Peter and Takako Jones Lab

03/29/2026

We were doing AI drug screening long before it was fashionable. Our approach is to first identify viable therapeutic targets that are key positive regulators of DUX4 (Himeda et al 2018), make conditional knockout mice to prove they are safe targets when knocked down (unpublished), then design small molecule compounds to inhibit their activity and test in FSHD muscle cells. Here, we partnered with Atomwise, Inc (now called Numerion Labs) who used their AI platform to screen millions of compounds resulting in ~70 to test in cells for repression of DUX4. We were successful in finding several great repressor molecules, however, not a great drug (yet). The screening project was started by Hannah Moore, an absolutely spectacular undergraduate researcher in the lab who has since moved on to Johns Hopkins PhD program, and then taken on by Dr. Ning Chang. Ning has since used this tool compound in an exciting study on regulation of DUX4 that will be coming soon.

Posted in the open-access preprint server while in review.

https://www.biorxiv.org/content/10.64898/2026.03.09.710626v2

12/19/2025

Here in the Jones Lab we are all FSHD research scientists at heart, we live and breathe science; however, we are not total lab geeks. We also like science fiction 😉. And we do love to support our lab family. After all, some important sci-fi author almost certainly once said “today’s science fiction is tomorrow’s science fact,” so where else are we going to get our ideas?

So here is the BIG NEWS: The Wake family is back! Yes, those oddball relatives of the Jones lab (at least it feels that way) return in the second book in the CRISPR Evolution series, “Finding the Gift”, And yes, I have actually read it. And it is great! And not just because the author is our own CRISPR Goddess.

The biomedical research world knows her as Charis Himeda, PhD, inventor of CRISPR inhibition for FSHD, expert in muscle gene regulation, and co-founder of Renogenyx, Inc. The literary world knows her as the award-winning author Charis Jones of https://www.charisjonesbooks.com/. And yes, FSHD patients and MyFSHD podcast listeners know her as The CRISPR Goddess (I know it gets a little confusing, but she has too many talents for just one name – and we appreciate the nod to the Jones Lab name).

Now, truth be told, Dr. Himeda has been with the Jones lab since 2011, but it was years before I would read any of her literary works because she has always been family and you know that you always have to read your family’s stuff and go to their plays and ballets and recitals and marvel at their art, and put it on the fridge and tell them it is all great (mine really was) when it is really only great because you appreciate your loved ones and want to encourage their efforts. It’s mostly great to you because of who they are. Yes, I am a terrible brother and uncle and cousin and family friend because I’m not going to faux appreciate a bunch of dribble just because I have too. But I digress…. I don’t know why but one night I finally actually read one of her short stories, “Green-eyed Monster,” probably because she won some prestigious awards to put on the lab fridge or perhaps because she was selected to contribute stories to real anthologies such as “Wild – Uncivilized Tales from Rocky Mountain Fiction Writers” and “The Best American Mystery and Suspense (2021)”, so I figured someone else likes this stuff, let’s see If she’s really “all that and a bag of chips” outside of lab. Honestly, she is. It was one of the best (published) short stories ever; and her unpublished ones are brilliant, too. It’s as if she is a writer and curing FSHD on the side instead of the other way around. Anyway, when “CRISPR Evolution” came out and she hinted some Jones Lab characteristics were infused, I actually read it and totally connected with the Wake family and their scientific frustrations, battles, and ethical dilemmas, etc... And while “Finding the Gift” continues with the same characters, it is notably different, although written with the same captivating brilliance and excitement as her other stories and will make you stay up too late as you won’t want to put it down (trite but true).

I don’t know that I like reading Sci-Fi in general, but I love this author and I love this series. So, spoil yourself and try them both.

12/16/2025

Happy Hanukkah, Merry Christmas, Happy New Year, and best wishes from the Jones Lab no matter how or if you celebrate the season.

Our 2025 Jones Lab Holiday Baking Day was wonderful, we love and appreciate our lab family. We were so happy that Maryam and Heinrich came back to the lab home from Cali. This year we even incorporated some spontaneous salsa dancing to take a break from decorating. Yes, the lab is getting smaller (only Brooke was unable to make it, and was missed), but as in the past the group is still shockingly efficient and impactful, in the kitchen AND in the lab. And I’ll need all this sugar with Yosuke’s paper, Ning and Hannah’s paper, and two diagnostic papers (Takako, Maryam, and Brooke) all needing to get out the door by the end of the year. Plus, the first pig paper is on its way, too.

In 2026 you will see our first FSHD-like pig paper, our pediatric Australian epigenetics paper, another advance in CRISPR inhibition technology, Ning’s mechanistic study of the locus, and several more epigenetic papers. We are also moving forward with our collaborations with hospitals in Vietnam, Ukraine, Egypt, Taiwan and Algeria to continue to help those in need. We are also very excited about working with the Chinese FSHD patient organization and help to facilitate a FSHD meeting in China in the fall.

2026 will also see several more clinical trials in the FSHD space. As with this year, some are worthwhile enrolling while others unfortunately, in our opinion, are not worth the time, effort or muscle. Stay tuned to the MyFSHD podcast for our unfiltered (and unsponsored) scientific opinions or feel free to email us directly with your questions, we are always happy to provide our scientific opinions and feedback.

We hope you all will stop by the lab if you are ever in the area and say Hi, we’d love to meet you in person, answer any questions, and show you around.

Thank you all for your support.

12/01/2025

Friends of FSH Research has always funded the most impactful FSHD research and, with your help, will continue to do so.

Giving Tuesday - join with us to find a cure!!

https://secure.givelively.org/donate/friends-of-fsh-research/2025-giving-tuesday-4acure

11/19/2025

11/19/2025

We are just back from Taiwan where we introduced FSHD to a number of scientists and clinicians and updated others familiar with FSHD on our FSHD research testing and therapeutics. And to be clear, just like our trips to China, Vietnam, Australia and Canada, not one penny of Jones Lab funding went to this trip either. All costs were covered by the inviting conferences or personally by Peter and Takako Jones. All donations to the Jones Lab and all grants to the Jones lab go 100% to our research projects.

We thank Dr. H. Sunny Sun, Professor, Institute of Molecular Genetics and the Director for the Center for Genomic Medicine at National Cheng Kung University Medical College and Dr. Wan-Chi Tsai, Associate Professor, Department of Medical Laboratory Science and Biotechnology at Kaohsiung Medical University for the invitations to speak at their events.

We gave the opening Keynote address at the “Multiomics and Precision Medicine Joint Conference” held at Taiwan National University in Taipei. The theme this year was “Big Data and the AI Revolution in Precision Medicine”, which is not exactly our wheelhouse. However, we and others already use AI approaches to advance FSHD so we briefly discussed that and then went out on a whim and spoke on the importance of finding, validating, and characterizing your patient population around the world, seeking patients everywhere so that you can truly use Big Data approaches and how this is extremely important for rare diseases such as FSHD. The title of our talk was “Facioscapulohumeral muscular dystrophy is a model epigenetic disease for diagnostics and therapy”. We discussed how our worldwide epigenetic testing for FSHD is finding FSHD patients and making things possible for the FSHD community. Additional discussions were on using DNA methylation as a diagnostic and a biomarker.

The conference banquet was a great Taiwanese dinner with attendees and we got to sit with another speaker, Dr. Yosuke Nakamura, a true pioneer in human genetics and mapping the human genome, cancer genetics, and now personalized medicine with too many honors to list. Currently the President of the National Institutes of Biomedical Innovation, Health and Nutrition in Osaka, Japan, he has had the most fascinating career with numerous impactful scientific breakthroughs while following the science with integrity and advocating for good science policy. I’ve been very disappointed with many in the FSHD space lately and it was very encouraging for us as we approach science the same patient-focused way of speaking the truth, taking a stand, and not bowing to pressures (he resigned a Cabinet post and left Japan in protest of unethical use of government science funding), and I’ll certainly take him up on his invitation to come to Osaka for a talk and meet with students.

Then off to the night market after dinner for some late-night Taiwanese treats with some former PhD students from out time at UIUC.

Our next stop was to tour the Center for Genomic Medicine at National Cheng Kung University Medical College in Tainan where we found help for optical genome mapping to genetically validate epigenetic FSHD in southeastern Asian populations. We know our epigenetic testing is extremely accurate, but it never hurts to prove it again on new populations and, scientifically, it is the right thing to do.

Our second talk was at the Conference on “Prevention, Diagnosis, and Treatment of Rare Diseases” at Kaohsiung Medical University. We presented a talk titled “Lessons learned from worldwide epigenetic testing for facioscapulohumeral muscular dystrophy” and discussed the value and risks of family and population screening for rare diseases with the other attendees (scientists, clinicians, and patient advocates) representing their rare disease populations.

Then the typhoon hit, but first a small earthquake. Neither amounted to much but closed most of the country down for a day and cancelled our planned birding tour. Hiked up the monkey mountain area looking for more FSHD 😜, then grabbed an Uber driver and worked something out through Google translate and saw some endangered black-faced spoonbills on the coast.

Overall, very successful trip and looking forward to going back to help them get our epigenetic testing set up in Taiwan.

09/10/2025

We posted what we think is a pretty cool developmental study onto the bioRxiv preprint server. Basically, we (as in Dr. Takako Jones) made transgenic mice that contain a single D4Z4 repeat and the upstream DUX4 regulatory regions from human chromosome 4q35 but replaced the DUX4 open reading frame with a reporter gene so that we could genetically mark and thus follow the cell lineages that expressed DUX4 during vertebrate development or after muscle injury in an FSHD context. In individuals without FSHD, these elements would all be epigenetically silent and not expressed; however, in individuals with FSHD, as well as these mice that have only 1 D4Z4 repeat unit, the region is epigenetically amenable to expression when these regulatory elements are active. This leads to a genetic recombination that permanently marks the cells (and all daughter cells) as having had the DUX4 regulatory regions turned on. You will see in the figures attached that the blue areas were regions that would be affected by DUX4 expression during embryonic development.

Dr. Yosuke Hiramuki joined our lab as a post-doc to work on these mice and did an outstanding job leading the developmental investigations.

Not surprisingly, we find DUX4 would be expressed in the adult limb muscles as well as the te**is. Interestingly, the DUX4 regulatory elements were also active in the developing limb and facial muscles during embryogenesis. However, what was really surprising was the histology showed that DUX4 regulatory elements were also expressed in pericyte lineages in adult muscles. Pericytes are multi-functional cells involved in blood flow and angiogenesis as well as skeletal muscle regeneration. This is exciting in that these cells had never been suggested to express DUX4 and may impact FSHD pathology in a way not previously considered.

These mice will also provide a useful tool for evaluating therapeutics that target DUX4 regulation in FSHD.

As with all our mouse models (and pigs), we will be giving them away to the field in the hope they can help advance therapeutics as well as our understanding of FSHD pathogenic mechanisms.

It is currently out for peer review, however, based on our recent experiences this could be many months and even years until final publication so we wanted to get this out for the field to evaluate and utilize the data and mice, if interested.

Thank you to Friends of FSH Research, the FSHD Canada Foundation, and the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS/NIH) for funding this work.

https://www.biorxiv.org/content/10.1101/2025.08.22.671867v1

08/14/2025

One of the keys to efficacious gene therapy in a patient is to package all components into a single AAV vector for safe systemic delivery, which is what Dr. Himeda accomplished several years ago and published (finally) here. Additional key steps that are ongoing are to make sure the viral dose is efficacious and therapeutic effect is durable, both accomplished using large animal models such as our FSHD-like minipig, and of course ensuring that the viral capsid going to clinic is a next-generation myotropic capsid so that an efficacious dose is safe and a safe dose is efficacious.

Time certainly is muscle, however, going to clinic with something suboptimal at best or with no chance of sustained (or even short-term) efficacy, as the case may be, might be good business, but would be irresponsible as scientists and disrespectful of the patient community. If you want to get there fast, go the long way and do it right. We will always follow the science and do what is best for the FSHD patient community.

For clinical relevance, AAV-delivered gene therapies must be contained within single vectors. Jones and colleagues have engineered all-in-one AAV vectors for CRISPR inhibition of pathogenic DUX4 expression in Facioscapulohumeral muscular dystrophy (FSHD). These vectors have been validated in FSHD my...

07/01/2025

Please take a minute to vote for FSHD Global and help raise awareness for FSHD and this great program! We are glad to be a part of it.

05/20/2025

I just returned from two weeks visiting Shanghai, China and Hanoi, Vietnam to help the respective FSHD research, clinical, and patient communities. It was both inspiring and humbling for me. We try to do our part to help everyone everywhere, but there is a huge unmet need. Yet everywhere I go people turn out to help, they go out of their way to make helpful connections, they make time and are wonderfully hospitable to me, and in turn become excited to see that we are there to help and that there really is a path forward with FSHD and other rare diseases.

In China, where they are now using our FSHD epigenetic diagnostic (research test in the USA) to quickly and cheaply identify FSHD patients, the researchers and doctors are eager for collaboration and our FSHD animal models to move further into FSHD therapeutics (I was introduced to some technology with amazing potential that would benefit everyone in FSHD – sorry I cannot divulge more, but I always say technology keeps moving forward and new technologies for disease suppression and muscle building keep coming). I spoke at two meetings, one an industry meeting for FSHD where I went over our FSHD-like mouse and minipig models, and the second a national neuromuscular disease meeting where I talked about our CRISPR-inhibition gene therapy. A huge thank you to Dr. Wenhua Zhu at Fudan University and Huashan Hospital for the invitation and to Aili (Eric) Aikepaier of the Chinese FSHD Youth Community for showing me around and taking me for Xinjiang food – wow, that was good!.

In Vietnam, I was able to show the MDs and geneticists I met how we are attacking FSHD with no-cost diagnostics and accessible/affordable research tools to identify the patient populations and drive therapeutic development as a blueprint for other rare diseases. And (I was told) my talk inspired the medical students, although I was taken aback a bit at their surprise that we are so willing to help them and that our diagnostic (research test in the USA) will not cost their patients anything, and that we can collaborate just because it is the right thing to do, not because we can see some sort of way to take advantage of them. Evidently westerners don’t have the greatest reputation for being helpful, I hope we can change that image. We don’t want anything in return, we just want to help them better help their neuromuscular disease patients through diagnostics and education. Now they are energized towards FSHD and I am super-excited to be working with Vietnam National Children’s Hospital and the prospects of helping the likely large and currently undiagnosed or misdiagnosed FSHD community there. I am always amazed by the impact of our no-cost FSHD diagnostic we make available worldwide. Treatment (including mental health) and therapeutics start with diagnostics, one needs to first know what disease they are dealing with. And while it is a horrible business model, our real business is overcoming barriers and helping those in need, and we will do everything in our power to keep this going. It is easy to say you want to help people, there is a lot of that going around the FSHD community, but actually doing it is another thing entirely. We know we are not alone. We are thankful for Friends of FSH Research and FSHD Global Research Foundation for helping with our testing, for example, Neil Camarta and FSHD Canada, and for people like Tamara Gottlieb and friends with Supplements, Nutrition and Peer Support who are providing wonderful and sometimes life changing options with nutrition, supplements, and exercise advice that I am able to pass along. BTW, the clinicians I met a dying to get this helpful information to pass on to their FSHD patients 😊

Overall, a truly amazing trip where I met so many new friends, reconnected with old friends, and had incredible experiences and food. Thank you Ms Tê Hi and Ms Hoa for setting up the clinical meetings in Vietnam, welcoming me into your homes, and showing me around Hanoi (I love the home cooking and traditional foods so much!) and great kindness and warm hearts of the Vietnamese people. I look forward to coming back again soon and hopefully having you all visit us in Nevada soon, too.

03/21/2025

Our collaborative work with Dr Zhu at Huashan Hospital and Fudan University is online now. They modified our FSHD methylation research testing technique to work with a slightly different next-generation sequencing platform (MiSeq) and validated our methylation testing protocol for FSHD in a large cohort of Chinese patients and healthy subjects. Several interesting findings include that we found no 4AL alleles in the cohort and all FSHD1 patients were 2-8RUs. The diagnostic methylation cut-offs are also quite sharp and yielded precise discrimination between the FSHD and not FSHD groups. Our soon to be published data from around the world shows more epigenetic variability and highlights that different ethnic populations have different epigenetic and genetic characteristics in respect to FSHD, something that others have found (for example in India and Japan), too. We are happy to be able to help FSHDers and their families everywhere in the world get answers and look forward to continued collaboration with our friends in China and around the world.

https://www.sciencedirect.com/science/article/abs/pii/S1525157825000595?CMX_ID=&SIS_ID=&dgcid=STMJ_219742_AUTH_SERV_PA&utm_acid=77889098&utm_campaign=STMJ_219742_AUTH_SERV_PA&utm_in=DM552106&utm_medium=email&utm_source=AC_

03/09/2025

It's International Women's Day 2025 highlighting women in STEM, but every day in the Jones Lab feels like International Women's Day as we are powered by amazing women scientists from all over the world. However, it wasn't by design; since our inception in 2001, just by picking the best and the brightest researchers for our lab has resulted in assembling the most brilliant, hardworking, dedicated and innovative FSHD lab we could imagine, and it’s mostly women. And if you think that I wanted a lab of women so I could push them around easier, well you don’t know anything about science in the new millennium caveman dude. This band of intimidating geniuses is kicking butt and doesn’t have time for games or to take names. So, what’s my job? I just stay out of the way and find them funding so they can work their magic and keep making breakthroughs.

Check out some of the highlights in the papers and pictures and stop by the lab to meet everyone yourself, you can’t help but be impressed.