Theodora

PhD student @ucddublin | Epigenetic mechanisms governing pediatric leukemias | @sysbioire @Researchirel

[Iannis Aifantis @iannisaifantis1]

We mapped 3D chromosome organization during normal human B-cell development and in pediatric B-ALL. Our study shows that leukemia subtypes acquire distinct 3D genome architectures that help activate oncogenic transcriptional programs. In ETV6::RUNX1 B-ALL, altered chromatin interactions converge on ERG, linking nuclear organization to leukemia cell survival and impaired differentiation. These findings highlight 3D genome remodeling as a key layer of leukemia biology and a potential source of new therapeutic vulnerabilities.

[Dan Landau @landau_lab]

Exciting breakthrough technology from the lab, now live in @CellCellPress ! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!

[Ansu Satpathy @Satpathology]

A holy grail for our lab has been tracking myeloid cells in human tumors in the same way that we track T and B cells with TCR/BCR.
@vincentzliu and @CalebLareau solved it!
We developed Mitotrek using scATAC-seq + mitochondrial DNA to do exactly this. Using Mitotrek, we find that new myeloid cells clones constantly infiltrate the tumor via circulating monocytes — and that their macrophage or dendritic cell fate is epigenetically programmed before tumor entry.
@10xGenomics @parkerici @CancerResearch @TheMarkFdn
https://t.co/Y37qbyw3F5

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Update - DOT1L provides transcriptional memory through PRC1.1 antagonism https://t.co/hR0W0bobWa

Chen Davidovich/Omer Gilan (Monash University) in Nat Cell Biol

#Epigenetics #DOT1L #Polycomb
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Gain deeper insights into gene regulation; https://t.co/WmSYDGWPJD

[Zihai Li, MD, PhD @Zihai]

Transcription factors for T cell differentiation cataloged. https://t.co/2nG6tUCqIE

[Hao Yin @HaoYin20]

DeepSpaceDB
https://t.co/FE7KDzA1io

>2k #SpatialTranscriptomics Visium samples

👉Interactive, downloadable data analysis
QC➡️ manual/LLM image annotation➡️
in-sample or cross-sample spot clustering BASS BayesSpace➡️
Spatially variable genes singleCellHaystack SPARK-X binSpect➡️
Cell type deconvolution RCTD SPOTlight

👉Cross-sample/Cross-study comparison
👉Analyze your own data
👉Database-wide gene/pathway inquiry

@alexisvdb #NucAcidRes 2026
https://t.co/3Bm62qd2P7

[Thomas Norman @thenormanlab]

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

[Andrey Tvardovskiy @ATvardovskiy]

Great to see it finally out!
"Mass spectrometry–based profiling of single-cell histone post-translational modifications"
Huge congratulations to @SimoneSidoli @cutleraging and co-authors!

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Update – Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models https://t.co/y045t3VuA8

#Epigenetic #DNAm #Cancer
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Gain deeper insights at https://t.co/WmSYDGXnzb

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Review - Epigenetic editing: from concept to clinic https://t.co/uRozZW2eEX

Marianne G. Rots (University of Groningen) reporting in Nat Rev Drug Disc

#Epigenetics #Review #EpigeneticEditing
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Gain deeper insights into gene regulation; https://t.co/WmSYDGWPJD

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Update - Addressing the specific roles of histone modifications in transcriptional repression https://t.co/iyllpZuHpG

Kristian Helin reporting in Nat Commun

#Epigenetics #HisMods #Chromatin
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Discover the breakthrough at https://t.co/WmSYDGXnzb

[Haematologica @Haematologica]

First-born twins have a higher risk of acute leukemia, but concordance between twins is rare, says a new California twin cohort study. Epigenetics may explain birth order differences.
https://t.co/MdzquMRnaH

[Rutger Gjaltema 🧬 @RutgerGjaltema]

Interesting: ChIP-Seq is biased in favor of gene promoters and against intergenic Regions. CUT&Tag identifies H3K9me3 at young repetitive elements undetectable by ChIP-Seq.
https://t.co/04UB7z1NSM

[Andy Lane @lane_andy]

Rapid epigenomic classification of acute leukemia | Nature Genetics https://t.co/jlbVWmTgsS

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Update - A subset of transposable elements as mechano-response enhancer elements in controlling human embryonic stem cell fate https://t.co/q7KLWJta5j

#Epigenetics #StemCells
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High-res insights without cell sorting; https://t.co/WmSYDGXnzb

[Stephen Turner 🦋 @stephenturner.us @strnr]

OmniPath (https://t.co/g2JRIODn2k): integrated knowledgebase for multi-omics analysis https://t.co/SYaCvU76su 🧬🖥️🧪

Python module https://t.co/n7As1pmtmv
R package https://t.co/bwzjAmuab8 #Rstats

[Calum Gabbutt @CalumGabbutt]

Cancer is an evolutionary disease, but does knowing a cancer’s evolutionary past help predict its future? Out today in @Nature, we learnt the evolution of 2000 lymphoid cancers and found it was highly correlated with clinical outcomes! (1/7, link below)

[Prof. Nikolai Slavov @slavov_n]

This article suggests that TF binding is determined by the sum of multiple, overlapping binding sites.

Thus, competition between paralogous TFs for shared high-affinity binding sites may be influences by flanking nucleotides from overlapping, lower-affinity binding sites.

🧵

[Cosmin Tudose @cosmint_]

Pleased that the 2nd part of my PhD in now available as a preprint! Here, we investigated the epigenomic and transcriptomic changes occurring upon PRC2 depletion in AML cells. https://t.co/xc0v6DUXW3. A thread🧵1/17

[Jonathan Bond @jbond2019]

Bond group out in force ⁦@News_IACR⁩ Congrats to Luke ⁦@iamnotaprawn⁩ for his poster 🏵️ and Theodora ⁦@TheodoraGrosu⁩ for selection for the Fitzpatrick medal competition ⁦@sysbioire⁩ ⁦@IrishCancerSoc⁩ ⁦@Researchirel⁩ ⁦@PrecisionOncIre⁩