Daniel Lipka
@dblipka.bsky.social
Physician Scientist at DKFZ & NCT Heidelberg
studying 🩸🧬 #epigenomics #DNAmethylation #singleCell #precisiononcology #JMML
www.translational-cancer-epigenomics.de
studying 🩸🧬 #epigenomics #DNAmethylation #singleCell #precisiononcology #JMML
www.translational-cancer-epigenomics.de
Pinned
Daniel Lipka
@dblipka.bsky.social
· Dec 6
ONLINE FIRST ALERT!
Molecular #Plasticity Results in #Oncofetal #Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
aacrjournals.org/bloodcancerd...
@aacrjournals.bsky.social
#childhoodcancer
#epigenetics
#precisiononcology
Molecular #Plasticity Results in #Oncofetal #Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
aacrjournals.org/bloodcancerd...
@aacrjournals.bsky.social
#childhoodcancer
#epigenetics
#precisiononcology
Very happy and proud to see this story finally published! 🎉🥳
#epigenetics #hematology #jmml #leukemia
#epigenetics #hematology #jmml #leukemia
Reposted by 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
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
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 ...
doi.org
February 4, 2026 at 6:28 PM
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
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
Reposted by Daniel Lipka
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
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
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...
doi.org
February 4, 2026 at 6:28 PM
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
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
Reposted by Daniel Lipka
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
#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
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...
aacrjournals.org
February 4, 2026 at 6:28 PM
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
#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
Reposted by Daniel Lipka
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...
Staying Current in Data Science and Computational Biology: 2026 Edition
Part 3 in a series of posts going back 14 years
doi.org
January 1, 2026 at 10:15 AM
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...
Reposted by Daniel Lipka
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!
December 27, 2025 at 3:50 PM
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!
Reposted by Daniel Lipka
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)
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...
www.biorxiv.org
December 24, 2025 at 3:06 PM
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)
Reposted by Daniel Lipka
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...
www.sciencedirect.com/science/arti...
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 …
www.sciencedirect.com
December 19, 2025 at 5:17 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Daniel Lipka
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
www.nct-heidelberg.de/das-nct/news...
@dkfz.bsky.social @mphartmann.bsky.social @dblipka.bsky.social
December 15, 2025 at 1:48 PM
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
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
December 7, 2025 at 3:34 PM
👉🏼 @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
Interested in DNA methylation and want to hear what we can learn from it regarding lineage commitment decisions in #hematopoiesis? #ASH25 #epigenomics #HemeSky
December 6, 2025 at 3:46 PM
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
#epigenetics #hematology #jmml #leukemia
ONLINE FIRST ALERT!
Molecular #Plasticity Results in #Oncofetal #Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
aacrjournals.org/bloodcancerd...
@aacrjournals.bsky.social
#childhoodcancer
#epigenetics
#precisiononcology
Molecular #Plasticity Results in #Oncofetal #Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia
aacrjournals.org/bloodcancerd...
@aacrjournals.bsky.social
#childhoodcancer
#epigenetics
#precisiononcology
December 6, 2025 at 1:07 AM
Very happy and proud to see this story finally published! 🎉🥳
#epigenetics #hematology #jmml #leukemia
#epigenetics #hematology #jmml #leukemia
Reposted by Daniel Lipka
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
🔗 https://ow.ly/G7Ol50XukwQ
#Genomics #HemeSky #MedSky
November 19, 2025 at 8:30 PM
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
🔗 https://ow.ly/G7Ol50XukwQ
#Genomics #HemeSky #MedSky
Reposted by Daniel Lipka
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, 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
October 24, 2025 at 3:09 PM
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, 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
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
#jmml #ewogmds #precisionmedicine www.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...
www.ewogberlin2025.org
September 19, 2025 at 5:07 PM
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
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org
Reposted by Daniel Lipka
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...
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!
keysym.us
September 16, 2025 at 4:01 PM
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-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/10.1007/s004...
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...
doi.org
September 15, 2025 at 12:29 PM
Of interest to the #epigenomics, #dnamethylation, #neurooncology, #oncology and #precisionmedicine communities! 🧬
Reposted by Daniel Lipka
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/10.1007/s004...
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...
doi.org
September 8, 2025 at 7:07 AM
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/10.1007/s004...
Reposted by Daniel Lipka
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
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
September 12, 2025 at 11:49 AM
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
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
Reposted by Daniel Lipka
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...
August 18, 2025 at 12:23 PM
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
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
+++ 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/...
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/...
August 30, 2025 at 10:51 AM
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
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
Reposted by Daniel Lipka
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...
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...
www.nature.com
August 29, 2025 at 7:27 PM
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...
Reposted by Daniel Lipka
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....
August 7, 2025 at 4:20 PM
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/...
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/...
August 25, 2025 at 8:45 PM
+++ 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/...
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/...
Reposted by Daniel Lipka
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
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
August 21, 2025 at 8:18 AM
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
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
Reposted by Daniel Lipka
🧵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
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9
August 16, 2025 at 8:01 AM
🧵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
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9