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Lab News

Peter and Takako Jones Lab

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Jones Lab Receives 3 Year Grant From Muscular Dystrophy Association

February 1, 2016

Peter and Takako Jones were awarded an MDA research grant for their FSHD-like mouse model

A major impediment to developing ameliorative treatments for FSHD has been the lack of a viable, robust, and consistent phenotypic FSHD-like animal model. We have addressed this void by generating a novel transgenic mouse model based on the widely accepted paradigm that FSHD is caused by increased somatic expression of the DUX4 gene, which triggers a cascade of events leading to pathophysiology. Thus, the DUX4 mRNA, DUX4 protein, and downstream events are all potential targets for therapeutic development. Our successfully engineered lines of mice contain the human DUX4 gene in the context of its native gene structure. Initial characterization of these mice indicates that they are healthy and fertile in the absence of inducing DUX4 expression. Induction of DUX4 causes a dose-dependent muscular dystrophy-like phenotype ranging from very mild to very severe. One can imagine that different disease courses may have different applications for therapeutic testing. Therefore, in this project we will determine the precise conditions necessary to develop multiple screenable FSHD-like phenotypes in this mouse model with varying courses of pathology. Successful completion of this project will provide the FSHD field with valuable tools for understanding the events downstream of DUX4 expression and for preclinical screening of different classes of potential FSHD therapeutics aimed at DUX4 and its downstream targets. It is our hope that enabling this vital step of the therapeutic development process will ultimately lead to ameliorative treatments for FSHD.

UMass Med Now reports on work in the Peter and Takako Jones lab

February 1, 2016

UMassMed Now reports on the Jones lab's participation in a recent Yahoo Sports video for The Vertical with Woj. Work performed in the Jones lab is supported by the Chris Carrino Foundation for FSHD, established by Chris Carrino, the radio broadcaster for the Brooklyn Nets, the NFL. Chris is an FSHD patient and his foundation is dedicated to raising FSHD awareness and funding for a cure.

Peter and Takako Jones lab features in Adrian Wojnarowski's The Vertical "Relentless Voice: The fight of Chris Carrino" on Yahoo Sports

January 29, 2016

The launch on Yahoo Sports of Adrian (Woj) Wojnarowski's site, The Vertical, featured Chris Carrino's story of living and working with FSHD. Chris is the radio broadcaster of the NBA's Brooklyn Nets and also broadcasts NFL games. Chris's foundation, The Chris Carrino Foundation for FSHD, raises money and awareness for FSHD research. The Peter and Takako Jones lab at UMMS was one of the first groups funded by the foundation and as been funded since 2013. The featured video describes how this funding was used to help generate our FSHD-like mouse models and to further our recent FSHD CRISPR work. We are grateful to be working together with the Carrino Foundation towards developing an FSHD therapy. Many thanks to Bryan Goodchild in the UMMS Office of Communications for shooting the UMMS video.

Huffington Post Science reports on Jones lab FSHD CRISPR work

November 28, 2015

huffington post tweetHuffington Post Science section reports on our CRISPR work: "How controversial gene editing could lead to groundbreaking cures"

The Huffington Post's science reporter Lila Shapiro interviewed Dr. Charis Himeda about our recent publication on CRISPR/dCas9 inhibition of pathogenic DUX4 expression is FSHD muscle cells.

Washington Post "Innovations" section covers Jones lab CRISPR work for FSHD

November 19, 2015

CRISPR work diagramThe Washington Post's Innovations section reports on our CRISPR work: "How CRISPR could lead to a cure for muscular dystrophy"

The Washington Post's science innovations reporter Dominic Basulto interviewed Dr. Charis Himeda about our recent publication on CRISPR/dCas9 inhibition of pathogenic DUX4 expression is FSHD muscle cells.

Jones Lab Awarded Grant from FSH Society

November 17, 2015

Jones lab awarded small research grant from the FSH Society "Characterization of Coriell FSHD family cell lines."

The FSH Society awarded the Jones lab a research grant for the molecular genetic characterization of lymphoblast cell lines residing at the Coriell Cell Repositories. These cell lines were generated >20yrs ago from clinical samples donated by 116 different individuals in 12 families. Roughly half of the subjects were clinically diagnosed with FSHD, however, none of these patients or samples have undergone genetic testing for FSHD. The samples have remained in cryostorage and not available for distribution since they are uncharacterized in respect to disease status. This funding will allow the Jones lab to produce the necessary genetic and epigenetic characterization to allow Coriell Cell Repositories to make these resources available to the FSHD community at large. We thank Dan Perez and the FSH Society for enabling this project to get to completion.

Charis Himeda Publishes Paper in the journal Molecular Therapy

November 3, 2015

CRISPR paperCharis Himeda's paper published online in the journal Molecular Therapy, "CRISPR/dCas9-mediated transcriptional inhibition ameliorates the epigenetic dysregulation at D4Z4 and represses DUX4-fl in FSH muscular dystrophy."

CRISPR Lay Description

Cell biology in 100 words:

In the simplest, nutshell version, the genome consists of all the DNA in a cell, which exists in the form of chromosomes. Genes are sequences of DNA that code for RNAs, which, in turn, code for proteins. When RNA and protein are actively being produced from a gene, the gene is referred to as expressed ("on" or "active"). Proteins, in general, are the machinery that run a cell. Some of this machinery is common to all cell types (things that every cell needs) and some of it is specialized for specific cell types (certain proteins allow a cell to function as a muscle cell as opposed to a blood cell or a liver cell).

Background on FSHD:

About half the human genome consists of repetitive DNA sequences that are normally repressed (collectively referred to as the "repeat genome"). The FSHD disease locus is within the repeat genome, at a large repeat called D4Z4. D4Z4 repeats are present in hundreds of copies at several different chromosomes. FSHD is caused by a shortening of the D4Z4 repeat (to less than 10 copies) on a specific type of chromosome 4. This shortening causes a loss of repression in the region, which allows the DUX4 gene (harbored within each copy of D4Z4 and normally silent in somatic cells) to be turned on from a single pathogenic repeat unit (the last unit of the array). The abnormal expression of DUX4 in skeletal muscle leads to FSHD.

Background on CRISPR:

CRISPR/Cas9 is a gene-editing technology that involves two key components: 1) the Cas9 protein from bacteria and 2) a guide RNA that targets Cas9 to a specific sequence within the genome. Normal Cas9 (the version most commonly used) is an enzyme that cuts DNA, allowing subsequent insertion of a changed or new DNA sequence into the genome at a specific location (thus the phrase "gene editing technology" associated with typical CRISPR/Cas9 approach). We used a non-cutting version of Cas9 ("dead Cas9" or dCas9) fused to another protein (KRAB) whose normal function is to turn off gene expression. Thus, in theory, dCas9-KRAB enables one to target and specifically silence the expression of any target gene.

CRISPR in the context of FSHD vs other diseases:

Most diseases are caused by mutation(s) in a single protein-encoding gene, which results in the production of a dysfunctional protein or no protein at all. Thus, researchers studying these "typical" diseases are using Cas9 to cut out the mutated part of the disease gene in order to replace it with the correct DNA sequence. For FSHD, we don't need to replace a missing/dysfunctional protein; rather, we need to stop production of a toxic protein. Hence, CRISPR inhibition with dCas9-KRAB (as opposed to editing with Cas9) may be uniquely suited to FSHD.

Major findings from our study:

Most genes are present in only two copies (one from each parent) and are very similar; therefore, targeting these sequences is conceptually quite simple. By contrast, only one specific copy of D4Z4-the last repeat unit on a specific type of chromosome 4-expresses DUX4, causing FSHD. This introduces a degree of complexity for genome targeting that is not normally encountered. It was unclear whether the existing CRISPR technology could be used to target a single pathogenic copy of D4Z4, amongst hundreds of other nearly identical sequences in the genome. In this study we showed that we could, in fact, target a repetitive region of the genome and repress expression of the pathogenic DUX4 gene using dCas9-KRAB.

Typically, researchers use Cas9 to edit problematic DNA sequences, and that approach is also being attempted for FSHD. However, cutting a repeat sequence that is present in hundreds of nearly identical copies could be very dangerous or even catastrophic for a cell. A key aspect of our study is that all D4Z4 repeats are normally in the OFF (unexpressed) state, and only in FSHD is the pathogenic D4Z4 in an ON (expressed) state, leading to abnormal expression of the DUX4 gene. We therefore decided to use dCas9-KRAB to try to return all D4Z4s to the OFF state. Those already OFF would remain OFF, and those ON would be switched to OFF, including the one D4Z4 that leads to FSHD. Our study shows that we can design and utilize guide RNAs to target the dCas9-KRAB repressor to the FSHD disease locus, effectively returning the DNA to its OFF state and repressing expression of the pathogenic DUX4 gene.

Our study is the first:

  1. to show that the repeat genome can be effectively targeted using CRISPR technology
  2. use of CRISPR inhibition for any human disease (as opposed to CRISPR editing, which is being widely used in other disease studies by other labs). Note: we did not develop the CRISPR inhibition tool (dCas9-KRAB)-it was developed by other labs.
  3. use of CRISPR technology in primary human muscle cells (which are closer to the cells in a patient's body than the more commonly used "immortalized" cell lines)

What makes this finding different from other work done to prevent/treat FSHD?

Many researchers are investigating ways to silence the expression of DUX4 or its downstream pathways that lead to FSHD. By contrast, we aimed to overcome the underlying genetic defect by returning the DNA at the FSHD disease locus to its normal repressed state. This approach has several advantages: 1) it should correct aspects of the disease caused by loss of repression at the disease locus, including the pathological expression of DUX4, 2) it should correct all aspects of the disease that are caused by DUX4 expression, and 3) repressive changes in the structure of the disease locus have the potential to be passed on to subsequent generations of cells. Specificity of the CRISPR technology is also an issue. In addition to binding their intended target sequence, guide RNAs also have an affinity for similar sequences in the genome, and can recruit the Cas9 cutting enzyme to these off-target locations. By using dCas9, we avoid the serious concern of cutting the genome at unintended places.

What do you hope will come of this? Is this a step to preventing FSHD entirely?

We believe that this work has laid the foundations for using CRISPR technology to treat FSHD in the future. Rapid advances in genome-editing platforms are actively underway, and will hopefully lead to more effective and specific correction of many diseases. For example, there has already been successful development of new Cas9 enzymes that are amenable to viral delivery, which is critical for moving towards therapy. Our work has demonstrated that, in principle, such a strategy is feasible for FSHD, by showing that the CRISPR system can be used to target and correct a very unusual part of the human genome. Ultimately, more work needs to be done before CRISPR technology for FSHD or any other disease will be ready to move into a clinical setting. It is imperative for us to have a better understanding of off-target effects and the long-term implications of gene editing/modification. Luckily, progress in the treatment of any disease is progress for all, since many therapies and technologies are broadly applicable, as are lessons learned at all stages of therapy development.

Putting CRISPR in the context of current research funding:

The CRISPR system was discovered in bacteria, as a defense mechanism that bacteria use to protect themselves against infection. It's a great example of a biological system with important implications for medicine, agriculture, etc. that would never have been discovered and developed as a gene modification tool without support for basic research-and it underscores the need to increase funding for basic research. Great discoveries have always come from unexpected places.

Our lab's funding:

This study was funded by the NIH and the AFM (Association Francaise contre les Myopathies). Other FSHD work in our lab is funded by the Chris Carrino Foundation for FSHD, the FSH Society, and the Muscular Dystrophy Association.