Sign in

Jason Buenrostro

@jbuenrostro.bsky.social
2.1K followers 166 following 36 posts

Epigenetics & Genomics Harvard University & Broad Institute www.macfound.org/fellows/class-of-2… buenrostrolab.com

PostsRepliesMedia
Reposted by Jason Buenrostro
Kaili Fan @kailifan.bsky.social · 05/10/2026
1/13 The human body runs on one genome—but every cell reads it differently. How? To find out, we need to measure both gene expression and chromatin accessibility in the same nucleus. So we did, across 21 adult tissues and nearly half a million nuclei. 🧵 🔗 www.biorxiv.org/content/10.6...
biorxiv.org
Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues
Diverse human cell types establish specialized functions through lineage- and context-specific regulatory programs. Interpreting non-coding genetic risk requires integrated multi-omic reference maps t...
1179
Jason Buenrostro @jbuenrostro.bsky.social · 18/07/2026
Thank you Broad Institute of MIT and Harvard for this profile. The last 2 years have been an extraordinary moment of creativity and inspiration. If you’re interested in joining us, PM me! We’re building new methods, models and ML tools - we’re recruiting at all levels!
0229
Reposted by Jason Buenrostro
Waggoner Lab @labwaggoner.bsky.social · 06/05/2026
@biorxivpreprint.bsky.social RUNX is a "master collaborator" in T cells, where RUNX2:KLF2 interactions specify exhaustion, which can be perturbed by mutating the RUNX2:KLF2 interface or amp'ed by synthetic tethering of RUNX2 to KLF2 @jbuenrostro.bsky.social @harvard.edu doi.org/10.64898/202...
052
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
We’re excited about this direction. Synthetic TF tethering may provide a general approach for engineering gene expression in cells, and a path toward more programmable control of cell identity. I’ll again thank @igvfconsortium.bsky.social and team. Please reach out with feedback.
020
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
We then engineered this interaction: we synthetically tethered RUNX2 and KLF2, forcing their collaboration to create a stronger and more specific gene expression response.
130
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
We next asked: how does KLF2 work? Using perturb-SHARE-seq, we applied seq2PRINT and found that RUNX TFs are highly collaborative, enabling cells to access diverse regulatory programs. Additional experiments revealed that RUNX2 and KLF2 physically interact to regulate key exhaustion genes. 🧬
nature.com
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
181
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
Fast forwarding through a lot of work: we screened ~3,500 TFs, profiled ~750K cells with perturb-SHARE-seq, and identified KLF2 as a potent context-specific repressor of exhaustion programs. These same programs are associated with favorable outcomes in CAR T therapy, motivating us to dig deeper.
230
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
We hypothesized that combinations of TFs are required to reprogram T cell identity. This is motivated by the observation that most cell reprogramming strategies require multiple factors. We therefore set out to identify TFs that collaborate within exhaustion-specific programs.
110
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
Many regulators of T cell exhaustion have been discovered. As our community saturates discovery of endogenous regulators, we reasoned there may be major opportunities to combine perturbations and/or design synthetic proteins.
110
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
My group has long used epigenomics to define cell types. Since joining @harvard.edu SCRB, we set out to create strategies to engineer cell fate and state. Here, we look to engineer CD8 T cells, where exhaustion limits their broader therapeutic use.
110
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
Can we control cells by forcing TFs to collaborate? Interested? Read our preprint! An awesome collaboration with @cgersbach.bsky.social, @igvfconsortium.bsky.social, Christian McRoberts Amador, @rachel-savage.bsky.social: www.biorxiv.org/content/10.6... 🧵
biorxiv.org
13310
Reposted by Jason Buenrostro
Surya Nagaraja @snaga13.bsky.social · 28/03/2026
A little late to Bluesky but my postdoc work w/ @jbuenrostro.bsky.social now out in @nature.com "Epigenetic memory of colitis promotes tumour growth" www.nature.com/articles/s41... We wanted to understand how transient inflammation can create an increase in cancer risk, even after full recovery 🧵
nature.com
Epigenetic memory of colitis promotes tumour growth - Nature
Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...
3429
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
Lead by @snaga13.bsky.social, special thanks to Omer Yilmaz, David Breault and Mike Greenberg for their collaboration and an additional thanks to @cancergrand.bsky.social @igvfconsortium.bsky.social for support
030
Reposted by Jason Buenrostro
Waggoner Lab @labwaggoner.bsky.social · 26/03/2026
The epigenome "remembers" inflammation and primes stem cells for cancer @snaga13.bsky.social @nature.com @jbuenrostro.bsky.social @harvard.edu www.nature.com/articles/s41... www.nature.com/articles/d41...
0132
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
This reframes how we think about cancer. It is not just about having the right mutation in the right cell type. It is also about a cell's prior experiences. In short, a cell’s history, written into its epigenome, can shape how disease unfolds.
151
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
We then introduced an oncogenic mutation. What we saw was striking: cells with prior inflammatory memory formed larger tumors, effectively lowering the threshold for transformation. Same mutation, different outcome depending on the cell’s past experiences.
151
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
The answer was yes! Using a new method (SHARE-TRACE), we found that inflammation rewires the epigenome of stem cells that persists long after recovery. These changes are clonal, encoded through TF activity, and stabilized over time by DNA methylation, forming a durable molecular memory.
140
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
To test this, we turned to a mouse model of chronic colitis, where we could control when inflammation happens, when it resolves, and what comes next. This gave us a clean way to ask: does past inflammation leave a lasting imprint on cells?
120
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
In my lab, we are driven by the simple idea: epigenomes are drivers of disease. We asked whether inflammation leaves lasting epigenetic changes that quietly predispose cells to become cancerous. The epigenome: genome.gov/genetics-glo...
genome.gov
Epigenome
The term epigenome is derived from the Greek word epi which literally means "above" the genome.
130
Jason Buenrostro @jbuenrostro.bsky.social · 26/03/2026
It’s well known that inflammation increases cancer risk, but how? The answer: the epigenome "remembers" inflammation and primes stem cells for cancer. Here is our paper: nature.com/articles/s41... And a special shoutout to the lead author @snaga13.bsky.social A 🧵
nature.com
Epigenetic memory of colitis promotes tumour growth - Nature
Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...
16226
Reposted by Jason Buenrostro
Broad Institute @broadinstitute.org · 25/03/2026
Chronic gut inflammation leaves behind “molecular scars” that may raise the risk for developing cancer, according to a new study showing that epigenetic memory of colitis, along with a cancer-promoting mutation, can accelerate tumor growth in mice. @jbuenrostro.bsky.social
broad.io
How inflammation may prime the gut for cancer
A study in mice suggests that even intestinal cells that appear healthy may hold epigenetic “memories” of earlier bouts of inflammation that can promote colon cancer later in life.
0116
Reposted by Jason Buenrostro
GenomeTDCC @genometdcc.org · 17/03/2026
Coming Soon: March 31 @2pm ET. 📅 Charting Cellular Futures: Lineage Recording & Regulatory Network Insights. Free webinar featuring @jshendure.bsky.social and @jbuenrostro.bsky.social. Register www.jax.org/GenomeTechDev26/ 🧪🧪💻
Free webinar featuring Jay Shendure and Jason Buenrostro. Charting Cellular Futures: Lineage Recording & Regulatory Network Insights. March 31 2pm ET. Register www.jax.org/GenomeTechDev26/
001
Reposted by Jason Buenrostro
Broad Institute @broadinstitute.org · 04/11/2025
Broad has launched the Biology of Adversity Project, led by @jbuenrostro.bsky.social a 2023 @macfound.org fellow, to uncover how adverse life experiences can inflict molecular “scars” in the genome and body and increase risk of heart disease and other disorders. Learn more: broad.io/BAP
Jason Buenrostro stands behind a podium speaking to an audience.
122
Jason Buenrostro @jbuenrostro.bsky.social · 21/10/2025
This is a great opportunity. Apply and join our community! academicjobsonline.org/ajo/jobs/30714
academicjobsonline.org
Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center
Job #AJO30714, Postdoctoral Associate, Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, US
062
Reposted by Jason Buenrostro
Ryan Flynn @raflynn5.bsky.social · 07/10/2025
We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...
biorxiv.org
DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells
The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...
37622
Reposted by Jason Buenrostro
Çağrı Çevrim @cagricevrim.bsky.social · 10/10/2025
I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉 @karalmckinley.bsky.social We built the first transgenic model of menstruation in mice. We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪 www.biorxiv.org/content/10.1... 🧵
biorxiv.org
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
1423482
Reposted by Jason Buenrostro
Vijay Ramani @vram142.bsky.social · 09/10/2025
Congratulations @karalmckinley.bsky.social & lab on their groundbreaking recent preprint establishing + characterizing a chemically inducible model of menstruation in mouse: www.biorxiv.org/content/10.1... My jaw dropped when I heard this presented earlier this year. Incredible.
biorxiv.org
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
16621
Reposted by Jason Buenrostro
Broad Institute @broadinstitute.org · 30/09/2025
Leading epigenetics researcher and longtime Broad member @jbuenrostro.bsky.social has been named core institute member of the Broad. His lab will study how cells change in response to life experiences, and how those alterations affect health and disease.
broad.io
Jason Buenrostro named core institute member at Broad
An expert in epigenetics and longtime member of the Broad community, Buenrostro will focus on how life experiences can alter the epigenome and increase risk of disease.
1213
Reposted by Jason Buenrostro
siddhartha jena @epijenatics.bsky.social · 11/09/2025
One last thing - I am on the job market! My lab will extend this approach to decode resilient chromatin: adaptations in proteins/DNA that allow for survival in harsh environments. These hold the 🔑 to designing cells that thrive under stress, esp. as we push the limits of where we take them ❄️🚀🪐🌱9/9
151
Reposted by Jason Buenrostro
siddhartha jena @epijenatics.bsky.social · 11/09/2025
Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9
biorxiv.org
Engineered histones reshape chromatin in human cells
Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...
2194
Reposted by Jason Buenrostro
siddhartha jena @epijenatics.bsky.social · 11/09/2025
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
18832
Reposted by Jason Buenrostro
Vinay Kartha @vkartha.bsky.social · 10/07/2025
Had a super week filled with great science, curiosity and discussions at this year's Gordon Research Conference on Human genetics and genomics. Also fun when you get to give a talk the same day as your postdoc advisor @jbuenrostro.bsky.social
061
Reposted by Jason Buenrostro
Xin Jin @xinjin.bsky.social · 20/06/2025
Honored to be an HHMI FHS! Grateful to brilliant colleagues who push me to think deeply, and to my students whose curiosity & energy make the lab a joy. My grad advisor said in genetic screens, you don’t get what you want—you get what you deserve. Hope we are deserving www.hhmi.org/programs/fre...
hhmi.org
The 2025 Freeman Hrabowski Scholars | HHMI
Freeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields.
16778
Reposted by Jason Buenrostro
Epigenome Technologies @epigenometech.bsky.social · 05/06/2025
Epigenetics Update - Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation bit.ly/4jtXApb Jason D. Buenrostro (MIT/Harvard) reporting in Science #Epigenetics #Chromatin --- Gain deeper insights into gene regulation; epigenometech.com
bit.ly
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...
0185
Reposted by Jason Buenrostro
Di Jiang @dijiang319.bsky.social · 29/05/2025
@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/... @jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu #ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy
science.org
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...
04113
Reposted by Jason Buenrostro
Broad Institute @broadinstitute.org · 29/05/2025
A new combination technique enables DNA sequencing and high-resolution imaging in intact cells — offering new insights into progeria and aging. broad.io/expansion-in-situ @jbuenrostro.bsky.social
0236
Reposted by Jason Buenrostro
Julia Belk @juliabelk.bsky.social · 18/04/2025
A lot of fun teaming up with Hsin and Howard on this, with key contributions from @ruochiz.bsky.social, @zchiang.bsky.social, and @jbuenrostro.bsky.social on the tech dev and @mattjones.bsky.social, Natasha Weiser, and Paul Mischel on the ecDNA analysis. (5/5)
162
Reposted by Jason Buenrostro
Anshul Kundaje @anshulkundaje.bsky.social · 21/02/2025
Disease diagnostics using machine learning of B cell and T cell receptor sequences www.science.org/doi/10.1126/... TL;DR: BCRs ARE ALL YOU NEED! (Well actually .... keep reading) 1/
science.org
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
69725
Reposted by Jason Buenrostro
Surya Nagaraja @snaga13.bsky.social · 18/02/2025
We’d like to thank our collaborators in the Yilmaz and Breault labs, and PROSPECT @cancerresearchuk.org / NCI for their support. Find out about binding partners, drugging AP-1, the new tools we made and more here at our pre-print: tinyurl.com/ColitisNagar... (14/14)
041
Reposted by Jason Buenrostro
Surya Nagaraja @snaga13.bsky.social · 18/02/2025
New to bluesky, but I’m excited to share my work over the last few years with @jbuenrostro.bsky.social! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagar.... Here’s a walkthrough of what we found (🧵)
16619
Reposted by Jason Buenrostro
Roxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 27/01/2025
To help people understand the importance of NIH, share what you’ve used their funding for (in easily understandable terms). I’ll start: my NIH postdoc funding helped me develop and test AI tools that could identify skin cancer across diverse skin tones.
41490186
Jason Buenrostro @jbuenrostro.bsky.social · 27/01/2025
Hey Jeff, just to clarify, we performed a genome wide analysis across all cell types seen in BMMCs. The results are quantified in Figure 3c. There’s also more examples in Ext Figure 6. Feel free to shoot me a message if you’re interested, could be fun to discuss.
110
Reposted by Jason Buenrostro
Ryan Flynn @raflynn5.bsky.social · 25/01/2025
"cryoET" ? (h/t Jon Perr in my lab) #CryoET #TeamTomo
2412
Reposted by Jason Buenrostro
Yan Hu @yanhu97.bsky.social · 23/01/2025
Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: www.nature.com/articles/s41...
nature.com
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
17731
Reposted by Jason Buenrostro
Nature @nature.com · 13/01/2025
A decade in, expansion microscopy is unlocking insights across biology and medicine go.nature.com/4adlNgg
go.nature.com
‘Expansion microscopy’ turns ten: how a tissue-swelling method brought super-resolution imaging to the masses
A decade in, expansion microscopy is unlocking insights across biology and medicine.
18519
Reposted by Jason Buenrostro
Stirling Churchman @stirlingchurchman.bsky.social · 31/12/2024
I’m celebrating tonight with my father in law, Jack Strominger, who is about to enjoy his 100th New Years! He wants to know whether any other scientist has published in their 100th year. He’s proud to have a paper in the works. I told him you all would know! Please RT
3237579
Reposted by Jason Buenrostro
Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
723189
Reposted by Jason Buenrostro
BrunetLab @brunetlab.bsky.social · 18/12/2024
Thrilled to see this paper out!! 🧪 Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors! Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social! rdcu.be/d33uQ 🧵
rdcu.be
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...
2230296
Reposted by Jason Buenrostro
Andrew Payne @andrewcpayne.bsky.social · 03/12/2024
🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains. Read more: e11.bio/news/roadmap
616954