MPNforum Magazine

 February, 2015

Zapping the JAK2 mutant clone… Inside the MPN Research Foundation … CRISPR Meetings & Mayhem … ..Bill Gates on CRISPR

Making medical history: For gene editing, for MPN patients. 

— by Zhenya Senyak

   Zhaohui Ye had a problem.  A very little problem.               

He was hunting for a small target.  It was a single gene, a few micronanometers of DNA, that had mutated and was blighting another MPN patient’s life. The gene was located somewhere on a six foot long DNA strand, nestled among 3 billion look-alike base pairs glittering on a double helix skeleton of sugar and phosphate

That mutated  JAK2 v617f gene is infinitesimal in size but capable of massive damage as it proliferates and expands in myeloproliferative neoplastic disease. Launching a search and destroy mission aimed at the JAK2 clone is a daunting task.

But his team had a special weapon  The CRISPR molecule carrying an RNA homing system and an advanced chemical weapon, the Cas9 cleaver.  They also had pinpointed the  location.

His team had the address.

JAK2 Home Address

Since 2005 everyone had the address of the JAK2 mutated gene on the small arm of Chromosome 9.  Doing something about it is the challenge.  In that location, the amino acid valine is replaced by phenylalanine at position 617.  That replacement created a gain of function mutation.

The gain of function is the ability of the JAK2 protein to stimulate blood line production. Additionally, the mutated clone activates signaling  proteins and pathways that promote survival and proliferation, thus delaying apoptosis or cellular death.  As a result the mutated JAK2 clone gradually overcomes the natural or wild type JAK2 gene.

Having the exact address is an advantage.   But the full gene itself is long — over 143,000 bases — so targeting the mutation with precision is a challenge.

Zhaohui’s solution:  Send a molecule to find a molecule.

Zhaohui and his team didn’t come up with this solution. Genetic engineers have been doing it for years,  laboriously constructing elaborate proteins to find and snip a mutated gene out of a DNA strand.  And Zhaohui didn’t invent the tool he was using this day.  But this tool,  discovered nearly three years ago, was slimmer, sleeker, easier to produce and deploy.  The CRISPR molecule needs only a small strand of RNA–  75-100 nucleotides — to guide Cas9 (the cleaver)  to hone in on the target gene.

He and his colleagues in Professor Linzhao Cheng’s Lab at the Institute for Cell Engineering at Johns Hopkins School of Medicine were about to do something central to MPN patients and decisive for the future of gene editing.  He intended to precisely snip a JAK2 mutated gene out of a reprogrammed human stem cell derived from a polycythemia patient. 

Beyond that, the Johns Hopkins team was comparing the precision of tools to locate and cleave genes precisely.  On the one hand, the CRISPR tool,  with its few bits of programmable RNA code and on the other the older TALENs (Transcription activator-like effector nucleases) gene editor, a more complex protein bound to a  restriction enzyme to cut a targeted gene.

The blood tissue used in this landmark experiment resulted from Zhaohui’s personal relationship to the MPNs.

“My research into MPN started when I was still a graduate student studying human stem cell biology in Linzhao’s lab, “said Zhaohui.

Zhaohui Ye

“When Yamanaka reported the first iPS [induced pluripotent stem cells] cell generation,[2006]  we realized this could provide novel disease models for mechanism studies.

“So we collaborated with Jerry Spivak and Alison Moliterno (who are in the same Division of Hematology) to generate the first human iPS cell lines from blood cells of MPD patients (back then it was not yet MPN, as you probably remember). After the first paper was published, Joe Prchal [University of Utah] was also very interested in using such a model system, so we have been collaborating. The cell lines [we] used … include one from Jerry/Alison and two from Joe. That’s the short story how I got into MPN. By no means a MPN expert, but I do find the disease fascinating from a biologist’s point of view of course.”

In the end, the Johns Hopkins team hit a  perfect bulls-eye, slicing the DNA within a single nucleotide and in the process made medical history. They also  strengthened CRISPR/Cas9’s growing popularity among genetic engineers.  The study results, published in advance in Molecular Therapy last month, are reported in MPNforum. 

The Spring Special CRISPR/Cas9 issue of the  MPN Quarterly Journal will carry more of our interview with Zhaohui Ye along with a technical review of this work, an update on current CRISPR work and the implications for MPN therapeutic application.

The MPN Research Foundation — A day at the office.

Photo: Associated Press

Chicago can be biting cold in January. But there, nestled among the ice patches, sooty snow banks and city traffic is the international headquarters of the MPN Research Foundation. MPNforum decided to report on the realities of the Foundation that has such a big footprint in our lives. And downtown Chicago is where it happens.

Every MPN patient and specialist knows the basic story. With a small staff, this single Foundation supplied badly needed funds to nearly every major breakthrough research affecting MPN patients today — from JAK2 to CAL-R and lots of stuff in between. The Foundation searched out innovative scientists, solicited and reviewed lengthy grant proposals, and coordinated teams of scientists in the process before it could write the check. 

Beyond funding research that led to transformational discoveries, the Foundation bankrolled significant MPN structural projects — providing the seed capital for the first MPN tissue bank, for MPD-RC, launching the MF Challenge Grants and dozens of projects still percolating in the labs.  In all:  $10 million for MPN basic research.

How do they do it…and even more mysterious, where does all this happen? Considering the MPN Research Foundation is all about high impact science and finance, you’d figure HQ would be glass-tower posh, thick rugs on the floor and high tech security.

Instead, I found a creaky old-fashioned elevator in a B List office building leading to a small, well-lit and tightly organized workspace. The five person core MPNRF crew is a close knit team that clearly likes each other and loves its work.

That affection would be put to the test in the day’s featured event: a marathon review of Foundation tasks.

The agenda for the review chaired by Michelle Woerhle was outlined in a four page task list that literally took all day to work through. We never got out of the conference room. Because of confidentiality agreements we can’t provide details — and most of it that wasn’t exciting is pretty routine and tedious anyhow — but we can do better than that. Instead of reporting on mundane tasks, high finance, and all the rest, we can show you what it’s like for the Foundation team after grinding hours in the conference room broken only by a take-out lunch from the local falafel joint:

Robert Rosen, Barbara VanHusen, Michelle Woerhle, Bill Crowley, and Raquel Nunez star in this little epic with Dr. John Crispino, Foundation science guru, coming by to help wrap things up…and finish off the pita and falafel

And here’s where we pass the hat…

There’s a new round of grants coming up and transformational science to discover and finance. The MPN Research Foundation is entirely funded by donations. This is our time to kick in.

Discovering new mutations and drug targets, exploring genetic engineering and immunotherapy…We’re so close to breakthrough treatment and a cure. Here’s our chance to be part of that historic effort. Dig deep.

(Clicking on the DONATE button will take you away from this page on to a form hosted by the MPN Research Foundation.)

For CRISPR It’s Showtime!

The CRISPR Precision Gene Editing Congress  in Cambridge, Massachusetts is a three day affair featuring roundtable discussions, presentations, interactive sessions and post conference workshops. In an explosive atmosphere of CRISPR growth and conflicting ownership claims. the Cambridge Event promises to advance CRISPR knowledge for scientists, clinicians and drug developers alike.

Because so much of genomic engineering is new, the Congress is also a chance to find many of the gene editing pioneers sharing early insights and exploring opportunities and challenges.  Harvard University, MIT and Editas Medicine —  the CRISPR technology company founded by Feng Zhang (Broad Institute, MIT), Jennifer Doudna (Howard Hughes, UC Berkeley),  George Church (Harvard, MIT),  J. Keith Joung (Harvard) and David Liu (Harvard)  — are well represented among presenters.

The event is organized around big themes – “Potential applications of CRISPR” – and technical issues like “Nucleic acid delivery systems for RNA therapy.” Concluding  post-conference workshops are focused on bringing CRISPR technology into the clinic and improving CRISPR-Cas nuclease specificity.

Cambridge-based Editas is on the faculty of the Gene Editing Congress in force.  But not represented at the meeting is Doudna or her co-developer of CRISPR/Cas9,  Emmanuelle Charpentier.   There are turf battles and conflicting patent claims over what the MIT Technology Review says “…may be the most important new genetic engineering technique since the beginning of the biotechnology age in the 1970’s.”

Editas’ Founder and Scientific Advisor  Feng Zhang won a patent that he assigned to the Broad Institute. Doudna disassociated herself from Editas.  The CRISPR development company she previously co-founded,  Caribou Biosciences, then licensed her own broad pending patent to Intellia, a new company formed to develop therapeutic products using CRISP/cas9.   Charpentier, Scientist and Co-founder of  CRISPR Therapeutics with Rodger Novak in Basel Switzerland assigned her patent rights to that company.

However the patent rights issues resolve, CRISPR Cas9 research and development work booms along… and the academic meetings and conferences go on. Here are a few others on the horizon.

Keystone Symposia
Big Sky, Montana
Precision Genome Engineering and Synthetic Biology
January 11—16, 2015 (Completed, abstracts available).
https://www.keystonesymposia.org/15A1

New Frontiers in Gene Editing Transitioning From the Lab to the Clinic
February 19-20, 2015 |
The InterContinental San Francisco | San Francisco, CA
http://www.triconference.com/gene-editing/

CRISPR Precision Gene Editing Congress
Cambridge, Massachusetts
February 25-27
http://crispr-congress.com

The CRISPR/Cas Revolution,
Cold Springs Harbor
September 24 – 27, 2015
http://meetings.cshl.edu/meetings/2015/crispr15.shtml

Innovative Genomics Initiative
Berkeley, California
CRISPR Workshop
July 20=-23, 2015
http://innovativegenomics.org/crispr-workshop-routes-to-designer-biology/

Bill Gates on CRISPR

MPD-RC has released its January Newsletter updating projects and clinical trials. It’s available here:

The Spring MPN Quarterly Journal will focus on CRISPR Cas9 and gene editing.

(New this issue!) The List and Map of 164 Patient-Recommended Hematologists –

The First Six Combined MPNclinics with Index

The Catalog of Articles. ..

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