Sign in

Daniel Lipka

@dblipka.bsky.social
3.5K followers 5.2K following 73 posts

Physician Scientist at DKFZ & NCT Heidelberg studying 🩸🧬 #epigenomics #DNAmethylation #singleCell #precisiononcology #JMML www.translational-cancer-epigenomics.de

PostsRepliesMedia
Reposted by Daniel Lipka
ISEH - International Society for Experimental Hematology @isehsociety.bsky.social · 30/09/2026
Tomorrow: Prof. Constanze Bonifer and Dr. Daniel Lipka share insights from their research and discuss how epigenetic approaches are advancing the field from clinical diagnosis to molecular disease mechanisms. Register for free: iseh.org/Webinars-Eve....
043
Reposted by Daniel Lipka
NCT Heidelberg @nct-heidelberg.bsky.social · 16/07/2026
Neue Erkenntnisse zu akuten Leukämien: Bestimmte Mutationen liefern Ansatzpunkte für gezieltere Therapien Forschende des NCT Heidelberg und des Deutschen Krebsforschungszentrums (@dkfz.bsky.social) haben erstmals systematisch ermittelt, wie bestimmte Mutationen akute myeloische Leukämien fördern.
123
Reposted by Daniel Lipka
Daniel Lipka @dblipka.bsky.social · 06/07/2026
‼️ Pre-print alert from the Lipka lab ‼️ Our latest work “Hierarchical classification of hematologic malignancies using epigenetic and genetic information” is now online! www.biorxiv.org/content/10.6... Thanks to all colleagues who contributed to this work! 🙏
biorxiv.org
Hierarchical classification of hematologic malignancies using epigenetic and genetic information
Molecular testing in hematology requires different assays for disease subgroup identification, risk stratification and selection of appropriate treatment regimens. Yet, molecular tests are not necessa...
0104
Reposted by Daniel Lipka
bioRxiv Cancer Bio @biorxiv-cancer.bsky.social · 10/07/2026
Hierarchical classification of hematologic malignancies using epigenetic and genetic information www.biorxiv.org/content/10.64898/20…
012
Daniel Lipka @dblipka.bsky.social · 06/07/2026
‼️ Pre-print alert from the Lipka lab ‼️ Our latest work “Hierarchical classification of hematologic malignancies using epigenetic and genetic information” is now online! www.biorxiv.org/content/10.6... Thanks to all colleagues who contributed to this work! 🙏
biorxiv.org
Hierarchical classification of hematologic malignancies using epigenetic and genetic information
Molecular testing in hematology requires different assays for disease subgroup identification, risk stratification and selection of appropriate treatment regimens. Yet, molecular tests are not necessa...
0104
Daniel Lipka @dblipka.bsky.social · 18/06/2026
😱 Seeing the global temperature change like this is absolutely shocking.... showyourstripes.info/c/globe
showyourstripes.info
Show Your Stripes
Visualising how the climate has changed for every country across the globe
043
Daniel Lipka @dblipka.bsky.social · 30/05/2026
Thank you for your nice words Vikram! 😊
000
Daniel Lipka @dblipka.bsky.social · 30/05/2026
13/ Huge congratulations to first author @mariamhakobyan.bsky.social and all collaborators and a big THANK YOU for all your efforts and support throughout the project! 🎉 📄 Paper link 👇 doi.org/10.1182/bloo... #AML #Leukemia #IDH1 #Epigenetics #HemeSky @dkfz.bsky.social @nct-heidelberg.bsky.social
doi.org
Mutant IDH1 blocks neutropoiesis by repressing myeloid progenitor programs
Key Points. IDH1-mutant AML exhibit more severe neutropenia than other AML subtypes and present an epigenetic scar from the neutrophil lineageIDH1 expressi
030
Reposted by Daniel Lipka
mariamhakobyan.bsky.social @mariamhakobyan.bsky.social · 29/05/2026
I’m excited to share that my PhD paper is officially out now in @bloodjournals.hematology.org Check out our discovery of how mutant IDH1 but not IDH2 leads to a lineage-specific differentiation block via epigenetic repression of lineage programs! 📄 Paper link below: 👇 doi.org/10.1182/bloo...
083
Daniel Lipka @dblipka.bsky.social · 29/05/2026
Very good point! 👍
010
Reposted by Daniel Lipka
Matthias Eberl @eberlmat.bsky.social · 29/05/2026
Data manipulation at a breathtaking scale by commercial providers of crucial research reagents. As if the few remaining lab scientists didn't face enough obstacles already.
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
45332
Daniel Lipka @dblipka.bsky.social · 29/05/2026
12/ To summarise: → IDH1 is highly expressed in myeloid progenitors (unlike IDH2) → Mutant IDH1 epigenetically silences Cebpe → neutrophil block → The block persists after IDH1 inhibition alone → IDH1i + hypomethylating agent fully rescues the defect
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
11/ The efficacy of combined IDH1i + Aza mirrors the superior outcomes seen with ivosidenib + Aza in the AGILE trial — and now we have a mechanistic explanation for why it works.
110
Daniel Lipka @dblipka.bsky.social · 29/05/2026
10/ 🔬The winning combination: IDH1 inhibitor + 5-azacitidine. This erased aberrant DNA methylation at the Cebpe locus, restored expression, and fully rescued neutrophil differentiation.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
9/ Great news: the differentiation block is reversible! ✅ Forcing CEBPE activation fully rescued neutrophil differentiation. ⚠️ IDH1 inhibition (AGI-5198) alone? It cleared D2HG and restored proliferation — yet Cebpe silencing and the neutrophil defect persisted.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
8/ ATAC-seq + Nanopore sequencing identified reduced chromatin accessibility and aberrant DNA hypermethylation at the Cebpe locus.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
7/ What's the molecular mechanism? Single-cell & bulk transcriptomics of Idh1-R132H neutrophil progenitors pointed to impaired activation of Cebpe 🎯 A master transcription factor for terminal neutrophil maturation, which fails to be activated in mutant progenitors.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
6/ To study this mechanistically, we used a heterozygous Idh1-R132H mouse model under the control of the endogenous promoter. Result: a clear, cell-intrinsic block in neutrophil differentiation with accumulation of myeloid progenitors and reduction in mature neutrophils
110
Daniel Lipka @dblipka.bsky.social · 29/05/2026
5/ This expression pattern is epigenetically regulated. A specific Idh1 transcript variant shows progressive DNA demethylation at its TSS specifically in the myeloid lineage — meaning myeloid progenitors are uniquely primed to express IDH1 at high levels.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
4/ 🤔But why would IDH1 mutations specifically affect neutrophils? Using single-cell RNA-seq data from human + mouse bone marrow, we found that IDH1 is strongly upregulated in myeloid progenitors, while IDH2 was expressed more homogeneously across all lineages.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
3/ This epigenetic clue had a clear clinical correlate. Across ~4,000 AML patients, IDH1-mutant patients had: 🔻 Significantly less bone marrow granulopoiesis 🔻 Lower absolute neutrophil counts in blood …compared to both IDH2-mutant and other AML subtypes.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
2/ We started by asking: do IDH1- and IDH2-mutant AMLs look different at the DNA methylation level? Analysing 473 AML patients, we found that IDH1-mutant — but not IDH2-mutant — AMLs carry an epigenetic "scar" from the neutrophil differentiation program.
100
Daniel Lipka @dblipka.bsky.social · 29/05/2026
🧵 NEW PAPER in @bloodjournal.bsky.social! Why do IDH1 mutations almost exclusively drive myeloid #leukemia, while IDH2 mutations occur in both myeloid AND lymphoid cancers? 🤔 #AML #Epigenetics Despite sharing the same biochemical mechanism, they are NOT equivalent. Here's what we found 👇
2329
Reposted by Daniel Lipka
Marcus Buschbeck and Lab @marcusbuschbeck.bsky.social · 07/05/2026
Please RT: Opportunity to join us as technician! We are looking for a technician to support us in our projects in MPN and other myeloid malignancies using epigenomics on primary samples and PDX mouse models. Where: @carrerasijc.bsky.social When: Anytime. What: 👉https://sl1nk.com/0ekf3z6
033
Reposted by Daniel Lipka
AACR Journals @aacrjournals.bsky.social · 27/04/2026
In this Blood Cancer Discovery study, the authors demonstrate that oncogenic PTPN11 mutations enhance cellular plasticity. This leads to partial restoration of fetal molecular programs, creating new therapeutically exploitable vulnerabilities. buff.ly/QiXstYy
121
Reposted by Daniel Lipka
Mark Hartmann @mphartmann.bsky.social · 04/02/2026
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
doi.org
Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia
AbstractAccumulating evidence links pediatric cancers to prenatal transformation events, yet the influence of the developmental stage on oncogenesis remains elusive. We investigated how hematopoietic ...
143
Reposted by Daniel Lipka
Mark Hartmann @mphartmann.bsky.social · 04/02/2026
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
doi.org
Molecular Plasticity Results in Oncofetal Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
AbstractPersistent fetal gene expression in childhood neoplasms is usually explained by a maturation block originating in the prenatal phase. In contrast, reactivation of fetal genes in adult malignan...
042
Reposted by Daniel Lipka
Mark Hartmann @mphartmann.bsky.social · 04/02/2026
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
aacrjournals.org
A Triumvirate of Transformation: Oncogene, Ontogeny, and Plasticity
Summary:. Cancer cells display extensive heterogeneity that influences therapy response and clinical outcome, yet the underlying mechanisms remain incompletely understood. Recent studies reveal that t...
174
Reposted by Daniel Lipka
Stephen Turner @stephenturner.us · 01/01/2026
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...
doi.org
Staying Current in Data Science and Computational Biology: 2026 Edition
Part 3 in a series of posts going back 14 years
13412
Reposted by Daniel Lipka
Stegle Lab @steglelab.bsky.social · 27/12/2025
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!
072
Reposted by Daniel Lipka
Alex Stark @alex-stark.bsky.social · 24/12/2025
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)
biorxiv.org
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...
210448
Reposted by Daniel Lipka
Rob Schneider @robertife.bsky.social · 19/12/2025
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...
sciencedirect.com
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 …
23411
Reposted by Daniel Lipka
NCT Heidelberg @nct-heidelberg.bsky.social · 15/12/2025
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
073
Daniel Lipka @dblipka.bsky.social · 07/12/2025
👉🏼 @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
0313
Daniel Lipka @dblipka.bsky.social · 06/12/2025
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!
050
Daniel Lipka @dblipka.bsky.social · 06/12/2025
Interested in DNA methylation and want to hear what we can learn from it regarding lineage commitment decisions in #hematopoiesis? #ASH25 #epigenomics #HemeSky
090
Daniel Lipka @dblipka.bsky.social · 06/12/2025
Very happy and proud to see this story finally published! 🎉🥳 #epigenetics #hematology #jmml #leukemia
0101
Reposted by Daniel Lipka
American Society of Hematology @ash.hematology.org · 19/11/2025
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. 🔗 ow.ly/G7Ol50XukwQ #Genomics #HemeSky #MedSky
052
Reposted by Daniel Lipka
John Greally @greally.bsky.social · 24/10/2025
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
figshare.com
1156
Daniel Lipka @dblipka.bsky.social · 19/09/2025
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
ewogberlin2025.org
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...
040
Reposted by Daniel Lipka
Karim-Jean Armache @kjarmache.bsky.social · 16/09/2025
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...
keysym.us
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!
1258
Daniel Lipka @dblipka.bsky.social · 15/09/2025
Of interest to the #epigenomics, #dnamethylation, #neurooncology, #oncology and #precisionmedicine communities! 🧬
020
Reposted by Daniel Lipka
Michael Scherer @scherermich.bsky.social · 08/09/2025
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...
doi.org
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...
0121
Reposted by Daniel Lipka
Epigenome Technologies @epigenometech.bsky.social · 12/09/2025
Epigenetics Update - Fluctuating DNA methylation tracks cancer evolution at clinical scale go.nature.com/3Ve4OUy #Epigenetics #Cancer #DNAme #DNAm --- Empower your research with high-res epigenetic insights at epigenometech.com
031
Reposted by Daniel Lipka
kasitc.bsky.social @kasitc.bsky.social · 18/08/2025
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...
29839
Daniel Lipka @dblipka.bsky.social · 30/08/2025
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
064
Reposted by Daniel Lipka
Mathieu Lupien @matlupien.bsky.social · 29/08/2025
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...
nature.com
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...
0348
Reposted by Daniel Lipka
Schubeler Lab @schubelerlab.bsky.social · 07/08/2025
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....
211549
Daniel Lipka @dblipka.bsky.social · 25/08/2025
+++ 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/...
083
Reposted by Daniel Lipka
Epigenome Technologies @epigenometech.bsky.social · 21/08/2025
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 --- High-resolution insights without cell sorting; epigenometech.com
162