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Qiao P, Zhang C, Shi Y, Du H. The role of alternative polyadenylation in breast cancer. Front Genet 2024; 15:1377275. [PMID: 38939531 PMCID: PMC11208690 DOI: 10.3389/fgene.2024.1377275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
Breast cancer (BC), as a highly prevalent malignant tumor worldwide, is still unclear in its pathogenesis and has poor therapeutic outcomes. Alternative polyadenylation (APA) is a post-transcriptional regulatory mechanism widely found in eukaryotes. Precursor mRNA (pre-mRNA) undergoes the APA process to generate multiple mRNA isoforms with different coding regions or 3'UTRs, thereby greatly increasing the diversity and complexity of the eukaryotic transcriptome and proteome. Studies have shown that APA is involved in the progression of various diseases, including cancer, and plays a crucial role. Therefore, clarifying the biological mechanisms of APA and its regulators in breast cancer will help to comprehensively understand the pathogenesis of breast cancer and provide new ideas for its prevention and treatment.
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Affiliation(s)
- Ping Qiao
- Department of Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Caihong Zhang
- Department of Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yingxu Shi
- Department of Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hua Du
- Department of Pathology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
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Shademan M, Mei H, van Engelen B, Ariyurek Y, Kloet S, Raz V. PABPN1 loss-of-function causes APA-shift in oculopharyngeal muscular dystrophy. HGG ADVANCES 2024; 5:100269. [PMID: 38213032 PMCID: PMC10840355 DOI: 10.1016/j.xhgg.2024.100269] [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: 08/29/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
Alternative polyadenylation (APA) at the 3' UTR of transcripts contributes to the cell transcriptome. APA is suppressed by the nuclear RNA-binding protein PABPN1. Aging-associated reduced PABPN1 levels in skeletal muscles lead to muscle wasting. Muscle weakness in oculopharyngeal muscular dystrophy (OPMD) is caused by short alanine expansion in PABPN1 exon1. The expanded PABPN1 forms nuclear aggregates, an OPMD hallmark. Whether the expanded PABPN1 affects APA and how it contributes to muscle pathology is unresolved. To investigate these questions, we developed a procedure including RNA library preparation and a simple pipeline calculating the APA-shift ratio as a readout for PABPN1 activity. Comparing APA-shift results to previously published PAS utilization and APA-shift results, we validated this procedure. The procedure was then applied on the OPMD cell model and on RNA from OPMD muscles. APA-shift was genome-wide in the mouse OPMD model, primarily affecting muscle transcripts. In OPMD individuals, APA-shift was enriched with muscle transcripts. In an OPMD cell model APA-shift was not significant. APA-shift correlated with reduced expression levels of a subset of PABPN1 isoforms, whereas the expression of the expanded PABPN1 did not correlate with APA-shift. PABPN1 activity is not affected by the expression of expanded PABPN1, but rather by reduced PABPN1 expression levels. In muscles, PABPN1 activity initially affects muscle transcripts. We suggest that muscle weakness in OPMD is caused by PABPN1 loss-of-function leading to APA-shift that primarily affects in muscle transcripts.
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Affiliation(s)
- Milad Shademan
- Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, the Netherlands
| | - Baziel van Engelen
- Department of Neurology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands.
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Sáez-Martínez P, Porcel-Pastrana F, Montero-Hidalgo AJ, Lozano de la Haba S, Sanchez-Sanchez R, González-Serrano T, Gómez-Gómez E, Martínez-Fuentes AJ, Jiménez-Vacas JM, Gahete MD, Luque RM. Dysregulation of RNA-Exosome machinery is directly linked to major cancer hallmarks in prostate cancer: Oncogenic role of PABPN1. Cancer Lett 2024; 584:216604. [PMID: 38244911 DOI: 10.1016/j.canlet.2023.216604] [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: 10/05/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Novel biomarkers and therapeutic strategies for prostate-cancer (PCa) are required to overcome its lethal progression. The dysregulation/implication of the RNA-Exosome-complex (REC; cellular machinery controlling the 3'-5'processing/degradation of most RNAs) in different cancer-types, including PCa, is poorly known. Herein, different cellular/molecular/preclinical approaches with human PCa-samples (tissues and/or plasma of 7 independent cohorts), and in-vitro/in-vivo PCa-models were used to comprehensively characterize the REC-profile and explore its role in PCa. Moreover, isoginkgetin (REC-inhibitor) effects were evaluated on PCa-cells. We demonstrated a specific dysregulation of the REC-components in PCa-tissues, identifying the Poly(A)-Binding-Protein-Nuclear 1 (PABPN1) factor as a critical regulator of major cancer hallmarks. PABPN1 is consistently overexpressed in different human PCa-cohorts and associated with poor-progression, invasion and metastasis. PABPN1 silencing decreased relevant cancer hallmarks in multiple PCa-models (proliferation/migration/tumourspheres/colonies, etc.) through the modulation of key cancer-related lncRNAs (PCA3/FALEC/DLEU2) and mRNAs (CDK2/CDK6/CDKN1A). Plasma PABPN1 levels were altered in patients with metastatic and tumour-relapse. Finally, pharmacological inhibition of REC-activity drastically inhibited PCa-cell aggressiveness. Altogether, the REC is drastically dysregulated in PCa, wherein this novel molecular event/mechanism, especially PABPN1 alteration, may be potentially exploited as a novel prognostic and therapeutic tool for PCa.
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Affiliation(s)
- Prudencio Sáez-Martínez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Francisco Porcel-Pastrana
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Antonio J Montero-Hidalgo
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Samanta Lozano de la Haba
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Rafael Sanchez-Sanchez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Anatomical Pathology Service, HURS, Cordoba, Spain
| | - Teresa González-Serrano
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Anatomical Pathology Service, HURS, Cordoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Urology Service, HURS/IMIBIC, Cordoba, Spain
| | - Antonio J Martínez-Fuentes
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | | | - Manuel D Gahete
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain; Hospital Universitario Reina Sofía (HURS), Cordoba, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.
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Qattan A. Genomic Alterations Affecting Competitive Endogenous RNAs (ceRNAs) and Regulatory Networks (ceRNETs) with Clinical Implications in Triple-Negative Breast Cancer (TNBC). Int J Mol Sci 2024; 25:2624. [PMID: 38473871 DOI: 10.3390/ijms25052624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The concept of competitive endogenous RNA regulation has brought on a change in the way we think about transcriptional regulation by miRNA-mRNA interactions. Rather than the relatively simple idea of miRNAs negatively regulating mRNA transcripts, mRNAs and other non-coding RNAs can regulate miRNAs and, therefore, broad networks of gene products through competitive interactions. While this concept is not new, its significant roles in and implications on cancer have just recently come to light. The field is now ripe for the extrapolation of technologies with a substantial clinical impact on cancer. With the majority of the genome consisting of non-coding regions encoding regulatory RNAs, genomic alterations in cancer have considerable effects on these networks that have been previously unappreciated. Triple-negative breast cancer (TNBC) is characterized by high mutational burden, genomic instability and heterogeneity, making this aggressive breast cancer subtype particularly relevant to these changes. In the past few years, much has been learned about the roles of competitive endogenous RNA network regulation in tumorigenesis, disease progression and drug response in triple-negative breast cancer. In this review, we present a comprehensive view of the new knowledge and future perspectives on competitive endogenous RNA networks affected by genomic alterations in triple-negative breast cancer. An overview of the competitive endogenous RNA (ceRNA) hypothesis and its bearing on cellular function and disease is provided, followed by a thorough review of the literature surrounding key competitive endogenous RNAs in triple-negative breast cancer, the genomic alterations affecting them, key disease-relevant molecular and functional pathways regulated by them and the clinical implications and significance of their dysregulation. New knowledge of the roles of these regulatory mechanisms and the current acceleration of research in the field promises to generate insights into the diagnosis, classification and treatment of triple-negative breast cancer through the elucidation of new molecular mechanisms, therapeutic targets and biomarkers.
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Affiliation(s)
- Amal Qattan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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Wang QH, Yan PC, Shi LZ, Teng YJ, Gao XJ, Yao LQ, Liang ZW, Zhou MH, Han W, Li R. PABPN1 functions as a predictive biomarker in colorectal carcinoma. Mol Biol Rep 2023; 51:40. [PMID: 38158471 DOI: 10.1007/s11033-023-08936-x] [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: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE PABPN1 acts as a modulator of poly(A) tail length and alternative polyadenylation. This research was aimed to explore the role of PABPN1 in colorectal cancer (CRC). METHODS Public databases were performed to analyze expression, location, roles of prognosis and tumor immunity and interaction with RNAs and proteins of PABPN1. To investigate PABPN1 expression in tissues, 78 CRC specimens were collected to conduct IHC, and 30 pairs of frozen CRC and corresponding adjacent normal tissues were used to conduct qRT-PCR and WB. In addition, in vitro experiments were then carried out to identify the role of PABPN1 in CRC. RESULTS Compared with normal tissues, PABPN1 expression was significant higher in CRC. Its high level predicted poor outcome of CRC. Th1 and Treg had significant negative relationships not only with PABPN1 expression, but also with six molecules interacting with PABPN1, including IFT172, KIAA0895L, RECQL4, WDR6, PABPC1 and NCBP1. In addition, PABPN1 had negative relationships with quite a few immune markers, such as CSF1R, IL-10, CCL2 and so on. In cellular experiments, silencing PABPN1 inhibited proliferation and promoted apoptosis in HCT-116 CRC cells. CONCLUSION In summary, PABPN1 might become a novel biomarker and correlate with tumor immunity in CRC.
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Affiliation(s)
- Qing-Hua Wang
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Pei-Ci Yan
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Zhou Shi
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ya-Jie Teng
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Qian Yao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Zhi-Wei Liang
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ming-Hui Zhou
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Wei Han
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China.
| | - Rui Li
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.
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