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To KKW, Huang Z, Zhang H, Ashby CR, Fu L. Utilizing non-coding RNA-mediated regulation of ATP binding cassette (ABC) transporters to overcome multidrug resistance to cancer chemotherapy. Drug Resist Updat 2024; 73:101058. [PMID: 38277757 DOI: 10.1016/j.drup.2024.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Multidrug resistance (MDR) is one of the primary factors that produces treatment failure in patients receiving cancer chemotherapy. MDR is a complex multifactorial phenomenon, characterized by a decrease or abrogation of the efficacy of a wide spectrum of anticancer drugs that are structurally and mechanistically distinct. The overexpression of the ATP-binding cassette (ABC) transporters, notably ABCG2 and ABCB1, are one of the primary mediators of MDR in cancer cells, which promotes the efflux of certain chemotherapeutic drugs from cancer cells, thereby decreasing or abolishing their therapeutic efficacy. A number of studies have suggested that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a pivotal role in mediating the upregulation of ABC transporters in certain MDR cancer cells. This review will provide updated information about the induction of ABC transporters due to the aberrant regulation of ncRNAs in cancer cells. We will also discuss the measurement and biological profile of circulating ncRNAs in various body fluids as potential biomarkers for predicting the response of cancer patients to chemotherapy. Sequence variations, such as alternative polyadenylation of mRNA and single nucleotide polymorphism (SNPs) at miRNA target sites, which may indicate the interaction of miRNA-mediated gene regulation with genetic variations to modulate the MDR phenotype, will be reviewed. Finally, we will highlight novel strategies that could be used to modulate ncRNAs and circumvent ABC transporter-mediated MDR.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Zoufang Huang
- Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Hang Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, United States
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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2
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Yu P, Song S, Zhang X, Cui S, Wei G, Huang Z, Zeng L, Ni T, Sun A. Downregulation of apoptotic repressor AVEN exacerbates cardiac injury after myocardial infarction. Proc Natl Acad Sci U S A 2023; 120:e2302482120. [PMID: 37816050 PMCID: PMC10589712 DOI: 10.1073/pnas.2302482120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023] Open
Abstract
Myocardial infarction (MI) is a leading cause of heart failure (HF), associated with morbidity and mortality worldwide. As an essential part of gene expression regulation, the role of alternative polyadenylation (APA) in post-MI HF remains elusive. Here, we revealed a global, APA-mediated, 3' untranslated region (3' UTR)-lengthening pattern in both human and murine post-MI HF samples. Furthermore, the 3' UTR of apoptotic repressor gene, AVEN, is lengthened after MI, contributing to its downregulation. AVEN knockdown increased cardiomyocyte apoptosis, whereas restoration of AVEN expression substantially improved cardiac function. Mechanistically, AVEN 3' UTR lengthening provides additional binding sites for miR-30b-5p and miR-30c-5p, thus reducing AVEN expression. Additionally, PABPN1 (poly(A)-binding protein 1) was identified as a potential regulator of AVEN 3' UTR lengthening after MI. Altogether, our findings revealed APA as a unique mechanism regulating cardiac injury in response to MI and also indicated that the APA-regulated gene, AVEN, holds great potential as a critical therapeutic target for treating post-MI HF.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Shujun Cui
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
| | - Zihang Huang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Linqi Zeng
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai200040, China
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot010021, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai201203, China
| | - Aijun Sun
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Anthropology and Human Genetics, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai200438, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai200032, China
- Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai201203, China
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3
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Liu H, Arsiè R, Schwabe D, Schilling M, Minia I, Alles J, Boltengagen A, Kocks C, Falcke M, Friedman N, Landthaler M, Rajewsky N. SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle. Mol Syst Biol 2023; 19:1-23. [PMID: 38778223 PMCID: PMC10568207 DOI: 10.15252/msb.202211427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 05/25/2024] Open
Abstract
RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene‐specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust‐cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM‐Drop‐seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single‐cell gene expression dynamics in continuous biological processes.
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Affiliation(s)
- Haiyue Liu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Roberto Arsiè
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Daniel Schwabe
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marcel Schilling
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Igor Minia
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christine Kocks
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Physics, Humboldt University Berlin, Berlin, Germany
| | - Nir Friedman
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Center for Computational Medicine, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Berlin, Germany.
- NeuroCure Cluster of Excellence, Berlin, Germany.
- German Cancer Consortium (DKTK), Berlin, Germany.
- National Center for Tumor Diseases (NCT), Berlin, Germany.
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4
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Moon Y, Burri D, Zavolan M. Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR Genom Bioinform 2023; 5:lqad079. [PMID: 37705828 PMCID: PMC10495540 DOI: 10.1093/nargab/lqad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3' ends via cleavage and polyadenylation at distinct polyadenylation (poly(A)) sites. The regulation of cell type-specific poly(A) site choice is not completely resolved, and requires quantitative poly(A) site usage data across cell types. 3' end-based single-cell RNA-seq can now be broadly used to obtain such data, enabling the identification and quantification of poly(A) sites with direct experimental support. We propose SCINPAS, a computational method to identify poly(A) sites from scRNA-seq datasets. SCINPAS modifies the read deduplication step to favor the selection of distal reads and extract those with non-templated poly(A) tails. This approach improves the resolution of poly(A) site recovery relative to standard software. SCINPAS identifies poly(A) sites in genic and non-genic regions, providing complementary information relative to other tools. The workflow is modular, and the key read deduplication step is general, enabling the use of SCINPAS in other typical analyses of single cell gene expression. Taken together, we show that SCINPAS is able to identify experimentally-supported, known and novel poly(A) sites from 3' end-based single-cell RNA sequencing data.
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Affiliation(s)
- Youngbin Moon
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dominik Burri
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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5
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Gallicchio L, Olivares GH, Berry CW, Fuller MT. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol 2023; 20:908-925. [PMID: 37906624 PMCID: PMC10730144 DOI: 10.1080/15476286.2023.2275109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
| | - Gonzalo H. Olivares
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Center for Integrative Biology (CIB), Universidad Mayor, Chile and Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
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