Pseudotime Based Discovery of Breast Cancer Heterogeneity

Aqila, Tasmia; Mamun, Abdullah Al; Mondal, Ananda Mohan

doi:10.1109/bibm47256.2019.8983300

Cited by 3 publications

(1 citation statement)

References 13 publications

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“…In our pseudotime graphs, we detected between two and four cellular subpopulations per cancer entity, which suggests a certain degree of tumor heterogeneity. Indeed, other studies have performed in-depth evaluation of intratumoral heterogeneity using pseudotime in the past [75,76]. The upregulation of specific ASIGs during pseudotemporal development was restricted to a narrow population in the tSNE plot.…”

Section: Discussionmentioning

confidence: 99%

Single-Cell Transcriptomics Reveals the Expression of Aging- and Senescence-Associated Genes in Distinct Cancer Cell Populations

Saul

Kosinsky

2021

Cells

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The human aging process is associated with molecular changes and cellular degeneration, resulting in a significant increase in cancer incidence with age. Despite their potential correlation, the relationship between cancer- and ageing-related transcriptional changes is largely unknown. In this study, we aimed to analyze aging-associated transcriptional patterns in publicly available bulk mRNA-seq and single-cell RNA-seq (scRNA-seq) datasets for chronic myelogenous leukemia (CML), colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer (LC), and pancreatic ductal adenocarcinoma (PDAC). Indeed, we detected that various aging/senescence-induced genes (ASIGs) were upregulated in malignant diseases compared to healthy control samples. To elucidate the importance of ASIGs during cell development, pseudotime analyses were performed, which revealed a late enrichment of distinct cancer-specific ASIG signatures. Notably, we were able to demonstrate that all cancer entities analyzed in this study comprised cell populations expressing ASIGs. While only minor correlations were detected between ASIGs and transcriptome-wide changes in PDAC, a high proportion of ASIGs was induced in CML, CRC, HCC, and LC samples. These unique cellular subpopulations could serve as a basis for future studies on the role of aging and senescence in human malignancies.

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Section: Discussionmentioning

confidence: 99%