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Archive for the ‘CRISPR/Cas9 & Gene Editing’ Category


Bioinformatic Tools for RNASeq: A Curation

Curator: Stephen J. Williams, Ph.D. 

 

Note:  This will be an ongoing curation as new information and tools become available.

RNASeq is a powerful tool for the analysis of the transcriptome profile and has been used to determine the transcriptional changes occurring upon stimuli such as drug treatment or detecting transcript differences between biological sample cohorts such as tumor versus normal tissue.  Unlike its genomic companion, whole genome and whole exome sequencing, which analyzes the primary sequence of the genomic DNA, RNASeq analyzes the mRNA transcripts, thereby more closely resembling the ultimate translated proteome. In addition, RNASeq and transcriptome profiling can determine if splicing variants occur as well as determining the nonexomic sequences, such as miRNA and lncRNA species, all of which have shown pertinence in the etiology of many diseases, including cancer.

However, RNASeq, like other omic technologies, generates enormous big data sets, which requires multiple types of bioinformatic tools in order to correctly analyze the sequence reads, and to visualize and interpret the output data.  This post represents a curation by the RNA-Seq blog of such tools useful for RNASeq studies and lists and reviews published literature using these curated tools.

 

From the RNA-Seq Blog

List of RNA-Seq bioinformatics tools

Posted by: RNA-Seq Blog in Data Analysis, Web Tools September 16, 2015 6,251 Views

from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools

A review of some of the literature using some of the aforementioned curated tools are discussed below:

 

A.   Tools Useful for Single Cell RNA-Seq Analysis

 

B.  Tools for RNA-Seq Analysis of the Sliceasome

 

C.  Tools Useful for RNA-Seq read assembly visualization

 

Other articles on RNA and Transcriptomics in this Open Access Journal Include:

NIH to Award Up to $12M to Fund DNA, RNA Sequencing Research: single-cell genomics, sample preparation, transcriptomics and epigenomics, and genome-wide functional analysis.

Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

Complex rearrangements and oncogene amplification revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Single-cell RNA-seq helps in finding intra-tumoral heterogeneity in pancreatic cancer

First challenge to make use of the new NCI Cloud Pilots – Somatic Mutation Challenge – RNA: Best algorithms for detecting all of the abnormal RNA molecules in a cancer cell

Evolution of the Human Cell Genome Biology Field of Gene Expression, Gene Regulation, Gene Regulatory Networks and Application of Machine Learning Algorithms in Large-Scale Biological Data Analysis

 

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Medicine in 2045 – Perspectives by World Thought Leaders in the Life Sciences & Medicine

Reporter: Aviva Lev-Ari, PhD, RN

 

This report is based on an article in Nature Medicine | VOL 25 | December 2019 | 1800–1809 | http://www.nature.com/naturemedicine

Looking forward 25 years: the future of medicine.

Nat Med 25, 1804–1807 (2019) doi:10.1038/s41591-019-0693-y

 

Aviv Regev, PhD

Core member and chair of the faculty, Broad Institute of MIT and Harvard; director, Klarman Cell Observatory, Broad Institute of MIT and Harvard; professor of biology, MIT; investigator, Howard Hughes Medical Institute; founding co-chair, Human Cell Atlas.

  • millions of genome variants, tens of thousands of disease-associated genes, thousands of cell types and an almost unimaginable number of ways they can combine, we had to approximate a best starting point—choose one target, guess the cell, simplify the experiment.
  • In 2020, advances in polygenic risk scores, in understanding the cell and modules of action of genes through genome-wide association studies (GWAS), and in predicting the impact of combinations of interventions.
  • we need algorithms to make better computational predictions of experiments we have never performed in the lab or in clinical trials.
  • Human Cell Atlas and the International Common Disease Alliance—and in new experimental platforms: data platforms and algorithms. But we also need a broader ecosystem of partnerships in medicine that engages interaction between clinical experts and mathematicians, computer scientists and engineers

Feng Zhang, PhD

investigator, Howard Hughes Medical Institute; core member, Broad Institute of MIT and Harvard; James and Patricia Poitras Professor of Neuroscience, McGovern Institute for Brain Research, MIT.

  • fundamental shift in medicine away from treating symptoms of disease and toward treating disease at its genetic roots.
  • Gene therapy with clinical feasibility, improved delivery methods and the development of robust molecular technologies for gene editing in human cells, affordable genome sequencing has accelerated our ability to identify the genetic causes of disease.
  • 1,000 clinical trials testing gene therapies are ongoing, and the pace of clinical development is likely to accelerate.
  • refine molecular technologies for gene editing, to push our understanding of gene function in health and disease forward, and to engage with all members of society

Elizabeth Jaffee, PhD

Dana and Albert “Cubby” Broccoli Professor of Oncology, Johns Hopkins School of Medicine; deputy director, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins.

  • a single blood test could inform individuals of the diseases they are at risk of (diabetes, cancer, heart disease, etc.) and that safe interventions will be available.
  • developing cancer vaccines. Vaccines targeting the causative agents of cervical and hepatocellular cancers have already proven to be effective. With these technologies and the wealth of data that will become available as precision medicine becomes more routine, new discoveries identifying the earliest genetic and inflammatory changes occurring within a cell as it transitions into a pre-cancer can be expected. With these discoveries, the opportunities to develop vaccine approaches preventing cancers development will grow.

Jeremy Farrar, OBE FRCP FRS FMedSci

Director, Wellcome Trust.

  • shape how the culture of research will develop over the next 25 years, a culture that cares more about what is achieved than how it is achieved.
  • building a creative, inclusive and open research culture will unleash greater discoveries with greater impact.

John Nkengasong, PhD

Director, Africa Centres for Disease Control and Prevention.

  • To meet its health challenges by 2050, the continent will have to be innovative in order to leapfrog toward solutions in public health.
  • Precision medicine will need to take center stage in a new public health order— whereby a more precise and targeted approach to screening, diagnosis, treatment and, potentially, cure is based on each patient’s unique genetic and biologic make-up.

Eric Topol, MD

Executive vice-president, Scripps Research Institute; founder and director, Scripps Research Translational Institute.

  • In 2045, a planetary health infrastructure based on deep, longitudinal, multimodal human data, ideally collected from and accessible to as many as possible of the 9+ billion people projected to then inhabit the Earth.
  • enhanced capabilities to perform functions that are not feasible now.
  • AI machines’ ability to ingest and process biomedical text at scale—such as the corpus of the up-to-date medical literature—will be used routinely by physicians and patients.
  • the concept of a learning health system will be redefined by AI.

Linda Partridge, PhD

Professor, Max Planck Institute for Biology of Ageing.

  • Geroprotective drugs, which target the underlying molecular mechanisms of ageing, are coming over the scientific and clinical horizons, and may help to prevent the most intractable age-related disease, dementia.

Trevor Mundel, MD

President of Global Health, Bill & Melinda Gates Foundation.

  • finding new ways to share clinical data that are as open as possible and as closed as necessary.
  • moving beyond drug donations toward a new era of corporate social responsibility that encourages biotechnology and pharmaceutical companies to offer their best minds and their most promising platforms.
  • working with governments and multilateral organizations much earlier in the product life cycle to finance the introduction of new interventions and to ensure the sustainable development of the health systems that will deliver them.
  • deliver on the promise of global health equity.

Josep Tabernero, MD, PhD

Vall d’Hebron Institute of Oncology (VHIO); president, European Society for Medical Oncology (2018–2019).

  • genomic-driven analysis will continue to broaden the impact of personalized medicine in healthcare globally.
  • Precision medicine will continue to deliver its new paradigm in cancer care and reach more patients.
  • Immunotherapy will deliver on its promise to dismantle cancer’s armory across tumor types.
  • AI will help guide the development of individually matched
  • genetic patient screenings
  • the promise of liquid biopsy policing of disease?

Pardis Sabeti, PhD

Professor, Harvard University & Harvard T.H. Chan School of Public Health and Broad Institute of MIT and Harvard; investigator, Howard Hughes Medical Institute.

  • the development and integration of tools into an early-warning system embedded into healthcare systems around the world could revolutionize infectious disease detection and response.
  • But this will only happen with a commitment from the global community.

Els Toreele, PhD

Executive director, Médecins Sans Frontières Access Campaign

  • we need a paradigm shift such that medicines are no longer lucrative market commodities but are global public health goods—available to all those who need them.
  • This will require members of the scientific community to go beyond their role as researchers and actively engage in R&D policy reform mandating health research in the public interest and ensuring that the results of their work benefit many more people.
  • The global research community can lead the way toward public-interest driven health innovation, by undertaking collaborative open science and piloting not-for-profit R&D strategies that positively impact people’s lives globally.

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CRISPR companies calling for article retraction from Nature Methods – If the same or similar sequence of letters appears elsewhere in the genome, that can result in an unintentional or off-target edit – Concerns of Harm caused by Gene Editing using CRISPR-Cas9

 

Reporter: Aviva Lev-Ari, PhD, RN

Storm around the call for “Nature Methods editorial board to retract this paper.”

A spokesperson at Springer Nature, which publishes Nature Methods, said the organization had received “a number of communications” already about the paper. “We are carefully considering all concerns that have been raised with us and are discussing them with the authors,” the journal said. Vinit Mahajan of Stanford University, who was the paper’s senior author, did not immediately respond to a request for comment. Another author, Alexander Bassuck of the University of Iowa, said he was traveling and unable to respond immediately.

 

The paper, titled

Unexpected mutations after CRISPR–Cas9 editing in vivo, triggered a rash of negative headlines after claiming the gene-editing tool caused widespread and unpredictable havoc in the genomes of edited mice, introducing hundreds of unintended errors.

The stock market value of Editas Medicine, Intellia Therapeutics, and CRISPR Therapeutics, which together have raised more than $1 billion to pursue CRISPR treatments, all fell sharply on the news.

CRISPR technology is widely touted as a revolutionary new means of easily altering DNA. But its promise is being exaggerated in media reports, including some that claim it will cure all genetic disease and solve the world’s food problems with superplants.

CRISPR can be programmed to cut specific sequences of DNA letters, thereby correcting or changing genes. While this versatility is what makes it powerful, if the same or similar sequence of letters appears elsewhere in the genome, that can result in an unintentional or off-target edit. Concern over the technique’s potential side effects is widely shared, even by some of its inventors.

The fear is that planned medical treatments using CRISPR could prove dangerous. A single erroneous cut could be disastrous for patients if it lands in a vital gene. Fifteen years ago, pioneering experiments in gene therapy were set back when unintentional genetic changes caused cancer in some children. Many scientists believe careful programming can eliminate most of the risk.

The ease of use of CRISPR means nearly any lab can try it. In China, some human experiments have already begun. The rush to use the method is part of what’s creating anxiety, since it makes mistakes more likely. Editas recently postponed its own planned study of CRISPR to correct an eye disease until next year.

According to Intellia, however, the authors showed “disregard” for what’s already known about CRISPR. “It is clear the authors are not experts on the CRISPR Cas9, whole genome sequencing, nor basic genetics. Their claim of ‘unexpected mutations’ clearly demonstrates their lack of scientific acumen around this topic,” the company said.

SOURCE

Gene-Editing Companies Hit Back at Paper That Criticized CRISPR

Report that suggested CRISPR is too dangerous to use as a drug was wrong, say biotech companies.

Jun 9, 2017

EmTech: Risks of Gene-Editing Drugs Need Study, Pioneer Warns

One of the inventors of gene editing says scientists should proceed cautiously before testing it in people.

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Human gene editing continues to hold a major fascination within a biomedical and biopharmaceutical industries. It’s extraordinary potential is now being realized but important questions as to who will be the beneficiaries of such breakthrough technologies remained to be answered. The session will discuss whether gene editing technologies can alleviate some of the most challenging unmet medical needs. We will discuss how research advances often never reach minority communities and how diverse patient populations will gain access to such breakthrough technologies. It is widely recognize that there are patient voids in the population and we will explore how community health centers might fill this void to ensure that state-of-the-art technologies can reach the forgotten patient groups . We also will touch ethical questions surrounding germline editing and how such research and development could impact the community at large.

Please follow LIVE on TWITTER using the following @ handles and # hashtags:

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CRISPR cuts turn gels into biological watchdogs

Reporter: Irina Robu, PhD

Genome editing if of significant interest in the prevention and treatment of human diseases including single-gene disorders such as cystic fibrosis, hemophilia and sickle cell disease. It also shows great promise for the prevention and treatment of diseases such as cancer, heart disease, mental illness and human immunodeficiency virus infection. However, ethical concerns arise when genome editing, using technologies such as CRISPR-Cas9 is used to alter human genomes.

James Collins, bioengineer at MIT and his team worked with water-filled polymers that are held together by strands of DNA, known as DNA hydrogels. To alter the properties of these materials, these scientists turned to a form of CRISPR that uses a DNA-snipping enzyme called Cas12a, which can be programed to recognize a specific DNA sequence. The enzyme then cuts its target DNA strand, then severs single strands of DNA nearby. This property lets scientists to build a series of CRISPR-controlled hydrogels encapsulating a target DNA sequence and single strands of DNA, which break up after Cas12a identifies the target sequence in a stimulus. The break-up of the single DNA strands activates the hydrogels to change shape or completely dissolve, releasing a payload.

According to Collins and his team, the programmed hydrogels will release enzymes, small molecules and human cells as part of a smart therapy in response to stimuli. However, in order to make it a smart therapeutic, the researchers in collaboration with Dan Luo, bioengineer at Cornell University placed the CRISPR- controlled hydrogels into electric circuits. The circuit is switched off in response to the detection of the genetic material of harmful pathogens such as Ebola virus and methicillin-resistant Staphylococcus aureus. The team used these hydrogels to develop a prototype diagnostic tool that sends a wireless signal to identify Ebola in lab samples.

Yet, it is evident that these CRISPR-controlled hydrogels show great potential for the prevention and treatment of diseases.

SOURCE

https://www.nature.com/articles/d41586-019-02542-3?utm_source=Nature+Briefing

 

 

 

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At Technical University of Munich (TUM) Successful Genetical modification of a patient’s own immune cells, T cell receptors, using CRISPR-Cas9 gene editing tool. The engineered T cells are very similar to the physiological immune cells.

Reporter: Aviva Lev-Ari, PhD, RN

 

Targeted exchange using the CRISPR-Cas9 gene scissors

The problem with conventional methods is that the genetic information for the new receptors is randomly inserted into the genome. This means that T cells are produced with both new and old receptors or with receptors having one old and one new chain. As a result, the cells do not function as effectively as physiological T cells and are also controlled differently. Moreover, there is a danger that the mixed chains could trigger dangerous side effects (Graft-versus-Host Disease, GvHD).

“Using the CRISPR method, we’ve been able to completely replace the natural receptors with new ones, because we’re able to insert them into the very same location in the genome. In addition, we’ve replaced the information for both chains so that there are no longer any mixed receptors,” explains Kilian Schober, who is a lead author of the new study along with his colleague Thomas Müller.

Near-natural properties

Thomas Müller explains the advantages of the modified T cells: “They’re much more similar to physiological T cells, yet they can be changed flexibly. They’re controlled like physiological cells and have the same structure, but are capable of being genetically modified.“ The scientists have demonstrated in a cell culture model that T cells modified in this way behave nearly exactly like their natural counterparts.

“Another advantage is that the new method allows multiple T cells to be modified simultaneously so that they’re able to recognize different targets and can be used in combination. This is especially interesting for cancer therapy, because tumors are highly heterogeneous,” Dirk Busch adds. In the future, the team plans to investigate the new cells and their properties in preclinical mouse models, an important step in preparing for clinical trials with humans.

Original Publication

Kilian Schober, Thomas R. Müller, Füsun Gökmen, Simon Grassmann, Manuel Effenberger, Mateusz Poltorak, Christian Stemberger, Kathrin Schumann, Theodore L. Roth, Alexander Marson and Dirk H. Busch: Orthotopic replacement of T-cell receptor ɑ- and β-chains with preservation of near-physiological, Nature Biomedical Engineering, June 12, 2019, DOI: 10.1038/s41551-019-0409-0

 

SOURCE

https://www.tum.de/nc/en/about-tum/news/press-releases/details/35560/

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@BroadInstitute a shift from Permanently editing DNA to Temporarily revising RNA – An approach with promise for addressing the risk of developing Alzheimer’s by deactivating APOE4 – RESCUE: RNA Editing for Specific C to U Exchange, the platform builds on REPAIR: RNA Editing for Programmable A to I

Reporter: Aviva Lev-Ari, PhD, RN

 

  • The RNA editors converted “the nucleotide base adenine to inosine, or letters A to I. Zhang and colleagues took the REPAIR fusion and evolved it in the lab until it could change cytosine to uridine, or C to U.”
  • Using Cas13, Zhang’s team was able to take the APOE4 gene — believed to carry the added risk of spurring Alzheimer’s — and changed it to a benign APOE2.

RNA-guided DNA insertion with CRISPR-associated transposases

Science  05 Jul 2019:
Vol. 365, Issue 6448, pp. 48-53
DOI: 10.1126/science.aax9181
SOURCE

Other related articles on CRISPR derived Gene Editing for Gene Therapy published in this Open Access on Online Scientific Journal include the following:

 

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

Forthcoming 12/2019, Volume Two

by

Prof. Marcus W. Feldman, PhD, Editor, Stanford University

Prof. Stephen J. Williams, PhD, Editor, Temple University

and Aviva Lev-Ari, PhD, RN, Editor, LPBI Group 

 

Part 2: CRISPR for Gene Editing and DNA Repair

2.1 The Science – 77 articles

2.2 Technologies and Methodologies – 27 articles

2.3 Clinical Aspects – 9 articles

2.4 Business and Legal – 18 articles

 

Series B: Frontiers in Genomics Research

 

  • VOLUME 1: Genomics Orientations for Personalized Medicine. On Amazon.com since 11/23/2015

http://www.amazon.com/dp/B018DHBUO6

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