ArticlePloS one2019
Alternative polyadenylation of single cells delineates cell types and serves as a prognostic marker in early stage breast cancer.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- ZFP36L1 and ZFP36L2 reduce cyclin D1 expression by decreasing expression of E2F1 and long 3'UTR isoform of CCND1 transcripts.Molecular and cellular biochemistry · 2025Article
- The role of alternative polyadenylation in breast cancer.Frontiers in genetics · 2024Review
- Dynamics of alternative polyadenylation in single root cells ofFrontiers in plant science · 2024Article
- Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma.Cancer informatics · 2024Article
- Cell-type-specific alternative polyadenylation promotes oncogenic gene expression in non-small cell lung cancer progression.Molecular therapy. Nucleic acids · 2023Article
- Omics Technologies Improving Breast Cancer Research and Diagnostics.International journal of molecular sciences · 2023Review
- Article
- Circular RNAs and Untranslated Regions in Acute Myeloid Leukemia.International journal of molecular sciences · 2023Review
- Regulation and function of alternative polyadenylation in development and differentiation.RNA biology · 2023Review
- Association of RNA-modification "writer" genes with prognosis and response to immunotherapy in patients with low-grade glioma.PloS one · 2023Article
- scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data.International journal of molecular sciences · 2022Article
- Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.Genome research · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Single cell RNA sequencing for breast cancer: present and future.Cell death discovery · 2021Review
- Immune-related genes with APA in microenvironment indicate risk stratification and clinical prognosis in grade II/III gliomas.Molecular therapy. Nucleic acids · 2021Article
- Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer.Molecular cancer · 2021Article
- Alternative Polyadenylation: a new frontier in post transcriptional regulation.Biomarker research · 2020Review
- Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders.Biomolecules · 2020Review
- Progress and Clinical Application of Single-Cell Transcriptional Sequencing Technology in Cancer Research.Frontiers in oncology · 2020Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative polyadenylation (APA) in 3' untranslated regions (3' UTR) plays an important role in regulating transcript abundance, localization, and interaction with microRNAs. Length-variation of 3'UTRs by APA contributes to efficient proliferation of cancer cells. In this study, we investigated APA in single cancer cells and tumor microenvironment cells to understand the physiological implication of APA in different cell types. We analyzed APA patterns and the expression level of genes from the 515 single-cell RNA sequencing (scRNA-seq) dataset from 11 breast cancer patients. Although the overall 3'UTR length of individual genes was distributed equally in tumor and non-tumor cells, we found a differential pattern of polyadenylation in gene sets between tumor and non-tumor cells. In addition, we found a differential pattern of APA across tumor types using scRNA-seq data from 3 glioblastoma patients and 1 renal cell carcinoma patients. In detail, 1,176 gene sets and 53 genes showed the distinct pattern of 3'UTR shortening and over-expression as signatures for five cell types including B lymphocytes, T lymphocytes, myeloid cells, stromal cells, and breast cancer cells. Functional categories of gene sets for cellular proliferation demonstrated concordant regulation of APA and gene expression specific to cell types. The expression of APA genes in breast cancer was significantly correlated with the clinical outcome of earlier stage breast cancer patients. We identified cell type-specific APA in single cells, which allows the identification of cell types based on 3'UTR length variation in combination with gene expression. Specifically, an immune-specific APA signature in breast cancer could be utilized as a prognostic marker of early stage breast cancer.
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