Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis

Fan, Huihui; Atiya, Huda I.; Wang, Yeh; Pisanic, Thomas R.; Wang, Jeff; Shih, Ie‐Ming; Foy, Kelly K.; Frisbie, Leonard; Chandler, Chelsea; Shen, Hui; Coffman, Lan

doi:10.1101/2020.02.25.964197

Cited by 2 publications

(2 citation statements)

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“…PEPATAC does not rely on any specific local or cloud computing infrastructure, and it has already been deployed successfully in various compute environments at multiple research institutes to yield several peer-reviewed studies 10–14 . To simplify installation, we also enable a computing environment with the command-line tools required to run PEPATAC using either docker or singularity with the bulker multi-container environment manager 15 .…”

Section: Introductionmentioning

confidence: 99%

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PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

Smith

Corces

et al. 2020

Preprint

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Motivation: As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. Results: PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. Availability: BSD2-licensed code and documentation at https://pepatac.databio.org.

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Section: Introductionmentioning

confidence: 99%

“…PEPATAC does not rely on any specific local or cloud computing infrastructure, and it has already been deployed successfully in various compute environments at multiple research institutes to yield numerous peerreviewed studies (10)(11)(12)(13)(14). While all ATAC-seq pipelines use several common bioinformatic tools (Fig.…”

Section: Introductionmentioning

confidence: 99%

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

Smith

Corces

et al. 2020

Preprint

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Loss of XIST lncRNA unlocks stemness and cellular plasticity in ovarian cancer

Naciri,

Liang,

Yang

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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Plasticity, a key hallmark of cancer, enables cells to transition into different states, driving tumor heterogeneity. This cellular plasticity is associated with cancer progression, treatment resistance, and relapse. Cancer stem cells (CSCs) play a central role in this process, yet the molecular factors underlying cancer cell stemness remain poorly understood. In this study, we explored the role of XIST (X-inactive specific transcript) long noncoding RNA in ovarian cancer stemness and plasticity through in silico and in vitro analyses. We found that XIST is significantly down-regulated in ovarian tumors, with low XIST expression linked to a higher stemness index and lower overall survival. Knocking down XIST in ovarian cancer cells enhanced stemness, particularly increasing mesenchymal-like CSCs, and under hypoxic conditions, it promoted epithelial-like CSC markers. Our findings suggest that XIST loss leads to CSC enrichment and cellular plasticity in ovarian cancer, pointing to potential therapeutic targets for patients with low XIST expression.

show abstract

Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis

Cited by 2 publications

References 57 publications

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

Loss of XIST lncRNA unlocks stemness and cellular plasticity in ovarian cancer

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