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Archive for the ‘Personalized and Precision Medicine & Genomic Research’ Category

Record Innovations in Drug Discovery by Koch Institute @MIT Members and Affiliates

Reporter: Aviva Lev-Ari, PhD, RN

 

 

In Good Company

Trovagene announced a new patent for the use of the drug onvansertib in combination with other anti-androgen drugs for the treatment of prostate cancer. Last fall, Trovagene secured exclusive rights to develop combination therapies and clinical biomarkers for prostate cancer based in part on Bridge Project-funded research. Read more.

Lyndra Therapeutics, co-founded by KI member Bob Langer, raised $55 million in its Series B round, with new investors including the Bill and Melinda Gates Foundation and Gilead Sciences. Phase 2 trials for its ultra long-acting drug delivery capsule are expected to begin next year. Read more.

Dragonfly Therapeutics, co-founded by KI director Tyler Jacks, has committed $10 million to launch the first clinical studies of its TriNKETs (Tri-specific, NK cell Engager Therapies) platform for both solid tumor and hematological cancers. Read more.

Following its record-breaking IPO, Moderna Therapeutics (co-founded by KI member Bob Langer) published preclinical data in Science Translational Medicine demonstrating the promise of its mRNA-2752 program in several cancers. Read more.

Dewpoint Therapeutics launched with a $60 million Series A, aims to translate recent insights into biomolecular condensates from the laboratory of co-founder and KI member Rick Young to drug discovery. Read more.

KI member Bob Langer and collaborator Omid Farokhzad co-founded Seer— combining nanotechnology, protein chemistry, and machine learning—to develop liquid biopsy tests for the early detection of cancer and other diseases. Read more.

Epizyme, co-founded by KI member Bob Horvitz, is submitting a New Drug Application to gain accelerated approval of tazemetostat for patients with relapsed or refractory follicular lymphoma. Read more.

Ribon Therapeutics, founded by former KI member Paul Chang, launched with $65 million in a Series B funding round with Victoria Richon, a veteran of Sanofi and Epizyme, at the helm. Ribon focuses on developing PARP7 inhibitors for cancer treatment. Read more.

SOURCE

From: MIT Koch Institute for Integrative Cancer Research <cancersolutions=mit.edu@cmail19.com> on behalf of MIT Koch Institute for Integrative Cancer Research <cancersolutions@mit.edu>

Reply-To: <ki-communications@mit.edu>

Date: Wednesday, February 6, 2019 at 3:15 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: Lung Microbiome Corrupted in Cancer; Angelika Amon wins 2019 Vilcek Award; Lunch Lines of Inquiry

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Cell Therapy Market to Grow Beyond Oncology As Big Pharma Expands Investments

Reporter: Irina Robu, PhD

Collaborations of Big Pharma with small to mid-segment companies are currently focusing R&D on precision medicine. The market is valued at $2.70 billion in 2017 and is expected to reach $8.21 billion in 2025. A varied therapeutic focus and implementation of advanced manufacturing technologies such as single-use bioreactors, will pave a way for unique cell-gene and stem cell – gene combination therapies.
Novartis and Gilead are the first companies to adopt pay for performance business for their CAR-T cell therapies. In addition to innovative pricing models, Pharma companies are also showing a preference for risk sharing and fast-to-market models in order to support the development of novel therapies. Moreover, developments in cell culturing techniques alongside the use of different stem cells such as adipose-derived stem cells, mesenchymal stem cells, and induced pluripotent stem cell will reinforce the market with superior treatment options for non-oncological conditions such as neurological, musculoskeletal, and dermatological conditions.

With the high request for cell therapies, numerous growth opportunities can occur such as:

  • With more than 959 ongoing regenerative medicine clinical trials, the market finds opportunity across both stem cell and non-stem cell-based therapies.
  • Curative combination therapies which help find application in identifying the right patient as well as predicting the immune response in cancer patients.
  • Implementation of IT solutions and single-use manufacturing techniques for optimizing small-volume, high-value manufacturing of novel cell therapies, thus dropping the time to market radically.
  • Emerging Business Models which aid market players focus on academic and research collaborations together with industry collaborations to support therapeutic and technological innovations.

Source

https://www.newswire.ca/news-releases/cell-therapy-market-to-grow-beyond-oncology-as-big-pharma-expands-investments-826628110.html

 

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@Amazon.com @pharma_BI BUNDLES for $274 #Patients #Voices #Precision #Medicine #Physiology #Genomics #Therapeutics #3D #BioPrinting: Series E: Volumes 1,2,3,4 by Editors:

Larry H Bernstein @bernstein_h  

Gail Thornton @GailThornt 

Aviva Lev-Ari @AVIVA1950 ‏

 

Article ID #263: @Amazon.com @pharma_BI BUNDLES for $274 #Patients #Voices #Precision #Medicine #Physiology #Genomics #Therapeutics #3D #BioPrinting: Series E: Volumes 1,2,3,4 by Editors:  Larry H Bernstein @bernstein_h   Gail Thornton @GailThornt  Aviva Lev-Ari @AVIVA1950. Published on 1/20/2019

WordCloud Image Produced by Adam Tubman

Series E: Patient-Centered Medicine – LINKS to e-Books & Cover Pages for Volumes 1,2,3,4

 

  • Volume 1: The VOICES of Patients, Hospitals CEOs, Health Care Providers, Caregivers and Families: Personal Experience with Critical Care and Invasive Medical Procedures. On Amazon.com  since 10/16/2017

https://www.amazon.com/dp/B076HGB6MZ

 
  • Volume 2: Medical Scientific Discoveries for the 21st Century & Interviews with Scientific Leaders. On Amazon.com since12/9/2017

https://www.amazon.com/dp/B078313281

 

 

 
  • Volume 3: Milestones in Physiology: Discoveries in Medicine, Genomics and Therapeutics. On Amazon.com since 12/27/2015

http://www.amazon.com/dp/B019VH97LU

 
  • Volume 4: Medical 3D BioPrinting – The Revolution in Medicine, Technologies for Patient-centered Medicine: From R&D in Biologics to New Medical Devices. On Amazon.com  since 12/30/2017

https://www.amazon.com/dp/B078QVDV2W

 

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The Puzzle of Stem Cells and Cancer Stem Cells: The MIT Stem Cell Initiative

Reporter: Irina Robu, PhD

The MIT Stem Cell Initiative is looking to research fundamental biological questions about normal adult stem cells and their malignant counterparts, cancer stem cells. The MIT Stem Cell Initiative is applying new technologies and approaches in pursuit of this goal. In particular, the MIT Stem Cell Initiative has focused on the breast and colon, as these tissues are quite different from each other, yet each constitutes a major portion of cancer occurrence. The program purposes are to

(a) identify the stem cells and cancer stem cells in various tissues and tumor types,

(b) control how these cells change during aging or with disease progression and

(c) determine the similarities and differences between

  • normal cells, and
  • cancer stem cells,

with the goal of finding weaknesses in cancer stem cells that can be feasible and exact targets for treatment.

In due course, the ability to identify, purify, and establish several populations of stem cells and cancer stem cells could aid researchers to understand the biology of these cells, and learn how to exploit them more efficiently in regenerative medicine applications and target them in cancer.

Normal adult stem cells are undifferentiated cells within a tissue that divide to produce two daughter cells and divide periodically to replenish or repair the tissue. One of the two daughter cells remain in the stem cell state and the other adopts a partially differentiated state, then goes on to divide and differentiate further to harvest multiple cell types that form that tissue. The division process is through a precise process to ensure that tissues are restricted to the appropriate size and cell content.

Cancer stem cells perform the same division but, rather than differentiating, the additional cells produced by the second daughter cell amass to form the bulk of the tumor.

  • Cancer stem cells can regrow the tumor, and
  • are frequently resistant to chemotherapy.

This exclusive ability of normal and cancer stem cells to both self-renew and form a tissue or tumor is referred to by researchers as “stemness,” and has important implications for biomedical applications.

As a result, cancer stem cells are thought to be responsible for

  • tumor recurrence after remission, and also for the
  • formation of metastases, which account for the majority of cancer-associated deaths.

Accordingly, an anti-cancer stem cell therapy that can target and kill cancer stem cells is one of the holy grail of cancer treatment as means to suppress both tumor recurrence and metastatic disease. One of the important tasks to studying normal and cancer stem cells, and to ultimately harnessing that knowledge is developing the ability to identify, purify, and propagate these cells. Accordingly, the main goal in stem cell and cancer stem cell research is discovering ways to distinguish them, preferably by identifying unique surface markers that can be used to cleanse stem cell and cancer stem cell populations and enable their study.

New technologies are permitting the researchers to make significant headway in these investigations, progress that was not possible just a few years ago. Explicitly, they are using

  • a mixture of specially cultured cells,
  • highly controllable mouse models of cancer, and s
  • ingle-cell RNA sequencing and
  • computational analysis techniques that are extremely matched to extracting an excessive deal of information from the moderately small number of stem cells.

SOURCE

http://news.mit.edu/2018/mit-initiative-delves-into-stem-cell-biology-1015

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37th Annual J.P. Morgan HEALTHCARE CONFERENCE: News at #JPM2019 for Jan. 10, 2019: Deals and Announcements

Reporter: Stephen J. Williams, Ph.D.

From Biospace.com

 

JP Morgan Healthcare Conference Update: Sage, Mersana, Shutdown Woes and Babies

Speaker presenting to audience at a conference

With the J.P. Morgan Healthcare Conference winding down, companies remain busy striking deals and informing investors about pipeline advances. BioSpace snagged some of the interesting news bits to come out of the conference from Wednesday.

SAGE Therapeutics – Following a positive Phase III report that its postpartum depression treatment candidate SAGE-217 hit the mark in its late-stage clinical trial, Sage Therapeutics is eying the potential to have multiple treatment options available for patients. At the start of J.P. Morgan, Sage said that patients treated with SAGE-217 had a statistically significant improvement of 17.8 points in the Hamilton Rating Scale for Depression, compared to 13.6 for placebo. The company plans to seek approval for SAGE-2017, but before that, the FDA is expected to make a decision on Zulresso in March. Zulresso already passed muster from advisory committees in November, and if approved, would be the first drug specifically for postpartum depression. In an interview with the Business Journal, Chief Business Officer Mike Cloonan said the company believes there is room in the market for both medications, particularly since the medications address different patient populations.

 

Mersana Therapeutics – After a breakup with Takeda Pharmaceutical and the shelving of its lead product, Cambridge, Mass.-based Mersana is making a new path. Even though a partial clinical hold was lifted following the death of a patient the company opted to shelve development of XMT-1522. During a presentation at JPM, CEO Anna Protopapas noted that many other companies are developing therapies that target the HER2 protein, which led to the decision, according to the Boston Business Journal. Protopapas said the HER2 space is highly competitive and now the company will focus on its other asset, XMT-1536, an ADC targeting NaPi2b, an antigen highly expressed in the majority of non-squamous NSCLC and epithelial ovarian cancer. XMT-1536 is currently in Phase 1 clinical trials for NaPi2b-expressing cancers, including ovarian cancer, non-small cell lung cancer and other cancers. Data on XMT-1536 is expected in the first half of 2019.

Novavax – During a JPM presentation, Stan Erck, CEO of Novavax, pointed to the company’s RSV vaccine, which is in late-stage development. The vaccine is being developed for the mother, in order to protect an infant. The mother transfers the antibodies to the infant, which will provide the baby with protection from RSV in its first six months. Erck called the program historic. He said the Phase III program is in its fourth year and the company has vaccinated 4,636 women. He said they are tracking the women and the babies. Researchers call the mothers every week through the first six months of the baby’s life to acquire data. Erck said the company anticipates announcing trial data this quarter. If approved, Erck said the market for the vaccine could be a significant revenue driver.

“You have 3.9 million birth cohorts and we expect 80 percent to 90 percent of those mothers to be vaccinated as a pediatric vaccine and in the U.S. the market rate is somewhere between $750 million and a $1 billion and then double that for worldwide market. So it’s a large market and we will be first to market in this,” Erck said, according to a transcript of the presentation.

Denali Therapeutics – Denali forged a collaboration with Germany-based SIRION Biotech to develop gene therapies for central nervous disorders. The two companies plan to develop adeno-associated virus (AAV) vectors to enable therapeutics to cross the blood-brain barrier for clinical applications in neurodegenerative diseases including Parkinson’s, Alzheimer’s disease, ALS and certain other diseases of the CNS.

AstraZeneca – Pharma giant AstraZeneca reported that in 2019 net prices on average across the portfolio will decrease versus 2018. With a backdrop of intense public and government scrutiny over pricing, Market Access head Rick Suarez said the company is increasing its pricing transparency. Additionally, he said the company is looking at new ways to price drugs, such as value-based reimbursement agreements with payers, Pink Sheet reported.

Amarin Corporation – As the company eyes a potential label expansion approval for its cardiovascular disease treatment Vascepa, Amarin Corporation has been proactively hiring hundreds of sales reps. In the fourth quarter, the company hired 265 new sales reps, giving the company a sales team of more than 400, CEO John Thero said. Thero noted that is a label expansion is granted by the FDA, “revenues will increase at least 50 percent over what we did in the prior year, which would give us revenues of approximate $350 million in 2019.”

Government Woes – As the partial government shutdown in the United States continues into its third week, biotech leaders at JPM raised concern as the FDA’s carryover funds are dwindling. With no new funding coming in, reviews of New Drug Applications won’t be able to continue past February, Pink Sheet said. While reviews are currently ongoing, no New Drug Applications are being accepted by the FDA at this time. With the halt of NDA applications, that has also caused some companies to delay plans for an initial public offering. It’s hard to raise potential investor excitement without the regulatory support of a potential drug approval. During a panel discussion, Jonathan Leff, a partner at Deerfield Management, noted that the ongoing government shutdown is a reminder of how “overwhelmingly dependent the whole industry of biotech and drug development is on government,” Pink Sheet said.

Other posts on the JP Morgan 2019 Healthcare Conference on this Open Access Journal include:

#JPM19 Conference: Lilly Announces Agreement To Acquire Loxo Oncology

36th Annual J.P. Morgan HEALTHCARE CONFERENCE January 8 – 11, 2018

37th Annual J.P. Morgan HEALTHCARE CONFERENCE: #JPM2019 for Jan. 8, 2019; Opening Videos, Novartis expands Cell Therapies, January 7 – 10, 2019, Westin St. Francis Hotel | San Francisco, California

37th Annual J.P. Morgan HEALTHCARE CONFERENCE: News at #JPM2019 for Jan. 8, 2019: Deals and Announcements

 

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2019 Trends in Precision Medicine: A Perspective from Foundation Medicine

Reporter: Aviva Lev-Ari, PhD, RN

 

BIOPHARMA, DIAGNOSTICS

Foundation Medicine appoints new CEO; exec provides forecasts for precision medicine in 2019

With the approval of Loxo’s Vitrakvi, pan-cancer drugs and an emphasis on real-world data are likely to become important trends trends this year.

A next-generation sequencing firm that last year became wholly owned by Swiss drugmaker Roche has appointed a new leader.

Cambridge, Massachusetts-based Foundation Medicine said Monday that it had appointed Cindy Perettie as CEO, effective Feb. 4. Succeeding Troy Cox, Perettie was most recently senior vice president for global oncology product strategy at Roche’s oncology unit. She previously had begun working for Genentech in 2004 and continued working there through that company’s 2009 acquisition by Roche, before moving to the Sarah Cannon Research Institute as president for global development innovations.

Foundation Medicine markets genomic sequencing products for use in oncology, including in next-generation sequencing for solid and hematological cancers and liquid biopsy. Roche, which was already a majority shareholder in the company, bought the rest of it in June for $2.4 billion.

The Roche acquisition and new executive appointment have come at a time when genomic sequencing has become a crucial component of precision medicine.

In an interview at the J.P. Morgan Healthcare Conference in San Francisco, Chief Business Officer Melanie Nallicheri did not comment on Perettie’s appointment, but discussed some of her expectations for what 2019 has in store for precision medicine.

In particular, she said the November approval of Loxo Oncology and Bayer’s Vitrakvi (larotrectinib) is a taste of things to come. “This is the second pan-cancer approval,” she said. “So the notion of really moving away from cancer as a tissue disease to cancer as a genomic disease, we’re starting to see that take hold.

Loxo has a partnership with Illumina to develop a companion diagnostic for Vitrakvi, though Nallicheri noted that Foundation Medicine works with the company as well. Eli Lilly & Co. said Monday it would acquire Loxo for $8 billion.

When there was only one such approval, namely for Merck & Co.’s Keytruda (pembrolizumab) in microsatellite instability-high and mismatch repair-deficiency cancers in 2017, it may have been possible to say that was a one-off, she said. But Vitrakvi’s approval changes that. Yet, even the Keytruda approval may be predictive. Quantitative biomarkers like MSI-H and tumor mutational burden can support approval, so that’s probably an important trend of which more will be seen.

Another area in which Nallicheri said Foundation Medicine can have a role is in providing real-world clinical data, which she said is also likely to become an important trend in 2019, particularly given the guidance from the Food and Drug Administration. A guidance released last month outlined a new framework for advancing real-world evidence to support drug and biologic development. In addition, in a breakout session at JPM Tuesday, executives from Roche emphasized the potential for historical data to serve as a synthetic control arm, pointing to the Swiss drugmaker’s $1.9 billion acquisition of Flatiron Health in February 2018. “The idea that you can replace control arms with historical data is tangible,” Roche CEO Severin Schwan said in the session. “This is not just a hypothesis – it’s real life.”

SOURCE

https://medcitynews.com/2019/01/foundation-medicine-appoints-new-ceo-exec-provides-forecasts-for-precision-medicine-in-2019/?rf=1

 

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

#JPM19 Conference: Lilly Announces Agreement To Acquire Loxo Oncology

PMC Strategic Plan for 2019

37th Annual J.P. Morgan HEALTHCARE CONFERENCE: #JPM2019 for Jan. 8, 2019; Opening Videos, Novartis expands Cell Therapies, January 7 – 10, 2019, Westin St. Francis Hotel | San Francisco, California

37th Annual J.P. Morgan HEALTHCARE CONFERENCE: News at #JPM2019 for Jan. 8, 2019: Deals and Announcements

 

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

  • VOLUME 2: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS & BioInformatics, Simulations and the Genome Ontology

https://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-two-genomics-methodologies-ngs-bioinformatics-simulations-and-the-genome-ontology/

Work-in-Progress

 

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Personalized Medicine Coalition (PMC), PMC’s Strategic Plan for 2019

Reporter: Aviva Lev-Ari, PhD, RN

 

​

​

 

Dear Colleague:


Recognizing that almost 40 percent of those who responded to the strategic planning survey underpinning the plan did not agree that “it is inevitable that all doctors will someday practice personalized medicine [because] the science and technology will demand it,” the Coalition has outlined robust efforts to encourage and nurture medical progress through education, advocacy, and evidence development.
On behalf of the Personalized Medicine Coalition (PMC), I am pleased to share PMC’s Strategic Plan for 2019.

Unless payers, providers, patients, and policymakers are aware of personalized medicine, it will be harder to increase research funding and propose smart public policies that encourage integrating diagnostics into therapeutic decisions.

And unless we develop the evidence base necessary to demonstrate the clinical and economic value of personalized medicine, those decision-makers are not going to embrace it, and, in fact, may propose policies, like “step therapy” — paying for what costs least first — that fly in the face of the principles of personalized medicine.

In short, in keeping with the scientific and technological progress of recent years, we need to redouble our efforts to deliver the promise of personalized medicine — better clinical outcomes and more efficient health systems. The stakes are very high.

We welcome your participation in PMC this year. Without it, progress will be much slower than any of us would like.

Please contact PMC Membership & Development Director Kayla Smith at ksmith@personalizedmedicinecoalition.org with questions about how to get involved with any of the projects listed in the plan.

Sincerely yours,

Edward Abrahams

President

SOURCE

rom: Personalized Medicine Coalition <messages@app.production.membersuite.com>

Reply-To: “Christopher Wells (PMC)” <cwells@personalizedmedicinecoalition.org>

Date: Wednesday, January 9, 2019 at 9:36 AM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: PMC Strategic Plan for 2019

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Role of Informatics in Precision Medicine: Notes from Boston Healthcare Webinar: Can It Drive the Next Cost Efficiencies in Oncology Care? Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Role of Informatics in Precision Medicine: Notes from Boston Healthcare Webinar: Can It Drive the Next Cost Efficiencies in Oncology Care?

Reporter: Stephen J. Williams, Ph.D.

 

Boston Healthcare sponsored a Webinar recently entitled ” Role of Informatics in Precision Medicine: Implications for Innovators”.  The webinar focused on the different informatic needs along the Oncology Care value chain from drug discovery through clinicians, C-suite executives and payers. The presentation, by Joseph Ferrara and Mark Girardi, discussed the specific informatics needs and deficiencies experienced by all players in oncology care and how innovators in this space could create value. The final part of the webinar discussed artificial intelligence and the role in cancer informatics.

 

Below is the mp4 video and audio for this webinar.  Notes on each of the slides with a few representative slides are also given below:

Please click below for the mp4 of the webinar:

 

 


  • worldwide oncology related care to increase by 40% in 2020
  • big movement to participatory care: moving decision making to the patient. Need for information
  • cost components focused on clinical action
  • use informatics before clinical stage might add value to cost chain

 

 

 

 

Key unmet needs from perspectives of different players in oncology care where informatics may help in decision making

 

 

 

  1.   Needs of Clinicians

– informatic needs for clinical enrollment

– informatic needs for obtaining drug access/newer therapies

2.  Needs of C-suite/health system executives

– informatic needs to help focus of quality of care

– informatic needs to determine health outcomes/metrics

3.  Needs of Payers

– informatic needs to determine quality metrics and managing costs

– informatics needs to form guidelines

– informatics needs to determine if biomarkers are used consistently and properly

– population level data analytics

 

 

 

 

 

 

 

 

 

 

 

 

What are the kind of value innovations that tech entrepreneurs need to create in this space? Two areas/problems need to be solved.

  • innovations in data depth and breadth
  • need to aggregate information to inform intervention

Different players in value chains have different data needs

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Data Depth: Cumulative Understanding of disease

Data Depth: Cumulative number of oncology transactions

  • technology innovators rely on LEGACY businesses (those that already have technology) and these LEGACY businesses either have data breath or data depth BUT NOT BOTH; (IS THIS WHERE THE GREATEST VALUE CAN BE INNOVATED?)
  • NEED to provide ACTIONABLE as well as PHENOTYPIC/GENOTYPIC DATA
  • data depth more important in clinical setting as it drives solutions and cost effective interventions.  For example Foundation Medicine, who supplies genotypic/phenotypic data for patient samples supplies high data depth
  • technologies are moving to data support
  • evidence will need to be tied to umbrella value propositions
  • Informatic solutions will have to prove outcome benefit

 

 

 

 

 

How will Machine Learning be involved in the healthcare value chain?

  • increased emphasis on real time datasets – CONSTANT UPDATES NEED TO OCCUR. THIS IS NOT HAPPENING BUT VALUED BY MANY PLAYERS IN THIS SPACE
  • Interoperability of DATABASES Important!  Many Players in this space don’t understand the complexities integrating these datasets

Other Articles on this topic of healthcare informatics, value based oncology, and healthcare IT on this OPEN ACCESS JOURNAL include:

Centers for Medicare & Medicaid Services announced that the federal healthcare program will cover the costs of cancer gene tests that have been approved by the Food and Drug Administration

Broad Institute launches Merkin Institute for Transformative Technologies in Healthcare

HealthCare focused AI Startups from the 100 Companies Leading the Way in A.I. Globally

Paradoxical Findings in HealthCare Delivery and Outcomes: Economics in MEDICINE – Original Research by Anupam “Bapu” Jena, the Ruth L. Newhouse Associate Professor of Health Care Policy at HMS

Google & Digital Healthcare Technology

Can Blockchain Technology and Artificial Intelligence Cure What Ails Biomedical Research and Healthcare

The Future of Precision Cancer Medicine, Inaugural Symposium, MIT Center for Precision Cancer Medicine, December 13, 2018, 8AM-6PM, 50 Memorial Drive, Cambridge, MA

Live Conference Coverage @Medcity Converge 2018 Philadelphia: Oncology Value Based Care and Patient Management

2016 BioIT World: Track 5 – April 5 – 7, 2016 Bioinformatics Computational Resources and Tools to Turn Big Data into Smart Data

The Need for an Informatics Solution in Translational Medicine

 

 

 

 

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Gene-editing Second International Summit in Hong Kong: George Church, “Let’s be quantitative before we start being accusatory”

Reporter: Aviva Lev-Ari, PhD, RN

2.1.4.3

2.1.4.3   Gene-editing Second International Summit in Hong Kong: George Church, “Let’s be quantitative before we start being accusatory”, 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

UPDATED on 11/30/2018

Gene editing takes a foreboding leap forward

He Jiankui. Photo: Zhang Wei/Chinese News Service/VCG via Getty Images

 

China is temporarily suspending the work of scientists who claimed twins were born after being genetically edited as embryos.

Why it matters: The scientific consensus is that gene editing embryos at this stage of science is “irresponsible.” But, while this particular experiment has not been verified, the fact is the technology is available to researchers, so there’s a growing call for international limitations on its use.

ICYMI: Chinese scientist He Jiankui announced earlier this week that twins were born after he used the gene-editing tool CRISPR-Cas9 to cut the CCR5 gene that’s known to play a role in HIV infection.

  • He stirred even more dismay when he mentioned the possibility of a second pregnancy.
  • China currently bans human implantation of gene-edited embryos. Its Ministry of Science and Technology is investigating the claims, per Xinhua.

There are concerns about the safety, efficacy and possible mosaicism, where a person can contain genes in both its edited and unedited forms, from cutting genes.

  • Editing embryos raises an even bigger concern: The genetic changes and all the unknowns around them can be passed down to future generations.

Between the lines: Not everyone viewed it as a complete disaster. For instance, Harvard Medical School’s George Daley suggested that it may be time to reconsider the massive amounts of research done over the past several years and look for plausible methods of moving forward.

What to watch: Scientists are cautious about predicting what the impact will be, in part because the details of this claim are thin. However, the debate is heating up and one concern is it will dampen important research.

  • Medical ethicist Jonathan Moreno from the University of Pennsylvania says the situation reminds him of other times in history where there were tremors in the science world, like the death of 18-year-old Jesse Gelsinger in 1999 from a gene therapy trial that led to years of diminished research.

The bottom line: The alarm over what could be next is real. But scientists hope the current debate will promote consensus on firm limits and promote transparency.

Go deeper:

SOURCE

From: Andrew Freedman <andrew.freedman@axios.com>

Date: Thursday, November 29, 2018 at 5:33 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: Axios Science: About that climate report — Gene editing takes a foreboding step — Building in harms’ way

He Jiankui spoke at the second international summit on human genome editing in Hong Kong. (Alex Hofford/EPA-EFE/Shutterstock)

CRISPR-baby scientist faces the music

The scientist who claims to have helped produce the first people born with edited genomes faced a tough crowd yesterday at a gene-editing summit in Hong Kong. He Jiankui gave a 20-minute talk about his unpublished work in animals and humans before opening a 40-minute Q&A session (watch it here). He faced difficult questions about the ethics of his work and his choice to keep it mostly under wraps until after the babies were born, and left many unanswered.

Meanwhile, prominent geneticist George Church is one of the few scientists who seem to be looking on the bright side of He’s controversial claim. “Let’s be quantitative before we start being accusatory,” Church told Science. “As long as these are normal, healthy kids it’s going to be fine for the field and the family.”

Nature | 9 min read & Science | 6 min read

Read more: Genome-edited baby claim provokes international outcry

SOURCE

From: Nature Briefing <briefing@nature.com>

Reply-To: Nature Briefing <briefing@nature.com>

Date: Thursday, November 29, 2018 at 12:18 PM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: CRISPR-baby scientist faces the music at gene-editing summit

See

SAVE

The ethical red flags of genetically edited babies

Driving the news: Chinese scientist He Jiankui announced Sunday night that a pair of twin girls had been born from embryos he modified using the gene-editing tool known as CRISPR.

  • He hasn’t provided solid proof, but if it‘s true, it would be the first time the technology has been used to engineer a human.

What they’re saying: The inventors of CRISPR technology did not seem pleased with the development — one called for a moratorium on implantation edited embryos into potential mothers.

  • “I hope we will be more cautious in the next thing we try to do, and think more carefully about when you should use technology versus when you could use technology,” said Jessica Berg, a bioethicist at Case Western Reserve University.

Between the lines: Several specific factors in He’s work sent up ethical red flags.

  • Many scientists had assumed that, when this technology was first used in humans, it would edit out mutations tied to a single gene that were certain to cause a child pain and suffering once it was born — essentially, as a last resort.
  • But He used CRISPR to, as he put it, “close a door” that HIV could have one day traveled through. That has prompted some speculation that this project was more about testing the technology than serving an acute medical need.
  • “That should make us very uneasy about the whole situation,” Berg said. “Of all the things to have started with, it does make you a little suspicious about this particular choice.”

The intrigue: There’s a lot we still don’t know about He’s work, and that’s also contributing to an attitude of skepticism.

  • How many embryos did he edit and implant before these live births?
  • How will he know it worked? As the children age, they’ll likely have their blood drawn and those samples will be exposed to HIV in a lab, but researchers aren’t going to tell them to go out and have unprotected sex or use intravenous drugs — another reason HIV seems like an odd starting place for human gene editing.
  • How did this even happen? The university where He worked said he was on leave, and Chinese officials have said he’s under investigation. But gene editing is a pretty hard thing to freelance.

The other side: He defended his work in a video message, saying, “I understand my work will be controversial but I believe families need this technology and I’m willing to take the criticism for them.”

  • “Their parents don’t want a designer baby, just a child who won’t suffer from a disease which medicine can now prevent,” He said.

Yes, but: Now that this threshold may have been crossed, attempts to create “designer babies” — within the limitations of what CRISPR can do — probably aren’t far off, some experts fear.

  • There are “likely to be places that are less regulated than others, where people are going to attempt to see what they can do,” Berg said. “I wouldn’t say everything in the world has changed now, but it’s certainly the next step.”
SOURCE

https://www.axios.com/genetic-editing-baby-china-ethics-controversy-b33f8414-8b83-445c-bad5-d8407f8841f4.html

https://pharmaceuticalintelligence.com/2018/11/26/jennifer-doudna-and-npr-science-correspondent-joe-palca-several-interviews/

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The Future of Precision Cancer Medicine, Inaugural Symposium, MIT Center for Precision Cancer Medicine, December 13, 2018, 8AM-6PM, 50 Memorial Drive, Cambridge, MA

Reporter: Aviva Lev-Ari, PhD, RN

#CPCM2018 @AVIVA1950 @pharma_BI

 

 

Aviva Lev-Ari, PhD, RN, Editor-in-Chief, will attend and cover this event in REAL TIME for

 http://pharmaceuticalintelligence.com 


Over the past decade, there have been major advancements in the field of precision medicine, leading to exciting new treatments for some cancer patients. Much attention has been focused on genomic profiling of tumors to identify genomic alterations that might guide selection of specific therapies for individual patients. Beyond genomics, however, there is a variety of other precision approaches that can identify and exploit cancer-specific biological mechanisms including proteomics, metabolomics, and computational modeling, resulting in the more effective use of existing cancer medicines. On Thursday, December 13, 2018, the MIT Center for Precision Cancer Medicine will hold its inaugural annual symposium in the Samberg Conference Center at MIT. This full-day event will feature leading researchers and clinicians, who will highlight recent advances in precision cancer medicine and share perspectives on the future. An industry panel will also discuss the barriers to instituting precision medicine into current and future clinical trials.

 


Keynote Address

Charles Sawyers

Charles Sawyers, MD

Chair, Human Oncology and Pathogenesis Program
Memorial Sloan Kettering Cancer Center

Speakers

Andrea Califano

Andrea Califano, PhD

Clyde and Helen Wu Professor of Chemical Systems Biology, Columbia University
Chair, Department of Systems Biology, Columbia University
Director, JP Sulzberger Columbia Genome Center
Associate Director, Herbert Irving Comprehensive Cancer Center

Chris Love

J. Christopher Love, PhD

Professor of Chemical Engineering, MIT
Associate Member, Ragon Institute of MGH, MIT and Harvard
Member, Koch Institute, MIT

Richard Marais

Richard Marais, PhD

Professor of Molecular Oncology
Director, CRUK Manchester Institute
The University of Manchester

Kenna Mills Shaw

Kenna Mills Shaw, PhD

Executive Director
Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy
MD Anderson Cancer Center

Alice Shaw

Alice Shaw, MD, PhD

Professor, Harvard Medical School
Director, Thoracic Cancer Program, Massachusetts General Hospital

Matt Vander Heiden

Matthew Vander Heiden, MD, PhD

Associate Professor of Biology, MIT
Associate Director, Koch Institute
Member, MIT Center for Precision Cancer Medicine

Mike Yaffe

Michael B. Yaffe, MD, PhD

David H. Koch Professor of Science, MIT
Professor of Biology and Biological Engineering, MIT
Director, MIT Center for Precision Cancer Medicine
Director, Koch Institute Clinical Investigator Program

Jean Zhao

Jean Zhao, PhD

Professor of Biological Chemistry and Molecular Pharmacology
Harvard Medical School and Dana-Farber Cancer Institute


Panelists: Barriers to Instituting Precision Medicine in Clinical Trials

Hammerman

Peter Hammerman, MD, PhD

Global Head, Translational Research
Oncology Disease Area
Novartis Institutes for BioMedical Research

Ho

Steffan N. Ho, MD, PhD

Vice President, Head of Translational Oncology
Pfizer Global Product Development

Shiva Malek

Shiva Malek, PhD

Director and Principal Scientist
Department of Discovery Oncology
Genentech Inc

Marks

Kevin Marks, PhD

VP of Biology
Agios Pharmaceuticals

Michael Rothenberg

S. Michael Rothenberg, MD, PhD

Vice-President, Research and Development
Loxo Oncology, Inc.

Angela Koehler

Moderator:

Angela Koehler, PhD

Goldblith Career Development Professor in Applied Biology, MIT
Member, Koch Institute for Integrative Cancer Research
Member, MIT Center for Precision Cancer Medicine

 

Speakers:

Panelists:

  • Peter Hammerman, Novartis Institutes for BioMedical Research
  • Steffan Ho, Pfizer
  • Shiva Malek, Genentech, Inc
  • Kevin Marks, Agios Pharmaceuticals
  • S. Michael Rothenberg, Loxo Oncology, Inc

Moderated by Angela Koehler, MIT’s Koch Institute

Agenda:

8:00 am Registration and continental breakfast

8:45 am Opening remarks by Michael Yaffe (MIT’s Koch Institute)

  • Season of great expectation, tumor genetics is just the beginning, beyond: science, engineering, medicine: beyond genomics: immunology, cell biology, early detection, new drug development for the undrugable, system biology, RNAi
  • Jack Tyler was the initiator to find a donor for CPCM

9:00 am Keynote Address by Charles L. Sawyers (Memorial Sloan Kettering Cancer Center)

  • developed a drug for prostate cancer
  • Clinical trained oncologist/genomics
  • Lineage Plasticity:
  1. luminal cells in histology of origin and basal cells and require androgen receptor AR) function
  2. deprive lunimal cells fro growth factor
  3. Hormonal therapy Leuprolite, degarelix [castration methastatic]
  4. after relapse 2nd generation anti-androgens abirateron
  5. PING MU ENZALUTAMIDE RESISTANCE P53/RB! DELETION CONFER
  6. TRANSCRIPTION CHANGE: ANTIADROGEN RESISTANCE
  7. Lineage shift Sox2 level goes up – prevent drug resistance, in vivo and in vitro
  8. SOX2 promotes lineage placticity and antiadrogen resistance in TP53 and RBI-deficient prostate cancer
  9. Evolution of Lineage plasticity over time
  10. AR Pathway inhibition accelerates lineage plasticity: synaptophysin-positive disease in-vivo
  11. scRNA-seq time course – modeled by diffusion map displayed in luminal and basal cells
  12. Emergence of EMT phenotype, with retention of epithelial features
  13. Use CRISPR to perturb luminal plasticity by phyeno type
  14. Genomic landscape of Primary Prostate Cancer: ERG gain drives luminal layer
  15. Different classes of FOXA1 mutations in Prostate organoid Cancer – Missense, inframe, truncated
  16. FOXA1 key in hormone receptor signaling
  17. Hypermorphic peaks – ATAC-seq neomorphic FOXA1 pioneering activity
  18. Common Prostate Cancer Genes:differentiation phenotypes: TP53 Loss, RB1 – Loss,
  19. work of Matan Hofree – four subtypes of luminal cells
  20. involution and regeneration of single cell RNAseq
  21. Transcriptional shifts in response to castration/androgen addback
  22. androgen addback: 50% of luminal cells are proliferation in 48 hours
  23. cell responsible for organ regeneration

 

9:45 am Alice T. Shaw (Massachusetts General Hospital)

  • evolution of drug resistance in Lung Cancer
  • oncogenic drivers in lung adenocarcenoma –
  1. EGFR – sensitizing 19.4% of all patients
  2. KRAS
  3. ALK
  4. ROS1
  5. CMET
  6. BRAF
  7. NTRK1
  8. RET

Delay and prevention of drug resistance: liquid biopsy of pleural fluids and serial blood collections

  • Crizotinib patient with ROS1 + nsclc
  • acquired mutation in ROS1 G2032R – resistance to Crizotinib – Michael Lawrence, MGH – analysis of mutation and resistance
  • Repotrectinib – for ROS1 – Resistance mediated by this mutation
  • If patient fails three antiinhibitor drugs: secondary ALK mutations mediate Crizotinib Resistance
  • 2nd generation of  ALK inhibitors are structurally Distinct molecules
  • Lorlatinib – 3rd generation –>> back to 1st generation Crizotinib
  • Clonal evolution of resistance in ALK in NSCLC
  • compound mutations in ALK mutations – Lorlatinib Resistance
  • Sequential TKI therapy foster the development of compound mutation refractory to all generations og ALK TKIs – compound mutation can’t be overcome
  • Intratumoral Heterogeneity revealed by multiregion sequencing of renal cell carcinoma and resected NSCLC
  • somatic mutations: Pre-treatment to Lorlatinib resistance
  • Clonal Analysis: Multiple Drivers of resistance underlie clinical relapse
  • genomic instability – eradicate residual disease to eliminate drug resistance and tolerance persistance

 

10:25 am Networking Break

10:45 am Richard Marais (Cancer Research UK, Manchester Institute)

  • Melanoma – Precision Medicin
  • Request – NOT TO PUBLISH on the INTERNET, some of the work presented is not PUBLISHED.
  • Request is honored

11:25 am Matthew Vander Heiden (MIT’s Koch Institute)

  • Targeting Metabolism is altered in cancer
  • Metabolism is glucose carbohydrates, lipids – conversion of nutrients into biomass: ATP, Protein, Nucleic acid,
  • Not -proliferating cells vs proliferating cells
  • genetic mutations, tissue of origin, lineage of cells — metabolism takes place: combination of these three facto
  • environment consists the metabolic network definers.d by cell intrinsic network
  • Assessment of nutrient levels in tumor microenvironment
  • Metabolite analysis: ion suppression vs nutrients
  • nutrients are available to cells in tumors
  • depletion of glucose vs enrichment
  • metabolite most different: Gluthamine, needed for cancer to grow
  • Lineage can contribute – tryptophane and argenine
  • gluthamine – Cyctine affect gluthamine sensitivity to gluthamine inhibitors
  • what you eat, where is the tumor locate, tissue environment — more important
  • therapeutic window: metabolism processes – cell proliferation
  • ability to make aspartate – given to mice pancreatic  — tumor grow faster
  • cellular oxidation state correlate with pyruvate oxidation — PDH Activator suppress oxidation
  • Aspartate vs NAD+/NADH – lactate TCA – form more carbon
  • PDH activation reduces Redux
  • Serine availability can limit proliferation even in cells with increase
  • Serine vs NAD regeneration
  • which cancer falls into which group : Serine pathway – increase serine synthesis: Melanoma vs Breast cancer
  • growth of breast cancer: Serine availability dependent – accelerate of inhibit growth by level of serine
  • Model for how nutrient limitation affect tumor growth, tumor size depends of serine levels

 

12:05 pm Box lunch

12:30 pm Industry panel: Barriers to instituting precision medicine into clinical trials

  • Long term benefits of Precision Medicine
  • What phynotype are now looked for?

Michael Rothenberg

  1. short term, identify mutations
  2. more testing is needed
  3. sequencing the therapies
  4. challenge getting tissue, doing experiments in house
  5. Industry needs Academia collaboration for accelerated innovations
  6. AI may lower the cost of drug discovery

KEVIN MARX:

  1. MECHANISM OF RESISTANCE – COMBINATORIAL DRUG DISCOVERY
  2. phynotyping, tissue acquisition immune phenotype, what drive therapeutic response?
  3. genetic drivers
  4. HR seeks Scientistist that worked in TEAMS, collaborative science

STEPHAN HO

  1. long term benefits are very important
  2. Stage III disease – technology advances
  3. advanced in the regulatory space
  4. smaller cohort size to approve a drug
  5. biologic complexity, driver oncogenes, precision to imprecision
  6. cost of risk in investment in innovations
  7. check point inhibitor – known biology and immuno-modulation, data hypothesis and moving forward
  8. Organizational culture, interaction in teams, functional behavior
  9. commit to deliverable, perfect timing contingent on work of others.

Peter Hammerman

  1. single cell tumor immunity in combination drug therapy
  2. Tumor monitoring over time
  3. Novartis is interested to collaborate with innovators in Academia and in other institutions
  4. critical thinking on DATA and on negative data
  5. Combination drug therapy: orthogonal mechanism of actions and drug classed – toxicity is an issue

Shiva Malek

  1. How to drug mutations on DATA
  2. Acquired and intrinsic mutations
  3. exposure and patient safety
  4. UCSF’s Ashkenazi’s Team and Genetech – basic biology area selection
  5. Failure are not talked about
  6. Round table for problem solvers, how you approach a problem
  7. translational work require skills beyond technical expertise
  8. learning the navigation inside an organization
  9. leadership in R&D, expected to demonstrate leadership, the Scientist needs to have command of the field and of desirable directions of research

 

2:00 pm J. Christopher Love (MIT’s Koch Institute)

Acceleration of the PROCESS to develop Precision Medicine products

  • design, build, test – PROCESS
  • New drugs and vaccines – the process is iterative
  • measurements, with use of smallest number of samples
  • deliver precision medical: small f patients or large population or
  • clinical samples provide rich source of information: Blood or tissue sample
  • Tissue – extract RNA, component cells, single-cell RNA sequencing,
  • Challenges of enabling scRNA-seq in clinical labs
  • Probability, scale, capture efficiencies, temporal uniformity
  • single-cell sequencing
  • Seq-Well: method for scRNA-Seq
  • New Chemistries for T-cell
  • Blood: cell, cfDNA, Exosomes
  • map cancer genome from blood
  • Tissue:
  • Single circulating Tumor cells:
  • yield genomic landscape of cancer
  • cell free DNA, vells, proteins, metabolite, Tumor is existence, draw blood
  • cfDNA Tumor Fraction is prognostic of survival in mTNBC
  • automate to 13 cancer types
  • Rs is now possible
  • reduce sample requirement
  • cost is low digital information from clinical samples
  • Keytruda – is a molecular Signature
  • low volume product, advanced preparation (mo-years) __>>> agile solutions (days to years)
  • bentchtop, on-demand manufacturing system: Production, Purification, Formulation
  • hand-free production of formulated G-CSF: comparable to licensed products.
  • Plug and play manufacturing using  InSeq
  • Novel MAbs from patients
  • Many molecules to many products

 

2:40 pm Andrea Califano (Columbia University, System Biology)

Mechanistic Framework for the systematic pharmacological targeting of Non-Oncogene Dependencies – Precise Precision Oncology

  • systematic elucidation od critical cancer cell dependencies
  • drug MOA
  • Tumor dependencies to Drug MOA
  • Tumor heterogeneity
  • ARACNe – regulatory targets of regulatory proteins
  • Combinational Therapy: HER@ inhibitor and JAK1/JAK2 inhibitor
  • Driver Mutations
  • ARACNe; MINDy DIGGIT; Expression VIPER: MetaVIPER
  • Aberrantly activated protein for Prioritizing treatment in patients
  • Checkpoint activity reversal – prioritize drugs based on
  • Tumor model selection: GIST
  • 260 patients, 14 untreatable cancers — N of 1 Study
  • Single cell Studies – active proteins in stem-like progenitor cells
  • Ivermectin Treatment vs Control (7d vs 14d)

 

3:20 pm Networking Break

3:40 pm Jean Zhao (Dana Farber Cancer Institute)

Immunotherapy and Targeted Therapy in Cancer Therapy

  • Targeting cancer with CDK4/6 inhibitors
  • CDK4/6 inhibitors causes tumor regression in breast cancer and regression of CT-26 colorectal cancer
  • CDK4/6DNMT1 inducing viral mimicry
  • PARP inhibitors  changing treatment in ovarian cancer
  • FDA approved three drugs for ovarian cancer
  • p53-null; BRCA-null; myc high – model testing

 

4:20 pm Kenna Mills Shaw (MD Anderson Cancer Center)

  • PM nor a Silver bullet nor a Dream Illusion
  • 2013: not all mutations are equally actionable
  • Context of Biomarkers
  • co-mutations in lung cancer identity – therapeutic vulnerability
  • NGS cost decrease leads to increases in Data generation
  • there are only 125 genes ACTIONABLE IN THE CLINIC
  • finding biomarkers beyond direct targets
  • clinical actionability:80K mutation – 32%
  • patients: No standard treatment available
  • Enrollment inGenotype Matched TRIALS
  • MUTATIONS SCREENED: LACK OF ENROLLMENT NOT DUE TO LACK OF MATCHING PROCESS
  • 69% GOT NEW REGIMEN, 17% did not come back — no one called them
  • 58% enrolled on genotrype-matched trials
  • Beyond NGS:

www.personalizedcancertherapy.org

  • DECISION SUPPORT IN REAL TIME IMPROVES “MATCHING” TO RIGHT DRUG.
  • MULTIFACTORS: CO-MOEBIDITIES, MICROBIOME, IMMUNE PHYNOTYPING, GENOMICS, MICROBIOME, ZIP CODE, INFECTION

5:00 pm Michael Yaffe (MIT)

  • AUGMENTED SYNTHETIC LETHALITY
  • CANCER CELLS ARE UNDER CONSTANT STRESS
  • inflammation
  • Therpeutics-targeted Synthetic Lethality
  • BRCA mutation seen in 10%-20% of patients
  • p53 mutations DNA demage – leads to apoptosis p38 MK2 as a pathway is taking over repair DNA and no apotosis occurs.
  • doxorubicin
  • Nanoparticle targeting of siRNAs to established tumors
  • The Concept of augmented Synthetic Lethality   —- enhance a prevosly known synthetic interaction by targeting additional pathways
  • combination of repair pathway  and checkpoint activation – lead to better therapeutic results
  • MK2 – targets hnRNP A0 (an RNA binding protein)  – Cleaved Caspase 3 – is synthetic lethal with p53 mutuant tumors, not just p53 null alleles
  • MK2 links Inflammation and Cancer – IBD –>> polyps and Colon Cancer
  • myeloid cell recruitment to inflammatory tumors in
  • MK2 KO mice: IL-4 –M2 magrophage – tumor progression; regulate the tumor microenvironment
  • IFNgamma –>M1 macrophages – tumor suppression

 

 

 

SOURCE

https://ki.mit.edu/news/events/cpcmsymposium-2018

https://www.eventbrite.com/e/mit-center-for-precision-cancer-medicine-inaugural-symposium-tickets-50424019600?utm_campaign=event_reminder&utm_medium=email&utm_source=eb_email&utm_term=eventname

https://www.eventbrite.com/e/mit-center-for-precision-cancer-medicine-inaugural-symposium-tickets-50424019600

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