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Gao Y, Lin KT, Jiang T, Yang Y, Rahman MA, Gong S, Bai J, Wang L, Sun J, Sheng L, Krainer AR, Hua Y. Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA. Nucleic Acids Res 2022; 50:731-749. [PMID: 35018432 PMCID: PMC8789036 DOI: 10.1093/nar/gkab1280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5′ splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action.
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Affiliation(s)
- Yuan Gao
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Tao Jiang
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Yang Yang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Mohammad A Rahman
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Shuaishuai Gong
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Junjie Sun
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Lei Sheng
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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3
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Rosen SM, Joshi M, Hitt T, Beggs AH, Agrawal PB. Knockin mouse model of the human CFL2 p.A35T mutation results in a unique splicing defect and severe myopathy phenotype. Hum Mol Genet 2021; 29:1996-2003. [PMID: 32160286 DOI: 10.1093/hmg/ddaa035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
Cofilin-2 is an actin-binding protein that is predominantly expressed in skeletal and cardiac muscles and belongs to the AC group of proteins, which includes cofilin-1 and destrin. In humans, cofilin-2 (CFL2) mutations have been associated with congenital myopathies that include nemaline and myofibrillar myopathy. To understand the pathogenicity of the human CFL2 mutation, p.A35T, that first linked cofilin-2 with the human disease, we created a knock-in mouse model. The Cfl2A35T/A35T (KI) mice were indistinguishable from their wild-type littermates at birth, but they rapidly worsened and died by postnatal day 9. The phenotypic, histopathologic and molecular findings mimicked the constitutive Cfl2-knockout (KO) mice described previously, including sarcomeric disruption and actin accumulations in skeletal muscles and negligible amounts of cofilin-2 protein. In addition, KI mice demonstrated a marked reduction in Cfl2 mRNA levels in various tissues including skeletal muscles. Further investigation revealed evidence of alternative splicing with the presence of two alternate transcripts of smaller size. These alternate transcripts were expressed at very low levels in the wild-type mice and were significantly upregulated in the mutant mice, indicating that pre-translational splicing defects may be a critical component of the disease mechanism associated with the mutation. Evidence of reduced expression of the full-length CFL2 transcript was also observed in the muscle biopsy sample of the patient with p.A35T mutation.
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Affiliation(s)
- Samantha M Rosen
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mugdha Joshi
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Talia Hitt
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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6
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Westbrook JA, Cairns DA, Peng J, Speirs V, Hanby AM, Holen I, Wood SL, Ottewell PD, Marshall H, Banks RE, Selby PJ, Coleman RE, Brown JE. CAPG and GIPC1: Breast Cancer Biomarkers for Bone Metastasis Development and Treatment. J Natl Cancer Inst 2016; 108:djv360. [PMID: 26757732 PMCID: PMC4808632 DOI: 10.1093/jnci/djv360] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 10/27/2015] [Indexed: 01/30/2023] Open
Abstract
Background: Bone is the predominant site of metastasis from breast cancer, and recent trials have demonstrated that adjuvant bisphosphonate therapy can reduce bone metastasis development and improve survival. There is an unmet need for prognostic and predictive biomarkers so that therapy can be appropriately targeted. Methods: Potential biomarkers for bone metastasis were identified using proteomic comparison of bone-metastatic, lung-metastatic, and nonmetastatic variants of human breast cancer MDA-MB-231 cells. Clinical validation was performed using immunohistochemical staining of tumor tissue microarrays from patients in a large randomized trial of adjuvant zoledronic acid (zoledronate) (AZURE-ISRCTN79831382). We used Cox proportional hazards regression, the Kaplan-Meier estimate of the survival function, and the log-rank test to investigate associations between protein expression, clinical variables, and time to distant recurrence events. All statistical tests were two-sided. Results: Two novel biomarker candidates, macrophage-capping protein (CAPG) and PDZ domain–containing protein GIPC1 (GIPC1), were identified for clinical validation. Cox regression analysis of AZURE training and validation sets showed that control patients (no zoledronate) were more likely to develop first distant recurrence in bone (hazard ratio [HR] = 4.5, 95% confidence interval [CI] = 2.1 to 9.8, P < .001) and die (HR for overall survival = 1.8, 95% CI = 1.01 to 3.24, P = .045) if both proteins were highly expressed in the primary tumor. In patients with high expression of both proteins, zoledronate had a substantial effect, leading to 10-fold hazard ratio reduction (compared with control) for first distant recurrence in bone (P = .008). Conclusions: The composite biomarker, CAPG and GIPC1 in primary breast tumors, predicted disease outcomes and benefit from zoledronate and may facilitate patient selection for adjuvant bisphosphonate treatment.
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Affiliation(s)
- Jules A Westbrook
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - David A Cairns
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Jianhe Peng
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Valerie Speirs
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Andrew M Hanby
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Ingunn Holen
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Steven L Wood
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Penelope D Ottewell
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Helen Marshall
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Rosamonde E Banks
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Peter J Selby
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Robert E Coleman
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
| | - Janet E Brown
- Affiliations of authors:Academic Unit of Clinical Oncology, University of Sheffield , Sheffield , UK (JAW*, IH, PDO, REC, JEB*); Cancer Research UK Leeds Centre (JAW, DAC, JP, SLW, REB, PJS, JEB), Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research (DAC*, HM), and Clinical and Biomedical Proteomics Group (JAW, DAC, JP, SLW, REB, PJS, JEB) and Pathology and Tumor Biology (VS, AMH), Leeds Institute of Cancer and Pathology, University of Leeds , UK ; Department of Oncology and Metabolism, University of Sheffield, Sheffield , UK (SLW*)
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