Posts Tagged ‘Proceedings of the National Academy of Sciences of the United States of America’

Multiple Lung Cancer Genomic Projects Suggest New Targets, Research Directions for Non-Small Cell Lung Cancer

Posted in Biological Networks, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Computational Biology/Systems and Bioinformatics, Gene Regulation and Evolution, Genome Biology, Health Economics and Outcomes Research, Personalized and Precision Medicine & Genomic Research, tagged antitumor therapy, Bioinformatics, Cancer - General, Cell Biology, Computational Biology/Systems and Bioinformatics, DNA, DNA Sequencing, driver mutations, gene expression, genetics, genome, genomics, informatics, Lung cancer, mutation, mutational analysis, National Institutes of Health, Non-small cell lung cancer, Personalized medicine, Proceedings of the National Academy of Sciences of the United States of America, Prostate cancer, research, smoking, The Cancer Genome Atlas (TCGA), The Clinical Lung Cancer Genome Project (CLCGP), whole exome sequencing on September 5, 2014| Leave a Comment »

Multiple Lung Cancer Genomic Projects Suggest New Targets, Research Directions for Non-Small Cell Lung Cancer

Curator, Writer: Stephen J. Williams, Ph.D.

UPDATED 10/10/2021

(photo credit: cancer.gov)

A report Lung Cancer Genome Surveys Find Many Potential Drug Targets, in the NCI Bulletin,

http://www.cancer.gov/ncicancerbulletin/091812/page2

summarizes the clinical importance of five new lung cancer genome sequencing projects. These studies have identified genetic and epigenetic alterations in hundreds of lung tumors, of which some alterations could be taken advantage of using currently approved medications.

The reports, all published this month, included genomic information on more than 400 lung tumors. In addition to confirming genetic alterations previously tied to lung cancer, the studies identified other changes that may play a role in the disease.

Collectively, the studies covered the main forms of the disease—lung adenocarcinomas, squamous cell cancers of the lung, and small cell lung cancers.

“All of these studies say that lung cancers are genomically complex and genomically diverse,” said Dr. Matthew Meyerson of Harvard Medical School and the Dana-Farber Cancer Institute, who co-led several of the studies, including a large-scale analysis of squamous cell lung cancer by The Cancer Genome Atlas (TCGA) Research Network.

Some genes, Dr. Meyerson noted, were inactivated through different mechanisms in different tumors. He cautioned that little is known about alterations in DNA sequences that do not encode genes, which is most of the human genome.

Four of the papers are summarized below, with the first described in detail, as the Nature paper used a multi-‘omics strategy to evaluate expression, mutation, and signaling pathway activation in a large cohort of lung tumors. A literature informatics analysis is given for one of the papers.  Please note that links on GENE names usually refer to the GeneCard entry.

Paper 1. Comprehensive genomic characterization of squamous cell lung cancers[1]

The Cancer Genome Atlas Research Network Project just reported, in the journal Nature, the results of their comprehensive profiling of 230 resected lung adenocarcinomas. The multi-center teams employed analyses of

• microRNA
• Whole Exome Sequencing including
  • Exome mutation analysis
  • Gene copy number
  • Splicing alteration
• Methylation
• Proteomic analysis

Summary:

Some very interesting overall findings came out of this analysis including:

• High rates of somatic mutations including activating mutations in common oncogenes
• Newly described loss of function MGA mutations
• Sex differences in EGFR and RBM10 mutations
• driver roles for NF1, MET, ERBB2 and RITI identified in certain tumors
• differential mutational pattern based on smoking history
• splicing alterations driven by somatic genomic changes
• MAPK and PI3K pathway activation identified by proteomics not explained by mutational analysis = UNEXPLAINED MECHANISM of PATHWAY ACTIVATION

however, given the plethora of data, and in light of a similar study results recently released, there appears to be a great need for additional mining of this CGAP dataset. Therefore I attempted to curate some of the findings along with some other recent news relevant to the surprising findings with relation to biomarker analysis.

Makeup of tumor samples

230 lung adenocarcinomas specimens were categorized by:

Subtype

33% acinar

25% solid

14% micro-papillary

9% papillary

8% unclassified

5% lepidic

4% invasive mucinous
Gender

Smoking status

81% of patients reported past of present smoking

The authors note that TCGA samples were combined with previous data for analysis purpose.

A detailed description of Methodology and the location of deposited data are given at the following addresses:

Publication TCGA Web Page: https://tcga-data.nci.nih.gov/docs/publications/luad_2014/

Sequence files: https://cghub.ucsc.edu

Results:

Gender and Smoking Habits Show different mutational patterns

 

WES mutational analysis

1. a) smoking status

– there was a strong correlations of cytosine to adenine nucleotide transversions with past or present smoking. In fact smoking history separated into transversion high (past and previous smokers) and transversion low (never smokers) groups, corroborating previous results.

→ mutations in groups              Transversion High                   Transversion Low

TP53, KRAS, STK11,                 EGFR, RB1, PI3CA

     KEAP1, SMARCA4 RBM10

 

1. b) Gender

Although gender differences in mutational profiles have been reported, the study found minimal number of significantly mutated genes correlated with gender. Notably:

• EGFR mutations enriched in female cohort
• RBM10 loss of function mutations enriched in male cohort

Although the study did not analyze the gender differences with smoking patterns, it was noted that RBM10 mutations among males were more prevalent in the transversion high group.

Whole exome Sequencing and copy number analysis reveal Unique, Candidate Driver Genes

Whole exome sequencing revealed that 62% of tumors contained mutations (either point or indel) in known cancer driver genes such as:

KRAS, EGFR, BRMF, ERBB2

However, authors looked at the WES data from the oncogene-negative tumors and found unique mutations not seen in the tumors containing canonical oncogenic mutations.

Unique potential driver mutations were found in

TP53, KEAP1, NF1, and RIT1

The genomics and expression data were backed up by a proteomics analysis of three pathways:

1. MAPK pathway
2. mTOR
3. PI3K pathway

…. showing significant activation of all three pathways HOWEVER the analysis suggested that activation of signaling pathways COULD NOT be deduced from DNA sequencing alone. Phospho-proteomic analysis was required to determine the full extent of pathway modification.

For example, many tumors lacked an obvious mutation which could explain mTOR or MAPK activation.

 

Altered cell signaling pathways included:

• Increased MAPK signaling due to activating KRAS
• Higher mTOR due to inactivating STK11 leading to increased proliferation, translation

Pathway analysis of mutations revealed alterations in multiple cellular pathways including:

• Reduced oxidative stress response
• Nucleosome remodeling
• RNA splicing
• Cell cycle progression
• Histone methylation

Summary:

Authors noted some interesting conclusions including:

1. MET and ERBB2 amplification and mutations in NF1 and RIT1 may be unique driver events in lung adenocarcinoma
2. Possible new drug development could be targeted to the RTK/RAS/RAF pathway
3. MYC pathway as another important target
4. Cluster analysis using multimodal omics approach identifies tumors based on single-gene driver events while other tumor have multiple driver mutational events (TUMOR HETEROGENEITY)

Paper 2. A Genomics-Based Classification of Human Lung Tumors[2]

The paper can be found at

http://stm.sciencemag.org/content/5/209/209ra153

by The Clinical Lung Cancer Genome Project (CLCGP) and Network Genomic Medicine (NGM),*,†

Paper Summary

This sequencing project revealed discrepancies between histologic and genomic classification of lung tumors.

Methodology

– mutational analysis by whole exome sequencing of 1255 lung tumors of histologically

defined subtypes

– immunohistochemistry performed to verify reclassification of subtypes based on sequencing data

Results

• 55% of all cases had at least one oncogenic alteration amenable to current personalized treatment approaches
• Marked differences existed between cluster analysis within and between preclassified histo-subtypes
• Reassignment based on genomic data eliminated large cell carcinomas
• Prospective classification of 5145 lung cancers allowed for genomic classification in 75% of patients
• Identification of EGFR and ALK mutations led to improved outcomes

Conclusions:

It is feasible to successfully classify and diagnose lung tumors based on whole exome sequencing data.

Paper 3. Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers[3]

A link to the paper can be found here with Graphic Summary: http://www.cell.com/cell/abstract/S0092-8674%2812%2901022-7?cc=y?cc=y

Methodology

• Whole genome sequencing and transcriptome sequencing of cancerous and adjacent normal tissues from 17 patients with NSCLC
• Integrated RNASeq with WES for analysis of
  • Variant analysis
  • Clonality by variant allele frequency anlaysis
  • Fusion genes
• Bioinformatic analysis
  • PathScan, KEGG for pathway analysis
  • COSMIC for reported mutations
  • ChimeraScan, defuse, BreakFusion for fusion protein analysis

Results

• 3,726 point mutations and more than 90 indels in the coding sequence
• Smokers with lung cancer show 10× the number of point mutations than never-smokers
• Novel lung cancer genes, including DACH1, CFTR, RELN, ABCB5, and HGF were identified

• Tumor samples from males showed high frequency of MYCBP2 MYCBP2 involved in transcriptional regulation of MYC.

• Variant allele frequency analysis revealed 10/17 tumors were at least biclonal while 7/17 tumors were monoclonal revealing majority of tumors displayed tumor heterogeneity
• Novel pathway alterations in lung cancer include cell-cycle and JAK-STAT pathways
• 14 fusion proteins found, including ROS1-ALK fusion. ROS1-ALK fusions have been frequently found in lung cancer and is indicative of poor prognosis[4].
• Novel metabolic enzyme fusions
• Alterations were identified in 54 genes for which targeted drugs are available.           Drug-gable mutant targets include: AURKC, BRAF, HGF, EGFR, ERBB4, FGFR1, MET, JAK2, JAK3, HDAC2, HDAC6, HDAC9, BIRC6, ITGB1, ITGB3, MMP2, PRKCB, PIK3CG, TERT, KRAS, MMP14

Table. Validated Gene-Fusions Obtained from Ref-Seq Data

Note: Gene columns contain links for GeneCard while Gene function links are to the    gene’s GO (Gene Ontology) function.

GeneA (5′)	GeneB (3′)	GeneA function (link to Gene Ontology)	GeneB function (link to Gene Ontology)		known function (refs)
GRIP1	TNIP1	glutamate receptor IP	transcriptional repressor
SGMS1	STK10	sphingolipid synthesis	ser/thr kinase
RASSF3	TTYH2	GTP-binding protein	chloride anion channel
KDELR2	ROS1, GOPC	ER retention seq. binding	proto-oncogenic tyr kinase
ACSL4	DCAF6	fatty acid synthesis	?
MARCH8	PRKG1	ubiquitin ligase	cGMP dependent protein kinase
APAF1	UNC13B, TLN1	caspase activation	cytoskeletal
EML4	ALK	microtubule protein	tyrosine kinase		♦
EDR3,PHC3	LOC441601	polycomb pr/DNA binding	?
DKFZp761L1918,RHPN2	ANKRD27	Rhophilin (GTP binding pr	ankyrin like
VANGL1	HAO2	tetraspanin family	oxidase
CACNA2D3	FLNB	VOC Ca++ channel	filamin (actin binding)

† Author’s Note:

There has been a recent literature on the importance of the EML4-ALK fusion protein in lung cancer. EML4-ALK positive lung tumors were found to be les chemo sensitive to cytotoxic therapy[5] and these tumor cells may exhibit an epitope rendering these tumors amenable to immunotherapy[6]. In addition, inhibition of the PI3K pathway has sensitized EMl4-ALK fusion positive tumors to ALK-targeted therapy[7]. EML4-ALK fusion positive tumors show dependence on the HSP90 chaperone, suggesting this cohort of patients might benefit from the new HSP90 inhibitors recently being developed[8].

Table. Significantly mutated genes (point mutations, insertions/deletions) with associated function.

Gene	Function
TP53	tumor suppressor
KRAS	oncogene
ZFHX4	zinc finger DNA binding
DACH1	transcription factor
EGFR	epidermal growth factor receptor
EPHA3	receptor tyrosine kinase
ENSG00000205044
RELN	cell matrix protein
ABCB5	ABC Drug Transporter

Table. Literature Analysis of pathways containing significantly altered genes in NSCLC reveal putative targets and risk factors, linkage between other tumor types, and research areas for further investigation.

Note: Significantly mutated genes, obtained from WES, were subjected to pathway analysis (KEGG Pathway Analysis) in order to see which pathways contained signicantly altered gene networks. This pathway term was then used for PubMed literature search together with terms “lung cancer”, “gene”, and “NOT review” to determine frequency of literature coverage for each pathway in lung cancer. Links are to the PubMEd search results.

KEGG pathway Name	# of PUBMed entries containing Pathway Name, Gene ANDLung Cancer
Cell cycle	1237
Cell adhesion molecules (CAMs)	372
Glioma	294
Melanoma	219
Colorectal cancer	207
Calcium signaling pathway	175
Prostate cancer	166
MAPK signaling pathway	162
Pancreatic cancer	88
Bladder cancer	74
Renal cell carcinoma	68
Focal adhesion	63
Regulation of actin cytoskeleton	34
Thyroid cancer	32
Salivary secretion	19
Jak-STAT signaling pathway	16
Natural killer cell mediated cytotoxicity	11
Gap junction	11
Endometrial cancer	11
Long-term depression	9
Axon guidance	8
Cytokine-cytokine receptor interaction	8
Chronic myeloid leukemia	7
ErbB signaling pathway	7
Arginine and proline metabolism	6
Maturity onset diabetes of the young	6
Neuroactive ligand-receptor interaction	4
Aldosterone-regulated sodium reabsorption	2
Systemic lupus erythematosus	2
Olfactory transduction	1
Huntington’s disease	1
Chemokine signaling pathway	1
Cardiac muscle contraction	1
Amyotrophic lateral sclerosis (ALS)	1

A few interesting genetic risk factors and possible additional targets for NSCLC were deduced from analysis of the above table of literature including HIF1-α, mIR-31, UBQLN1, ACE, mIR-193a, SRSF1. In addition, glioma, melanoma, colorectal, and prostate and lung cancer share many validated mutations, and possibly similar tumor driver mutations.

 please click on graph for larger view

Paper 4. Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing[9]

For full paper and graphical summary please follow the link: http://www.cell.com/cell/abstract/S0092-8674%2812%2901061-6

Highlights

• Exome and genome characterization of somatic alterations in 183 lung adenocarcinomas
• 12 somatic mutations/megabase
• U2AF1, RBM10, and ARID1A are among newly identified recurrently mutated genes
• Structural variants include activating in-frame fusion of EGFR
• Epigenetic and RNA deregulation proposed as a potential lung adenocarcinoma hallmark

Summary

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

Paper 5. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer[10]

Highlights

• Whole exome and transcriptome (RNASeq) sequencing 29 small-cell lung carcinomas
• High mutation rate 7.4 protein-changing mutations/million base pairs
• Inactivating mutations in TP53 and RB1
• Functional mutations in CREBBP, EP300, MLL, PTEN, SLIT2, EPHA7, FGFR1 (determined by literature and database mining)
• The mutational spectrum seen in human data also present in a Tp53-/- Rb1-/- mouse lung tumor model

 

Curator Graphical Summary of Interesting Findings From the Above Studies

The above figure (please click on figure) represents themes and findings resulting from the aforementioned studies including

questions which will be addressed in Future Posts on this site.

UPDATED 10/10/2021

The following article uses RNASeq to screen lung adenocarcinomas for fusion proteins in patients with either low or high tumor mutational burden. Findings included presence of MET fusion proteins in addition to other fusion proteins irrespective if tumors were driver negative by DNASeq screening.

High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Source:

High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Ryma Benayed, Michael Offin, Kerry Mullaney, Purvil Sukhadia, Kelly Rios, Patrice Desmeules, Ryan Ptashkin, Helen Won, Jason Chang, Darragh Halpenny, Alison M. Schram, Charles M. Rudin, David M. Hyman, Maria E. Arcila, Michael F. Berger, Ahmet Zehir, Mark G. Kris, Alexander Drilon and Marc Ladanyi

Clin Cancer Res August 1 2019 (25) (15) 4712-4722; DOI: 10.1158/1078-0432.CCR-19-0225

Abstract

Purpose: Targeted next-generation sequencing of DNA has become more widely used in the management of patients with lung adenocarcinoma; however, no clear mitogenic driver alteration is found in some cases. We evaluated the incremental benefit of targeted RNA sequencing (RNAseq) in the identification of gene fusions and MET exon 14 (METex14) alterations in DNA sequencing (DNAseq) driver–negative lung cancers.

Experimental Design: Lung cancers driver negative by MSK-IMPACT underwent further analysis using a custom RNAseq panel (MSK-Fusion). Tumor mutation burden (TMB) was assessed as a potential prioritization criterion for targeted RNAseq.

Results: As part of prospective clinical genomic testing, we profiled 2,522 lung adenocarcinomas using MSK-IMPACT, which identified 195 (7.7%) fusions and 119 (4.7%) METex14 alterations. Among 275 driver-negative cases with available tissue, 254 (92%) had sufficient material for RNAseq. A previously undetected alteration was identified in 14% (36/254) of cases, 33 of which were actionable (27 in-frame fusions, 6 METex14). Of these 33 patients, 10 then received matched targeted therapy, which achieved clinical benefit in 8 (80%). In the 32% (81/254) of DNAseq driver–negative cases with low TMB [0–5 mutations/Megabase (mut/Mb)], 25 (31%) were positive for previously undetected gene fusions on RNAseq, whereas, in 151 cases with TMB >5 mut/Mb, only 7% were positive for fusions (P < 0.0001).

Conclusions: Targeted RNAseq assays should be used in all cases that appear driver negative by DNAseq assays to ensure comprehensive detection of actionable gene rearrangements. Furthermore, we observed a significant enrichment for fusions in DNAseq driver–negative samples with low TMB, supporting the prioritization of such cases for additional RNAseq.

Translational Relevance

Inhibitors targeting kinase fusions have shown dramatic and durable responses in lung cancer patients, making their comprehensive detection critical. Here, we evaluated the incremental benefit of targeted RNA sequencing (RNAseq) in the identification of gene fusions in patients where no clear mitogenic driver alteration is found by DNA sequencing (DNAseq)–based panel testing. We found actionable alterations (kinase fusions or MET exon 14 skipping) in 13% of cases apparently driver negative by previous DNAseq testing. Among the driver-negative samples tested by RNAseq, those with low tumor mutation burden (TMB) were significantly enriched for gene fusions when compared with the ones with higher TMB. In a clinical setting, such patients should be prioritized for RNAseq. Thus, a rational, algorithmic approach to the use of targeted RNA-based next-generation sequencing (NGS) to complement large panel DNA-based NGS testing can be highly effective in comprehensively uncovering targetable gene fusions or oncogenic isoforms not just in lung cancer but also more generally across different tumor types.

A Commentary is in the same issue at https://clincancerres.aacrjournals.org/content/25/15/4586?iss=15

Wake Up and Smell the Fusions: Single-Modality Molecular Testing Misses Drivers

by Kurtis D. Davies and Dara L. Aisner

Abstract

Multitarget assays have become common in clinical molecular diagnostic laboratories. However, all assays, no matter how well designed, have inherent gaps due to technical and biological limitations. In some clinical cases, testing by multiple methodologies is needed to address these gaps and ensure the most accurate molecular diagnoses.

See related article by Benayed et al., p. 4712

In this issue of Clinical Cancer Research, Benayed and colleagues illustrate the growing need to consider multiple molecular testing methodologies for certain clinical specimens (1). The rapidly expanding list of actionable molecular alterations across cancer types has resulted in the wide adoption of multitarget testing approaches, particularly those based on next-generation sequencing (NGS). NGS-based assays are commonly viewed as “one-stop shops” to detect a vast array of molecular variants. However, as Benayed and colleagues discuss, even well-designed and highly vetted NGS assays have inherent gaps that, under certain circumstances, are ideally addressed by analyzing the sample using an alternative approach.

In the article, the authors examined a cohort of lung adenocarcinoma patient samples that had been deemed “driver- negative” via MSK-IMPACT, an FDA-cleared test that is widely considered by experts in the field to be one of the best examples of a DNA-based large gene panel NGS assay (2). Of 589 driver-negative cases, 254 had additional material amenable for a different approach: RNA-based NGS designed specifically for gene fusion and oncogenic gene isoform detection. After accounting for quality control failures, 232 samples were successfully sequenced, and, among these, 36 samples (representing an astonishing 15.5% of tested cases) were found to be positive for a driver gene fusion or oncogenic isoform that had not been detected by DNA-based NGS. The real-world value derived from this orthogonal testing schema was more than theoretical, with 8 of 10 (80%) patients demonstrating clinical benefit when treated according to the alteration identified via the RNA-based approach.

To detect gene rearrangements that lead to oncogenic gene fusions (and to detect mutations and insertions/deletions that lead to MET exon 14 skipping), MSK-IMPACT employs hybrid capture-based enrichment of selected intronic regions from genomic DNA. While this approach has proven to be successful in a variety of settings, there are associated limitations that were determined in this study to underlie the discrepancies between MSK-IMPACT and the RNA-based assay. First, some introns that are involved in clinically actionable rearrangement events are very large, thus requiring substantial sequencing capital that can represent a disproportionate fraction of the assay. Despite the ability via NGS to perform sequencing at a large scale, this sequencing capacity is still finite, and thus decisions must be made to sacrifice coverage of certain large genomic regions to ensure sufficient sequencing depth for other desired genomic targets. In the case of MSK-IMPACT (and most other DNA-based NGS assays), certain important introns in NTRK3 and NRG1 are not included in covered content, simply because they are too large (>90 Kb each). The second primary problem with DNA-based analysis of introns is that they often contain highly repetitive elements that are extremely difficult to assess via NGS due to their recurring presence across the genome. Attempts to sequence these regions are largely unfruitful because any sequencing data obtained cannot be specifically aligned/mapped to the desired targeted region of the genome (3). This is particularly true for intron 31 of ROS1, because it contains two repetitive long interspersed nuclear elements, and many DNA-based assays, including MSK-IMPACT, poorly cover this intron (4). In this study by Benayed and colleagues, the most common discrepant alteration was fusion involving ROS1, which accounted for 10 of 36 (28%) cases. At least six of these, those that demonstrated fusion to ROS1 exon 32, were likely directly explained by incomplete intron 31 sequencing. RNA-based analysis is able to overcome the above described limitations owing to the simple fact that sequencing is focused on exons post-splicing and the need to sequence introns is entirely avoided (Fig. 1).

• Download figure
• Open in new tab
• Download powerpoint

Figure 1.

Schematic representation of underlying genomic complexities that can lead to false-negative gene fusion results in DNA-based NGS analysis. In some cases, RNA-based approaches may overcome the limitations of DNA-based testing.

Lack of sufficient intronic coverage could not account for all of the discrepancies between DNA-based and RNA-based analysis however. Six samples in the cohort were found to be positive for MET exon 14 skipping based on RNA. In five of these, genomic alterations in MET introns 13 or 14 were observed, however they did not conform to canonical splice site alterations and thus were not initially called (although this was addressed by bioinformatics updates). In RNA-based testing, however, determination of exon skipping is simplified such that, regardless of the specific genomic alteration that interferes with splicing, absence of the exon in the transcript is directly observed (5). In another two of the discrepant cases, tumor purity was observed to be low in the sample, meaning that the expected variant allele frequency (VAF) for a genomic event would also likely be low, potentially below detectable levels. However, overexpression of the fusions at the transcript level was theorized to compensate for low VAF (Fig. 1). Additional explanations for discordant findings between the assays included sample-specific poor sequencing in selected introns and complex rearrangements that hindered proper capture (Fig. 1).

The take home message from Benayed and colleagues is simply this: there is no perfect assay that will detect 100% of the potential actionable alterations in patient samples. Even an extremely well designed, thoroughly vetted, and FDA-cleared assay such as MSK-IMPACT will have inherent and unavoidable “holes” due to intrinsic limitations. The solution to this dilemma, as adeptly described by Benayed and colleagues, is additional testing using a different approach. While in an ideal world every clinical tumor sample would be tested by multiple modalities to ensure the most comprehensive clinical assessment, the reality is that these samples are often scant and testing is fiscally burdensome (and often not reimbursed). Therefore, algorithms to determine which samples should be reflexed to secondary assays after testing with a primary assay are critical for maximizing benefit. In this study, the first algorithmic step was lack of an identified driver (because activated oncogenic drivers tend to exist exclusively of each other), which amounted to 23% of samples tested with the primary assay. In addition, the authors found a significantly higher rate of actionable gene fusions in samples with a low (<5 mut/Mb) tumor mutational burden, meaning that this metric, which was derived from the primary assay, could also be used to help inform decision making regarding additional testing. While this scenario is somewhat specific to lung cancer, similar approaches could be prescribed on a cancer type–specific basis.

These findings should be considered a “wake-up call” for oncologists in regard to the ordering and interpretation of molecular testing. It is clear from these and other published findings that advanced molecular analysis has limitations that require nuanced technical understanding. As this arena evolves, it is critical for oncologists (and trainees) to gain an increased comprehension of how to identify when the “gaps” in a test might be most clinically relevant. This requires a level of technical cognizance that has been previously unexpected of clinical practitioners, yet is underscored by the reality that opportunities for effective targeted therapy can and will be missed if the treating oncologist is unaware of how to best identify patients for whom additional testing is warranted. This study also highlights the mantra of “no test is perfect” regardless of prestige of the testing institution, number of past tests performed, or regulatory status. NGS, despite its benefits, does not mean all-encompassing. It is only through the adaptability of laboratories to utilize knowledge such as is provided by Benayed and colleagues that advances in laboratory medicine can be quickly deployed to maximize benefits for oncology patients.

References:

1. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012, 489(7417):519-525.
2. A genomics-based classification of human lung tumors. Science translational medicine 2013, 5(209):209ra153.
3. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J et al: Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012, 150(6):1121-1134.
4. Takeuchi K, Soda M, Togashi Y, Suzuki R, Sakata S, Hatano S, Asaka R, Hamanaka W, Ninomiya H, Uehara H et al: RET, ROS1 and ALK fusions in lung cancer. Nature medicine 2012, 18(3):378-381.
5. Morodomi Y, Takenoyama M, Inamasu E, Toyozawa R, Kojo M, Toyokawa G, Shiraishi Y, Takenaka T, Hirai F, Yamaguchi M et al: Non-small cell lung cancer patients with EML4-ALK fusion gene are insensitive to cytotoxic chemotherapy. Anticancer research 2014, 34(7):3825-3830.
6. Yoshimura M, Tada Y, Ofuzi K, Yamamoto M, Nakatsura T: Identification of a novel HLA-A 02:01-restricted cytotoxic T lymphocyte epitope derived from the EML4-ALK fusion gene. Oncology reports 2014, 32(1):33-39.
7. Yang L, Li G, Zhao L, Pan F, Qiang J, Han S: Blocking the PI3K pathway enhances the efficacy of ALK-targeted therapy in EML4-ALK-positive nonsmall-cell lung cancer. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2014.
8. Workman P, van Montfort R: EML4-ALK fusions: propelling cancer but creating exploitable chaperone dependence. Cancer discovery 2014, 4(6):642-645.
9. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A et al: Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012, 150(6):1107-1120.
10. Peifer M, Fernandez-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T et al: Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nature genetics 2012, 44(10):1104-1110.

Other posts on this site which refer to Lung Cancer and Cancer Genome Sequencing include:

Multi-drug, Multi-arm, Biomarker-driven Clinical Trial for patients with Squamous Cell Carcinoma called the Lung Cancer Master Protocol, or Lung-MAP launched by NCI, Foundation Medicine, and Five Pharma Firms

US Personalized Cancer Genome Sequencing Market Outlook 2018 –

Comprehensive Genomic Characterization of Squamous Cell Lung Cancers

International Cancer Genome Consortium Website has 71 Committed Cancer Genome Projects Ongoing

Non-small Cell Lung Cancer drugs – where does the Future lie?

Lung cancer breathalyzer trialed in the UK

Diagnosing Lung Cancer in Exhaled Breath using Gold Nanoparticles

Multi-drug, Multi-arm, Biomarker-driven Clinical Trial for patients with Squamous Cell Carcinoma called the Lung Cancer Master Protocol, or Lung-MAP launched by NCI, Foundation Medicine, and Five Pharma Firms

Share this:

• Click to share on Twitter (Opens in new window)
• Click to share on LinkedIn (Opens in new window)
• Click to share on Facebook (Opens in new window)
• Click to print (Opens in new window)
• Click to email a link to a friend (Opens in new window)

Like this:

Like Loading...

Read Full Post »

Heroes in Medical Research: Developing Models for Cancer Research

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Genome Biology, Health Economics and Outcomes Research, Human Immune System in Health and in Disease, Scientist: Career considerations, Translational Research, tagged animal models of disease, Aviva Lev-Ari, Cancer - General, cancer models, Cell Biology, cloning, Conditions and Diseases, Developmental biology, DNA, gene expression, genetics, history of science, mouse model, National Institutes of Health, Proceedings of the National Academy of Sciences of the United States of America, research, scientific discovery on April 4, 2014| Leave a Comment »

Heroes in Medical Research: Developing Models for Cancer Research

Author, Curator: Stephen J. Williams, Ph.D.

 

The current rapid progress in cancer research would have never come about if not for the dedication of past researchers who had developed many of the scientific tools we use today. In this issue of Heroes in Medical Research I would like to give tribute to the researchers who had developed the some of the in-vivo and in-vitro models which are critical for cancer research.

 

The Animal Modelers in Cancer Research

Helen Dean King, Ph.D. (1869-1955)

Helen Dean King, Ph.D. from www.ExplorePAhistory.com; photo Courtesy of the Wistar Institute Archive Collection, Philadelphia, PA

 

 

The work of Dr. Helen Dean King on rat inbreeding led to development of strains of laboratory animals. Dr. King taught at Bryn Mawr College, then worked at University of Pennsylvania and the Wistar Institute under famed geneticist Thomas Hunt Morgan, researching if inbreeding would produce harmful genetic traits.   At University of Pennsylvania she examined environmental and genetic factors on gender determination.

 

 

 

 

Important papers include [1-6]as well as the following contributions:

“Studies in Inbreeding”, “Life Processes in Gray Norway Rats During Fourteen Years in Captivity”, doctoral thesis on embryologic development in toads (1899)

 

Milestones include:

 

1909    started albino rat breeding and bred 20 female and male from same litter (King colony) to 25

successive generations (inbreeding did not cause harmful traits)

 

1919     started to domesticate the wild Norwegian rats that ran thru Philadelphia (six pairs Norway rats

thru 28 generations)

A good reference for definitions of rat inbreeding versus line generation including a history of Dr. King’s work can be found at the site: Munificent Mischief Rattery and a brief history here.[7] In addition, Dr. King had investigated using rat strains as a possible recipient for tumor cells. The work was an important advent to the use of immunodeficient models for cancer research.

 

As shown below Philadelphia became a hotbed for research into embryology, development, genetics, and animal model development.

 

Beatrice Mintz, Ph.D.

(Beatrice Minz, Ph.D.; photo credit Fox Chase Cancer Center, www.pubweb.fccc.edu)

Dr. Mintz, an embryologist and cancer researcher from Fox Chase Cancer Center in Philadelphia, PA, contributed some of the most seminal discoveries leading to our current understanding of genetics, embryo development, cellular differentiation, and oncogenesis, especially melanoma, while pioneering techniques which allowed the development of genetically modified mice.

If you get the privilege of hearing her talk, take advantage of it. Dr. Mintz is one of those brilliant scientists who have the ability to look at a clinical problem from the viewpoint of a basic biological question and, at the same time, has the ability to approach the well-thought out questions with equally well thought out experimental design. For example, Dr. Mintz asked if a cell’s developmental fate was affected by location in the embryo. This led to her work by showing teratocarcinoma tumor cells in the developing embryo could revert to a more normal phenotype, essentially proving two important concepts in development and tumor biology:

1. The existence of pluripotent stem cells
2. That tumor cells are affected by their environment (which led to future concepts of the importance of tumor microenvironment on tumor growth

Other seminal discoveries included:

• Development of the first mouse chimeras using novel cell fusion techniques
• With Rudolf Jaenisch in 1974, showed integration of viral DNA from SV40, could be integrated into the DNA of developing mice and persist into adulthood somatic cells, the first transgenesis in mice which led ultimately to:
• Development of the first genetically modified mouse model of human melanoma in 1993

Her current work, seen on the faculty webpage here, is developing mice with predisposition to melanoma to uncover risk factors associated with the early development of melanoma.

In keeping with the Philadelphia tradition another major mouse model which became seminal to cancer drug discovery was co-developed in the same city, same institute and described in the next section.

It is interesting to note that the first cloning of an animal, a frog, had taken place at the Institute for Cancer Research, later becoming Fox Chase Cancer Center, which was performed by Drs. Robert Briggs and Thomas J. King and reported in the 152 PNAS paper Transplantation of Living Nuclei From Blastula Cells into Enucleated Frogs’ Eggs.[8]

 

 The Immunodeficient Animal as a Model System for Cancer Research – Dr. Mel Bosma, Ph.D.

 

Melvin J. Bosma, Ph.D.; photo credit Fox Chase Cancer Center

In the summer of 1980 at Fox Chase Cancer Center, Dr. Melvin J. Bosma and his co-researcher wife Gayle discovered mice with deficiencies in common circulating antibodies and since, these mice were littermates, realized they had found a genetic defect which rendered the mice immunodeficient (upon further investigation these mice were unable to produce mature B and T cells). These mice were the first scid (severe combined immunodeficiency) colony. The scid phenotype was later found to be a result of a spontaneous mutation in the enzyme Prkdc {protein kinase, DNA activated, catalytic polypeptide} involved in DNA repair, and ultimately led to a defect in V(D)J recombination of immunoglobulins.

The emergence of this scid mouse was not only crucial for AIDS research but was another turning point in cancer research , as researchers now had a robust in-vivo recipient for human tumor cells. The orthotopic xenograft of human tumor cells now allowed for studies on genetic and microenvironmental factors affecting tumorigenicity, as well as providing a model for chemotherapeutic drug development (see Suggitt for review and references)[9]. A discussion of the pros and cons of the xenograft system for cancer drug discovery would be too voluminous for this post and would warrant a full review by itself. But before the advent of such scid mouse systems researchers relied on spontaneous and syngeneic mouse tumor models such as the B16 mouse melanoma and Lewis lung tumor model.

Other scid systems have been developed such as in the dog, horse, and pig. Please see the following post on this site The SCID Pig: How Pigs are becoming a Great Alternate Model for Cancer Research. The athymic (nude) mouse (nu/nu) also is a popular immunodeficient mouse model used for cancer research

Two other in-vivo tumor models: Patient Derived Xenografts (PDX) and Genetically Engineered Mouse models (GEM) deserve their own separate discussion however the success of these new models can be attributed to the hard work of the aforementioned investigators. Therefore I will post separately and curate PDX and GEM models of cancer and highlight some new models which are having great impact on cancer drug development.

 

References

1.         Loeb L, King HD: Transplantation and Individuality Differential in Strains of Inbred Rats. The American journal of pathology 1927, 3(2):143-167.

2.         Lewis MR, Aptekman PM, King HD: Retarding action of adrenal gland on growth of sarcoma grafts in rats. J Immunol 1949, 61(4):315-319.

3.         Aptekman PM, Lewis MR, King HD: Tumor-immunity induced in rats by subcutaneous injection of tumor extract. J Immunol 1949, 63(4):435-440.

4.         Lewis MR, Aptekman PM, King HD: Inactivation of malignant tissue in tumor-immune rats. J Immunol 1949, 61(4):321-326.

5.         Lewis MR, King HD, et al.: Further studies on oncolysis and tumor immunity in rats. J Immunol 1948, 60(4):517-528.

6.         Aptekman PM, Lewis MR, King HD: A method of producing in inbred albino rats a high percentage of immunity from tumors native in their strain. J Immunol 1946, 52:77-86.

7.         Ogilvie MB: Inbreeding, eugenics, and Helen Dean King (1869-1955). Journal of the history of biology 2007, 40(3):467-507.

8.         Briggs R, King TJ: Transplantation of Living Nuclei From Blastula Cells into Enucleated Frogs’ Eggs. Proceedings of the National Academy of Sciences of the United States of America 1952, 38(5):455-463.

9.         Suggitt M, Bibby MC: 50 years of preclinical anticancer drug screening: empirical to target-driven approaches. Clinical cancer research : an official journal of the American Association for Cancer Research 2005, 11(3):971-981.

 

Other posts on this site about Cancer, Animal Models of Disease, and other articles in this series include:

The SCID Pig: How Pigs are becoming a Great Alternate Model for Cancer Research

A Synthesis of the Beauty and Complexity of How We View Cancer

Guidelines for the welfare and use of animals in cancer research

Importance of Funding Replication Studies: NIH on Credibility of Basic Biomedical Studies

FDA Guidelines For Developmental and Reproductive Toxicology (DART) Studies for Small Molecules

Report on the Fall Mid-Atlantic Society of Toxicology Meeting “Reproductive Toxicology of Biologics: Challenges and Considerations:

What`s new in pancreatic cancer research and treatment?

Heroes in Medical Research: Dr. Carmine Paul Bianchi Pharmacologist, Leader, and Mentor

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

Richard Lifton, MD, PhD of Yale University and Howard Hughes Medical Institute: Recipient of 2014 Breakthrough Prizes Awarded in Life Sciences for the Discovery of Genes and Biochemical Mechanisms that cause Hypertension

Reuben Shaw, Ph.D., a geneticist and researcher at the Salk Institute: Metabolism Influences Cancer

 

Share this:

• Click to share on Twitter (Opens in new window)
• Click to share on LinkedIn (Opens in new window)
• Click to share on Facebook (Opens in new window)
• Click to print (Opens in new window)
• Click to email a link to a friend (Opens in new window)

Like this:

Like Loading...

Read Full Post »

IRF-1 Deficiency Skews the Differentiation of Dendritic Cells

Posted in Biological Networks, Gene Regulation and Evolution, Cell Biology, Signaling & Cell Circuits, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, International Global Work in Pharmaceutical, Molecular Genetics & Pharmaceutical, Pharmaceutical Industry Competitive Intelligence, Technology Transfer: Biotech and Pharmaceutical, tagged Adaptive immune system, Conditions and Diseases, CTLA-4, Dendritic cell, immune system, Immunology, Interleukin 10, Interleukin 6, IRF1, Proceedings of the National Academy of Sciences of the United States of America, Regulatory T cell on March 5, 2013| Leave a Comment »

IRF-1 Deficiency Skews the Differentiation of Dendritic Cells

Reporter: Larry H Bernstein, MD, FCAP

 

 

IFN Regulatory Factor-1 Negatively Regulates CD4+CD25+ Regulatory T Cell Differentiation by Repressing Foxp3 Expression1

 

Alessandra Fragale*, Lucia Gabriele†, Emilia Stellacci*, Paola Borghi†,…. and Angela Battistini2,*
The Journal of Immunology   Aug 1, 2008; 181(3): 1673-1682

Regulatory T (Treg) cells are critical in inducing and maintaining tolerance. Despite progress in understanding the basis of immune tolerance,

• mechanisms and molecules involved in the generation of Treg cells remain poorly understood.

IFN regulatory factor (IRF)-1 is a pleiotropic transcription factor implicated in the regulation of various immune processes. In this study, we report that IRF-1 negatively regulates CD4+CD25+ Treg cell

• development and function by specifically repressing Foxp3 expression.

IRF-1-deficient (IRF-1−/−) mice showed a selective and marked increase of highly activated and differentiated CD4+CD25+Foxp3+ Treg cells in thymus and in all peripheral lymphoid organs. Furthermore,

• IRF-1−/− CD4+CD25− T cells showed extremely high bent to differentiate into CD4+CD25+Foxp3+ Treg cells, whereas
• restoring IRF-1 expression in IRF-1−/− CD4+CD25− T cells
  • impaired their differentiation into CD25+Foxp3+ cells.

Functionally, both isolated and TGF-β-induced CD4+CD25+ Treg cells from IRF-1−/− mice

• exhibited more increased suppressive activity than wild-type Treg cells.

Such phenotype and functional characteristics were explained at a mechanistic level by the finding that

• IRF-1 binds a highly conserved IRF consensus element sequence (IRF-E) in the foxp3 gene promoter in vivo and
• negatively regulates its transcriptional activity.

We conclude that IRF-1 is a key negative regulator of CD4+CD25+ Treg cells

• through direct repression of Foxp3 expression.

Introduction

Tolerance is critical for prevention of autoimmunity and maintenance of immune homeostasis by active suppression of inappropriate immune responses. Suppression has a dedicated population of  T cells that

• control the responses of other T cells.

This cell population, referred to as regulatory T (Treg)3 cells, actually comprises several subsets, including naturally occurring CD4+CD25+ Treg cells that arise in thymus. Once generated,

• thymic Treg cells are exported to peripheral tissues, and
• comprise 5–10% of peripheral CD4+ T cells (1, 2, 3).

CD4+CD25+ Treg cells are characterized by

• constitutive expression of IL-2Rα (CD25), CTLA-4, and glucocorticoid-induced TNFR family-related gene; moreover,
• they express CD62 ligand (CD62L) and are mainly CD45RBlow (4).

In contrast to cell surface markers, which can be shared with other T cells populations,

• the forkhead/winged-helix family transcriptional repressor Foxp3 is
• specifically expressed in CD4+CD25+ Treg cells and
• rigorously controls their development and function (5, 6, 7).

Functionally after TCR stimulation, CD4+CD25+ Treg cells can

• mediate strong suppression of proliferation and
• IL-2 production by CD4+ T cells both in vivo and in vitro (8).

Although mechanisms of suppression are not fully understood,

• they appear to be cell contact-mediated, whereas
• the relative contribution of soluble cytokines remains controversial
  • with differences between in vitro and in vivo results (1, 8, 9).

Indeed, the involvement of cytokines in the suppressor function of CD4+CD25+ Treg cells has been proposed in vivo,

• where they are able to produce IL-10 and TGF-β (10, 11, 12), and
• importantly, IL-10 activity has been recently associated with the function of TGF-β-induced CD4+CD25−CD45RBlow cells (13).

Beside naturally occurring CD4+CD25+ Treg cells, CD4+CD25+ Treg cells can also be

• induced (inTreg) in vivo or in vitro after TCR stimulation and TGF-β treatment,
• acquiring expression of CD25 and Foxp3 both in mice (14, 15, 16) and humans (17, 18, 19, 20),
  • although with characteristic functional differences (20).

Despite extensive studies on the role of Foxp3 in inducing and maintaining tolerance, little information on regulation of its expression is available. Transcription factors of the IFN regulatory factor (IRF) family participate in

• the early host response to pathogens,
• in immunomodulation and
• hematopoietic differentiation (21).

Nine members of this family have been identified based on a unique helix-turn-helix DNA binding domain, located at

• the N terminus that is responsible for binding to the IRF consensus element (IRF-E) (21).

The first member of the family, IRF-1, was originally identified as a protein that binds

• the cis-acting DNA elements in the ifnβ gene promoter and the IRF-E (also referred to as the IFN-stimulated response element; ISRE),
• in the promoters of IFN-αβ-stimulated genes (22).

IRF-1 is expressed at low basal levels in all cell types examined, but

• accumulates in response to several stimuli and cytokines including IFN-γ, the strongest IRF-1 inducer (22).

Intensive functional analyses conducted on this transcription factor have revealed a remarkable functional diversity in the

• regulation of cellular responses through the
• modulation of different sets of genes,
• depending on

1. cell type,
2. state of the cell, and/or
3. nature of the stimuli (21).

We and others have shown that IRF-1 affects the differentiation of both lymphoid and myeloid lineages (22, 23, 24, 25, 26, 27, 28). In particular, studies in knockout (KO) mice have implicated IRF-1

in the regulation of various immune processes:

1. impairment of CD8+ T cell and NK cell maturation,
2. impaired IL-12 macrophage production,
3. exclusive Th2 differentiation, and
4. defective Th1 responses…………. have all been observed (22, 23, 24, 25, 26).

As a result, IRF-1−/− mice are highly susceptible to infections, for which effective host control

• is associated with a Th1 immune response (24).

In contrast, these mice are characterized by

• increased resistance to several autoimmune diseases such as

1. collagen-induced arthritis,
2. experimental autoimmune encephalomyelitis,
3. Helicobacter pylori-induced gastritis,
4. induced lymphocytic thyroiditis,
5. insulitis, or
6. diabetes (29, 30, 31, 32).

Recently, we reported that IRF-1−/− mice display a prevalence of

• dendritic cell (DC) subsets with immature and tolerogenic features that were
  • unable to undergo full maturation after stimulation.

Moreover, IRF-1−/− DC conferred

• increased suppressive activity to CD4+CD25+ Treg cells (33).

Because there is growing evidence that immature or partially matured DC can induce tolerance (34, 35), we hypothesized that IRF-1 could play a role in

• Treg development and function.

In this study, we analyzed the CD4+CD25+ compartment in IRF-1−/− mice and

• we found that in vivo IRF-1 deficiency resulted in a
• selective and marked increase in highly differentiated and activated CD4+CD25+Foxp3+ Treg cells, whereas

reintroduction of IRF-1 by retrovirus transduction

• impaired TGF-β-mediated differentiation of IRF-1−/− CD4+CD25− T cells into CD4+CD25+Foxp3+ Treg cells.

At molecular level, we show that IRF-1 plays a direct role in the generation and expansion of CD4+CD25+ Treg cells

• specifically repressing Foxp3 transcriptional activity.

Our results, therefore, highlight a unique role for IRF-1 as regulator of Foxp3, thus pointing to IRF-1 as a specific tool to control altered tolerance.

Results

CD4+CD25+ Treg from IRF-1−/− mice are increased and functionally more suppressive than WT Treg cells

The distribution and the phenotype of CD4+CD25+Foxp3+ Treg in lymphoid organs of IRF-1−/− mice were determined by flow cytometry.

the number of ex vivo double positive CD4+CD25+ cells was significantly increased in spleens and skin draining and mesenteric lymph nodes (2.8-, 2.3-, and 2.1-fold increase, respectively), and to a lesser extent, in thymus (1.6-fold increase) of IRF-1−/− mice as compared with WT mice. Consistently with previous reports (23, 41), no differences in CD4+ T cell and total cell numbers in all lymphoid organs from WT or IRF-1−/− mice were found (data not shown). Strikingly, intracellular analysis of Foxp3 expression showed that this factor was increasingly expressed in CD4+CD25+ Treg cells from spleens as well as from other lymphoid organs of IRF-1−/− mice

FACS analysis of splenic magnetically sorted CD4+CD25+ Treg cells was performed to evaluate the expression of activation markers.  IRF-1−/− Treg cells were to a large extent characteristic of a marked activated and differentiated phenotype.

Because there is accumulating evidence that activity of CD4+CD25+ Treg cells in vivo involves some immunosuppressive cytokines (9, 10, 11, 12), we also compared the cytokine profile of IRF-1−/− CD4+CD25+ Treg cells with the profile of WT counterparts . Lower levels of proinflammatory cytokines, such as TNF-α and IFN-γ, whereas higher levels of IL-4 were expressed in CD4+CD25+ Treg cells as well as in CD4+CD25− T lymphocytes from KO as compared with WT cells. Notably, only IRF-1−/− Treg cells showed a clear-cut increase in the expression of IL-10. By contrast, TGF-β was expressed at similar levels in CD4+CD25+ Treg cells from both IRF-1−/− and WT mice. Accordingly with mRNA data, IL-10 secretion in supernatants of TCR-stimulated CD4+CD25+ cocultures from IRF-1−/− mice was significantly increased (3-fold), whereas

• IFN-γ secretion was decreased (2.5-fold) compared with cocultures from WT mice (Fig. 2⇑C).

As the functional hallmark of Treg cells is their ability to suppress the expansion of effector T cells, we next evaluated this activity performing suppression assays (1, 2, 3, 8). Importantly, CD4+CD25+ Treg cells from IRF-1−/− mice were found significantly more efficient than WT Treg cells in suppressing the proliferation of syngeneic CD4+CD25− responder T cells in a dose-dependent fashion. Next, to verify whether IRF-1−/− Treg cells suppression ability was retained vs WT responder T cells, we performed suppression assays using IRF-1−/− Treg and WT responders and vice versa. The suppressive activity of IRF-1−/− Treg cells toward WT responders was dose-dependently increased, as well.

IRF-1−/− CD4+CD25− T cells show high bent to convert into CD4+CD25+ Treg cells

It has been reported in mice and human that TGF-β promotes the induction of peripheral CD4+CD25− T cells into CD4+CD25+ Treg cells (inTreg), that acquire Foxp3 expression and regulatory functions.

In presence of TGF-β, 44.2% of CD4+CD25+ inTreg cells were generated in the coculture of CD4+CD25− T cells from IRF-1−/− mice, whereas

• only 24% of double positive cells were detected in the corresponding coculture from WT mice.

Notably, even in absence of TGF-β, 25.4% CD4+CD25+ inTreg were generated in the coculture of CD4+CD25− T cells from IRF-1−/− mice, as

• compared with 16.5% of Treg cells generated in WT cocultures.

Importantly, an increased number of CD4+CD25+-gated Foxp3+ cells were observed in IRF-1−/− inTreg cells in the presence (4.5-fold increase) or in the absence (8-fold increase) of TGF-β compared with WT inTreg cells. Next, to evaluate quantitatively Foxp3 expression levels in TGF-β-induced Treg vs ex vivo freshly purified Treg cells, quantitative real-time PCR was performed. A clear-cut

induction of Foxp3 mRNA (4.5-fold increase) was detected in TGF-β-treated IRF-1−/− cells compared with WT cells. Of note, these levels were comparable with those present in freshly isolated IRF-1−/− CD4+CD25+ cells. Strikingly, also untreated IRF-1−/− T cells showed higher levels of Foxp3 mRNA than WT untreated cells (6-fold increase) and similar to levels present in freshly purified WT CD4+CD25+ Treg cells.

The functionality of CD4+CD25+Foxp3+ inTreg cells was then assessed by suppression assays. TGF-β-treated IRF-1−/− inTreg cells were significantly more effective than the WT counterpart cells

• in suppressing proliferation of effector T cells in a dose-dependent way.

Interestingly, a saturating amount of anti-IL-10 m Abs neutralized the suppression ability of  inTreg cells from both IRF-1−/− and WT mice even though the effect was much more marked in IRF-1−/− inTreg cells. Control Abs did not exhibit any effect.

Restoring IRF-1 expression in IRF-1−/− CD4+CD25− T cells impairs their differentiation into CD4+CD25+Foxp3+ cells

To address the specificity of IRF-1 role in differentiation of CD4+CD25+ Treg cells from CD25− cells, we investigate whether

• forced expression of IRF-1 in CD4+CD25− IRF-1−/− T cells could rescue the WT phenotype.
• bicistronic retroviral vectors expressing murine IRF-1 and human CD8 protein as surface marker (MigR1 IRF-1-CD8) or CD8 alone (MigR1 EV-CD8) were generated.

Splenic CD4+CD25− cells from IRF-1−/− mice were stimulated with plate-bound anti-CD3 and anti-CD28 Abs and infected with either retrovirus.

• 31.6% of MigR1 EV-CD8 CD4+ retrovirus-infected cells were CD25+, by contrast
• only 17.7% of MigR1 IRF-1-CD8 retrovirus-infected cells were double positive.

Consistently, Foxp3 expression in CD8+-gated cells was significantly decreased in MigR1 IRF-1-CD8-infected cells as compared with

• those infected with MigR1 EV-CD8 vectors,
• strongly supporting the evidence that IRF-1 specifically impairs CD4+CD25+ cell differentiation.

IRF-1 binds an IRF-E on the Foxp3 core promoter and inhibits its transcriptional activity

To shed light on the molecular mechanisms responsible for the striking effect exerted by IRF-1 on the development and function of CD4+CD25+ Treg cells, we investigated whether IRF-1, which is a regulator of key immunomodulatory genes (21), could directly regulate the foxp3 gene promoter activity. The proximal promoter of human foxp3 gene has been recently characterized and localized at −511/+176 bp upstream of the 5′ untranslated region (38). By the Genomatix software, we analyzed this region and found an IRF-E spanning from −234 to −203 bp . This region has been found highly homologous to mouse and rat foxp3 promoter, and of note, the IRF-E is perfectly conserved between humans and these species (38). To determine whether IRF-1 could bind this sequence, DNA affinity purification assays were performed with cell extracts from Jurkat T cells, which display discrete basal levels of IRF-1, and from the same cells treated with IFN-γ to maximally stimulate IRF-1 expression. A total of 200 μg of nuclear extracts was incubated with oligonucleotides containing the WT or the a mutated version of IRF-E. The isolated complexes were then examined by immunoblotting against IRF-1. A specific binding of IRF-1 to Foxp3 oligonucleotide was evident. The binding was strongly stimulated by IFN-γ treatment and, interestingly, it was comparable to that obtained when the same extracts were incubated with a synthetic oligonucleotide corresponding to C13, the canonical IRF-1 consensus sequence (21). IRF-1 binding was highly specific because a mutated version of the Foxp3/IRF-E, or an unrelated oligonucleotide corresponding to the STAT binding site present on the β-casein gene promoter, did not retain any protein from the same extracts. To functionally characterize the specific binding of IRF-1 to the foxp3 gene promoter, we cloned the encompassing part of the proximal promoter containing the IRF-E from −296 to +7 bp of foxp3 gene promoter upstream the luciferase reporter gene. The effect of IRF-1 was evaluated in Jurkat T cells transiently cotransfected with the luciferase reporter gene and increasing doses of an IRF-1-expressing vector.

The results indicated that the basal transcriptional activity of the foxp3 gene promoter

• was substantially reduced in the presence of IRF-1 and the effect was dose-dependent.

Conversely, the basal activity of the foxp3 gene promoter construct mutated in the IRF-E

• was not affected by IRF-1 overexpression.

Interestingly, IRF-2, a repressor of IRF-1 transcriptional activity on most promoters (21), neither affected the promoter activity nor counteracted the inhibitory effect exerted by IRF-1.  IRF-1, IRF-2, as well as the IFN-γ treatment drastically reduced the transcriptional activity of the il4 gene promoter, whereas

• the low molecular mass polypeptide lmp2 construct was stimulated by IRF-1 and by IFN-γ treatment, but it was not affected by IRF-2.

All together these results demonstrate the specificity and functional relevance of IRF-1 binding to the foxp3 proximal promoter.

Foxp3 is a direct target of IRF-1 in human and mouse primary CD4+CD25− T cells and CD4+CD25+ Treg cells

To assess the biological relevance of the the reported effects of IRF-1 on Treg development and on the regulation of Foxp3 expression, we performed experiments with primary cells. We first assessed by Western blot IRF-1 expression levels in CD4+CD25+ Treg cells vs CD4+CD25− T cells magnetically sorted from PBMC of healthy donors or from mice spleens. Strikingly, we found that IRF-1 was down-regulated in double positive cells as compared with CD4+CD25− T cells both in mouse and human primary cells. To determine whether IRF-1 binds the Foxp3 oligonucleotides in primary Treg cells, pull-down assays with the same extracts were then performed. IRF-1 binding to Foxp3 oligonucleotide was significantly decreased in primary CD4+CD25+ Treg cells compared with CD4+CD25− T cells from both species. Foxp3 staining of CD4+CD25− T cells and CD4+CD25+ human Treg cells confirmed that these cells expressed low and high levels of Foxp3, respectively, and

• Foxp3 expression was further increased by IL-2 treatment.

To test whether IRF-1 expression was also down-modulated during the acquisition of Treg cell phenotype upon TGF-β treatment, freshly purified TCR-activated CD4+CD25− T cells from both species were cultured with TGF-β, or left untreated, for 3 days and Western blot analysis was performed. When cells were cultured in presence of TGF-β, IRF-1 expression was substantially decreased, as compared with untreated cells. Pull-down assays revealed that IRF-1 binding to Foxp3 oligonucleotide was decreased in TGF-β-treated primary cells compared with untreated cells, as well. Consistently, FACS analysis of these cultures indicated that ∼35% of TGF-β-treated CD4+ cells were Foxp3+ in human and ∼10% in mouse TGF-β treated cultures, respectively. By contrast, even though 46.3% of human untreated cells were CD25+ only 5% were Foxp3+.

Next, we assessed the in vivo IRF-1 binding to foxp3 gene in human and mouse primary magnetically sorted CD4+CD25− T cells and CD4+CD25+ Treg cells, using ChIP assay with anti-IRF-1 Abs. After DNA immunoprecipitation, subsequent real-time PCR amplification of the foxp3 gene surrounding the IRF-E site showed significant IRF-1 binding to Foxp3 promoter in CD4+CD25−Foxp3− T cells, and by contrast, a 5-fold decrease of IRF-1 binding in CD4+CD25+Foxp3high human Treg cells (Fig. 6⇑C). Similarly, the binding of IRF-1 to the Foxp3 promoter in the mouse Treg cells was decreased by ∼50%.

Finally, to assess the functionality of the in vivo IRF-1 binding, negatively selected primary human and mouse CD4+ T lymphocytes were nucleofected with the Foxp3 luciferase reporter gene along with expression vector for IRF-1. Fig. 6⇑E shows the results obtained with T cells from three different healthy donors and Fig. 6⇑F shows a representative experiment with mouse T cells from three independent experiments. In all samples, a discrete basal activity of foxp3 gene promoter was present and this activity was significantly repressed by IRF-1.

Discussion

The identification of molecules controlling Treg differentiation and function is important not only in understanding host immune responses in malignancy and autoimmunity but also in shaping immune response.

In this study, we have shown that IRF-1, a transcription factor involved in the IFN signaling, selectively affects CD4+CD25+ Treg cell development and function, unraveling a novel immunoregulatory function of IRF-1 in addition to its well-established role in balancing Th1 vs Th2 type immune responses. Several lines of evidence support this conclusion:

1) IRF-1−/− mice show a selective and marked increase in all lymphoid organs of CD4+CD25+Foxp3+ Treg cells; 2) CD4+CD25+ from IRF-1−/− mice are characterized by a highly activated and differentiated  phenotype and higher levels of Foxp3 that make them to be functionally more suppressive than WT Treg cells;

3) after TGF-β treatment, and importantly also in its absence, CD4+CD25− T cells from KO mice promptly converted into CD4+CD25+Foxp3+ Treg with a higher suppressive activity than WT cells;

4) forced retrovirus-mediated expression of IRF-1 in IRF-1−/− CD4+CD25− T cells impairs their differentiation into CD25+Foxp3+ cells; and 5) IRF-1 directly regulates transcriptional activity of the foxp3 gene promoter.

The phenotypical and functional characteristics of IRF-1−/− Treg cells strongly support the conclusion that IRF-1 can be considered a key negative regulator of CD4+CD25+ Treg cells.

The increased frequency of differentiated and activated CD4+CD25+ Treg cells characterized by an immunosuppressive cytokine profile described in this study

• may provide a mechanistic base for the reduced incidence and severity of several autoimmune diseases characterizing IRF-1−/− mice .

In this regard, it has been recently shown that CD4+CD25+ Treg cells were increased in IRF-1−/− mice backcrossed with the MRL/lpr mice, which showed reduced glomerulonephritis.

The increased production of the immunosuppressive cytokine IL-10 by isolated Treg cells from IRF-1−/− mice and the reverted suppression ability of inTreg by anti-IL-10 Abs suggest that this cytokine could play a key role in their suppressor function. Consistently, IL-10 activity has been recently associated with the function of TGF-β-induced CD4+CD25−CD45RBlow cells because their suppressive activity was abrogated with anti-IL-10R Ab treatment (13). Moreover, several reports focused on the in vivo IL-10 role in peripheral CD4+CD25+ Treg cell function in various autoimmunity models (10, 11, 12), although IL-10 seems not required for the functions of thymically derived Treg cells (1). In contrast with the increased IL-10 production, T cells from IRF-1−/− mice failed to produce significant amounts of proinflammatory cytokines such as IFN-γ or TNF-α. Accordingly, an inverse relationship between in vivo IFN-γ administration and generation or activation of CD4+CD25+ Treg cells has been recently shown (45). Moreover, in humans, it has been reported that TNF-α inhibits the suppressive function of both naturally occurring CD4+CD25+ Treg and TGF-β-induced Treg cells, and an anti-TNF Ab therapy reversed their suppressive activity by down-modulating the expression of Foxp3 (46). These latter and our results are apparently in contrast with what was recently reported on the stimulating role of IFN-γ on Foxp3 induction and conversion of CD4+CD25− T cells to CD4+ Treg cells in the IFN-γ KO model (47). In this regard, it is noteworthy to underline that, as it has been also suggested, although knocking down genes involved in up-regulation of IFN-γ expression do not significantly influence autoimmunity, by contrast the absence of genes expressed in response to IFN-γ, including IRF-1, lead to greatly reduced autoimmunity (48). Thus, although the exact mechanism underlying IFN-γ and TNF-α interference with the elicitation of Treg cells remains to be defined, we can speculate that induction of IRF-1 expression, which is up-regulated by IFN-γ and TNF-α, may represent a mechanism through which proinflammatory cytokines negatively affect Foxp3 expression, thereby influencing generation or activation of CD4+CD25+ Treg cells.

It is well known that Foxp3 plays a pivotal role in the regulatory functions of CD4+CD25+ T cells both in humans and in animal models. Thus, the key question in the field of Treg biology is which are molecules and signals that govern Foxp3 transcription.

We identify Foxp3 as specific target of IRF-1 and we show

• that it binds to foxp3 gene promoter in vitro and in vivo and represses its expression.

Structure of the human foxp3 gene promoter and elements necessary for its induction in T cells have been reported. We have identified an IRF-E sequence at 203 bp upstream of the transcriptional start site that is highly conserved. This element is bound by IRF-1 as proven by pull-down experiments and by ChIP analysis in intact cells, and IRF-1 binding resulted in a specific,

• dose-dependent repression of the foxp3 proximal promoter.

Notably, treatments with IFN-γ, a major IRF-1 inducer, significantly inhibited foxp3 gene promoter transcriptional activity, whereas IRF-2 did not have any effects. It is noteworthy that the foxp3 gene is highly conserved between mouse and man species, and in particular, the core promoter and the IRF-E identified in this study are perfectly conserved between mouse and human. Such conservation underscores the importance of this motif as regulatory element and provides additional evidence for the role of IRF-1 in regulating foxp3 gene expression.  IRF-1 binds this sequence and negatively regulates its expression in both human and mouse cells. The molecular interactions enabling IRF-1 to inhibit Foxp3 are not yet identified, although our preliminary results show that IRF-1 may compete with c-Myb for the binding to the same overlapping consensus sequence on the foxp3 gene promoter.

In summary, the current study provides evidence that IRF-1 affects CD4+CD25+ development and function by Foxp3 repression. Thus, our data demonstrate a new important contribution by which IRF-1 affects T cell differentiation and provide new important insights into molecular mechanisms controlling immune homeostasis.

Related articles

• Toll-Like Receptor 4 Engagement Drives Differentiation of Human and Murine Dendritic Cells from a Pro- into an Anti-Inflammatory Mode (plosone.org)
• New Strategy for Autoimmune Disease Treatment (azonano.com)
• Natural Sciences Repository Publishes New Information on Cell Treatment and Tumor Cells (prweb.com)
• Lactobacillus reuteri DSM 17938 Changes the Frequency of Foxp3+ Regulatory T Cells in the Intestine and Mesenteric Lymph Node in Experimental Necrotizing Enterocolitis (plosone.org)
• Partial Depletion of Regulatory T Cells Does Not Influence the Inflammation Caused by High Dose Hemi-Body Irradiation (plosone.org)
• Foxp3+ Treg Expanded from Patients with Established Diabetes Reduce Helios Expression while Retaining Normal Function Compared to Healthy Individuals (plosone.org)

Th1-Th2-Th17-Treg origin (Photo credit: Wikipedia)

 

00

Share this:

• Click to share on Twitter (Opens in new window)
• Click to share on LinkedIn (Opens in new window)
• Click to share on Facebook (Opens in new window)
• Click to print (Opens in new window)
• Click to email a link to a friend (Opens in new window)

Like this:

Like Loading...

Read Full Post »

RNA Virus Genome as Bacterial Chromosome

Posted in Advanced Drug Manufacturing Technology, Biological Networks, Gene Regulation and Evolution, Cell Biology, Signaling & Cell Circuits, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Infectious Disease & New Antibiotic Targets, International Global Work in Pharmaceutical, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Industry Competitive Intelligence, Technology Transfer: Biotech and Pharmaceutical, tagged bacteria, Bacterial artificial chromosome, chromosome, Complementary DNA, Messenger RNA, Proceedings of the National Academy of Sciences of the United States of America, RNA on March 5, 2013| Leave a Comment »

RNA Virus Genome as Bacterial Chromosome

Reporter: Larry H Bernstein, MD, FCAP

 

Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome

F Almazan, JM Gonzalez, Z Penzes, A Izeta, E Calvo, J Plana-Duran, and L Enjuanes

PNAS  May 9, 2000; 97(10): 5516–5521.

the application of two strategies,

• cloning of the cDNAs into a bacterial artificial chromosome and
• nuclear expression of RNAs that are typically produced within the cytoplasm

is useful for the engineering of large RNA molecules.
A cDNA encoding an infectious coronavirus RNA genome

• has been cloned as a bacterial artificial chromosome.

The rescued coronavirus

• conserved all of the genetic markers introduced throughout the sequence and
• showed a standard mRNA pattern and

the antigenic characteristics expected for the synthetic virus.
The cDNA was transcribed

• within the nucleus, and
• the RNA translocated to the cytoplasm.

Interestingly, the recovered virus had

• essentially the same sequence as the original one, and
  • no splicing was observed.

During the engineering of the infectious cDNA,

• the spike gene of the virus was replaced by
• the spike gene of an enteric isolate.

The synthetic virus

• replicated abundantly in the enteric tract and was fully virulent, demonstrating that
• the tropism and virulence of the recovered coronavirus can be modified.

the application of two strategies,

• cloning of the cDNAs into a bacterial artificial chromosome and
• nuclear expression of RNAs that are typically produced within the cytoplasm,
  • is useful for the engineering of large RNA molecules.

A cDNA encoding an infectious coronavirus RNA genome has been cloned as a bacterial artificial chromosome. The rescued coronavirus

• conserved all of the genetic markers introduced throughout the sequence and
• showed a standard mRNA pattern and
• the antigenic characteristics expected for the synthetic virus.
  • The cDNA was transcribed within the nucleus, and
  • the RNA translocated to the cytoplasm.

Interestingly, the recovered virus had essentially the same sequence as the original one, and no splicing was observed. During the engineering of the infectious cDNA, the spike gene of the virus was replaced by the spike gene of an enteric isolate. The synthetic virus

• replicated abundantly in the enteric tract and
• was fully virulent,

demonstrating that the tropism and virulence of the recovered coronavirus can be modified.}
http://www.PNAS.org/Engineering_the_largest_RNAvirus_genome_as_an_infectious_bacterial_artificial_chromosome/

Description: The interaction of mRNA in a cell. Source: http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/mrna.shtml (file) License: “All of the illustrations in the Talking Glossary of Genetics are freely available and may be used without special permission.” http://www.genome.gov/page.cfm?pageID=10003803 (Photo credit: Wikipedia)

RNA Protein Virus (Photo credit: Wikipedia)

This image was created as part of the Philip Greenspun illustration project. (Photo credit: Wikipedia)

Related articles

• Cloning the vaccinia virus genome as a bacterial artificial chromosome (pharmaceuticalintelligence.com)
• Regulators Discover a Hidden Viral Gene in Commercial GMO Crops (beyond2012zeitgeist.com)
• Ryogen Receives Nine Human Gene Patents in 2012 for Total of 23-Patent Portfolio (prweb.com)
• Research and Markets: Cytogenetics – Technologies, Markets and Companies – 2013 (prweb.com)
• RNA Guided Human Gene and Genome Engineering and Radical life extension, disease prevention and cures (nextbigfuture.com)
• In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus (plosone.org)
• What about Circular RNAs? (pharmaceuticalintelligence.com)
• Genomics of Bacterial and Archaeal Viruses (pharmaceuticalintelligence.com)
• How Genes Function (pharmaceuticalintelligence.com)
• When Clinical Application of miRNAs? (pharmaceuticalintelligence.com)

00

Share this:

• Click to share on Twitter (Opens in new window)
• Click to share on LinkedIn (Opens in new window)
• Click to share on Facebook (Opens in new window)
• Click to print (Opens in new window)
• Click to email a link to a friend (Opens in new window)

Like this:

Like Loading...

Read Full Post »

Older Posts »

• Follow Blog via Email

  Enter your email address to follow this blog and receive notifications of new posts by email.

  Email Address

  Follow

  Join 9,308 other subscribers

• Recent Posts

  • Artificial Intelligence (AI) Used to Successfully Determine Most Likely Repurposed Antibiotic Against Deadly Superbug Acinetobacter baumanni May 26, 2023
  • Testimonial on the English to Spanish Translation JOINT Project that yielded the “BioMed e-Series Spanish-language Edition” on Amazon.com May 24, 2023
  • percutaneous Left Ventricular Assist Device (pLVAD) – An Israeli startup, Magenta Medical, behind the world’s smallest heart pump has raised $55 million May 5, 2023
  • microRNA (miRNA) miR-483-5p has a key role in preventing stress-related anxiety by acting on its target gene Pgap2 that curbs the development of this type of anxiety May 3, 2023
  • Prediction of exact requirement of exogenous hormone doses in contraceptives to reduce health issues April 25, 2023
  • Alliance for Cancer Gene Therapy to honor Dr. Crystal Mackall with Edward Netter Leadership Award April 8, 2023
  • Creating a Twitter Space for @pharma_BI for Live Broadcasts March 14, 2023
  • The Vibrant Philly Biotech Scene: Recent Happenings & Deals March 11, 2023
  • Peak oxygen uptake (VO2peak) quantified fitness: Lifelong and late-onset athletes had higher VO2peak than non-athletes March 7, 2023
  • Merck’s sotatercept overachieves, PCSK9 inhibitor passes phase 2 March 6, 2023

• Archives

  Archives Select Month May 2023  (4) April 2023  (2) March 2023  (5) February 2023  (2) January 2023  (3) December 2022  (2) October 2022  (6) September 2022  (2) August 2022  (1) July 2022  (3) June 2022  (3) May 2022  (8) April 2022  (10) March 2022  (7) February 2022  (7) January 2022  (3) December 2021  (3) November 2021  (4) October 2021  (11) September 2021  (5) August 2021  (8) July 2021  (21) June 2021  (8) May 2021  (10) April 2021  (8) March 2021  (15) February 2021  (17) January 2021  (20) December 2020  (10) November 2020  (12) October 2020  (26) September 2020  (17) August 2020  (22) July 2020  (27) June 2020  (33) May 2020  (26) April 2020  (42) March 2020  (22) February 2020  (11) January 2020  (7) December 2019  (20) November 2019  (13) October 2019  (11) September 2019  (3) August 2019  (8) July 2019  (25) June 2019  (47) May 2019  (40) April 2019  (27) March 2019  (29) February 2019  (17) January 2019  (50) December 2018  (14) November 2018  (17) October 2018  (18) September 2018  (17) August 2018  (8) July 2018  (20) June 2018  (22) May 2018  (17) April 2018  (12) March 2018  (20) February 2018  (26) January 2018  (16) December 2017  (6) November 2017  (20) October 2017  (13) September 2017  (16) August 2017  (16) July 2017  (19) June 2017  (20) May 2017  (32) April 2017  (21) March 2017  (10) February 2017  (24) January 2017  (21) December 2016  (43) November 2016  (8) October 2016  (40) September 2016  (67) August 2016  (59) July 2016  (75) June 2016  (37) May 2016  (95) April 2016  (152) March 2016  (175) February 2016  (196) January 2016  (139) December 2015  (90) November 2015  (287) October 2015  (237) September 2015  (115) August 2015  (96) July 2015  (63) June 2015  (44) May 2015  (53) April 2015  (76) March 2015  (95) February 2015  (83) January 2015  (75) December 2014  (75) November 2014  (88) October 2014  (135) September 2014  (117) August 2014  (88) July 2014  (88) June 2014  (109) May 2014  (60) April 2014  (85) March 2014  (58) February 2014  (72) January 2014  (107) December 2013  (104) November 2013  (136) October 2013  (62) September 2013  (32) August 2013  (46) July 2013  (74) June 2013  (110) May 2013  (112) April 2013  (86) March 2013  (92) February 2013  (63) January 2013  (63) December 2012  (46) November 2012  (71) October 2012  (84) September 2012  (82) August 2012  (122) July 2012  (59) June 2012  (34) May 2012  (46) April 2012  (2)

• Categories

  Categories Select Category 3D Printing for Medical Application  (232)    3D Plotting Scaffolds  (43)    BioInks  (33)       Biopolymer Blend Open Porous  (17)       Dental Applications  (10)    BioPrinting in Regenerative Medicine  (74)       Cell Level  (14)       MicroEngineering Cell-Tissue & Systems  (30)       Tissue Engineering  (35)    Cardiovascular and Vascular Systems  (27)       Artificial Vascular Structures  (9)       Cardiovascular Tissue  (8)    Drug Development using MultiOrgan Chip  (11)    Drug Development/Formulation using 3D Printing  (8)    MEMS  (16)       Bio-MEMS  (12)    Organ-on-a-Chip  (11)    Programmable Sensors (Carbon Nano Tubes)  (5) 3rd Party IP: Drug DIscovery  (1) 4D Printing and Meta Materials  (9) Academic Publishing  (222)    Key Opinion Leaders in eScientific Publishing – Interviews with  (8) Advanced Drug Manufacturing Technology  (92)    Antimalarial Preparation  (8)    Autologous Cell Therapy  (11)    Automated Cell Processing  (12) Allergy and Infectious Diseases  (12) Alzheimer’s Disease  (158)    Etiology  (76)    Medical Device Therapies for Altzheimer’s Disease  (14)    Pharmacotherapy and Cell Activity  (48) Anticancer Resistance  (28) Art Exhibits on the Human Condition  (1) Art Inspires Science  (3) Artificial Heart  (2) Artificial Intelligence – General  (184)    An executive’s guide to AI  (9)    Artificial Intelligence – Breakthroughs in Theories and Technologies  (91)    Artificial Intelligence Applications in Health Care  (92)       Artificial Intelligence in CANCER  (25)       Artificial Intelligence in Health Care – Tools & Innovations  (54)    Artificial Intelligence in Medicine – Application for Diagnosis  (50)       Artificial intelligence applications for cardiology  (22)          AI-assisted Cardiac MRI  (9)       Artificial Intelligence in Psychiatry  (5)       Deep Learning in Pathology  (13)    Artificial Intelligence in Medicine – Applications in Therapeutics  (46)    Machine Learning  (40)       Deep Learning  (5)       Natural Language Processing (NLP)  (20)    Machine learning in predicting type 2 diabetes  (1) Auditory and vision  (13) Autism Spectrum Disorders  (10) Autoimmune Inflammatory DIseases  (19)    Crohn’s disease  (5)    Tolerance-inducing Autoimmune Disease Therapeutics  (2)    Ulcerative Colitis  (3) Autophagosome  (2) Bacterial Resistance  (25) Behavior  (26) Behavioral Genetics  (21) Big Data  (75)    Intelligent Information Systems  (46) Bio Instrumentation in Experimental Life Sciences Research  (364)    Analytical Instruments Industry  (5)    Microfuidics  (7) Bio-Ethics  (14) BioBanking  (33) Biodegradable Drug-eluting Material  (7) Bioengineering & reverse engineering design  (41) BioIT: BioInformatics  (142) BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceutical R&D Informatics, Clinical Genomics, Cancer Informatics  (123)    Advanced Computing Platform  (30)       Blockchain Transactions System  (6)          Platform for Content Monetization embedded Content Promotion  (1)    Pancreatic adenocarcinoma classifier  (3)    Simulation Modeling in NGS  (3) Biological Engineering  (40) Biological Networks  (189) Biological Networks, Gene Regulation and Evolution  (473)    Virology  (10) Biomarkers & Medical Diagnostics  (564)    VOC – Volatile Organic Compounds as BioMarkers  (2) Biomedical Measurement Science  (172) BioSimilars  (111) BioTechnology – Venture Creation  (125)    Foundations for supporting Science and Education  (12)    Philanthropy to Academic Institution  (2) BioTechnology – Venture Creation, Venture Capital  (105)    Seeking Talent  (3) BiVAD  (1) Blindness  (6) Bone Disease and Musculoskeletal Disease  (82) Brain Basis of Emotion  (5) Business Career Consideration  (1) Ca2+ triggered activation  (59) Calcium  (19) Calcium Signaling  (67) Calmodulin Kinase and Contraction  (34) Cancer – General  (176) Cancer and Current Therapeutics  (396)    interventional oncology  (42)       Breast Cancer – impalpable breast lesions  (17)       Prostate Cancer: Monitoring vs Treatment  (8) CANCER BIOLOGY & Innovations in Cancer Therapy  (1,091)    Anaerobic Glycolysis  (51)    Cachexia  (18)    Cancer Genomics  (69)       Circulating Tumor Cells (CTC)  (19)          Liquid Biopsy Chip detects an array of metastatic cancer cell markers in blood  (14)             mRNA  (5)          MagSifter chip  (1)       KRAS Mutation  (6)       Li-fraumeni syndrome.  (3)       TP53 – Germline mutations  (5)    cancer metabolism  (20)    Funding Opportunities for Cancer Research  (11)    Genomic Expression  (143)    Glioblastoma  (7)    Hexokinase  (14)    Loss of function gene  (18)    Metabolic Immuno-Oncology  (16)    Metastasis Process  (13)    Methylation  (31)    Microbiome and Responses to Cancer Therapy  (5)    Monoclonal Immunotherapy  (27)    mtDNA  (13)    Oxidative phosphorylation  (56)    Pancreatic cancer  (9)    Pyruvate Kinase  (27)    The NCI Formulary  (1)    tumor microenvironment  (13)    Warburg effect  (50) Cancer Informatics  (93) Cancer Prevention: Research & Programs  (125) Cancer Screening  (102) Cancer Vaccines: Targeting Cancer Genes for Immunotherapy  (25)    Engineering Enhanced Cancer Vaccines  (3) cancer-general  (1) Cardiac and Cardiovascular Surgical Procedures  (319)    Aortic Valve: TAVR, TAVI vs Open Heart Surgery  (86)       Prosthesis-Patient Mismatch (PPM) in TAVI vs SAVR  (1)       TAVI vs Open Heart Surgery  (5)       Transcatheter Aortic Valve Replacement via the Transcarotid Access  (1)       Transcaval TAVR Procedure  (2)       Valve-in-Valve Procedure  (3)    Atrial Fibrilation (a-Fib), Cardiac Pacing and Arrhythmias  (17)    BackBeat’s Cardiac Neuromodulation Therapy (CNT) bioelectronic therapy  (1)    CABG  (46)    Cancer Surgery of the Heart  (10)    Cardiovascular Fluid Management: algorithms  (1)    Heart Transplant  (14)    Heart-Lung Transplant  (9)    Implantation  (2)    Left Main Coronary Artery Disease (LMCAD)  (3)    Mechanical Assist Devices: LVAD, RVAD, BiVAD, Artificial Heart  (19)    Mitral Valve: Repair and Replacement  (63)       TMVR – Transcatheter Mitral Valve Repair  (4)    PCI  (104)       Bioresorbable Vascular Scaffold (BVS)  (3)       Invasive FFR for PCI  (2)       Multivessel PCI FFR Guidance  (1)       Robotic-assisted percutaneous coronary intervention  (1)       Stent Retriever in endovascular thrombectomy  (2)    Peripheral Arterial Disease & Peripheral Vascular Surgery  (62)       Abdominal Aorta  (19)       Carotid Artery  (15)       Limb ischemia  (4)       Thoracic Aorta  (15)    Pulmonary Valve Replacement and Repair  (2)    Renal Denervation  (20)    Replacement  (1)    Robotically assisted Cardiothoracic Surgery  (1)    Tricuspid Valve Repair  (6)    Vena Caval Filters: Device for Prevention of Pulmonary Embolism and Thrombosis  (1) Cardiovascular Pharmacogenomics  (168) Cargo  (3) Cell Biology  (320) Cell Biology, Signaling & Cell Circuits  (662)    Apoptosis  (16)    Autophagy-Modulating Proteins  (5)    “Antibody–enzyme conjugates”  (4)    Cell Processing System in Cell Therapy Process Development  (24)    Endoplasmic reticulum  (2)    Enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)  (3)    Ubiquitin  (9) Cerebrovascular and Neurodegenerative Diseases  (122)    Stroke  (8) Chemical Biology and its relations to Metabolic Disease  (460)    #BIGAxisSummit  (1)    Gut Microbiome and Obesity  (7) Chemical Genetics  (349) Child and Adolescent Psychiatry  (13) Childhood cancer  (15) Childhood malnutrition  (3) children  (1) Circulating Progenitor Cells  (27)    Bone marrow derived cells  (17)    Endothelial cells  (7)    Umbilical cord cells  (6) Clinical & Translational  (234) Clinical Diagnostics  (216)    Mass automation of plasma proteins  (13) Clinical Genomics  (135) Coagulation Therapy and Internal Bleeding  (83) Cognition  (46) Commercialization  (20) Components and IRB related issues  (4) Computational Biology/Systems and Bioinformatics  (464)    Computational Histopathology  (2)    Meta-analysis of transcriptome data  (8) Conference Coverage with Social Media  (475)    MassBio  (3) coronavirus  (18) COVID-19  (20) CRISPR/Cas9 & Gene Editing  (188)    CRISPR alternative for editing genes without cutting  (14)       CAST – Alternative to CRISPR/Cas9  (3)       Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration  (4)    CRISPR applied to Human Germ Line  (10)       Gene Editing Impact on Longevity  (4) CT  (19) Cytokines  (19) Cytoskeleton  (84) Developmental biology  (105) Diabetes Mellitus  (141)    Artificial Pancreas for Type 2 Diabetes  (1)    Artificial Pancreas for Type1 Diabetes  (5)    Gestational diabetes  (2) Diagnostic Immunology  (56) Diagnostics and Lab Tests  (127)    Liquid Biopsy: Circulating Tumor Cells in Urine and Blood  (8) Digital HealthCare – biotech & internet joint ventures  (46) Disease Biology  (332) Disease Biology, Small Molecules in Development of Therapeutic Drugs  (483) DNA repair  (71)    Apoptosis  (11)    Autophagy  (12)    Cell death pathways  (18)    Proteolysis  (8)    Proteosome  (8) Drug Delivery Platform Technology  (155)    Drug Carrier Design  (19)       Medication Remote Compliance Monitoring  (3)    Exosomes: Natural Carriers for siRNA Delivery  (9) Drug Toxicity  (74) Ecosystems & Industrial Concentration in the Medical Device Sector  (172)    Cardiac & Vascular Repair Tools Subsegment  (128)    Exec Compensation in the Cardiac & Vascular Repair Tools Subsegment  (14)    Massachusetts Niche Suppliers and National Leaders  (20) Electronic Health Record  (9) Embryology  (24) Empathy  (6) Endocrine Diseases  (59) Enzyme Induction  (45)    ion-transporting enzyme  (1)    K + -ATPase.  (1)    Na +  (2) Epigenetics and Environmental Factors  (31) Ethics and Leadership  (10) Executive Compensation – Big Pharma  (3) Fat soluble vitamins  (4) FDA  (68) FDA Regulatory Affairs  (355)    FDA, CE Mark & Global Regulatory Affairs: process management and strategic planning – GCP, GLP, ISO 14155  (52)    ISO 10993 for Product Registration: FDA & CE Mark for Development of Medical Devices and Diagnostics  (30) Fetal Ultrasound  (2) Fiction and medicine  (5) Frontiers in Cardiology and Cardiovascular Disorders  (916)    Acute Myocardial Infarction  (60)       Cardiogenic Shock  (4)    Anemia in CVD Patients  (6)    Cardio-Oncology  (4)    Cardiomyopathy  (57)    Cardiovascular Research  (183)       Myocardial metabolism, Myocardial ischemia, myocardial perfusion, Myocardial adenine nucleotide metabolism  (62)       Pre-Clinical Animal Model Development  (23)    Chronic Thromboembolic Pulmonary Hypertension (CTEPH) and Pulmonary Arterial Hypertension (PAH)  (19)    Cost of Inpatient Stay for Cardiovascular Diagnosis for Admission  (1)    Electrophysiology  (107)       Ablation Procedure vs Drug Therapy  (2)       Arrhythmia Detection with Machine Learning Algorithms  (6)       Cardiotoxic Risks of Immune Checkpoint Inhibitors  (1)       Genomic Analysis of EKG Electrophysiology Genomics  (2)       implantable cardioverter defibrillator (ICD) and External Defibrillation  (1)       implantable pacemaker  (2)       Rare heart rhythm disorders and Long QT syndrome (LQTS)  (5)    Epigenetics and Cardiovascular Risks  (55)    Heart Failure (HF)  (46)       Acute coronary syndrome  (6)       congestive heart failure  (17)    Medical Devices R&D and Inventions  (207)       Assist Devices: LV  (3)       RV  (1)       Stents & Tools  (89)       Valves & Tools  (64)    Origins of Cardiovascular Disease  (416)       Atherogenic Processes & Pathology  (177)       Congenital Heart Disease  (34)          Genetic Mutations in Congenital Heart Disease  (4)       inflammation independent of lipid levels  (11)       Systemic Inflammatory Diseases as CVD Risk  (10)    Pharmacotherapy of Cardiovascular Disease  (352)       HTN  (172)       HTN in Youth  (7)       Resident-cell-based  (43)       Subarachnoid Hemorrhage (SAH)  (1)       Transthyretin amyloid cardiomyopathy (ATTR-CM)  (1)    Spontaneous Coronary Artery Dissection (SCAD)  (6)    Stroke  (13)       endovascular thrombectomy  (5)    Vascular Diseases  (20)       mesenteric ischemia  (3) Future Pandemics Inform-graphics  (1) Gastroenterology  (37) Gene Regulation  (227) Gene Regulation and Evolution  (135) Genetics & Innovations in Treatment  (172) Genetics & Pharmaceutical  (199) Genome Biology  (958)    Exosomes  (24)    Gene Therapy & Gene Editing Development  (38)    mRNA Therapeutics  (17)    Mutagenesis  (26)    Single Cell Genomics  (22)    Single-cell sequencing  (18)    Variation in human protein-coding regions  (31) Genomic Endocrinology  (41) Genomic Testing: Methodology for Diagnosis  (412) Genomics Pharmacy  (37) Global Market of Medical Devices Technology  (2) Global Medical Publishers by Country  (3) Global Partnering & Biotech Investment  (45) GLP  (4) Glycobiology: Biopharmaceutical Production  (14) Glycobiology: Biopharmaceutical Production, Pharmacodynamics and Pharmacokinetics  (26) Health Care System by Country  (45)    AI Models in Healthcare  (6)    Centers for Medicare & Medicaid Services  (7)    Health in Israel  (2)    United States  (21)       Hospital-based Medical Innovations  (7)       Medical Recertification and Maintenance of Certification (MOC)  (1) Health Economics and Outcomes Research  (377)    Women Health  (14)       Heart and Brain Disease in Women  (3) Health Law & Patient Safety  (160)    and Bioethics  (13)    Biotechnology  (11)    Health Law Policy  (10) HealthCare IT  (136) Healthcare Reform  (110)    Accountable Care Organizations  (25)    Affordable Care Act  (29)       Repair  (1)       Repeal ACA  (1)       Replace  (1)    Federal Budget Appropriations  (25)    Healthcare costs and reimbursement  (54)    Indigent Nutrition  (13)    Medicare and Medicaid  (20)    Prescription Drugs Costs  (21)    Skilled Nursing Facilities  (6)    Technology Capital Expenses  (15)    Uninsured and Underinsured  (19) Hematology  (99)    Acute lymphocytic leukemia  (18)    Acute myelocytic leukemia  (21)    Hematopoiesis  (48)    Lymphoma  (21) History and physical exam  (6) Human aging  (27) Human Immune System in Health and in Disease  (235) Human Sensation and Cellular Transduction: Physiology and Therapeutics  (20) Image Processing/Computing  (41) Imaging-based Cancer Patient Management  (116) Immuno-Oncology & Genomics  (125)    mRNA platform in Drug DIscovery  (6) Immunodiagnostics  (126)    Cancer-Immune Interactions  (20)    CNS-Immune Interface  (3)    Neuronal Circuits  (4) Immunology  (112)    Adaptive Immune Response to Biomaterials and Tissue Repair  (9)    Antibody Responses Predict Antigen Exposure  (15)    Cytokine Receptor Structure  (7)    Human Antibody Response  (15)    Human Circulating Antibody Repertoire  (9)    Human Naive B Cell Repertoire  (8)    MHC Repertoires for Antigen Prediction  (8)    Protection Against Autoimmune Disease  (7)    Synthetic Immunology: Hacking Immune Cells  (12) Immunotherapy  (119)    CAR-T  (13)    combination immunotherapies.  (11)    Efficacy of Anti-Tumor T Cells  (11)    Engineering Better T Cells  (7)    Immune Engineering  (13)    Immune Modulatory  (13)    Integrin-targeted Combination Immunotherapy  (5)    Modulating Macrophages in Cancer Immunotherapy  (11)    NK Cell-Based Cancer Immunotherapy  (16)    Synergistic Innate and Adaptive Immunotherapy  (13) Income Disparity  (2) Infectious Disease & New Antibiotic Targets  (162)    Antibiotic resistance  (7)    Viral diseases  (37)       Myocarditis  (1) Infectious Disease Immunodiagnostics  (56)    Virology – Vector-borne DIsease  (17) Inflammasome  (26)    Anti-tumor necrosis factor drugs (TNF inhibitors)  (2) Innovation in Immunology Diagnostics  (105)    Universal Immune Cell Therapies (uICT)  (9) Innovations  (185)    R&D Expenditure  (8) Innovations in Neurophysiology & Neuropsychology  (142)    Age and Life Expectancy  (1)    autism spectrum disorder  (1)    Circadian Rhythm and Sleep  (6)    hNPCs  (1)    Nervous System Function  (2)    Relapsing Multiple Sclerosis  (1) Intellectual Property  (75)    Disputes and Settlements  (8)    IP Valuation Models – Pricing Intangible Assets  (5)    Patent Law in Biotech  (12) Intellectual Property, Innovations, Commercialization, Investment in technological breakthrough  (106) International Global Work in Pharmaceutical  (188) Interventional Oncology: Radiofrequency Ablation, Transarterial Chemoembolization, Microwave Ablation and Irreversible Electroporation (IRE)  (12) Interviews with Scientific Leaders  (298)    Albany Medical Center Prize in Medicine and Biomedical Research  (1)    Annual Breakthrough Prize  (2)    Annual Lewis S. Rosenstiel Award  (1)    Awards in Cardiology and Cardiovascular Medicine  (3)    CEOs of Biotech Companies  (2)    Gerald D Aurbach Award for Outstanding Translational Research  (1)    Interviews with Key Opinion Leaders (KOLs)  (7)    James Prize in Science and Technology Integration  (1)    Jessie Stevenson Kovalenko Medal – Medical Sciences  (1)    Lemelson-MIT Prize  (1)    Life Sciences Breakthrough Prize  (3)    Mosteller Statistician of the Year Award  (1)    Mourning the Loss of a Scientific Leader  (2)    National Academy of Sciences AWARDS  (2)    Nobel Prize WInners  (20)    Noble Prize (Not Nobel Prize)  (1)    Paul Marks Prize for Cancer Research  (1)    Russ Prize recognizes bioengineering achievements worldwide  (1)    The Dan David Prize  (5)    Warren Alpert Foundation Prize Recipients  (3)    Wolf Prize  (1)    Wolf Prize in Medicine  (1)    women in science  (3) Investment in Technological Breakthrough  (59) Ionic Transporters Na+  (25) IP Development by LPBI Group Team  (9) IP Development by LPBI Group Team & Other Organizations  (7) ISO 14155  (3) Joint Venture – SBH & M3DP: SOP and Arrangements  (1) Justice & Law  (1) K  (15) Lab-on-a-chip  (2) Landscape  (1) Lasers and photonics  (18)    Midrange IR spectroscopy  (1) Law and Medicine Conflicts  (13) Leadership, Power, Social Interlocking Connections  (13) Lipid metabolism  (108)    Fatty acids  (37)    Lipids  (37)    PCSK9 Inhibitor Therapy  (19) Lipidomics  (10) Liposome  (3) Liver & Digestive Diseases Research  (119) LPBI Group, e-Scientific Media, DFP, R&D-M3DP, R&D-Drug Discovery, US Patents: SOPs and Team Management  (129)    Award Nominations  (5)    BioMed e-Books e-Series by LPBI Group  (8)    Feedback from Investors: LPBI Portfolio of Five Businesses  (2)    LPBI Group Founder – Aviva Lev-Ari  (22)    PhD  (1)    RN  (1) LPBI Management  (15) Massachusetts Academy of Sciences (MAS)    (2) Materials Science & Engineering  (36)    Organic BioElectronics  (1) Math  (13)    Great Discoveries  (7) Mechanical Assist Devices: LVAD  (4) Medical and Population Genetics  (190) Medical Devices R&D Investment  (239)    21st Century Cures Act  (2)    CE Mark & Global Regulatory Affairs: process management and strategic planning – GCP  (13)    Rhythm management device hardware: dual-chamber pacemakers  (1)       Systolic HTN  (1) Medical Imaging Technology  (55) Medical Imaging Technology, Image Processing/Computing, MRI, CT, Nuclear Medicine, Ultra Sound  (160)    Circumferential-Intravascular-Radioluminescence-Photoacoustic-Imaging (CIRPI)  (3)    Echocardiography  (2)    MRI  (17)    Noninvasive Diagnostic Fractional Flow Reserve (FFR) CT  (5)    Ultra Sound  (7) Melatonin & Circadian Regulation  (9) memory loss  (1) Metabolism  (235)    Biochemical pathways  (141)       Enzymes and isoenzymes  (71)          Dehydrogenase  (15)          Kinase  (27)          Phosphatase  (8)          Phosphorylase  (21)          tyrosine decarboxylases  (2)    Inosine nucleotides  (8)    Leloir pathway  (6)    microbiome  (6)    Pentose monophosphate shunt  (14)    Pyridine nucleotides  (28)       Pyridine nucleotide transhydrogenase  (7) Metabolomics  (317) Methods  (37) Mg++  (10) Microbiologial genetics  (33) Microbiology  (67)    Virology  (14) Micronutrients  (15) Microvesicle  (6) Microwave Ablation and Irreversible Electroporation (IRE)  (1) Mobile Healthcare  (4) Molecular Genetics & Pharmaceutical  (374)    Organoids  (3) Monoclonal antibody therapy  (13) Mutant Gene Expression  (41) Myocardial adenine nucleotide metabolism  (5) Myocardial Ischemia  (25) Myocardial Metabolism  (35) Na-K transport  (39) Na-K-ATPase  (26) Nanotechnology for Drug Delivery  (96) Nephrology  (46) Nephrology & Regenerative medicine  (9) Neurodegenerative Diseases  (86)    hNPCs  (3)    MS  (5) Neurohumoral Transmission  (66)    Ca2+ triggered activation  (19)    Calmodulin  (12)    Parkinson’s disease dyskinesia levodopa  (3)    PKC  (13)    Synaptic vesicle  (20) Neurological Diseases  (120) Neuroscience  (126) Next Generation Sequencing (NGS)  (24)    Nanopore sequencing  (1) NIH Common Fund  (1) Nitric Oxide in Health and Disease  (135) Nuclear Medicine  (11) Nutrigenomics  (67) Nutrition  (193)    Nutritional Supplements: Atherogenesis, lipid metabolism  (48) Nutrition and Phytochemistry  (60)    Minerals in Medicine  (4)    Plant extract  (22) Nutrition Disorders  (29) Nutritional Supplements: Atherogenesis  (30) Obesity  (17) Oligonucleotide Therapeutics & Delivery  (7) Oncolytic virus & OncoViro-Therapy  (21)    Synthetic Virology  (1) Organ-on-a-Chip & 3D Printing in Life Sciences  (7) Pain: Etiology, Genetics & Innovations in Treatment  (24) Parasitology  (5)    Malaria  (4)    Tropical diseases  (1) Patents  (34) Patient Experience  (64)    Art therapy  (1)    Hospital reputation  (7)    Humor  (1)    Music therapy  (2)    Pain Alleviation  (7)    Patient Outlook  (28)    Reputation of Interventionist  (4)    Support Staff  (13)    Supportive therapies  (6)       laughfter  (1)    Surgical Procedure  (7) Patient Experience: Personal Memories of Invasive Medical Intervantion  (30) Patient’s Voice: Personal Experience with Invasive Medical Procedures  (18) Perioperative Statins at Noncardiac Surgery  (1) Personal Health Applications: Tech Innovations serves HealhCare  (35) Personalized and Precision Medicine & Genomic Research  (715)    Longevity  (1)    New Drug Approval  (4)    Patient-centered Medicine  (34)       cell-based therapy  (8)       stem cell biology and patient-specific  (6)    Personalized Medicine Coalition  (8)    Precision Cancer Medicine  (17) Phagophore  (1) Pharmaceutical Analytics  (258)    Pharmacologic toxicities  (61) Pharmaceutical Discovery  (106)    Rapid automation of plasma protein pools  (16) Pharmaceutical Drug Discovery  (195)    Drug Development Process  (52)       Drug Discovery Chemistry  (27)    drug repurposing  (9) Pharmaceutical Industry Competitive Intelligence  (338)    Pharmacovigilance  (6)    Value-based Drug Pricing  (8) Pharmaceutical R&D Informatics  (42) Pharmaceutical R&D Investment  (297) Pharmacodynamics and Pharmacokinetics  (23) Pharmacogenomics  (156) Photography Collection  (1) Physics  (12) Placenta  (7) Population genetics  (25) Population Health Management  (190)    Evolution of Biology Through Culture  (13)    U.S. Employment-to-Population Ratio  (8) Population Health Management, Genetics & Pharmaceutical  (621)    COVID-19  (155)       Biomarkers: Inflammation  (36)       Cancer Researchers Fighting COVID-19  (14)       COVID-19 effects on Human Heart  (15)       COVID-19: Pandemic Surgery Guidance  (19)       Economic Impact of Coronavirus Pandemic  (41)       number of asymptomatic infections  (27)       Treatment Protocols for COVID-19  (62)    SARS-CoV-2  (138)       Coronavirus Gene Expression  (65)          SARS-CoV-2 circulating variants   (14)          SARS-CoV-2 Viral Variants  (18)       Glycosylation and its Role in SARS-CoV-2 Viral Pathogenesis  (2)       Immune-Mediation (independent immunopathology: lung and reticuloendothelial system)  (29)       Mechanisms of infection by SARS-CoV-2  (21)       SAR-Cov-2 a vasculotropic (blood vessels) RNA Virus  (35)          SARS-COV2 Hijacking the Complement and Coagulation Systems  (19)       Seasonality & Environmental Factors in Resurgence  (26)       Serology tests for coronavirus antibodies  (44)       T-cell response to SARS-CoV-2 infection  (14)       Vaccinology  (51)          Mechanism of Thrombosis with AZ & J&J COVID-19 Vaccines  (5)       Virtual Drug Molecule Screening targeting SAR-CoV-2 proteins  (8)    Virus Infective Acute Respiratory Syndrome: SARS-CoV  (92) Population Health Management, Nutrition and Phytochemistry  (150) Preimplantation Genetic Diagnosis and Reproductive Genomics  (12) Protein-energy malnutrition  (11) Proteomics  (359)    Amino acids  (51)    Proteins  (133) Pulmonary diseases  (16)    Lung and pulmonology  (15) Pulmonary pathology  (8) Radio Frequency (RF)-based Surgical Solutions  (2) REAL TIME Conference Coverage Twitter’s Hashtags and Handles per Presentation/session  (30) Regenerative Biology and Medicine  (91) Regulated Clinical Trials: Design, Methods, Components and IRB related issues  (265) Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics  (112) Reproductive Biology & Bio Instrumentation  (77) RNA Biology  (80)    RNA interference (RNAi) therapeutic  (4) RNA Biology, Cancer and Therapeutics  (61) RVAD  (1) SBIR, SBA, NIH, NSF  (3) Schizophrenia  (16) Scientific & Biotech Conferences: Press Coverage  (172) Scientific Publishing  (606)    Curation  (583)       Curation methodology  (40)       De novo synthesis  (16)       Dialectic  (17)       Discovery process  (71)       Evolutionary cognition  (52)       Experimental validation  (90)       Explanatory  (91)       Historical relevance  (71)       Technology Advance Assessment of  (69)       Theoretic convergence  (27)    Open Access Journals  (36) Scientist: Career considerations  (193)    Big Data & Analytics  (14)    Data Science  (10)    Women in Life Sciences  (11) Scoop.it  (19) Sensors & Analytics  (17) Sepsis  (2) Severe Autism  (3) Signaling  (99)    Phosphorylation  (41)    S-nitrosylation  (12)    Ubiquitinylation  (32) Signaling & Cell Circuits  (128) single cell sequencing  (1) Small Molecules in Development of Therapeutic Drugs  (69) Social Development  (15) Specialized 3D BioPrinters (Cornea  (1) Statistical Methods for Research Evaluation  (136) Stem Cells for Regenerative Medicine  (174)    Cardiac muscle regeneration  (18)    Competition in regenerative stem cell science  (17)    Human neural progenitor cells  (7)    Skeletal muscle regeneration  (8) STORM  (2) Stress Disorders  (18) Substance Abuse  (4) Systemic Inflammatory Response Related Disorders  (159)    Inflammatory Pathophysiology  (7) Technology Transfer: Biotech and Pharmaceutical  (351) therapeutics  (2) Tissue Engineering and Regenerative Medicine  (21) Tissue Microenvironment  (3) Transarterial Chemoembolization  (2) Transcriptomics  (42) Transformative Technologies in Healthcare  (13) Translational Science  (224)    Best evidence  (52)    Bias measurement tools  (2)    Evidence-based decision-making  (27)    Inferential analysis  (25)    Intra-rater error  (1)    Quality Assurance  (8)    Random Error  (2)    Systematic Error (Bias)  (6)    Total error  (2)    Translational Effectiveness  (49)    Translational Research  (88) Trends in Global Economy  (6) Uncategorized  (1,008) Unfolded Protein Response (UPR)  (5) US and Global Economy: Trends and Findings  (8) Venture Capital  (44)    Income Geographic Distribution  (2)    Institutional Capital Raised by Female Founders  (5) virology  (9) Vision  (6) Voices of Patients and Healthcare Providers  (21) Water Transporters  (7) Wearable Tech + Digital Health  (3) Anemia  (21) Neutropenia  (8) Neutrophilia  (9) Platelet count disorder  (9) Folate and B12  (7) Iron deficiency  (5) Myelodysplasia  (12) Myelofibrosis  (10)

• Meta

  • Log in
  • Entries feed
  • Comments feed
  • WordPress.org

• • 2012pharmaceutical
  • Amandeep Kaur
  • Aashir Awan, Phd
  • Abhisar Anand
  • Adina Hazan
  • Alan F. Kaul, PharmD., MS, MBA, FCCP
  • alexcrystal6
  • anamikasarkar
  • apreconasia
  • aviralvatsa
  • David Orchard-Webb, PhD
  • danutdaagmailcom
  • Demet Sag, Ph.D., CRA, GCP
  • Dror Nir
  • dsmolyar
  • Ethan Coomber
  • evelinacohn
  • Gail S Thornton
  • Irina Robu
  • jayzmit48
  • jdpmd
  • jshertok
  • kellyperlman
  • Ed Kislauskis
  • larryhbern
  • Madison Davis
  • marzankhan
  • megbaker58
  • ofermar2020
  • Dr. Pati
  • pkandala
  • ritusaxena
  • Rick Mandahl
  • sjwilliamspa
  • Srinivas Sriram
  • stuartlpbi
  • Dr. Sudipta Saha
  • tildabarliya
  • zraviv06
  • zs22