1
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Ishigami Y, Wong MS, Martí-Gómez C, Ayaz A, Kooshkbaghi M, Hanson SM, McCandlish DM, Krainer AR, Kinney JB. Specificity, synergy, and mechanisms of splice-modifying drugs. Nat Commun 2024; 15:1880. [PMID: 38424098 PMCID: PMC10904865 DOI: 10.1038/s41467-024-46090-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5' splice site sequences, suggest that branaplam recognizes 5' splice sites via two distinct interaction modes, and contradict the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.
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Affiliation(s)
- Yuma Ishigami
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mandy S Wong
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Beam Therapeutics, Cambridge, MA, 02142, USA
| | | | - Andalus Ayaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mahdi Kooshkbaghi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- The Estée Lauder Companies, New York, NY, 10153, USA
| | | | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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2
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Xiang X, Bhowmick K, Shetty K, Ohshiro K, Yang X, Wong LL, Yu H, Latham PS, Satapathy SK, Brennan C, Dima RJ, Chambwe N, Sharifova G, Cacaj F, John S, Crawford JM, Huang H, Dasarathy S, Krainer AR, He AR, Amdur RL, Mishra L. Mechanistically based blood proteomic markers in the TGF-β pathway stratify risk of hepatocellular cancer in patients with cirrhosis. Genes Cancer 2024; 15:1-14. [PMID: 38323119 PMCID: PMC10843195 DOI: 10.18632/genesandcancer.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/05/2023] [Indexed: 02/08/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer worldwide but is often diagnosed at an advanced incurable stage. Yet, despite the urgent need for blood-based biomarkers for early detection, few studies capture ongoing biology to identify risk-stratifying biomarkers. We address this gap using the TGF-β pathway because of its biological role in liver disease and cancer, established through rigorous animal models and human studies. Using machine learning methods with blood levels of 108 proteomic markers in the TGF-β family, we found a pattern that differentiates HCC from non-HCC in a cohort of 216 patients with cirrhosis, which we refer to as TGF-β based Protein Markers for Early Detection of HCC (TPEARLE) comprising 31 markers. Notably, 20 of the patients with cirrhosis alone presented an HCC-like pattern, suggesting that they may be a group with as yet undetected HCC or at high risk for developing HCC. In addition, we found two other biologically relevant markers, Myostatin and Pyruvate Kinase M2 (PKM2), which were significantly associated with HCC. We tested these for risk stratification of HCC in multivariable models adjusted for demographic and clinical variables, as well as batch and site. These markers reflect ongoing biology in the liver. They potentially indicate the presence of HCC early in its evolution and before it is manifest as a detectable lesion, thereby providing a set of markers that may be able to stratify risk for HCC.
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Affiliation(s)
- Xiyan Xiang
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
- These authors contributed equally to this work
| | - Krishanu Bhowmick
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
- These authors contributed equally to this work
| | - Kirti Shetty
- Division of Gastroenterology and Hepatology, University of Maryland, Baltimore, MD 21201, USA
| | - Kazufumi Ohshiro
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
| | - Xiaochun Yang
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
| | - Linda L. Wong
- Department of Surgery, University of Hawaii, Honolulu, HI 96813, USA
| | - Herbert Yu
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Patricia S. Latham
- Department of Pathology, The George Washington University, Washington, DC 20037, USA
| | - Sanjaya K. Satapathy
- Department of Medicine, Sandra Atlas Bass Center for Liver Diseases and Transplantation, North Shore University Hospital/Northwell Health, Manhasset, NY 11030, USA
| | - Christina Brennan
- Office of Clinical Research, Northwell Health, Lake Success, NY 11042, USA
- The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Richard J. Dima
- Office of Clinical Research, Northwell Health, Lake Success, NY 11042, USA
| | - Nyasha Chambwe
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Gulru Sharifova
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Fellanza Cacaj
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
| | - Sahara John
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
| | | | - Hai Huang
- The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Srinivasan Dasarathy
- Division of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44106, USA
| | | | - Aiwu R. He
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC 20007, USA
| | - Richard L. Amdur
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
- Quantitative Intelligence, The Institutes for Health Systems Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Lopa Mishra
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory, Division of Gastroenterology and Hepatology, Northwell Health, Manhasset, NY 11030, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Surgery, The George Washington University, Washington, DC 20037, USA
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3
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Wan L, Lin KT, Rahman MA, Ishigami Y, Wang Z, Jensen MA, Wilkinson JE, Park Y, Tuveson DA, Krainer AR. Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer. Cancer Discov 2023; 13:1678-1695. [PMID: 37098965 PMCID: PMC10330071 DOI: 10.1158/2159-8290.cd-22-1013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/14/2023] [Accepted: 03/22/2023] [Indexed: 04/27/2023]
Abstract
Inflammation is strongly associated with pancreatic ductal adenocarcinoma (PDAC), a highly lethal malignancy. Dysregulated RNA splicing factors have been widely reported in tumorigenesis, but their involvement in pancreatitis and PDAC is not well understood. Here, we report that the splicing factor SRSF1 is highly expressed in pancreatitis, PDAC precursor lesions, and tumors. Increased SRSF1 is sufficient to induce pancreatitis and accelerate KRASG12D-mediated PDAC. Mechanistically, SRSF1 activates MAPK signaling-partly by upregulating interleukin 1 receptor type 1 (IL1R1) through alternative-splicing-regulated mRNA stability. Additionally, SRSF1 protein is destabilized through a negative feedback mechanism in phenotypically normal epithelial cells expressing KRASG12D in mouse pancreas and in pancreas organoids acutely expressing KRASG12D, buffering MAPK signaling and maintaining pancreas cell homeostasis. This negative feedback regulation of SRSF1 is overcome by hyperactive MYC, facilitating PDAC tumorigenesis. Our findings implicate SRSF1 in the etiology of pancreatitis and PDAC, and point to SRSF1-misregulated alternative splicing as a potential therapeutic target. SIGNIFICANCE We describe the regulation of splicing factor SRSF1 expression in the context of pancreas cell identity, plasticity, and inflammation. SRSF1 protein downregulation is involved in a negative feedback cellular response to KRASG12D expression, contributing to pancreas cell homeostasis. Conversely, upregulated SRSF1 promotes pancreatitis and accelerates KRASG12D-mediated tumorigenesis through enhanced IL1 and MAPK signaling. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- Ledong Wan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Yuma Ishigami
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhikai Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Mads A. Jensen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John E. Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David A. Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
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4
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Jbara A, Lin KT, Stossel C, Siegfried Z, Shqerat H, Amar-Schwartz A, Elyada E, Mogilevsky M, Raitses-Gurevich M, Johnson JL, Yaron TM, Ovadia O, Jang GH, Danan-Gotthold M, Cantley LC, Levanon EY, Gallinger S, Krainer AR, Golan T, Karni R. RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature 2023; 617:147-153. [PMID: 36949200 PMCID: PMC10156590 DOI: 10.1038/s41586-023-05820-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases1-3. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in PDA. RNA-sequencing and splicing analysis of RBFOX2 target genes revealed enrichment of genes in the RHO GTPase pathways, suggesting a role of RBFOX2 splicing activity in cytoskeletal organization and focal adhesion formation. Modulation of RBFOX2-regulated splicing events, such as via myosin phosphatase RHO-interacting protein (MPRIP), is associated with PDA metastases, altered cytoskeletal organization and the induction of focal adhesion formation. Our results implicate the splicing-regulatory function of RBFOX2 as a tumour suppressor in PDA and suggest a therapeutic approach for metastatic PDA.
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Affiliation(s)
- Amina Jbara
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chani Stossel
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Haya Shqerat
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ela Elyada
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maxim Mogilevsky
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ofek Ovadia
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gun Ho Jang
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Steven Gallinger
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | | | - Talia Golan
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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5
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Zhang Q, Yang L, Liu YH, Wilkinson JE, Krainer AR. Antisense oligonucleotide therapy for H3.3K27M diffuse midline glioma. Sci Transl Med 2023; 15:eadd8280. [PMID: 37043556 PMCID: PMC10263181 DOI: 10.1126/scitranslmed.add8280] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023]
Abstract
Diffuse midline gliomas (DMGs) are pediatric high-grade brain tumors in the thalamus, midbrain, or pons; the latter subgroup are termed diffuse intrinsic pontine gliomas (DIPG). The brain stem location of these tumors limits the clinical management of DIPG, resulting in poor outcomes for patients. A heterozygous, somatic point mutation in one of two genes coding for the noncanonical histone H3.3 is present in most DIPG tumors. This dominant mutation in the H3-3A gene results in replacement of lysine 27 with methionine (K27M) and causes a global reduction of trimethylation on K27 of all wild-type histone H3 proteins, which is thought to be a driving event in gliomagenesis. In this study, we designed and systematically screened 2'-O-methoxyethyl phosphorothioate antisense oligonucleotides (ASOs) that direct RNase H-mediated knockdown of H3-3A mRNA. We identified a lead ASO that effectively reduced H3-3A mRNA and H3.3K27M protein and restored global H3K27 trimethylation in patient-derived neurospheres. We then tested the lead ASO in two mouse models of DIPG: an immunocompetent mouse model using transduced mutant human H3-3A cDNA and an orthotopic xenograft with patient-derived cells. In both models, ASO treatment restored K27 trimethylation of histone H3 proteins and reduced tumor growth, promoted neural stem cell differentiation into astrocytes, neurons, and oligodendrocytes, and increased survival. These results demonstrate the involvement of the H3.3K27M oncohistone in tumor maintenance, confirm the reversibility of the aberrant epigenetic changes it promotes, and provide preclinical proof of concept for DMG antisense therapy.
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Affiliation(s)
- Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
- Stony Brook University, Graduate Program in Molecular and Cell Biology, Stony Brook, NY, 11794
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
- Stony Brook University, Graduate Program in Genetics, Stony Brook, NY, 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - John E. Wilkinson
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109
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6
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Wan L, Kral AJ, Voss D, Krainer AR. Preclinical Screening of Splice-Switching Antisense Oligonucleotides in PDAC Organoids. bioRxiv 2023:2023.03.31.535161. [PMID: 37066201 PMCID: PMC10103938 DOI: 10.1101/2023.03.31.535161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Aberrant alternative splicing is emerging as a cancer hallmark and a potential therapeutic target. It is the result of dysregulated splicing factors or genetic alterations in splicing-regulatory cis -elements. Targeting individual altered splicing events associated with cancer-cell dependencies is a potential therapeutic strategy, but several technical limitations need to be addressed. Patient-derived organoids (PDOs) are a promising platform to recapitulate key aspects of disease states and to facilitate drug development for precision medicine. Here, we report an efficient antisense-oligonucleotide (ASO) transfection method to systematically evaluate and screen individual splicing events as therapeutic targets in pancreatic ductal adenocarcinoma (PDAC) organoids. This optimized delivery method allows fast and efficient screening of ASOs that reverse oncogenic alternative splicing. In combination with advancements in chemical modifications and ASO-delivery strategies, this method has the potential to accelerate the discovery of anti-tumor ASO drugs that target pathological alternative splicing.
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7
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Abstract
"RNA therapeutics" refers to a disease treatment or drug that utilizes RNA as a component. In this context, RNA may be the direct target of a small-molecule drug or RNA itself may be the drug, designed to bind to a protein, or to mimic or target another RNA. RNA has gained attention in the drug-development world, as recent clinical successes and breakthrough technologies have revolutionized the drug-like qualities of the molecule or its usefulness as a drug target. In this special issue of RNA, we gathered expert perspectives on the past, present, and future of the field, to serve as a primer and also a challenge to the broad scientific community to incorporate RNA into their experimental design and problem-solving process, and to imagine and realize the potential of RNA as a therapeutic drug or target.
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Affiliation(s)
- Michelle L Hastings
- Rosalind Franklin University of Medicine and Science, Chicago, Illinois 60064, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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8
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Ishigami Y, Wong MS, Aldaravi CMG, Kooshkbaghi M, Ayaz A, McCandlish DM, Krainer AR, Kinney JB. Specificity, cooperativity, synergy, and mechanisms of splice-modifying drugs. Biophys J 2023; 122:271a. [PMID: 36783339 DOI: 10.1016/j.bpj.2022.11.1547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Yuma Ishigami
- Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | | | - Carlos M G Aldaravi
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | - Mahdi Kooshkbaghi
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | - Andalus Ayaz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | | | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
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9
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Kim YJ, Krainer AR. Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Mol Cells 2023; 46:10-20. [PMID: 36697233 PMCID: PMC9880599 DOI: 10.14348/molcells.2023.2172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Antisense oligonucleotide (ASO) technology has become an attractive therapeutic modality for various diseases, including Mendelian disorders. ASOs can modulate the expression of a target gene by promoting mRNA degradation or changing pre-mRNA splicing, nonsense-mediated mRNA decay, or translation. Advances in medicinal chemistry and a deeper understanding of post-transcriptional mechanisms have led to the approval of several ASO drugs for diseases that had long lacked therapeutic options. For instance, an ASO drug called nusinersen became the first approved drug for spinal muscular atrophy, improving survival and the overall disease course. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Although Trikafta and other CFTR-modulation therapies benefit most CF patients, there is a significant unmet therapeutic need for a subset of CF patients. In this review, we introduce ASO therapies and their mechanisms of action, describe the opportunities and challenges for ASO therapeutics for CF, and discuss the current state and prospects of ASO therapies for CF.
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Affiliation(s)
- Young Jin Kim
- Department of Pediatrics, Mount Sinai Hospital, New York, NY 10029, USA
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10
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Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell 2022; 185:2057-2070.e15. [PMID: 35688133 DOI: 10.1016/j.cell.2022.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/17/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022]
Abstract
Spinal muscular atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped, cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide (ASO) that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7. We show that by promoting transcriptional elongation, the histone deacetylase inhibitor VPA cooperates with a nusinersen-like ASO to promote E7 inclusion. Surprisingly, the ASO promotes the deployment of the silencing histone mark H3K9me2 on the SMN2 gene, creating a roadblock to RNA polymerase II elongation that inhibits E7 inclusion. By removing the roadblock, VPA counteracts the chromatin effects of the ASO, resulting in higher E7 inclusion without large pleiotropic effects. Combined administration of the nusinersen-like ASO and VPA in SMA mice strongly synergizes SMN expression, growth, survival, and neuromuscular function.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jose N Stigliano
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina.
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11
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Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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12
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Kim YJ, Sivetz N, Layne J, Voss DM, Yang L, Zhang Q, Krainer AR. Exon-skipping antisense oligonucleotides for cystic fibrosis therapy. Proc Natl Acad Sci U S A 2022; 119:e2114858118. [PMID: 35017301 PMCID: PMC8784140 DOI: 10.1073/pnas.2114858118] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), and the CFTR-W1282X nonsense mutation causes a severe form of CF. Although Trikafta and other CFTR-modulation therapies benefit most CF patients, targeted therapy for patients with the W1282X mutation is lacking. The CFTR-W1282X protein has residual activity but is expressed at a very low level due to nonsense-mediated messenger RNA (mRNA) decay (NMD). NMD-suppression therapy and read-through therapy are actively being researched for CFTR nonsense mutants. NMD suppression could increase the mutant CFTR mRNA, and read-through therapies may increase the levels of full-length CFTR protein. However, these approaches have limitations and potential side effects: because the NMD machinery also regulates the expression of many normal mRNAs, broad inhibition of the pathway is not desirable, and read-through drugs are inefficient partly because the mutant mRNA template is subject to NMD. To bypass these issues, we pursued an exon-skipping antisense oligonucleotide (ASO) strategy to achieve gene-specific NMD evasion. A cocktail of two splice-site-targeting ASOs induced the expression of CFTR mRNA without the premature-termination-codon-containing exon 23 (CFTR-Δex23), which is an in-frame exon. Treatment of human bronchial epithelial cells with this cocktail of ASOs that target the splice sites flanking exon 23 results in efficient skipping of exon 23 and an increase in CFTR-Δex23 protein. The splice-switching ASO cocktail increases the CFTR-mediated chloride current in human bronchial epithelial cells. Our results set the stage for developing an allele-specific therapy for CF caused by the W1282X mutation.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Nicole Sivetz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Jessica Layne
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Dillon M Voss
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Ma WK, Voss DM, Scharner J, Costa ASH, Lin KT, Jeon HY, Wilkinson JE, Jackson M, Rigo F, Bennett CF, Krainer AR. ASO-based PKM splice-switching therapy inhibits hepatocellular carcinoma growth. Cancer Res 2021; 82:900-915. [PMID: 34921016 DOI: 10.1158/0008-5472.can-20-0948] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
The M2 pyruvate kinase (PKM2) isoform is upregulated in most cancers and plays a crucial role in regulation of the Warburg effect, which is characterized by the preference for aerobic glycolysis over oxidative phosphorylation for energy metabolism. PKM2 is an alternative-splice isoform of the PKM gene and is a potential therapeutic target. Antisense oligonucleotides (ASO) that switch PKM splicing from the cancer-associated PKM2 to the PKM1 isoform have been shown to induce apoptosis in cultured glioblastoma cells when delivered by lipofection. Here, we explore the potential of ASO-based PKM splice switching as a targeted therapy for liver cancer. A more potent lead cEt/DNA ASO induced PKM splice-switching and inhibited the growth of cultured hepatocellular carcinoma (HCC) cells. This PKM isoform switch increased pyruvate-kinase activity and altered glucose metabolism. In an orthotopic HCC xenograft mouse model, the lead ASO and a second ASO targeting a non-overlapping site inhibited tumor growth. Finally, in a genetic HCC mouse model, a surrogate mouse-specific ASO induced Pkm splice switching and inhibited tumorigenesis, without observable toxicity. These results lay the groundwork for a potential ASO-based splicing therapy for HCC.
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Affiliation(s)
| | - Dillon M Voss
- Medical Scientist Training Program (MSTP), Stony Brook University School of Medicine
| | | | - Ana S H Costa
- Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai
| | | | | | - John E Wilkinson
- Unit for Laboratory Animal Medicine, University of Michigan–Ann Arbor
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15
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Wan L, Lin KT, Rahman MA, Wang Z, Park Y, Tuveson DA, Krainer AR. Abstract PR-011: Loss of compensatory feedback mechanism involving splicing factor SRSF1 accelerates KrasG12D-mediated pancreatic cancer initiation. Cancer Res 2021. [DOI: 10.1158/1538-7445.panca21-pr-011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS is recurrently mutated in pancreatic ductal adenocarcinoma (PDAC), triggering the formation of acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN). However, the majority of pancreatic cells from KC (LSL-KrasG12D/+; Pdx-1-Cre) mice carrying the KrasG12D mutation remain morphologically normal for a long time, suggesting the existence of compensatory feedback mechanisms that buffer KrasG12D signaling, and that additional steps are required for disrupting cell homeostasis and promoting transformation. Here we found that splicing factor SRSF1, which is associated with cell transformation, is downregulated in the majority of morphologically normal pancreas cells with the KrasG12D mutation as a compensatory feedback mechanism. To assess the role of SRSF1 in PDAC, we generated a transgenic mouse strain (SC) with Dox-inducible pancreatic-specific expression of SRSF1 protein. Elevated SRSF1 alone is sufficient to induce pancreatitis and ADM transformation. By further crossing the SC strain with KrasG12D alone (KSC) or together with Trp53R172H (KPSC), we found that increasing SRSF1 accelerated KrasG12D-mediated tumor initiation and resulted in more aggressive PDAC. To address the underlying mechanisms of SRSF1’s involvement in the homeostatic response to KrasG12D mutation and in PDAC initiation, we generated organoid lines from the above mouse strains. Following Dox induction, elevated SRSF1 with Kras WT or KrasG12D consistently activated MAPK signaling, which is one of the top negatively enriched pathways in response to KrasG12D. Furthermore, SRSF1 promoted the expression of Il1r1—an IL1 receptor associated with the activation of MAPK signaling—by regulating an alternative-splicing event in the 5’UTR to generate a more stable mRNA isoform. We conclude that decreased SRSF1 is a compensatory feedback mechanism in pancreatic cells against the KrasG12D mutation, whose disruption facilitates PDAC initiation.
Citation Format: Ledong Wan, Kuan-Ting Lin, Mohammad A. Rahman, Zhikai Wang, Youngkyu Park, David A. Tuveson, Adrian R. Krainer. Loss of compensatory feedback mechanism involving splicing factor SRSF1 accelerates KrasG12D-mediated pancreatic cancer initiation [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PR-011.
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Affiliation(s)
- Ledong Wan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Zhikai Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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16
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Abou-el-Enein M, Angelis A, Appelbaum FR, Andrews NC, Bates SE, Bierman AS, Brenner MK, Cavazzana M, Caligiuri MA, Clevers H, Cooke E, Daley GQ, Dzau VJ, Ellis LM, Fineberg HV, Goldstein LS, Gottschalk S, Hamburg MA, Ingber DE, Kohn DB, Krainer AR, Maus MV, Marks P, Mummery CL, Pettigrew RI, Rutter JL, Teichmann SA, Terzic A, Urnov FD, Williams DA, Wolchok JD, Lawler M, Turtle CJ, Bauer G, Ioannidis JP. Evidence generation and reproducibility in cell and gene therapy research: A call to action. Mol Ther Methods Clin Dev 2021; 22:11-14. [PMID: 34377737 PMCID: PMC8322039 DOI: 10.1016/j.omtm.2021.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Mohamed Abou-el-Enein
- Division of Medical Oncology, Department of Medicine and Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Joint USC/CHLA Cell Therapy Program, University of Southern California and Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Aris Angelis
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London, UK
- Department of Health Policy and LSE Health, London School of Economics and Political Science, London, UK
| | - Frederick R. Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nancy C. Andrews
- Department of Pharmacology and Cancer Biology and Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Susan E. Bates
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Arlene S. Bierman
- Center for Evidence and Practice Improvement, Agency for Healthcare Research and Quality, Rockville, MD, USA
| | - Malcolm K. Brenner
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Marina Cavazzana
- Biotherapy Department, Necker Children’s Hospital, Assistance Publique-Hopitaux de Paris, Paris, France
- Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Quest, INSERM, Paris, France
| | - Michael A. Caligiuri
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emer Cooke
- European Medicines Agency, Amsterdam, the Netherlands
| | - George Q. Daley
- Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Lee M. Ellis
- Department of Surgical Oncology and Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Lawrence S.B. Goldstein
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Margaret A. Hamburg
- American Association for the Advancement of Science (AAAS), Washington, DC, USA
- National Academy of Medicine, Washington, DC, USA
| | - Donald E. Ingber
- Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA
| | - Donald B. Kohn
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- The Eli & Edith Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Marcela V. Maus
- Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Peter Marks
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roderic I. Pettigrew
- ENMED, Colleges of Medicine and Engineering, Texas A&M University, Houston, TX, USA
| | - Joni L. Rutter
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge, UK
| | - Andre Terzic
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fyodor D. Urnov
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David A. Williams
- Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Jedd D. Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Belfast, UK
| | - Cameron J. Turtle
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gerhard Bauer
- Institute for Regenerative Cures, University of California, Davis, Sacramento, CA, USA
| | - John P.A. Ioannidis
- Stanford Prevention Research Center, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Epidemiology and Population Health and Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
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17
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Ajiro M, Awaya T, Kim YJ, Iida K, Denawa M, Tanaka N, Kurosawa R, Matsushima S, Shibata S, Sakamoto T, Studer R, Krainer AR, Hagiwara M. Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nat Commun 2021; 12:4507. [PMID: 34301951 PMCID: PMC8302731 DOI: 10.1038/s41467-021-24705-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/21/2021] [Indexed: 01/10/2023] Open
Abstract
Approximately half of genetic disease-associated mutations cause aberrant splicing. However, a widely applicable therapeutic strategy to splicing diseases is yet to be developed. Here, we analyze the mechanism whereby IKBKAP-familial dysautonomia (FD) exon 20 inclusion is specifically promoted by a small molecule splice modulator, RECTAS, even though IKBKAP-FD exon 20 has a suboptimal 5' splice site due to the IVS20 + 6 T > C mutation. Knockdown experiments reveal that exon 20 inclusion is suppressed in the absence of serine/arginine-rich splicing factor 6 (SRSF6) binding to an intronic splicing enhancer in intron 20. We show that RECTAS directly interacts with CDC-like kinases (CLKs) and enhances SRSF6 phosphorylation. Consistently, exon 20 splicing is bidirectionally manipulated by targeting cellular CLK activity with RECTAS versus CLK inhibitors. The therapeutic potential of RECTAS is validated in multiple FD disease models. Our study indicates that small synthetic molecules affecting phosphorylation state of SRSFs is available as a new therapeutic modality for mechanism-oriented precision medicine of splicing diseases.
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Affiliation(s)
- Masahiko Ajiro
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobuo Tanaka
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shingo Matsushima
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Saiko Shibata
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsunori Sakamoto
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Rolenz Studer
- Center for Stem Cell Biology, Sloan Kettering Institute, New York, NY, USA
| | | | - Masatoshi Hagiwara
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. .,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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18
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Frederiksen SB, Holm LL, Larsen MR, Doktor TK, Andersen HS, Hastings ML, Hua Y, Krainer AR, Andresen BS. Identification of SRSF10 as a regulator of SMN2 ISS-N1. Hum Mutat 2020; 42:246-260. [PMID: 33300159 DOI: 10.1002/humu.24149] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/22/2020] [Accepted: 12/06/2020] [Indexed: 01/02/2023]
Abstract
Understanding the splicing code can be challenging as several splicing factors bind to many splicing-regulatory elements. The SMN1 and SMN2 silencer element ISS-N1 is the target of the antisense oligonucleotide drug, Spinraza, which is the treatment against spinal muscular atrophy. However, limited knowledge about the nature of the splicing factors that bind to ISS-N1 and inhibit splicing exists. It is likely that the effect of Spinraza comes from blocking binding of these factors, but so far, an unbiased characterization has not been performed and only members of the hnRNP A1/A2 family have been identified by Western blot analysis and nuclear magnetic resonance to bind to this silencer. Employing an MS/MS-based approach and surface plasmon resonance imaging, we show for the first time that splicing factor SRSF10 binds to ISS-N1. Furthermore, using splice-switching oligonucleotides we modulated the splicing of the SRSF10 isoforms generating either the long or the short protein isoform of SRSF10 to regulate endogenous SMN2 exon 7 inclusion. We demonstrate that the isoforms of SRSF10 regulate SMN1 and SMN2 splicing with different strength correlating with the length of their RS domain. Our results suggest that the ratio between the SRSF10 isoforms is important for splicing regulation.
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Affiliation(s)
- Sabrina B Frederiksen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Lise L Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Henriette S Andersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Center for Genetic Diseases, Chicago Medical School and School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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19
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Abstract
Antisense oligonucleotides represent a novel therapeutic platform for the discovery of medicines that have the potential to treat most neurodegenerative diseases. Antisense drugs are currently in development for the treatment of amyotrophic lateral sclerosis, Huntington's disease, and Alzheimer's disease, and multiple research programs are underway for additional neurodegenerative diseases. One antisense drug, nusinersen, has been approved for the treatment of spinal muscular atrophy. Importantly, nusinersen improves disease symptoms when administered to symptomatic patients rather than just slowing the progression of the disease. In addition to the benefit to spinal muscular atrophy patients, there are discoveries from nusinersen that can be applied to other neurological diseases, including method of delivery, doses, tolerability of intrathecally delivered antisense drugs, and the biodistribution of intrathecal dosed antisense drugs. Based in part on the early success of nusinersen, antisense drugs hold great promise as a therapeutic platform for the treatment of neurological diseases.
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Affiliation(s)
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
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20
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Abstract
RNA splicing, the spliceosome-catalyzed process by which pre-messenger RNA (pre-mRNA) is processed to mature mRNA, is altered in a number of ways in cancer. Tumor-specific splicing alterations are created by mutations that disrupt splicing-regulatory elements within genes and impair splicing recognition or by altering the RNA-binding preferences of individual splicing factors. This SnapShot summarizes our current understanding of splicing-factor alterations in cancers. To view this SnapShot, open or download the PDF.
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Affiliation(s)
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Omar Abdel-Wahab
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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21
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Lin KT, Krainer AR. PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics 2020; 35:5048-5054. [PMID: 31135034 DOI: 10.1093/bioinformatics/btz438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/24/2019] [Accepted: 05/22/2019] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet). RESULTS PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers. AVAILABILITY AND IMPLEMENTATION PSI-Sigma is implemented is available at https://github.com/wososa/PSI-Sigma.
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Affiliation(s)
- Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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22
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Sheng L, Rigo F, Bennett CF, Krainer AR, Hua Y. Comparison of the efficacy of MOE and PMO modifications of systemic antisense oligonucleotides in a severe SMA mouse model. Nucleic Acids Res 2020; 48:2853-2865. [PMID: 32103257 PMCID: PMC7102994 DOI: 10.1093/nar/gkaa126] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a motor neuron disease. Nusinersen, a splice-switching antisense oligonucleotide (ASO), was the first approved drug to treat SMA. Based on prior preclinical studies, both 2′-O-methoxyethyl (MOE) with a phosphorothioate backbone and morpholino with a phosphorodiamidate backbone—with the same or extended target sequence as nusinersen—displayed efficient rescue of SMA mouse models. Here, we compared the therapeutic efficacy of these two modification chemistries in rescue of a severe mouse model using ASO10-29—a 2-nt longer version of nusinersen—via subcutaneous injection. Although both chemistries efficiently corrected SMN2 splicing in various tissues, restored motor function and improved the integrity of neuromuscular junctions, MOE-modified ASO10-29 (MOE10-29) was more efficacious than morpholino-modified ASO10-29 (PMO10-29) at the same molar dose, as seen by longer survival, greater body-weight gain and better preservation of motor neurons. Time-course analysis revealed that MOE10-29 had more persistent effects than PMO10-29. On the other hand, PMO10-29 appears to more readily cross an immature blood-brain barrier following systemic administration, showing more robust initial effects on SMN2 exon 7 inclusion, but less persistence in the central nervous system. We conclude that both modifications can be effective as splice-switching ASOs in the context of SMA and potentially other diseases, and discuss the advantages and disadvantages of each.
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Affiliation(s)
- Lei Sheng
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Department of Orthopedics, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA.,Institute of Neuroscience, Soochow University, 199 Ren-Ai Road, Suzhou, Jiangsu 215123, China
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23
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Scharner J, Ma WK, Zhang Q, Lin KT, Rigo F, Bennett CF, Krainer AR. Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res 2020; 48:802-816. [PMID: 31802121 PMCID: PMC6954394 DOI: 10.1093/nar/gkz1132] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/03/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Splice-switching antisense oligonucleotides (ASOs), which bind specific RNA-target sequences and modulate pre-mRNA splicing by sterically blocking the binding of splicing factors to the pre-mRNA, are a promising therapeutic modality to treat a range of genetic diseases. ASOs are typically 15–25 nt long and considered to be highly specific towards their intended target sequence, typically elements that control exon definition and/or splice-site recognition. However, whether or not splice-modulating ASOs also induce hybridization-dependent mis-splicing of unintended targets has not been systematically studied. Here, we tested the in vitro effects of splice-modulating ASOs on 108 potential off-targets predicted on the basis of sequence complementarity, and identified 17 mis-splicing events for one of the ASOs tested. Based on analysis of data from two overlapping ASO sequences, we conclude that off-target effects are difficult to predict, and the choice of ASO chemistry influences the extent of off-target activity. The off-target events caused by the uniformly modified ASOs tested in this study were significantly reduced with mixed-chemistry ASOs of the same sequence. Furthermore, using shorter ASOs, combining two ASOs, and delivering ASOs by free uptake also reduced off-target activity. Finally, ASOs with strategically placed mismatches can be used to reduce unwanted off-target splicing events.
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Affiliation(s)
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
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24
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Rahman MA, Lin KT, Bradley RK, Abdel-Wahab O, Krainer AR. Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes Dev 2020; 34:413-427. [PMID: 32001512 PMCID: PMC7050488 DOI: 10.1101/gad.332270.119] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Oncogenic mutations in the RNA splicing factors SRSF2, SF3B1, and U2AF1 are the most frequent class of mutations in myelodysplastic syndromes and are also common in clonal hematopoiesis, acute myeloid leukemia, chronic lymphocytic leukemia, and a variety of solid tumors. They cause genome-wide splicing alterations that affect important regulators of hematopoiesis. Several mRNA isoforms promoted by the various splicing factor mutants comprise a premature termination codon (PTC) and are therefore potential targets of nonsense-mediated mRNA decay (NMD). In light of the mechanistic relationship between splicing and NMD, we sought evidence for a specific role of mutant SRSF2 in NMD. We show that SRSF2 Pro95 hot spot mutations elicit enhanced mRNA decay, which is dependent on sequence-specific RNA binding and splicing. SRSF2 mutants enhance the deposition of exon junction complexes (EJCs) downstream from the PTC through RNA-mediated molecular interactions. This architecture then favors the association of key NMD factors to elicit mRNA decay. Gene-specific blocking of EJC deposition by antisense oligonucleotides circumvents aberrant NMD promoted by mutant SRSF2, restoring the expression of PTC-containing transcript. Our study uncovered critical effects of SRSF2 mutants in hematologic malignancies, reflecting the regulation at multiple levels of RNA metabolism, from splicing to decay.
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Affiliation(s)
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Omar Abdel-Wahab
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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25
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Aznarez I, Nomakuchi TT, Tetenbaum-Novatt J, Rahman MA, Fregoso O, Rees H, Krainer AR. Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Rep 2019; 23:2186-2198. [PMID: 29768215 PMCID: PMC5999336 DOI: 10.1016/j.celrep.2018.04.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/20/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022] Open
Abstract
The splicing factor SRSF1 promotes nonsense-mediated mRNA decay (NMD), a quality control mechanism that degrades mRNAs with premature termination codons (PTCs). Here we show that transcript-bound SRSF1 increases the binding of NMD factor UPF1 to mRNAs while in, or associated with, the nucleus, bypassing UPF2 recruitment and promoting NMD. SRSF1 promotes NMD when positioned downstream of a PTC, which resembles the mode of action of exon junction complex (EJC) and NMD factors. Moreover, splicing and/or EJC deposition increase the effect of SRSF1 on NMD. Lastly, SRSF1 enhances NMD of PTC-containing endogenous transcripts that result from various events. Our findings reveal an alternative mechanism for UPF1 recruitment, uncovering an additional connection between splicing and NMD. SRSF1’s role in the mRNA’s journey from splicing to decay has broad implications for gene expression regulation and genetic diseases.
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Affiliation(s)
- Isabel Aznarez
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | | | - Oliver Fregoso
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Holly Rees
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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26
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Park S, Brugiolo M, Akerman M, Das S, Urbanski L, Geier A, Kesarwani AK, Fan M, Leclair N, Lin KT, Hu L, Hua I, George J, Muthuswamy SK, Krainer AR, Anczuków O. Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep 2019; 29:2672-2688.e7. [PMID: 31775037 PMCID: PMC6936330 DOI: 10.1016/j.celrep.2019.10.110] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Misregulation of alternative splicing is a hallmark of human tumors, yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer and uncover differences and redundancies in their targets and biological functions. We identify splicing factors frequently altered in human breast tumors and assay their oncogenic functions using breast organoid models. We demonstrate that not all splicing factors affect mammary tumorigenesis in MCF-10A cells. Specifically, the upregulation of SRSF4, SRSF6, or TRA2β disrupts acinar morphogenesis and promotes cell proliferation and invasion in MCF-10A cells. By characterizing the targets of these oncogenic splicing factors, we identify shared spliced isoforms associated with well-established cancer hallmarks. Finally, we demonstrate that TRA2β is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo, and its levels correlate with breast cancer patient survival.
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Affiliation(s)
- SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Mattia Brugiolo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Envisagenics Inc., New York, NY, USA,These authors contributed equally
| | - Shipra Das
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,These authors contributed equally
| | - Laura Urbanski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | | | | | - Martin Fan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nathan Leclair
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Leo Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ian Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Senthil K. Muthuswamy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Correspondence: (O.A.), (A.R.K.)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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27
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Yoshimi A, Lin KT, Wiseman DH, Rahman MA, Pastore A, Wang B, Lee SCW, Micol JB, Zhang XJ, de Botton S, Penard-Lacronique V, Stein EM, Cho H, Miles RE, Inoue D, Albrecht TR, Somervaille TCP, Batta K, Amaral F, Simeoni F, Wilks DP, Cargo C, Intlekofer AM, Levine RL, Dvinge H, Bradley RK, Wagner EJ, Krainer AR, Abdel-Wahab O. Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature 2019; 574:273-277. [PMID: 31578525 PMCID: PMC6858560 DOI: 10.1038/s41586-019-1618-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/28/2019] [Indexed: 12/17/2022]
Abstract
Transcription and pre-mRNA splicing are key steps in the control of gene expression and mutations in genes regulating each of these processes are common in leukaemia1,2. Despite the frequent overlap of mutations affecting epigenetic regulation and splicing in leukaemia, how these processes influence one another to promote leukaemogenesis is not understood and, to our knowledge, there is no functional evidence that mutations in RNA splicing factors initiate leukaemia. Here, through analyses of transcriptomes from 982 patients with acute myeloid leukaemia, we identified frequent overlap of mutations in IDH2 and SRSF2 that together promote leukaemogenesis through coordinated effects on the epigenome and RNA splicing. Whereas mutations in either IDH2 or SRSF2 imparted distinct splicing changes, co-expression of mutant IDH2 altered the splicing effects of mutant SRSF2 and resulted in more profound splicing changes than either mutation alone. Consistent with this, co-expression of mutant IDH2 and SRSF2 resulted in lethal myelodysplasia with proliferative features in vivo and enhanced self-renewal in a manner not observed with either mutation alone. IDH2 and SRSF2 double-mutant cells exhibited aberrant splicing and reduced expression of INTS3, a member of the integrator complex3, concordant with increased stalling of RNA polymerase II (RNAPII). Aberrant INTS3 splicing contributed to leukaemogenesis in concert with mutant IDH2 and was dependent on mutant SRSF2 binding to cis elements in INTS3 mRNA and increased DNA methylation of INTS3. These data identify a pathogenic crosstalk between altered epigenetic state and splicing in a subset of leukaemias, provide functional evidence that mutations in splicing factors drive myeloid malignancy development, and identify spliceosomal changes as a mediator of IDH2-mutant leukaemogenesis.
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Affiliation(s)
- Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel H Wiseman
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | | | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Xiao Jing Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Eytan M Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel E Miles
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Todd R Albrecht
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Kiran Batta
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Fabio Amaral
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Fabrizio Simeoni
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Deepti P Wilks
- Manchester Cancer Research Centre Biobank, The University of Manchester, Manchester, UK
| | - Catherine Cargo
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Heidi Dvinge
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric J Wagner
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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28
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Li JJ, Lin X, Tang C, Lu YQ, Hu X, Zuo E, Li H, Ying W, Sun Y, Lai LL, Chen HZ, Guo XX, Zhang QJ, Wu S, Zhou C, Shen X, Wang Q, Lin MT, Ma LX, Wang N, Krainer AR, Shi L, Yang H, Chen WJ. Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice. Natl Sci Rev 2019; 7:92-101. [PMID: 34691481 PMCID: PMC8446915 DOI: 10.1093/nsr/nwz131] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022] Open
Abstract
We here report a genome-editing strategy to correct spinal muscular atrophy (SMA). Rather
than directly targeting the pathogenic exonic mutations, our strategy employed Cas9 and
guide-sgRNA for the targeted disruption of intronic splicing-regulatory elements. We
disrupted intronic splicing silencers (ISSs, including ISS-N1 and ISS + 100) of survival
motor neuron (SMN) 2, a key modifier gene of SMA, to enhance exon 7 inclusion and
full-length SMN expression in SMA iPSCs. Survival of splicing-corrected iPSC-derived motor
neurons was rescued with SMN restoration. Furthermore, co-injection of Cas9 mRNA from
Streptococcus pyogenes (SpCas9) or Cas9 from Staphylococcus
aureus (SaCas9) alongside their corresponding sgRNAs targeting ISS-N1 into
zygotes rescued 56% and 100% of severe SMA transgenic mice
(Smn−/−, SMN2tg/−). The median
survival of the resulting mice was extended to >400 days. Collectively, our study
provides proof-of-principle for a new strategy to therapeutically intervene in SMA and
other RNA-splicing-related diseases.
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Affiliation(s)
- Jin-Jing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiang Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Cheng Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying-Qian Lu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xinde Hu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Erwei Zuo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - He Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqin Ying
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yidi Sun
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu-Lu Lai
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Hai-Zhu Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xin-Xin Guo
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qi-Jie Zhang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Shuang Wu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Changyang Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaowen Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Ting Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Li-Xiang Ma
- Department of Anatomy, Histology & Embryology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Linyu Shi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
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29
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Sinha R, Kim YJ, Nomakuchi T, Sahashi K, Hua Y, Rigo F, Bennett CF, Krainer AR. Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice. Nucleic Acids Res 2019; 46:4833-4844. [PMID: 29672717 PMCID: PMC6007753 DOI: 10.1093/nar/gky249] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/28/2018] [Indexed: 12/19/2022] Open
Abstract
Familial dysautonomia (FD) is a rare inherited neurodegenerative disorder caused by a point mutation in the IKBKAP gene that results in defective splicing of its pre-mRNA. The mutation weakens the 5′ splice site of exon 20, causing this exon to be skipped, thereby introducing a premature termination codon. Though detailed FD pathogenesis mechanisms are not yet clear, correcting the splicing defect in the relevant tissue(s), thus restoring normal expression levels of the full-length IKAP protein, could be therapeutic. Splice-switching antisense oligonucleotides (ASOs) can be effective targeted therapeutics for neurodegenerative diseases, such as nusinersen (Spinraza), an approved drug for spinal muscular atrophy. Using a two-step screen with ASOs targeting IKBKAP exon 20 or the adjoining intronic regions, we identified a lead ASO that fully restored exon 20 splicing in FD patient fibroblasts. We also characterized the corresponding cis-acting regulatory sequences that control exon 20 splicing. When administered into a transgenic FD mouse model, the lead ASO promoted expression of full-length human IKBKAP mRNA and IKAP protein levels in several tissues tested, including the central nervous system. These findings provide insights into the mechanisms of IKBKAP exon 20 recognition, and pre-clinical proof of concept for an ASO-based targeted therapy for FD.
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Affiliation(s)
- Rahul Sinha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University School of Medicine, Stony Brook, NY 11790, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University School of Medicine, Stony Brook, NY 11790, USA
| | - Kentaro Sahashi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92008, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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30
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Feng H, Bao S, Rahman MA, Weyn-Vanhentenryck SM, Khan A, Wong J, Shah A, Flynn ED, Krainer AR, Zhang C. Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol Cell 2019; 74:1189-1204.e6. [PMID: 31226278 PMCID: PMC6676488 DOI: 10.1016/j.molcel.2019.02.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/30/2022]
Abstract
RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence motifs in their target transcripts, but precisely defining their binding specificity remains challenging. Crosslinking and immunoprecipitation (CLIP) allows for mapping of the exact protein-RNA crosslink sites, which frequently reside at specific positions in RBP motifs at single-nucleotide resolution. Here, we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the discovered motifs by genome-wide analysis of allelic binding sites. Our analyses revealed that the prototypical SR protein SRSF1 recognizes clusters of GGA half-sites in addition to its canonical GGAGGA motif. Therefore, SRSF1 regulates splicing of a much larger repertoire of transcripts than previously appreciated, including HNRNPD and HNRNPDL, which are involved in multivalent protein assemblies and phase separation.
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Affiliation(s)
- Huijuan Feng
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | | | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Aziz Khan
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Justin Wong
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Ankeeta Shah
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Elise D Flynn
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
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31
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Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I. Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell 2019; 35:369-384.e7. [PMID: 30799057 PMCID: PMC6424627 DOI: 10.1016/j.ccell.2019.01.010] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/26/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are essential modulators of transcription and translation frequently dysregulated in cancer. We systematically interrogated RBP dependencies in human cancers using a comprehensive CRISPR/Cas9 domain-focused screen targeting RNA-binding domains of 490 classical RBPs. This uncovered a network of physically interacting RBPs upregulated in acute myeloid leukemia (AML) and crucial for maintaining RNA splicing and AML survival. Genetic or pharmacologic targeting of one key member of this network, RBM39, repressed cassette exon inclusion and promoted intron retention within mRNAs encoding HOXA9 targets as well as in other RBPs preferentially required in AML. The effects of RBM39 loss on splicing further resulted in preferential lethality of spliceosomal mutant AML, providing a strategy for treatment of AML bearing RBP splicing mutations.
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Affiliation(s)
- Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xufeng Chen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jochen Imig
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kathryn Hockemeyer
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Yohana E Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michelle Ki
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lillian Bitner
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andreas Kloetgen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Taisuke Uehara
- Tsukuba Research Laboratories, Eisai Company, Ltd, Tsukuba, Ibaraki 300-4352, Japan
| | - Takashi Owa
- Tsukuba Research Laboratories, Eisai Company, Ltd, Tsukuba, Ibaraki 300-4352, Japan
| | - Raoul Tibes
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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32
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Sheng L, Wan B, Feng P, Sun J, Rigo F, Bennett CF, Akerman M, Krainer AR, Hua Y. Downregulation of Survivin contributes to cell-cycle arrest during postnatal cardiac development in a severe spinal muscular atrophy mouse model. Hum Mol Genet 2019; 27:486-498. [PMID: 29220503 DOI: 10.1093/hmg/ddx418] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the leading genetic cause of infant mortality, characterized by progressive degeneration of spinal-cord motor neurons, leading to atrophy of skeletal muscles. However, accumulating evidence indicates that it is a multi-system disorder, particularly in its severe forms. Several studies delineated structural and functional cardiac abnormalities in SMA patients and mouse models, yet the abnormalities have been primarily attributed to autonomic dysfunction. Here, we show in a severe mouse model that its cardiomyocytes undergo G0/G1 cell-cycle arrest and enhanced apoptosis during postnatal development. Microarray and real-time RT-PCR analyses revealed that a set of genes associated with cell cycle and apoptosis were dysregulated in newborn pups. Of particular interest, the Birc5 gene, which encodes Survivin, an essential protein for heart development, was down-regulated even on pre-symptomatic postnatal day 0. Interestingly, cultured cardiomyocytes depleted of SMN recapitulated the gene expression changes including downregulation of Survivin and abnormal cell-cycle progression; and overexpression of Survivin rescued the cell-cycle defect. Finally, increasing SMN in SMA mice with a therapeutic antisense oligonucleotide improved heart pathology and recovered expression of deregulated genes. Collectively, our data demonstrate that the cardiac malfunction of the severe SMA mouse model is mainly a cell-autonomous defect, caused by widespread gene deregulation in heart tissue, particularly of Birc5, resulting in developmental abnormalities through cell-cycle arrest and apoptosis.
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Affiliation(s)
- Lei Sheng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Bo Wan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Pengchao Feng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Junjie Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.,Envisagenics, Inc., New York, NY 10017, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
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33
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Wong MS, Kinney JB, Krainer AR. Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell 2018; 71:1012-1026.e3. [PMID: 30174293 DOI: 10.1016/j.molcel.2018.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/18/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023]
Abstract
Pre-mRNA splicing is an essential step in the expression of most human genes. Mutations at the 5' splice site (5'ss) frequently cause defective splicing and disease due to interference with the initial recognition of the exon-intron boundary by U1 small nuclear ribonucleoprotein (snRNP), a component of the spliceosome. Here, we use a massively parallel splicing assay (MPSA) in human cells to quantify the activity of all 32,768 unique 5'ss sequences (NNN/GYNNNN) in three different gene contexts. Our results reveal that although splicing efficiency is mostly governed by the 5'ss sequence, there are substantial differences in this efficiency across gene contexts. Among other uses, these MPSA measurements facilitate the prediction of 5'ss sequence variants that are likely to cause aberrant splicing. This approach provides a framework to assess potential pathogenic variants in the human genome and streamline the development of splicing-corrective therapies.
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Affiliation(s)
- Mandy S Wong
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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34
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Lin KT, Ma WK, Scharner J, Liu YR, Krainer AR. A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res 2018; 28:gr.227181.117. [PMID: 29449409 PMCID: PMC5848607 DOI: 10.1101/gr.227181.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/24/2018] [Indexed: 01/05/2023]
Abstract
Pre-mRNA splicing can contribute to the switch of cell identity that occurs in carcinogenesis. Here, we analyze a large collection of RNA-seq data sets and report that splicing changes in hepatocyte-specific enzymes, such as AFMID and KHK, are associated with HCC patients' survival and relapse. The switch of AFMID isoforms is an early event in HCC development and is associated with driver mutations in TP53 and ARID1A The switch of AFMID isoforms is human-specific and not detectable in other species, including primates. Finally, we show that overexpression of the full-length AFMID isoform leads to a higher NAD+ level, lower DNA-damage response, and slower cell growth in HepG2 cells. The integrative analysis uncovered a mechanistic link between splicing switches, de novo NAD+ biosynthesis, driver mutations, and HCC recurrence.
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Affiliation(s)
- Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Juergen Scharner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan 11031
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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35
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Wu X, Wang SH, Sun J, Krainer AR, Hua Y, Prior TW. A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy. Hum Mol Genet 2018; 26:2768-2780. [PMID: 28460014 DOI: 10.1093/hmg/ddx166] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 04/25/2017] [Indexed: 01/14/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by reduced expression of survival of motor neuron (SMN), a protein expressed in humans by two paralogous genes, SMN1 and SMN2. These genes are nearly identical, except for 10 single-nucleotide differences and a 5-nucleotide insertion in SMN2. SMA is subdivided into four main types, with type I being the most severe. SMN2 copy number is a key positive modifier of the disease, but it is not always inversely correlated with clinical severity. We previously reported the c.859G > C variant in SMN2 exon 7 as a positive modifier in several patients. We have now identified A-44G as an additional positive disease modifier, present in a group of patients carrying 3 SMN2 copies but displaying milder clinical phenotypes than other patients with the same SMN2 copy number. One of the three SMN2 copies appears to have been converted from SMN1, but except for the C6T transition, no other changes were detected. Analyzed with minigenes, SMN1C6T displayed a ∼20% increase in exon 7 inclusion, compared to SMN2. Through systematic mutagenesis, we found that the improvement in exon 7 splicing is mainly attributable to the A-44G transition in intron 6. Using RNA-affinity chromatography and mass spectrometry, we further uncovered binding of the RNA-binding protein HuR to the -44 region, where it acts as a splicing repressor. The A-44G change markedly decreases the binding affinity of HuR, resulting in a moderate increase in exon 7 inclusion.
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Affiliation(s)
- Xingxing Wu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Shu-Huei Wang
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Junjie Sun
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215123, China
| | - Thomas W Prior
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
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36
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Abstract
Tumor-associated alterations in RNA splicing result either from mutations in splicing-regulatory elements or changes in components of the splicing machinery. This review summarizes our current understanding of the role of splicing-factor alterations in human cancers. We describe splicing-factor alterations detected in human tumors and the resulting changes in splicing, highlighting cell-type-specific similarities and differences. We review the mechanisms of splicing-factor regulation in normal and cancer cells. Finally, we summarize recent efforts to develop novel cancer therapies, based on targeting either the oncogenic splicing events or their upstream splicing regulators.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Doktor TK, Hua Y, Andersen HS, Brøner S, Liu YH, Wieckowska A, Dembic M, Bruun GH, Krainer AR, Andresen BS. RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns. Nucleic Acids Res 2016; 45:395-416. [PMID: 27557711 PMCID: PMC5224493 DOI: 10.1093/nar/gkw731] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 11/21/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity is correlated with decreased snRNP assembly activity. In particular, the minor spliceosomal snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in patient cells and animal models. SMA is characterized by loss of motor neurons, but the underlying mechanism is largely unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show elevated U12-intron retention in all examined tissues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN in HeLa cells. Furthermore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and that many transcriptional changes are reversed. Finally, we report on missplicing of several Ca2+ channel genes that may explain disrupted Ca2+ homeostasis in SMA and activation of Cdk5.
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Affiliation(s)
- Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Henriette Skovgaard Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Sabrina Brøner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Anna Wieckowska
- Department of Gamete and Embryo Biology, Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-243 Olsztyn, Poland
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark .,The Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
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38
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Bruun GH, Doktor TK, Borch-Jensen J, Masuda A, Krainer AR, Ohno K, Andresen BS. Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol 2016; 14:54. [PMID: 27380775 PMCID: PMC4932749 DOI: 10.1186/s12915-016-0279-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/23/2016] [Indexed: 01/14/2023] Open
Abstract
Background Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. Results Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5’ splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5′ splice site can be blocked by SSOs to activate the exon. Conclusions The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0279-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gitte H Bruun
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Jonas Borch-Jensen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY, 11724, USA
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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Arun G, Diermeier S, Akerman M, Chang KC, Wilkinson J, Hearn S, Kim Y, MacLeod A, Krainer AR, Norton L, Brogi E, Egeblad M, Spector DL. Abstract PR11: Differentiation of mammary tumors and reduction in metastasis upon Malat1 LncRNA loss. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-pr11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genome-wide studies have identified thousands of long non-coding RNAs (lncRNAs) lacking protein-coding capacity. MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is among the most abundant and highly conserved nuclear restricted lncRNAs whose expression is mis-regulated in many cancers including breast cancer. RNA-FISH experiments on primary tumor and metastatic nodules from patients with luminal type breast cancer revealed that MALAT1 lncRNA is 4-5 times up regulated in metastatic nodules compared to primary tumors. This strongly suggests that MALAT1 plays an important role in the metastatic progression of luminal breast cancers. We have used the MMTV-PyMT mouse model of luminal B breast cancer to characterize the role of Malat1 in primary breast cancer and its subsequent metastasis. Malat1 lncRNA was knocked down via subcutaneous administration of antisense oligonucleotides (ASOs) at a dose of 125mg/kg/week over a period of 7 weeks after which animals were sacrificed and primary tumors and lungs were removed for molecular and histological analyses. Malat1 ASO treatment resulted in ~60% knockdown in the primary tumor concomitant with a significant reduction in tumor progression rate as well as a change in the differentiation status. Detailed histo-pathological analysis of ASO treated tumors showed an increase in well-differentiated ductular tumors, whereas scrambled ASO treated tumors progressed to solid carcinomas. Most interestingly, a marked decrease was observed in the incidence of lung metastases; ~70% fewer metastatic nodules in Malat1 ASO treated animals than scrambled ASO treated animals. Further, Malat1 ASO treated ex-vivo generated mammary gland organoids from MMTV-PyMT mice, resulted in an inhibition of branching morphogenesis, which recapitulates the invasive process that initiate metastases in vivo. RNA-seq analysis of the primary tumors and tumor derived organoids treated with Malat1 ASO showed up-regulation of genes involved in differentiation and down regulation of genes involved in migration and proliferation. Further, Malat1 knock-down also resulted in aberrant splicing of many genes including critical transcription factors. Together, our data indicates that Malat1 lncRNA regulates critical processes in breast cancer pathogenesis and represents a promising therapeutic target for treatment.
This abstract is also presented as Poster B02.
Citation Format: Gayatri Arun, Sarah Diermeier, Martin Akerman, Kung-Chi Chang, J.Erby Wilkinson, Stephen Hearn, Youngsoo Kim, A.Robert MacLeod, Adrian R. Krainer, Larry Norton, Edi Brogi, Mikala Egeblad, David L. Spector. Differentiation of mammary tumors and reduction in metastasis upon Malat1 LncRNA loss. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr PR11.
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Affiliation(s)
- Gayatri Arun
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | | | - Stephen Hearn
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
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Anczuków O, Das S, Lin KT, Wu J, Akerman M, Muthuswamy SK, Krainer AR. Abstract A50: Nonredundant functions of splicing factors in breast-cancer initiation and metastasis. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.advbc15-a50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Alternative splicing is a key control point in gene expression, whose misregulation contributes to cancer malignancy. Although certain splicing factors (SFs) and their targets are altered in human tumors, the functional significance of these alterations remains unclear. We previously demonstrated that the splicing factor SRSF1 is upregulated in human breast tumors and promotes transformation in vivo and in vitro. SRSF1 is a prototypical member of the SR protein family, composed of 12 structurally related proteins. However, little is known about differences and redundancies in their splicing targets and biological functions. Here, we investigated whether additional SFs also promoted breast cancer, using transformation models that mimic the relevant biological context. In parallel, we used RNA sequencing (RNA-seq) to systematically identify their oncogenic splicing targets.
By mining a large collection of human tumors from the TCGA project, we defined the molecular portraits of SFs alterations in breast tumors. We identified five SFs amplified and/or overexpressed in at least 10% of breast tumors. We then used SF-overexpressing human mammary epithelial MCF-10A cells grown in organotypic 3-D culture; these cells form polarized growth-arrested acinar structures, similar to the terminal units of mammary ducts. Various breast-cancer oncogenes are known to disrupt acinar growth and/or architecture. Interestingly, only certain SFs were oncogenic in this context, differentially affecting cell proliferation, apoptosis, or acinar organization, suggesting non-redundant functions. We then characterized the splicing targets relevant for SF-mediated transformation. We developed a bioinformatics pipeline to identify and quantify splicing variation in RNA-seq data. We defined the global repertoire of SF-regulated splicing events in 3-D culture and compared the target specificities of various SR proteins. In addition, we identified splicing targets regulated both in 3-D culture as well as in human breast tumors. Strikingly, SFs that promoted similar phenotypic changes shared a significant number of splicing targets, suggesting that they regulate common genes to promote tumor initiation. Furthermore, specific SFs affected targets previously associated with epithelial to mesenchymal transition, and increased cell migration or invasion. Finally, we uncovered that the splicing regulator TRA2β is required for the maintenance of metastatic properties of human breast-cancer cells in 3-D culture and in mouse orthotopic models. Furthermore, TRA2β levels correlate with increased metastatic incidence in breast cancer patients. Thus TRA2β represent a potential target for therapeutics development.
In summary, we gained new insights into the biological functions of SR proteins and identified novel oncogenic SF-regulated splicing events involved in tumor initiation and metastasis.
Citation Format: Olga Anczuków, Shipra Das, Kuan-Ting Lin, Jie Wu, Martin Akerman, Senthil K. Muthuswamy, Adrian R. Krainer. Nonredundant functions of splicing factors in breast-cancer initiation and metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A50.
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Affiliation(s)
- Olga Anczuków
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Shipra Das
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Kuan-Ting Lin
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Jie Wu
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
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Anczuków O, Akerman M, Cléry A, Wu J, Shen C, Shirole NH, Raimer A, Sun S, Jensen MA, Hua Y, Allain FHT, Krainer AR. SRSF1-Regulated Alternative Splicing in Breast Cancer. Mol Cell 2016; 60:105-17. [PMID: 26431027 DOI: 10.1016/j.molcel.2015.09.005] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 07/24/2015] [Accepted: 08/28/2015] [Indexed: 12/28/2022]
Abstract
Splicing factor SRSF1 is upregulated in human breast tumors, and its overexpression promotes transformation of mammary cells. Using RNA-seq, we identified SRSF1-regulated alternative splicing (AS) targets in organotypic three-dimensional MCF-10A cell cultures that mimic a context relevant to breast cancer. We identified and validated hundreds of endogenous SRSF1-regulated AS events. De novo discovery of the SRSF1 binding motif reconciled discrepancies in previous motif analyses. Using a Bayesian model, we determined positional effects of SRSF1 binding on cassette exons: binding close to the 5' splice site generally promoted exon inclusion, whereas binding near the 3' splice site promoted either exon skipping or inclusion. Finally, we identified SRSF1-regulated AS events deregulated in human tumors; overexpressing one such isoform, exon-9-included CASC4, increased acinar size and proliferation, and decreased apoptosis, partially recapitulating SRSF1's oncogenic effects. Thus, we uncovered SRSF1 positive and negative regulatory mechanisms, and oncogenic AS events that represent potential targets for therapeutics development.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Antoine Cléry
- Institute for Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jie Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Chen Shen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Nitin H Shirole
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Amanda Raimer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shuying Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Mads A Jensen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yimin Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Arun G, Diermeier S, Akerman M, Chang KC, Wilkinson JE, Hearn S, Kim Y, MacLeod AR, Krainer AR, Norton L, Brogi E, Egeblad M, Spector DL. Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss. Genes Dev 2015; 30:34-51. [PMID: 26701265 PMCID: PMC4701977 DOI: 10.1101/gad.270959.115] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/24/2015] [Indexed: 12/29/2022]
Abstract
Genome-wide analyses have identified thousands of long noncoding RNAs (lncRNAs). Malat1 (metastasis-associated lung adenocarcinoma transcript 1) is among the most abundant lncRNAs whose expression is altered in numerous cancers. Here we report that genetic loss or systemic knockdown of Malat1 using antisense oligonucleotides (ASOs) in the MMTV (mouse mammary tumor virus)-PyMT mouse mammary carcinoma model results in slower tumor growth accompanied by significant differentiation into cystic tumors and a reduction in metastasis. Furthermore, Malat1 loss results in a reduction of branching morphogenesis in MMTV-PyMT- and Her2/neu-amplified tumor organoids, increased cell adhesion, and loss of migration. At the molecular level, Malat1 knockdown results in alterations in gene expression and changes in splicing patterns of genes involved in differentiation and protumorigenic signaling pathways. Together, these data demonstrate for the first time a functional role of Malat1 in regulating critical processes in mammary cancer pathogenesis. Thus, Malat1 represents an exciting therapeutic target, and Malat1 ASOs represent a potential therapy for inhibiting breast cancer progression.
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Affiliation(s)
- Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sarah Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kung-Chi Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
| | - J Erby Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Youngsoo Kim
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11790, USA
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Nomakuchi TT, Rigo F, Aznarez I, Krainer AR. Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay. Nat Biotechnol 2015; 34:164-6. [PMID: 26655495 PMCID: PMC4744113 DOI: 10.1038/nbt.3427] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/09/2015] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular quality-control mechanism that is thought to exacerbate the phenotype of certain pathogenic nonsense mutations by preventing the expression of semi-functional proteins. NMD also limits the efficacy of read-through compound (RTC)-based therapies. Here, we report a gene-specific method of NMD inhibition using antisense oligonucleotides (ASOs), and combine this approach with an RTC to effectively restore the expression of full-length protein from a nonsense-mutant allele.
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Affiliation(s)
- Tomoki T Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Stony Brook University School of Medicine, Stony Brook, New York, USA
| | - Frank Rigo
- Isis Pharmaceuticals, Carslbad, California, USA
| | - Isabel Aznarez
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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Abstract
Alterations in RNA splicing are frequent in human tumors. Two recent studies of lymphoma and breast cancer have identified components of the spliceosome - the core splicing machinery - that are essential for malignant transformation driven by the transcription factor MYC. These findings provide a direct link between MYC and RNA splicing deregulation, and raise the exciting possibility of targeting spliceosome components in MYC-driven tumors.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
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Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 2015; 162:900-10. [PMID: 26276636 PMCID: PMC4642453 DOI: 10.1016/j.cell.2015.07.038] [Citation(s) in RCA: 634] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/30/2015] [Accepted: 07/22/2015] [Indexed: 01/27/2023]
Abstract
CTCF and the associated cohesin complex play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context, the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. These findings reveal how 3D chromosome architecture can be encoded by linear genome sequences.
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Affiliation(s)
- Ya Guo
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Quan Xu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168(th) Street, New York, NY 10032, USA
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Jinhuan Li
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - David U Gorkin
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Inkyung Jung
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haiyang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Yanan Zhai
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Yuanxiao Tang
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Yichao Lu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Yonghu Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Zhilian Jia
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Wei Li
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Michael Q Zhang
- Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA; MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Bing Ren
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168(th) Street, New York, NY 10032, USA.
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China.
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Akerman M, Fregoso OI, Das S, Ruse C, Jensen MA, Pappin DJ, Zhang MQ, Krainer AR. Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol 2015; 16:119. [PMID: 26047612 PMCID: PMC4502471 DOI: 10.1186/s13059-015-0682-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
Background During spliceosome assembly, protein-protein interactions (PPI) are sequentially formed and disrupted to accommodate the spatial requirements of pre-mRNA substrate recognition and catalysis. Splicing activators and repressors, such as SR proteins and hnRNPs, modulate spliceosome assembly and regulate alternative splicing. However, it remains unclear how they differentially interact with the core spliceosome to perform their functions. Results Here, we investigate the protein connectivity of SR and hnRNP proteins to the core spliceosome using probabilistic network reconstruction based on the integration of interactome and gene expression data. We validate our model by immunoprecipitation and mass spectrometry of the prototypical splicing factors SRSF1 and hnRNPA1. Network analysis reveals that a factor’s properties as an activator or repressor can be predicted from its overall connectivity to the rest of the spliceosome. In addition, we discover and experimentally validate PPIs between the oncoprotein SRSF1 and members of the anti-tumor drug target SF3 complex. Our findings suggest that activators promote the formation of PPIs between spliceosomal sub-complexes, whereas repressors mostly operate through protein-RNA interactions. Conclusions This study demonstrates that combining in-silico modeling with biochemistry can significantly advance the understanding of structure and function relationships in the human spliceosome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0682-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Present address: Envisagenics, Inc, 315 Main St., 2nd floor, Huntington, NY, 11743, USA
| | - Oliver I Fregoso
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Watson School of Biological Sciences, Cold Spring Harbor, NY, 11724, USA.,Present address: Fred Hutchinson Cancer Research Center, Division of Human Biology, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Shipra Das
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Cristian Ruse
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Present address: New England Biolabs, 240 County Road, Ipswich, MA, 01938, UK
| | - Mads A Jensen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Present address: Santaris Pharma A/S, Horsholm, Denmark
| | | | - Michael Q Zhang
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA.,Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China
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Abstract
Efficient transcription of the HIV-1 genome is regulated by Tat, which recruits P-TEFb from the 7SK small nuclear ribonucleoprotein (snRNP) and other nucleoplasmic complexes to phosphorylate RNA polymerase II and other factors associated with the transcription complex. Although Tat activity is dependent on its binding to the viral TAR sequence, little is known about the cellular factors that might also assemble onto this region of the viral transcript. Here, we report that the splicing factor SRSF1 (SF2/ASF) and Tat recognize overlapping sequences within TAR and the 7SK RNA. SRSF1 expression can inhibit Tat transactivation by directly competing for its binding to TAR. Additionally, we provide evidence that SRSF1 can increase the basal level of viral transcription in the absence of Tat. We propose that SRSF1 activates transcription in the early stages of viral infection by recruiting P-TEFb to TAR from the 7SK snRNP. Whereas in the later stages, Tat substitutes for SRSF1 by promoting release of the stalled polymerase and more efficient transcriptional elongation.
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Affiliation(s)
- Sean Paz
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
| | | | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
- To whom correspondence should be addressed. Tel: +1 5612970627;
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48
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Affiliation(s)
- Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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49
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Staropoli JF, Li H, Chun SJ, Allaire N, Cullen P, Thai A, Fleet CM, Hua Y, Bennett CF, Krainer AR, Kerr D, McCampbell A, Rigo F, Carulli JP. Rescue of gene-expression changes in an induced mouse model of spinal muscular atrophy by an antisense oligonucleotide that promotes inclusion of SMN2 exon 7. Genomics 2015; 105:220-8. [PMID: 25645699 DOI: 10.1016/j.ygeno.2015.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/25/2015] [Indexed: 01/09/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by disruption of the survival motor neuron 1 (SMN1) gene, partly compensated for by the paralogous gene SMN2. Exon 7 inclusion is critical for full-length SMN protein production and occurs at a much lower frequency for SMN2 than for SMN1. Antisense oligonucleotide (ASO)-mediated blockade of an intron 7 splicing silencer was previously shown to promote inclusion of SMN2 exon 7 in SMA mouse models and mediate phenotypic rescue. However, downstream molecular consequences of this ASO therapy have not been defined. Here we characterize the gene-expression changes that occur in an induced model of SMA and show substantial rescue of those changes in central nervous system tissue upon intracerebroventricular administration of an ASO that promotes inclusion of exon 7, with earlier administration promoting greater rescue. This study offers a robust reference set of preclinical pharmacodynamic gene expression effects for comparison of other investigational therapies for SMA.
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Affiliation(s)
- John F Staropoli
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Huo Li
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Seung J Chun
- Neuroscience Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Norm Allaire
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Patrick Cullen
- Neuroscience Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Alice Thai
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Christina M Fleet
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Yimin Hua
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - C Frank Bennett
- Neuroscience Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Doug Kerr
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Alexander McCampbell
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA
| | - Frank Rigo
- Neuroscience Drug Discovery, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - John P Carulli
- Division of Genetics and Genomics, Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, USA.
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Hua Y, Liu YH, Sahashi K, Rigo F, Bennett CF, Krainer AR. Motor neuron cell-nonautonomous rescue of spinal muscular atrophy phenotypes in mild and severe transgenic mouse models. Genes Dev 2015; 29:288-97. [PMID: 25583329 PMCID: PMC4318145 DOI: 10.1101/gad.256644.114] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Survival of motor neuron (SMN) deficiency causes spinal muscular atrophy (SMA), but restoring SMN in motor neurons only partially rescues SMA in mouse models. Hua et al. address the relative importance of SMN restoration in the CNS versus peripheral tissues in mouse models by using a therapeutic splice-switching antisense oligonucleotide to restore SMN and a complementary decoy oligonucleotide to neutralize its effects in the CNS. Increasing SMN exclusively in peripheral tissues completely rescued necrosis in mild SMA mice and robustly extended survival in severe SMA mice, with significant improvements in vulnerable tissues and motor function. Survival of motor neuron (SMN) deficiency causes spinal muscular atrophy (SMA), but the pathogenesis mechanisms remain elusive. Restoring SMN in motor neurons only partially rescues SMA in mouse models, although it is thought to be therapeutically essential. Here, we address the relative importance of SMN restoration in the central nervous system (CNS) versus peripheral tissues in mouse models using a therapeutic splice-switching antisense oligonucleotide to restore SMN and a complementary decoy oligonucleotide to neutralize its effects in the CNS. Increasing SMN exclusively in peripheral tissues completely rescued necrosis in mild SMA mice and robustly extended survival in severe SMA mice, with significant improvements in vulnerable tissues and motor function. Our data demonstrate a critical role of peripheral pathology in the mortality of SMA mice and indicate that peripheral SMN restoration compensates for its deficiency in the CNS and preserves motor neurons. Thus, SMA is not a cell-autonomous defect of motor neurons in SMA mice.
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Affiliation(s)
- Yimin Hua
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Institute of Neuroscience, Soochow University, Suzhou, Jiangsu 215021, China; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kentaro Sahashi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Frank Rigo
- Isis Pharmaceuticals, Carlsbad, California 92010, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
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