1
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Ruta V, Naro C, Pieraccioli M, Leccese A, Archibugi L, Cesari E, Panzeri V, Allgöwer C, Arcidiacono PG, Falconi M, Carbone C, Tortora G, Borrelli F, Attili F, Spada C, Quero G, Alfieri S, Doglioni C, Kleger A, Capurso G, Sette C. An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer. Cell Rep Med 2024; 5:101411. [PMID: 38325381 PMCID: PMC10897606 DOI: 10.1016/j.xcrm.2024.101411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/19/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis. PDAC presents with molecularly distinct subtypes, with the basal-like one being associated with enhanced chemoresistance. Splicing dysregulation contributes to PDAC; however, its involvement in subtype specification remains elusive. Herein, we uncover a subtype-specific splicing signature associated with prognosis in PDAC and the splicing factor Quaking (QKI) as a determinant of the basal-like signature. Single-cell sequencing analyses highlight QKI as a marker of the basal-like phenotype. QKI represses splicing events associated with the classical subtype while promoting basal-like events associated with shorter survival. QKI favors a plastic, quasi-mesenchymal phenotype that supports migration and chemoresistance in PDAC organoids and cell lines, and its expression is elevated in high-grade primary tumors and metastatic lesions. These studies identify a splicing signature that defines PDAC subtypes and indicate that QKI promotes an undifferentiated, plastic phenotype, which renders PDAC cells chemoresistant and adaptable to environmental changes.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | - Adriana Leccese
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | | | - Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Chantal Allgöwer
- Institute for Molecular Oncology and Stem Cell Biology, Ulm University Hospital, 89081 Ulm, Germany
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Massimo Falconi
- Vita-Salute San Raffaele University, 20132 Milan, Italy; Pancreas and Transplantation Surgical Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | | | - Giampaolo Tortora
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Medical Oncology, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | | | - Fabia Attili
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
| | | | - Giuseppe Quero
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Gemelli Pancreatic Advanced Research Center (CRMPG), Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Sergio Alfieri
- Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy; Gemelli Pancreatic Advanced Research Center (CRMPG), Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Claudio Doglioni
- Vita-Salute San Raffaele University, 20132 Milan, Italy; Division of Pathology, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy
| | - Alexander Kleger
- Institute for Molecular Oncology and Stem Cell Biology, Ulm University Hospital, 89081 Ulm, Germany; Division of Interdisciplinary Pancreatology, Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, 20132 Milan, Italy; Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy.
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2
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He S, Liang Y, Tan Y, Liu Q, Liu T, Lu X, Zheng S. Positioning determines function: Wandering PKM2 performs different roles in tumor cells. Cell Biol Int 2024; 48:20-30. [PMID: 37975488 DOI: 10.1002/cbin.12103] [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: 07/17/2023] [Revised: 10/01/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Short for pyruvate kinase M2 subtype, PKM2 can be said of all-round player that is notoriously known for its metabolic involvement in glycolysis. Holding a dural role as a metabolic or non-metabolic (kinase) enzyme, PKM2 has drawn extensive attention over its biological roles implicated in tumor cells, including proliferation, migration, invasion, metabolism, and so on. wandering PKM2 can be transboundary both intracellularly and extracellularly. Specifically, PKM2 can be nuclear, cytoplasmic, mitochondrial, exosomal, or even circulate within the body. Importantly, PKM2 can function as an RNA-binding protein (RBP) to self-support its metabolic function. Despite extensive investigations or reviews available surrounding the biological roles of PKM2 from different angles in tumor cells, little has been described regarding some novel role of PKM2 that has been recently found, including, for example, acting as RNA-binding protein, protection of Golgi apparatus, and remodeling of microenvironment, and so forth. Given these findings, in this review, we summarize the recent advancements made in PKM2 research, mainly from non-metabolic respects. By the way, PKM1, another paralog of PKM2, seems to have been overlooked or under-investigated since its discovery. Some recent discoveries made about PKM1 are also preliminarily mentioned and discussed.
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Affiliation(s)
- Shuo He
- Department of Pathology, Basic Medicine College, Xinjiang Medical University, Urumqi, China
| | - Yan Liang
- Department of Pathology, Basic Medicine College, Xinjiang Medical University, Urumqi, China
| | - Yiyi Tan
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Tao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Xiaomei Lu
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Shutao Zheng
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
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3
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Caggiano C, Pieraccioli M, Pitolli C, Babini G, Zheng D, Tian B, Bielli P, Sette C. The androgen receptor couples promoter recruitment of RNA processing factors to regulation of alternative polyadenylation at the 3' end of transcripts. Nucleic Acids Res 2022; 50:9780-9796. [PMID: 36043441 PMCID: PMC9508809 DOI: 10.1093/nar/gkac737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer (PC) relies on androgen receptor (AR) signaling. While hormonal therapy (HT) is efficacious, most patients evolve to an incurable castration-resistant stage (CRPC). To date, most proposed mechanisms of acquired resistance to HT have focused on AR transcriptional activity. Herein, we uncover a new role for the AR in alternative cleavage and polyadenylation (APA). Inhibition of the AR by Enzalutamide globally regulates APA in PC cells, with specific enrichment in genes related to transcription and DNA topology, suggesting their involvement in transcriptome reprogramming. AR inhibition selects promoter-distal polyadenylation sites (pAs) enriched in cis-elements recognized by the cleavage and polyadenylation specificity factor (CPSF) complex. Conversely, promoter-proximal intronic pAs relying on the cleavage stimulation factor (CSTF) complex are repressed. Mechanistically, Enzalutamide induces rearrangement of APA subcomplexes and impairs the interaction between CPSF and CSTF. AR inhibition also induces co-transcriptional CPSF recruitment to gene promoters, predisposing the selection of pAs depending on this complex. Importantly, the scaffold CPSF160 protein is up-regulated in CRPC cells and its depletion represses HT-induced APA patterns. These findings uncover an unexpected role for the AR in APA regulation and suggest that APA-mediated transcriptome reprogramming represents an adaptive response of PC cells to HT.
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Affiliation(s)
- Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | - Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
| | | | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy.,IRCCS Fondazione Santa Lucia, Rome 00143, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome 00168, Italy.,IRCCS Fondazione Policlinico A. Gemelli, Rome 00168, Italy
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4
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Pu F, Liu J, Jing D, Chen F, Huang X, Shi D, Wu W, Lin H, Zhao L, Zhang Z, Lv X, Wang B, Zhang Z, Shao Z. LncCCAT1 interaction protein PKM2 upregulates SREBP2 phosphorylation to promote osteosarcoma tumorigenesis by enhancing the Warburg effect and lipogenesis. Int J Oncol 2022; 60:44. [PMID: 35244192 PMCID: PMC8923656 DOI: 10.3892/ijo.2022.5334] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022] Open
Abstract
Pyruvate kinase M2 (PKM2) plays an important role in the consumption of glucose and the production of lactic acid, the striking feature of cancer metabolism. The association of PKM2 with osteosarcoma (OS) has been reported but its role in OS has yet to be elucidated. To study this, PKM2‑bound RNAs in HeLa cells, a type of cancer cells widely used in the study of molecular function and mechanism, were obtained. Peak calling analysis revealed that PKM2 binds to long noncoding RNAs (lncRNAs), which are associated with cancer pathogenesis and development. Validation of the PKM2‑lncRNA interaction in the human OS cell line revealed that lncRNA colon cancer associated transcript‑1 (lncCCAT1) interacted with PKM2, which upregulated the phosphorylation of sterol regulatory element‑binding protein 2 (SREBP2). These factors promoted the Warburg effect, lipogenesis, and OS cell growth. PKM2 appears to be a key regulator in OS by binding to lncCCAT1. This further extends the biological functions of PKM2 in tumorigenesis and makes it a novel potential therapeutic for OS.
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Affiliation(s)
- Feifei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jianxiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Doudou Jing
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Fengxia Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xin Huang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Deyao Shi
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Wei Wu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Hui Lin
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Lei Zhao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhenhao Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiao Lv
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Baichuan Wang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhicai Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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5
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Wang X, Ge X, Liao W, Cao Y, Li R, Zhang F, Zhao B, Du J. ZFP36 promotes VDR mRNA degradation to facilitate cell death in oral and colonic epithelial cells. Cell Commun Signal 2021; 19:85. [PMID: 34380509 PMCID: PMC8355874 DOI: 10.1186/s12964-021-00765-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vitamin D receptor (VDR) plays a vital protective role in oral and colonic epithelial cells. Albeit we know that VDR expression is reduced in the mucosal epithelial layers of autoimmune diseases, the mechanism by which VDR is decreased remains elusive. METHODS VDR and zinc finger protein 36 (ZFP36) levels in human samples and cell lines were detected by real-time PCR, western blot and immunostaining. Luciferase report assay was used to test cis-elements in VDR gene promoter, real-time PCR was applied to measure mRNA decay and western blot was performed to evaluate protein degradation. RNA affinity chromatography assay was used to test protein-mRNA interaction. Co-immunoprecipitation was used to detect protein-protein interaction. The role of ZFP36 in AU-rich elements (AREs) in the 3' untranslated region (UTR) of VDR mRNA was also measured by luciferase report assay. RESULTS We identify ZFP36 can bind with the AREs in the 3'UTR of VDR mRNA, leading to mRNA degradation in oral and colonic epithelial cells under inflammatory circumstance. Either ZFP36 protein or AREs of VDR mRNA mutation abolishes this protein-mRNA binding process. After the key amino acid's mutation, ZFP36 fails to decrease VDR mRNA expression. We also find that VDR physically binds with Y box-binding protein 1 (YBX-1) to block YBX-1's nuclear translocation and ameliorate cell death in the presence of inflammation. CONCLUSION These findings provide insights into the cause of VDR decrease in oral and colonic epithelial cells under inflammatory condition and explain how VDR maintains cell viability in these cells. Video abstract.
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Affiliation(s)
- Xiangyu Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China.,Department of Child Dental and Preventive Dentistry, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China.,Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, No. 56 Xinjian South Road, Taiyuan, 030001, Shanxi, China
| | - Xuejun Ge
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China.,Department of Endodontics, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Wang Liao
- Department of Cardiology, Hainan General Hospital, Hainan Clinical Medicine Research Institution, Haikou, China
| | - Yong Cao
- Division of Gastroenterology, Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ran Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China.,Department of Child Dental and Preventive Dentistry, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Fang Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China.,Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, No. 56 Xinjian South Road, Taiyuan, 030001, Shanxi, China
| | - Bin Zhao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China.,Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, No. 56 Xinjian South Road, Taiyuan, 030001, Shanxi, China
| | - Jie Du
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, No. 63 Xinjian South Road, Taiyuan, 030001, Shanxi, China. .,Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, No. 56 Xinjian South Road, Taiyuan, 030001, Shanxi, China. .,Institute of Biomedical Research, Shanxi Medical University, Taiyuan, Shanxi, China.
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Farini D, Cesari E, Weatheritt RJ, La Sala G, Naro C, Pagliarini V, Bonvissuto D, Medici V, Guerra M, Di Pietro C, Rizzo FR, Musella A, Carola V, Centonze D, Blencowe BJ, Marazziti D, Sette C. A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum. Cell Rep 2021; 31:107703. [PMID: 32492419 DOI: 10.1016/j.celrep.2020.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/13/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Tight coordination of gene expression in the developing cerebellum is crucial for establishment of neuronal circuits governing motor and cognitive function. However, transcriptional changes alone do not explain all of the switches underlying neuronal differentiation. Here we unveiled a widespread and highly dynamic splicing program that affects synaptic genes in cerebellar neurons. The motifs enriched in modulated exons implicated the splicing factor Sam68 as a regulator of this program. Sam68 controls splicing of exons with weak branchpoints by directly binding near the 3' splice site and competing with U2AF recruitment. Ablation of Sam68 disrupts splicing regulation of synaptic genes associated with neurodevelopmental diseases and impairs synaptic connections and firing of Purkinje cells, resulting in motor coordination defects, ataxia, and abnormal social behavior. These findings uncover an unexpectedly dynamic splicing regulatory network that shapes the synapse in early life and establishes motor and cognitive circuitry in the developing cerebellum.
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Affiliation(s)
- Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Robert J Weatheritt
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Gina La Sala
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Davide Bonvissuto
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Vanessa Medici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Chiara Di Pietro
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Francesca Romana Rizzo
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy; San Raffaele Pisana and University San Raffaele, IRCCS, Rome, Italy
| | | | - Valeria Carola
- Fondazione Santa Lucia, IRCCS, Rome, Italy; Department of Dynamic and Clinical Psychology, University of Rome Sapienza, Rome, Italy
| | - Diego Centonze
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy; Unit of Neurology, IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Daniela Marazziti
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Rome, Italy
| | - Claudio Sette
- Fondazione Santa Lucia, IRCCS, Rome, Italy; Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.
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7
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Zhu S, Chen W, Wang J, Qi L, Pan H, Feng Z, Tian D. SAM68 promotes tumorigenesis in lung adenocarcinoma by regulating metabolic conversion via PKM alternative splicing. Theranostics 2021; 11:3359-3375. [PMID: 33537092 PMCID: PMC7847678 DOI: 10.7150/thno.51360] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/18/2020] [Indexed: 01/26/2023] Open
Abstract
Background: A metabolic "switch" from oxidative phosphorylation to glycolysis provides tumor cells with energy and biosynthetic substrates, thereby promoting tumorigenesis and malignant progression. However, the mechanisms controlling this metabolic switch in tumors is not entirely clear. Methods: Clinical specimens were used to determine the effect of SAM68 on lung adenocarcinoma (LUAD) tumorigenesis and metastasis, and mouse models and molecular biology assays were performed to elucidate the function and underlying mechanisms in vitro and in vivo. Results:SAM68 mRNA levels were higher in LUAD tissue than in normal lung tissue, indicating that SAM68 expression is upregulated in LUAD. Patients with LUAD with SAM68high (n = 257) had a higher frequency of tumor recurrence (p = 0.025) and recurrence-free survival (p = 0.013) than did those with SAM68low (n = 257). Patients with SAM68high mRNA levels (n = 257) were at a higher risk for cancer-related death (p = 0.006), and had shorter overall survival (p = 0.044) than did those with SAM68low. SAM68 promotes tumorigenesis and metastasis of LUAD cells in vitro and in vivo by regulating the cancer metabolic switch. SAM68 drives cancer metabolism by mediating alternative splicing of pyruvate kinase (PKM) pre-mRNAs, and promoting the formation of PKM2. Mechanistically, SAM68 increased the binding of the splicing repressor hnRNP A1 to exon 9 of PKM, thereby enhancing PKM2 isoform formation and PKM2-dependent aerobic glycolysis and tumorigenesis. Conclusions: SAM68 promotes LUAD cell tumorigenesis and cancer metabolic programming via binding of the 351-443 aa region of SAM68 to the RGG motif of hnRNP A1, driving hnRNP A1-dependent PKM splicing, contributing to increased oncogene PKM2 isoform formation and inhibition of PKM1 isoform formation. SAM68 is therefore a promising therapeutic target for the treatment of LUAD.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/metabolism
- Adenocarcinoma of Lung/mortality
- Adenocarcinoma of Lung/pathology
- Alternative Splicing
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Exons
- Gene Expression Regulation, Neoplastic
- Glycolysis/genetics
- Heterogeneous Nuclear Ribonucleoprotein A1/genetics
- Heterogeneous Nuclear Ribonucleoprotein A1/metabolism
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/mortality
- Lung Neoplasms/pathology
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred NOD
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Oxidative Phosphorylation
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Signal Transduction
- Survival Analysis
- Thyroid Hormones/genetics
- Thyroid Hormones/metabolism
- Tumor Burden
- Xenograft Model Antitumor Assays
- Thyroid Hormone-Binding Proteins
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Affiliation(s)
- Song Zhu
- Department of Radiotherapy, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
| | - Weiping Chen
- Department of Respiratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
| | - Jizhong Wang
- Department of Cardiology, Vascular Center, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, People's Republic of China
| | - Ling Qi
- Department of Central Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
| | - Huilin Pan
- Department of Radiotherapy, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
| | - Zhengfu Feng
- Department of Radiotherapy, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
| | - Dongbo Tian
- Department of Respiratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P. R. China
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8
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Panzeri V, Manni I, Capone A, Naro C, Sacconi A, Di Agostino S, de Latouliere L, Montori A, Pilozzi E, Piaggio G, Capurso G, Sette C. The RNA-binding protein MEX3A is a prognostic factor and regulator of resistance to gemcitabine in pancreatic ductal adenocarcinoma. Mol Oncol 2020; 15:579-595. [PMID: 33159833 PMCID: PMC7858117 DOI: 10.1002/1878-0261.12847] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/16/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer. Most patients present with advanced disease at diagnosis, which only permits palliative chemotherapeutic treatments. RNA dysregulation is a hallmark of most human cancers, including PDAC. To test the impact of RNA processing dysregulation on PDAC pathology, we performed a bioinformatics analysis to identify RNA-binding proteins (RBPs) associated with prognosis. Among the 12 RBPs associated with progression-free survival, we focused on MEX3A because it was recently shown to mark an intestinal stem cell population that is refractory to chemotherapeutic treatments, a typical feature of PDAC. Increased expression of MEX3A was correlated with higher disease stage in PDAC patients and with tumor development in a mouse model of PDAC. Depletion of MEX3A in PDAC cells enhanced sensitivity to chemotherapeutic treatment with gemcitabine, whereas its expression was increased in PDAC cells selected upon chronic exposure to the drug. RNA-sequencing analyses highlighted hundreds of genes whose expression is sensitive to MEX3A expression, with significant enrichment in cell cycle genes. MEX3A binds to its target mRNAs, like cyclin-dependent kinase 6 (CDK6), and promotes their stability. Accordingly, knockdown of MEX3A caused a significant reduction in PDAC cell proliferation and in progression to the S phase of the cell cycle. These findings uncover a novel role for MEX3A in the acquisition and maintenance of chemoresistance by PDAC cells, suggesting that it may represent a novel therapeutic target for PDAC.
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Affiliation(s)
- Valentina Panzeri
- Department of Science Medical/Chirurgic and Translational Medicine, University of Rome "Sapienza", Italy.,Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Isabella Manni
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,IRCCS Fondazione Policlinico Agostino Gemelli, Rome, Italy
| | - Andrea Sacconi
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Luisa de Latouliere
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Montori
- Department of Clinical and Molecular Medicine, UOC Anatomia Patologica, Sant' Andrea Hospital, Sapienza University of Rome, Italy
| | - Emanuela Pilozzi
- Department of Clinical and Molecular Medicine, UOC Anatomia Patologica, Sant' Andrea Hospital, Sapienza University of Rome, Italy
| | - Giulia Piaggio
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Gabriele Capurso
- PancreatoBiliary Endoscopy and EUS Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
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9
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Du J, Liao W, Liu W, Deb DK, He L, Hsu PJ, Nguyen T, Zhang L, Bissonnette M, He C, Li YC. N 6-Adenosine Methylation of Socs1 mRNA Is Required to Sustain the Negative Feedback Control of Macrophage Activation. Dev Cell 2020; 55:737-753.e7. [PMID: 33220174 DOI: 10.1016/j.devcel.2020.10.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/12/2020] [Accepted: 10/29/2020] [Indexed: 12/16/2022]
Abstract
Bacterial infection triggers a cytokine storm that needs to be resolved to maintain the host's wellbeing. Here, we report that ablation of m6A methyltransferase subunit METTL14 in myeloid cells exacerbates macrophage responses to acute bacterial infection in mice, leading to high mortality due to sustained production of pro-inflammatory cytokines. METTL14 depletion blunts Socs1 m6A methylation and reduces YTHDF1 binding to the m6A sites, which diminishes SOCS1 induction leading to the overactivation of TLR4/NF-κB signaling. Forced expression of SOCS1 in macrophages depleted of METTL14 or YTHDF1 rescues the hyper-responsive phenotype of these macrophages in vitro and in vivo. We further show that LPS treatment induces Socs1 m6A methylation and sustains SOCS1 induction by promoting Fto mRNA degradation, and forced FTO expression in macrophages mimics the phenotype of METTL14-depleted macrophages. We conclude that m6A methylation-mediated SOCS1 induction is required to maintain the negative feedback control of macrophage activation in response to bacterial infection.
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Affiliation(s)
- Jie Du
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA; Institute of Biomedical Research, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wang Liao
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA; Department of Cardiology, Hainan General Hospital, Hainan Clinical Research Institute, Haikou, Hainan, China
| | - Weicheng Liu
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA
| | - Dilip K Deb
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA
| | - Lei He
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA
| | - Phillip J Hsu
- Departments of Chemistry, Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Tivoli Nguyen
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA
| | - Linda Zhang
- Departments of Chemistry, Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Marc Bissonnette
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Departments of Chemistry, Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yan Chun Li
- Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, IL, USA.
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10
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Cesari E, Loiarro M, Naro C, Pieraccioli M, Farini D, Pellegrini L, Pagliarini V, Bielli P, Sette C. Combinatorial control of Spo11 alternative splicing by modulation of RNA polymerase II dynamics and splicing factor recruitment during meiosis. Cell Death Dis 2020; 11:240. [PMID: 32303676 PMCID: PMC7165175 DOI: 10.1038/s41419-020-2443-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 11/29/2022]
Abstract
Homologous recombination and chromosome segregation in meiosis rely on the timely expression of two splice variants of the endonuclease SPO11, named α and β, which respectively skip or include exon 2. However, in spite of its physiological importance, the mechanism underlying Spo11 alternative splicing in meiosis is still unknown. By screening the activity of factors that are predicted to bind the alternatively spliced region of Spo11, we identified hnRNPH as a key regulator of SPO11α splicing in mouse spermatocytes. Although hnRNPH was not upregulated in meiosis concomitantly with the switch in splicing, its recruitment to Spo11 pre-mRNA was favored by selective modulation of RNA polymerase II (RNAPII) phosphorylation and processivity in proximity of exon 2. The hnRNPH binding sites were localized near those of splicing factors that promote SPO11β splicing, suggesting that hnRNPH favors exon 2 skipping by competing out positive regulators. Indeed, hnRNPH binds proximal to a consensus motif for Sam68, a positive regulator of SPO11β splicing in vitro and in vivo, and it interferes with Sam68 binding to the Spo11 pre-mRNA. Thus, our work reveals that modulation of RNAPII dynamics in concert with hnRNPH recruitment exerts a combinatorial control of the timely regulated Spo11 splicing during meiosis.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Maria Loiarro
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Marco Pieraccioli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Donatella Farini
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Livia Pellegrini
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy. .,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy.
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11
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Naro C, Pellegrini L, Jolly A, Farini D, Cesari E, Bielli P, de la Grange P, Sette C. Functional Interaction between U1snRNP and Sam68 Insures Proper 3' End Pre-mRNA Processing during Germ Cell Differentiation. Cell Rep 2020; 26:2929-2941.e5. [PMID: 30865884 DOI: 10.1016/j.celrep.2019.02.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/15/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Male germ cells express the widest repertoire of transcript variants in mammalian tissues. Nevertheless, factors and mechanisms underlying such pronounced diversity are largely unknown. The splicing regulator Sam68 is highly expressed in meiotic cells, and its ablation results in defective spermatogenesis. Herein, we uncover an extensive splicing program operated by Sam68 across meiosis, primarily characterized by alternative last exon (ALE) regulation in genes of functional relevance for spermatogenesis. Lack of Sam68 preferentially causes premature transcript termination at internal polyadenylation sites, a feature observed also upon depletion of the spliceosomal U1snRNP in somatic cells. Notably, Sam68-regulated ALEs are characterized by proximity between U1snRNP and Sam68 binding motifs. We demonstrate a physical association between Sam68 and U1snRNP and show that U1snRNP recruitment to Sam68-regulated ALEs is impaired in Sam68-/- germ cells. Thus, our study reveals an unexpected cooperation between Sam68 and U1snRNP that insures proper processing of transcripts essential for male fertility.
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Affiliation(s)
- Chiara Naro
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Livia Pellegrini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ariane Jolly
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Eleonora Cesari
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pierre de la Grange
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.
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12
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Pagliarini V, Jolly A, Bielli P, Di Rosa V, De la Grange P, Sette C. Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization. Nucleic Acids Res 2020; 48:633-645. [PMID: 31777926 PMCID: PMC6954450 DOI: 10.1093/nar/gkz1117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/12/2019] [Accepted: 11/22/2019] [Indexed: 01/01/2023] Open
Abstract
The Spinal Muscular Atrophy (SMA) gene SMN was recently duplicated (SMN1 and SMN2) in higher primates. Furthermore, invasion of the locus by repetitive elements almost doubled its size with respect to mouse Smn, in spite of an almost identical protein-coding sequence. Herein, we found that SMN ranks among the human genes with highest density of Alus, which are evolutionary conserved in primates and often occur in inverted orientation. Inverted repeat Alus (IRAlus) negatively regulate splicing of long introns within SMN, while promoting widespread alternative circular RNA (circRNA) biogenesis. Bioinformatics analyses revealed the presence of ultra-conserved Sam68 binding sites in SMN IRAlus. Cross-link-immunoprecipitation (CLIP), mutagenesis and silencing experiments showed that Sam68 binds in proximity of intronic Alus in the SMN pre-mRNA, thus favouring circRNA biogenesis in vitro and in vivo. These findings highlight a novel layer of regulation in SMN expression, uncover the crucial impact exerted by IRAlus and reveal a role for Sam68 in SMN circRNA biogenesis.
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Affiliation(s)
- Vittoria Pagliarini
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome 00168, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome 00168, Italy
| | - Ariane Jolly
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, Paris 75013, France
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Valentina Di Rosa
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy
| | - Pierre De la Grange
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, Paris 75013, France
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Heart, Rome 00168, Italy.,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome 00143, Italy
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13
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Caggiano C, Pieraccioli M, Panzeri V, Sette C, Bielli P. c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer. Nucleic Acids Res 2020; 47:6160-6171. [PMID: 31066450 PMCID: PMC6614821 DOI: 10.1093/nar/gkz344] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified the promoter region of the Sam68 gene (KHDRBS1) and the proto-oncogenic transcription factor c-MYC as a key regulator of Sam68 expression. Upregulation of Sam68 and c-MYC correlate in PCa patients. c-MYC directly binds to and activates the Sam68 promoter. Furthermore, c-MYC affects productive splicing of the nascent Sam68 transcript by modulating the transcriptional elongation rate within the gene. Importantly, c-MYC-dependent expression of Sam68 is under the tight control of external cues, such as androgens and/or mitogens. These findings uncover an unexpected coordination of transcription and splicing of Sam68 by c-MYC, which may represent a key step in PCa tumorigenesis.
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Affiliation(s)
- Cinzia Caggiano
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marco Pieraccioli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Valentina Panzeri
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Science medical/chirurgic and translational medicine, University of Rome Sapienza,00189 Rome, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy
| | - Pamela Bielli
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
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14
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Identification of Upregulated HNRNPs Associated with Poor Prognosis in Pancreatic Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5134050. [PMID: 31355266 PMCID: PMC6637714 DOI: 10.1155/2019/5134050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/03/2019] [Accepted: 06/12/2019] [Indexed: 12/27/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (HNRNPs) are reported to play a crucial role in the pathogenic process of multiple malignancies. However, the expression patterns and prognostic values of HNRNPs in pancreatic cancer (PC) are lacking. In this study, several public databases were explored to identify the commonly upregulated HNRNPs in PC. The clinical significance of HNRNPL (heterogeneous nuclear ribonucleoproteins L) in PC was analyzed. We further performed a series of experiments to elucidate the biological functions of HNRNPL. Bioinformatics analysis including pathway enrichment and interactors with HNRNPL was used to explain the potential mechanisms of HNRNPL in PC pathogenesis. Herein, we reported that HNRNPL was commonly overexpressed in public databases and that high expression of HNRNPL in PC was positively associated with aggressive disease and poor overall survival. Downregulation of HNRNPL suppressed the abilities of migration and epithelial mesenchymal transition of PC cells in vitro, while depletion of HNRNPL did not affect the proliferation rate of PC cells. We further showed that HNRNPL might combine with RNA-binding protein, PTBP1, and function as a part of the spliceosome to regulate alternative splicing of target genes in the occurrence and development of PC. HNRNPL could be employed as an innovative prognostic biomarker and therapeutic target for PC.
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15
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The RNA binding protein Sam68 controls T helper 1 differentiation and anti-mycobacterial response through modulation of miR-29. Cell Death Differ 2018; 26:1169-1180. [PMID: 30258098 DOI: 10.1038/s41418-018-0201-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/08/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022] Open
Abstract
Polarization of naive T cells into interferon (IFN)-γ-producing T helper 1 (Th1) cells is an essential event in the inflammatory response to pathogens. Herein, we identify the RNA binding protein Sam68 as a specific modulator of Th1 differentiation. Sam68-knockout (ko) naive T cells are strongly defective in IL-12-mediated Th1 polarization and express low levels of T-bet and Eomes. Consequently, Sam68-ko Th1 cells are significantly impaired in IFN-γ production. Moreover, we found that Sam68 is required for the induction of an inflammatory Th1 response during Mycobacterium bovis Bacillus Calmette-Guerin (BCG) infection, thus limiting bacterial dissemination in the lungs. Mechanistically, Sam68 directly binds to the microRNA miR-29, a negative regulator of Th1 response, and inhibits its expression during BCG infection. These findings uncover a novel post-transcriptional mechanism required for the Th1-mediated defense against intracellular pathogens and identify a new function for Sam68 in the regulation of the immune response.
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16
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Bielli P, Panzeri V, Lattanzio R, Mutascio S, Pieraccioli M, Volpe E, Pagliarulo V, Piantelli M, Giannantoni A, Di Stasi SM, Sette C. The Splicing Factor PTBP1 Promotes Expression of Oncogenic Splice Variants and Predicts Poor Prognosis in Patients with Non-muscle-Invasive Bladder Cancer. Clin Cancer Res 2018; 24:5422-5432. [PMID: 30012566 DOI: 10.1158/1078-0432.ccr-17-3850] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/02/2018] [Accepted: 07/10/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Non-muscle-invasive bladder cancer (NMIBC) is a malignant disease characterized by high heterogeneity, which corresponds to dysregulated gene expression and alternative splicing (AS) profiles. Bioinformatics analyses of splicing factors potentially linked to bladder cancer progression identified the heterogeneous nuclear ribonucleoprotein I (i.e., PTBP1) as candidate. This study aimed at investigating whether PTBP1 expression associates with clinical outcome in patients with NMIBC.Experimental Design: A cohort of 152 patients presenting with primary NMIBC (pTa-pT1) was enrolled. Primary NMIBCs were assessed for PTBP1 expression by IHC, and the results were correlated with clinical data using Kaplan-Meier curves and Cox regression analyses. Cell proliferation and survival assays were performed to assess the function of PTBP1. Furthermore, the impact of PTBP1 on the AS pattern of specific bladder cancer-related genes was investigated in cancer cell lines and in patients' specimens.Results: Public datasets querying highlighted a positive correlation between PTBP1 expression and NMIBC progression, which was then confirmed by IHC analysis. High PTBP1 expression was associated with worse clinical outcome in terms of incidence of tumor relapse and survival in patients with NMIBC. Interestingly, downregulation of PTBP1 in bladder cancer cell lines affected prosurvival features. Accordingly, PTBP1 modulated AS of bladder cancer-related genes in cell lines and patient's specimens.Conclusions: PTBP1 expression correlates with disease progression, poor prognosis, and worse survival in patients with NMIBC. Downregulation of PTBP1 expression affects prosurvival features of bladder cancer cells and modulates AS of genes with relevance for bladder cancer, suggesting its role as an outcome-predictor in this disease. Clin Cancer Res; 24(21); 5422-32. ©2018 AACR.
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Affiliation(s)
- Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Valentina Panzeri
- Fondazione Santa Lucia IRCCS, Rome, Italy.,Department of Science Medical/Chirurgic and Translational Medicine, University of Rome "Sapienza", Rome, Italy.,Institute of Human Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rossano Lattanzio
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy.,Center of Excellence on Aging and Translational Medicine (CeSi-Met), G. d'Annunzio University, Chieti, Italy
| | - Simona Mutascio
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Marco Pieraccioli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | | | - Vincenzo Pagliarulo
- Department of Emergency and Organ Transplantation, University Aldo Moro, Bari, Italy
| | - Mauro Piantelli
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - Antonella Giannantoni
- Department of Surgical and Biomedical Sciences, University of Perugia, Perugia, Italy
| | - Savino M Di Stasi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Claudio Sette
- Fondazione Santa Lucia IRCCS, Rome, Italy. .,Institute of Human Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
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