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Hu Z, Li M, Chen Y, Chen L, Han Y, Chen C, Lu X, You N, Lou Y, Huang Y, Huo Z, Liu C, Liang C, Liu S, Deng K, Chen L, Chen S, Wan G, Wu X, Fu Y, Xu A. Disruption of PABPN1 phase separation by SNRPD2 drives colorectal cancer cell proliferation and migration through promoting alternative polyadenylation of CTNNBIP1. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1212-1225. [PMID: 38811444 DOI: 10.1007/s11427-023-2495-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/26/2023] [Indexed: 05/31/2024]
Abstract
Generally shortened 3' UTR due to alternative polyadenylation (APA) is widely observed in cancer, but its regulation mechanisms for cancer are not well characterized. Here, with profiling of APA in colorectal cancer tissues and poly(A) signal editing, we firstly identified that the shortened 3' UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration. We found that liquid-liquid phase separation (LLPS) of PABPN1 is reduced albeit with higher expression in cancer, and the reduction of LLPS leads to the shortened 3' UTR of CTNNBIP1 and promotes cell proliferation and migration. Notably, the splicing factor SNRPD2 upregulated in colorectal cancer, can interact with glutamic-proline (EP) domain of PABPN1, and then disrupt LLPS of PABPN1, which attenuates the repression effect of PABPN1 on the proximal poly(A) sites. Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1, suggesting that regulation of APA by interfering LLPS of 3' end processing factor may have the potential as a new way for the treatment of cancer.
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Affiliation(s)
- Zhijie Hu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengxia Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yufeng Chen
- Department of General Surgery (Colorectal Surgery) & Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases & Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Liutao Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuting Han
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengyong Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Lu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nan You
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yawen Lou
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yingye Huang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhanfeng Huo
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chao Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cheng Liang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Susu Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ke Deng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liangfu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guohui Wan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaojian Wu
- Department of General Surgery (Colorectal Surgery) & Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases & Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
| | - Yonggui Fu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Smith IC, Chakraborty S, Bourque PR, Sampaio ML, Melkus G, Lochmüller H, Woulfe J, Parks RJ, Brais B, Warman-Chardon J. Emerging and established biomarkers of oculopharyngeal muscular dystrophy. Neuromuscul Disord 2023; 33:824-834. [PMID: 37926637 DOI: 10.1016/j.nmd.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is a rare, primarily autosomal dominant, late onset muscular dystrophy commonly presenting with ptosis, dysphagia, and subsequent weakness of proximal muscles. Although OPMD diagnosis can be confirmed with high confidence by genetic testing, the slow progression of OPMD poses a significant challenge to clinical monitoring and a barrier to assessing the efficacy of treatments during clinical trials. Accordingly, there is a pressing need for more sensitive measures of OPMD progression, particularly those which do not require a muscle biopsy. This review provides an overview of progress in OPMD biomarkers from clinical assessment, quantitative imaging, histological assessments, and genomics, as well as hypothesis-generating "omics" approaches. The ongoing search for biomarkers relevant to OPMD progression needs an integrative, longitudinal approach combining validated and experimental approaches which may include clinical, imaging, demographic, and biochemical assessment methods. A multi-omics approach to biochemical biomarker discovery could help provide context for differences found between individuals with varying levels of disease activity and provide insight into pathomechanisms and prognosis of OPMD.
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Affiliation(s)
- Ian C Smith
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | | | - Pierre R Bourque
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada
| | - Marcos L Sampaio
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Medical Imaging, The Ottawa Hospital, Ottawa, Ontario K1Y 4E9, Canada; Department of Radiology, Radiation Oncology and Medical Physics, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Gerd Melkus
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Medical Imaging, The Ottawa Hospital, Ottawa, Ontario K1Y 4E9, Canada; Department of Physics, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Hanns Lochmüller
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - John Woulfe
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
| | - Robin J Parks
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada
| | - Bernard Brais
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Jodi Warman-Chardon
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada; Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada.
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3
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Hu Z, Li M, Huo Z, Chen L, Liu S, Deng K, Lu X, Chen S, Fu Y, Xu A. U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors. J Mol Cell Biol 2022; 14:6694001. [PMID: 36073763 PMCID: PMC9926334 DOI: 10.1093/jmcb/mjac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, both alternative splicing and alternative polyadenylation (APA) play essential roles in the gene regulation network. U1 small ribonucleoprotein particle (U1 snRNP) is a major component of spliceosome, and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3' end processing factors. However, here we show that both knockdown and overexpression of SNRPA, SNRPC, SNRNP70, and SNRPD2, the U1 snRNP proteins, promote the usage of proximal APA sites at the transcriptome level. SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate, which may reduce the repressive effects of PABPN1 on the proximal APA sites. Additionally, SNRNP70 can also promote the proximal APA sites by recruiting CPSF6, suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent. Consequently, these results reveal that, on the contrary to U1 snRNP complex, the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3' end processing machinery.
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Affiliation(s)
| | | | | | - Liutao Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Susu Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Ke Deng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Xin Lu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | | | - Anlong Xu
- Correspondence to: Anlong Xu, E-mail:
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4
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Banerjee A, Phillips BL, Deng Q, Seyfried NT, Pavlath GK, Vest KE, Corbett AH. Proteomic analysis reveals that wildtype and alanine-expanded nuclear poly(A)-binding protein exhibit differential interactions in skeletal muscle. J Biol Chem 2019; 294:7360-7376. [PMID: 30837270 DOI: 10.1074/jbc.ra118.007287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is a late-onset, primarily autosomal dominant disease caused by a short GCN expansion in the PABPN1 (polyadenylate-binding protein nuclear 1) gene that results in an alanine expansion at the N terminus of the PABPN1 protein. Expression of alanine-expanded PABPN1 is linked to the formation of nuclear aggregates in tissues from individuals with OPMD. However, as with other nuclear aggregate-associated diseases, controversy exists over whether these aggregates are the direct cause of pathology. An emerging hypothesis is that a loss of PABPN1 function and/or aberrant protein interactions contribute to pathology in OPMD. Here, we present the first global proteomic analysis of the protein interactions of WT and alanine-expanded PABPN1 in skeletal muscle tissue. These data provide both insight into the function of PABPN1 in muscle and evidence that the alanine expansion alters the protein-protein interactions of PABPN1. We extended this analysis to demonstrate altered complex formation with and loss of function of TDP-43 (TAR DNA-binding protein 43), which we show interacts with alanine-expanded but not WT PABPN1. The results from our study support a model where altered protein interactions with alanine-expanded PABPN1 that lead to loss or gain of function could contribute to pathology in OPMD.
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Affiliation(s)
| | - Brittany L Phillips
- From the Department of Biology and.,the Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Quidong Deng
- the Department of Biochemistry, Center for Neurodegenerative Diseases and
| | | | - Grace K Pavlath
- the Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, and
| | - Katherine E Vest
- the Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
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5
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Richard P, Roth F, Stojkovic T, Trollet C. Distrofia muscolare oculofaringea. Neurologia 2017. [DOI: 10.1016/s1634-7072(16)81777-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Pain C, Dumont J, Dumoulin M. Camelid single-domain antibody fragments: Uses and prospects to investigate protein misfolding and aggregation, and to treat diseases associated with these phenomena. Biochimie 2015; 111:82-106. [DOI: 10.1016/j.biochi.2015.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/23/2015] [Indexed: 12/19/2022]
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7
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Chang SH, Chang WL, Lu CC, Tarn WY. Alanine repeats influence protein localization in splicing speckles and paraspeckles. Nucleic Acids Res 2014; 42:13788-98. [PMID: 25414336 PMCID: PMC4267627 DOI: 10.1093/nar/gku1159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ.
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Affiliation(s)
- Shuo-Hsiu Chang
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Lun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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8
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Raz Y, Raz V. Oculopharyngeal muscular dystrophy as a paradigm for muscle aging. Front Aging Neurosci 2014; 6:317. [PMID: 25426070 PMCID: PMC4226162 DOI: 10.3389/fnagi.2014.00317] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/28/2014] [Indexed: 12/04/2022] Open
Abstract
Symptoms in late-onset neuromuscular disorders initiate only from midlife onward and progress with age. These disorders are primarily determined by identified hereditable mutations, but their late-onset symptom manifestation is not fully understood. Here, we review recent research developments on the late-onset autosomal dominant oculopharyngeal muscular dystrophy (OPMD). OPMD is caused by an expansion mutation in the gene encoding for poly-adenylate RNA binding protein1 (PABPN1). The molecular pathogenesis for the disease is still poorly understood. Despite a ubiquitous expression of PABPN1, symptoms in OPMD are limited to skeletal muscles. We discuss recent studies showing that PABPN1 levels in skeletal muscles are lower compared with other tissues, and specifically in skeletal muscles, PABPN1 expression declines from midlife onward. In OPMD, aggregation of expanded PABPN1 causes an additional decline in the level of the functional protein, which is associated with severe muscle weakness in OPMD. Reduced PABNPN1 expression in muscle cell culture causes myogenic defects, suggesting that PABPN1 loss-of-function causes muscle weakness in OPMD and in the elderly. Molecular signatures of OPMD muscles are similar to those of normal muscle aging, although expression trends progress faster in OPMD. We discuss a working hypothesis that aging-associated factors trigger late-onset symptoms in OPMD, and contribute to accelerated muscle weakness in OPMD. We focus on the pharyngeal and eyelid muscles, which are often affected in OPMD patients. We suggest that muscle weakness in OPMD is a paradigm for muscle aging.
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Affiliation(s)
- Yotam Raz
- Department of Human Genetics, Leiden University Medical Center , Leiden , Netherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Center , Leiden , Netherlands
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9
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A Novel Feed-Forward Loop between ARIH2 E3-Ligase and PABPN1 Regulates Aging-Associated Muscle Degeneration. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1119-1131. [DOI: 10.1016/j.ajpath.2013.12.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/13/2013] [Accepted: 12/02/2013] [Indexed: 11/15/2022]
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10
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Goodwin M, Swanson MS. RNA-binding protein misregulation in microsatellite expansion disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:353-88. [PMID: 25201111 PMCID: PMC4483269 DOI: 10.1007/978-1-4939-1221-6_10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA-binding proteins (RBPs) play pivotal roles in multiple cellular pathways from transcription to RNA turnover by interacting with RNA sequence and/or structural elements to form distinct RNA-protein complexes. Since these complexes are required for the normal regulation of gene expression, mutations that alter RBP functions may result in a cascade of deleterious events that lead to severe disease. Here, we focus on a group of hereditary disorders, the microsatellite expansion diseases, which alter RBP activities and result in abnormal neurological and neuromuscular phenotypes. While many of these diseases are classified as adult-onset disorders, mounting evidence indicates that disruption of normal RNA-protein interaction networks during embryogenesis modifies developmental pathways, which ultimately leads to disease manifestations later in life. Efforts to understand the molecular basis of these disorders has already uncovered novel pathogenic mechanisms, including RNA toxicity and repeat-associated non-ATG (RAN) translation, and current studies suggest that additional surprising insights into cellular regulatory pathways will emerge in the future.
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Affiliation(s)
- Marianne Goodwin
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Cancer Genetics Research Complex, 2033 Mowry Road, Gainesville, FL, 32610-3610, USA
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11
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Anvar SY, Raz Y, Verway N, van der Sluijs B, Venema A, Goeman JJ, Vissing J, van der Maarel SM, 't Hoen PAC, van Engelen BGM, Raz V. A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging. Aging (Albany NY) 2013; 5:412-26. [PMID: 23793615 PMCID: PMC3824410 DOI: 10.18632/aging.100567] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is caused by trinucleotide repeat expansion mutations in Poly(A) binding protein 1 (PABPN1). PABPN1 is a regulator of mRNA stability and is ubiquitously expressed. Here we investigated how symptoms in OPMD initiate only at midlife and why a subset of skeletal muscles is predominantly affected. Genome-wide RNA expression profiles from Vastus lateralis muscles human carriers of expanded-PABPN1 at pre-symptomatic and symptomatic stages were compared with healthy controls. Major expression changes were found to be associated with age rather than with expression of expanded-PABPN1, instead transcriptomes of OPMD and elderly muscles were significantly similar (P<0.05). Using k-means clustering we identified age-dependent trends in both OPMD and controls, but trends were often accelerated in OPMD. We report an age-regulated decline in PABPN1 levels in Vastus lateralis muscles from the fifth decade. In concurrence with severe muscle degeneration in OPMD, the decline in PABPN1 accelerated in OPMD and was specific to skeletal muscles. Reduced PABPN1 levels (30% to 60%) in muscle cells induced myogenic defects and morphological signatures of cellular aging in proportion to PABPN1 expression levels. We suggest that PABPN1 levels regulate muscle cell aging and OPMD represents an accelerated muscle aging disorder.
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Affiliation(s)
- Seyed Yahya Anvar
- Center for Human and Clinical Genetics, Leiden University Medical Center, the Netherlands
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12
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Raz V, Sterrenburg E, Routledge S, Venema A, van der Sluijs BM, Trollet C, Dickson G, van Engelen BGM, van der Maarel SM, Antoniou MN. Nuclear entrapment and extracellular depletion of PCOLCE is associated with muscle degeneration in oculopharyngeal muscular dystrophy. BMC Neurol 2013; 13:70. [PMID: 23815790 PMCID: PMC3717027 DOI: 10.1186/1471-2377-13-70] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 06/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Muscle fibrosis characterizes degenerated muscles in muscular dystrophies and in late onset myopathies. Fibrotic muscles often exhibit thickening of the extracellular matrix (ECM). The molecular regulation of this process is not fully understood. In oculopharyngeal muscular dystrophy (OPMD), an expansion of an alanine tract at the N-terminus of poly(A)-binding protein nuclear 1 (PABPN1) causes muscle symptoms. OPMD patient muscle degeneration initiates after midlife, while at an earlier age carriers of alanine expansion mutant PABPN1 (expPABPN1) are clinically pre-symptomatic. OPMD is characterized by fibrosis in skeletal muscles but the causative molecular mechanisms are not fully understood. METHODS We studied the molecular processes that are involved in OPMD pathology using cross-species mRNA expression profiles in muscles from patients and model systems. We identified significant dysregulation of the ECM functional group, among which the procollagen C-endopeptidase enhancer 1 gene (PCOLCE) was consistently down-regulated across species. We investigated PCOLCE subcellular localization in OPMD muscle samples and OPMD model systems to investigate any functional relevance of PCOLCE down-regulation in this disease. RESULTS We found that muscle degeneration in OPMD is associated with PCOLCE down-regulation. In addition to its known presence at the ECM, we also found PCOLCE within the nucleus of muscle cells. PCOLCE sub-cellular localization changes during myoblast cell fusion and is disrupted in cells expressing mutant expPABPN1. Our results show that PCOLCE binds to soluble PABPN1 and co-localizes with aggregated PABPN1 with a preference for the mutant protein. In muscle biopsies from OPMD patients we find that extracellular PCOLCE is depleted with its concomitant enrichment within the nuclear compartment. CONCLUSIONS PCOLCE regulates collagen processing at the ECM. Depletion of extracellular PCOLCE is associated with the expression of expPABPN1 in OPMD patient muscles. PCOLCE is also localized within the nucleus where it binds to PABPN1, suggesting that PCOLCE shuttles between the ECM and the nucleus. PCOLCE preferentially binds to expPABPN1. Nuclear-localized PCOLCE is enriched in muscle cells expressing expPABPN1. We suggest that nuclear entrapment of PCOLCE and its extracellular depletion represents a novel molecular mechanism in late-onset muscle fibrosis.
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Affiliation(s)
- Vered Raz
- Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands.
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13
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Raz V, Butler-Browne G, van Engelen B, Brais B. 191st ENMC International Workshop: Recent advances in oculopharyngeal muscular dystrophy research: From bench to bedside 8-10 June 2012, Naarden, The Netherlands. Neuromuscul Disord 2013; 23:516-23. [DOI: 10.1016/j.nmd.2013.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Indexed: 10/27/2022]
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14
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Hughes JN, Thomas PQ. Molecular pathology of polyalanine expansion disorders: new perspectives from mouse models. Methods Mol Biol 2013; 1017:135-51. [PMID: 23719913 DOI: 10.1007/978-1-62703-438-8_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Disease-causing polyalanine (PA) expansion mutations have been identified in nine genes, eight of which encode transcription factors (TFs) with important roles in development. In vitro and cell overexpression studies have shown that expanded PA tracts result in protein misfolding and the formation of aggregates. This feature of PA proteins is reminiscent of the related polyglutamine (PQ) disease proteins, which have been shown to cause disease via a gain-of-function (GOF) mechanism. However, in sharp contrast to PQ disorders, the disease phenotypes associated with PA mutations are more consistent with a LOF and/or mild GOF mechanism, suggesting that their molecular pathology is inherently different to PQ disorders. Elucidating the cellular impact of PA mutations in vivo has been difficult to address as, unlike the late-onset polyglutamine disorders, all PA disorders associated with TF gene mutations are congenital. However, in recent years, significant advances have been made through the analysis of engineered (knock-in) and spontaneous PA mouse models. Here we review these recent findings and propose an updated model of the molecular and cellular mechanism of PA disorders that incorporates both LOF and GOF features.
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Affiliation(s)
- James N Hughes
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
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de Klerk E, Venema A, Anvar SY, Goeman JJ, Hu O, Trollet C, Dickson G, den Dunnen JT, van der Maarel SM, Raz V, 't Hoen PAC. Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation. Nucleic Acids Res 2012; 40:9089-101. [PMID: 22772983 PMCID: PMC3467053 DOI: 10.1093/nar/gks655] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The choice for a polyadenylation site determines the length of the 3′-untranslated region (3′-UTRs) of an mRNA. Inclusion or exclusion of regulatory sequences in the 3′-UTR may ultimately affect gene expression levels. Poly(A) binding protein nuclear 1 (PABPN1) is involved in polyadenylation of pre-mRNAs. An alanine repeat expansion in PABPN1 (exp-PABPN1) causes oculopharyngeal muscular dystrophy (OPMD). We hypothesized that previously observed disturbed gene expression patterns in OPMD muscles may have been the result of an effect of PABPN1 on alternative polyadenylation, influencing mRNA stability, localization and translation. A single molecule polyadenylation site sequencing method was developed to explore polyadenylation site usage on a genome-wide level in mice overexpressing exp-PABPN1. We identified 2012 transcripts with altered polyadenylation site usage. In the far majority, more proximal alternative polyadenylation sites were used, resulting in shorter 3′-UTRs. 3′-UTR shortening was generally associated with increased expression. Similar changes in polyadenylation site usage were observed after knockdown or overexpression of expanded but not wild-type PABPN1 in cultured myogenic cells. Our data indicate that PABPN1 is important for polyadenylation site selection and that reduced availability of functional PABPN1 in OPMD muscles results in use of alternative polyadenylation sites, leading to large-scale deregulation of gene expression.
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Affiliation(s)
- Eleonora de Klerk
- Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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16
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Righolt CH, van 't Hoff MLR, Vermolen BJ, Young IT, Raz V. Robust nuclear lamina-based cell classification of aging and senescent cells. Aging (Albany NY) 2012; 3:1192-201. [PMID: 22199022 PMCID: PMC3273899 DOI: 10.18632/aging.100414] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Changes in the shape of the nuclear lamina are exhibited in senescent cells, as well as in cells expressing mutations in lamina genes. To identify cells with defects in the nuclear lamina we developed an imaging method that quantifies the intensity and curvature of the nuclear lamina. We show that this method accurately describes changes in the nuclear lamina. Spatial changes in nuclear lamina coincide with redistribution of lamin A proteins and local reduction in protein mobility in senescent cell. We suggest that local accumulation of lamin A in the nuclear envelope leads to bending of the structure. A quantitative distinction of the nuclear lamina shape in cell populations was found between fresh and senescent cells, and between primary myoblasts from young and old donors. Moreover, with this method mutations in lamina genes were significantly distinct from cells with wild-type genes. We suggest that this method can be applied to identify abnormal cells during aging, in in vitro propagation, and in lamina disorders.
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Bengoechea R, Tapia O, Casafont I, Berciano J, Lafarga M, Berciano MT. Nuclear speckles are involved in nuclear aggregation of PABPN1 and in the pathophysiology of oculopharyngeal muscular dystrophy. Neurobiol Dis 2012; 46:118-29. [PMID: 22249111 DOI: 10.1016/j.nbd.2011.12.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 12/19/2011] [Accepted: 12/31/2011] [Indexed: 10/14/2022] Open
Abstract
Nuclear speckles are essential nuclear compartments involved in the assembly, delivery and recycling of pre-mRNA processing factors, and in the post-transcriptional processing of pre-mRNAs. Oculopharyngeal muscular dystrophy (OPMD) is caused by a small expansion of the polyalanine tract in the poly(A)-binding protein nuclear 1 (PABPN1). Aggregation of expanded PABPN1 into intranuclear inclusions (INIs) in skeletal muscle fibers is the pathological hallmark of OPMD. In this study what we have analyzed in muscle fibers of OPMD patients and in primary cultures of human myoblasts are the relationships between nuclear speckles and INIs, and the contribution of the former to the biogenesis of the latter. While nuclear speckles concentrate snRNP splicing factors and PABPN1 in control muscle fibers, they are depleted of PABPN1 and appear closely associated with INIs in muscle fibers of OPMD patients. The induction of INI formation in human myoblasts expressing either wild type GFP-PABPN1 or expanded GFP-PABPN1-17ala demonstrates that the initial aggregation of PABPN1 proteins and their subsequent growth in INIs occurs at the edges of the nuclear speckles. Moreover, the growing of INIs gradually depletes PABPN1 proteins and poly(A) RNA from nuclear speckles, although the existence of these nuclear compartments is preserved. Time-lapse experiments in cultured myoblasts confirm nuclear speckles as biogenesis sites of PABPN1 inclusions. Given the functional importance of nuclear speckles in the post-transcriptional processing of pre-mRNAs, the INI-dependent molecular reorganization of these nuclear compartments in muscle fibers may cause a severe dysfunction in nuclear trafficking and processing of polyadenylated mRNAs, thereby contributing to the molecular pathophysiology of OPMD. Our results emphasize the potential importance of nuclear speckles as nuclear targets of neuromuscular disorders.
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Affiliation(s)
- Rocío Bengoechea
- Department of Anatomy and Cell Biology and Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Cantabria, Santander, Spain
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