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Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Zhou, Jay et al. report that in mantle cell lymphoma and T cell leukaemia, lineage-determining transcription factors share a mechanism to regulate how multiple enhancers control oncogene expression through topological conformation and interaction.

Yeqiao Zhou
Atishay Jay
Robert B. Faryabi
Research02 Dec 2025
Nature Cell Biology

Volume: 28, P: 149-165
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

The role of enhancer-promoter hubs in the regulation of gene expression in cancer remains to be explored. Here, the authors identify enhancer-promoter hubs in breast cancer, lymphoma, and leukemia and suggest their potential role in promoting oncogenesis and drug resistance.

Brent S. Perlman
Noah Burget
Robert B. Faryabi
ResearchOpen Access14 Sept 2024
Nature Communications

Volume: 15, P: 1-21
AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Annotation of cell types and quantification of their relative localization in tissues remain challenging. Here, the authors present AnnoSpat (Annotator and Spatial Pattern Finder), a computational tool that can automatically identify cell types and quantify cell-cell proximity relationships.

Aanchal Mongia
Fatema Tuz Zohora
Robert B. Faryabi
ResearchOpen Access03 May 2024
Nature Communications

Volume: 15, P: 1-19
Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

The DNA-binding domains of transcription factors have been well characterized, but whether their intrinsically disordered regions control cell fate is unclear. Here, the authors show the functional and mechanistic importance of an intrinsically disordered region of TCF-1 in T cell development.

Naomi Goldman
Aditi Chandra
Golnaz Vahedi
Research17 Aug 2023
Nature Immunology

Volume: 24, P: 1698-1710
ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells

Verma et al. report that ALC1 loss confers PARP inhibitor hypersensitivity in homologous recombination-deficient cells through reducing chromatin accessibility.

Priyanka Verma
Yeqiao Zhou
Roger A. Greenberg
Research18 Jan 2021
Nature Cell Biology

Volume: 23, P: 160-171
TooManyCells identifies and visualizes relationships of single-cell clades

The TooManyCells approach to scRNA-seq data facilitates efficient and unbiased identification and visualization of cell clades and rare subpopulations. Application of TooManyCells to drug-resistant leukemia cells identifies a rare resistant-like subpopulation of treatment-naive cells.

Gregory W. Schwartz
Yeqiao Zhou
Robert B. Faryabi
Research02 Mar 2020
Nature Methods

Volume: 17, P: 405-413

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Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells

TooManyCells identifies and visualizes relationships of single-cell clades

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