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Chen B, Chen X, Hu R, Li H, Wang M, Zhou L, Chen H, Wang J, Zhang H, Zhou X, Zhang H. Alternative polyadenylation regulates the translation of metabolic and inflammation-related proteins in adipose tissue of gestational diabetes mellitus. Comput Struct Biotechnol J 2024; 23:1298-1310. [PMID: 38560280 PMCID: PMC10978812 DOI: 10.1016/j.csbj.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/25/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
In gestational diabetes mellitus (GDM), adipose tissue undergoes metabolic disturbances and chronic low-grade inflammation. Alternative polyadenylation (APA) is a post-transcriptional modification mechanism that generates mRNA with variable lengths of 3' untranslated regions (3'UTR), and it is associated with inflammation and metabolism. However, the role of APA in GDM adipose tissue has not been well characterized. In this study, we conducted transcriptomic and proteomic sequencing on subcutaneous and omental adipose tissues from both control and GDM patients. Using Dapars, a novel APA quantitative algorithm, we delineated the APA landscape of adipose tissue, revealing significant 3'UTR elongation of mRNAs in the GDM group. Omental adipose tissue exhibited a significant correlation between elongated 3'UTRs and reduced translation levels of genes related to metabolism and inflammation. Validation experiments in THP-1 derived macrophages (TDMs) demonstrated the impact of APA on translation levels by overexpressing long and short 3'UTR isoforms of a representative gene LRRC25. Additionally, LRRC25 was validated to suppress proinflammatory polarization in TDMs. Further exploration revealed two underexpressed APA trans-acting factors, CSTF3 and PPP1CB, in GDM omental adipose tissue. In conclusion, this study provides preliminary insights into the APA landscape of GDM adipose tissue. Reduced APA regulation in GDM omental adipose tissue may contribute to metabolic disorders and inflammation by downregulating gene translation levels. These findings advance our understanding of the molecular mechanisms underlying GDM-associated adipose tissue changes.
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Affiliation(s)
- Bingnan Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Ruohan Hu
- Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Hongli Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Min Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Linwei Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hao Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Jianqi Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hanwen Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Xiaobo Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hua Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
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Luo X, Wei Q, Jiang X, Chen N, Zuo X, Zhao H, Liu Y, Liu X, Xie L, Yang Y, Liu T, Yi P, Xu J. CSTF3 contributes to platinum resistance in ovarian cancer through alternative polyadenylation of lncRNA NEAT1 and generating the short isoform NEAT1_1. Cell Death Dis 2024; 15:432. [PMID: 38898019 PMCID: PMC11187223 DOI: 10.1038/s41419-024-06816-1] [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: 12/13/2023] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
Platinum-based chemotherapy is the standard postoperative adjuvant treatment for ovarian cancer (OC). Despite the initial response to chemotherapy, 85% of advanced OC patients will have recurrent disease. Relapsed disease and platinum resistance are the major causes of death in OC patients. In this study, we compared the global regulation of alternative polyadenylation (APA) in platinum-resistant and platinum-sensitive tissues of OC patients by analyzing a set of single-cell RNA sequencing (scRNA-seq) data from public databases and found that platinum-resistant patients exhibited global 3' untranslated region (UTR) shortening due to the different usage of polyadenylation sites (PASs). The APA regulator CSTF3 was the most significantly upregulated gene in epithelial cells of platinum-resistant OC. CSTF3 knockdown increased the sensitivity of OC cells to platinum. The lncRNA NEAT1 has two isoforms, short (NEAT1_1) and long (NEAT1_2) transcript, because of the APA processing in 3'UTR. We found that CSTF3 knockdown reduced the usage of NEAT1 proximal PAS to lengthen the transcript and facilitate the expression of NEAT1_2. Downregulation of the expression of NEAT1 (NEAT1_1/_2), but not only NEAT1_2, also increased the sensitivity of OC cells to platinum. Overexpressed NEAT1_1 reversed the platinum resistance of OC cells after knocking down CSTF3 expression. Furthermore, downregulated expression of CSTF3 and NEAT1_1, rather than NEAT1_2, was positively correlated with inactivation of the PI3K/AKT/mTOR pathway in OC cells. Together, our findings revealed a novel mechanism of APA regulation in platinum-resistant OC. CSTF3 directly bound downstream of the NEAT1 proximal PAS to generate the short isoform NEAT1_1 and was conducive to platinum resistance, which provides a potential biomarker and therapeutic strategy for platinum-resistant OC patients.
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Affiliation(s)
- Xin Luo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinglv Wei
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyan Jiang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ningxuan Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinzhao Zuo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongyan Zhao
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yujiao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lingcui Xie
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jing Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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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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Capela AM, Tavares-Marcos C, Estima-Arede HF, Nóbrega-Pereira S, Bernardes de Jesus B. NORAD-Regulated Signaling Pathways in Breast Cancer Progression. Cancers (Basel) 2024; 16:636. [PMID: 38339387 PMCID: PMC10854850 DOI: 10.3390/cancers16030636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Long non-coding RNA activated by DNA damage (NORAD) has recently been associated with pathologic mechanisms underlying cancer progression. Due to NORAD's extended range of interacting partners, there has been contradictory data on its oncogenic or tumor suppressor roles in BC. This review will summarize the function of NORAD in different BC subtypes and how NORAD impacts crucial signaling pathways in this pathology. Through the preferential binding to pumilio (PUM) proteins PUM1 and PUM2, NORAD has been shown to be involved in the control of cell cycle, angiogenesis, mitosis, DNA replication and transcription and protein translation. More recently, NORAD has been associated with PUM-independent roles, accomplished by interacting with other ncRNAs, mRNAs and proteins. The intricate network of NORAD-mediated signaling pathways may provide insights into the potential design of novel unexplored strategies to overcome chemotherapy resistance in BC treatment.
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Affiliation(s)
| | | | | | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
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5
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Cacioppo R, Akman HB, Tuncer T, Erson-Bensan AE, Lindon C. Differential translation of mRNA isoforms underlies oncogenic activation of cell cycle kinase Aurora A. eLife 2023; 12:RP87253. [PMID: 37384380 DOI: 10.7554/elife.87253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Aurora Kinase A (AURKA) is an oncogenic kinase with major roles in mitosis, but also exerts cell cycle- and kinase-independent functions linked to cancer. Therefore, control of its expression, as well as its activity, is crucial. A short and a long 3'UTR isoform exist for AURKA mRNA, resulting from alternative polyadenylation (APA). We initially observed that in triple-negative breast cancer, where AURKA is typically overexpressed, the short isoform is predominant and this correlates with faster relapse times of patients. The short isoform is characterized by higher translational efficiency since translation and decay rate of the long isoform are targeted by hsa-let-7a tumor-suppressor miRNA. Additionally, hsa-let-7a regulates the cell cycle periodicity of translation of the long isoform, whereas the short isoform is translated highly and constantly throughout interphase. Finally, disrupted production of the long isoform led to an increase in proliferation and migration rates of cells. In summary, we uncovered a new mechanism dependent on the cooperation between APA and miRNA targeting likely to be a route of oncogenic activation of human AURKA.
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Hesna Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Taner Tuncer
- Department of Biology, Ondokuz Mayis Universitesi, Samsun, Turkey
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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Watt K, Postovit LM. Tailoring 3' UTRs alters metastatic potential. Nat Cell Biol 2023; 25:805-807. [PMID: 37156910 DOI: 10.1038/s41556-023-01127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Kathleen Watt
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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Xiao S, Gu H, Deng L, Yang X, Qiao D, Zhang X, Zhang T, Yu T. Relationship between NUDT21 mediated alternative polyadenylation process and tumor. Front Oncol 2023; 13:1052012. [PMID: 36816917 PMCID: PMC9933127 DOI: 10.3389/fonc.2023.1052012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3' end of RNA polymerase II transcripts from over 60% of human genes. APA and microRNA regulation are both mechanisms of post-transcriptional regulation of gene expression. As a key molecular mechanism, Alternative polyadenylation often results in mRNA isoforms with the same coding sequence but different lengths of 3' UTRs, while microRNAs regulate gene expression by binding to specific mRNA 3' UTRs. Nudix Hydrolase 21 (NUDT21) is a crucial mediator involved in alternative polyadenylation (APA). Different studies have reported a dual role of NUDT21 in cancer (both oncogenic and tumor suppressor). The present review focuses on the functions of APA, miRNA and their interaction and roles in development of different types of tumors.NUDT21 mediated 3' UTR-APA changes can be used to generate specific signatures that can be used as potential biomarkers in development and disease. Due to the emerging role of NUDT21 as a regulator of the aforementioned RNA processing events, modulation of NUDT21 levels may be a novel viable therapeutic approach.
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Affiliation(s)
- Shan Xiao
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China
| | - Huan Gu
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Deng
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China
| | - Xiongtao Yang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Qiao
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xudong Zhang
- Department of Anesthesia, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tian Zhang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Tao Yu, ; Tian Zhang,
| | - Tao Yu
- Department of Oncology, Affiliated Hospital of Southwest Medical University of China, Luzhou, China,Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Tao Yu, ; Tian Zhang,
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8
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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10
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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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11
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Fan W, Ding J, Liu S, Zhong W. Development and validation of novel prognostic models based on RNA-binding proteins in breast cancer. J Int Med Res 2022; 50:3000605221106285. [PMID: 35770997 PMCID: PMC9252011 DOI: 10.1177/03000605221106285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives We aimed to construct novel prognostic models based on RNA-binding proteins (RBPs) in breast cancer (BRCA) and explore their roles in this disease and their effects on tumor-infiltrating immune cells (TIICs). Methods Datasets were downloaded from the Gene Expression Omnibus (GEO) database. Functions and prognostic values of RBPs were systematically investigated using a series of bioinformatics analysis methods. TIICs were assessed using CIBERSORT. Results Overall, 138 differentially expressed RBPs were identified, of which 86 were upregulated and 52 were downregulated. Of these, 13 RBPs were identified as prognosis-related and adopted to construct an overall survival (OS) model, while 12 RBPs were used for the relapse-free survival (RFS) model. High-risk patients had poorer OS and RFS rates than low-risk patients. The results indicate that the OS and RFS models are good prognostic models with reliable predictive abilities. In addition, the proportions of CD8, CD4 naïve, and CD4 memory resting T cells, as well as resting dendritic cells, were significantly different between the low-risk and high-risk groups in the OS model. Conclusions OS and RFS signatures can be used as reliable BRCA prognostic biomarkers. This work will help understand the prognostic roles and functions of RBPs in BRCA.
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Affiliation(s)
- Wei Fan
- Department of Breast Cancer, Hubei Cancer Hospital; Tongji Medical College, Huazhong University of Science and Technology and Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan, Hubei, China
| | - Jun Ding
- Department of Neurology, Wuhan First Hospital, Wuhan, Hubei, China
| | - Shushu Liu
- Department of Breast Cancer, Hubei Cancer Hospital; Tongji Medical College, Huazhong University of Science and Technology and Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan, Hubei, China
| | - Wei Zhong
- Department of Breast Cancer, Hubei Cancer Hospital; Tongji Medical College, Huazhong University of Science and Technology and Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan, Hubei, China
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12
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PUMILIO proteins promote colorectal cancer growth via suppressing p21. Nat Commun 2022; 13:1627. [PMID: 35338151 PMCID: PMC8956581 DOI: 10.1038/s41467-022-29309-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2022] [Indexed: 12/17/2022] Open
Abstract
PUMILIO (PUM) proteins belong to the highly conserved PUF family post-transcriptional regulators involved in diverse biological processes. However, their function in carcinogenesis remains under-explored. Here, we report that Pum1 and Pum2 display increased expression in human colorectal cancer (CRC). Intestine-specific knockout of Pum1 and Pum2 in mice significantly inhibits the progression of colitis-associated cancer in the AOM/DSS model. Knockout or knockdown of Pum1 and/or Pum2 in human CRC cells result in a significant decrease in the tumorigenicity and delayed G1/S transition. We identify p21/Cdkn1a as a direct target of PUM1. Abrogation of the PUM1 binding site in the p21 mRNA also results in decreased cancer cell growth and delayed G1/S transition. Furthermore, intravenous injection of nanoparticle-encapsulated anti-Pum1 and Pum2 siRNAs reduces colorectal tumor growth in murine orthotopic colon cancer models. These findings reveal the requirement of PUM proteins for CRC progression and their potential as therapeutic targets. RNA binding proteins can contribute to colorectal cancer (CRC) initiation and development. Here the authors show that PUMILIO proteins, PUM1 and PUM2 contribute to CRC growth by inhibiting p21 expression.
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13
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Davis AG, Johnson DT, Zheng D, Wang R, Jayne ND, Liu M, Shin J, Wang L, Stoner SA, Zhou JH, Ball ED, Tian B, Zhang DE. Alternative polyadenylation dysregulation contributes to the differentiation block of acute myeloid leukemia. Blood 2022; 139:424-438. [PMID: 34482400 PMCID: PMC8777198 DOI: 10.1182/blood.2020005693] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/16/2021] [Indexed: 01/22/2023] Open
Abstract
Posttranscriptional regulation has emerged as a driver for leukemia development and an avenue for therapeutic targeting. Among posttranscriptional processes, alternative polyadenylation (APA) is globally dysregulated across cancer types. However, limited studies have focused on the prevalence and role of APA in myeloid leukemia. Furthermore, it is poorly understood how altered poly(A) site usage of individual genes contributes to malignancy or whether targeting global APA patterns might alter oncogenic potential. In this study, we examined global APA dysregulation in patients with acute myeloid leukemia (AML) by performing 3' region extraction and deep sequencing (3'READS) on a subset of AML patient samples along with healthy hematopoietic stem and progenitor cells (HSPCs) and by analyzing publicly available data from a broad AML patient cohort. We show that patient cells exhibit global 3' untranslated region (UTR) shortening and coding sequence lengthening due to differences in poly(A) site (PAS) usage. Among APA regulators, expression of FIP1L1, one of the core cleavage and polyadenylation factors, correlated with the degree of APA dysregulation in our 3'READS data set. Targeting global APA by FIP1L1 knockdown reversed the global trends seen in patients. Importantly, FIP1L1 knockdown induced differentiation of t(8;21) cells by promoting 3'UTR lengthening and downregulation of the fusion oncoprotein AML1-ETO. In non-t(8;21) cells, FIP1L1 knockdown also promoted differentiation by attenuating mechanistic target of rapamycin complex 1 (mTORC1) signaling and reducing MYC protein levels. Our study provides mechanistic insights into the role of APA in AML pathogenesis and indicates that targeting global APA patterns can overcome the differentiation block in patients with AML.
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Affiliation(s)
- Amanda G Davis
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Daniel T Johnson
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ruijia Wang
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Nathan D Jayne
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Mengdan Liu
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Jihae Shin
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Luyang Wang
- Program in Gene Expression and Regulation, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA
| | | | - Jie-Hua Zhou
- Division of Blood and Marrow Transplantation, Department of Medicine; and
| | - Edward D Ball
- Division of Blood and Marrow Transplantation, Department of Medicine; and
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
- Program in Gene Expression and Regulation, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA
| | - Dong-Er Zhang
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
- Department of Pathology, University of California San Diego, La Jolla, CA
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14
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Li J, Chen W, Cao Y, Li ZR. The Identification of Alternative Polyadenylation in Stomach Adenocarcinomas Using the Genotype-Tissue Expression Project and the Cancer Genome Atlas- Stomach Adenocarcinoma Profiles. Int J Gen Med 2021; 14:6035-6045. [PMID: 34588807 PMCID: PMC8475968 DOI: 10.2147/ijgm.s329064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/27/2021] [Indexed: 12/09/2022] Open
Abstract
Objective Alternative polyadenylation (APA) is a common mechanism that is present in most human genes and determines the length of the messenger ribonucleic acid (mRNA) three prime untranslated region (3ʹ-UTR), which can give rise to changes in mRNA stability and localization. However, little is known about the specific changes related to APA in stomach adenocarcinomas (STADs). Methods We integrated RNA sequencing data from The Cancer Genome Atlas and Genotype-Tissue Expression project to comprehensively analyze APA events in 289 cases of STAD. Results Our results showed that APA events were widespread in patients with STAD and were rich in genes related to known STAD pathways. The APA events result in the loss of tumor-suppressing micro-ribonucleic acid (miRNA) binding sites and increased heterogeneity in the length of the 3ʹ-UTR altered genes. Survival analysis revealed that specific subsets of 3ʹ-UTR-altered genes independently characterized a poor prognostic cohort among patients with STAD, thereby indicating the potential of APA as a new prognostic biomarker. Conclusion Our single-cancer analysis showed that by losing miRNA regulation, APA can become a driving factor for regulating the expression of oncogenic genes in STAD and promote its development. Our research revealed that APA events regulated STAD genes that were functionally related, thereby providing a new approach for gaining a better understanding of the progress of STADs and a means for identifying new drug targets as avenues of treatment.
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Affiliation(s)
- Jian Li
- Department of Gastrointestinal Surgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, 330000, People's Republic of China
| | - Wen Chen
- Key Laboratory of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, People's Republic of China
| | - Yi Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, People's Republic of China
| | - Zheng-Rong Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, People's Republic of China
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15
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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16
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Li X, Yang J, Chen X, Cao D, Xu EY. PUM1 represses CDKN1B translation and contributes to prostate cancer progression. J Biomed Res 2021; 35:371-382. [PMID: 34531333 PMCID: PMC8502688 DOI: 10.7555/jbr.35.20210067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Posttranscriptional regulation of cancer gene expression programs plays a vital role in carcinogenesis; identifying the critical regulators of tumorigenesis and their molecular targets may provide novel strategies for cancer diagnosis and therapeutics. Highly conserved RNA-binding protein Pumilio-1 (PUM1) regulates mouse growth and cell proliferation, propelling us to examine its role in cancer. We found human PUM1 is highly expressed in a diverse group of cancer, including prostate cancer; enhanced PUM1 expression is also correlated with reduced survival among prostate cancer patients. Detailed expression analysis in twenty prostate cancer tissues showed enhanced expression of PUM1 at mRNA and protein levels. Knockdown of PUM1 reduced prostate cancer cell proliferation and colony formation, and subcutaneous injection of PUM1 knockdown cells led to reduced tumor size. Downregulation of PUM1 in prostate cancer cells consistently elevated cyclin-dependent kinase inhibitor 1B (CDKN1B) protein expression through increased translation but did not impact its mRNA level, while overexpression of PUM1 reduced CDKN1B protein level. Our finding established a critical role of PUM1 mediated translational control, particularly the PUM1-CDKN1B axis, in prostate cancer cell growth and tumorigenesis. We proposed that PUM1-CDKN1B regulatory axis may represent a novel mechanism for the loss of CDKN1B protein expression in diverse cancers and potential targets for therapeutics development.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jian Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dandan Cao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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17
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Abstract
The protein-coding regions of mRNAs have the information to make proteins and hence have been at the center of attention for understanding altered protein functions in disease states, including cancer. Indeed, the discovery of genomic alterations and driver mutations that change protein levels and/or activity has been pivotal in our understanding of cancer biology. However, to better understand complex molecular mechanisms that are deregulated in cancers, we also need to look at non-coding parts of mRNAs, including 3'UTRs (untranslated regions), which control mRNA stability, localization, and translation efficiency. Recently, these rather overlooked regions of mRNAs are gaining attention as mounting evidence provides functional links between 3'UTRs, protein functions, and cancer-related molecular mechanisms. Here, roles of 3'UTRs in cancer biology and mechanisms that result in cancer-specific 3'-end isoform variants will be reviewed. An increased appreciation of 3'UTRs may help the discovery of new ways to explain as of yet unknown oncogene activation and tumor suppressor inactivation cases in cancers, and provide new avenues for diagnostic and therapeutic applications.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological Sciences and Cancer Systems Biology Laboratory, Middle East Technical University (METU, ODTU), Dumlupinar Blv No: 1, Universiteler Mah, 06800, Ankara, Turkey.
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18
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Role of PUM RNA-Binding Proteins in Cancer. Cancers (Basel) 2021; 13:cancers13010129. [PMID: 33401540 PMCID: PMC7796173 DOI: 10.3390/cancers13010129] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary PUM1 and PUM2 are RNA-binding Pumilio proteins controlling the accessibility of hundreds of mRNAs for translation in a variety of human tissues. As a result, PUMs exemplify one of the mechanisms safeguarding the cellular proteome. PUM expression is disturbed in cancer, resulting in dysregulation of their target mRNAs. These targets encode factors responsible for processes usually affected in cancer, such as proliferation, apoptosis, and the cell cycle. This review describes PUM1 and PUM2 ribonucleoprotein networks and highlights the mechanisms underlying the regulatory role of PUM proteins and, most importantly, the emerging impact of PUM dysregulation in cancer. It also emphasizes the importance of upcoming studies on PUM proteins in the context of cancer, as they may provide new therapeutic targets in the future. Abstract Until recently, post-transcriptional gene regulation (PTGR), in contrast to transcriptional regulation, was not extensively explored in cancer, even though it seems to be highly important. PUM proteins are well described in the PTGR of several organisms and contain the PUF RNA-binding domain that recognizes the UGUANAUA motif, located mostly in the 3′ untranslated region (3′UTR) of target mRNAs. Depending on the protein cofactors recruited by PUM proteins, target mRNAs are directed towards translation, repression, activation, degradation, or specific localization. Abnormal profiles of PUM expression have been shown in several types of cancer, in some of them being different for PUM1 and PUM2. This review summarizes the dysregulation of PUM1 and PUM2 expression in several cancer tissues. It also describes the regulatory mechanisms behind the activity of PUMs, including cooperation with microRNA and non-coding RNA machineries, as well as the alternative polyadenylation pathway. It also emphasizes the importance of future studies to gain a more complete picture of the role of PUM proteins in different types of cancer. Such studies may result in identification of novel targets for future cancer therapies.
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19
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Qin X, Liu Z, Yan K, Fang Z, Fan Y. Integral Analysis of the RNA Binding Protein-associated Prognostic Model for Renal Cell Carcinoma. Int J Med Sci 2021; 18:953-963. [PMID: 33456353 PMCID: PMC7807188 DOI: 10.7150/ijms.50704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
RNA binding protein (RBPs) dysregulation has been reported in various malignant tumors and plays a pivotal role in tumor carcinogenesis and progression. However, the underlying mechanisms in renal cell carcinoma (RCC) are still unknown. In the present study, we performed a bioinformatics analysis using data from TCGA database to explore the expression and prognostic value of RBPs. We identified 125 differently expressed RBPs between tumor and normal tissue in RCC patients, including 87 upregulated and 38 downregulated RBPs. Eight RBPs (RPL22L1, RNASE2, RNASE3, EZH2, DDX25, DQX1, EXOSC5, DDX47) were selected as prognosis-related RBPs and used to construct a risk score model. In the risk score model, the high-risk subgroup had a poorer overall survival (OS) than the low-risk subgroup, and we divided the 539 RCC patients into two groups and conducted a time-dependent receiver operating characteristic (ROC) analysis to further test the prognostic ability of the eight hub RBPs. The area under the curve (AUC) of the ROC curve was 0.728 in train-group and 0.688 in test-group, indicating a good prognostic model. More importantly, we established a nomogram based on the selected eight RBPs. The eight selected RBPS have predictive value for RCC patients, with potential applications in clinical decision-making and individualized treatment.
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Affiliation(s)
- Xin Qin
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Zhengfang Liu
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Keqiang Yan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China.,Department of Medicine, Center for Molecular Medicine (CMM) and Bioclinicum, Karolinska Institute and Karolinska University Hospital Solna, Solna 171 64, Sweden
| | - Yidong Fan
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, PR China
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20
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Wang L, Lang GT, Xue MZ, Yang L, Chen L, Yao L, Li XG, Wang P, Hu X, Shao ZM. Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers. Am J Cancer Res 2020; 10:10531-10547. [PMID: 32929364 PMCID: PMC7482814 DOI: 10.7150/thno.40944] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high heterogeneity. However, the alternative polyadenylation (APA) profiles of TNBC remain unknown. Here, we aimed to define the characteristics of the APA events at post-transcription level among TNBCs. Methods: Using transcriptome microarray data, we analyzed APA profiles of 165 TNBC samples and 33 paired normal tissues. A pooled short hairpin RNA screen targeting 23 core cleavage and polyadenylation (C/P) genes was used to identify key C/P factors. Results: We established an unconventional APA subtyping system composed of four stable subtypes: 1) luminal androgen receptor (LAR), 2) mesenchymal-like immune-activated (MLIA), 3) basal-like (BL), 4) suppressed (S) subtypes. Patients in the S subtype had the worst disease-free survival comparing to other patients (log-rank p = 0.021). Enriched clinically actionable pathways and putative therapeutic APA events were analyzed among each APA subtype. Furthermore, CPSF1 and PABPN1 were identified as the master C/P factors in regulating APA events and TNBC proliferation. The depletion of CPSF1 or PABPN1 weakened cell proliferation, enhanced apoptosis, resulted in cell cycle redistribution and a reversion of APA events of genes associated with tumorigenesis, proliferation, metastasis and chemosensitivity in breast cancer. Conclusions: Our findings advance the understanding of tumor heterogeneity regulation in APA and yield new insights into therapeutic target identification in TNBC.
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21
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Kaczmarek Michaels K, Mohd Mostafa S, Ruiz Capella J, Moore CL. Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases. Nucleic Acids Res 2020; 48:5407-5425. [PMID: 32356874 PMCID: PMC7261179 DOI: 10.1093/nar/gkaa292] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Adjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3′ end processing machinery to the vicinity of pA sites.
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Affiliation(s)
- Katarzyna Kaczmarek Michaels
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Salwa Mohd Mostafa
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Julia Ruiz Capella
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
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22
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Qin H, Ni H, Liu Y, Yuan Y, Xi T, Li X, Zheng L. RNA-binding proteins in tumor progression. J Hematol Oncol 2020; 13:90. [PMID: 32653017 PMCID: PMC7353687 DOI: 10.1186/s13045-020-00927-w] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.
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Affiliation(s)
- Hai Qin
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Haiwei Ni
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yichen Liu
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China
| | - Yaqin Yuan
- Guizhou Medical Device Testing Center, Guiyang, 550004, Guizhou, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, People's Republic of China.
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23
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Coordinated AR and microRNA regulation in prostate cancer. Asian J Urol 2020; 7:233-250. [PMID: 32742925 PMCID: PMC7385519 DOI: 10.1016/j.ajur.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/22/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) remains a key driver of prostate cancer (PCa) progression, even in the advanced castrate-resistant stage, where testicular androgens are absent. It is therefore of critical importance to understand the molecular mechanisms governing its activity and regulation during prostate tumourigenesis. MicroRNAs (miRs) are small ∼22 nt non-coding RNAs that regulate target gene, often through association with 3′ untranslated regions (3′UTRs) of transcripts. They display dysregulation during cancer progression, can function as oncogenes or tumour suppressors, and are increasingly recognised as targets or regulators of hormonal action. Thus, understanding factors which modulate miRs synthesis is essential. There is increasing evidence for complex and dynamic bi-directional cross-talk between the multi-step miR biogenesis cascade and the AR signalling axis in PCa. This review summarises the wealth of mechanisms by which miRs are regulated by AR, and conversely, how miRs impact AR's transcriptional activity, including that of AR splice variants. In addition, we assess the implications of the convergence of these pathways on the clinical employment of miRs as PCa biomarkers and therapeutic targets.
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24
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Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020; 10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
A crucial feature of gene expression involves RNA processing to produce 3′ ends through a process termed 3′ end cleavage and polyadenylation (CPA). This ensures the nascent RNA molecule can exit the nucleus and be translated to ultimately give rise to a protein which can execute a function. Further, alternative polyadenylation (APA) can produce distinct transcript isoforms, profoundly expanding the complexity of the transcriptome. CPA is carried out by multi-component protein complexes interacting with multiple RNA motifs and is tightly coupled to transcription, other steps of RNA processing, and even epigenetic modifications. CPA and APA contribute to the maintenance of a multitude of diverse physiological processes. It is therefore not surprising that disruptions of CPA and APA can lead to devastating disorders. Here, we review potential CPA and APA mechanisms involving both loss and gain of function that can have tremendous impacts on health and disease. Ultimately we highlight the emerging diagnostic and therapeutic potential CPA and APA offer.
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Affiliation(s)
- Jamie Nourse
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefano Spada
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, Germany
- Correspondence:
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Li M, Li AQ, Zhou SL, Lv H, Wei P, Yang WT. RNA-binding protein MSI2 isoforms expression and regulation in progression of triple-negative breast cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:92. [PMID: 32448269 PMCID: PMC7245804 DOI: 10.1186/s13046-020-01587-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND The RNA-binding protein Musashi-2 (MSI2) has been implicated in the tumorigenesis and tumor progression of some human cancers. MSI2 has also been reported to suppress tumor epithelial-to-mesenchymal transition (EMT) progression in breast cancer, and low MSI2 expression is associated with poor outcomes for breast cancer patients; however, the underlying mechanisms have not been fully investigated. This study investigated the expression and phenotypic functions of two major alternatively spliced MSI2 isoforms (MSI2a and MSI2b) and the potential molecular mechanisms involved in triple-negative breast cancer (TNBC) progression. METHODS The Illumina sequencing platform was used to analyze the mRNA transcriptomes of TNBC and normal tissues, while quantitative reverse transcription-polymerase chain reaction and immunohistochemistry validated MSI2 isoform expression in breast cancer tissues. The effects of MSI2a and MSI2b on TNBC cells were assayed in vitro and in vivo. RNA immunoprecipitation (RIP) and RNA sequencing were performed to identify the potential mRNA targets of MSI2a, and RIP and luciferase analyses were used to confirm the mRNA targets of MSI2. RESULTS MSI2 expression in TNBC tissues was significantly downregulated compared to that in normal tissues. In TNBC, MSI2a expression was associated with poor overall survival of patients. MSI2a overexpression in vitro and in vivo inhibited TNBC cell invasion as well as extracellular signal-regulated kinase 1/2 (ERK1/2) activity. However, MSI2b overexpression had no significant effects on TNBC cell migration. Mechanistically, MSI2a expression promoted TP53INP1 mRNA stability by its interaction with the 3'-untranslated region of TP53INP1 mRNA. Furthermore, TP53INP1 knockdown reversed MSI2a-induced suppression of TNBC cell invasion, whereas ectopic expression of TP53INP1 and inhibition of ERK1/2 activity blocked MSI2 knockdown-induced TNBC cell invasion. CONCLUSIONS The current study demonstrated that MSI2a is the predominant functional isoform of MSI2 proteins in TNBC, that its downregulation is associated with TNBC progression and poor prognosis and that MSI2a expression inhibited TNBC invasion by stabilizing TP53INP1 mRNA and inhibiting ERK1/2 activity. Overall, our study provides new insights into the isoform-specific roles of MSI2a and MSI2b in the tumor progression of TNBC, allowing for novel therapeutic strategies to be developed for TNBC.
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Affiliation(s)
- Ming Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China
| | - An-Qi Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China
| | - Shu-Ling Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China
| | - Hong Lv
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China
| | - Ping Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Institute of Pathology, Fudan University, Shanghai, China. .,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Institute of Pathology, Fudan University, Shanghai, China.
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Lin K, Qiang W, Zhu M, Ding Y, Shi Q, Chen X, Zsiros E, Wang K, Yang X, Kurita T, Xu EY. Mammalian Pum1 and Pum2 Control Body Size via Translational Regulation of the Cell Cycle Inhibitor Cdkn1b. Cell Rep 2020; 26:2434-2450.e6. [PMID: 30811992 PMCID: PMC6444939 DOI: 10.1016/j.celrep.2019.01.111] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 12/20/2018] [Accepted: 01/29/2019] [Indexed: 11/24/2022] Open
Abstract
Body and organ size regulation in mammals involves multiple signaling pathways and remains largely enigmatic. Here, we report that Pum1 and Pum2, which encode highly conserved PUF RNA-binding proteins, regulate mouse body and organ size by post-transcriptional repression of the cell cycle inhibitor Cdkn1b. Binding of PUM1 or PUM2 to Pumilio binding elements (PBEs) in the 3’ UTR of Cdkn1b inhibits translation, promoting G1-S transition and cell proliferation. Mice with null mutations in Pum1 and Pum2 exhibit gene dosage-dependent reductions in body and organ size, and deficiency for Cdkn1b partially rescues postnatal growth defects in Pum1−/− mice. We propose that coordinated tissue-specific expression of Pum1 and Pum2, which involves auto-regulatory and reciprocal post-transcriptional repression, contributes to the precise regulation of body and organ size. Hence PUM-mediated post-transcriptional control of cell cycle regulators represents an additional layer of control in the genetic regulation of organ and body size. Lin et al. show that the RNA-binding proteins PUM1 and PUM2 regulate translation of cell cycle proteins such as CDKN1B by binding to their 3’ UTR and achieve precise control of organ and body size in a gene dosage-sensitive manner via auto and reciprocal gene expression regulation.
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Affiliation(s)
- Kaibo Lin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Wenan Qiang
- Department of Obstetrics and Gynecology (Reproductive Science in Medicine), Center for Developmental Therapeutics, Northwestern University, Chicago, IL 60611, USA
| | - Mengyi Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yan Ding
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qinghua Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Emese Zsiros
- Department of Obstetrics and Gynecology (Reproductive Science in Medicine), Center for Developmental Therapeutics, Northwestern University, Chicago, IL 60611, USA
| | - Kun Wang
- Department of Chemistry, Nanjing Normal University, Nanjing 210023, China
| | - Xiaodi Yang
- Department of Chemistry, Nanjing Normal University, Nanjing 210023, China
| | - Takeshi Kurita
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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Ozaki H, Hayashi T, Umeda M, Nikaido I. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. BMC Genomics 2020; 21:177. [PMID: 32122302 PMCID: PMC7053140 DOI: 10.1186/s12864-020-6542-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 01/29/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking. RESULTS Here, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of "local" region-specific, cell-to-cell heterogeneity in read coverage. We applied Millefy to scRNA-seq data sets of mouse embryonic stem cells and triple-negative breast cancers and showed variability of transcribed regions including antisense RNAs, 3 ' UTR lengths, and enhancer RNA transcription. CONCLUSIONS Millefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https://github.com/yuifu/millefy) and as a Docker image for use with Jupyter Notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).
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Affiliation(s)
- Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575 Japan
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577 Japan
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Mana Umeda
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
- Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575 Japan
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29
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Venkat S, Tisdale AA, Schwarz JR, Alahmari AA, Maurer HC, Olive KP, Eng KH, Feigin ME. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma. Genome Res 2020; 30:347-360. [PMID: 32029502 PMCID: PMC7111527 DOI: 10.1101/gr.257550.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/04/2020] [Indexed: 01/08/2023]
Abstract
Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3'-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA events across the tumor landscape; however, little is known about tumor type-specific alterations that may uncover novel events and vulnerabilities. Here, we integrate RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA events in 148 pancreatic ductal adenocarcinomas (PDACs). We report widespread, recurrent, and functionally relevant 3'-UTR alterations associated with gene expression changes of known and newly identified PDAC growth-promoting genes and experimentally validate the effects of these APA events on protein expression. We find enrichment for APA events in genes associated with known PDAC pathways, loss of tumor-suppressive miRNA binding sites, and increased heterogeneity in 3'-UTR forms of metabolic genes. Survival analyses reveal a subset of 3'-UTR alterations that independently characterize a poor prognostic cohort among PDAC patients. Finally, we identify and validate the casein kinase CSNK1A1 (also known as CK1alpha or CK1a) as an APA-regulated therapeutic target in PDAC. Knockdown or pharmacological inhibition of CSNK1A1 attenuates PDAC cell proliferation and clonogenic growth. Our single-cancer analysis reveals APA as an underappreciated driver of protumorigenic gene expression in PDAC via the loss of miRNA regulation.
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Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Johann R Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - H Carlo Maurer
- Klinikum rechts der Isar, II. Medizinische Klinik, Technische Universität München, 81675 Munich, Germany
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Division of Digestive and Liver Diseases, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
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Functions, mechanisms and regulation of Pumilio/Puf family RNA binding proteins: a comprehensive review. Mol Biol Rep 2019; 47:785-807. [PMID: 31643042 DOI: 10.1007/s11033-019-05142-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
The Pumilio (Pum)/Puf family proteins are ubiquitously present across eukaryotes, including yeast, plants and humans. They generally bind to the 3' untranslated regions of single stranded RNA targets in a sequence specific manner and destabilize them, although a few reports suggest their role in stabilizing the target transcripts. The Pum isoforms are implicated in a wide array of biological processes including stem cell maintenance, development, ribosome biogenesis as well as human diseases. Further studies on Pum would be interesting and important to understand their evolutionarily conserved and divergent features across species, which can have potential implications in medicine, plant sciences as well as basic molecular and cell biological studies. A large number of research reports exists, pertaining to various aspects of Pum, in individual experimental systems. This review is a comprehensive summary of the functions, types, mechanism of action as well as the regulation of Pum in various species. Also, the research questions to be addressed in future are discussed.
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Clinical relevance of H-RAS, K-RAS, and N-RAS mRNA expression in primary breast cancer patients. Breast Cancer Res Treat 2019; 179:403-414. [PMID: 31646390 DOI: 10.1007/s10549-019-05474-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/10/2019] [Indexed: 01/12/2023]
Abstract
PURPOSE The RAS family comprises three proto-oncogenes (H-RAS, K-RAS, and N-RAS) and is among the most widely studied of oncogenes. The present study aimed at investigating the clinical relevance of mRNA levels of the three isoforms in a large group of breast cancer patients with a long-term follow-up. METHODS 198 previously untreated patients were enrolled in the study. mRNA levels of K-RAS, H-RAS, and N-RAS were measured using microarray (Affymetrix HG-U133A). RESULTS Elevated H-RAS levels were found significantly more frequently in patients with larger (p = 0.021) and ER-positive tumors (p = 0.048), while elevated K-RAS levels were associated with nodal positivity (p = 0.001) and HER2-positivity (p = 0.010). Patients with high N-RAS mRNA levels were more likely to be diagnosed with triple-negativity (p < 0.001) and higher grading (p = 0.001). Patients with high K-RAS levels were more likely to show an elevated H-RAS (p = 0.003). After a median follow-up of 183 months, patients with high N-RAS expression had significantly reduced overall survival (OS) compared with patients with low N-RAS (mean: 146.9 vs. 211.0 months; median 169.3 vs. not reached; p = 0.009). In patients with non-metastatic disease at the time of tissue sampling, mean disease-free survival (DFS) was 150.1 months for patients with high N-RAS versus 227.7 months with low N-RAS; median DFS was not reached (p = 0.004). The expression of H-RAS and K-RAS was not associated with DFS/OS. In the multivariable analysis, distant metastasis, HER2 positivity, and elevated N-RAS mRNA levels independently predicted reduced OS, while nodal status, HER2 status, and N-RAS predicted reduced DFS. CONCLUSIONS Elevated N-RAS mRNA levels predict impaired clinical outcome; hypothetically, further exploration of the RAS signaling pathway might enable identifying potential targeted treatment strategies. The association between high N-RAS levels and the most aggressive among breast cancer subtypes, the triple-negative phenotype, for which targeted approaches are still lacking, underlines the need to further investigate the RAS family.
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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Schuster SL, Hsieh AC. The Untranslated Regions of mRNAs in Cancer. Trends Cancer 2019; 5:245-262. [PMID: 30961831 PMCID: PMC6465068 DOI: 10.1016/j.trecan.2019.02.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
Abstract
The 5' and 3' untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular homeostasis. When these processes go awry through mutation or misexpression of certain regulatory elements, the subsequent deregulation of oncogenic gene expression can drive or enhance cancer pathogenesis. Although the number of known cancer-related mutations in UTR regulatory elements has recently increased markedly as a result of advances in whole-genome sequencing, little is known about how the majority of these genetic aberrations contribute functionally to disease. In this review we explore the regulatory functions of UTRs, how they are co-opted in cancer, new technologies to interrogate cancerous UTRs, and potential therapeutic opportunities stemming from these regions.
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Affiliation(s)
- Samantha L Schuster
- Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrew C Hsieh
- Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA; School of Medicine and Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Grozdanov PN, Masoumzadeh E, Latham MP, MacDonald CC. The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity. Nucleic Acids Res 2018; 46:12022-12039. [PMID: 30257008 PMCID: PMC6294498 DOI: 10.1093/nar/gky862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/31/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023] Open
Abstract
Cleavage and polyadenylation (C/P) of mRNA is an important cellular process that promotes increased diversity of mRNA isoforms and could change their stability in different cell types. The cleavage stimulation factor (CstF) complex, part of the C/P machinery, binds to U- and GU-rich sequences located downstream from the cleavage site through its RNA-binding subunit, CstF-64. Less is known about the function of the other two subunits of CstF, CstF-77 and CstF-50. Here, we show that the carboxy-terminus of CstF-77 plays a previously unrecognized role in enhancing C/P by altering how the RNA recognition motif (RRM) of CstF-64 binds RNA. In support of this finding, we also show that CstF-64 relies on CstF-77 to be transported to the nucleus; excess CstF-64 localizes to the cytoplasm, possibly via interaction with cytoplasmic RNAs. Reverse genetics and nuclear magnetic resonance studies of recombinant CstF-64 (RRM-Hinge) and CstF-77 (monkeytail-carboxy-terminal domain) indicate that the last 30 amino acids of CstF-77 increases the stability of the RRM, thus altering the affinity of the complex for RNA. These results provide new insights into the mechanism by which CstF regulates the location of the RNA cleavage site during C/P.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Michael P Latham
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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36
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Wang L, Hu X, Wang P, Shao ZM. Integrative 3' Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer. Oncologist 2018; 24:22-30. [PMID: 30082491 DOI: 10.1634/theoncologist.2017-0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/09/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets. Samples from GSE31519 were divided into training set (n = 164) and validation set (n = 163), and GSE76275 was used to construct testing set (n = 164). We built a six-member 3'UTR panel (ADD2, COL1A1, APOL2, IL21R, PKP2, and EIF4G3) using an elastic net model to estimate the risk of lymph node metastasis (LNM). Receiver operating characteristic and logistic analyses were used to assess the association between the panel and LNM status. RESULTS The six-member 3'UTR-panel showed a high distinguishing power with an area under the curve of 0.712, 0.729, and 0.708 in the training, validation, and testing sets, respectively. After adjustment by tumor size, the 3'UTR panel retained significant predictive power in the training, validation, and testing sets (odds ratio = 4.93, 4.58, and 3.59, respectively; p < .05 for all). A combinatorial analysis of the 3'UTR panel and tumor size yielded an accuracy of 97.2%, 100%, and 100% in training, validation, and testing set, respectively. CONCLUSION This study established an integrative 3'UTR-based model as a promising predictor for nodal negativity in operable TNBC. Although a prospective study is needed to validate the model, our results may permit a no axillary surgery option for selected patients. IMPLICATIONS FOR PRACTICE Currently, sentinel lymph node biopsy is the standard approach for surgical staging in breast cancer patients with negative axillae. Prediction estimation for lymph node metastasis of breast cancer relies on clinicopathological characteristics, which is unreliable, especially in triple-negative breast cancer (TNBC)-a highly heterogeneous disease. The authors developed and validated an effective prediction model for the lymph node status of patients with TNBC, which integrates 3'UTR markers and tumor size. This is the first 3'UTR-based model that will help identify TNBC patients with low risk of nodal involvement who are most likely to benefit from exemption axillary surgery.
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Affiliation(s)
- Lei Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Peng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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De Keuckelaere E, Hulpiau P, Saeys Y, Berx G, van Roy F. Nanos genes and their role in development and beyond. Cell Mol Life Sci 2018; 75:1929-1946. [PMID: 29397397 PMCID: PMC11105394 DOI: 10.1007/s00018-018-2766-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022]
Abstract
The hallmark of Nanos proteins is their typical (CCHC)2 zinc finger motif (zf-nanos). Animals have one to four nanos genes. For example, the fruit fly and demosponge have only one nanos gene, zebrafish and humans have three, and Fugu rubripes has four. Nanos genes are mainly known for their evolutionarily preserved role in germ cell survival and pluripotency. Nanos proteins have been reported to bind the C-terminal RNA-binding domain of Pumilio to form a post-transcriptional repressor complex. Several observations point to a link between the miRNA-mediated repression complex and the Nanos/Pumilio complex. Repression of the E2F3 oncogene product is, indeed, mediated by cooperation between the Nanos/Pumilio complex and miRNAs. Another important interaction partner of Nanos is the CCR4-NOT deadenylase complex. Besides the tissue-specific contribution of Nanos proteins to normal development, their ectopic expression has been observed in several cancer cell lines and various human cancers. An inverse correlation between the expression levels of human Nanos1 and Nanos3 and E-cadherin was observed in several cancer cell lines. Loss of E-cadherin, an important cell-cell adhesion protein, contributes to tumor invasion and metastasis. Overexpression of Nanos3 induces epithelial-mesenchymal transition in lung cancer cell lines partly by repressing E-cadherin. Other than some most interesting data from Nanos knockout mice, little is known about mammalian Nanos proteins, and further research is needed. In this review, we summarize the main roles of Nanos proteins and discuss the emerging concept of Nanos proteins as oncofetal antigens.
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Affiliation(s)
- Evi De Keuckelaere
- VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
- Molecular Cell Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Paco Hulpiau
- VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
- Molecular Cell Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Yvan Saeys
- VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, S9, 9000, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frans van Roy
- VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium.
- Molecular Cell Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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NUDT21 negatively regulates PSMB2 and CXXC5 by alternative polyadenylation and contributes to hepatocellular carcinoma suppression. Oncogene 2018; 37:4887-4900. [PMID: 29780166 DOI: 10.1038/s41388-018-0280-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/21/2023]
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism and involved in many diseases, including cancer. CFIm25, a subunit of the cleavage factor I encoded by NUDT21, is required for 3'RNA cleavage and polyadenylation. Although it has been recently reported to be involved in glioblastoma tumor suppression, its roles and the underlying functional mechanism remain unclear in other types of cancer. In this study, we characterized NUDT21 in hepatocellular carcinoma (HCC). Reduced expression of NUDT21 was observed in HCC tissue compared to adjacent non-tumorous compartment. HCC patients with lower NUDT21 expression have shorter overall and disease-free survival times than those with higher NUDT21 expression after surgery. Knockdown of NUDT21 promotes HCC cell proliferation, metastasis, and tumorigenesis, whereas forced expression of NUDT21 exhibits the opposite effects. We then performed global APA site profiling analysis in HCC cells and identified considerable number of genes with shortened 3'UTRs upon the modulation of NUDT21 expression. In particular, we further characterized the NUDT21-regulated genes PSMB2 and CXXC5. We found NUDT21 knockdown increases usage of the proximal polyadenylation site in the PSMB2 and CXXC5 3' UTRs, resulting in marked increase in the expression of PSMB2 and CXXC5. Moreover, knockdown of PSMB2 or CXXC5 suppresses HCC cell proliferation and invasion. Taken together, our study demonstrated that NUDT21 inhibits HCC proliferation, metastasis and tumorigenesis, at least in part, by suppressing PSMB2 and CXXC5, and thereby provided a new insight into understanding the connection of HCC suppression and APA machinery.
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Turner RE, Pattison AD, Beilharz TH. Alternative polyadenylation in the regulation and dysregulation of gene expression. Semin Cell Dev Biol 2017; 75:61-69. [PMID: 28867199 DOI: 10.1016/j.semcdb.2017.08.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
Abstract
Transcriptional control shapes a cell's transcriptome composition, but it is RNA processing that refines its expression. The untranslated regions (UTRs) of mRNA are hotspots for regulatory control. Features in these can impact mRNA stability, localisation and translation. Here we describe how alternative cleavage and polyadenylation can change mRNA fate by changing the length of its 3'UTR.
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Affiliation(s)
- Rachael Emily Turner
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia
| | - Andrew David Pattison
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia
| | - Traude Helene Beilharz
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia.
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 462] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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Gao J, Wang X, Zhang Q. Evolutionary Conservation of pou5f3 Genomic Organization and Its Dynamic Distribution during Embryogenesis and in Adult Gonads in Japanese Flounder Paralichthys olivaceus. Int J Mol Sci 2017; 18:ijms18010231. [PMID: 28124980 PMCID: PMC5297860 DOI: 10.3390/ijms18010231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 01/06/2023] Open
Abstract
Octamer-binding transcription factor 4 (Oct4) is a member of POU (Pit-Oct-Unc) transcription factor family Class V that plays a crucial role in maintaining the pluripotency and self-renewal of stem cells. Though it has been deeply investigated in mammals, its lower vertebrate homologue, especially in the marine fish, is poorly studied. In this study, we isolated the full-length sequence of Paralichthys olivaceus pou5f3 (Popou5f3), and we found that it is homologous to mammalian Oct4. We identified two transcript variants with different lengths of 3′-untranslated regions (UTRs) generated by alternative polyadenylation (APA). Quantitative real-time RT-PCR (qRT-PCR), in situ hybridization (ISH) and immunohistochemistry (IHC) were implemented to characterize the spatial and temporal expression pattern of Popou5f3 during early development and in adult tissues. Our results show that Popou5f3 is maternally inherited, abundantly expressed at the blastula and early gastrula stages, then greatly diminishes at the end of gastrulation. It is hardly detectable from the heart-beating stage onward. We found that Popou5f3 expression is restricted to the adult gonads, and continuously expresses during oogenesis while its dynamics are downregulated during spermatogenesis. Additionally, numerous cis-regulatory elements (CRE) on both sides of the flanking regions show potential roles in regulating the expression of Popou5f3. Taken together, these findings could further our understanding of the functions and evolution of pou5f3 in lower vertebrates, and also provides fundamental information for stem cell tracing and genetic manipulation in Paralichthys olivaceus.
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Affiliation(s)
- Jinning Gao
- College of Marine Life Science, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao 266003, China.
- Center for Developmental Cardiology, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Xubo Wang
- College of Marine Life Science, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao 266003, China.
| | - Quanqi Zhang
- College of Marine Life Science, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao 266003, China.
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Abstract
INTRODUCTION Ovarian cancer remains the most lethal gynecologic malignancy. Although standard platinum-based chemotherapy results in high response rates, more than 70% of patients with advanced disease will experience recurrence within 5 years. Therefore, novel treatment strategies to increase primary efficacy, decrease recurrence after primary treatment and improve the response rate for recurrent disease are needed. AREAS COVERED This review covers antiangiogenesis therapy and the efficacy of bevacizumab as primary treatment and in platinum-sensitive and resistant recurrent disease. EXPERT OPINION The evidence provided from Phase III trials has supported the efficacy of bevacizumab in primary and recurrent ovarian cancer management. Future investigation is needed to improve clinical performance (via biomarkers of efficacy, early discontinuation, additional agents, etc.), as well as, more sensitive tools to assess direct patient impact.
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Affiliation(s)
- Takahito M Miyake
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert L Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1155 Herman Pressler, Unit 1362, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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