Healthcare analytics, AI solutions for biological big data, providing an AI platform for the biotech, life sciences, medical and pharmaceutical industries, as well as for related technological approaches, i.e., curation and text analysis with machine learning and other activities related to AI applications to these industries.
Mozilla Science Lab Promotes Data Reproduction Through Open Access: Report from 9/10/2015 Online Meeting
Reporter: Stephen J. Williams, Ph.D.
Mozilla Inc. is developing a platform for scientists to discuss the issues related to developing a framework to share scientific data as well as tackle the problems of scientific reproducibility in an Open Access manner. According to their blog
We’re excited to announce the launch of the Mozilla Science Lab, a new initiative that will help researchers around the world use the open web to shape science’s future.
Scientists created the web — but the open web still hasn’t transformed scientific practice to the same extent we’ve seen in other areas like media, education and business. For all of the incredible discoveries of the last century, science is still largely rooted in the “analog” age. Credit systems in science are still largely based around “papers,” for example, and as a result researchers are often discouraged from sharing, learning, reusing, and adopting the type of open and collaborative learning that the web makes possible.
The Science Lab will foster dialog between the open web community and researchers to tackle this challenge. Together they’ll share ideas, tools, and best practices for using next-generation web solutions to solve real problems in science, and explore ways to make research more agile and collaborative.
On their blog they highlight various projects related to promoting Open Access for scientific data
On September 10, 2015 Mozilla Science Lab had their scheduled meeting on scientific data reproduce ability. The meeting was free and covered by ethernet and on social media. The Twitter hashtag for updates and meeting discussion is #mozscience (https://twitter.com/search?q=%23mozscience )
Questions regarding coding projects – Abby will coordinate efforts on coding into their codebase
The journal will publish and authors and reviewers get a badge and their efforts and comments will appear on GigaScience: Giga Science will give credit for your reviews – supports an Open Science Discussion
Miss the submission deadline? You can still apply to join our Open Research Accelerator and join us for the event (PLUS get a DOI for your submission and 1:1 help)
ReScience is dedicated to publishing replications of previously published computational studies, along with all the code required to replicate the results.
ReScience lives entirely on GitHub. Submissions take the form of a Git repository, and review takes place in the open through GitHub issues. This also means that ReScience is free for everyone (authors, readers, reviewers, editors… well, I said everyone, right?), as long as GitHub is willing to host it.
ReScience was launched just a few days ago and is evolving quickly. To stay up to date, follow @ReScienceEds on Twitter. If you want to volunteer as a reviewer, please contact the editorial board.
The ReScience Journal Reproducible Science is Good. Replicated Science is better.
ReScience is a peer-reviewed journal that targets computational research and encourages the explicit reproduction of already published research promoting new and open-source implementations in order to ensure the original research is reproducible. To achieve such a goal, the whole editing chain is radically different from any other traditional scientific journal. ReScience lives on github where each new implementation is made available together with the comments, explanations and tests. Each submission takes the form of a pull request that is publicly reviewed and tested in order to guarantee any researcher can re-use it. If you ever reproduced computational result from the literature, ReScience is the perfect place to publish this new implementation. The Editorial Board
Notes from his talk:
– must be able to replicate paper’s results as written according to experimental methods
– All authors on ReScience need to be on GitHub
– not accepting MatLab replication; replication can involve computational replication;
Research Ideas and Outcomes Journal – Daniel Mietchen @EvoMRI
Postdoc at Natural Museum of London doing data mining; huge waste that 90% research proposals don’t get used so this journal allows for publishing proposals
Learned how to write proposals by finding a proposal online open access
Reviewing system based on online reviews like GoogleDocs where people view, comment
Growing editorial and advisory board; venturing into new subject areas like humanities, economics, biological research so they are trying to link diverse areas under SOCIAL IMPACT labeling
BIG question how to get scientists to publish their proposals especially to improve efficiency of collaboration and reduce too many duplicated efforts as well as reagent sharing
Crowdfunding platform used as post publication funding mechanism; still in works
They need a lot of help on the editorial board so if have a PhD PLEASE JOIN
CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development
UPDATED 6/11/2021
CRISPR Diagnostics: CRISPR-dx Comes of Age: Tool in Drug Development
The past five years has seen a rapid expansion of the ability of CRISPR based tools toward diagnostic testing. Recently, CRISPR has been used to detect SARS-CoV-2 in patients. An article in the journal Science describes the different classes of CRISPR diagnostics in use today .
Update near end of post
UPDATED 8/08/2020
Association to Causation: Using GWAS to Identify Druggable Targets
A Gen Webinar Thursday, August 6, 2020; 11:00am – 12:30pm EST
See at end of post
Curator: Stephen J. Williams, Ph.D.
Article 21.4.8- CRISPRCas9 Finds Its Way As an Important Tool For Drug Discovery & Development
CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development, 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
The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR)adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA.
CRISPR/Cas systems are part of the adaptive immune system of bacteria and archaea, protecting them against invading nucleic acids such as viruses by cleaving the foreign DNA in a sequence-dependent manner. Although CRISPR arrays were first identified in the Escherichia coli genome in 1987 (Ishino et al., 1987), their biological function was not understood until 2005, when it was shown that the spacers were homologous to viral and plasmid sequences suggesting a role in adaptive immunity (Bolotin et al., 2005; Mojica et al., 2005; Pourcel et al., 2005). Two years later, CRISPR arrays were confirmed to provide protection against invading viruses when combined with Cas genes (Barrangou et al., 2007). The mechanism of this immune system based on RNA-mediated DNA targeting was demonstrated shortly thereafter (Brounset al., 2008; Deltcheva et al., 2011; Garneau et al., 2010; Marraffini and Sontheimer, 2008).
Jennifer Doudna, PhD Professor of Molecular and Cell Biology and Chemistry, University of California, Berkeley Investigator, Howard Hughes Medical Institute has recently received numerous awards and accolades for the discovery of CRISPR/Cas9 as a tool for mammalian genetic manipulation as well as her primary intended research target to understand bacterial resistance to viral infection.
A good post on the matter and Dr. Doudna can be seen below:
In Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting inheritable metabolic disorders in which may benefit from a CRISPR-Cas9 mediated therapy is discussed. However this curation is meant to focus on CRISPR/CAS9 AS A TOOL IN PRECLINICAL DRUG DEVELOPMENT.
Three Areas of Importance of CRISPR/Cas9 as a TOOL in Preclinical Drug Discovery Include:
Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE
CRISPR/CAS9 Use in Developing Models of Disease
CRISPR/CAS9 Use as aDiagnostic Tool
Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES
I. Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE
The advent of the first tools for manipulating genetic material (cloning, PCR, transgenic technology, and before microarray and other’omic methods) allowed scientists to probe novel, individual gene functions as well as their variants and mutants in a “one-gene-at-a time” process. In essence, a gene (or mutant gene) was sequenced, cloned into expression vectors and transfected into recipient cells where function was evaluated.
However, some of the experimental issues with this methodology involved
Lack of knowledge of insertion site of the transgene – this leads to off-target effects usually due to insertion of a transgene in front of unwanted promoters or insertion at a site resulting in gene disruption or even mutagenesis. In an extreme case, such as transposon-induced mutagenesis may lead to transformation as described in an earlier post on this site How Mobile Elements in “Junk” DNA Promote Cancer – Part 1: Transposon-mediated Tumorigenesis
Most transfections experiments result in NON ISOGENIC cell lines – by definition the insertion of a transgene alters the genetic makeup of a cell line. Simple transfection experiments with one transgene compared to a “null” transfectant compares non-isogenic lines, possibly confusing the interpretation of gene-function studies. Therefore a common technique is to develop cell lines with inducible gene expression, thereby allowing the investigator to compare a gene’s effect in ISOGENIC cell lines.
Use of CRSPR in Highthrough-put Screening of Genetic Function
A very nice presentation and summary of CRSPR’s use in determining gene function in a high-throughput manner can be found below
an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq), relies on capture of double-stranded oligodeoxynucleotides into DSBs. Application of GUIDE-seq to 13 RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or chromatin immunoprecipitation sequencing (ChIP-seq). GUIDE-seq also identified RGN-independent genomic breakpoint ‘hotspots’.
1) In this talk Dr. Tyler Jacks discussed his use of CRSPR to generate a mouse model of liver tumor in an immunocompetent mouse. Some notes from this talk are given below
B) Engineering Cancer Genomes: Tyler Jacks, Ph.D.; Director, Koch Institute for Integrative Cancer Research
Cancer GEM’s (genetically engineered mouse models of cancer) had moved from transgenics to defined oncogenes
Observation that p53 -/- mice develop spontaneous tumors (lymphomas)
then GEMs moved to Cre/Lox systems to generate mice with deletions however these tumor models require lots of animals, much time to create, expensive to keep;
figured can use CRSPR/Cas9 as rapid, inexpensive way to generate engineered mice and tumor models
he used CRSPR/Cas9 vectors targeting PTEN to introduce PTEN mutations in-vivo to hepatocytes; when they also introduced p53 mutations produced hemangiosarcomas; took ONLY THREE months to produce detectable tumors
also produced liver tumors by using CRSPR/Cas9 to introduce gain of function mutation in β-catenin
2) In the Upcoming Meeting New Frontiers in Gene Editing multiple uses of CRISPR technology is discussed in relation to gene knockout/function studies, tumor model development and
New Frontiers in Gene Editing
Session Spotlight: BUILDING IN VIVO MODELS FOR DRUG DISCOVERY
Genome Editing Animal Models in Drug Discovery Myung Shin, Ph.D., Senior Principal Scientist, Biology-Discovery, Genetics and Pharmacogenomics, Merck Research Laboratories
Recent advances in genome editing have greatly accelerated and expanded the ability to generate animal models. These tools allow generating mouse models in condensed timeline compared to that of conventional gene-targeting knock-out/knock-in strategies. Moreover, the genome editing methods have expanded the ability to generate animal models beyond mice. In this talk, we will discuss the application of ZFN and CRISPR to generate various animal models for drug discovery programs.
In vivo Cancer Modeling and Genetic Screening Using CRISPR/Cas9 Sidi Chen, Ph.D., Postdoctoral Fellow, Laboratories of Dr. Phillip A. Sharp and Dr. Feng Zhang, Koch Institute for Integrative Cancer Research at MIT and Broad Institute of Harvard and MIT
Here we describe a genome-wide CRISPR-Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a non-metastatic mouse cancer cell line using a genome-scale library. The mutant cell pool rapidly generates metastases when transplanted into immunocompromised mice. Enriched sgRNAs in lung metastases and late stage primary tumors were found to target a small set of genes, suggesting specific loss-of-function mutations drive tumor growth and metastasis.
FEATURED PRESENTATION: In vivo Chromosome Engineering Using CRISPR-Cas9 Andrea Ventura, M.D., Ph.D., Assistant Member, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center
We will discuss our experience using somatic genome editing to engineer oncogenic chromosomal rearrangements in vivo. More specifically, we will present the results of our ongoing efforts aimed at modeling cancers driven by chromosomal rearrangements using viral mediated delivery of Crispr-Cas9 to adult animals.
RNAi and CRISPR/Cas9-Based in vivo Models for Drug Discovery Christof Fellmann, Ph.D., Postdoctoral Fellow, Laboratory of Dr. Jennifer Doudna, Department of Molecular and Cell Biology, The University of California, Berkeley
Genetically engineered mouse models (GEMMs) are a powerful tool to study disease initiation, treatment response and relapse. By combining CRISPR/Cas9 and “Sensor” validated, tetracycline-regulated “miR-E” shRNA technology, we have developed a fast and scalable platform to generate RNAi GEMMs with reversible gene silencing capability. The synergy of CRISPR/Cas9 and RNAi enabled us to not only model disease pathogenesis, but also mimic drug therapy in mice, providing us capability to perform preclinical studies in vivo.
In vivo Genome Editing Using Staphylococcus aureus Cas9 Fei Ann Ran, Ph.D., Post-doctoral Fellow, Laboratory of Dr. Feng Zhang, Broad Institute and Junior Fellow, Harvard Society of Fellows
The RNA-guided Cas9 nuclease from the bacterial CRISPR/Cas system has been adapted as a powerful tool for facilitating targeted genome editing in eukaryotes. Recently, we have identified an additional small Cas9 nuclease from Staphylococcus aureus that can be packaged with its guide RNA into a single adeno-associated virus (AAV) vector for in vivo applications. We demonstrate the use of this system for effective gene modification in adult animals and further expand the Cas9 toolbox for in vivo genome editing.
OriGene, Making the Right Tools for CRISPR Research Xuan Liu, Ph.D., Senior Director, Marketing, OriGene
CRISPR technology has quickly revolutionized the scientific community. Its simplicity has democratized the genome editing technology and enabled every lab to consider its utility in gene function research. As the largest tool box for gene functional research, OriGene created a large collection of CRISPR-related tools, including various all-in-one vectors for gRNA cloning, donor vector backbones, genome-wide knockout kits, AAVS1 insertion vectors, etc. OriGene’s high quality products will accelerate CRISPR research.
A critical component of producing transgenic animals is the ability of each successive generations to pass on the transgene. In her post on this site, A NEW ERA OF GENETIC MANIPULATION Dr. Demet Sag discusses the molecular biology of Cas9 systems and their efficiency to cause point mutations which can be passed on to subsequent generations
“
This group developed a new technology for editing genes that can be transferable change to the next generation by combining microbial immune defense mechanism, CRISPR/Cas9 that is the latest ground breaking technology for translational genomics with gene therapy-like approach.
In short, this so-called “mutagenic chain reaction” (MCR) introduces a recessive mutation defined by CRISPR/Cas9 that lead into a high rate of transferable information to the next generation. They reported that when they crossed the female MCR offspring to wild type flies, the yellow phenotype observed more than 95 percent efficiency.
“
The advantage of CRISPR/Cas9 over ZFNs or TALENs is its scalability and multiplexibility in that multiple sites within the mammalian genome can be simultaneously modified, providing a robust, high-throughput approach for gene editing in mammalian cells.
Applied StemCell, Inc. offers various services related to animal models including conventional transgenic rats, and phenotype analysis using knock-in, knock-out strategies.
Further explanation of their use of CRSPR can be found at the site below:
III. Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES
As of now it is unclear as to the strategy of pharma in how to use this technology for toxicology testing however a few companies have licensed the technology to use across their R&D platforms including
A recent paper used a sister technique TALEN to generate knock-in pigs which suggest that it would be possible to generate pigs with human transgenes, especially in human liver isozymes in orer to study hepatotoxicity of drugs.
Associate Professor UCSF Investigator Chan Zuckerberg Biohub
Kevin Holden, PhD
Head of Science Synthego
Abhi Saharia, PhD
VP, Commercial Development Synthego
Human genetics provides perhaps the single best opportunity to innovate and improve clinical success rates, through the identification of novel drug targets for complex disease. Even as correlation identifies multiple genetic variants associated with disease, it is challenging to conduct requisite functional studies to identify the causal variants, especially since most association signals map to non-coding regions of the genome.
Genetic editing technologies, such as CRISPR, have enabled the modeling of associated variants at their native loci, including non-coding loci, empowering the identification of underlying biological mechanisms of disease with potential causal genes. However, genome editing is largely manual today severely limiting scale, and forcing the use of rational filters to prioritize which variants to investigate functionally.
In this GEN webinar, we will discuss several strategies enabling large-scale functional investigation of disease-associated variants in a cost- and time-effective manner, including different types of pooled CRISPR-based screens and the development of a fully automated genome engineering platform. We will also review how optimization of genome engineering on this platform enables the engineering of disease-associated variants at scale in pluripotent cells.
They will be presenting on use of wide scale CRSPR screens to validate druggable targets
The presenters will also discuss new platforms for these wide scale screens
Big gap between accumulation of genetic variant information and functions of these variants
CRSPRi or CRSPa (siRNA coupled or enhancer coupled CRSPR guides)
Arrayed screens: multiplate guide RNAs and phenotype measured (phenotype can be morphology, complex biological systems like organoids or non autonomous functions
Using pooled screens and use of suitable cell model critical for this strategy
For example in iPSC vs. neurons has different expression patterns upon same CRSPR of UBA1
Advantage is using CRSPR to take iPSC from diseased variant patient to make a corrected isogenic control then introduce gRNAs and use modifier screens to determine phenotypes
Generated a platform called CRISPRbrain.org to do bioinformatics on various experiments with different guide RNAs (CRSPRs)
Nature medicine paper did GWAS and found 27 SNV associated with high risk disease and a rational filter focused on 1 SNV in noncoding region but why study a single variant and if studied all 27 would they have been able to identify a more representative druggable set?
Goal is to reduce or eliminate these rational filters
Syntheco uses an electroporation with ribonucleic proteins (RNP) to give highest efficiency and minimizes off target as complex is only in cells for a short period of time
They confirm they are doing single cell cloning by using automated microscopy to confirm single cell growth in each cloning well
Engineering iPSc genetically modified cells at scale
The closer you get to your target site the more efficient your CRSPR so a big factor when making guides, especially for knock-in CRSPR
Adding a small molecule non homologous end joining inhibitor increases efficiency to 95%
Cold shocking the cells also assists in homologous repair
Use cleavage resistant templates
III. CRISPR/CAS9 AS A DIAGNOSTIC TOOL
In the journal Science, Omar Abudayyeh and Jonathan Gootenberg discuss how CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). In addition they discuss the work by Jiao et al. in combining this technique to develop a rapid and sensitive SARS-CoV2 diagnostic test.
Omar O. Abudayyeh, Jonathan S. Gootenberg. Science 28 May 2021: CRISPR Diagnostics Vol. 372, Issue 6545, pp. 914-915; DOI: 10.1126/science.abi9335
Summary
Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.
Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.
There are multiple types of CRISPR systems comprising basic components of a single protein or protein complex, which cuts a specific DNA or RNA target programmed by a complementary guide sequence in a CRISPR-associated RNA (crRNA). The type V and VI systems and the CRISPR-associated endonucleases Cas12 (2, 3) and Cas13 (4, 5) bind and cut DNA or RNA, respectively. Furthermore, upon recognizing a target DNA or RNA sequence, Cas12 and Cas13 proteins exhibit “collateral activity” whereby any DNA or RNA, respectively, in the sample is cleaved regardless of its nucleic acid sequence (4, 6). Thus, reporter DNAs or RNAs, which allow for visual or fluorescent detection upon cleavage, can be added to a sample to infer the presence or absence of specific DNA or RNA species (4–8).
Initial versions of CRISPR-dx utilizing Cas13 alone were sensitive to the low picomolar range, corresponding to a limit of detection of millions of molecules in a microliter sample. To improve sensitivity, preamplification methods, such as recombinase polymerase amplification (RPA), PCR, loop-mediated isothermal amplification (LAMP), or nucleic acid sequence–based amplification (NASBA), can be used with Cas12 or Cas13 to enable a limit of detection down to a single molecule (8). This preamplification approach, applicable to both Cas12 and Cas13 (6, 7), enabled a suite of detection methods and multiplexing up to four orthogonal targets (7). Additional developments expanded CRISPR-dx readouts beyond fluorescence, including lateral flow (7), colorimetric (9), and electronic or material responsive readouts (10), allowing for instrument-free approaches. In addition, post–collateral-cleavage amplification methods, such as the use of the CRISPR-associated enzyme Csm6, have been combined with Cas13 to further increase the speed of CRISPR-dx tests (7). As an alternative to collateral-cleavage–based detection, type III CRISPR systems, which involve large multiprotein complexes capable of targeting both DNA and RNA, have been used for SARS-CoV-2 detection through production of colorimetric or fluorometric readouts (11).
FDA-authorized CRISPR-dx tests are currently only for use in centralized labs, because the most common CRISPR detection protocols require fluid handling steps and two different incubations, precluding their immediate use at the point of care. Single-step formulations have been developed to overcome this limitation, and these “one-pot” versions of CRISPR-dx are simple to run, operate at a single temperature, and run without complex equipment, producing either fluorescence or lateral flow readouts. The programmability of CRISPR makes new diagnostic tests easier to develop, and within months of the release of the SARS-CoV-2 genome, many COVID-19–specific CRISPR tests were reported and distributed around the world.
The broader capability for Cas enzyme–enhanced nucleic acid binding or cleavage has led to several other detection modalities. Cas9-based methods for cleaving nucleic acids in solution for diagnostic purposes have been combined with other detection platforms, such as destruction of undesired amplicons for preparation of next-generation sequencing libraries (12), or selective removal of alleles for nucleotide-specific detection (13). Alternatively, the programmable cleavage event from the Cas nuclease can be used to initiate an amplification reaction (14). Cas9-based DNA targeting has also been used for nucleotide detection in combination with solid-state electronics, promising an amplification-free platform for detection. In this platform, called CRISPR-Chip, the Cas9 protein binds nucleotide targets of interest (often in the context of the native genome) to graphene transistors, where the presence of these targets alters either current or voltage (15). By utilizing additional Cas9 orthologs and specific guide designs, CRISPR-Chip approaches have been tuned for single–base-pair sensitivity (15). Because they are integrated with electronic readers, CRISPR-Chip platforms may allow facile point-of-care detection with handheld devices.
Different classes of CRISPR diagnostics. GRAPHIC: ERIN DANIEL
Jiao et al. use a distinct characteristic of type II CRISPR systems, which involve Cas9, to develop a new type of noncollateral based CRISPR detection. Unlike Cas12s and Cas13, Cas9-crRNA complex formation requires an additional RNA known as the trans-activating CRISPR RNA (tracrRNA). By sequencing RNAs bound to Cas9 from Campylobacter jejuni in its natural host, the authors identified unexpected crRNAs, called noncanonical crRNA (ncrRNA), that corresponded to endogenous transcripts. Upon investigation of this surprising observation, it became clear that the tracrRNA was capable of hybridizing to semi-complementary sequences from a variety of RNA sources, leading to biogenesis of ncrRNAs of various sizes. Recognizing that they could program tracrRNAs to target a transcript of interest, the authors generated a reprogrammed tracrRNA (Rptr) that could bind and cleave a desired transcript, converting a piece of that transcript into a functional guide RNA. By then creating fluorescent DNA sensors that would be cleaved by the Rptr and ncrRNAs, the sensing of RNA by Cas9 could be linked to a detectable readout. This platform, called LEOPARD (leveraging engineered tracrRNAs and on-target DNAs for parallel RNA detection), can be combined with gel-based readouts and enables multiplexed detection of several different sequences in a single reaction (see the figure).
Jiao et al. also combined LEOPARD with PCR in a multistep workflow to detect SARS-CoV-2 genomes from patients with COVID-19. Although more work is needed to integrate this Cas9-based detection modality into a single step with RPA or LAMP to create a portable and sensitive isothermal test, an advantage of this approach is the higher-order multiplexing that can be achieved, allowing multiple pathogens, diseases, or variants to be detected simultaneously. More work is also needed to combine this technology with extraction-free methods for better ease of use; alternative readouts to gel-based readouts, such as lateral flow and colorimetric readouts, would be beneficial for point-of-care detection.
In just 5 years, the CRISPR-dx field has rapidly expanded, growing from a set of peculiar molecular biology discoveries to multiple FDA-authorized COVID-19 tests and spanning four of the six major subtypes of CRISPR systems. Despite the tremendous promise of CRISPR-dx, substantial challenges remain to adapting these technologies for point-of-care and at-home settings. Simplification of the chemistries to operate as a single reaction in a matter of minutes would be revolutionary, especially if the reaction could be run at room temperature without any complex or expensive equipment. These improvements to CRISPR-dx assays can be achieved by identification or engineering of additional Cas enzymes with lower-temperature requirements, higher sensitivity, or faster kinetics, enabling rapid and simple amplification-free detection with single-molecule sensitivity.
Often overlooked is the necessity for a sample DNA or RNA preparation step that is simple enough to be added directly to the CRISPR reaction to maintain a simple workflow for point-of-care testing. In addition, higher-order multiplexing developments would allow for expansive testing menus and approach the possibility of testing for all known diseases. As these advancements are realized, innovative uses of CRISPR-dx will continue in areas such as surveillance, integration with biomaterials, and environmental monitoring. In future years, CRISPR-dx assays may become universal in the clinic and at home, reshaping how diseases are diagnosed.
Leaders in Pharmaceutical Business Intelligence would like to announce their First Volume of their BioMedical E-Book Series A: eBooks on Cardiovascular Diseases
This book is a comprehensive review of Nitric Oxide, its discovery, function, and related opportunities for Targeted Therapy written by Experts, Authors, Writers. This book is a series of articles delineating the basic functioning of the NOS isoforms, their production widely by endothelial cells, and the effect of NITRIC OXIDE production by endothelial cells, by neutrophils and macrophages, the effect on intercellular adhesion, and the effect of circulatory shear and turbulence on NITRIC OXIDE production. The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012. All new articles on this subject, will continue to be incorporated, as published, in real time in the e-Book which is a live book.
We invite e-Readers to write an Article Reviews on Amazon for this e-Book.
All forthcoming BioMed e-Book Titles can be viewed at:
Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.
Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:
delivering curation and summary interpretations of latest findings and innovations on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
providing a social platform for scientists and clinicians to enter into discussion using social media
compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform
This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.
Table of Contents forPerspectives on Nitric Oxide in Disease Mechanisms
Chapter 1: Nitric Oxide Basic Research
Chapter 2: Nitric Oxide and Circulatory Diseases
Chapter 3: Therapeutic Cardiovascular Targets
Chapter 4: Nitric Oxide and Neurodegenerative Diseases
Chapter 5: Bone Metabolism
Chapter 6: Nitric Oxide and Systemic Inflammatory Disease
Chapter 7: Nitric Oxide: Lung and Alveolar Gas Exchange
This e-Book is a comprehensive review of recent Original Research on METABOLOMICS and related opportunities for Targeted Therapy written by Experts, Authors, Writers. This is the first volume of the Series D: e-Books on BioMedicine – Metabolomics, Immunology, Infectious Diseases. It is written for comprehension at the third year medical student level, or as a reference for licensing board exams, but it is also written for the education of a first time baccalaureate degree reader in the biological sciences. Hopefully, it can be read with great interest by the undergraduate student who is undecided in the choice of a career. The results of Original Research are gaining value added for the e-Reader by the Methodology of Curation.The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012. All new articles on this subject, will continue to be incorporated, as published with periodical updates.
We invite e-Readers to write an Article Reviews on Amazon for this e-Book on Amazon.
All forthcoming BioMed e-Book Titles can be viewed at:
Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.
Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:
delivering curation and summary interpretations of latest findings and innovations on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
providing a social platform for scientists and clinicians to enter into discussion using social media
compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform
This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.
Table of Contents forMetabolic Genomics & Pharmaceutics, Vol. I
Chapter 1: Metabolic Pathways
Chapter 2: Lipid Metabolism
Chapter 3: Cell Signaling
Chapter 4: Protein Synthesis and Degradation
Chapter 5: Sub-cellular Structure
Chapter 6: Proteomics
Chapter 7: Metabolomics
Chapter 8: Impairments in Pathological States: Endocrine Disorders; Stress
Hypermetabolism and Cancer
Chapter 9: Genomic Expression in Health and Disease
Cancer Biology and Genomics for Disease Diagnosis (Vol. I) Now Available for Amazon Kindle
Reporter: Stephen J Williams, PhD
Article ID #179: Cancer Biology and Genomics for Disease Diagnosis (Vol. I) Now Available for Amazon Kindle. Published on 8/14/2015
WordCloud Image Produced by Adam Tubman
Leaders in Pharmaceutical Business Intelligence would like to announce the First volume of their BioMedical E-Book Series C: e-Books on Cancer & Oncology
This e-Book is a comprehensive review of recent Original Research on Cancer & Genomics including related opportunities for Targeted Therapy written by Experts, Authors, Writers. This ebook highlights some of the recent trends and discoveries in cancer research and cancer treatment, with particular attention how new technological and informatics advancements have ushered in paradigm shifts in how we think about, diagnose, and treat cancer. The results of Original Research are gaining value added for the e-Reader by the Methodology of Curation.The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012. All new articles on this subject, will continue to be incorporated, as published with periodical updates.
We invite e-Readers to write an Article Reviews on Amazon for this e-Book on Amazon. All forthcoming BioMed e-Book Titles can be viewed at:
Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.
Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:
delivering curation and summary interpretations of latest findings and innovations
on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
providing a social platform for scientists and clinicians to enter into discussion using social media
compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform
This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.
Table of Contents for Cancer Biology and Genomics for Disease Diagnosis
Preface
Introduction The evolution of cancer therapy and cancer research: How we got here?
Part I. Historical Perspective of Cancer Demographics, Etiology, and Progress in Research
Chapter 1: The Occurrence of Cancer in World Populations
Chapter 2. Rapid Scientific Advances Changes Our View on How Cancer Forms
Chapter 3: A Genetic Basis and Genetic Complexity of Cancer Emerge
Chapter 4: How Epigenetic and Metabolic Factors Affect Tumor Growth
Chapter 5: Advances in Breast and Gastrointestinal Cancer Research Supports Hope for Cure
Part II. Advent of Translational Medicine, “omics”, and Personalized Medicine Ushers in New Paradigms in Cancer Treatment and Advances in Drug Development
Chapter 6: Treatment Strategies
Chapter 7: Personalized Medicine and Targeted Therapy
Part III.Translational Medicine, Genomics, and New Technologies Converge to Improve Early Detection
Chapter 8: Diagnosis
Chapter 9: Detection
Chapter 10: Biomarkers
Chapter 11: Imaging In Cancer
Chapter 12: Nanotechnology Imparts New Advances in Cancer Treatment, Detection, & Imaging
Epilogue by Larry H. Bernstein, MD, FACP: Envisioning New Insights in Cancer Translational Biology
With the support from DARPA and private investors, a company was created, Tribogenics, to produce an unconventional x-ray source https://gigaom.com/2011/12/06/darpa-backed-start-up-builds-iphone-sized-x-ray-machines/ that doesn’t need vacuum, cooling system, and high voltage generator. The CEO of that company explains the applications in medicine: http://exponential.singularityu.org/medicine/dale-fox. The new x-ray source is non-expensive and affordable for more people in the field of medicine. Dale Fox, the CEO of Tribogenics company stated that about 4 billion people can benefit from this new x-ray source. The prospects for the new x-ray source and devices associated with are favorable for a steady growth, the year 2015 is a turning point in the production of the new devices for medical industry.
SOURCE
Camara, C. G., Escobar, J. V., Hird, J. R. & Putterman, S. J. Nature455, 1089–1092 (2008).
Nature455, 1089-1092 (23 October 2008) | doi:10.1038/nature07378; Received 30 December 2007; Accepted 27 August 2008
Correlation between nanosecond X-ray flashes and stick–slip friction in peeling tape
Carlos G. Camara1,2, Juan V. Escobar1,2, Jonathan R. Hird1 & Seth J. Putterman1
Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California 90095, USA
Relative motion between two contacting surfaces can produce visible light, called triboluminescence1. This concentration of diffuse mechanical energy into electromagnetic radiation has previously been observed to extend even to X-ray energies2. Here we report that peeling common adhesive tape in a moderate vacuum produces radio and visible emission3, 4, along with nanosecond, 100-mW X-ray pulses that are correlated with stick–slip peeling events. For the observed 15-keV peak in X-ray energy, various models5, 6 give a competing picture of the discharge process, with the length of the gap between the separating faces of the tape being 30 or 300μm at the moment of emission. The intensity of X-ray triboluminescence allowed us to use it as a source for X-ray imaging. The limits on energies and flash widths that can be achieved are beyond current theories of tribology.
The actual level of the society we live in depends on the prior progress done by all member of the society in which we include the scientists with two distinct branches: the experimentalist and the theoretician. In the past, according with the history of sciences the experimentalist and theoretician was the same person. Today there is a split between the two due to a deep division of work that is imposed by complexity of work, complexity of products, and complexity of thoughts.
One important aspect of the work of the experimentalist is that it is well appreciated among anyone involved on producing real things like: cars, planes, machinery, computers, iPhones, houses, etc. The work of theoretician is also appreciated by scientists, teachers, researchers, and less appreciated by product developers or tool refiners for machines and mundane installations because simply their theory doesn’t directly apply to that particular field. This aspect of appreciation, in which I believe is related to the level of education, becomes a subjective factor. It depends on how well key people in the social chain of development are thinking on doing things better with the goal to get the fastest pace on progress.
For a society to grow, it is important to unite all possible constructive factors in one productive direction. This process is like unifying all known physical fields in one self-consistent theory that will explain everything. Unfortunately, this scientific event did not practically happen yet. However, corrective patches exist that explain why today some categories of professionals get busier and new professions appear branching farther on the division of the work, that ignites new opportunities for many with a good cause. As we know, the capacity of brain to process information is very high, therefore a straightforward solution for the society to keep fast pace on progress is to produce highly qualified individuals to deal with these problems. The experimentalist and the theoretician started to play an important role on this historic development path. In free societies, like ours, the accommodation of all disciplines is based on competition that drives the will of people to pursue the career in the direction where theirs skills are maximized and their talents recognized. It looks like today, many people put a lot of credit on their education, many of them qualifying for two or more disciplines on the market competition. As a fact, today we cannot see often the two skills of the experimentalist and the theoretician together for a single individual. Not because the life is too short, but because there seems to be a limitation in understanding different or opposite things. In the history of sciences and arts we saw that the math does not stick with some degree with the arts. However, great people managed both skills like Aldous Huxley, who beautifully explained in a narrated manner, the Pythagorean Theorem in the story titled “Young Archimedes”.
An obvious practical question is what we can do when the competition is touching all of us, scientists, as well as non-scientists, with complex question imposed by actual technological level of the society? The solution is go back to the school! Read as much as you can, ask passionately a scientist, a doctor, a friend, a teacher, an engineer, a physicist. Be realist on what you know and how much you know. New players are coming for sure, irrespective of age, social position, or educational strength. Let’s give all candidates a chance to compete fairly, without prejudgments, and have great respect for all of them.
Notes from Opening Plenary Session – The Genome and Beyond from the 2015 AACR Meeting in Philadelphia PA; Sunday April 19, 2015
Reporter: Stephen J. Williams, Ph.D.
The following contain notes from the Sunday April 19, 2015 AACR Meeting (Pennsylvania Convention Center, Philadelphia PA) 9:30 AM Opening Plenary Session
A) Insights From Cancer Genomes: Michael R. Stratton, Ph.D.; Director of the Wellcome Trust Sanger Institute
How do we correlate mutations with causative factors of carcinogenesis and exposure?
Cancer was thought as a disease of somatic mutations
UV skin exposure – see C>T transversion in TP53 while tobacco exposure and lung cancer see more C>A transversion; Is it possible to determine EXPOSURE SIGNATURES?
Use a method called non negative matrix factorization (like face pattern recognition but a mutation pattern recognition)
Performed sequence analysis producing 12,000 mutation catalogs with 8,000 somatic mutation signatures
Found more mutations than expected; some mutation signatures found in all cancers, while some signatures in half of cancers, and some signatures not found in cancer
For example found 3 mutation signatures in ovarian cancer but 13 for breast cancers (80,000 mutations); his signatures are actually spectrums of mutations
kataegis: defined as localized hypermutation; an example is a signature he found related to AID/APOBEC family (involved in IgG variability); kataegis is more prone in hematologic cancers than solid cancers
recurrent tumors show a difference in mutation signatures than primary tumor before drug treatment
B) Engineering Cancer Genomes: Tyler Jacks, Ph.D.; Director, Koch Institute for Integrative Cancer Research
Cancer GEM’s (genetically engineered mouse models of cancer) had moved from transgenics to defined oncogenes
Observation that p53 -/- mice develop spontaneous tumors (lymphomas)
then GEMs moved to Cre/Lox systems to generate mice with deletions however these tumor models require lots of animals, much time to create, expensive to keep;
figured can use CRSPR/Cas9 as rapid, inexpensive way to generate engineered mice and tumor models
he used CRSPR/Cas9 vectors targeting PTEN to introduce PTEN mutations in-vivo to hepatocytes; when they also introduced p53 mutations produced hemangiosarcomas; took ONLY THREE months to produce detectable tumors
also produced liver tumors by using CRSPR/Cas9 to introduce gain of function mutation in β-catenin
The three “E’s” of cancer immunoediting: Elimination, Equilibrium, and Escape
First evidence for immunoediting came from mice that were immunocompetent resistant to 3 methylcholanthrene (3mca)-induced tumorigenesis but RAG2 -/- form 3mca-induced tumors
RAG2-/- unedited (retain immunogenicity); tumors rejected by wild type mice
Edited tumors (aren’t immunogenic) led to tolerization of tumors
Can use genomic studies to identify mutant proteins which could be cancer specific immunoepitopes
MHC (major histocompatibility complex) tetramers: can develop vaccines against epitope and personalize therapy but only good as checkpoint block (anti-PD1 and anti CTLA4) but personalized vaccines can increase therapeutic window so don’t need to start PD1 therapy right away
E) Report on the Melanoma Keynote 006 Trial comparing pembrolizumab and ipilimumab (PD1 inhibitors)
Results of this trial were published the morning of the meeting in the New England Journal of Medicine and can be found here.
A few notes:
From the paper: The anti–PD-1 antibody pembrolizumab prolonged progression-free survival and overall survival and had less high-grade toxicity than did ipilimumab in patients with advanced melanoma. (Funded by Merck Sharp & Dohme; KEYNOTE-006 ClinicalTrials.gov number, NCT01866319.)
Xue W, Chen S, Yin H, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG et al: CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature 2014, 514(7522):380-384.
Other related articles on Cancer Genomics and Social Media Coverage were published in this Open Access Online Scientific Journal, include the following:
Opening Ceremony and Award Presentations from the 2015 AACR Meeting in Philadelphia PA; Pennsylvania Convention Center, Sunday April 19, 2015: 8:15 AM
Reporter: Stephen J. Williams, Ph.D.
Article ID #176: Opening Ceremony and Award Presentations from the 2015 AACR Meeting in Philadelphia PA. Published on 4/29/2015
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The following contain notes from the Sunday April 19, 2015 AACR Meeting (Pennsylvania Convention Center, Philadelphia PA) 8:15 AM Opening Ceremony and Awards Presentation
Ninth Annual AACR Team Science Award
Recipient: Designing Androgen Receptor (AR) Inhibitor Team
The Designing AR Inhibitors Team is a multi-institutional team that is composed of Charles Sawyers, MD, PhD, team leader, director of the Human Oncology and Pathogenesis Program at Memorial Sloan Kettering Cancer Center in New York, AACR past-president, and Howard Hughes Medical Institute investigator; Howard Scher, MD, chief of genitourinary oncology service and D. Wayne Calloway chair in urologic oncology at Memorial Sloan Kettering; and Michael Jung, PhD, distinguished professor in the Department of Chemistry and Biochemistry at the UCLA.
The team was honored for their collective work in discovering and developing the novel antiandrogen enzalutamide (Xtandi) for the treatment of metastatic castration-resistant prostate cancer in a collaboration that started ten years ago.
Twelfth Annual AACR Award for Lifetime Achievement in Cancer Research
Recipient: Mario R. Capecchi, Ph.D.
Dr. Capecchi is a geneticist who won the Nobel prize for creating technologies that resulted in the first knockout mouse. For this work, Capecchi won the 2007 Nobel prize for medicine or physiology, along with Martin Evans and Oliver Smithies, who also contributed.
AACR Distinguished Public Service Award
Recipient : Miri Ziv Director General of Israel Cancer
Instrumental in getting national Israeli mammography screening
Efforts led to national skin cancer screening program in Israel
Prevention/control programs
In 1995 representative to European Breast League
Ninth Annual AACR Margaret Foti Award for Leadership and Extraordinary Achievements in Cancer Research
Recipient: Donald S. Coffey, Ph.D.
Dr. Coffey discovered the nuclear matrix and made pivotal discoveries understanding the process of DNA synthesis. He is the leader of the National Prostate Coalition and efforts led to the development of the Prostate Specific Antigen (PSA) as a prostate cancer biomarker. Now his lab is assessing the role of chaos, fractals and complexity in the self-organization of DNA, cells and tissue in relation to tumor biology.
In a side note, both Dr. Foti and Dr. Coffey had the same mentor, Dr. Sydney Weinhouse and Professor Leslie Helleman, who both studied the oxidation of free fatty acids and took Otto Warburg’s hypothesis a step further to understand how more complex cancer metabolism was than Otto had imagined.
Other award winners were:
Dr. Richard Pasdur of the FDA who won the Public Service Award
In memorial
Dr. Upton (M.D.) pathologist head of NCI and established EPA
Dr. Emmanuel Farber, M.D., Ph.D. – biology of tobacco control and issued the historical Surgeon
General’s report on smoking
Dr. June Biedler, Ph.D. – showed multidrug resistance and defined cytogenetics of neuroblastoma
Other related articles on Cancer History and Social Media Coverage were published in this Open Access Online Scientific Journal, include the following:
Notes On Tumor Heterogeneity: Targets and Mechanisms, from the 2015 AACR Meeting in Philadelphia PA
Reporter: Stephen J. Williams, Ph.D.
The following contain notes from the Sunday April 19, 2015 AACR Meeting (Pennsylvania Convention Center, Philadelphia PA) 1 PM Major Symposium Session on Tumor Heterogeneity: Targets and Mechanism chaired by Dr. Charles Swanton.
Tumor heterogeneity is a common feature of many malignancies, especially the solid tumors and can drive the evolution and adaptation of the growing tumor, complicating therapy and resulting in therapeutic failure, including resistance. This session at AACR described the mechanisms, both genetic and epigenetic, which precipitate intratumor heterogeneity and how mutational processes and chromosomal instability may impact the tumor progression and the origin of driver events during tumor evolution. Finally the session examined possible therapeutic strategies to take advantage of, and overcome, tumor evolution. The session was chaired by Dr. Charles Swanton. For a more complete description of his work, tumor heterogeneity, and an interview on this site please click on the link below:
This paper described the longitudinal Whole Genome Sequencing (WGS) study of a 35 year old female whose primary glioblastoma (GBM) was followed through temozolomide treatment and ultimately recurrence.
In 2008 patient was diagnosed with primary GBM (three biopsies of unrelated sites were Grade II and Grade IV; temozolomide therapy for three years then relapse in 2011
WGS of 2 areas of primary tumor showed extensive mutational and copy number heterogeneity; was able to identify clonal TP53 mutations and clonal IDH1 mutation in primary tumor with different patterns of clonality based on grade
Amplifications on chromosome 4 and 12 (PDGFRA, KIT, CDK4)
After three years of temozolomide multiple translocations found in chromosome 4 and 12 (6 translocations)
Clonal IDH1 R132H mutation in primary tumor only at very low frequency in recurrent tumor
The WGS on recurrent tumor (sequencing took ONLY 9 days from tumor resection to sequence results) showed mutation cluster in KIT/PDGFRA.PI3K.mTOR axis so patient treated with imatinib
However despite rapid sequencing and a personalized approach based on WGS results, tumor progressed and patient died shortly: tumor evolution is HUGE hurdle for personalized medicine
As Dr. Swanton stated:
“we are underestimating the frequency of polyclonal evolution”
analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions.
identified later subclonal “actionable” mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), EGFR (L858R), and KRAS (G12D), which may compromise the efficacy of targeted therapy approaches.
> 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K (phosphatidylinositol 3-kinase)–AKT–mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal
Mutations in the RAS–MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling
Branched chain can converge on single resistance mechanism; clonal resistance (for example to PI3K inhibitors can get multiple PTEN mutations in various metastases
Targeting Tumor Heterogeneity
Identify high risk occupants (have to know case history)
Mutational landscape interferes with anti-PD1 therapies
Low frequency mutations affect outcome
Notes from Dr. Catherine J. Wu, Dana-Farber Cancer Institute: The evolutionary landscape of CLL: Therapeutic implications
Clonal evolution a key feature of cancer progression and relapse
Hypothesis: evolutionary dynamics (heterogeneity) in chronic lymphocytic leukemia (CLL) contributes to variations in response and disease “tempo”
Used whole exome sequencing and copy number data of 149 CLL cases to discover early and late cancer drivers: clonal patterns (Landau et. al, Cell 2013); some drivers correspond to poor clinical outcome
Methylation studies suggest that there is epigenetic heterogeneity which may drive CLL clonal evolution
Developing methodology to integrate WES to determine mutations with immunogenic potential for development of personalized immunotherapy for CLL and other malignancies
McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C: Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Science translational medicine 2015, 7(283):283ra254.
Other related articles on Tumor Heterogeneity were published in this Open Access Online Scientific Journal, include the following:
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