking will be powered by online One-2-One meeting system and dedicated meeting facilities to make the event more transactional and productive.

WATCH VIDEO

http://labiotech.eu/interviewing-the-biotech-which-raised-the-biggest-european-round-in-2016-so-far/

 

SOURCE

http://labiotech.eu/interviewing-the-biotech-which-raised-the-biggest-european-round-in-2016-so-far/

 

Other related articles published on this Open Access Online Scientific Journal include the following:

14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment
30th September – 1st October 2014 • Congress Center Basel
SACHS Associates, London
http://www.sachsforum.com/zurich14/index.html

http://pharmaceuticalintelligence.com/2014/03/25/14th-annual-biotech-in-europe-forum-for-global-partnering-investment-930-1012014-•-congress-center-basel-sachs-associates-london/

The 2nd ANNUAL Sachs Cancer Bio Partnering & Investment Forum in Drug Development, 19th March 2014 • New York Academy of Sciences • USA
http://pharmaceuticalintelligence.com/2014/03/21/real-time-cancer-conference-coverage-a-novel-methodology-for-authentic-reporting-on-presentations-and-discussions-launched-via-twitter-com-the-2nd-annual-sachs-cancer-bio-partnering-investmen/