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Yoshida M, Oda C, Mishima K, Tsuji I, Obika S, Shimojo M. An antisense amido-bridged nucleic acid gapmer oligonucleotide targeting SRRM4 alters REST splicing and exhibits anti-tumor effects in small cell lung cancer and prostate cancer cells. Cancer Cell Int 2023; 23:8. [PMID: 36650528 PMCID: PMC9847160 DOI: 10.1186/s12935-022-02842-1] [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: 10/15/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Antisense oligonucleotide (ASO) medicine for clinical applications has been becoming a reality. We previously developed a gapmer ASO targeting Ser/Arg repetitive matrix 4 (SRRM4) that is abnormally expressed in small cell lung cancer (SCLC). However the detailed mechanism of ASO through repressing SRRM4 has not been completely elucidated. Further, effectiveness of SRRM4 ASO to prostate cancer (PCa) cells expressing SRRM4 similar to SCLC remains to be elucidated. RE1-silencing transcription factor (REST) is a tumor suppressor, and its splicing isoform (sREST) is abnormally expressed by SRRM4 and causes carcinogenesis with neuroendocrine phenotype in SCLC. The present study aimed to understand the contribution of REST splicing by SRRM4 ASO administration. METHODS SRRM4 expression and REST splicing were analyzed by RT-qPCR and conventional RT-PCR after treating SRRM4 ASO, and cell viability was analyzed in vitro. Exogenous reconstitution of Flag-tagged REST plasmid in SCLC cells and the splice-switching oligonucleotide (SSO) specific for REST was analyzed for cell viability. Furthermore, we expanded the application of SRRM4 ASO in PCa cells abnormally expressing SRRM4 mRNA in vitro. RESULTS SRRM4 ASO successfully downregulated SRRM4 expression, followed by repressed cell viability of SCLC and PCa cells in a dose-dependent manner. Administration of SRRM4 ASO then modified the alternative splicing of REST, resulting reduced cell viability. REST SSO specifically modified REST splicing increased REST expression, resulting in reduced cell viability. CONCLUSIONS Our data demonstrate that a gapmer ASO targeting SRRM4 (SRRM4 ASO) reduces cell viability through splicing changes of REST, followed by affecting REST-controlled genes in recalcitrant tumors SCLC and PCa cells.
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Affiliation(s)
- Misa Yoshida
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Chihiro Oda
- grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Keishiro Mishima
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Itsuki Tsuji
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Satoshi Obika
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, 565-0871 Japan ,grid.482562.fNational Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka 567-0085 Japan
| | - Masahito Shimojo
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
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2
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D’Abronzo LS, Lombard AP, Ning S, Armstong CM, Leslie AR, Sharifi M, Schaaf ZA, Lou W, Gao AC. Wntless expression promotes lineage plasticity and is associated with neuroendocrine prostate cancer. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:299-310. [PMID: 36313205 PMCID: PMC9605943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Resistance to androgen receptor (AR) targeted therapies remains as the main reason for most prostate cancer related deaths. Lineage plasticity resulting in altered, treatment insensitive prostate tumor cell phenotypes such neuroendocrine differentiated prostate cancer is a common manifestation within resistant tumors upon AR-targeted therapies. The mechanisms responsible for lineage plasticity in prostate cancer remain incompletely understood. Here we demonstrate that the enzalutamide resistant MDVR cell line possesses lineage plastic characteristics associated with overexpression of the Wnt transporter Wntless (WLS). Furthermore, we present evidence that overexpression of WLS is common in varying cell line models of lineage plastic prostate cancer, is higher in neuroendocrine patient samples, and positively correlates with the neuroendocrine marker SYP in clinical data. Targeting WLS in lineage plastic cellular models reduces viability and represses lineage plasticity associated gene expression. Our study provides insight into the importance of WLS to the development of lethal resistant prostate cancer and provides a potential target for the treatment of advanced disease.
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Affiliation(s)
- Leandro S D’Abronzo
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Alan P Lombard
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
- UC Davis Comprehensive Cancer Center, University of California DavisSacramento, California, USA
- Department of Biochemistry and Molecular Medicine, University of California DavisSacramento, California, USA
| | - Shu Ning
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Cameron M Armstong
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Amy R Leslie
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Masuda Sharifi
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Zachary A Schaaf
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Wei Lou
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
| | - Allen C Gao
- Department of Urologic Surgery, University of California DavisSacramento, California, USA
- UC Davis Comprehensive Cancer Center, University of California DavisSacramento, California, USA
- VA Northern California Health Care SystemSacramento, California, USA
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3
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Advances in neuroendocrine prostate cancer research: From model construction to molecular network analyses. J Transl Med 2022; 102:332-340. [PMID: 34937865 DOI: 10.1038/s41374-021-00716-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is the most common cancer among men and has a high incidence and associated mortality worldwide. It is an androgen-driven disease in which tumor growth is triggered via ligand-mediated signaling through the androgen receptor (AR). Recent evidence suggests that the widespread use of effective AR pathway inhibitors may increase the occurrence of neuroendocrine prostate cancer (NEPC), an aggressive and treatment-resistant AR-negative variant; however, mechanisms controlling NEPC development remain to be elucidated. Various preclinical models have recently been developed to investigate the mechanisms driving the NEPC differentiation. In the present study, we summarized strategies for the development of NEPC models and proposed a novel method for model evaluation, which will help in the timely and accurate identification of NEPC by virtue of its ability to recapitulate the heterogeneity of prostate cancer. Moreover, we discuss the origin and the mechanism of NEPC. The understanding of the regulatory network mediating neuroendocrine differentiation presented in this review could provide valuable insights into the identification of novel drug targets for NEPC as well as into the causes of antiandrogenic drug resistance.
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4
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Reprogramming landscape highlighted by dynamic transcriptomes in therapy-induced neuroendocrine differentiation. Comput Struct Biotechnol J 2022; 20:5873-5885. [DOI: 10.1016/j.csbj.2022.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022] Open
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5
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Head SA, Hernandez-Alias X, Yang JS, Ciampi L, Beltran-Sastre V, Torres-Méndez A, Irimia M, Schaefer MH, Serrano L. Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers. PLoS Biol 2021; 19:e3001138. [PMID: 33621242 PMCID: PMC7935315 DOI: 10.1371/journal.pbio.3001138] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 03/05/2021] [Accepted: 02/04/2021] [Indexed: 01/14/2023] Open
Abstract
RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3–27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the SF Serine/Arginine Repetitive Matrix 4 (SRRM4), whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here, we demonstrate that despite having low expression in normal nonneural tissues, SRRM4 is further silenced in tumors, resulting in the suppression of normal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced SF across all tumor types analyzed, implying a general advantage of microexon down-regulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and up-regulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and toward differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake. Using data from The Cancer Genome Atlas, this study shows that the splicing factor SRRM4 and its program of differentiation-promoting microexons are downregulated across tumor types with remarkable consistency, providing tumors with a proliferative advantage.
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Affiliation(s)
- Sarah A. Head
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jae-Seong Yang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Violeta Beltran-Sastre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Méndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Martin H. Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- * E-mail: (SAH); (MHS); (LS)
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
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6
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Lovnicki J, Gan Y, Feng T, Li Y, Xie N, Ho CH, Lee AR, Chen X, Nappi L, Han B, Fazli L, Huang J, Gleave ME, Dong X. LIN28B promotes the development of neuroendocrine prostate cancer. J Clin Invest 2021; 130:5338-5348. [PMID: 32634132 DOI: 10.1172/jci135373] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Therapy-induced neuroendocrine prostate cancer (t-NEPC) is a highly aggressive subtype of prostate cancer with poor patient survival. Emerging evidence indicates that t-NEPC can develop when prostate adenocarcinoma cells acquire cancer stem-like cell signaling in the presence of androgen receptor inhibition, followed by redifferentiation toward neuroendocrine lineage and subsequent t-NEPC progression. Whether the stem-like signaling is controlled by the core pluripotency stem cell genes (e.g., LIN28 and SOX2) remains unknown. Here, we report that the transcription of the LIN28B isoform and SOX2 were co-upregulated in t-NEPC patient tumors, patient-derived xenografts, transgenic mice, and cell models. Immunohistochemistry validated that LIN28B and SOX2 protein expression were elevated in t-NEPC patient biopsies. Using prostate adenocarcinoma and t-NEPC cell models, we demonstrated that LIN28B induced a stem-like gene network, neuroendocrine biomarkers, and neuroendocrine cell morphology. LIN28B depletion by CRISPR inhibited t-NEPC tumorigenesis and xenograft growth. These LIN28B functions were mediated mainly through the suppression of let-7 miRNA expression, resulting in de-repression of the transcription factor HMGA2 and HMGA2-mediated SOX2 expression. This study revealed a mechanism by which t-NEPC can develop through the LIN28B/let-7/SOX2 axis that regulates a cancer cell stem-like gene network, highlighting LIN28B as a potential therapeutic target in t-NEPC.
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Affiliation(s)
- Jessica Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yu Gan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Feng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Key Laboratory of Experimental Teratology, Ministry of Education, and Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ning Xie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chia-Hao Ho
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xufeng Chen
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lucia Nappi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bo Han
- Key Laboratory of Experimental Teratology, Ministry of Education, and Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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7
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SRRM4 Expands the Repertoire of Circular RNAs by Regulating Microexon Inclusion. Cells 2020; 9:cells9112488. [PMID: 33207694 PMCID: PMC7697094 DOI: 10.3390/cells9112488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)-which occur in 30% of functional mRNA transcripts-have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLBRA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family.
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8
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Franko A, Berti L, Guirguis A, Hennenlotter J, Wagner R, Scharpf MO, de Angelis MH, Wißmiller K, Lickert H, Stenzl A, Birkenfeld AL, Peter A, Häring HU, Lutz SZ, Heni M. Characterization of Hormone-Dependent Pathways in Six Human Prostate-Cancer Cell Lines: A Gene-Expression Study. Genes (Basel) 2020; 11:E1174. [PMID: 33036464 PMCID: PMC7599530 DOI: 10.3390/genes11101174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa), the most incident cancer in men, is tightly regulated by endocrine signals. A number of different PCa cell lines are commonly used for in vitro experiments, but these are of diverse origin, and have very different cell-proliferation rates and hormone-response capacities. By analyzing the gene-expression pattern of main hormone pathways, we systematically compared six PCa cell lines and parental primary cells. We compared these cell lines (i) with each other and (ii) with PCa tissue samples from 11 patients. We found major differences in the gene-expression levels of androgen, insulin, estrogen, and oxysterol signaling between PCa tissue and cell lines, and between different cell lines. Our systematic characterization gives researchers a solid basis to choose the appropriate PCa cell model for the hormone pathway of interest.
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Affiliation(s)
- Andras Franko
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
| | - Lucia Berti
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
| | - Alke Guirguis
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, 72076 Tübingen, Germany;
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tübingen, 72076 Tübingen, Germany; (J.H.); (A.S.)
| | - Robert Wagner
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
| | - Marcus O. Scharpf
- Institute of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany;
| | - Martin Hrabĕ de Angelis
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Katharina Wißmiller
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany;
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Department of Medicine, Technical University of Munich, 81675 München, Germany
| | - Heiko Lickert
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany;
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Department of Medicine, Technical University of Munich, 81675 München, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tübingen, 72076 Tübingen, Germany; (J.H.); (A.S.)
| | - Andreas L. Birkenfeld
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
| | - Andreas Peter
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, 72076 Tübingen, Germany;
| | - Hans-Ulrich Häring
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
| | - Stefan Z. Lutz
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Clinic for Geriatric and Orthopedic Rehabilitation Bad Sebastiansweiler, 72116 Mössingen, Germany
| | - Martin Heni
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology, and Nephrology, University Hospital Tübingen, 72076 Tübingen, Germany; (A.F.); (R.W.); (A.L.B.); (H.-U.H.); (S.Z.L.); (M.H.)
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, 72076 Tübingen, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; (M.H.d.A.); (H.L.)
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, 72076 Tübingen, Germany;
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9
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Coleman DJ, Sampson DA, Sehrawat A, Kumaraswamy A, Sun D, Wang Y, Schwartzman J, Urrutia J, Lee AR, Coleman IM, Nelson PS, Dong X, Morrissey C, Corey E, Xia Z, Yates JA, Alumkal JJ. Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. Neoplasia 2020; 22:253-262. [PMID: 32403054 PMCID: PMC7218227 DOI: 10.1016/j.neo.2020.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023] Open
Abstract
Neuroendocrine prostate cancer (NEPC) is the most virulent form of prostate cancer. Importantly, our recent work examining metastatic biopsy samples demonstrates NEPC is increasing in frequency. In contrast to prostate adenocarcinomas that express a luminal gene expression program, NEPC tumors express a neuronal gene expression program. Despite this distinction, the diagnosis of NEPC is often challenging, demonstrating an urgent need to identify new biomarkers and therapeutic targets. Our prior work demonstrated that the histone demethylase LSD1 (KDM1A) is important for survival of prostate adenocarcinomas, but little was known about LSD1's role in NEPC. Recently, a neural-specific transcript variant of LSD1-LSD1+8a-was discovered and demonstrated to activate neuronal gene expression in neural cells. The splicing factor SRRM4 was previously shown to promote LSD1+8a splicing in neuronal cells, and SRRM4 promotes NEPC differentiation and cell survival. Therefore, we sought to determine if LSD1+8a might play a role in NEPC and whether LSD1+8a splicing was linked to SRRM4. To investigate a potential role for LSD1+8a in NEPC, we examined a panel of prostate adenocarcinoma and NEPC patient-derived xenografts and metastatic biopsies. LSD1+8a was expressed exclusively in NEPC samples and correlated significantly with elevated expression of SRRM4. Using SRRM4-overexpressing cell lines, we determined that SRRM4 mediates alternative splicing of LSD1+8a. Finally, using gain of function studies, we confirmed that LSD1+8a and SRRM4 co-regulate target genes distinct from canonical LSD1. Our findings suggest further study of the interplay between SRRM4 and LSD1+8a and mechanisms by which LSD1+8a regulates gene expression in NEPC is warranted.
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Affiliation(s)
- Daniel J Coleman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - David A Sampson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Archana Sehrawat
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Anbarasu Kumaraswamy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Jacob Schwartzman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joshua Urrutia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Joel A Yates
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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10
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Dong X, Chen R. Understanding aberrant RNA splicing to facilitate cancer diagnosis and therapy. Oncogene 2019; 39:2231-2242. [PMID: 31819165 DOI: 10.1038/s41388-019-1138-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Almost all genes in normal cells undergo alternative RNA splicing to generate a greater extent of diversification of gene products for normal cellular functions. RNA splicing is tightly regulated and closely interplays with genetic and epigenetic machinery. While DNA polymorphism and somatic mutations modulate alternative splicing patterns, RNA splicing also controls genomic stability, chromatin organization, and transcriptome. Tumor cells, in turn, often take advantage of aberrant RNA splicing to develop, grow and progress into therapy-resistant tumors. Understanding alternative RNA splicing in tumor cells would, therefore, provide us opportunities to gain further insights into tumor biology, identify diagnostic or prognosis biomarkers, as well as to design effective therapeutic means to control tumor progression. Here, we provide an overview of RNA splicing mechanisms and use prostate cancer as an example to review recent advancements in our understanding of RNA splicing in cancer progression and therapy resistance. We also discuss emerging diagnostic and therapeutic potentials of RNA splicing events or RNA splicing factors.
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Affiliation(s)
- Xuesen Dong
- Department of Urologic Sciences, Faculty of Medicine, The University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada. .,The Vancouver Prostate Centre, Vancouver General Hospital, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada.
| | - Ruiqi Chen
- Faculty of Medicine, University of Toronto, 27 King's College Circle 8, Toronto, ON, M5S 1A1, Canada
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11
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Maldonado-Ruiz LP, Montenegro-Cadena L, Blattner B, Menghwar S, Zurek L, Londono-Renteria B. Differential Tick Salivary Protein Profiles and Human Immune Responses to Lone Star Ticks ( Amblyomma americanum) From the Wild vs. a Laboratory Colony. Front Immunol 2019; 10:1996. [PMID: 31555263 PMCID: PMC6724717 DOI: 10.3389/fimmu.2019.01996] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022] Open
Abstract
Ticks are a growing concern to human and animal health worldwide and they are leading vectors of arthropod-borne pathogens in the United States. Ticks are pool blood feeders that can attach to the host skin for days to weeks using their saliva to counteract the host defenses. Tick saliva, as in other hematophagous arthropods, contains pharmacological and immunological active compounds, which modulate local and systemic immune responses and induce antibody production. In the present study, we explore differences in the salivary gland extract (SGE) protein content of Amblyomma americanum ticks raised in a laboratory colony (CT) vs. those collected in the field (FT). First, we measured the IgG antibody levels against SGE in healthy volunteers residing in Kansas. ELISA test showed higher IgG antibody levels when using the SGE from CT as antigen. Interestingly, antibody levels against both, CT-SGE and FT-SGE, were high in the warm months (May-June) and decreased in the cold months (September-November). Immunoblot testing revealed a set of different immunogenic bands for each group of ticks and mass spectrometry data revealed differences in at 19 proteins specifically identified in the CT-SGE group and 20 from the FT-SGE group. Our results suggest that differences in the salivary proteins between CT-SGE and FT-SGE may explain the differential immune responses observed in this study.
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Affiliation(s)
- L Paulina Maldonado-Ruiz
- Medical/Veterinary Entomology Laboratory, Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Lidia Montenegro-Cadena
- Vector Biology Laboratory, Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Brittany Blattner
- Vector Biology Laboratory, Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Sapna Menghwar
- Vector Biology Laboratory, Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Ludek Zurek
- Department of Pathology and Parasitology, CEITEC Center for Zoonoses, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia
| | - Berlin Londono-Renteria
- Vector Biology Laboratory, Department of Entomology, Kansas State University, Manhattan, KS, United States
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12
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Li Y, Xie N, Chen R, Lee AR, Lovnicki J, Morrison EA, Fazli L, Zhang Q, Musselman CA, Wang Y, Huang J, Gleave ME, Collins C, Dong X. RNA Splicing of the BHC80 Gene Contributes to Neuroendocrine Prostate Cancer Progression. Eur Urol 2019; 76:157-166. [PMID: 30910347 DOI: 10.1016/j.eururo.2019.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/08/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Prostate adenocarcinoma (AdPC) progression to treatment-induced neuroendocrine prostate cancer (t-NEPC) is associated with poor patient survival. While AdPC and t-NEPC share similar genomes, they possess distinct transcriptomes, suggesting that RNA splicing and epigenetic mechanisms may regulate t-NEPC development. OBJECTIVE To characterize the role of alternative RNA splicing of the histone demethylase BHC80 during t-NEPC progression. DESIGN, SETTING, AND PARTICIPANTS The expression of BHC80 splice variants (BHC80-1 and BHC80-2) were compared between AdPC and t-NEPC patient tumors. Regulatory mechanisms of RNA splicing of the BHC80 gene were studied, and the signal pathways mediated by BHC80 splice variants were investigated in t-NEPC cell and xenograft models. RESULTS Global transcriptome analyses identified that the BHC80-2 variant is highly expressed in t-NEPC. Compared with the known histone demethylation activities of the BHC80 gene, we discovered a novel nonepigenetic action of BHC80-2, whereby BHC80-2 is localized in the cytoplasm to trigger the MyD88-p38-TTP pathway, which results in increased RNA stability of multiple tumor-promoting cytokines. While BHC80-2 does not induce neuroendocrine differentiation of cancer cells, it stimulates cell proliferation and tumor progression independent of androgen receptor signaling. Blockade of BHC80-2-regulated MyD88 signaling suppresses growth of several t-NEPC cell spheroid and xenograft models. CONCLUSIONS Gain of function of BHC80-2 through alternative RNA splicing activates immune responses of cancer cells to promote t-NEPC development. PATIENT SUMMARY The main obstacle to develop effective therapies for patients with t-NEPC is the lack of understanding on how t-NEPC is developed. Our study not only identifies a previously unknown BHC80-2-MyD88 signaling pathway that plays an important role during t-NEPC development, but also provides a proof of principle that targeting this signal pathway may offer an avenue to treat t-NEPC.
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Affiliation(s)
- Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ning Xie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ruiqi Chen
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jessica Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Qingfu Zhang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA; China Medical University, Shenyang, China
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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13
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Li Y, Zhang Q, Lovnicki J, Chen R, Fazli L, Wang Y, Gleave M, Huang J, Dong X. SRRM4 gene expression correlates with neuroendocrine prostate cancer. Prostate 2019; 79:96-104. [PMID: 30155992 DOI: 10.1002/pros.23715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/14/2018] [Indexed: 12/29/2022]
Abstract
Neuroendocrine prostate cancer (NEPC) is an aggressive subtype of castrate-resistant prostate cancer characterized by poor patient outcome. Whole transcriptome sequencing analyses identified a NEPC-specific RNA splicing program that is predominantly controlled by the SRRM4 gene, suggesting that SRRM4 drives NEPC development. However, whether SRRM4 expression in patients may aid pathologists in diagnosing NEPC and predicting patient survival remains to be determined. In this study, we have applied RNA in situ hybridization and immunohistochemistry assays to measure the expressions of SRRM4, NEPC markers (SYP, CD56, and CHGA), and adenocarcinoma (AdPC) markers (AR, PSA) in a series of tissue microarrays constructed from castrate-resistant prostate tumors, treatment-naïve tumors collected from radical prostatectomy, and tumors treated with neoadjuvant hormonal therapy (NHT) for 0-12 months. Three pathologists also independently evaluated tumor histology and NEPC marker status. Here, we report that SRRM4 in castrate-resistant tumors is highly expressed in NEPC, strongly correlated with SYP, CD56, and CHGA expressions (Pearson correlation r = 0.883, 0.675, and 0.881; P < 0.0001) and negatively correlated with AR and PSA expressions (Pearson correlation r = -0.544 and -0.310; P < 0.05). Overall survival is 12.3 months for patients with SRRM4 positive tumors, comparing to 23 months for patients with SRRM4 negative tumors. In treatment-naïve AdPC, low SRRM4 expression is detected in ∼16% tumor cores. It correlates with SYP and CHGA expressions, but not Gleason scores. AdPC treated with >7 month NHT has significantly higher SRRM4 expression. Based on these findings, we conclude that SRRM4 expression in castrate-resistant tumors is highly correlated with NEPC and poor patient survival. It may serve as a diagnosis and prognosis biomarker of NEPC.
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Affiliation(s)
- Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Qingfu Zhang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
- China Medical University, Shenyang, China
| | - Jessica Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ruiqi Chen
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Lee AR, Gan Y, Xie N, Ramnarine VR, Lovnicki JM, Dong X. Alternative RNA splicing of the GIT1 gene is associated with neuroendocrine prostate cancer. Cancer Sci 2019; 110:245-255. [PMID: 30417466 PMCID: PMC6317919 DOI: 10.1111/cas.13869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 12/23/2022] Open
Abstract
Potent androgen receptor pathway inhibition (ARPI) therapies have given rise to a lethal, aggressive subtype of castration-resistant prostate cancer (CRPC) called treatment-induced neuroendocrine prostate cancer (t-NEPC). Now, t-NEPC poses a major clinical problem as approximately 20% of CRPC cases bear this subtype-a rate of occurrence that is predicted to rise with the widespread use of ARPI therapies. Unfortunately, there are no targeted therapies currently available to treat t-NEPC as the origin and molecular underpinnings of t-NEPC development remain unclear. In the present study, we identify that RNA splicing of the G protein-coupled receptor kinase-interacting protein 1 (GIT1) gene is a unique event in t-NEPC patients. Specifically, upregulation of the GIT1-A splice variant and downregulation of the GIT1-C variant expressions are associated with t-NEPC patient tumors, patient-derived xenografts, and cell models. RNA-binding assays show that RNA splicing of GIT1 is directly driven by SRRM4 and is associated with the neuroendocrine phenotype in CRPC cohorts. We show that GIT1-A and GIT1-C regulate differential transcriptomes in prostate cancer cells, where GIT1-A regulates genes associated with morphogenesis, neural function, environmental sensing via cell-adhesion processes, and epigenetic regulation. Consistent with our transcriptomic analyses, we report opposing functions of GIT1-A and GIT1-C in the stability of focal adhesions, whereby GIT1-A promotes focal adhesion stability. In summary, our study is the first to report that alternative RNA splicing of the GIT1 gene is associated with t-NEPC and reprograms its function involving FA-mediated signaling and cell processes, which may contribute to t-NEPC development.
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Affiliation(s)
- Ahn R. Lee
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
| | - Yu Gan
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
- Department of UrologyXiangya HospitalCentral South UniversityChangshaChina
| | - Ning Xie
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
| | - Varune R. Ramnarine
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
| | - Jessica M. Lovnicki
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
| | - Xuesen Dong
- Vancouver Prostate CentreDepartment of Urologic SciencesUniversity of British ColumbiaVancouverCanada
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15
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Ramnarine VR, Alshalalfa M, Mo F, Nabavi N, Erho N, Takhar M, Shukin R, Brahmbhatt S, Gawronski A, Kobelev M, Nouri M, Lin D, Tsai H, Lotan TL, Karnes RJ, Rubin MA, Zoubeidi A, Gleave ME, Sahinalp C, Wyatt AW, Volik SV, Beltran H, Davicioni E, Wang Y, Collins CC. The long noncoding RNA landscape of neuroendocrine prostate cancer and its clinical implications. Gigascience 2018; 7:4994835. [PMID: 29757368 PMCID: PMC6007253 DOI: 10.1093/gigascience/giy050] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/01/2018] [Indexed: 01/29/2023] Open
Abstract
Background Treatment-induced neuroendocrine prostate cancer (tNEPC) is an aggressive variant of late-stage metastatic castrate-resistant prostate cancer that commonly arises through neuroendocrine transdifferentiation (NEtD). Treatment options are limited, ineffective, and, for most patients, result in death in less than a year. We previously developed a first-in-field patient-derived xenograft (PDX) model of NEtD. Longitudinal deep transcriptome profiling of this model enabled monitoring of dynamic transcriptional changes during NEtD and in the context of androgen deprivation. Long non-coding RNA (lncRNA) are implicated in cancer where they can control gene regulation. Until now, the expression of lncRNAs during NEtD and their clinical associations were unexplored. Results We implemented a next-generation sequence analysis pipeline that can detect transcripts at low expression levels and built a genome-wide catalogue (n = 37,749) of lncRNAs. We applied this pipeline to 927 clinical samples and our high-fidelity NEtD model LTL331 and identified 821 lncRNAs in NEPC. Among these are 122 lncRNAs that robustly distinguish NEPC from prostate adenocarcinoma (AD) patient tumours. The highest expressed lncRNAs within this signature are H19, LINC00617, and SSTR5-AS1. Another 742 are associated with the NEtD process and fall into four distinct patterns of expression (NEtD lncRNA Class I, II, III, and IV) in our PDX model and clinical samples. Each class has significant (z-scores >2) and unique enrichment for transcription factor binding site (TFBS) motifs in their sequences. Enriched TFBS include (1) TP53 and BRN1 in Class I, (2) ELF5, SPIC, and HOXD1 in Class II, (3) SPDEF in Class III, (4) HSF1 and FOXA1 in Class IV, and (5) TWIST1 when merging Class III with IV. Common TFBS in all NEtD lncRNA were also identified and include E2F, REST, PAX5, PAX9, and STAF. Interrogation of the top deregulated candidates (n = 100) in radical prostatectomy adenocarcinoma samples with long-term follow-up (median 18 years) revealed significant clinicopathological associations. Specifically, we identified 25 that are associated with rapid metastasis following androgen deprivation therapy (ADT). Two of these lncRNAs (SSTR5-AS1 and LINC00514) stratified patients undergoing ADT based on patient outcome. Discussion To date, a comprehensive characterization of the dynamic landscape of lncRNAs during the NEtD process has not been performed. A temporal analysis of the PDX-based NEtD model has for the first time provided this dynamic landscape. TFBS analysis identified NEPC-related TF motifs present within the NEtD lncRNA sequences, suggesting functional roles for these lncRNAs in NEPC pathogenesis. Furthermore, select NEtD lncRNAs appear to be associated with metastasis and patients receiving ADT. Treatment-related metastasis is a clinical consequence of NEPC tumours. Top candidate lncRNAs FENDRR, H19, LINC00514, LINC00617, and SSTR5-AS1 identified in this study are implicated in the development of NEPC. We present here for the first time a genome-wide catalogue of NEtD lncRNAs that characterize the transdifferentiation process and a robust NEPC lncRNA patient expression signature. To accomplish this, we carried out the largest integrative study that applied a PDX NEtD model to clinical samples. These NEtD and NEPC lncRNAs are strong candidates for clinical biomarkers and therapeutic targets and warrant further investigation.
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Affiliation(s)
- Varune Rohan Ramnarine
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Fan Mo
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Noushin Nabavi
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Robert Shukin
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sonal Brahmbhatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alexander Gawronski
- Department of Computer Science, Simon Fraser University, Burnaby, BC, Canada
| | - Maxim Kobelev
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Mannan Nouri
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Harrison Tsai
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - R Jefferey Karnes
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Amina Zoubeidi
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cenk Sahinalp
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Himisha Beltran
- Department of Medicine, Weill Cornell Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | | | - Yuzhuo Wang
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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16
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Zhang D, Tang DG. "Splice" a way towards neuroendocrine prostate cancer. EBioMedicine 2018; 35:12-13. [PMID: 30177243 PMCID: PMC6161471 DOI: 10.1016/j.ebiom.2018.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dingxiao Zhang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dean G Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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17
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Lee AR, Gan Y, Tang Y, Dong X. A novel mechanism of SRRM4 in promoting neuroendocrine prostate cancer development via a pluripotency gene network. EBioMedicine 2018; 35:167-177. [PMID: 30100395 PMCID: PMC6154886 DOI: 10.1016/j.ebiom.2018.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background Prostate adenocarcinoma (AdPC) cells can undergo lineage switching to neuroendocrine cells and develop into therapy-resistant neuroendocrine prostate cancer (NEPC). While genomic/epigenetic alterations are shown to induce neuroendocrine differentiation via an intermediate stem-like state, RNA splicing factor SRRM4 can transform AdPC cells into NEPC xenografts through a direct neuroendocrine transdifferentiation mechanism. Whether SRRM4 can also regulate a stem-cell gene network for NEPC development remains unclear. Methods Multiple AdPC cell models were transduced by lentiviral vectors encoding SRRM4. SRRM4-mediated RNA splicing and neuroendocrine differentiation of cells and xenografts were determined by qPCR, immunoblotting, and immunohistochemistry. Cell morphology, proliferation, and colony formation rates were also studied. SRRM4 transcriptome in the DU145 cell model was profiled by AmpliSeq and analyzed by gene enrichment studies. Findings SRRM4 induces an overall NEPC-specific RNA splicing program in multiple cell models but creates heterogeneous transcriptomes. SRRM4-transduced DU145 cells present the most dramatic neuronal morphological changes, accelerated cell proliferation, and enhanced resistance to apoptosis. The derived xenografts show classic phenotypes similar to clinical NEPC. Whole transcriptome analyses further reveal that SRRM4 induces a pluripotency gene network consisting of the stem-cell differentiation gene, SOX2. While SRRM4 overexpression enhances SOX2 expression in both time- and dose-dependent manners in DU145 cells, RNA depletion of SOX2 compromises SRRM4-mediated stimulation of pluripotency genes. More importantly, this SRRM4-SOX2 axis is present in a subset of NEPC patient cohorts, patient-derived xenografts, and clinically relevant transgenic mouse models. Interpretation We report a novel mechanism by which SRRM4 drives NEPC progression via a pluripotency gene network. Fund Canadian Institutes of Health Research, National Nature Science Foundation of China, and China Scholar Council.
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Affiliation(s)
- Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, 2660 Oak Street, Vancouver, BC, Canada.
| | - Yu Gan
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, 2660 Oak Street, Vancouver, BC, Canada; Xiangya Hospital, Department of Urology, Central South University, Changsha, Hunan, China; Third Xiangya Hospital, Department of Urology, Central South University, Changsha, Hunan, China.
| | - Yuxin Tang
- Third Xiangya Hospital, Department of Urology, Central South University, Changsha, Hunan, China.
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, 2660 Oak Street, Vancouver, BC, Canada.
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18
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Gan Y, Li Y, Long Z, Lee AR, Xie N, Lovnicki JM, Tang Y, Chen X, Huang J, Dong X. Roles of Alternative RNA Splicing of the Bif-1 Gene by SRRM4 During the Development of Treatment-induced Neuroendocrine Prostate Cancer. EBioMedicine 2018; 31:267-275. [PMID: 29759485 PMCID: PMC6013970 DOI: 10.1016/j.ebiom.2018.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/12/2018] [Accepted: 05/01/2018] [Indexed: 02/02/2023] Open
Abstract
Treatment-induced neuroendocrine prostate cancer (t-NEPC) is an aggressive subtype of prostate cancer (PCa) that becomes more prevalent when hormonal therapy, chemotherapy, or radiation therapy is applied to patients with metastatic prostate adenocarcinoma (AdPC). How AdPC cells survive these anti-cancer therapies and progress into t-NEPC remains unclear. By comparing the whole transcriptomes between AdPC and t-NEPC, we identified Bif-1, an apoptosis-associated gene, which undergoes alternative RNA splicing in t-NEPC. We found that while Bif-1a is the predominant variant of the Bif-1 gene in AdPC, two neural-specific variants, Bif-1b and Bif-1c, are highly expressed in t-NEPC patients, patient derived xenografts, and cell models. The neural-specific RNA splicing factor, SRRM4, promotes Bif-1b and Bif-1c splicing, and the expression of SRRM4 in tumors is strongly associated with Bif-1b/-1c levels. Furthermore, we showed that Bif-1a is pro-apoptotic, while Bif-1b and Bif-1c are anti-apoptotic in PCa cells under camptothecin and UV light irritation treatments. Taken together, our data indicate that SRRM4 regulates alternative RNA splicing of the Bif-1 gene that enables PCa cells resistant to apoptotic stimuli under anti-cancer therapies, and may contribute to AdPC progression into t-NEPC. Alternative RNA splicing of the apoptosis-related gene, Bif-1, is associated with the development of t-NEPC. SRRM4 regulates alternative RNA splicing of the Bif-1 gene. Bif-1a in AdPC cells is pro-apoptotic, while neural Bif-1 variants, Bif-1b/-1c, enable tumor cells resistant to apoptosis.
Treatment-induced neuroendocrine prostate cancer (t-NEPC) is an aggressive subtype of castration-resistant prostate cancer. It becomes more prevalent when more potent androgen receptor inhibitors are applied to patients. However, mechanisms by which t-NEPC develops remain unclear. Here we report alternative RNA splicing of the apoptosis-related gene, Bif-1, may contribute to t-NEPC establishment. We show that the expression of neural Bif-1 variants is upregulated in t-NEPC, and confers tumor cells resistance to apoptotic stimuli. We propose that tumor cells have to first develop mechanisms to counteract therapy-induced cell death before they can undergo neuroendocrine differentiation for t-NEPC.
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Affiliation(s)
- Yu Gan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada; Department of Urology, Xiangya Hospital, Central South University, Changsha, China; Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada.
| | - Zhi Long
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada; Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada.
| | - Ning Xie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada.
| | - Jessica M Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada.
| | - Yuxin Tang
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Xiang Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Canada.
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19
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Lee AR, Che N, Lovnicki JM, Dong X. Development of Neuroendocrine Prostate Cancers by the Ser/Arg Repetitive Matrix 4-Mediated RNA Splicing Network. Front Oncol 2018; 8:93. [PMID: 29666783 PMCID: PMC5891588 DOI: 10.3389/fonc.2018.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE). Recent reports indicate that the overall genomic landscapes of castration-resistant tumors with AdPC phenotypes and CRPC-NE are not significantly altered. However, CRPC-NE tumors have been found to contain a NE-specific pattern throughout their epigenome and splicing transcriptome, which are significantly modified. The molecular mechanisms by which CRPC-NE develops remain unclear, but several factors have been implicated in the progression of the disease. Recently, Ser/Arg repetitive matrix 4 (SRRM4), a neuronal-specific RNA splicing factor that is upregulated in CRPC-NE tumors, has been shown to establish a CRPC-NE-unique splicing transcriptome, to induce a NE-like morphology in AdPC cells, and, most importantly, to transform AdPC cells into CRPC-NE xenografts under ARPI. Moreover, the SRRM4-targeted splicing genes are highly enriched in various neuronal processes, suggesting their roles in facilitating a CRPC-NE program. This article will address the importance of SRRM4-mediated alternative RNA splicing in reprogramming translated proteins to facilitate NE differentiation, survival, and proliferation of cells to establish CRPC-NE tumors. In addition, we will discuss the potential roles of SRRM4 in conjunction with other known pathways and factors important for CRPC-NE development, such as the AR pathway, TP53 and RB1 genes, the FOXA family of proteins, and environmental factors. This study aims to explore the multifaceted functions of SRRM4 and SRRM4-mediated splicing in driving a CRPC-NE program as a coping mechanism for therapy resistance, as well as define future SRRM4-targeted therapeutic approaches for treating CRPC-NE or mitigating its development.
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Affiliation(s)
- Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Che
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jessica M Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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