Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing

Craig, Amanda J.; Silveira, Maruhen A. Datsch; Ma, Lichun; Revsine, Mahler; Wang, Limin; Heinrich, Sophia; Rae, Zachary; Ruchinskas, Allison; Dadkhah, Kimia; Do, Whitney; Behrens, Shay; Mehrabadi, Farid R.; Dominguez, Dana A.; Forgues, Marshonna; Budhu, Anuradha; Chaisaingmongkol, Jittiporn; Hernandez, Jonathan M.; Davis, Jeremy L.; Tran, Bao; Marquardt, Jens U.; Ruchirawat, Mathuros; Kelly, Michael; Greten, Tim F.; Wang, Xin W.

doi:10.1016/j.celrep.2023.113446

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2024

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Cited by 7 publications

References 46 publications

(86 reference statements)

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Morphomolecular Pathology and Genomic Insights into the Cells of Origin of Cholangiocarcinoma and Combined Hepatocellular-Cholangiocarcinoma

Guest,

Goeppert,

Nault

et al. 2024

The American Journal of Pathology

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Morphomolecular Pathology and Genomic Insights into the Cells of Origin of Cholangiocarcinoma and Combined Hepatocellular-Cholangiocarcinoma

Guest,

Goeppert,

Nault

et al. 2024

The American Journal of Pathology

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Applications of single-cell multi-omics in liver cancer

Peeters,

Cappuyns,

Piqué-Gili

et al. 2024

JHEP Reports

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EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data

Kelly,

Scherer,

Braun

et al. 2024

Preprint

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Epigenetic heterogeneity is a fundamental property of biological systems, and is recognized as a potential driver of tumor plasticity and therapy resistance. Single-cell epigenomics technologies have been widely employed to study epigenetic variation between - but not within - cellular clusters. We introduce epiCHAOS: a quantitative metric of cell-to-cell epigenetic heterogeneity, applicable to any single-cell epigenomics data type. After validation in synthetic datasets, we applied epiCHAOS to investigate global and region-specific patterns of epigenetic heterogeneity across diverse biological systems. EpiCHAOS provides an excellent approximation of stemness and plasticity in development and malignancy, making it a valuable addition to single-cell cancer epigenomics analyses.

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Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing

Cited by 7 publications

References 46 publications

Morphomolecular Pathology and Genomic Insights into the Cells of Origin of Cholangiocarcinoma and Combined Hepatocellular-Cholangiocarcinoma

Morphomolecular Pathology and Genomic Insights into the Cells of Origin of Cholangiocarcinoma and Combined Hepatocellular-Cholangiocarcinoma

Applications of single-cell multi-omics in liver cancer

EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data

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