51
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Du C, Li SW, Singh SX, Roso K, Sun MA, Pirozzi CJ, Yang R, Li JL, He Y. Epigenetic Regulation of Fanconi Anemia Genes Implicates PRMT5 Blockage as a Strategy for Tumor Chemosensitization. Mol Cancer Res 2021; 19:2046-2056. [PMID: 34521764 DOI: 10.1158/1541-7786.mcr-21-0093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/16/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
Strengthened DNA repair pathways in tumor cells contribute to the development of resistance to DNA-damaging agents. Consequently, targeting proteins in these pathways is a promising strategy for tumor chemosensitization. Here, we show that the expression of a subset of Fanconi anemia (FA) genes is attenuated in glioblastoma tumor cells deficient in methylthioadenosine phosphorylase (MTAP), a common genetic alteration in a variety of cancers. Subsequent experiments in cell line models of different cancer types illustrate that this reduced transcription of FA genes can be recapitulated by blockage of Protein Arginine Methyltransferase 5 (PRMT5), a promising therapeutically targetable epigenetic regulator whose enzymatic activity is compromised in MTAP-deficient cells. Further analyses provide evidence to support that PRMT5 can function as an epigenetic regulator that contributes to the increased expression of FA genes in cancer cells. Most notably and consistent with the essential roles of FA proteins in resolving DNA damage elicited by interstrand crosslinking (ICL) agents, PRMT5 blockage, as well as MTAP loss, sensitizes tumor cells to ICL agents both in vitro and in xenografts. Collectively, these findings reveal a novel epigenetic mechanism underlying the upregulated expression of FA genes in cancer cells and suggest that therapeutically targeting PRMT5 can have an additional benefit of chemosensitizing tumor cells to ICL agents. IMPLICATIONS: PRMT5 positively regulates the expression of FA genes. Inhibition of PRMT5 attenuates FA-dependent DNA repair pathway and sensitizes tumor cells to ICL agents.
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Affiliation(s)
- Changzheng Du
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina.,School of Medicine, Southern University of Science and Technology, and Southern University of Science and Technology Hospital, Nanshan District, Shenzhen, Guangdong, China
| | - Steven W Li
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Simranjit X Singh
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina.,Pathology Graduate Program, Duke University Medical Center, Durham, North Carolina
| | - Kristen Roso
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Michael A Sun
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina.,Pathology Graduate Program, Duke University Medical Center, Durham, North Carolina
| | - Christopher J Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Rui Yang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina. .,Department of Pathology, Duke University Medical Center, Durham, North Carolina
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52
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Gao J, Liu R, Feng D, Huang W, Huo M, Zhang J, Leng S, Yang Y, Yang T, Yin X, Teng X, Yu H, Yuan B, Wang Y. Snail/PRMT5/NuRD complex contributes to DNA hypermethylation in cervical cancer by TET1 inhibition. Cell Death Differ 2021; 28:2818-2836. [PMID: 33953349 PMCID: PMC8408166 DOI: 10.1038/s41418-021-00786-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023] Open
Abstract
The biological function of PRMT5 remains poorly understood in cervical cancer metastasis. Here, we report that PRMT5 physically associates with the transcription factor Snail and the NuRD(MTA1) complex to form a transcriptional-repressive complex that catalyzes the symmetrical histone dimethylation and deacetylation. This study shows that the Snail/PRMT5/NuRD(MTA1) complex targets genes, such as TET1 and E-cadherin, which are critical for epithelial-mesenchymal transition (EMT). This complex also affects the conversion of 5mC to 5hmC. This study demonstrates that the Snail/PRMT5/NuRD(MTA1) complex promotes the invasion and metastasis of cervical cancer in vitro and in vivo. This study also shows that PRMT5 expression is upregulated in cervical cancer and various human cancers, and the PRMT5 inhibitor EPZ015666 suppresses EMT and the invasion potential of cervical cancer cells by disinhibiting the expression of TET1 and increasing 5hmC, suggesting that PRMT5 is a potential target for cancer therapy.
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Affiliation(s)
- Jie Gao
- grid.265021.20000 0000 9792 1228Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China ,grid.27255.370000 0004 1761 1174The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Ruiqiong Liu
- grid.27255.370000 0004 1761 1174The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Dandan Feng
- grid.265021.20000 0000 9792 1228Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Huang
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Miaomiao Huo
- grid.506261.60000 0001 0706 7839Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyao Zhang
- grid.506261.60000 0001 0706 7839Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Leng
- grid.265021.20000 0000 9792 1228Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Yang
- grid.265021.20000 0000 9792 1228Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianshu Yang
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xin Yin
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xu Teng
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Hefen Yu
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Baowen Yuan
- grid.506261.60000 0001 0706 7839Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Wang
- grid.265021.20000 0000 9792 1228Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China ,grid.506261.60000 0001 0706 7839Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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53
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Mueller HS, Fowler CE, Dalin S, Moiso E, Udomlumleart T, Garg S, Hemann MT, Lees JA. Acquired resistance to PRMT5 inhibition induces concomitant collateral sensitivity to paclitaxel. Proc Natl Acad Sci U S A 2021; 118:e2024055118. [PMID: 34408017 PMCID: PMC8403834 DOI: 10.1073/pnas.2024055118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Epigenetic regulators play key roles in cancer and are increasingly being targeted for treatment. However, for many, little is known about mechanisms of resistance to the inhibition of these regulators. We have generated a model of resistance to inhibitors of protein arginine methyltransferase 5 (PRMT5). This study was conducted in KrasG12D;Tp53-null lung adenocarcinoma (LUAD) cell lines. Resistance to PRMT5 inhibitors (PRMT5i) arose rapidly, and barcoding experiments showed that this resulted from a drug-induced transcriptional state switch, not selection of a preexisting population. This resistant state is both stable and conserved across variants arising from distinct LUAD lines. Moreover, it brought with it vulnerabilities to other chemotherapeutics, especially the taxane paclitaxel. This paclitaxel sensitivity depended on the presence of stathmin 2 (STMN2), a microtubule regulator that is specifically expressed in the resistant state. Remarkably, STMN2 was also essential for resistance to PRMT5 inhibition. Thus, a single gene is required for both acquisition of resistance to PRMT5i and collateral sensitivity to paclitaxel in our LUAD cells. Accordingly, the combination of PRMT5i and paclitaxel yielded potent and synergistic killing of the murine LUAD cells. Importantly, the synergy between PRMT5i and paclitaxel also extended to human cancer cell lines. Finally, analysis of The Cancer Genome Atlas patient data showed that high STMN2 levels correlate with complete regression of tumors in response to taxane treatment. Collectively, this study reveals a recurring mechanism of PRMT5i resistance in LUAD and identifies collateral sensitivities that have potential clinical relevance.
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Affiliation(s)
- Helen S Mueller
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Colin E Fowler
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Simona Dalin
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Enrico Moiso
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tee Udomlumleart
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Salil Garg
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114
| | - Michael T Hemann
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jacqueline A Lees
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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54
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Genomic Mapping of Splicing-Related Genes Identify Amplifications in LSM1, CLNS1A, and ILF2 in Luminal Breast Cancer. Cancers (Basel) 2021; 13:cancers13164118. [PMID: 34439272 PMCID: PMC8391113 DOI: 10.3390/cancers13164118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary The alternative splicing (AS) process is highly relevant, affecting most of the hallmarks of cancer, such as proliferation, angiogenesis, and metastasis. Our study evaluated alterations in 304 splicing-related genes and their prognosis value in breast cancer patients. Amplifications in CLNS1A, LSM1, and ILF2 genes in luminal patients were significantly associated with poor outcome. Downregulation of these genes in luminal cell lines showed an antiproliferative effect. Pharmacological modulation of transcription and RNA regulation is key for the optimal development of therapeutic strategies against key proteins. Administration of a BET inhibitor and BET-PROTAC reduced the expression of these identified genes and displayed a significant antiproliferative effect on these cell models. In conclusion, we describe novel splicing genes amplified in luminal breast tumors that are associated with detrimental prognosis and can be modulated pharmacologically. It opens the door for further studies confirming the effect of these genes in patients treated with BET inhibitors. Abstract Alternative splicing is an essential biological process, which increases the diversity and complexity of the human transcriptome. In our study, 304 splicing pathway-related genes were evaluated in tumors from breast cancer patients (TCGA dataset). A high number of alterations were detected, including mutations and copy number alterations (CNAs), although mutations were less frequently present compared with CNAs. In the four molecular subtypes, 14 common splice genes showed high level amplification in >5% of patients. Certain genes were only amplified in specific breast cancer subtypes. Most altered genes in each molecular subtype clustered to a few chromosomal regions. In the Luminal subtype, amplifications of LSM1, CLNS1A, and ILF2 showed a strong significant association with prognosis. An even more robust association with OS and RFS was observed when expression of these three genes was combined. Inhibition of LSM1, CLNS1A, and ILF2, using siRNA in MCF7 and T47D cells, showed a decrease in cell proliferation. The mRNA expression of these genes was reduced by treatment with BET inhibitors, a family of epigenetic modulators. We map the presence of splicing-related genes in breast cancer, describing three novel genes, LSM1, CLNS1A, and ILF2, that have an oncogenic role and can be modulated with BET inhibitors.
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55
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, Sellers WR. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell 2021; 81:3481-3495.e7. [PMID: 34358446 DOI: 10.1016/j.molcel.2021.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.
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Affiliation(s)
| | | | | | | | - Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Adam Skepner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Donald Raymond
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Salvatore LaRussa
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - David C McKinney
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | - Dale Porter
- Broad Institute, Cambridge, MA, USA; Cedilla Therapeutics, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian McMillan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA; Tango Therapeutics, Cambridge, MA, USA
| | - William R Sellers
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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56
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Protein arginine methylation: from enigmatic functions to therapeutic targeting. Nat Rev Drug Discov 2021; 20:509-530. [PMID: 33742187 DOI: 10.1038/s41573-021-00159-8] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) are emerging as attractive therapeutic targets. PRMTs regulate transcription, splicing, RNA biology, the DNA damage response and cell metabolism; these fundamental processes are altered in many diseases. Mechanistically understanding how these enzymes fuel and sustain cancer cells, especially in specific metabolic contexts or in the presence of certain mutations, has provided the rationale for targeting them in oncology. Ongoing inhibitor development, facilitated by structural biology, has generated tool compounds for the majority of PRMTs and enabled clinical programmes for the most advanced oncology targets, PRMT1 and PRMT5. In-depth mechanistic investigations using genetic and chemical tools continue to delineate the roles of PRMTs in regulating immune cells and cancer cells, and cardiovascular and neuronal function, and determine which pathways involving PRMTs could be synergistically targeted in combination therapies for cancer. This research is enhancing our knowledge of the complex functions of arginine methylation, will guide future clinical development and could identify new clinical indications.
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57
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Kim H, Kim H, Feng Y, Li Y, Tamiya H, Tocci S, Ronai ZA. PRMT5 control of cGAS/STING and NLRC5 pathways defines melanoma response to antitumor immunity. Sci Transl Med 2021; 12:12/551/eaaz5683. [PMID: 32641491 DOI: 10.1126/scitranslmed.aaz5683] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/08/2020] [Indexed: 12/12/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) controls diverse cellular processes and is implicated in cancer development and progression. Here, we report an inverse correlation between PRMT5 function and antitumor immunity. PRMT5 expression was associated with an antitumor immune gene signature in human melanoma tissue. Reducing PRMT5 activity antagonized melanoma growth in immunocompetent but not immunocompromised mice. PRMT5 methylation of IFI16 [interferon-γ (IFN-γ)-inducible protein 16] or its murine homolog IFI204, which are components of the cGAS/STING (stimulator of IFN genes) pathway, attenuated cytosolic DNA-induced IFN and chemokine expression in melanoma cells. PRMT5 also inhibited transcription of the gene encoding NLRC5 (nucleotide-binding oligomerization domain-like receptor family caspase recruitment domain containing 5), a protein that promotes the expression of genes implicated in major histocompatibility complex class I (MHCI) antigen presentation. PRMT5 knockdown augmented IFN and chemokine production and increased MHCI abundance in melanoma. Increased expression of IFI204 and NLRC5 was associated with decreased melanoma growth in murine models, and increased expression of IFI16 and NLRC5 correlated with prolonged survival of patients with melanoma. Combination of pharmacological (GSK3326595) or genetic (shRNA) inhibition of PRMT5 with immune checkpoint therapy limited growth of murine melanoma tumors (B16F10 and YUMM1.7) and enhanced therapeutic efficacy, compared with the effect of either treatment alone. Overall, our findings provide a rationale to test PRMT5 inhibitors in immunotherapy-based clinical trials as a means to enhance an antitumor immune response.
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Affiliation(s)
- Hyungsoo Kim
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA.
| | - Heejung Kim
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA
| | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA
| | - Yan Li
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA
| | - Hironari Tamiya
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA
| | - Stefania Tocci
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA.,Technion Integrated Cancer Center, Technion, Haifa 3109601, Israel
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 90237, USA.
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58
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Ho JSY, Di Tullio F, Schwarz M, Low D, Incarnato D, Gay F, Tabaglio T, Zhang J, Wollmann H, Chen L, An O, Chan THM, Hall Hickman A, Zheng S, Roudko V, Chen S, Karz A, Ahmed M, He HH, Greenbaum BD, Oliviero S, Serresi M, Gargiulo G, Mann KM, Hernando E, Mulholland D, Marazzi I, Wee DKB, Guccione E. HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness. eLife 2021; 10:e59654. [PMID: 34075878 PMCID: PMC8346284 DOI: 10.7554/elife.59654] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/30/2021] [Indexed: 12/25/2022] Open
Abstract
High spliceosome activity is a dependency for cancer cells, making them more vulnerable to perturbation of the splicing machinery compared to normal cells. To identify splicing factors important for prostate cancer (PCa) fitness, we performed pooled shRNA screens in vitro and in vivo. Our screens identified heterogeneous nuclear ribonucleoprotein M (HNRNPM) as a regulator of PCa cell growth. RNA- and eCLIP-sequencing identified HNRNPM binding to transcripts of key homeostatic genes. HNRNPM binding to its targets prevents aberrant exon inclusion and backsplicing events. In both linear and circular mis-spliced transcripts, HNRNPM preferentially binds to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM-dependent linear-splicing events using splice-switching-antisense-oligonucleotides was sufficient to inhibit PCa cell growth. This suggests that PCa dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Our results have further been confirmed in other solid tumors. Taken together, our data reveal a role for HNRNPM in supporting cancer cell fitness. Inhibition of HNRNPM activity is therefore a potential therapeutic strategy in suppressing growth of PCa and other solid tumors.
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Affiliation(s)
- Jessica SY Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Federico Di Tullio
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Megan Schwarz
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Diana Low
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Danny Incarnato
- IIGM (Italian Institute for Genomic Medicine)TorinoItaly
- Dipartimento di Scienze della Vita e Biologia dei Sistemi Università di TorinoTorinoItaly
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of GroningenGroningenNetherlands
| | - Florence Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - JingXian Zhang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Heike Wollmann
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Alexander Hall Hickman
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- NTU Institute of Structural Biology, Nanyang Technological UniversitySingaporeSingapore
| | - Vladimir Roudko
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Sujun Chen
- Department of Medical Biophysics, University of TorontoTorontoCanada
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
- Ontario Institute for Cancer ResearchTorontoCanada
| | - Alcida Karz
- Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical CenterNew YorkUnited States
- Department of Pathology, New York University Langone Medical CenterNew YorkUnited States
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
| | - Housheng Hansen He
- Department of Medical Biophysics, University of TorontoTorontoCanada
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Pathology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Salvatore Oliviero
- IIGM (Italian Institute for Genomic Medicine)TorinoItaly
- Dipartimento di Scienze della Vita e Biologia dei Sistemi Università di TorinoTorinoItaly
| | - Michela Serresi
- Max Delbruck Center for Molecular MedicineBerlin-BuchGermany
| | | | - Karen M Mann
- Department of Molecular Oncology, Moffitt Cancer CenterTampaUnited States
| | - Eva Hernando
- Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical CenterNew YorkUnited States
- Department of Pathology, New York University Langone Medical CenterNew YorkUnited States
| | - David Mulholland
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Dave Keng Boon Wee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
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59
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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60
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Zhang L, Zhang Y, Hu X. Targeting the transcription cycle and RNA processing in cancer treatment. Curr Opin Pharmacol 2021; 58:69-75. [PMID: 33964728 DOI: 10.1016/j.coph.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022]
Abstract
The transcriptional program and RNA splicing machinery are highly and frequently dysregulated in human cancers due to genomic and epigenomic alterations during tumorigenesis. This leads to cancer-specific dependencies on components of the transcriptional program and RNA splicing machinery, providing alternative and targetable 'Achilles' heels' for cancer treatment in the clinic. To target these vulnerabilities in cancer cells, potent and specific transcriptional CDK inhibitors and chemical compounds that impair splicing have been developed and evaluated in preclinical cancer models. Several novel combination approaches with immune or targeted therapies have also been proposed for cancer treatment. More recently, inhibitors targeting transcriptional CDKs, splicing, or PRMT5 have shown promising therapeutic potential in preclinical studies, and many of them have rapidly advanced into early clinical trials for treatment of human cancer.
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Affiliation(s)
- Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Youyou Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaowen Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
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61
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Firestone RS, Feng M, Basu I, Peregrina K, Augenlicht LH, Schramm VL. Transition state analogue of MTAP extends lifespan of APC Min/+ mice. Sci Rep 2021; 11:8844. [PMID: 33893330 PMCID: PMC8065027 DOI: 10.1038/s41598-021-87734-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/23/2021] [Indexed: 01/03/2023] Open
Abstract
A mouse model of human Familial Adenomatous Polyposis responds favorably to pharmacological inhibition of 5'-methylthioadenosine phosphorylase (MTAP). Methylthio-DADMe-Immucillin-A (MTDIA) is an orally available, transition state analogue inhibitor of MTAP. 5'-Methylthioadenosine (MTA), the substrate for MTAP, is formed in polyamine synthesis and is recycled by MTAP to S-adenosyl-L-methionine (SAM) via salvage pathways. MTDIA treatment causes accumulation of MTA, which inhibits growth of human head and neck (FaDu) and lung (H359, A549) cancers in immunocompromised mouse models. We investigated the efficacy of oral MTDIA as an anti-cancer therapeutic for intestinal adenomas in immunocompetent APCMin/+ mice, a murine model of human Familial Adenomatous Polyposis. Tumors in APCMin/+ mice were decreased in size by MTDIA treatment, resulting in markedly improved anemia and doubling of mouse lifespan. Metabolomic analysis of treated mice showed no changes in polyamine, methionine, SAM or ATP levels when compared with control mice but indicated an increase in MTA, the MTAP substrate. Generation of an MTDIA-resistant cell line in culture showed a four-fold amplification of the methionine adenosyl transferase (MAT2A) locus and expression of this enzyme. MAT2A is downstream of MTAP action and catalyzes synthesis of the SAM necessary for methylation reactions. Immunohistochemical analysis of treated mouse intestinal tissue demonstrated a decrease in symmetric dimethylarginine, a PRMT5-catalyzed modification. The anti-cancer effects of MTDIA indicate that increased cellular MTA inhibits PRMT5-mediated methylations resulting in attenuated tumor growth. Oral dosing of MTDIA as monotherapy has potential for delaying the onset and progression of colorectal cancers in Familial Adenomatous Polyposis (FAP) as well as residual duodenal tumors in FAP patients following colectomy. MTDIA causes a physiologic inactivation of MTAP and may also have efficacy in combination with inhibitors of MAT2A or PRMT5, known synthetic-lethal interactions in MTAP-/- cancer cell lines.
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Affiliation(s)
- Ross S Firestone
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Indranil Basu
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Karina Peregrina
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Leonard H Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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62
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PRMT5: a putative oncogene and therapeutic target in prostate cancer. Cancer Gene Ther 2021; 29:264-276. [PMID: 33854218 DOI: 10.1038/s41417-021-00327-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 11/08/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) was discovered two decades ago. The first decade focused on the biochemical characterization of PRMT5 as a regulator of many cellular processes in a healthy organism. However, over the past decade, evidence has accumulated to suggest that PRMT5 may function as an oncogene in multiple cancers via both epigenetic and non-epigenetic mechanisms. In this review, we focus on recent progress made in prostate cancer, including the role of PRMT5 in the androgen receptor (AR) expression and signaling and DNA damage response, particularly DNA double-strand break repair. We also discuss how PRMT5-interacting proteins that are considered PRMT5 cofactors may cooperate with PRMT5 to regulate PRMT5 activity and target gene expression, and how PRMT5 can interact with other epigenetic regulators implicated in prostate cancer development and progression. Finally, we suggest that targeting PRMT5 may be employed to develop multiple therapeutic approaches to enhance the treatment of prostate cancer.
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63
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Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Res 2021; 31:1106-1119. [PMID: 33832989 PMCID: PMC8168582 DOI: 10.1101/gr.273904.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/01/2021] [Indexed: 12/24/2022]
Abstract
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 (Gabbr1) are highly expressed in mESCs but are absent from the cytoplasm. Instead, incompletely spliced Gabbr1 RNA remains sequestered on chromatin, where it is bound by PTBP1, similar to certain long noncoding RNAs. Upon neuronal differentiation, Gabbr1 RNA becomes fully processed and exported for translation. Thus, splicing repression and chromatin anchoring of RNA combine to allow posttranscriptional regulation of Gabbr1 over development. For this and other genes, polyadenylated RNA abundance does not indicate functional gene expression. Our data sets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
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Affiliation(s)
- Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, California 90095, USA.,Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Han Young Lim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
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64
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Gordon JM, Phizicky DV, Neugebauer KM. Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision. Curr Opin Genet Dev 2021; 67:67-76. [PMID: 33291060 PMCID: PMC8084925 DOI: 10.1016/j.gde.2020.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023]
Abstract
Thousands of genes produce polyadenylated mRNAs that still contain one or more introns. These transcripts are known as retained intron RNAs (RI-RNAs). In the past 10 years, RI-RNAs have been linked to post-transcriptional alternative splicing in a variety of developmental contexts, but they can also be dead-end products fated for RNA decay. Here we discuss the role of intron retention in shaping gene expression programs, as well as recent evidence suggesting that the biogenesis and fate of RI-RNAs is regulated by nuclear organization. We discuss the possibility that proximity of RNA to nuclear speckles - biomolecular condensates that are highly enriched in splicing factors and other RNA binding proteins - is associated with choices ranging from efficient co-transcriptional splicing, export and stability to regulated post-transcriptional splicing and possible vulnerability to decay.
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Affiliation(s)
- Jackson M Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - David V Phizicky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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65
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Samuel SF, Barry A, Greenman J, Beltran-Alvarez P. Arginine methylation: the promise of a 'silver bullet' for brain tumours? Amino Acids 2021; 53:489-506. [PMID: 33404912 PMCID: PMC8107164 DOI: 10.1007/s00726-020-02937-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Despite intense research efforts, our pharmaceutical repertoire against high-grade brain tumours has not been able to increase patient survival for a decade and life expectancy remains at less than 16 months after diagnosis, on average. Inhibitors of protein arginine methyltransferases (PRMTs) have been developed and investigated over the past 15 years and have now entered oncology clinical trials, including for brain tumours. This review collates recent advances in the understanding of the role of PRMTs and arginine methylation in brain tumours. We provide an up-to-date literature review on the mechanisms for PRMT regulation. These include endogenous modulators such as alternative splicing, miRNA, post-translational modifications and PRMT-protein interactions, and synthetic inhibitors. We discuss the relevance of PRMTs in brain tumours with a particular focus on PRMT1, -2, -5 and -8. Finally, we include a future perspective where we discuss possible routes for further research on arginine methylation and on the use of PRMT inhibitors in the context of brain tumours.
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Affiliation(s)
| | - Antonia Barry
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | - John Greenman
- Department of Biomedical Sciences, University of Hull, Hull, UK
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66
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Li WJ, He YH, Yang JJ, Hu GS, Lin YA, Ran T, Peng BL, Xie BL, Huang MF, Gao X, Huang HH, Zhu HH, Ye F, Liu W. Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth. Nat Commun 2021; 12:1946. [PMID: 33782401 PMCID: PMC8007824 DOI: 10.1038/s41467-021-21963-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/12/2021] [Indexed: 02/05/2023] Open
Abstract
Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy. Arginine methyltransferases (PRMTs) are involved in the regulation of various physiological and pathological conditions. Using proteomics, the authors here profile the methylation substrates of PRMTs 4, 5 and 7 and characterize the roles of these enzymes in cancer-associated splicing regulation.
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Affiliation(s)
- Wen-Juan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yao-Hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jing-Jing Yang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yi-An Lin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ting Ran
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Ling Peng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ming-Feng Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Gao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hai-Hua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Helen He Zhu
- Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Ye
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Fujian, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.
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67
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Tyzack GE, Neeves J, Crerar H, Klein P, Ziff O, Taha DM, Luisier R, Luscombe NM, Patani R. Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. Brain 2021; 144:1985-1993. [PMID: 33693641 PMCID: PMC8370440 DOI: 10.1093/brain/awab078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
We recently described aberrantly increased cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as new hallmarks of amyotrophic lateral sclerosis (ALS). However, the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep sequencing of nuclear and cytoplasmic fractions of human induced pluripotent stem cells undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins. Remarkably, TDP-43, SFPQ and FUS—RNA binding proteins known for nuclear-to-cytoplasmic mislocalization in ALS—abundantly and specifically bind to this aberrant cytoplasmic pool of IRTs. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.
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Affiliation(s)
- Giulia E Tyzack
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jacob Neeves
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Hamish Crerar
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Pierre Klein
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Oliver Ziff
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Doaa M Taha
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Zoology Department, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Raphaëlle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, CH - 1920 Martigny, Switzerland
| | - Nicholas M Luscombe
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
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68
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Metz PJ, Ching KA, Xie T, Delgado Cuenca P, Niessen S, Tatlock JH, Jensen-Pergakes K, Murray BW. Symmetric Arginine Dimethylation Is Selectively Required for mRNA Splicing and the Initiation of Type I and Type III Interferon Signaling. Cell Rep 2021; 30:1935-1950.e8. [PMID: 32049022 DOI: 10.1016/j.celrep.2020.01.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/07/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing is well understood to enhance proteome diversity as cells respond to stimuli. However, mechanistic understanding for how the spliceosome processes precursor messenger RNA (mRNA) transcripts to achieve template diversification is incomplete. We use recently developed enzymatic inhibitors of protein arginine methyltransferase 5 (PRMT5) and human naive T lymphocyte activation as a model system to uncover a precise set of mRNA transcripts that require symmetric arginine dimethylation. This methylation-dependent splicing selectivity is associated with a limited set of signaling pathways that are affected when PRMT5 is inhibited. Specifically, we identify a conserved role for symmetric arginine dimethylation in the induction of antiviral type I and type III interferon signaling following T cell receptor and pattern recognition receptor stimulation in human T lymphocytes and undifferentiated human THP-1 monocytes. Altogether, these findings reveal a mechanism by which cells may be enabled to precisely modulate transcript heterogeneity to orchestrate specific functional outcomes.
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Affiliation(s)
- Patrick J Metz
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA.
| | - Keith A Ching
- Computational Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Tao Xie
- Computational Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Paulina Delgado Cuenca
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Sherry Niessen
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - John H Tatlock
- Worldwide Medicinal Chemistry, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Kristen Jensen-Pergakes
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Brion W Murray
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
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69
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Marjon K, Kalev P, Marks K. Cancer Dependencies: PRMT5 and MAT2A in MTAP/p16-Deleted Cancers. ANNUAL REVIEW OF CANCER BIOLOGY 2021. [DOI: 10.1146/annurev-cancerbio-030419-033444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Discovery of targeted therapies that selectively exploit the genetic inactivation of specific tumor suppressors remains a major challenge. This includes the prevalent deletion of the CDKN2A/ MTAP locus, which was first reported nearly 40 years ago. The more recent advent of RNA interference and functional genomic screening technologies led to the identification of hidden collateral lethalities occurring with passenger deletions of MTAP in cancer cells. In particular, small-molecule inhibition of the type II arginine methyltransferase PRMT5 and the S-adenosylmethionine-producing enzyme MAT2A each presents a precision medicine approach for the treatment of patients whose tumors have homozygous loss of MTAP. In this review, we highlight key aspects of MTAP, PRMT5, and MAT2A biology to provide a conceptual framework for developing novel therapeutic strategies in tumors with MTAP deletion and to summarize ongoing efforts to drug PRMT5 and MAT2A.
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Affiliation(s)
- Katya Marjon
- Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Peter Kalev
- Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Kevin Marks
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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70
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Goenka A, Tiek D, Song X, Huang T, Hu B, Cheng SY. The Many Facets of Therapy Resistance and Tumor Recurrence in Glioblastoma. Cells 2021; 10:cells10030484. [PMID: 33668200 PMCID: PMC7995978 DOI: 10.3390/cells10030484] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is the most lethal type of primary brain cancer. Standard care using chemo- and radio-therapy modestly increases the overall survival of patients; however, recurrence is inevitable, due to treatment resistance and lack of response to targeted therapies. GBM therapy resistance has been attributed to several extrinsic and intrinsic factors which affect the dynamics of tumor evolution and physiology thus creating clinical challenges. Tumor-intrinsic factors such as tumor heterogeneity, hypermutation, altered metabolomics and oncologically activated alternative splicing pathways change the tumor landscape to facilitate therapy failure and tumor progression. Moreover, tumor-extrinsic factors such as hypoxia and an immune-suppressive tumor microenvironment (TME) are the chief causes of immunotherapy failure in GBM. Amid the success of immunotherapy in other cancers, GBM has occurred as a model of resistance, thus focusing current efforts on not only alleviating the immunotolerance but also evading the escape mechanisms of tumor cells to therapy, caused by inter- and intra-tumoral heterogeneity. Here we review the various mechanisms of therapy resistance in GBM, caused by the continuously evolving tumor dynamics as well as the complex TME, which cumulatively contribute to GBM malignancy and therapy failure; in an attempt to understand and identify effective therapies for recurrent GBM.
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Affiliation(s)
| | | | | | | | | | - Shi-Yuan Cheng
- Correspondence: ; Tel.: +1-312-503-3043; Fax: +1-312-503-5603
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71
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Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. Nat Commun 2021; 12:979. [PMID: 33579912 PMCID: PMC7881162 DOI: 10.1038/s41467-021-21204-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is a deadly cancer in which cancer stem cells (CSCs) sustain tumor growth and contribute to therapeutic resistance. Protein arginine methyltransferase 5 (PRMT5) has recently emerged as a promising target in GBM. Using two orthogonal-acting inhibitors of PRMT5 (GSK591 or LLY-283), we show that pharmacological inhibition of PRMT5 suppresses the growth of a cohort of 46 patient-derived GBM stem cell cultures, with the proneural subtype showing greater sensitivity. We show that PRMT5 inhibition causes widespread disruption of splicing across the transcriptome, particularly affecting cell cycle gene products. We identify a GBM splicing signature that correlates with the degree of response to PRMT5 inhibition. Importantly, we demonstrate that LLY-283 is brain-penetrant and significantly prolongs the survival of mice with orthotopic patient-derived xenografts. Collectively, our findings provide a rationale for the clinical development of brain penetrant PRMT5 inhibitors as treatment for GBM.
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Affiliation(s)
- Patty Sachamitr
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Jolene C Ho
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Felipe E Ciamponi
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lilian Lee
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naghmeh Rastegar
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | | | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Heather Whetstone
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mathieu Durand
- RNomics Platform, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Kirsten Hart
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Joseph Veyhl
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Wenjun Chen
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Nhat Tran
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Bang-Chi Duong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Ahmed M Aman
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Xinghui Che
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xiaoyang Lan
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Owen Whitley
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Olga Zaslaver
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Laura M Richards
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ian Restall
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Amy Caudy
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Maple Flavored Solutions, LLC, Stony Brook, NY, USA
| | - Hannes L Röst
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Sunit Das
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Cusimano
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
| | - Julian Spears
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Medical Imaging, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - H Artee Luchman
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katlin B Massirer
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
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72
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Kalev P, Hyer ML, Gross S, Konteatis Z, Chen CC, Fletcher M, Lein M, Aguado-Fraile E, Frank V, Barnett A, Mandley E, Goldford J, Chen Y, Sellers K, Hayes S, Lizotte K, Quang P, Tuncay Y, Clasquin M, Peters R, Weier J, Simone E, Murtie J, Liu W, Nagaraja R, Dang L, Sui Z, Biller SA, Travins J, Marks KM, Marjon K. MAT2A Inhibition Blocks the Growth of MTAP-Deleted Cancer Cells by Reducing PRMT5-Dependent mRNA Splicing and Inducing DNA Damage. Cancer Cell 2021; 39:209-224.e11. [PMID: 33450196 DOI: 10.1016/j.ccell.2020.12.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/30/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
The methylthioadenosine phosphorylase (MTAP) gene is located adjacent to the cyclin-dependent kinase inhibitor 2A (CDKN2A) tumor-suppressor gene and is co-deleted with CDKN2A in approximately 15% of all cancers. This co-deletion leads to aggressive tumors with poor prognosis that lack effective, molecularly targeted therapies. The metabolic enzyme methionine adenosyltransferase 2α (MAT2A) was identified as a synthetic lethal target in MTAP-deleted cancers. We report the characterization of potent MAT2A inhibitors that substantially reduce levels of S-adenosylmethionine (SAM) and demonstrate antiproliferative activity in MTAP-deleted cancer cells and tumors. Using RNA sequencing and proteomics, we demonstrate that MAT2A inhibition is mechanistically linked to reduced protein arginine methyltransferase 5 (PRMT5) activity and splicing perturbations. We further show that DNA damage and mitotic defects ensue upon MAT2A inhibition in HCT116 MTAP-/- cells, providing a rationale for combining the MAT2A clinical candidate AG-270 with antimitotic taxanes.
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Affiliation(s)
- Peter Kalev
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Marc L Hyer
- Pharmacology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Stefan Gross
- Biochemistry and Biophysics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Zenon Konteatis
- Chemistry, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Chi-Chao Chen
- Bioinformatics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Mark Fletcher
- Bioinformatics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Max Lein
- Drug Metabolism and Pharmacokinetics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Elia Aguado-Fraile
- Clinical Biomarkers, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Victoria Frank
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Amelia Barnett
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Everton Mandley
- Pharmacology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Joshua Goldford
- Cell Metabolism, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Yue Chen
- Drug Metabolism and Pharmacokinetics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Katie Sellers
- Cell Metabolism, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Sebastian Hayes
- Cell Metabolism, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Kate Lizotte
- Cell Metabolism, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Phong Quang
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Yesim Tuncay
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Michelle Clasquin
- Cell Metabolism, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Rachel Peters
- Toxicology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Jaclyn Weier
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Eric Simone
- Chemistry, Manufacturing and Control, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Joshua Murtie
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA; Pharmacology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Wei Liu
- Bioinformatics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Raj Nagaraja
- Drug Metabolism and Pharmacokinetics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Lenny Dang
- Biochemistry and Biophysics, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Zhihua Sui
- Chemistry, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Scott A Biller
- Chemistry, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Jeremy Travins
- Chemistry, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Kevin M Marks
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA
| | - Katya Marjon
- Biology, Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA.
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73
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Grinev VV, Barneh F, Ilyushonak IM, Nakjang S, Smink J, van Oort A, Clough R, Seyani M, McNeill H, Reza M, Martinez-Soria N, Assi SA, Ramanouskaya TV, Bonifer C, Heidenreich O. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nat Commun 2021; 12:520. [PMID: 33483506 PMCID: PMC7822815 DOI: 10.1038/s41467-020-20848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5'-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.
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Affiliation(s)
- Vasily V. Grinev
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Farnaz Barneh
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Ilya M. Ilyushonak
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Sirintra Nakjang
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Job Smink
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Anita van Oort
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Richard Clough
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Michael Seyani
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Hesta McNeill
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Mojgan Reza
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Natalia Martinez-Soria
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Salam A. Assi
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Tatsiana V. Ramanouskaya
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Constanze Bonifer
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Olaf Heidenreich
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK ,grid.1006.70000 0001 0462 7212Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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74
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Yuan Y, Nie H. Protein arginine methyltransferase 5: a potential cancer therapeutic target. Cell Oncol (Dordr) 2021; 44:33-44. [PMID: 33469838 DOI: 10.1007/s13402-020-00577-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND PRMT5 is a type II protein arginine methyltransferase that methylates histone or non-histone proteins. Arginine methylation by PRMT5 has been implicated in gene transcription, ribosome biogenesis, RNA transport, pre-mRNA splicing and signal transduction. High expression of PRMT5 has been observed in various cancers and PRMT5 overexpression has been reported to improve cancer cell survival, proliferation, migration and metabolism and to inhibit cancer cell apoptosis. In addition, PRMT5 has been found to be required for cancer stem cell survival, self-renewal and differentiation. Several microRNAs have been shown to regulate PRMT5 expression. As PRMT5 has oncogene-like properties, several PRMT5 inhibitors have been used to explore their efficacy as potential drugs for different types of cancer, and three of them are now being tested in clinical trials. CONCLUSIONS In this review, we summarize current knowledge on the role of PRMT5 in cancer development and progression, including its functions and underlying mechanisms. In addition, we highlight the rapid development of PRMT5 inhibitors and summarize ongoing clinical trials for cancer therapy. By affecting both tumor cells and the tumor microenvironment, PRMT5 inhibitors may serve as effective anti-cancer agents, especially when combined with immune therapies.
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Affiliation(s)
- Yuanyang Yuan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, China
| | - Hong Nie
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, China.
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75
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Liang Z, Liu L, Wen C, Jiang H, Ye T, Ma S, Liu X. Clinicopathological and Prognostic Significance of PRMT5 in Cancers: A System Review and Meta-Analysis. Cancer Control 2021; 28:10732748211050583. [PMID: 34758643 PMCID: PMC8591649 DOI: 10.1177/10732748211050583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Since protein arginine methyltransferase 5 (PRMT5) is abnormally expressed in various tumors, in this study we aim to assess the association between PRMT5 and clinicopathological and prognostic features. METHODS Electronic databases including PubMed, Web of Science, Scopus, ScienceDirect, and the Cochrane Library were searched until July 25, 2021. The critical appraisal of the eligible studies was performed using the Newcastle-Ottawa Quality Assessment Scale. Pooled hazard ratios (HR) and pooled odds ratios (OR) were calculated to assess the effect. Engauge Digitizer version 12.1, STATA version 15.1, and R version 4.0.5 were used to obtain and analysis the data. RESULTS A total of 32 original studies covering 15,583 patients were included. In our data, it indicated that high level of PRMT5 was significantly correlated with advanced tumor stage (OR = 2.12, 95% CI: 1.22-3.70, P =.008; I2 = 80.7%) and positively correlated with poor overall survival (HR = 1.59, 95% CI: 1.46-1.73, P < .001; I2 = 50%) and progression-free survival (HR = 1.53, 95% CI: 1.24-1.88, P < .001; I2 = 0%). In addition, sub-group analysis showed that high level of PRMT5 was associated with poor overall survival for such 5 kinds of cancers as hepatocellular carcinoma, pancreatic cancer, breast cancer, gastric cancer, and lung cancer. CONCLUSION For the first time we found PRMT5 was pan-cancerous as a prognostic biomarker and high level of PRMT5 was associated with poor prognosis for certain cancers.
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Affiliation(s)
- Zhenzhen Liang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, 130021, China
| | - Lianchang Liu
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, 130021, China
| | - Chaowei Wen
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Heya Jiang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Tianxia Ye
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Shumei Ma
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiaodong Liu
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, 130021, China
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
- Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, 325035, China
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76
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Jia Z, Yue F, Chen X, Narayanan N, Qiu J, Syed SA, Imbalzano AN, Deng M, Yu P, Hu C, Kuang S. Protein Arginine Methyltransferase PRMT5 Regulates Fatty Acid Metabolism and Lipid Droplet Biogenesis in White Adipose Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002602. [PMID: 33304767 PMCID: PMC7709973 DOI: 10.1002/advs.202002602] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 02/06/2023]
Abstract
The protein arginine methyltransferase 5 (PRMT5) is an emerging regulator of cancer and stem cells including adipogenic progenitors. Here, a new physiological role of PRMT5 in adipocytes and systemic metabolism is reported. Conditional knockout mice were generated to ablate the Prmt5 gene specifically in adipocytes (Prmt5AKO). The Prmt5AKO mice exhibit sex- and depot-dependent progressive lipodystrophy that is more pronounced in females and in visceral (than subcutaneous) white fat. The lipodystrophy and associated energy imbalance, hyperlipidemia, hepatic steatosis, glucose intolerance, and insulin resistance are exacerbated by high-fat-diet. Mechanistically, Prmt5 methylates and releases the transcription elongation factor SPT5 from Berardinelli-Seip congenital lipodystrophy 2 (Bscl2, encoding Seipin) promoter, and Prmt5AKO disrupts Seipin-mediated lipid droplet biogenesis. Prmt5 also methylates Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a) and promotes lipogenic gene expression, and Prmt5AKO suppresses SREBP1a-dependent fatty acid metabolic pathways in adipocytes. Thus, PRMT5 plays a critical role in regulating lipid metabolism and lipid droplet biogenesis in adipocytes.
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Affiliation(s)
- Zhihao Jia
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Feng Yue
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Xiyue Chen
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Naagarajan Narayanan
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Jiamin Qiu
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Meng Deng
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Peng Yu
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
- Medical Big Data CenterSichuan UniversityChengdu610041China
| | - Changdeng Hu
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
| | - Shihuan Kuang
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
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77
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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78
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Tan ZW, Fei G, Paulo JA, Bellaousov S, Martin SES, Duveau DY, Thomas CJ, Gygi SP, Boutz PL, Walker S. O-GlcNAc regulates gene expression by controlling detained intron splicing. Nucleic Acids Res 2020; 48:5656-5669. [PMID: 32329777 PMCID: PMC7261177 DOI: 10.1093/nar/gkaa263] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/18/2020] [Accepted: 04/07/2020] [Indexed: 12/28/2022] Open
Abstract
Intron detention in precursor RNAs serves to regulate expression of a substantial fraction of genes in eukaryotic genomes. How detained intron (DI) splicing is controlled is poorly understood. Here, we show that a ubiquitous post-translational modification called O-GlcNAc, which is thought to integrate signaling pathways as nutrient conditions fluctuate, controls detained intron splicing. Using specific inhibitors of the enzyme that installs O-GlcNAc (O-GlcNAc transferase, or OGT) and the enzyme that removes O-GlcNAc (O-GlcNAcase, or OGA), we first show that O-GlcNAc regulates splicing of the highly conserved detained introns in OGT and OGA to control mRNA abundance in order to buffer O-GlcNAc changes. We show that OGT and OGA represent two distinct paradigms for how DI splicing can control gene expression. We also show that when DI splicing of the O-GlcNAc-cycling genes fails to restore O-GlcNAc homeostasis, there is a global change in detained intron levels. Strikingly, almost all detained introns are spliced more efficiently when O-GlcNAc levels are low, yet other alternative splicing pathways change minimally. Our results demonstrate that O-GlcNAc controls detained intron splicing to tune system-wide gene expression, providing a means to couple nutrient conditions to the cell's transcriptional regime.
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Affiliation(s)
- Zhi-Wei Tan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - George Fei
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Sara E S Martin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Damien Y Duveau
- National Institutes of Health Chemical Genomics Center, Rockville, MD 20850, USA
| | - Craig J Thomas
- National Institutes of Health Chemical Genomics Center, Rockville, MD 20850, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Paul L Boutz
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.,Center for Biomedical Informatics, University of Rochester, Rochester, NY 14642, USA.,Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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79
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Parra M, Zhang W, Vu J, DeWitt M, Conboy JG. Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts. RNA (NEW YORK, N.Y.) 2020; 26:996-1005. [PMID: 32312846 PMCID: PMC7373989 DOI: 10.1261/rna.075028.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
The decoy exon model has been proposed to regulate a subset of intron retention (IR) events involving predominantly larger introns (>1 kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides may be able to block decoy splice sites in endogenous pre-mRNA, thereby reducing IR and increasing productive gene expression. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from ∼80% to ∼20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since antisense targeting of decoy 5' splice sites greatly reduced (SNRNP70) or nearly eliminated (SF3B1) IR in two widely expressed splicing factors, and also greatly reduced IR in transcripts encoding the erythroid-specific structural protein, α-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR and suggest that dynamic regulation of decoy exons could be a mechanism to fine-tune gene expression post-transcriptionally in many cell types.
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Affiliation(s)
- Marilyn Parra
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Weiguo Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jonathan Vu
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Mark DeWitt
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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80
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Cherry S, Lynch KW. Alternative splicing and cancer: insights, opportunities, and challenges from an expanding view of the transcriptome. Genes Dev 2020; 34:1005-1016. [PMID: 32747477 PMCID: PMC7397854 DOI: 10.1101/gad.338962.120] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over the past decade there has been increased awareness of the potential role of alternative splicing in the etiology of cancer. In particular, advances in RNA-Sequencing technology and analysis has led to a wave of discoveries in the last few years regarding the causes and functional relevance of alternative splicing in cancer. Here we discuss the current understanding of the connections between splicing and cancer, with a focus on the most recent findings. We also discuss remaining questions and challenges that must be addressed in order to use our knowledge of splicing to guide the diagnosis and treatment of cancer.
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Affiliation(s)
- Sara Cherry
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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81
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Protein Arginine Methyltransferase 5 as a Therapeutic Target for KRAS Mutated Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12082091. [PMID: 32731506 PMCID: PMC7465151 DOI: 10.3390/cancers12082091] [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: 06/30/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Nearly 45% of colorectal cancer (CRC) patients harbor a mutation in their KRAS gene for which, despite many years of research, there are still no targeted therapies available. Protein Arginine Methyltransferase 5 (PRMT5) is a transcription regulator for multiple cellular processes that is currently being tested as a potential target in several cancer types. PRMT5 has been previously shown to be overexpressed in approximately 75% of CRC patient tumor samples, as well as negatively correlated with CRC patient survival. Here, we provide evidence that PRMT5 can act as a surrogate target for mutated KRAS in CRC. Our findings show that PRMT5 expression is upregulated, as well as positively correlated with KRAS expression, in CRC patient datasets. Moreover, our results reveal that PRMT5 is further overexpressed in KRAS mutant CRC cells when compared to KRAS wild type (WT) CRC cells at both the transcriptional and translational levels. Additionally, our data demonstrate that this further overexpression of PRMT5 in the KRAS mutant CRC cells affects an even greater degree of growth inhibition, apoptosis, and cell cycle arrest, following treatment with PRMT5 inhibitor, when compared to the KRAS WT CRC cells. Our research therefore suggests for the first time that PRMT5 and KRAS may crosstalk, and thus, PRMT5 can potentially be used as a surrogate target for mutated KRAS in CRC.
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82
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Barczak W, Jin L, Carr SM, Munro S, Ward S, Kanapin A, Samsonova A, La Thangue NB. PRMT5 promotes cancer cell migration and invasion through the E2F pathway. Cell Death Dis 2020; 11:572. [PMID: 32709847 PMCID: PMC7382496 DOI: 10.1038/s41419-020-02771-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022]
Abstract
The pRb-E2F pathway is a critical point of regulation in the cell cycle and loss of control of the pathway is a hallmark of cancer. E2F1 is the major target through which pRb exerts its effects and arginine methylation by PRMT5 plays a key role in dictating E2F1 activity. Here we have explored the functional role of the PRMT5-E2F1 axis and highlight its influence on different aspects of cancer cell biology including viability, migration, invasion and adherence. Through a genome-wide expression analysis, we identified a distinct set of genes under the control of PRMT5 and E2F1, including some highly regulated genes, which influence cell migration, invasio and adherence through a PRMT5-dependent mechanism. Most significantly, a coincidence was apparent between the expression of PRMT5 and E2F1 in human tumours, and elevated levels of PRMT5 and E2F1 correlated with poor prognosis disease. Our results suggest a causal relationship between PRMT5 and E2F1 in driving the malignant phenotype and thereby highlight an important pathway for therapeutic intervention.
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Affiliation(s)
- Wojciech Barczak
- Laboratory of Cancer Biology Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Li Jin
- Laboratory of Cancer Biology Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Simon Mark Carr
- Laboratory of Cancer Biology Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Shonagh Munro
- Argonaut Therapeutics Ltd Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK
| | - Samuel Ward
- Argonaut Therapeutics Ltd Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK
| | - Alexander Kanapin
- Centre for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Anastasia Samsonova
- Centre for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Nicholas B La Thangue
- Laboratory of Cancer Biology Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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83
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Abstract
Protein methyl transferases play critical roles in numerous regulatory pathways that underlie cancer development, progression and therapy-response. Here we discuss the function of PRMT5, a member of the nine-member PRMT family, in controlling oncogenic processes including tumor intrinsic, as well as extrinsic microenvironmental signaling pathways. We discuss PRMT5 effect on histone methylation and methylation of regulatory proteins including those involved in RNA splicing, cell cycle, cell death and metabolic signaling. In all, we highlight the importance of PRMT5 regulation and function in cancer, which provide the foundation for therapeutic modalities targeting PRMT5.
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Affiliation(s)
- Hyungsoo Kim
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
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84
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Yue L, Wan R, Luan S, Zeng W, Cheung TH. Dek Modulates Global Intron Retention during Muscle Stem Cells Quiescence Exit. Dev Cell 2020; 53:661-676.e6. [DOI: 10.1016/j.devcel.2020.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/06/2020] [Accepted: 05/09/2020] [Indexed: 12/21/2022]
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85
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Zhou Y, Han C, Wang E, Lorch AH, Serafin V, Cho BK, Gutierrez Diaz BT, Calvo J, Fang C, Khodadadi-Jamayran A, Tabaglio T, Marier C, Kuchmiy A, Sun L, Yacu G, Filip SK, Jin Q, Takahashi YH, Amici DR, Rendleman EJ, Rawat R, Bresolin S, Paganin M, Zhang C, Li H, Kandela I, Politanska Y, Abdala-Valencia H, Mendillo ML, Zhu P, Palhais B, Van Vlierberghe P, Taghon T, Aifantis I, Goo YA, Guccione E, Heguy A, Tsirigos A, Wee KB, Mishra RK, Pflumio F, Accordi B, Basso G, Ntziachristos P. Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia. Cancer Discov 2020; 10:1388-1409. [PMID: 32444465 DOI: 10.1158/2159-8290.cd-19-1436] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/21/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
Splicing alterations are common in diseases such as cancer, where mutations in splicing factor genes are frequently responsible for aberrant splicing. Here we present an alternative mechanism for splicing regulation in T-cell acute lymphoblastic leukemia (T-ALL) that involves posttranslational stabilization of the splicing machinery via deubiquitination. We demonstrate there are extensive exon skipping changes in disease, affecting proteasomal subunits, cell-cycle regulators, and the RNA machinery. We present that the serine/arginine-rich splicing factors (SRSF), controlling exon skipping, are critical for leukemia cell survival. The ubiquitin-specific peptidase 7 (USP7) regulates SRSF6 protein levels via active deubiquitination, and USP7 inhibition alters the exon skipping pattern and blocks T-ALL growth. The splicing inhibitor H3B-8800 affects splicing of proteasomal transcripts and proteasome activity and acts synergistically with proteasome inhibitors in inhibiting T-ALL growth. Our study provides the proof-of-principle for regulation of splicing factors via deubiquitination and suggests new therapeutic modalities in T-ALL. SIGNIFICANCE: Our study provides a new proof-of-principle for posttranslational regulation of splicing factors independently of mutations in aggressive T-cell leukemia. It further suggests a new drug combination of splicing and proteasomal inhibitors, a concept that might apply to other diseases with or without mutations affecting the splicing machinery.This article is highlighted in the In This Issue feature, p. 1241.
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Affiliation(s)
- Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Adam H Lorch
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Blanca T Gutierrez Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Julien Calvo
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christian Marier
- Genome Technology Center, New York University School of Medicine, New York, New York
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Limin Sun
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - George Yacu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Szymon K Filip
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Radhika Rawat
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Silvia Bresolin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Maddalena Paganin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Yuliya Politanska
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hiam Abdala-Valencia
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Bruno Palhais
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Ernesto Guccione
- Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adriana Heguy
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Genome Technology Center, New York University School of Medicine, New York, New York
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Keng Boon Wee
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Rama K Mishra
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Center for Molecular Innovation and Drug Discovery, Northwestern University, Chicago, Illinois
| | - Francoise Pflumio
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Benedetta Accordi
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois. .,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
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86
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Wang E, Aifantis I. RNA Splicing and Cancer. Trends Cancer 2020; 6:631-644. [PMID: 32434734 DOI: 10.1016/j.trecan.2020.04.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/01/2023]
Abstract
RNA splicing is an essential process that governs many aspects of cellular proliferation, survival, and differentiation. Considering the importance of RNA splicing in gene regulation, alterations in this pathway have been implicated in many human cancers. Large-scale genomic studies have uncovered a spectrum of splicing machinery mutations that contribute to tumorigenesis. Moreover, cancer cells are capable of hijacking the expression of RNA-binding proteins (RBPs), leading to dysfunctional gene splicing and tumor-specific dependencies. Advances in next-generation RNA sequencing have revealed tumor-specific isoforms associated with these alterations, including the presence of neoantigens, which serve as potential immunotherapeutic targets. In this review, we discuss the various mechanisms by which cancer cells exploit RNA splicing to promote tumor growth and the current therapeutic landscape for splicing-based therapies.
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Affiliation(s)
- Eric Wang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
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87
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Zhang Y, Liu Y, Liu H, Zhao Z, Wu F, Zeng F. Clinical and Biological Significances of a Methyltransferase-Related Signature in Diffuse Glioma. Front Oncol 2020; 10:508. [PMID: 32373523 PMCID: PMC7185060 DOI: 10.3389/fonc.2020.00508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/20/2020] [Indexed: 12/17/2022] Open
Abstract
Methylation of DNA, RNA or protein is a reversible modification. The proteins and genes that regulate this modification can be a candidate target for tumor therapy. However, the characteristics of methyltransferase related genes in glioma remain obscure. In this study, we systematically analyzed the relationship between methyltransferase-related genes expression profiles and outcomes in glioma patients based on The Cancer Genome Atlas and Chinese Glioma Genome Atlas RNA sequencing datasets. Consensus clustering identified two robust groups with significantly different pathological features and prognosis. Then a methyltransferase-related risk signature was built by a Cox proportional hazards model with elastic net penalty. Moreover, the risk score is associated with patients' clinical and molecular features and can be used as an independent prognostic indicator for patients with glioma. Furthermore, genes associated with the high-risk group were involved in various aspects of the malignant progression of glioma via Gene Ontology analysis and Gene Set Enrichment Analysis. In summary, our study identified a methyltransferase-related risk signature for predicting the prognosis of gliomas.
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Affiliation(s)
- Ying Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Hanjie Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Fan Zeng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
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88
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 379] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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89
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Tan DQ, Li Y, Yang C, Li J, Tan SH, Chin DWL, Nakamura-Ishizu A, Yang H, Suda T. PRMT5 Modulates Splicing for Genome Integrity and Preserves Proteostasis of Hematopoietic Stem Cells. Cell Rep 2020; 26:2316-2328.e6. [PMID: 30811983 DOI: 10.1016/j.celrep.2019.02.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/26/2018] [Accepted: 02/01/2019] [Indexed: 12/15/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is essential for hematopoiesis, while PRMT5 inhibition remains a promising therapeutic strategy against various cancers. Here, we demonstrate that hematopoietic stem cell (HSC) quiescence and viability are severely perturbed upon PRMT5 depletion, which also increases HSC size, PI3K/AKT/mechanistic target of rapamycin (mTOR) pathway activity, and protein synthesis rate. We uncover a critical role for PRMT5 in maintaining HSC genomic integrity by modulating splicing of genes involved in DNA repair. We found that reducing PRMT5 activity upregulates exon skipping and intron retention events that impair gene expression. Genes across multiple DNA repair pathways are affected, several of which mediate interstrand crosslink repair and homologous recombination. Consequently, loss of PRMT5 activity leads to endogenous DNA damage that triggers p53 activation, induces apoptosis, and culminates in rapid HSC exhaustion, which is significantly delayed by p53 depletion. Collectively, these findings establish the importance of cell-intrinsic PRMT5 activity in HSCs.
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Affiliation(s)
- Darren Qiancheng Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Desmond Wai Loon Chin
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ayako Nakamura-Ishizu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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90
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Webb LM, Sengupta S, Edell C, Piedra-Quintero ZL, Amici SA, Miranda JN, Bevins M, Kennemer A, Laliotis G, Tsichlis PN, Guerau-de-Arellano M. Protein arginine methyltransferase 5 promotes cholesterol biosynthesis-mediated Th17 responses and autoimmunity. J Clin Invest 2020; 130:1683-1698. [PMID: 32091410 PMCID: PMC7108896 DOI: 10.1172/jci131254] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) catalyzes symmetric dimethylation (SDM) of arginine, a posttranslational modification involved in oncogenesis and embryonic development. However, the role and mechanisms by which PRMT5 modulates Th cell polarization and autoimmune disease have not yet been elucidated. Here, we found that PRMT5 promoted SREBP1 SDM and the induction of cholesterol biosynthetic pathway enzymes that produce retinoid-related orphan receptor (ROR) agonists that activate RORγt. Specific loss of PRMT5 in the CD4+ Th cell compartment suppressed Th17 differentiation and protected mice from developing experimental autoimmune encephalomyelitis (EAE). We also found that PRMT5 controlled thymic and peripheral homeostasis in the CD4+ Th cell life cycle and invariant NK (iNK) T cell development and CD8+ T cell maintenance. This work demonstrates that PRMT5 expression in recently activated T cells is necessary for the cholesterol biosynthesis metabolic gene expression program that generates RORγt agonistic activity and promotes Th17 differentiation and EAE. These results point to Th PRMT5 and its downstream cholesterol biosynthesis pathway as promising therapeutic targets in Th17-mediated diseases.
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MESH Headings
- Animals
- Autoimmunity
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/pathology
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cholesterol/genetics
- Cholesterol/immunology
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Mice
- Mice, Transgenic
- Natural Killer T-Cells/immunology
- Natural Killer T-Cells/pathology
- Nuclear Receptor Subfamily 1, Group F, Member 3/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/immunology
- Protein-Arginine N-Methyltransferases/genetics
- Protein-Arginine N-Methyltransferases/immunology
- Sterol Regulatory Element Binding Protein 1/genetics
- Sterol Regulatory Element Binding Protein 1/immunology
- Th17 Cells/immunology
- Th17 Cells/pathology
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Affiliation(s)
- Lindsay M Webb
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Biomedical Sciences Graduate Program, and
| | - Shouvonik Sengupta
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Biomedical Sciences Graduate Program, and
| | - Claudia Edell
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Zayda L Piedra-Quintero
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Stephanie A Amici
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Janiret Narvaez Miranda
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | | | - Austin Kennemer
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Georgios Laliotis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University Comprehensive Cancer Center
| | - Philip N Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University Comprehensive Cancer Center
| | - Mireia Guerau-de-Arellano
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Institute for Behavioral Medicine Research
- Department of Microbial Infection and Immunity, and
- Department of Neuroscience, The Ohio State University, Columbus, Ohio, USA
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91
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Ullrich S, Guigó R. Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development. Nucleic Acids Res 2020; 48:1327-1340. [PMID: 31879760 PMCID: PMC7026658 DOI: 10.1093/nar/gkz1180] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 12/02/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previously reported granulocytes. During B-cell differentiation, we found an increase in IR from the bone marrow precursors to cells residing in secondary lymphoid organs. B-cells that undergo affinity maturation to become antibody producing plasma cells steadily decrease retention. In general, we found an inverse relationship between global IR levels and both the proliferative state of cells, and the global levels of expression of splicing factors. IR dynamics during B-cell differentiation appear to be conserved between human and mouse, suggesting that IR plays an important biological role, evolutionary conserved, during blood cell differentiation. By correlating the expression of non-core splicing factors with global IR levels, and analyzing RNA binding protein knockdown and eCLIP data, we identify a few splicing factors likely playing an evolutionary conserved role in IR regulation. Our work provides new insights into the role of IR during hematopoiesis, and on the main factors involved in regulating IR.
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Affiliation(s)
- Sebastian Ullrich
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
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92
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Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN. Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Nat Commun 2020; 11:1438. [PMID: 32188845 PMCID: PMC7080807 DOI: 10.1038/s41467-020-15171-6] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/06/2020] [Indexed: 01/01/2023] Open
Abstract
While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations. We report nanopore sequencing of full-length cDNA from CLL samples with and without SF3B1 mutation, as well as normal B cell samples, giving a total of 149 million pass reads. We present FLAIR (Full-Length Alternative Isoform analysis of RNA), a computational workflow to identify high-confidence transcripts, perform differential splicing event analysis, and differential isoform analysis. Using nanopore reads, we demonstrate differential 3' splice site changes associated with SF3B1 mutation, agreeing with previous studies. We also observe a strong downregulation of intron retention events associated with SF3B1 mutation. Full-length transcript analysis links multiple alternative splicing events together and allows for better estimates of the abundance of productive versus unproductive isoforms. Our work demonstrates the potential utility of nanopore sequencing for cancer and splicing research.
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Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Cameron M Soulette
- Department of Molecular Cell & Developmental Biology, University of California, Santa Cruz, CA, 95062, USA
| | - Marijke J van Baren
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Kevyn Hart
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institiute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA.
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93
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The X-linked trichothiodystrophy-causing gene RNF113A links the spliceosome to cell survival upon DNA damage. Nat Commun 2020; 11:1270. [PMID: 32152280 PMCID: PMC7062854 DOI: 10.1038/s41467-020-15003-7] [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: 01/24/2019] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
Prolonged cell survival occurs through the expression of specific protein isoforms generated by alternate splicing of mRNA precursors in cancer cells. How alternate splicing regulates tumor development and resistance to targeted therapies in cancer remain poorly understood. Here we show that RNF113A, whose loss-of-function causes the X-linked trichothiodystrophy, is overexpressed in lung cancer and protects from Cisplatin-dependent cell death. RNF113A is a RNA-binding protein which regulates the splicing of multiple candidates involved in cell survival. RNF113A deficiency triggers cell death upon DNA damage through multiple mechanisms, including apoptosis via the destabilization of the prosurvival protein MCL-1, ferroptosis due to enhanced SAT1 expression, and increased production of ROS due to altered Noxa1 expression. RNF113A deficiency circumvents the resistance to Cisplatin and to BCL-2 inhibitors through the destabilization of MCL-1, which thus defines spliceosome inhibitors as a therapeutic approach to treat tumors showing acquired resistance to specific drugs due to MCL-1 stabilization. Alternate splicing of mRNA precursors has been linked to tumor development. Here the authors reveal a role of the E3 ligase RNF113A in spliceosome regulation affecting cell survival upon DNA damage.
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94
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Broseus L, Ritchie W. Challenges in detecting and quantifying intron retention from next generation sequencing data. Comput Struct Biotechnol J 2020; 18:501-508. [PMID: 32206209 PMCID: PMC7078297 DOI: 10.1016/j.csbj.2020.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/29/2019] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computational assumptions that may lead to dramatically different results. We describe the various approaches for mitigating errors in detecting intron retention and for discovering IR signatures between different conditions.
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95
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Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J 2020; 39:e102729. [PMID: 31782550 PMCID: PMC6996502 DOI: 10.15252/embj.2019102729] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de-phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.
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Grants
- JP26113002 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06279 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17H03630 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17K19335 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP19K06478 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
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Affiliation(s)
| | - Shungo Adachi
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Tohru Natsume
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Junichi Iwakiri
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Goro Terai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Kiyoshi Asai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Tetsuro Hirose
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
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96
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Ge L, Wang H, Xu X, Zhou Z, He J, Peng W, Du F, Zhang Y, Gong A, Xu M. PRMT5 promotes epithelial-mesenchymal transition via EGFR-β-catenin axis in pancreatic cancer cells. J Cell Mol Med 2020; 24:1969-1979. [PMID: 31851779 PMCID: PMC6991680 DOI: 10.1111/jcmm.14894] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/13/2019] [Accepted: 11/16/2019] [Indexed: 12/17/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) has been implicated in the development and progression of human cancers. However, few studies reveal its role in epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. In this study, we find that PRMT5 is up-regulated in pancreatic cancer, and promotes proliferation, migration and invasion in pancreatic cancer cells, and promotes tumorigenesis. Silencing PRMT5 induces epithelial marker E-cadherin expression and down-regulates expression of mesenchymal markers including Vimentin, collagen I and β-catenin in PaTu8988 and SW1990 cells, whereas ectopic PRMT5 re-expression partially reverses these changes, indicating that PRMT5 promotes EMT in pancreatic cancer. More importantly, we find that PRMT5 knockdown decreases the phosphorylation level of EGFR at Y1068 and Y1172 and its downstream p-AKT and p-GSK3β, and then results in down-regulation of β-catenin. Expectedly, ectopic PRMT5 re-expression also reverses the above changes. It is suggested that PRMT5 promotes EMT probably via EGFR/AKT/β-catenin pathway. Taken together, our study demonstrates that PRMT5 plays oncogenic roles in the growth of pancreatic cancer cell and provides a potential candidate for pancreatic cancer treatment.
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Affiliation(s)
- Lu Ge
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
- Department of GastroenterologyDanyang People's HospitalZhenjiangChina
| | - Huizhi Wang
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
| | - Xiao Xu
- Department of Cell BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Zhengrong Zhou
- Department of Cell BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Junbo He
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
| | - Wanxin Peng
- Department of Cell BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Fengyi Du
- Department of Cell BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Youli Zhang
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
| | - Aihua Gong
- Department of Cell BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Min Xu
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
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97
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Splicing Dysregulation as Oncogenic Driver and Passenger Factor in Brain Tumors. Cells 2019; 9:cells9010010. [PMID: 31861467 PMCID: PMC7016899 DOI: 10.3390/cells9010010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/21/2022] Open
Abstract
Brain tumors are a heterogeneous group of neoplasms ranging from almost benign to highly aggressive phenotypes. The malignancy of these tumors mostly relies on gene expression reprogramming, which is frequently accompanied by the aberrant regulation of RNA processing mechanisms. In brain tumors, defects in alternative splicing result either from the dysregulation of expression and activity of splicing factors, or from mutations in the genes encoding splicing machinery components. Aberrant splicing regulation can generate dysfunctional proteins that lead to modification of fundamental physiological cellular processes, thus contributing to the development or progression of brain tumors. Herein, we summarize the current knowledge on splicing abnormalities in brain tumors and how these alterations contribute to the disease by sustaining proliferative signaling, escaping growth suppressors, or establishing a tumor microenvironment that fosters angiogenesis and intercellular communications. Lastly, we review recent efforts aimed at developing novel splicing-targeted cancer therapies, which employ oligonucleotide-based approaches or chemical modulators of alternative splicing that elicit an impact on brain tumor biology.
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98
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Ferreira de Freitas R, Ivanochko D, Schapira M. Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor. Molecules 2019; 24:E4492. [PMID: 31817960 PMCID: PMC6943651 DOI: 10.3390/molecules24244492] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Protein methyltransferases (PMTs) are enzymes involved in epigenetic mechanisms, DNA repair, and other cellular machineries critical to cellular identity and function, and are an important target class in chemical biology and drug discovery. Central to the enzymatic reaction is the transfer of a methyl group from the cofactor S-adenosylmethionine (SAM) to a substrate protein. Here we review how the essentiality of SAM for catalysis is exploited by chemical inhibitors. Occupying the cofactor binding pocket to compete with SAM can be hindered by the hydrophilic nature of this site, but structural studies of compounds now in the clinic revealed that inhibitors could either occupy juxtaposed pockets to overlap minimally, but sufficiently with the bound cofactor, or induce large conformational remodeling leading to a more druggable binding site. Rather than competing with the cofactor, other inhibitors compete with the substrate and rely on bound SAM, either to allosterically stabilize the substrate binding site, or for direct SAM-inhibitor interactions.
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Affiliation(s)
- Renato Ferreira de Freitas
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP 09606-070, Brazil
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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99
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Tiek DM, Khatib SA, Trepicchio CJ, Heckler MM, Divekar SD, Sarkaria JN, Glasgow E, Riggins RB. Estrogen-related receptor β activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma. FASEB J 2019; 33:13476-13491. [PMID: 31570001 PMCID: PMC6894094 DOI: 10.1096/fj.201901075r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/26/2019] [Indexed: 11/11/2022]
Abstract
Glioblastoma (GBM; grade 4 glioma) is a highly aggressive and incurable tumor. GBM has recently been characterized as highly dependent on alternative splicing, a critical driver of tumor heterogeneity and plasticity. Estrogen-related receptor β (ERR-β) is an orphan nuclear receptor expressed in the brain, where alternative splicing of the 3' end of the pre-mRNA leads to the production of 3 validated ERR-β protein products: ERR-β short form (ERR-βsf), ERR-β2, and ERR-β exon 10 deleted. Our prior studies have shown the ERR-β2 isoform to play a role in G2/M cell cycle arrest and induction of apoptosis, in contrast to the function of the shorter ERR-βsf isoform in senescence and G1 cell cycle arrest. In this study, we sought to better define the role of the proapoptotic ERR-β2 isoform in GBM. We show that the ERR-β2 isoform is located not only in the nucleus but also in the cytoplasm. ERR-β2 suppresses GBM cell migration and interacts with the actin nucleation-promoting factor cortactin, and an ERR-β agonist is able to remodel the actin cytoskeleton and similarly suppress GBM cell migration. We further show that inhibition of the splicing regulatory cdc2-like kinases in combination with an ERR-β agonist shifts isoform expression in favor of ERR-β2 and potentiates inhibition of growth and migration in GBM cells and intracranial tumors.-Tiek, D. M., Khatib, S. A., Trepicchio, C. J., Heckler, M. M., Divekar, S. D., Sarkaria, J. N., Glasgow, E., Riggins, R. B. Estrogen-related receptor β activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma.
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Affiliation(s)
- Deanna M. Tiek
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Subreen A. Khatib
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland, USA; and
| | - Colin J. Trepicchio
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Mary M. Heckler
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Shailaja D. Divekar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Jann N. Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric Glasgow
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rebecca B. Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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100
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Owens JL, Beketova E, Liu S, Tinsley SL, Asberry AM, Deng X, Huang J, Li C, Wan J, Hu CD. PRMT5 Cooperates with pICln to Function as a Master Epigenetic Activator of DNA Double-Strand Break Repair Genes. iScience 2019; 23:100750. [PMID: 31884170 PMCID: PMC6941881 DOI: 10.1016/j.isci.2019.100750] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/06/2019] [Accepted: 11/22/2019] [Indexed: 01/21/2023] Open
Abstract
DNA double-strand break (DSB) repair is critical for cell survival and genome integrity. Upon recognition of DSBs, repair proteins are transiently upregulated to facilitate repair through homologous recombination (HR) or non-homologous end joining (NHEJ). We present evidence that PRMT5 cooperates with pICln to function as a master epigenetic activator of DNA damage response (DDR) genes involved in HR, NHEJ, and G2 arrest (including RAD51, BRCA1, and BRCA2) to upregulate gene expression upon DNA damage. Contrary to the predominant role of PRMT5 as an epigenetic repressor, our results demonstrate that PRMT5 and pICln can activate gene expression, potentially independent of PRMT5's obligate cofactor MEP50. Targeting PRMT5 or pICln hinders repair of DSBs in multiple cancer cell lines, and both PRMT5 and pICln expression positively correlates with DDR genes across 32 clinical cancer datasets. Thus, targeting PRMT5 or pICln may be explored in combination with radiation or chemotherapy for cancer treatment. PRMT5 activates transcription of DSB repair genes upon DNA damage pICln cooperates with PRMT5 to activate transcription of DSB repair genes Targeting PRMT5 is effective to sensitize multiple cancer types to radiation PRMT5 expression positively correlates with DSB repair genes in cancer tissues
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Affiliation(s)
- Jake L Owens
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Elena Beketova
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Samantha L Tinsley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew M Asberry
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN 47907, USA
| | - Xuehong Deng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, University of Florida College of Pharmacy, Gainesville, FL 32610, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA; The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University - Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Chang-Deng Hu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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