iPhone Application: The CareKit by Apple – Embedded Algorithms in every Diagnosis Tool
Reporter: Aviva Lev-Ari, PhD, RN
Apple’s CareKit: Useful Tool for Health and the Encryption Debate
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Endovascular procedures associated with lower mortality, LOS, cost vs. surgical bypass: Results of Critical Limb Ischemia National Study
Reporter: Aviva Lev-Ari, PhD, RN
SOURCE
Mar. 21, 2016 /
a new comprehensive analysis of a nationwide hospital sample of nearly 650,000 patients conducted from 2003 to 2011.
Mehdi Shishehbor, DO, MPH, PhD
“We found that rates of surgery for CLI are going down while rates of endovascular procedures are going up,” says Mehdi Shishehbor, DO, MPH, PhD, Director of Endovascular Services at Cleveland Clinic. “Meanwhile hospital admissions for CLI have remained constant even as rates of amputation and death from CLI have gone down. This suggests there’s something at work other than improved medical therapy for CLI.”
Dr. Shishehbor led the Cleveland Clinic-conducted analysis, which was just published in Journal of the American College of Cardiology and will also be presented at the 65th Annual Scientific Session of the American College of Cardiology (ACC.16) in Chicago in early April.
Key findings
The researchers’ key findings are reflected in the figure below and include the following:
Figure. Nationwide trends in CLI hospital admissions and outcomes over time, based on the analysis by Shishehbor and colleagues. Reprinted from Agarwal S, Sud K, Shishehbor MH, J Am Coll Cardiol. 2016 Mar 21 [Epub ahead of print], ©2016, with permission from the American College of Cardiology Foundation.
- The annual rate of CLI admissions remained relatively constant (at ~150/100,000 population) throughout the 2003-2011 period despite a progressive increase in the rate of admissions for PAD. “The rise in PAD might be secondary to the rise in prevalence of cardiovascular risk factors, which we observed,” notes Dr. Shishehbor. “An increase in the rate of PAD-related admissions, with the constant rate of CLI-related admissions, might suggest early detection of PAD, leading to improved PAD management and the relative stabilization of CLI rates.”
- The proportion of patients with CLI undergoing surgical revascularization declined significantly during the study period (from 13.9 percent in 2003 to 8.8 percent in 2011) while the proportion undergoing endovascular treatment rose significantly (from 5.1 percent to 11.0 percent).
- There was a steady and significant decline in rates of in-hospital death and major amputation across the study period among patients with CLI as well as a significant overall decline in mean length of stay. Despite these improvements, mean hospitalization cost remained unchanged throughout the study period.
- Compared with surgical revascularization, endovascular treatment of CLI was associated with significantly lower in-hospital mortality, mean LOS and mean hospitalization cost — even after adjustment for potential confounders — despite statistically comparable rates of major amputation.
SOURCE
Posted in Peripheral Arterial Disease & Peripheral Vascular Surgery | Tagged critical limb ischemia (CLI), endovascular procedures, Journal of the American College of Cardiology, mehdi shishehbor, peripheral artery disease (PAD) | Leave a Comment »
Wearable Tech + Digital Health NYC and NeuroTech NYC, New York Academy of Sciences, June 7 – 8, 2016
Wearable Tech + Digital Health NYC and NeuroTech NYC, New York Academy of Sciences, June 7 – 8, 2016
Reporter: Aviva Lev-Ari, PhD, RN
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SOURCE
From: Lisa Weiner Intrator <lisa=applysci.com@mail100.atl71.mcdlv.net> on behalf of Lisa Weiner Intrator <lisa@applysci.com>
Reply-To: Lisa Weiner Intrator <lisa@applysci.com>
Date: Wednesday, March 23, 2016 at 4:40 AM
To: <AvivaLev-Ari>, <PhD>, Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>
Subject: Join MIT, TAU, DARPA, UnitedHealth, Takeda, Mt Sinai, neurosteer, Harvard, NASA at Wearable Tech + Digital Health + NeuroTech NYC – June 7-8, 2016
Posted in Digital HealthCare – biotech & internet joint ventures, Scientific & Biotech Conferences: Press Coverage | Leave a Comment »
Scientists eliminate HIV1 DNA from the genome and prevent reinfection
Reporter: Aviva Lev-Ari, PhD, RN
A specialized gene editing system designed by scientists at the Lewis Katz School of Medicine at Temple University is paving the way to an eventual cure for patients infected with HIV, the virus that causes AIDS. In a study published online this month in the Nature journal, Scientific Reports, the researchers show that they can both effectively and safely eliminate the virus from the DNA of human cells grown in culture.
According to senior investigator on the new study, Kamel Khalili, PhD, Laura H. Carnell Professor and Chair of the Department of Neuroscience, Director of the Center for Neurovirology, and Director of the Comprehensive NeuroAIDS Center at the Lewis Katz School of Medicine at Temple University (LKSOM), “Antiretroviral drugs are very good at controlling HIV infection. But patients on antiretroviral therapy who stop taking the drugs suffer a rapid rebound in HIV replication.” The presence of numerous copies of HIV weakens the immune system and eventually causes acquired immune deficiency syndrome, or AIDS.
Curing HIV/AIDS – which has claimed the lives of more than 25 million people since it was first discovered in the 1980s – is the ultimate goal in HIV research. But eliminating the virus after it has become integrated into CD4+ T-cells, the cells primarily infected with HIV, has proven difficult. Recent attempts have focused on intentionally reactivating HIV, aiming to stimulate a robust immune response capable of eradicating the virus from infected cells. However, to date, none of these “shock and kill” approaches has been successful.
Dr. Khalili and colleagues decided to try a different approach, specifically targeting HIV-1 proviral DNA (the integrated viral genome) using uniquely tailored gene editing technology. Their system includes a guide RNA that specifically locates HIV-1 DNA in the T-cell genome, and a nuclease enzyme, which cuts the strands of T-cell DNA. Once the nuclease has edited out the HIV-1 DNA sequence, the loose ends of the genome are reunited by the cell’s own DNA repair machinery.
In previous work, Dr. Khalili’s team had demonstrated the ability of their technology to snip out HIV-1 DNA from human cell lines. In their latest study, however, they concentrated on latently and productively infected CD4+ T cells to show not only that the technology eliminates the virus from cells but also that its persistent presence in HIV-1-eradicated cells actually protects them against reinfection. More importantly, they carried their work over to ex vivo experiments, in which T-cells from patients infected with HIV were grown in cell culture, showing that treatment with the gene editing system can suppress viral replication and dramatically reduce viral load in patient cells.
Sourced through Scoop.it from: www.templehealth.org
Posted in DNA repair, Virology | Leave a Comment »
Black fever parasite beats drugs by adding just two DNA bases to its genome
Reporter: Aviva Lev-Ari, PhD, RN
Wellcome Trust Sanger Institute scientists show how the parasite responsible for the neglected tropical disease Black Fever (visceral leishmaniasis) can become immune to drug treatment. Studying the whole genomes of more than 200 samples of Leishmania donovani revealed that the addition of just two bases of DNA to a gene known as LdAQP1 stops the parasite from absorbing antimonial drugs.
While antimonials are no longer the first-line treatment for the disease, the discovery does show that whole-genome sequencing of L. donovani parasites could be used to study and track the emergence of resistance to frontline drugs – alerting health workers to potential hot spots of resistance.
Black Fever is the second most deadly parasitic disease after malaria, affecting nearly 300,000 people every year and killing up to 50,000. The parasite is mainly found in the Indian subcontinent, where up to 80 per cent of the disease occurs. To best understand how the parasite evolves and track the spread of drug resistance, researchers need a way to survey and monitor the parasite’s population structure. Unfortunately standard techniques to do this have proved fruitless because the strains of L. donovani parasite are so genetically similar.
Exploring the genetic landscape of L. donovani at such depth and breadth yielded new insights into the parasites’ ability to develop drug resistance, and its evolutionary history. In particular, the researchers found that the insertion of just two bases of DNA into the genome of approximately 35,000,000 bases helped the parasite to overcome antimonial drugs.
Sourced through Scoop.it from: www.sanger.ac.uk
Posted in DNA repair | Leave a Comment »
Best in Precision Medicine: RNA May Surpass DNA in Precision Medicine
Curator: Larry H. Bernstein, MD, FCAP
2.1.5.21 Best in Precision Medicine: RNA May Surpass DNA in Precision Medicine, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
- “A more complicated application of CRISPR technology is to use it for gene activation,” adds Dr. Tedesco. “Cellecta plans to optimize this application to bring forth highly efficient, inexpensive, high-throughput genetic screens based on their pooled libraries.
RNA May Surpass DNA in Precision Medicine
http://www.genengnews.com/gen-news-highlights/rna-may-surpass-dna-in-precision-medicine/81252507/
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Scientists based at the Translational Genomics Research Institute have published a review heralding the promise of RNA sequencing (RNA-seq) for precision medicine. The scientists also note that progress will be needed on analytical, bioinformatics, and regulatory fronts, particularly in light of the transcriptome’s variety, dynamism, and wealth of detail. In this image, one aspect of RNA-seq is shown, the alignment with intron-split short reads. It reflects the alignment of mRNA sequence obtained via high-throughput sequencing and the expected behavior of the alignment to the reference genome when the read falls in an exon–exon junction. [Rgocs, Wikipedia]
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It’s not an either/or situation. Both DNA sequencing and RNA sequencing hold clinical promise—diagnostically, prognostically, and therapeutically. It must be said, however, that RNA sequencing reflects the dynamic nature of gene expression, shifting with the vagaries of health and disease. Also, RNA sequencing captures more biochemical complexity, in the sense that it allows for the detection of a wide variety of RNA species, including mRNA, noncoding RNA, pathogen RNA, chimeric gene fusions, transcript isoforms, and splice variants, and provides the capability to quantify known, predefined RNA species and rare RNA transcript variants within a sample.
All these potential advantages were cited in a paper that appeared March 21 in Nature Reviews Genetics, in an article entitled, “Translating RNA Sequencing into Clinical Diagnostics: Opportunities and Challenges.” The paper, contributed by scientists based at the Translational Genomics Research Institute (TGen), was definitely optimistic about the clinical utility of RNA sequencing, but it also highlighted the advances that would have to occur if RNA sequencing is to achieve its promise.
In general, the very things that make RNA sequencing so interesting are the same things that make it so challenging. RNA sequencing would take the measure of a world—the transcriptome—that is incredibly rich. To capture all the relevant subtleties of the transcriptome, scientists will have to develop sensitive, precise, and trustworthy analytical techniques. What’s more, scientists will need to find efficient and reliable means of processing and interpreting all of the transcriptome data they will collect. Finally, they will need to continue integrating RNA-based knowledge with DNA-based knowledge. That is, RNA sequencing results can be used to guide the interpretation of DNA sequencing results.
In their Nature Reviews Genetics paper, the TGen scientists review the state of RNA sequencing and offer specific recommendations to enhance its clinical utility. The TGen scientists make a special point about the promise held by extracellular RNA (exRNA). Because exRNA can be monitored by simply taking a blood sample, as opposed to taking a tumor biopsy, it could serve as a noninvasive diagnostic indicator of disease.
“Detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq represent some of the most immediate opportunities,” wrote the authors. “However, it is the diversity of RNA species detected through RNA-seq that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including the potential of extracellular RNAs as non-invasive diagnostic indicators of disease.”
The first test measuring exRNA was released earlier this year, the paper said, for use measuring specific exRNAs in lung cancer patients. And, the potential for using RNA-seq in cancer is expanding rapidly. Commercial RNA-seq tests are now available, and they provide the opportunity for clinicians to profile cancer more comprehensively and use this information to guide treatment selection for their patients.
In addition, the authors reported on several recent applications for RNA-seq in the diagnosis and management of infectious diseases, such as monitoring for drug-resistant populations during therapy and tracking the origin and spread of the Ebola virus.
Despite these advances, the authors also sounded a few cautionary notes. “There are currently few agreed upon methods for isolation or quantitative measurements and a current lack of quality controls that can be used to test platform accuracy and sample preparation quality,” they wrote. “Analytical, bioinformatics, and regulatory challenges exist, and ongoing efforts toward the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.”
Overall, the authors remain hopeful that precision medicine will embrace RNA sequencing. For example, lead author Sara Byron, research assistant professor in TGen’s Center for Translational Innovation, said, “RNA is a dynamic and diverse biomolecule with an essential role in numerous biological processes. From a molecular diagnostic standpoint, RNA-based measurements have the potential for broad application across diverse areas of human health, including disease diagnosis, prognosis, and therapeutic selection.”
Gene Editing Casts a Wide Net
With CRISPR, Gene Editing Can Trawl the Murk, Catching Elusive Phenotypes amidst the Epigenetic Ebb and Flow
http://www.genengnews.com/gen-articles/gene-editing-casts-a-wide-net/5713/
Gene-editing advances will not only open new avenues toward curing genetic diseases but will also rapidly increase the pace of new scientific discoveries about human and other types of genomes. [iStock/adventtr]
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Genome editing, a much-desired means of accomplishing gene knockout, gene activation, and other tasks, once seemed just beyond the reach of most research scientists and drug developers. But that was before the advent of CRISPR technology, an easy, versatile, and dependable means of implementing genetic modifications. It is in the process of democratizing genome editing.
CRISPR stands for “clustered, regularly interspaced, short palindromic repeats,” segments of DNA that occur naturally in many types of bacteria. These segments function as part of an ancient immune system. Each segment precedes “spacer DNA,” a short base sequence that is derived from a fragment of foreign DNA. Spacers serve as reminders of past encounters with phages or plasmids.
The CRISPR-based immune system encompasses several mechanisms, including one in which CRISPR loci are transcribed into small RNAs that may complex with a nuclease called CRISPR-associated protein (Cas). Then the RNA guides Cas, which cleaves invading DNA on the basis of sequence complementarity.
In the laboratory, CRISPR sequences are combined with a short RNA complementary to a target gene site. The result is a complex in which the RNA guides Cas to a preselected target.
Cas produces precise site-specific DNA breaks, which, with imperfect repair, cause gene mutagenesis. In more recent applications, Cas can serve as an anchor for other proteins, such as transcriptional factors and epigenetic enzymes. This system, it seems, has almost limitless versatility.
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Edited Stem Cells
The Sanger Institute Mouse Genetic Program, along with other academic institutions around the world, provides access to thousands of genetically modified mouse strains. “Genetic engineering of mouse embryonic stem (ES) cells by homologous recombination is a powerful technique that has been around since the 1980s,” says William Skarnes, Ph.D., senior group leader at the Wellcome Trust Sanger Institute.
“A significant drawback of the ES technology is the time required to achieve a germline transmission of the modified genetic locus,” he continues. “While we have an exhaustive collection of modified ES cells, only about 5,000 knockout mice, or a quarter of mouse genome, were derived on the basis of this methodology.”
The dominant position of the mouse ES cell engineering is now effectively challenged by the CRISPR technology. Compared with very low rates of homologous recombination in fertilized eggs, CRISPR generates high levels of mutations, and off-target effects may be so few as to be undetectable.
“We used the whole-genome sequencing to thoroughly assess off-target mutations in the offspring of CRISPR-engineered founder animals,” informs Dr. Skarnes. “A mutated Cas9 nuclease was deployed to increase specificity, resulting in nearly perfect targeting.”
Dr. Skarnes explains that the major mouse genome centers are now switching to CRISPR to complete the creation of the world-wide repository of mouse knockouts. His own research is now focused on genetically engineered induced pluripotent stem cells (iPSCs). These cells are adult cells that have been reprogrammed to an embryonic stem cell–like state, and are thus devoid of ethical issues associated with research on human embryonic stem cells. The ultimate goal is to establish a world-wide panel of reference iPSCs created by high-throughput genetic editing of every single human gene.
“We are poised to begin a large-scale phenotypic analysis of human genes,” declares Dr. Skarnes. His lab is releasing the first set of functional data on 100 DNA repair genes. “By knocking out individual proteins involved in DNA repair and sequencing the genomes of mutant cells,” declares Dr. Skarnes, “we hope to better understand the mutational signatures that occur in cancer.”
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Pooled CRISPR Libraries
Researchers hope to gain a better understanding of the mutational signatures found in cancers by using CRISPR techniques to knock out individual proteins involved in DNA repair and then sequencing the genomes of mutant cells. [iStock/zmeel]Connecting a phenotype to the underlying genomics requires an unbiased screening of multiple genes at once. “Pooled CRISPR libraries provide an opportunity to cast a wide net at a reasonably low cost,” says Donato Tedesco, Ph.D., lead research scientist at Cellecta. “Screening one gene at a time on genome scale is a significant investment of time and money that not everyone can afford, especially when looking for common genetic drivers across many cell models.”
Building on years of experience with shRNA libraries, Cellecta is uniquely positioned to prepare pooled CRISPR libraries for genome-wide or targeted screens of gene families. While shRNA interferes with gene translation, CRISPR disrupts a gene and the genomic level due to imperfections in the DNA repair mechanism.
To determine if these different mechanisms for inactivating genes affect the results of genetic screens, the team conducted a side-by-side comparison of Cellecta’s Human Genome-Wide Module 1 shRNA Library, which expresses 50,000 shRNA targeting 6,300 human genes, with the library of 50,000 gRNA targeting the same gene set. The concordance between approaches was very high, suggesting that these technologies may be complementary and used for cross-confirmation of results.
Also, a recently completed Phase I NIH SBIR Grant was used to create and test guiding strand RNA (sgRNA) structures to drastically improve efficiency of gene targeting. For this work, Cellecta used a pool library strategy to simultaneously test multiple sgRNA structures for their efficiency and specificity. An early customized Cellecta pooled gRNA library was successfully utilized for screening for epigenetic genes. This particular screen is highly dependent on a complete loss of function, and could not have been accomplished by shRNA inhibition.
Scientists from Epizyme interrogated 600 genes in a panel of 100 cell lines and, in addition to finding many epigenetic genes required for proliferation in nearly all cell lines, were able to identify validate several essential epigenetic genes required only in subsets of cells with specific genetic lesions. In other words, pooled cell line screening was able to distinguish targets that are likely to produce toxic side effects in certain types of cancer cells from gene targets that are essential in most cells.
“A more complicated application of CRISPR technology is to use it for gene activation,” adds Dr. Tedesco. “Cellecta plans to optimize this application to bring forth highly efficient, inexpensive, high-throughput genetic screens based on their pooled libraries.
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Chemically Modified sgRNA
Scientists based at Agilent Research Laboratories and Stanford University worked together to demonstrate that chemically modified single guide RNA can be used to enhance the genome editing of primary hepatopoietic stem cells and T cells. This image, which is from the Stanford laboratory of Matthew Porteus, M.D., Ph.D., shows CD34+ human hematopoietic stem cells that were edited to turn green. Editing involved inserting a construct for green fluorescent protein. About 1,000 cells are pictured here.Researchers at Agilent Technologies applied their considerable experience in DNA and RNA synthesis to develop a novel chemical synthesis method that can generate long RNAs of 100 nucleotides or more, such as single guide RNAs (sgRNAs) for CRISPR genome editing. “We have used this capability to design and test numerous chemical modifications at different positions of the RNA molecule,” said Laurakay Bruhn, Ph.D., section manager, biological chemistry, Agilent.
Agilent Research Laboratories worked closely with the laboratory of Matthew Porteus, M.D., Ph.D., an associate professor of pediatrics and stem cell transplantation at Stanford University. The Agilent and Stanford researchers collaborated to further explore the benefits of chemically modified sgRNAs in genome editing of primary hematopoetic stem cells and T cells.
Dr. Porteus’ lab chose three key target genes implicated in the development of severe combined immunodeficiency (SCID), sickle cell anemia, and HIV transmission. Editing these genes in the patient-derived cells offers an opportunity for novel precision therapies, as the edited cells can renew, expand, and colonize the donor’s bone marrow.
Dr. Bruhn emphasized the importance of editing specificity, so that no other cellular function is affected by the change. The collaborators focused on three chemical modifications strategically placed at each end of sgRNAs that Agilent had previously tested to show they maintained sgRNA function. A number of other optimization strategies in cell culturing and transfection were explored to ensure high editing yields.
“Primary cells are difficult to manipulate and edit in comparison with cell lines already adapted to cell culture,” maintains Dr. Bruhn. Widely varied cellular properties of primary cells may require experimental adaptation of editing techniques for each primary cell type.
The resulting data showed that chemical modifications can greatly enhance efficiency of gene editing. The next step would translate these findings into animal models. Another advantage of chemical synthesis of RNA is that it can potentially be used to make large enough quantities for therapeutics.
“We are working with Agilent’s Nucleic Acid Solution Division—a business focused on GMP manufacturing of oligonucleotides for therapeutics—to engage with customers interested in this capability and better understand how we might be able to help them accomplish their goals,” says Dr. Bruhn.
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Customized Animal Models
“Given their gene-knockout capabilities, zinc-finger-based technologies and CRISPR-based technologies opened the doors for creation of animal models that more closely resemble human disease than mouse models,” says Myung Shin, Ph.D., senior principal scientist, Merck & Co. Dr. Shin’s team supports Merck’s drug discovery and development program by creating animal models mimicking human genetics.
For example, Dr. Shin’s team has worked with the Dahl salt-sensitive strain of rats, a widely studied model of hypertension. “We used zinc-finger nucleases to generate a homozygous knockout of a renal outer medullary potassium channel (ROMK) gene,” elaborates Dr. Shin. “The resulting model represents a major advance in elucidating the role of ROMK gene.”
According to Dr. Shin, the model may also provide a bridge between genetics and physiology, particularly in studies of renal regulation and blood pressure. In one study, the model generated animal data that suggest ROMK plays a key role in kidney development and sodium absorption. Work along these lines may lead to a pharmacological strategy to manage hypertension.
In another study, the team applied zinc-finger nuclease strategy to knockout the coagulation Factor XII, and thoroughly characterize them in thrombosis and hemostasis studies. Results confirmed and extended previous literature findings suggesting Factor XII as a potential target for antithrombotic therapies that carry minimal bleeding risk. The model can be further utilized to study safety profiles and off-target effects of such novel Factor XII inhibitors.
“We use one-cell embryos to conduct genome editing with zinc-fingers and CRISPR,” continues Dr. Shin. “The ease of this genetic manipulation speeds up generation of animal models for testing of various hypotheses.”
A zinc finger–generated knockout of the multidrug resistance protein MDR 1a P-glycoprotein became an invaluable tool for evaluating drug candidates for targets located in the central nervous system. For example, it demonstrated utility in pharmacological analyses.
Dr. Shin’s future research is directed toward preclinical animal models that would contain specific nucleotide changes corresponding to those of humans. “CRISPR technology,” insists Dr. Shin, “brings an unprecedented power to manipulate genome at the level of a single nucleotide, to create gain- or loss-of-function genetic alterations, and to deeply understand the biology of a disease.”
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Transcriptionally Active dCas9
“Epigenome editing is important for several reasons,” says Charles Gersbach, Ph.D., an associate professor of biomedical engineering at Duke University. “It is a tool that helps us answer fundamental questions about biology. It advances disease modeling and drug screening. And it may, in the future, serve as mode of genetic therapy.”
“One part of our research focuses on studying the function of epigenetic marks,” Dr. Gersback continues. “While many of these marks are catalogued, and some have been associated with the certain gene-expression states, the exact causal link between these marks and their effect on gene expression is not known. CRISPR technology can potentially allow for targeted direct manipulation of each epigenetic mark, one at a time.”
Dr. Gersback’s team mutated the Cas9 nuclease to create deactivated Cas9 (dCas9), which is devoid of endonuclease activity. Although the dCas9 protein lacks catalytic activity, it may still serve as an anchor for a plethora of other important proteins, such as transcription factors and methyltransferases.
In an elegant study, Dr. Gersbach and colleagues demonstrated that recruitment of a histone acetyltransferase by dCas9 to a genomic site activates nearby gene expression. Moreover, the activation occurred even when the acetyltransferase domain was targeted to a distal enhancer. Similarly, recruitment of KRAB repressor to a distant site silenced the target gene in a very specific manner. These findings support the important role of three-dimensional chromatin structures in gene activation.
“Genome regulation by epigenetic markers is not static,” maintains Dr. Gersbach. “It responds to changes in the environment and other stimuli. It also changes during cell differentiation. We designed an inducible system providing us with an ability to execute dynamic control over the target genes.”
In a light-activated CRISPR-Cas9 effector (LACE) system, blue light may be used to control the recruitment of the transcriptional factor VP64 to target DNA sequences. The system has been used to provide robust activation of four target genes with only minimal background activity. Selective illumination of culture plates created a pattern of gene expression in a population of cells, which could be used to mimic what is observed in natural tissues.
Together with collaborators at Duke University, Dr. Gersbach intends to carry out the high-throughput analysis of all currently identified regulatory elements in the genome. “Our ultimate goal,” he declares, “is to assign function to all of these elements.”
Posted in CRISPR/Cas9 & Gene Editing, Proteomics, RNA Biology | Tagged CRISPR, precision medicine | Leave a Comment »
Controversial Case of Sarepta’s eteplirsen, for DMD gained a Support Letter to FDA by Site Investigators and Advisers working on the drug
Reporter: Aviva Lev-Ari, PhD, RN
UPDATED on 7/21/2025
What does Elevidys’ future look like now?
Some backstory first: The FDA first approved Elevidys in June 2023, granting it accelerated clearance for Duchenne patients who were 4 or 5 years old and could still walk. One year later, the agency expanded the treatment’s OK to include ambulatory and non-ambulatory Duchenne patients who were 4 years of age or older.
Both decisions were controversial, as Sarepta’s trial data for Elevidys didn’t prove the therapy could significantly improve motor function. But the Duchenne community mostly embraced Elevidys, propelling it to the fastest market launch of any gene therapy approved in the U.S.
Safety concerns prompted by the recent deaths could now change that. But without Sarepta’s cooperation, the FDA’s options for stopping Elevidys sales altogether are limited. And those it does have at its disposal are likely to take time.
In refusing the FDA’s request to halt sales, Sarepta maintained there has been no new information indicating greater safety risk in younger, ambulatory patients. Both of the Elevidys patients who died were teenagers whose disease had eroded their ability to walk.
The distinction is clinically important as Elevidys is dosed by weight, so younger, lighter patients receive less of the drug. And as they’re earlier in their disease course, the treatment window to forestall further damage may be greater.
The distinction also has regulatory implications. In June 2024, when the FDA expanded Elevidys’ approval it did so by converting its accelerated approval to full for ambulatory patients. In non-ambulatory patients, Elevidys’ clearance remains “accelerated,” which indicates Sarepta is required to produce further evidence of its benefit in this group.
For the time being, the FDA has informed Sarepta that Elevidys’ indication should be limited to ambulatory patients only. The agency said in a statement that it is “committed to further investigating the safety of the product in ambulatory patients and will take additional steps to protect patients as needed.” — Ned Pagliarulo
Why did the FDA wait to step in?
The FDA claimed Friday it took “swift action” by suspending multiple Sarepta trials and requesting the company halt all Elevidys shipments. It took those steps following “new safety concerns” that the agency said showed patients may be exposed to “unreasonable and significant risk of illness or injury.”
“We believe in access to drugs for unmet medical needs but are not afraid to take immediate action when a serious safety signal emerges,” FDA Commissioner Martin Makary said in the statement.
SOURCE
UPDATED on 6/22/2023
After delays, Sarepta’s DMD gene therapy Elevidys finally makes it past the FDA finish line
By Zoey BeckerJun 22, 2023 02:25pm
UPDATED on 12/12/2019
In stunning twist, FDA approves Sarepta’s Duchenne drug it rejected
Vyondys 53, a type of nucleic acid therapy, is now conditionally cleared for the roughly 8% of patients with Duchenne who are “amenable” to exon 53 skipping, the mechanism by which the drug works. Sarepta said it would price Vyondys 53 “at parity” with Exondys 51, which controversially won FDA approval in 2016. Exondys 51 costs about $300,000 per year per child.
Exondys 51 was the first medicine specifically approved to treat Duchenne. Its approval sparked internal debate at the FDA, with agency officials at the Division of Neurology Products, the director of the Office of New Drugs and the acting chief scientist arguing in favor of rejection. They were overruled by Janet Woodcock, head of the FDA’s Center for Drug Evaluation and Research.
The FDA’s rejection of Vyondys 53 had stirred speculation the agency had done so for political reasons tied to the controversy over Exondys 51.
Company CEO Doug Ingram steadfastly refused to say much about the decision other than that it related to infection and kidney toxicity risks, and asked the patient community to not pressure the agency to change its mind.
Approval is conditional on Sarepta running a confirmatory study to prove Vyondys 53 delivers a clinical benefit. The data Sarepta used to support its application showed that treatment increased levels of dystrophin, a critical muscle protein missing in patients with DMD, from 0.1% of normal to 1.02% on average after 48 weeks.
SOURCE
https://www.biopharmadive.com/news/fda-surprise-approval-sarepta-vyondys-53-duchenne-drug/569015/
On 1/23/2016 I published
Gene Editing for Exon 51: Why CRISPR Snipping might be better than Exon Skipping for DMD
Reporter: Aviva Lev-Ari, PhD, RN
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Monday, March 21, 2016 | By John Carroll
Sarepta ($SRPT) enjoyed a rare spike in its share price today after several dozen experts in Duchenne muscular dystrophy, including a host of site investigators and advisers working on the drug, circulated a detailed letter explaining why the FDA should support the company’s application for eteplirsen–despite a withering internal assessment from agency insiders. On a point-by-point basis these physicians took exception to the FDA review, noting that despite the extremely small number of patients in the key study–with data on only 12 boys–their experience observing patients in their practices suggest that the drug was clearly effective. As news of the letter spread, Sarepta’s share price surged 20%. “The collective signatories note that the group of 12 eteplirsen treated boys, even accounting for daily deflazacort usage or twice-weekly prednisone, is clearly performing better than our collective clinical experience and the published literature would predict,” the lineup of physicians asserts. “Collectively, a portion of us represent a group of physicians who have observed over 5,000 DMD patients in our practices over an average of more than 15 years. Published external natural history data and our clinical experience strongly support that the 12 boys treated for over 4 years show a milder clinical progression, likely due to a positive treatment effect of eteplirsen.” A quick check of Sarepta’s websites and online records also revealed that many of the as-advertised experts have close ties to Sarepta, often listed as the very investigators who have been helping Sarepta gather the controversial data together and analyze it for regulators. Among those who have worked on drug trials related to eteplirsen and signed the letter are UCLA’s Perry Shieh (a principal investigator for one study), Stanford’s John Day (who lists Confirmatory Study of Eteplirsen in DMD Patients on his resume; and Kathy Mathews at the University of Iowa (a hub site investigator and principal). Harvard Med School’s Louis Kunkel and the University of Washington’s Jeff Chamberlain, who signed on to the company’s advisory board, are also signers on the lobbying letter, along with many trial site leaders, including Anne Connolly, Susan Apkon, Nancy Kuntz and Basil Darras, all listed on Sarepta’s website. Dr. M. Carrie Miceli and Dr. Stanley Nelson, co-director of the Center for Muscular Dystrophy at UCLA, took the lead on the letter, which was dated February 24 and addressed to Dr. Billy Dunn, director of the division of neurology products at the FDA. The wife/husband team launched a public campaign advocating for new drugs to be approved for Duchenne, which afflicts their teenage son. Miceli, Nelson and Chamberlain also sit on the advisory board of CureDuchenne, an advocacy group which has offered its full-throated support of eteplirsen’s approval, along with Sarepta CEO Ed Kaye. In their view, which you can see here, the best approach would be to go ahead and approve eteplirsen and then go ahead and let upcoming data provide confirmatory results. “The FDA Briefing Document also implies that the ongoing non-placebo controlled confirmatory eteplirsen trial (NCT02255552) and additional eteplirsen safety studies (NCT02420379 and NCT02286947) initiated in response to FDA guidance may not be considered sufficiently robust to allow for approval,” the letter reads. “Given the relative paucity of patients with amenable mutations, the flexibility afforded by FDASIA, and the fact that many of the boys between the ages of 4 and 21 years with relevant mutations are already receiving eteplirsen in the context of these trials, it would be difficult to conduct a large placebo controlled study in the near future. Thus, it would be dubiously ethical to veer from the currently recommended study path at this point. In keeping with the criteria imposed by FDASIA for accelerated approval for rare disease with unmet need, we conclude that the aggregate data, described in the briefing documents, are providing substantial evidence of efficacy and use in the greater population of boys amenable to exon 51 skipping is appropriate. We suggest that the most scientifically robust way forward and the most ethical choice for the Duchenne community is in the context of an accelerated approval followed by a confirmatory trial.” Just how persuasive this group can be, with such close ties to Sarepta, won’t be clear until April 25, when the FDA’s advisory committee will finally meet for a review. The FDA’s internal assessment virtually dismissed Sarepta’s case. But the biotech has enjoyed intense support from parents and patients–as well as the professional community, which has played a big role in testing the drug. Related Articles: Sarepta has a new date with an FDA AdComm for Duchenne drug eteplirsen Sarepta shrinks as execs wait for FDA’s decision on Duchenne drug Sarepta faces another FDA delay with its much-scrutinized DMD drug Sarepta shares crash on a harsh FDA review of Duchenne’s drug |
SOURCE
From: FierceBiotech <editors@FierceBiotech.com>
Reply-To: <editors@FierceBiotech.com>
Date: Tuesday, March 22, 2016 at 1:31 PM
To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>
Subject: | 03.22.16 | Eli Lilly raises big questions in quest to salvage Alzheimer’s drug; Sarepta investigators join lobbying effort for eteplirsen
Posted in Exosomes, Genome Biology, Innovations in Neurophysiology & Neuropsychology | Tagged Gene Editing for Exon 51: Why CRISPR Snipping might be better than Exon Skipping for DMD | Leave a Comment »
Ions, molecules, and bio-markers measurements using BioMEMS
Curator: Danut Dragoi, PhD
Small or large molecules and ions are traditionally determined in specific clinical labs facilities utilizing complex instrumentation and standard operation procedures. Same analytical clinical results can be obtained today from specialized miniaturized bioMEMS. The miniaturized instrumentation and procedures use less sample and highly sophisticated algorithms for data processing, usually intended without sample preparation or lengthy time analysis. These features reduce the costs associated with the lab work, provide rapid results to the patient and doctors. In this presentation, the talk is focused on ions, molecules, and bio-markers measurements using BioMEMS as shown in the first slide.
Slide #2
An overview of the presentation includes the items shown below.
Slide #3 shows a palm size DNA and RNA sequencer, see link in here, that I assume astronaut Scot Kelly recently used in outer space, International Space Station, to monitor his DNA and RNA changes as an effect of low gravitation and cosmic radiation, during his close to one year work in outer space. The tiny new device shown in the picture below called the MinION™, is developed by Oxford Nanopore Technologies, promises to help scientists sequence DNA in space. NASA’s Biomolecule Sequencer investigation is a technology demonstration of the device.
Slide #4
The physical principle of the DNA sequencer is based on the perturbation of the electric current that flows trough the nanopore plate when one strand of DNA macromolecule, with nucleotides attached, goes through a small pore of 5 nm diameter. In this way, by recording the electrical signals, the genetic code is revealed, see link in here.
Slide #5
The picture in slide #5 taken from here, shows how the physical principle explained before is applied.
Slide #6
The one-strip bio-sensor structure, common for glucose concentration measurements shows three layers of electrodes, see link in here, that provide an electrical signal proportional to the amount of glucose in a tiny amount of blood.
Slide #7
This slide explains the principle and the chemical reaction at the electrodes for a common glucosometer, see link in here.
Slide #8
The principle of glucosometer can be applied to other molecules, such as bio-markers that represent large molecules associated with an antigen tumor in human plasma, see link in here. Photo image below is for a portable strip reader.
Slide #9
The chemical reactions specific to a glucose meter, shown bellow, are taken from here.
Slide #10
The schematic below shows how one strip biosensor for bio-markers works, see link in here. The complexity of a bio-marker molecule requires conditional measurements for accuracy and reproducible results.
Slide #11
The schematic below is a continuation of slide #10 in which standard bio-markers are introduced in order to have a comparison between a test line and a control line besides additional antigens, gold antigen conjugate, and antibodies.Details of how all these markers interact on the strip biosensor, see link in here.
Slide #12
In this slide, which is a continuation of slides #10 and slide #11, the goat anti-mouse IgG is introduced as a control sample in the control line.
Slide #13
In many situations, one strip amperometric (electrical current) is not enough to perform the measurements, as in salt daily intake determination, see link in here.The analyte in this case is determined from the analysis of an image taken from the strips, see link in here.
Slide #14
The technique described in here, has two strips for measurements. In this way the ions in human body fluids, like Na+ can be successfully determined utilizing BioMEMS such as that described in here, and here.
Slide #15
NB-Inspired from Na+ ions determination, a possibility of similar measurements exists for K+ ions.
Slide #17
Slide #17 introduces the long range surface plasmon polariton (LRSPP) technique , which is similar to surface enhanced Raman scattering (SERS) technique. When the sample is functionalized with G protein than the interaction between components is reflected in the optical cavity power measurements, which is exploited on determining the ratio of light kappa and lambda polymeric chains.
Slide #18
The slide shows an optical plasmonic biosensor for leukemia detection, see link in here.
Slide #19
The schematic on slide #19 shows how specificity of protein G, human IgG kappa and lambda, goat anti-human IgG kappa and lambda as pure standards work on optical plasmonic method.
Slide#20
The output optical power of the LRSPP device versus time of introducing the analyte and the standards shows specific signal shifts for anti-human lambda IgG on HKS (high kappa serum) and anti-human kappa IgG on HKS. If the ratio of the two signal is outside of a small given range, see link in here, than the measurements indicate the presence of the cancer cells.
Slide #21
This slide shows the description of chemiluminescence method applied on a chip, see link in here, that become more popular with the development of measurements on micro-fluids using sensitive photo detectors arrays.
Slide #22
The schematic below, taken from here, shows three sections of the chip, in which tiny capillaries lines take the sample without micro-pumping using the capillary effect, separates the light molecules from the heavy, and bring them in an area where chemiluminiscent effect takes place, emitted photons detected by an array of sensitive detectors and their signal electronically processed.
Slide #23
This slide highlights the detection process that takes place towards the end of the capillary, see link in here.
Slide #24
This slide illustrates a sample of signals adapted from a photo-detector array, see link in here.
Slide #25
In conclusion, heavy analytes of bio samples can be determined with BioMEMS based chemiluminescence effect, many analyte solutions can get through a relative long capillary path using BioMEMS that are prone to miniaturization. The method of detecting photons from analyte interaction with a bioenzime-substrate with mono and multi-strips trend to be the generalization of actual R & D miniaturized devices. The new analytical micro-devices based on sensitive photo-detectors array reduces the actual costs of clinical analyzes and increases the speed of analytical process.
Source
https://www.nanoporetech.com/community/start-using-minion
http://www.nasa.gov/centers/ames/research/technology-onepagers/nanopores_gene_sequencing.html
Click to access amperometric-test-strips-for-point-of-care-biosensors-an-overview.pdf
Click to access AJBMS_2009_1_07.pdf
https://sites.google.com/site/inescmn/home/research/mems-and-lab-on-chip-devices/lab-on-chip-devices
Posted in Bio-MEMS, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy | Tagged bioMEMS | Leave a Comment »
Roche/Genentech’s Late-Stage Pipeline beyond Cancer: Ocrelizumab, against primary progressive MS & relapsing/remitting MS – $2.7 billion peak sales forecast
Reporter: Aviva Lev-Ari, PhD, RN
SOURCE
Beyond Cancer
1. ocrelizumab, $2.7 billion peak sales forecast
What has the multiple sclerosis market excited about ocrelizumab is its success against primary progressive MS. Until orcrelizumab, no treatment in history has succeeded in a Phase III trial against this extremely debilitating form of MS.
Ocrelizumab is also being positioned for relapsing/remitting MS. Clinical trial data released in October showed that the treatment cut MS relapses by almost half compared with Merck’s competing drug, Rebif.
On a commercial basis, ocrelizumab’s expanded label (to include both forms of MS) should greatly increase its revenue potential. While a conservative estimate of ocrelizumab’s peak sales puts it at $2.7 billion, some see a peak sales potential for ocrelizumab in the neighborhood of $6 billion. That’s certainly a long shot, but not out of the question, since it is based on a MS market that is now worth $19 billion growing at 5% annually, with ocrelizumab eventually reaching a 30% market share.
Roche has stated plans for applying for regulatory approval for ocrelizumab in the first half of 2016. The drug’s accelerated approval status means an expedited review, with the FDA likely to take action on the application within 6 months. While ocrelizumab’s timeline depends on many variables, there is potential for sales to begin by year-end 2016.
Cancer Indications
2. Atezolizumab: $2.5 billion peak sales projected
Roche’s immuno-oncology drug atezolizumab follows ocrelizumab in blockbuster potential. Drugs such as atezolizumab (atezo) work by turning off cancer’s ability to remain undetected by the immune system, and atezo has put up some impressive data in its clinical trials. For example, in its POPLAR trial against advanced non-small-cell lung cancer, atezo doubled the likelihood of survival in patients taking the drug relative to placebo.
Being first matters, however. The market already has powerful competitors for atezo in Merck’s Keytruda and Bristol-Myers Squibb‘s (NYSE:BMY) Opdivo. On the other hand, both Keytruda and Opdivo are PD-1 treatments, and atezo works through another mechanism, PD-L1.
Genentech researchers believe PD-L1 is a more significant engine in cancer than PD-1. If they are correct, atezo will have a more long-lasting effect on stopping cancer growth, which would make the drug a potential first choice. Roche is driving some 36 studies toward making a broad case for atezo with the FDA. Encouraging data keeps coming in. But investors should realize that how this drug will perform against competition from Keytruda and Opdivo is still very much an open question.
A more immediate commercial advantage for atezo is that Roche has a powerful in-house diagnostic division providing tools that can tag patients likely to respond to the drug. Many cancer therapies are ineffective with a large percentage of patients, and by specifically identifying those cancer patients who should benefit, Roche can personalize cancer treatment. That’s a big plus with payers, who naturally want to conserve their money for therapies more likely to be effective. As personalized medicine becomes steadily more widespread, full-year sales for Roche’s diagnostic division have grown–increasing 6% in 2015 to $10.7 billion.
Atezo’s breakthrough therapy designation gives it a solid chance of rolling out this year, but some industry watchers are deferring atezo’s projected launch date until 2017. Calculating a launch date is an inexact science, so that’s certainly possible.
3. Venetoclax: $1.4 billion projected for Roche
Roche’s third blockbuster speeding toward FDA approval is AbbVie partnered venetoclax. The drug is targeted to treat a highly virulent form of leukemia (chronic lymphocytic leukemia), specifically in those patients with a mutation that makes the cancer more aggressive and often results in shortened survival. Late-stage trials are also ongoing in non-Hodgkin’s lymphoma, acute myeloid leukemia, and multiple myeloma.
Roche has U.S. marketing rights to the drug, and FiercePharma estimates Roche’s share of peak sales at $1.4 billion by 2020. The drug, which has already been fast-tracked for approval under the agency’s breakthrough designation last May, scored a priority review from the FDA in January. Roche expects FDA clearance in 2016.
SOURCE
Other related articles published in this Open Access Online Scientific Journal include the following:
Immune-Oncology Molecules In Development & Articles on Topic in @pharmaceuticalintelligence.com
Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN
Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Screening, Genomic Expression, Innovations in Neurophysiology & Neuropsychology, Pharmaceutical Analytics, Pharmaceutical Discovery, Pharmaceutical Drug Discovery, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Informatics, Pharmaceutical R&D Investment, Pharmacogenomics | Tagged Atezolizuma, ocrelizumab, Venetoclaxb | Leave a Comment »
Tim Cook on iPhone Data Privacy
Reporter: Aviva Lev-Ari, PhD, RN
VIEW VIDEO
The chief executive of Apple, Timothy D. Cook, said that the company did not expect to be at odds with the government over iPhone encryption, but that it would not back down.
By REUTERS on Publish DateMarch 21, 2016. Photo by Marcio Jose Sanchez/Associated Press. Watch in Times Video »
Apple also touted the iPhone’s potential usefulness in medical research and personal medical monitoring. It introduced new software on Monday to help developers create apps for both purposes, showcasing as an example a large project to study people with Parkinson’s disease.
Even then, Apple stressed its commitment to protecting customer data, saying that any sharing of health information would require a customer’s explicit permission.
“Nothing is more sensitive than your health data,” said Jeff Williams, Apple’s chief operating officer.
SOURCE
Posted in Digital HealthCare – biotech & internet joint ventures | Leave a Comment »
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