Daniel Lipka

Same mutation ≠ same leukemia.

Wagenblast et al. show:
• fetal HSCs readily transform
• postnatal HSCs become resistant
• fetal programs create targetable vulnerabilities

Ontogeny matters: state-of-origin shapes biology & therapy response.
doi.org/10.1158/2159...

#pediatric #AML #stemcells

JMML stem cells aren’t epigenetically “stuck” in a fetal state.

They mature postnatally—yet show striking transcriptional plasticity, with oncofetal reprogramming in high-risk disease, challenging the classic “maturation block” model.
doi.org/10.1158/2643...

#JMML #epigenetics #hematology #cancer

New Spotlight in @aacrjournals.bsky.social

#Oncogene × #Ontogeny × #Plasticity shape leukemia biology & therapy response.

Two complementary studies show: mutations alone don’t explain disease behavior—developmental state and cellular plasticity matter.

aacrjournals.org/bloodcancerd...

🩸🧬
EpiSci

Staying Current in Data Science and Computational Biology: 2026 Edition Part 3 in a series of posts going back 14 years

Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...

You’ll help build interoperable, FAIR tools across @scverse.bsky.social and @bioconductor.bsky.social ecosystems. You will work together with a cross-institute team composed of @lucamarconato.bsky.social, @arturmansl.bsky.social and many contributors from #scverse and #Bioconductor!

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations Histone modifications play crucial roles in genome function. However, how chromatin integrates physiological and metabolic responses at the molecular …

Excited to share new manuscript on histone acylations, exploring how H4K16 acylations regulate inter and intranucleosomal interactions and how they confer resilience to metabolic challenges in vivo. Thanks to all authors +1 author @sandrani.bsky.social Enjoy 👇👇
www.sciencedirect.com/science/arti...

Neue Erkenntnisse zu frühkindlicher Leukämie: Leukämiezellen können Programme aus der fetalen Entwicklung erneut aktivieren. Die Ergebnisse eröffnen neue Angriffspunkte für Diagnostik und Therapie.
www.nct-heidelberg.de/das-nct/news...

@dkfz.bsky.social @mphartmann.bsky.social @dblipka.bsky.social

👉🏼 @milsommick.bsky.social talking about the role of inflammation on HSC aging in the “Game of Clones” Scientific Session at #ASH25. #epigenomics #hematopoiesis #HemeSky @dkfz.bsky.social

Thank you Tim! Yes, our story has definitely evolved a lot during the review process.
And yes: I will have BCD @aacrjournals.bsky.social definitely on my list for future submissions and so should you!

Interested in DNA methylation and want to hear what we can learn from it regarding lineage commitment decisions in #hematopoiesis? #ASH25 #epigenomics #HemeSky

Very happy and proud to see this story finally published! 🎉🥳
#epigenetics #hematology #jmml #leukemia

The future of hematological genomics is here. The ASH HematOmics Program (ASHOP) developed with St. Jude & the Munich Leukemia Laboratory offers free access to powerful genomic visualization tools for blood disease research.
🔗 https://ow.ly/G7Ol50XukwQ
#Genomics #HemeSky #MedSky

The figures from this book are all freely available through
@figshare.com, hopefully helpful for presentations and teaching:

figshare.com/projects/Epi...

Please let me know if you find any inaccuracies and I'll fix them. I've already updated one of the figures.

#EpigeneticsBook

On the Verge to Malignancy: Cytopenia and Beyond - Ewog Symposium On the Verge to Malignancy: Cytopenia and Beyond International Symposium on bone marrow failure, predisposition, MDS and MPD in the Young Dear colleagues and friends, we are pleased to wel...

Great to meet friends and colleagues at this year’s EWOG-MDS meeting in Berlin. We had great discussions and developed new project ideas and collaborations with the aim of improving risk stratification and patient care for JMML patients.
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org

Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!

On behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...

Of interest to the #epigenomics, #dnamethylation, #neurooncology, #oncology and #precisionmedicine communities! 🧬

DNA methylation analysis reveals an epigenetic signature distinctive of high-grade oligodendroglioma - Acta Neuropathologica IDH-mutant gliomas represent a subtype of diffuse gliomas that primarily affect patients in early to mid-adolescence. These tumors are classified into three distinct CNS WHO grades of malignancy. Accu...

DNA-methylation-based deconvolution can be a powerful tool for identifying novel disease subgroups. In our paper in Acta Neuropathologica, we show how this can be leveraged in IDH-mutant gliomas - specifically in oligodendrogliomas.
doi.org/10.1007/s004...

Epigenetics Update - Fluctuating DNA methylation tracks cancer evolution at clinical scale go.nature.com/3Ve4OUy

#Epigenetics #Cancer #DNAme #DNAm
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Empower your research with high-res epigenetic insights at epigenometech.com

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

Still two weeks left to apply to the #postdoc position in my lab via the @dkfz.bsky.social fellowship program.
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology

Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins - Nature Communications Epigenome editing programs gene silencing without inducing DNA breaks but challenges in delivery into human cells limit its broader use. Here, the authors present the RENDER platform, which uses virus...

Every so often, a paper lands at exactly the right moment. This one’s a gem. Can’t wait to try out this new strategy for delivering CRISPRoff chromatin-editing tools into our favorite cellular model system. Congrats to James K Nuñez and his team: www.nature.com/articles/s41...

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

+++ Postdoc Opportunity +++
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...

Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...

Epigenetics Update - Thymic epithelial cells amplify epigenetic noise to promote immune tolerance
go.nature.com/45srCWG

Andrew S. Koh (University of Chicago) reporting in Nature

#Epigenetics #Noise #Chromatin #Immunity
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High-resolution insights without cell sorting; epigenometech.com

🧵Radiotherapy immune signaling is modular, redundant — and has a limit.

Together with
@joschakraske

@peterhuber_hd

@halama_immuno

@UKHD_radonc
our new study in fully human systems shows that:

t.co/GzH3N6gElf

1/9

Plant #epigenetics colleagues, is this the consensus opinion?

"...these methylation marks and epiallelic variations found in natural populations are mainly attributed to genetic variations in epigenetic machinery and transposable element (TE) insertions"

pmc.ncbi.nlm.nih.gov/articles/PMC...

IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells Nature Communications - Here, the authors show that IRX3 is a transcriptional master regulator of multiple histone- and chromatin-remodeling enzymes and the SUMOylation pathway in adipocyte...

I am delighted to share a publication in @natcomms.nature.com. IRX3, linked to obesity via the FTO locus, influences fat vs bone cell fate. It is the result of a wonderful collaboration between S. Dankel, G. Mellgren @unibergen.bsky.social and my lab @biovitenskap.bsky.social 🍾
👉 rdcu.be/ezA5o

MRC Postdoctoral Research Scientists x 5 - MRC Laboratory of Medical Sciences Applications are now open for up to five postdoctoral positions in the area of developmental epigenetics.

There’s still time to apply for one of our five advertised postdoctoral positions in developmental epigenetics!

Click here to find out more and apply: lms.mrc.ac.uk/work/vacanci...

Applications close 12th August

#HiringNow #Jobs #Epigenetics

Happy to share our recent publication on benchmarking peak calling methods for CUT&RUN.
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social

#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome