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An H, Xia A, Liu S, Luo D, Geng L, Li B, Sun B, Xu Z. RBM39 Promotes Base Excision Repair to Facilitate the Progression of HCC by Stabilising OGG1 mRNA. Cell Prolif 2025:e70059. [PMID: 40364450 DOI: 10.1111/cpr.70059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/27/2025] [Accepted: 04/29/2025] [Indexed: 05/15/2025] Open
Abstract
Targeting base excision repair (BER) has been an attractive strategy in cancer therapeutics. RNA-binding motif protein 39 (RBM39) modulates the alternative splicing of numerous genes involved in cancer occurrence and progression. However, whether and how RBM39 regulates BER in hepatocellular carcinoma (HCC) remain unclear. Here, we found that under oxidative stress, RBM39 degradation or knockdown decreased BER efficiency in HCC cells using a well-designed BER reporter. Further assays showed that RBM39 promoted HCC cell proliferation, migration, and invasion, enhancing cell survival and inhibiting apoptosis. Mechanistically, RBM39 interacted with the mRNA of the essential glycosidase 8-oxoguanine-DNA glycosylase 1 (OGG1), thereby stabilising OGG1 mRNA. This in turn increases OGG1 expression and promotes BER efficiency in HCC. Moreover, data suggested that RBM39 degradation, combined with oxidative damage, could be more effective for HCC treatment than monotherapy, both in vitro and in xenograft mice models. Overall, we demonstrated that RBM39 regulated OGG1 stabilisation and improved BER efficiency, suggesting that combining the RBM39 degradant indisulam with the oxidising agent KBrO3 could be an emerging strategy for HCC treatment.
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Affiliation(s)
- Hongda An
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
| | - Anliang Xia
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- MOE Innovation Center for Basic Research in Tumor Immunotherapy, Hefei, China
- Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, China
| | - Siyuan Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- MOE Innovation Center for Basic Research in Tumor Immunotherapy, Hefei, China
- Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, China
| | - Dongjun Luo
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
| | - Longpo Geng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- MOE Innovation Center for Basic Research in Tumor Immunotherapy, Hefei, China
- Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, China
| | - Binghua Li
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- MOE Innovation Center for Basic Research in Tumor Immunotherapy, Hefei, China
- Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, China
| | - Zhu Xu
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- MOE Innovation Center for Basic Research in Tumor Immunotherapy, Hefei, China
- Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, China
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Li TF, Rothhaar P, Lang A, Grünvogel O, Colasanti O, Ugarte SMO, Traut J, Piras A, Acosta-Rivero N, Gonçalves Magalhães V, Springer E, Betz A, Huang HE, Park J, Qiu R, Gnouamozi GE, Mehnert AK, Thi VLD, Urban S, Muckenthaler M, Schlesner M, Wohlleber D, Binder M, Bartenschlager R, Pichlmair A, Lohmann V. RBM39 shapes innate immunity by controlling the expression of key factors of the interferon response. Front Immunol 2025; 16:1568056. [PMID: 40330464 PMCID: PMC12054253 DOI: 10.3389/fimmu.2025.1568056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Accepted: 03/18/2025] [Indexed: 05/08/2025] Open
Abstract
Background and aims The contribution of innate immunity to clearance of viral infections of the liver, in particular sensing via Toll-like receptor 3 (TLR3), is incompletely understood. We aimed to identify the factors contributing to the TLR3 response in hepatocytes via CRISPR/Cas9 screening. Methods A genome-wide CRISPR/Cas9 screen on the TLR3 pathway was performed in two liver-derived cell lines, followed by siRNA knockdown validation. SiRNA knockdown and indisulam treatment were used to study the role of RNA-binding motif protein 39 (RBM39) in innate immunity upon poly(I:C) or cytokine treatment and viral infections. Transcriptome, proteome, and alternative splicing were studied via RNA sequencing and mass spectrometry upon depletion of RBM39. Results Our CRISPR/Cas9 screen identified RBM39, which is highly expressed in hepatocytes, as an important regulator of the TLR3 pathway. Knockdown of RBM39 or treatment with indisulam, an aryl sulfonamide drug targeting RBM39 for proteasomal degradation, strongly reduced the induction of interferon-stimulated genes (ISGs) in response to double-stranded RNA (dsRNA) or viral infections. RNA sequencing (seq) and mass spectrometry identified that transcription and/or splicing of the key pathway components IRF3, RIG-I, and MDA5 were affected by RBM39 depletion, along with multiple other cellular processes identified previously. RBM39 knockdown further restrained type I and type III IFN pathways by reducing the expression of individual receptor subunits and STAT1/2. The function of RBM39 was furthermore not restricted to hepatocytes. Conclusion We identified RBM39 as a regulatory factor of cell intrinsic innate immune signaling. Depletion of RBM39 impaired TLR3, RIG-I/MDA5, and IFN responses by affecting the basal expression of key pathway components.
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Affiliation(s)
- Teng-Feng Li
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Paul Rothhaar
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Arthur Lang
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Oliver Grünvogel
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ombretta Colasanti
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Santa Mariela Olivera Ugarte
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Jannik Traut
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Antonio Piras
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nelson Acosta-Rivero
- Department of Infectious Diseases, Molecular Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | - Emely Springer
- Institute of Molecular Immunology, University Hospital Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Andreas Betz
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Hao-En Huang
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Jeongbin Park
- Bioinformatics and Omics Data Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruiyue Qiu
- Heidelberg University, Medical Faculty, Department of Pediatric Oncology, Hematology, Immunology and Pneumology, Heidelberg, Germany
| | - Gnimah Eva Gnouamozi
- Department of Infectious Diseases, Molecular Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ann-Kathrin Mehnert
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Viet Loan Dao Thi
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Martina Muckenthaler
- Heidelberg University, Medical Faculty, Department of Pediatric Oncology, Hematology, Immunology and Pneumology, Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, University Hospital Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marco Binder
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host-Interactions, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
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Wang Y, Yang X, Yang Z, Chen Z, Jiang H, Wang Y, Shen D, Su G. RBM39 Functions as a Potential Oncogene Through the NF-κB Signaling Pathway in Colorectal Cancer Cells. J Cancer 2025; 16:2233-2249. [PMID: 40302803 PMCID: PMC12036102 DOI: 10.7150/jca.105120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 03/02/2025] [Indexed: 05/02/2025] Open
Abstract
Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer and is the second leading cause of cancer-related deaths globally. Recently, RNA-binding protein 39(RBM39), a critical factor in tumor-targeted mRNA and protein expression, has played a vital role in tumorigenesis and has broad development prospects in clinical treatment and drug research. However, the functional roles of RBM39 in the progression of CRC remain largely unexplored. This study found that RBM39 is notably overexpressed at both the mRNA and protein levels in CRC tissues compared with normal adjacent tissues. RBM39 was identified as a potential therapeutic target for colorectal cancer. Elevated RBM39 mRNA levels in CRC patients indicated worse survival probabilities. We show that RBM39 enhances the proliferation, migration, and invasion ability of CRC cells. Furthermore, we have made an innovative discovery that increased RBM39 inhibits apoptosis in CRC cells. Mechanistically, RNA-seq analysis indicated that RBM39 activates the NF-κB pathway, which plays a pivotal role in driving the malignant biological behaviors of colorectal cancer. Notably, these findings represent a novel contribution to our understanding of the mechanistic underpinnings of CRC, as they have not been previously documented in the literature. In the in vivo nude mouse xenograft model, our study demonstrates that the targeted knockdown of RBM39 markedly suppresses tumor formation, highlighting a novel therapeutic strategy for combating colorectal cancer. In conclusion, RBM39 emerges as a promising candidate for clinical diagnosis and targeted treatment of colorectal cancer, with implications for future research in tumor biology and therapeutic strategies.
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Affiliation(s)
- YaTao Wang
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen,361003, Fujian Province, China
- The Sixth People's Hospital of Luoyang, 471003, Luoyang, Henan Province, China
| | - XueSi Yang
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen,361003, Fujian Province, China
| | - ZhangQuan Yang
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen,361003, Fujian Province, China
| | - ZiRui Chen
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen,361003, Fujian Province, China
| | - HaiFeng Jiang
- Department of Critical Care Medicine, Second People's Hospital of Yibin City, Yibin, 644000, Sichuan Province, China
| | - YiCong Wang
- Gastrointestinal Oncology, The Affiliated Hospital of Qinghai University, Xining 810000, Qinghai Province, China
| | - DongYan Shen
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, Fujian Province, China
| | - GuoQiang Su
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen,361003, Fujian Province, China
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, 350122, China
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Wang J, Zheng L, Chen W, Zhang X, Lv D, Zeng C, Zhang C, Zhang R, Kang T, Zhong L. Targeting RBM39 suppresses tumor growth and sensitizes osteosarcoma cells to cisplatin. Oncogene 2025; 44:575-586. [PMID: 39633066 DOI: 10.1038/s41388-024-03242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 11/19/2024] [Accepted: 11/28/2024] [Indexed: 12/07/2024]
Abstract
Osteosarcoma is one of the most common malignant primary bone tumors and lacks effective therapeutic targets. Recent studies have reported that RNA binding proteins (RBPs) could serve as promising therapeutic targets for cancers, as their critical roles in transcriptional regulation and RNA splicing. Nevertheless, the potential of pharmacologically inhibiting RBPs as a therapeutic strategy for patients with osteosarcoma remains unclear. In this study, we identified the RNA-binding protein RBM39 as a promising therapeutic target for osteosarcoma. RBM39 is essential for cell viability, and a higher expression of RBM39 was associated with poor prognosis in osteosarcoma. Mechanistically, RBM39 served as a coactivator of c-Jun to transcriptionally upregulate DKK1, leading to the activation of the GSK3β-NF-κB pathway. Importantly, our results reveal that the pharmacological depletion of RBM39 by using the anti-cancer aryl sulfonamide (E7820), a drug known for its oral bioavailability and safe administration, effectively represses osteosarcoma growth and sensitizes osteosarcoma cells to cisplatin treatment both in vitro and in vivo. Our findings unveil the crucial role of RBM39 in modulating tumor growth and cisplatin sensitivity in osteosarcoma cells, suggesting that the combination of aryl sulfonamides with cisplatin may benefit patients with osteosarcoma.
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Affiliation(s)
- Jingxuan Wang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanqi Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xia Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongming Lv
- Department of Burns, Wound Repair and Reconstruction, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Changlin Zhang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li Zhong
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.
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Ma J, Li S, Wang T, Tao Z, Huang S, Lin N, Zhao Y, Wang C, Li P. Cooperative condensation of RNA-DIRECTED DNA METHYLATION 16 splicing isoforms enhances heat tolerance in Arabidopsis. Nat Commun 2025; 16:433. [PMID: 39762263 PMCID: PMC11704304 DOI: 10.1038/s41467-025-55850-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 01/02/2025] [Indexed: 01/11/2025] Open
Abstract
Dissecting the mechanisms underlying heat tolerance is important for understanding how plants acclimate to heat stress. Here, we identify a heat-responsive gene in Arabidopsis thaliana, RNA-DIRECTED DNA METHYLATION 16 (RDM16), which encodes a pre-mRNA splicing factor. Knockout mutants of RDM16 are hypersensitive to heat stress, which is associated with impaired splicing of the mRNAs of 18 out of 20 HEAT SHOCK TRANSCRIPTION FACTOR (HSF) genes. RDM16 forms condensates upon exposure to heat. The arginine residues in intrinsically disordered region 1 (IDR1) of RDM16 are responsible for RDM16 condensation and its function in heat stress tolerance. Notably, RDM16 produces two alternatively spliced transcripts designated RDM16-LONG (RDL) and RDM16-SHORT (RDS). RDS also forms condensates and can promote RDL condensation to improve heat tolerance. Our findings provide insight into the cooperative condensation of the two RDM16 isoforms encoded by RDM16 splice variants in enhancing heat tolerance in Arabidopsis.
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Affiliation(s)
- Jing Ma
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shuai Li
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Tengyue Wang
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhen Tao
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shijie Huang
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Ning Lin
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yibing Zhao
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Chuanhong Wang
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China.
| | - Peijin Li
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China.
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Jang JH, Kim JY, Lee TJ. Recent advances in anticancer mechanisms of molecular glue degraders: focus on RBM39-dgrading synthetic sulfonamide such as indisulam, E7820, tasisulam, and chloroquinoxaline sulfonamide. Genes Genomics 2024; 46:1345-1361. [PMID: 39271535 DOI: 10.1007/s13258-024-01565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
Abstract
Synthetic sulfonamide anticancer drugs, including E7820, indisulam, tasisulam, and chloroquinoxaline sulfonamide, exhibit diverse mechanisms of action and therapeutic potential, functioning as molecular glue degraders. E7820 targets RBM39, affecting RNA splicing and angiogenesis by suppressing integrin α2. Phase I studies have demonstrated some stability in advanced solid malignancies; however, further efficacy studies are required. Indisulam causes G1 cell cycle arrest and delays the G1/S transition by modulating splicing through RBM39 degradation via DCAF15. Despite its limited initial efficacy, it shows promise in combination therapies, particularly for hematopoietic malignancies and gliomas. Tasisulam inhibits VEGF signaling, suppresses angiogenesis, and induces apoptosis. Although early trials indicated broad activity, safety concerns have halted its development. Chloroquinoxaline sulfonamide, initially investigated for cell cycle arrest and topoisomerase II inhibition, was discontinued owing to its limited efficacy and toxicity, despite promising initial results. Recent studies revealed the structural interaction of E7820 with DCAF15 and RBM39, although phase II trials on myeloid malignancies have shown limited efficacy. Indisulam is effective against glioblastoma and neuroblastoma, with potential synergy in combination therapies and metabolic disruption. Recent research on tasisulam reveals its potential in cancer therapy by targeting RBM39 degradation through DCAF15-mediated pathways. Understanding these mechanisms could lead to new treatments that affect alternative splicing and improve cancer therapies Overall, although these drugs exhibit promising mechanisms of action, further research is required to optimize their clinical efficacy and safety.
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Affiliation(s)
- Ji Hoon Jang
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea
| | - Joo-Young Kim
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea
| | - Tae-Jin Lee
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea.
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Chan EKL, Pollard KM, Fritzler MJ. Eng Meng Tan. Ann Rheum Dis 2024; 83:1256-1259. [PMID: 38830750 PMCID: PMC11503108 DOI: 10.1136/ard-2024-226025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Affiliation(s)
- Edward K L Chan
- Oral Biology, Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA
| | - K Michael Pollard
- Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Marvin J Fritzler
- Medicine, University of Calgary, Health Sciences Centre, Calgary, Alberta, Canada
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Zhang X, Yang L, Liu X, Nie Z, Liu M, Wang T, Lu Y, Pan Y, Zhan Y, Wang Z, Luo J. Regulatory role of RBM39 in acute myeloid leukemia: Mediation through the PI3K/AKT pathway. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119607. [PMID: 37852323 DOI: 10.1016/j.bbamcr.2023.119607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) presents ongoing therapeutic challenges due to its intricate molecular pathogenesis. This study aimed to elucidate the role of RNA binding motif protein 39 (RBM39) in AML cell proliferation, apoptosis, and chemosensitivity, and its potential modulation of the PI3K/AKT pathway. METHODS In vitro and in vivo experiments were conducted using AML cell lines (K562 and U937) and bone marrow mononuclear cells (BM-MNCs) from AML patients and healthy donors. RBM39 mRNA and protein levels were measured using qRT-PCR and Western blotting. Cells were transfected with sh-RBM39 or sh-control, and then treated with daunorubicin (DNR) or homoharringtonine (HHT) at varied concentrations. Cell proliferation, chemosensitivity, and apoptosis were assessed through CCK-8 assay and Annexin V-APC/PI staining. RNA sequencing identified differentially expressed genes (DEGs) post RBM39 knockdown. An in vivo xenograft AML model using E7070, a selective RBM39 inhibitor, was employed to evaluate RBM39 modulation effects. RESULTS Elevated RBM39 levels were found in AML patients and cell lines compared to controls. RBM39 knockdown promoted apoptosis, curtailed cell proliferation, and enhanced chemosensitivity to DNR and HHT in vitro. Drug-resistant or relapsed AML patients displayed higher RBM39 levels. RNA sequencing after RBM39 knockdown revealed downregulated PI3K/AKT signaling. The xenograft model validated in vitro results, as E7070 treatment suppressed AML xenograft growth via RBM39-mediated PI3K/AKT pathway suppression. CONCLUSION RBM39 plays a pivotal role in AML progression through the PI3K/AKT signaling pathway. Targeting RBM39, potentially with E7070, could inhibit proliferation and induce apoptosis in AML cells, offering a promising avenue for future AML research and treatment.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Lin Yang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaojun Liu
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ziyuan Nie
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Menghan Liu
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tianyang Wang
- Department of Hepatobiliary Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yaqiong Lu
- Department of Hematology Oncology, Hebei Children's Hospital, Shijiazhuang, China
| | - Yuxia Pan
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ying Zhan
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhenzhen Wang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianmin Luo
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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Bonner EA, Lee SC. Therapeutic Targeting of RNA Splicing in Cancer. Genes (Basel) 2023; 14:1378. [PMID: 37510283 PMCID: PMC10379351 DOI: 10.3390/genes14071378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
RNA splicing is a key regulatory step in the proper control of gene expression. It is a highly dynamic process orchestrated by the spliceosome, a macro-molecular machinery that consists of protein and RNA components. The dysregulation of RNA splicing has been observed in many human pathologies ranging from neurodegenerative diseases to cancer. The recent identification of recurrent mutations in the core components of the spliceosome in hematologic malignancies has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. This review article will discuss our current understanding of how aberrant RNA splicing regulation drives tumor initiation and progression. We will also review current therapeutic modalities and highlight emerging technologies designed to target RNA splicing for cancer treatment.
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Affiliation(s)
- Elizabeth A. Bonner
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA;
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stanley C. Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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10
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Eléouët M, Lu C, Zhou Y, Yang P, Ma J, Xu G. Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194902. [PMID: 36535628 DOI: 10.1016/j.bbagrm.2022.194902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
RNA-binding protein 39 (RBM39) involves in pre-mRNA splicing and transcriptional regulation. RBM39 is dysregulated in many cancers and its upregulation enhances cancer cell proliferation. Recently, it has been discovered that aryl sulfonamides act as molecular glues to recruit RBM39 to the CRL4DCAF15 E3 ubiquitin ligase complex for its ubiquitination and proteasomal degradation. Therefore, various studies have focused on the degradation of RBM39 by aryl sulfonamides in the aim of finding new cancer therapeutics. These discoveries also attracted focus for thorough study on the biological functions of RBM39. RBM39 was found to regulate the splicing and transcription of genes mainly involved in pre-mRNA splicing, cell cycle regulation, DNA damage response, and metabolism, but the understanding of these regulations is still in its infancy. This article reviews the advances of the current literature and discusses the remaining key issues on the biological function and dynamic regulation of RBM39 at the post-translational level.
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Affiliation(s)
- Morgane Eléouët
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China; Synbio Technologies Company, BioBay C20, 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Yijia Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Ping Yang
- Synbio Technologies Company, BioBay C20, 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Jingjing Ma
- Department of Pharmacy, Medical Center of Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
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11
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Tong L, Sun J, Zhang X, Ge D, Yang Y, Zhou J, Wang D, Hu X, Liu H, Bai C. Diagnostic value of tumor associated autoantibody panel in early detection of lung cancer in Chinese population: Protocol for a prospective, observational, and multicenter clinical trial. CLINICAL EHEALTH 2022. [DOI: 10.1016/j.ceh.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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12
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Zhang R, Wang W, Zhang N, Chen X, Liu W, Zhang L, Liu N. Systematic pan-cancer analysis identifies RBM39 as an immunological and prognostic biomarker. J Cell Mol Med 2022; 26:4859-4871. [PMID: 35989423 PMCID: PMC9465192 DOI: 10.1111/jcmm.17517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/27/2022] Open
Abstract
RNA‐binding Motif Protein39 (RBM39) is identified as a splicing factor and transcription coactivator. Despite mounting evidence that RBM39 plays a critical role in the development of specific malignancies, no systematic pan‐cancer investigation of RBM39 has been conducted. As a result, we set out to investigate RBM39’s prognostic significance and putative immunological activities in 33 different cancers. Based on TCGA and CCLE, GTEx, cBioportal and HPA, we used a series of bioinformatics approaches to explore the potential oncogenic role of RBM39, including analysis of the expression of the pan‐cancer species RBM39, the prognostic relationship between RBM39 expression and overall survival (OS), disease‐specific survival (DSS) and progression‐free interval (PFI), the relationship between RBM39 expression and clinical phenotype, analysis of the relationship between RBM39 expression and tumour mutational burden (TMB), microsatellite instability (MSI), DNA methylation and immune cell infiltration. Our results showed that RBM39 is overexpressed in most cancers. RBM39 was positively or negatively correlated with the prognosis of different tumours. RBM39 expression was associated with TMB and MSI in 9 and 12 cancer types. In addition, RBM39 expression was associated with DNA methylation in almost all tumours. There are eight tumours were screened for further study, including BRCA, COAD, HNSC, LIHC, LUSC, SKCM, STAD, UCEC. In the screed tumours, RBM39 was found to be negatively correlated with the infiltration of most immune cells. In addition, the correlation with RBM39 expression varied by immune cell subtype. Based on RBM39’s role in tumorigenesis and tumour immunity, we suggest it can serve as a surrogate prognostic marker.
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Affiliation(s)
- Rui Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Nie Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xueting Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Wanming Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Longzhen Zhang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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13
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Zhang J, Guo X, Jin B, Zhu Q. Editorial: Tumor-associated antigens and their autoantibodies, from discovering to clinical utilization. Front Oncol 2022; 12:970623. [PMID: 35936692 PMCID: PMC9346231 DOI: 10.3389/fonc.2022.970623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jianying Zhang
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, United States
- *Correspondence: Jianying Zhang, ; Xiangqian Guo,
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
- *Correspondence: Jianying Zhang, ; Xiangqian Guo,
| | - Bilian Jin
- Cancer Center, Dalian Medical University, Dalian, China
| | - Qing Zhu
- West China Hospital, Sichuan University, Chengdu, China
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14
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RNA-binding protein 39: a promising therapeutic target for cancer. Cell Death Discov 2021; 7:214. [PMID: 34389703 PMCID: PMC8363639 DOI: 10.1038/s41420-021-00598-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/04/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
RNA-binding motif protein 39 (RBM39), as a key factor in tumor-targeted mRNA and protein expression, not only plays a vital role in tumorigenesis, but also has broad development prospects in clinical treatment and drug research. Moreover, since RBM39 was identified as a target of sulfonamides, it has played a key role in the emerging field of molecule drug development. Hence, it is of great significance to study the interaction between RBM39 and tumors and the clinical application of drug-targeted therapy. In this paper, we describe the possible multi-level regulation of RBM39, including gene transcription, protein translation, and alternative splicing. Importantly, the molecular function of RBM39 as an important splicing factor in most common tumors is systematically outlined. Furthermore, we briefly introduce RBM39’s tumor-targeted drug research and its clinical application, hoping to give reference significance for the molecular mechanism of RBM39 in tumors, and provide reliable ideas for in-depth research for future therapeutic strategies.
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15
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.30.454526. [PMID: 34373855 PMCID: PMC8351778 DOI: 10.1101/2021.07.30.454526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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16
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Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.05.451199. [PMID: 34729561 PMCID: PMC8562547 DOI: 10.1101/2021.07.05.451199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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17
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Wang JY, Zhang W, Roehrl VB, Roehrl MW, Roehrl MH. An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.05.438500. [PMID: 33851168 PMCID: PMC8043459 DOI: 10.1101/2021.04.05.438500] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To understand how COVID-19 may induce autoimmune diseases, we have been compiling an atlas of COVID-autoantigens (autoAgs). Using dermatan sulfate (DS) affinity enrichment of autoantigenic proteins extracted from HS-Sultan lymphoblasts, we identified 362 DS-affinity proteins, of which at least 201 (56%) are confirmed autoAgs. Comparison with available multi-omic COVID data shows that 315 (87%) of the 362 proteins are affected in SARS-CoV-2 infection via altered expression, interaction with viral components, or modification by phosphorylation or ubiquitination, at least 186 (59%) of which are known autoAgs. These proteins are associated with gene expression, mRNA processing, mRNA splicing, translation, protein folding, vesicles, and chromosome organization. Numerous nuclear autoAgs were identified, including both classical ANAs and ENAs of systemic autoimmune diseases and unique autoAgs involved in the DNA replication fork, mitotic cell cycle, or telomerase maintenance. We also identified many uncommon autoAgs involved in nucleic acid and peptide biosynthesis and nucleocytoplasmic transport, such as aminoacyl-tRNA synthetases. In addition, this study found autoAgs that potentially interact with multiple SARS-CoV-2 Nsp and Orf components, including CCT/TriC chaperonin, insulin degrading enzyme, platelet-activating factor acetylhydrolase, and the ezrin-moesin-radixin family. Furthermore, B-cell-specific IgM-associated ER complex (including MBZ1, BiP, heat shock proteins, and protein disulfide-isomerases) is enriched by DS-affinity and up-regulated in B-cells of COVID-19 patients, and a similar IgH-associated ER complex was also identified in autoreactive pre-B1 cells in our previous study, which suggests a role of autoreactive B1 cells in COVID-19 that merits further investigation. In summary, this study demonstrates that virally infected cells are characterized by alterations of proteins with propensity to become autoAgs, thereby providing a possible explanation for infection-induced autoimmunity. The COVID autoantigen-ome provides a valuable molecular resource and map for investigation of COVID-related autoimmune sequelae and considerations for vaccine design.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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18
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Dopie J, Sweredoski MJ, Moradian A, Belmont AS. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins. J Cell Biol 2021; 219:151914. [PMID: 32609799 PMCID: PMC7480118 DOI: 10.1083/jcb.201910207] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/03/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
We present a simple ratio method to infer protein composition within cellular structures using proximity labeling approaches but compensating for the diffusion of free radicals. We used tyramide signal amplification (TSA) and label-free mass spectrometry (MS) to compare proteins in nuclear speckles versus centromeres. Our “TSA-MS ratio” approach successfully identified known nuclear speckle proteins. For example, 96% and 67% of proteins in the top 30 and 100 sorted proteins, respectively, are known nuclear speckle proteins, including proteins that we validated here as enriched in nuclear speckles. We show that MFAP1, among the top 20 in our list, forms droplets under certain circumstances and that MFAP1 expression levels modulate the size, stability, and dynamics of nuclear speckles. Localization of MFAP1 and its binding partner, PRPF38A, in droplet-like nuclear bodies precedes formation of nuclear speckles during telophase. Our results update older proteomic studies of nuclear speckles and should provide a useful reference dataset to guide future experimental dissection of nuclear speckle structure and function.
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Affiliation(s)
- Joseph Dopie
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Annie Moradian
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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19
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Xu Y, Nijhuis A, Keun HC. RNA-binding motif protein 39 (RBM39): An emerging cancer target. Br J Pharmacol 2020; 179:2795-2812. [PMID: 33238031 DOI: 10.1111/bph.15331] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/13/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
RNA-binding motif protein 39 (RBM39) is an RNA-binding protein involved in transcriptional co-regulation and alternative RNA splicing. Recent studies have revealed that RBM39 is the unexpected target of aryl sulphonamides, which act as molecular glues between RBM39 and the DCAF15-associated E3 ubiquitin ligase complex leading to selective degradation of the target. Loss of RBM39 leads to aberrant splicing events and differential gene expression, thereby inhibiting cell cycle progression and causing tumour regression in a number of preclinical models. Many clinical studies have shown that aryl sulphonamides were well tolerated, but their clinical performance was limited due to an insufficient understanding of the target, RBM39 biology and a lack of predictive biomarkers. This review summarises the current knowledge of RBM39 function and discusses the therapeutic potential of this spliceosome target in cancer therapy.
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Affiliation(s)
- Yuewei Xu
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Anke Nijhuis
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Hector C Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
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20
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Shi Y, Bray W, Smith AJ, Zhou W, Calaoagan J, Lagisetti C, Sambucetti L, Crews P, Lokey RS, Webb TR. An exon skipping screen identifies antitumor drugs that are potent modulators of pre-mRNA splicing, suggesting new therapeutic applications. PLoS One 2020; 15:e0233672. [PMID: 32469945 PMCID: PMC7259758 DOI: 10.1371/journal.pone.0233672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
Agents that modulate pre-mRNA splicing are of interest in multiple therapeutic areas, including cancer. We report our recent screening results with the application of a cell-based Triple Exon Skipping Luciferase Reporter (TESLR) using a library that is composed of FDA approved drugs, clinical compounds, and mechanistically characterized tool compounds. Confirmatory assays showed that three clinical antitumor therapeutic candidates (milciclib, PF-3758309 and PF-562271) are potent splicing modulators and that these drugs are, in fact, nanomolar inhibitors of multiple kinases involved in the regulation the spliceosome. We also report the identification of new SF3B1 antagonists (sudemycinol C and E) and show that these antagonists can be used to develop a displacement assay for SF3B1 small molecule ligands. These results further support the broad potential for the development of agents that target the spliceosome for the treatment of cancer and other diseases, as well as new avenues for the discovery of new chemotherapeutic agents for a range of diseases.
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Affiliation(s)
- Yihui Shi
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
| | - Walter Bray
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States of America
| | - Alexander J. Smith
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States of America
| | - Wei Zhou
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
| | - Joy Calaoagan
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
| | - Chandraiah Lagisetti
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
| | - Lidia Sambucetti
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States of America
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States of America
| | - Thomas R. Webb
- Bioscience Division, SRI International, Menlo Park, CA, United States of America
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States of America
- * E-mail:
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21
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Prieto C, Kharas MG. RNA Regulators in Leukemia and Lymphoma. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a034967. [PMID: 31615866 DOI: 10.1101/cshperspect.a034967] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Posttranscriptional regulation of mRNA is a powerful and tightly controlled process in which cells command the integrity, diversity, and abundance of their protein products. RNA-binding proteins (RBPs) are the principal players that control many intermediary steps of posttranscriptional regulation. Recent advances in this field have discovered the importance of RBPs in hematological diseases. Herein we will review a number of RBPs that have been determined to play critical functions in leukemia and lymphoma. Furthermore, we will discuss the potential therapeutic strategies that are currently being studied to specifically target RBPs in these diseases.
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Affiliation(s)
- Camila Prieto
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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22
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Královicová J, Ševcíková I, Stejskalová E, Obuca M, Hiller M, Stanek D, Vorechovský I. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res 2019; 46:6166-6187. [PMID: 29788428 PMCID: PMC6093180 DOI: 10.1093/nar/gky389] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/01/2018] [Indexed: 12/27/2022] Open
Abstract
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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Affiliation(s)
- Jana Královicová
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Ševcíková
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Eva Stejskalová
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Mina Obuca
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - David Stanek
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Igor Vorechovský
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
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23
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Zhang W, Rho JH, Roehrl MW, Roehrl MH, Wang JY. A repertoire of 124 potential autoantigens for autoimmune kidney diseases identified by dermatan sulfate affinity enrichment of kidney tissue proteins. PLoS One 2019; 14:e0219018. [PMID: 31237920 PMCID: PMC6592568 DOI: 10.1371/journal.pone.0219018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/13/2019] [Indexed: 12/30/2022] Open
Abstract
Autoantigens are the molecular targets in autoimmune diseases. They are a cohort of seemingly unrelated self-molecules present in different parts of the body, yet they can trigger a similar chain of autoimmune responses such as autoantibody production. We previously reported that dermatan sulfate (DS) can bind self-molecules of dying cells to stimulate autoreactive CD5+ B cells to produce autoantibodies. The formation of autoantigen-DS complexes converts the normally non-antigenic self-molecules to none-self antigens, and thus DS-affinity represents a common underlying biochemical property for autoantigens. This study sought to apply this property to identify potential autoantigens in the kidney. Total proteins were extracted from mouse kidney tissues and loaded onto DS-Sepharose resins. Proteins without affinity were washed off the resins, whereas those with increasing DS-affinity were eluted with step gradients of increasing salt strength. Fractions with strong and moderate DS-affinity were sequenced by mass spectrometry and yielded 25 and 99 proteins, respectively. An extensive literature search was conducted to validate whether these had been previously reported as autoantigens. Of the 124 proteins, 79 were reported autoantigens, and 19 out of 25 of the strong-DS-binding ones were well-known autoantigens. Moreover, these proteins largely fell into the two most common autoantibody categories in autoimmune kidney diseases, including 40 ANA (anti-nuclear autoantibodies) and 25 GBM (glomerular basement membrane) autoantigens. In summary, this study compiles a large repertoire of potential autoantigens for autoimmune kidney diseases. This autoantigen-ome sheds light on the molecular etiology of autoimmunity and further supports our hypothesis DS-autoantigen complexes as a unifying principle of autoantigenicity.
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Affiliation(s)
- Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York, United States of America
- * E-mail: (JYW); (MHR)
| | - Julia Y. Wang
- Curandis, Scarsdale, New York, United States of America
- * E-mail: (JYW); (MHR)
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24
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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: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [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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25
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Wang P, Qin J, Ye H, Li L, Wang X, Zhang J. Using a panel of multiple tumor-associated antigens to enhance the autoantibody detection in the immunodiagnosis of ovarian cancer. J Cell Biochem 2018; 120:3091-3100. [PMID: 30484895 DOI: 10.1002/jcb.27497] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 07/25/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND Ovarian cancer (OC) is a major malignancy affecting a large population over the world, and a biomarker that holds diagnostic potential is of critical importance. Recently, autoantibodies have been indicated as biomarkers in multiple cancer research. The current study was designed to explore the practice of using autoantibodies in diagnostic settings by the enzyme-linked immunosorbent assay of sera with a panel of tumor-associated antigens (TAAs). METHODS A panel of 12 TAAs was selected to detect the corresponding autoantibodies in sera sampled from 132 OC patients as case group and 147 normal healthy individuals as the control group. The diagnostic potential of this panel was evaluated by conventional evaluation, receiver operating characteristic (ROC) curve analyses, and classification tree analysis. RESULTS When the cutoff values were set as mean ± 2 SD for normal healthy individuals, the positive rates of antibodies to any single TAA were less than 20% both in OC and in normal healthy individuals. In a parallel screening approach, a panel of nine TAAs (p53, C-myc, p90, p62, AHSG, 14-3-3zeta, RalA, Koc, and p16), obtained optimal diagnostic performance in OC with the sensitivity of 61.4% at the 85.0% specificity. In addition, when the nine TAAs were combined with CA125, the sensitivity and specificity were improved to 94.7% and 78.2%, respectively. The ROC curve analyses showed that only the area under the receiver operating characteristic curves (AUCs) of antibodies against C-myc, Koc, and RalA was beyond 0.6, which were 0.732, 0.668, and 0.665, respectively. The AUC of the combination was up to 0.914 (P < 0.05). Decision tree analysis showed that C-myc, HCC1.3, RalA, and CA125 held high potential in the detection of OC. The panel of nine TAAs also identified 78.8% of OC patients who had normal CA125 levels in their serum samples, indicating that elevated CA125 and anti-TAA antibodies appeared to be independent but supplementary biomarkers for diagnosing OC. CONCLUSIONS In summary, the current study further supports that a customized TAA panel can serve as a promising and powerful tool for immunodiagnosis of OC and may be particularly useful in patients with normal CA125 levels.
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Affiliation(s)
- Peng Wang
- Department of epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jiejie Qin
- Department of epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- Department of epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Liuxia Li
- Department of obstetrics and gynecology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xiao Wang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianying Zhang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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26
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Koziol JA, Imai H, Dai L, Zhang JY, Tan EM. Early detection of hepatocellular carcinoma using autoantibody profiles from a panel of tumor-associated antigens. Cancer Immunol Immunother 2018; 67:835-841. [PMID: 29497780 DOI: 10.1007/s00262-018-2135-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 02/20/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Multiple antigen miniarrays used for detecting autoantibodies to tumor-associated antigens (TAAs) can be a useful approach for cancer detection and diagnosis. We here address a very specific question: might there be autoimmune responses to TAAs which precede clinical detection of hepatocellular carcinoma (HCC) in HBV and HCV chronic liver disease patients under continuous medical surveillance, and if so, could these anti-TAAs be added to the armamentarium of diagnostic tests? METHODS We here examine the utility of a panel of 12 TAAs for the diagnosis of hepatocellular carcinoma (HCC). We derived a predictive rule for the presence of HCC based on the panel, from a cohort comprising 160 HCC patients and 90 normals. We then applied this rule to sequential anti-TAA data from a cohort of 17 HCC patients, from whom this information was available prior to diagnosis. RESULTS The predictors (autoantibodies to HCC1, P16, P53, P90, and survivin) indicated the presence of HCC prior to diagnosis in 16 of the 17 patients, at a median lead time of 0.75 year. CONCLUSIONS We believe these findings warrant further study of anti-TAA profiles as biomarkers for primary or early diagnosis of HCC.
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Affiliation(s)
- James A Koziol
- Department of Molecular and Experimental Medicine, MEM290, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | | | - Liping Dai
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian-Ying Zhang
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,University of Texas at El Paso, Texas, USA
| | - Eng M Tan
- Department of Molecular and Experimental Medicine, MEM290, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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27
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Dai L, Peng XX, Tan EM, Zhang JY. Tumor-associated antigen CAPERα and microvessel density in hepatocellular carcinoma. Oncotarget 2017; 7:16985-95. [PMID: 26934653 PMCID: PMC4941365 DOI: 10.18632/oncotarget.7707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/31/2016] [Indexed: 02/05/2023] Open
Abstract
PURPOSE CAPERα, a tumor-associated antigen, was identified from a cDNA clone with autoantibody from a patient with hepatocellular carcinoma (HCC). It has been implicated, by way of alternative splicing of VEGF pre-mRNA, in the regulation of microvessel formation in Ewing's sarcoma. In this study, we looked for possible association of alterations in CAPERα with microvessel density in HCC. METHODS Enzyme-linked immunosorbent assay using recombinant CAPERα as antigen were used to detect antibody against CAPERα. Immunohistochemistry (IHC) on liver sections was performed to analyze expression profiles of CAPERα, VEGF and CD34 in HCC and control tissues and was further used to assess the correlation of expression among CAPERα, VEGF and CD34 in HCC development. RESULTS Autoantibody to CAPERα was highest in HCC (22/76, 28.9%), not detected in prostate cancer (0/79) and at 3.4% (3/88) in breast cancer. In immunohistochemical analysis of grades II and III HCC tissues, significantly decreased immunostaining for CAPERα was observed and this correlated directly with decreased immunostaining for VEGF (R=0.534, P=0.0003). Using CD34 immunostaining for detecting newly formed microvessels, strong staining was observed in grades II and III HCC. Normal liver sections, all of which have high expression of CAPERα were totally negative for CD34 immunostaining. A significant inverse correlation was seen between CAPERα and CD34 immunostaining (R=-0.481, P=0.0012). CONCLUSIONS Decreased expression of CAPERα appears to be correlated with appearance of microvessels. It would be of interest to elucidate the cause of altered CAPERα since new formation of microvessels is important in progression of HCC.
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Affiliation(s)
- Liping Dai
- Department of Biological Sciences & NIH-Sponsored Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Xuan-Xian Peng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Eng M Tan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jian-Ying Zhang
- Department of Biological Sciences & NIH-Sponsored Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
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28
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Li P, Shi JX, Xing MT, Dai LP, Li JT, Zhang JY. Evaluation of serum autoantibodies against tumor-associated antigens as biomarkers in lung cancer. Tumour Biol 2017; 39:1010428317711662. [DOI: 10.1177/1010428317711662] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Pei Li
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Jian-Xiang Shi
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
- Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Meng-Tao Xing
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Li-Ping Dai
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
- Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ji-Tian Li
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Jian-Ying Zhang
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
- Henan Key Laboratory for Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
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29
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Sun H, Shi JX, Zhang HF, Xing MT, Li P, Dai LP, Luo CL, Wang X, Wang P, Ye H, Li LX, Zhang JY. Serum autoantibodies against a panel of 15 tumor-associated antigens in the detection of ovarian cancer. Tumour Biol 2017; 39:1010428317699132. [PMID: 28618923 DOI: 10.1177/1010428317699132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In this study, enzyme-linked immunosorbent assay has been used to examine the frequencies of serum autoantibodies against two candidate tumor-associated antigens intensively selected from the Human Protein Atlas database, in combination with 13 tumor-associated antigens available from our lab in sera from 44 OC patients and 50 normal healthy controls. Conventional evaluation (mean + 3SD as the cutoff value to determine a positive reactivity), receiver operating characteristic curve analyses, and classification tree analysis were further used to evaluate the diagnostic performance of autoantibodies against these tumor-associated antigens (anti-tumor-associated antigens) in ovarian cancer. For single anti-tumor-associated antigen, when the cutoff values were set as mean + 3SD of normal healthy controls, NPM1, MDM2, PLAT, p53, and c-Myc could achieve sensitivity higher than 20% at 98% specificity. Combinational utilization of autoantibodies against MDM2, PLAT, NPM1, 14-3-3 Zeta, p53, and RalA achieved the optimal diagnostic performance with 72.7% sensitivity at 96% specificity. Receiver operating characteristic curve analysis showed that the area under the receiver operating characteristic curves of autoantibodies against c-Myc, NPM1, MDM2, p16, p53, and 14-3-3 Zeta were greater than 0.80. This indicated that these tumor-associated antigens held high potential to serve as diagnostic biomarkers in ovarian cancer detection. Decision tree analysis indicated that anti-c-Myc held high potential in the detection of ovarian cancer. Further studies are warranted to validate the diagnostic performance of these anti-tumor-associated antigens with high area under the receiver operating characteristic curve, including autoantibodies against c-Myc, MDM2, PLAT, NPM1, 14-3-3 Zeta, p53, and RalA.
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Affiliation(s)
- Hao Sun
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Jian-Xiang Shi
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Hong-Fei Zhang
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Meng-Tao Xing
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Pei Li
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Li-Ping Dai
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cheng-Lin Luo
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Xiao Wang
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liu-Xia Li
- 2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian-Ying Zhang
- 1 Affiliated Cancer Hospital of Zhengzhou University, College of Public Health, Zhengzhou University, Zhengzhou, China.,2 Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA.,3 Henan Academy of Medical and Pharmaceutical Sciences and Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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30
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Wu C, Xu B, Li X, Ma W, Zhang P, Chen X, Wu J. Tracing and Characterizing the Development of Transplanted Female Germline Stem Cells In Vivo. Mol Ther 2017; 25:1408-1419. [PMID: 28528817 DOI: 10.1016/j.ymthe.2017.04.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/16/2017] [Accepted: 04/23/2017] [Indexed: 12/25/2022] Open
Abstract
It has long been believed that most female mammalian species lose the ability to generate oocytes in postnatal ovaries. Recent evidence has demonstrated the isolation and culture of female germline stem cells (FGSCs) from adult mice and humans. However, the process and mechanisms of FGSC differentiation in vivo following transplantation have not yet been studied. Here, we isolated and characterized FGSCs from a single EGFP-transgenic mouse, and traced the development and behavior of transplanted FGSCs (F-TFs) in vivo. Comparisons of folliculogenesis between recipients with FGSC transplantation and wild-type (WT) mice were performed by single follicle RNA-sequencing (RNA-seq). Results showed that FGSCs exhibited a homing ability and began to differentiate into early-stage oocytes only when they reached the edge of the ovarian cortex. The F-TFs restored function of premature ovarian failure (gdf9iCre; PtenloxP/loxP genotype) and generated offspring. Furthermore, results demonstrated that the developmental mechanisms of follicles derived from F-TFs were similar to that of WT follicles. Weighted gene co-expression network analysis identified two potential sub-networks and core genes that played a critical role in follicular development. These findings provide a theoretical basis and lay a technology platform for specific or personalized medical treatment of ovarian failure or other ovarian diseases.
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Affiliation(s)
- Changqing Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Xu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyong Li
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenzhi Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China
| | - Ping Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Xuejin Chen
- Department of Laboratory Animal Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China.
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31
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Selective degradation of splicing factor CAPERα by anticancer sulfonamides. Nat Chem Biol 2017; 13:675-680. [DOI: 10.1038/nchembio.2363] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/01/2017] [Indexed: 02/07/2023]
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32
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Han T, Goralski M, Gaskill N, Capota E, Kim J, Ting TC, Xie Y, Williams NS, Nijhawan D. Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science 2017; 356:science.aal3755. [DOI: 10.1126/science.aal3755] [Citation(s) in RCA: 309] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/27/2017] [Indexed: 12/11/2022]
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33
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Macdonald IK, Parsy-Kowalska CB, Chapman CJ. Autoantibodies: Opportunities for Early Cancer Detection. Trends Cancer 2017; 3:198-213. [PMID: 28718432 DOI: 10.1016/j.trecan.2017.02.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/18/2022]
Abstract
Cancer cells can induce an immunological response resulting in the production of tumor-associated (TA) autoantibodies. These serum immunobiomarkers have been detected for a range of cancers at an early stage before the development of clinical symptoms. Their measurement is minimally invasive and cost effective using established technologies. TA autoantibodies are present in a clinically significant number of individuals and could supplement current screening modalities to aid early diagnosis of high-risk populations and assist the clinical management of patients. Here we review their production, discovery, and validation as biomarkers for cancer and their current and future potential as clinical tools.
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34
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Dai L, Tsay JCJ, Li J, Yie TA, Munger JS, Pass H, Rom WN, Zhang Y, Tan EM, Zhang JY. Autoantibodies against tumor-associated antigens in the early detection of lung cancer. Lung Cancer 2016; 99:172-179. [PMID: 27565936 DOI: 10.1016/j.lungcan.2016.07.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/13/2016] [Accepted: 07/17/2016] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Autoantibodies against tumor-associated antigens (TAAs) identified in patients with advanced lung cancer may be detected in subjects with early lung cancer or even predate the diagnosis. The purpose of this study is to address the temporal relationship between lung cancer development and serum autoantibody response. MATERIALS AND METHODS Two cohorts of patients with newly diagnosed lung cancer were included. The first cohort included 90 sera from patients with lung cancer (Stages I-III) and 89 normal control sera. In the second cohort, 93 serial serum samples from 25 patients with CT-scan screen-detected stage I lung cancer were collected before the diagnosis of lung cancer (average 32 months) and 56 controls were matched on age, gender, and smoking. Autoantibody levels were measured by immunoassay. RESULTS Measurement of autoantibodies against seven TAAs (14-3-3ζ, c-Myc, MDM2, NPM1, p16, p53 and cyclin B1) individually could discriminate lung cancer patients from normal individuals in the first cohort and the area under curve (AUC) was 0.863 based on a panel of seven autoantibodies, with sensitivity of 68.9% and specificity of 79.5%. Autoantibodies in serial pre-diagnostic serum samples against the same panel of seven TAAs were detected prior to lung cancer diagnosis with sensitivity of 76.0% and specificity of 73.2% (AUC) (95%CI): 0.885 (0.797-0.973)). Elevated autoantibody levels could be detected greater than four years prior to lung cancer diagnosis. CONCLUSION A panel of seven TAAs may enhance the early detection of lung cancer, consistent with a humoral immune response to TAAs that can be detected months to years prior to the diagnosis.
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Affiliation(s)
- Liping Dai
- Center for Tumor Biotherapy, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China; Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA; Henan Academy of Medical and Pharmaceutical Sciences & Henan Key Laboratory for Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jitian Li
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Ting-An Yie
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - John S Munger
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Harvey Pass
- Department of Cardiothoracic Surgery, New York University School of Medicine, New York, NY 10016, USA
| | - William N Rom
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Yi Zhang
- Center for Tumor Biotherapy, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Eng M Tan
- The Scripps Research Institute, San Diego, CA 92037, USA
| | - Jian-Ying Zhang
- Center for Tumor Biotherapy, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China; Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA; Henan Academy of Medical and Pharmaceutical Sciences & Henan Key Laboratory for Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan 450052, China.
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35
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Fritzler MJ, Chan EKL. Dr Eng M. Tan: a tribute to an enduring legacy in autoimmunity. Lupus 2016; 26:208-217. [PMID: 27539991 DOI: 10.1177/0961203316664598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
At the age of ninety years, Dr Eng Meng Tan has had a remarkable impact on the accumulated knowledge of autoimmune diseases, including seminal findings in systemic lupus erythematosus (SLE) and a wide range of other autoimmune diseases. Dating to the first description of the Sm (Smith) autoantibody in SLE, his focus has been the use of autoantibodies as probes to identify and elucidate novel cellular molecules and then translating these discoveries into biomarkers and immunoassays for a wide range of these diseases and, later, cancer. He led efforts to standardize autoantibody nomenclature and testing protocols. Through his mentorship a great number of trainees and collaborators have had remarkably successful careers, and by that virtue he has garnered a remarkable continuing legacy.
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Affiliation(s)
- M J Fritzler
- 1 University of Calgary, Cumming School of Medicine, Calgary, Canada
| | - E K L Chan
- 2 Department of Oral Biology, University of Florida, Gainesville, USA
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36
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Mai S, Qu X, Li P, Ma Q, Cao C, Liu X. Global regulation of alternative RNA splicing by the SR-rich protein RBM39. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1014-24. [PMID: 27354116 DOI: 10.1016/j.bbagrm.2016.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 02/05/2023]
Abstract
BACKGROUND RBM39 is a serine/arginine-rich RNA-binding protein that is highly homologous to the splicing factor U2AF65. However, the role of RBM39 in alternative splicing is poorly understood. METHODS In this study, RBM39-mediated global alternative splicing was investigated using RNA-Seq and genome-wide RBM39-RNA interactions were mapped via cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq) in wild-type and RBM39-knockdown MCF-7 cells. RESULTS RBM39 was involved in the up- or down-regulation of the transcript levels of various genes. Hundreds of alternative splicing events regulated by endogenous RBM39 were identified. The majority of these events were cassette exons. Genes containing RBM39-regulated alternative exons were found to be linked to G2/M transition, cellular response to DNA damage, adherens junctions and endocytosis. CLIP-Seq analysis showed that the binding site of RBM39 was mainly in proximity to 5' and 3' splicing sites. Considerable RBM39 binding to mRNAs encoding proteins involved in translation was observed. Of particular importance, ~20% of the alternative splicing events that were significantly regulated by RBM39 were similarly regulated by U2AF65. CONCLUSIONS RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65. GENERAL SIGNIFICANCE The current study offers a genome-wide view of RBM39's regulatory function in alternative splicing. RBM39 may play important roles in multiple cellular processes by regulating both alternative splicing of RNA molecules and transcript levels.
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Affiliation(s)
- Sanyue Mai
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Xiuhua Qu
- General Navy Hospital of PLA, 6 Fucheng Rd, Haidian District, Beijing 100037, China
| | - Ping Li
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Qingjun Ma
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
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37
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Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol 2016; 72:497-511. [PMID: 27050129 PMCID: PMC4822562 DOI: 10.1107/s2059798316001248] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
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Affiliation(s)
- Galina A. Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Eigen Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Carol L. Farr
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott A. Lesley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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38
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Mai S, Qu X, Li P, Ma Q, Liu X, Cao C. Functional interaction between nonreceptor tyrosine kinase c-Abl and SR-Rich protein RBM39. Biochem Biophys Res Commun 2016; 473:355-360. [PMID: 27018250 DOI: 10.1016/j.bbrc.2016.03.108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 11/28/2022]
Abstract
RBM39, also known as splicing factor HCC1.4, acts as a transcriptional coactivator for the steroid nuclear receptors JUN/AP-1, ESR1/ER-α and ESR2/ER-β. RBM39 is involved in the regulation of the transcriptional responses of these steroid nuclear receptors and promotes transcriptional initiation. In this paper, we report that RBM39 interacts with the nonreceptor tyrosine kinase c-Abl. Both the Src homology (SH) 2 and SH3 domains of c-Abl interact with RBM39. The major tyrosine phosphorylation sites on RBM39 that are phosphorylated by c-Abl are Y95 and Y99, as demonstrated by liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) and mutational analysis. c-Abl was shown boost the transcriptional coactivation activity of RBM39 for ERα and PRβ in a tyrosine kinase-dependent manner. The results suggest that mammalian c-Abl plays an important role in steroid hormone receptor-mediated transcription by regulating RBM39.
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Affiliation(s)
- Sanyue Mai
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Xiuhua Qu
- General Navy Hospital of PLA, 6 Fucheng Rd, Haidian District, Beijing 100037, China
| | - Ping Li
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Qingjun Ma
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Xuan Liu
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
| | - Cheng Cao
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
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39
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Abstract
Orphan receptors comprise nearly half of all members of the nuclear receptor superfamily. Despite having broad structural similarities to the classical estrogen receptors, estrogen-related receptors (ERRs) have their own unique DNA response elements and functions. In this study, we focus on 2 ERRβ splice variants, short form ERRβ (ERRβsf) and ERRβ2, and identify their differing roles in cell cycle regulation. Using DY131 (a synthetic agonist of ERRβ), splice-variant selective shRNA, and exogenous ERRβsf and ERRβ2 cDNAs, we demonstrate the role of ERRβsf in mediating the G1 checkpoint through p21. We also show ERRβsf is required for DY131-induced cellular senescence. A key novel finding of this study is that ERRβ2 can mediate a G2/M arrest in response to DY131. In the absence of ERRβ2, the DY131-induced G2/M arrest is reversed, and this is accompanied by p21 induction and a G1 arrest. This study illustrates novel functions for ERRβ splice variants and provides evidence for splice variant interaction.
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Affiliation(s)
- Mary Mazzotta Heckler
- a Lombardi Comprehensive Cancer Center; the Department of Oncology ; Georgetown University School of Medicine ; Washington , DC USA
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40
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Hong Y, Huang J. Autoantibodies against tumor-associated antigens for detection of hepatocellular carcinoma. World J Hepatol 2015; 7:1581-1585. [PMID: 26085917 PMCID: PMC4462696 DOI: 10.4254/wjh.v7.i11.1581] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common tumors worldwide. The survival rate after the onset of symptoms is generally less than one year for the late presentation of HCC, and reliable tools for early diagnosis are lacking. Therefore, novel biomarkers for the early detection of HCC are urgently required. Recent studies show that the abnormal release of proteins by tumor cells can elicit humoral immune responses to self-antigens called tumor-associated antigens (TAAs). The corresponding autoantibodies can be detected before the clinical diagnosis of cancer. Therefore, there is growing interest in using serum autoantibodies as cancer biomarkers. In this review, we focus on the advances in research on autoantibodies against TAAs as serum biomarker for detection of HCC, the mechanism of the production of TAAs, and the association of autoantibodies with patients' clinical characteristics.
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Affiliation(s)
- Yu Hong
- Yu Hong, Jian Huang, Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jian Huang
- Yu Hong, Jian Huang, Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
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41
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Antonacci S, Forand D, Wolf M, Tyus C, Barney J, Kellogg L, Simon MA, Kerr G, Wells KL, Younes S, Mortimer NT, Olesnicky EC, Killian DJ. Conserved RNA-binding proteins required for dendrite morphogenesis in Caenorhabditis elegans sensory neurons. G3 (BETHESDA, MD.) 2015; 5:639-53. [PMID: 25673135 PMCID: PMC4390579 DOI: 10.1534/g3.115.017327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 01/22/2023]
Abstract
The regulation of dendritic branching is critical for sensory reception, cell-cell communication within the nervous system, learning, memory, and behavior. Defects in dendrite morphology are associated with several neurologic disorders; thus, an understanding of the molecular mechanisms that govern dendrite morphogenesis is important. Recent investigations of dendrite morphogenesis have highlighted the importance of gene regulation at the posttranscriptional level. Because RNA-binding proteins mediate many posttranscriptional mechanisms, we decided to investigate the extent to which conserved RNA-binding proteins contribute to dendrite morphogenesis across phyla. Here we identify a core set of RNA-binding proteins that are important for dendrite morphogenesis in the PVD multidendritic sensory neuron in Caenorhabditis elegans. Homologs of each of these genes were previously identified as important in the Drosophila melanogaster dendritic arborization sensory neurons. Our results suggest that RNA processing, mRNA localization, mRNA stability, and translational control are all important mechanisms that contribute to dendrite morphogenesis, and we present a conserved set of RNA-binding proteins that regulate these processes in diverse animal species. Furthermore, homologs of these genes are expressed in the human brain, suggesting that these RNA-binding proteins are candidate regulators of dendrite development in humans.
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Affiliation(s)
- Simona Antonacci
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Daniel Forand
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Margaret Wolf
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Courtney Tyus
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Julia Barney
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Leah Kellogg
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Margo A Simon
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Genevieve Kerr
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Kristen L Wells
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Serena Younes
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, Colorado 80208
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
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42
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Shao C, Yang B, Wu T, Huang J, Tang P, Zhou Y, Zhou J, Qiu J, Jiang L, Li H, Chen G, Sun H, Zhang Y, Denise A, Zhang DE, Fu XD. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nat Struct Mol Biol 2014; 21:997-1005. [PMID: 25326705 PMCID: PMC4429597 DOI: 10.1038/nsmb.2906] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/25/2014] [Indexed: 12/24/2022]
Abstract
The U2AF heterodimer has been well studied for its role in defining functional 3' splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3' splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3' splice site associated either with the alternative exon, to cause exon skipping, or with the competing constitutive exon, to induce exon inclusion. We further demonstrate partial functional impairment with leukemia-associated mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.
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Affiliation(s)
- Changwei Shao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Tongbin Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Jie Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Li Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Geng Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alain Denise
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Dong-Er Zhang
- UC San Diego Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Xiang-Dong Fu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
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43
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Shao C, Yang B, Wu T, Huang J, Tang P, Zhou Y, Zhou J, Qiu J, Jiang L, Li H, Chen G, Sun H, Zhang Y, Denise A, Zhang DE, Fu XD. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nat Struct Mol Biol 2014. [PMID: 25326705 DOI: 10.1038/nsmb2906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The U2AF heterodimer has been well studied for its role in defining functional 3' splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3' splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3' splice site associated either with the alternative exon, to cause exon skipping, or with the competing constitutive exon, to induce exon inclusion. We further demonstrate partial functional impairment with leukemia-associated mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.
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Affiliation(s)
- Changwei Shao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Tongbin Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Jie Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Li Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Geng Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alain Denise
- Laboratoire de Recherche en Informatique, Institut de Génétique et Microbiologie I, Université Paris-Sud and Centre National de la Recherche Scientifique, Orsay, France
| | - Dong-Er Zhang
- UC San Diego Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Xiang-Dong Fu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
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44
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Kumar P P, Emechebe U, Smith R, Franklin S, Moore B, Yandell M, Lessnick SL, Moon AM. Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex. eLife 2014; 3. [PMID: 24876127 PMCID: PMC4071561 DOI: 10.7554/elife.02805] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/22/2014] [Indexed: 12/19/2022] Open
Abstract
Cellular senescence is a crucial tumor suppressor mechanism. We discovered a CAPERα/TBX3 repressor complex required to prevent senescence in primary cells and mouse embryos. Critical, previously unknown roles for CAPERα in controlling cell proliferation are manifest in an obligatory interaction with TBX3 to regulate chromatin structure and repress transcription of CDKN2A-p16INK and the RB pathway. The IncRNA UCA1 is a direct target of CAPERα/TBX3 repression whose overexpression is sufficient to induce senescence. In proliferating cells, we found that hnRNPA1 binds and destabilizes CDKN2A-p16INK mRNA whereas during senescence, UCA1 sequesters hnRNPA1 and thus stabilizes CDKN2A-p16INK. Thus CAPERα/TBX3 and UCA1 constitute a coordinated, reinforcing mechanism to regulate both CDKN2A-p16INK transcription and mRNA stability. Dissociation of the CAPERα/TBX3 co-repressor during oncogenic stress activates UCA1, revealing a novel mechanism for oncogene-induced senescence. Our elucidation of CAPERα and UCA1 functions in vivo provides new insights into senescence induction, and the oncogenic and developmental properties of TBX3. DOI:http://dx.doi.org/10.7554/eLife.02805.001 Cell division and growth are essential for survival. But it is equally important that cells can stop dividing, because failing to do so can lead to the uncontrolled tumor growth seen in cancer. One such quality control mechanism is called senescence, which stops the growth and multiplication of cells that are old, damaged or behaving in ways that may harm the organism. All cells eventually stop dividing and undergo senescence, but a number of factors may trigger the process early, such as DNA damage, stress or the appearance of cancer-causing proteins. Senescence can be harmful if it occurs too early in life and interferes with normal growth. Severe birth defects—including fatal heart problems and limb malformations—occur if senescence is inappropriately triggered early in development. Mutations in a gene encoding a protein called TBX3 have been linked to these severe birth defects. Normally, TBX3 stops the production of other proteins that trigger senescence in early development, and helps to maintain stable conditions in adult cells. Understanding how it does so could help scientists understand normal cell function and aging, and also help to find ways to trigger senescence in cancerous cells. Kumar et al. found that a protein called CAPERα—for short Coactivator of AP1 and Estrogen Receptor—forms a complex with TBX3 that stops cells dividing in living organisms in at least two different ways. One way is by altering how DNA is folded. The other way involves a non-coding strand of RNA from a gene called UCA1: this RNA prevents the degradation of proteins that stop cell division. In normal proliferating cells, the CAPERα/TBX3 protein complex prevents the production of UCA1 RNA. In contrast, in cells that received a cancer causing stimulus, TBX3 and CAPERα physically separate: this activates production of UCA1 RNA and causes senescence. Further studies will be required to establish exactly how the CAPERα/TBX3 protein complex interacts with DNA and RNA to control senescence and prevent cancer. DOI:http://dx.doi.org/10.7554/eLife.02805.002
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Affiliation(s)
- Pavan Kumar P
- Weis Center for Research, Geisinger Clinic, Danville, United States
| | - Uchenna Emechebe
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, United States
| | - Richard Smith
- The Centre for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, United States
| | - Barry Moore
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Stephen L Lessnick
- Department of Pediatrics, University of Utah, Salt Lake City, United States
| | - Anne M Moon
- Weis Center for Research, Geisinger Clinic, Danville, United States
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Loerch S, Maucuer A, Manceau V, Green MR, Kielkopf CL. Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. J Biol Chem 2014; 289:17325-37. [PMID: 24795046 DOI: 10.1074/jbc.m114.558825] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
U2AF homology motifs (UHMs) mediate protein-protein interactions with U2AF ligand motifs (ULMs) of pre-mRNA splicing factors. The UHM-containing alternative splicing factor CAPERα regulates splicing of tumor-promoting VEGF isoforms, yet the molecular target of the CAPERα UHM is unknown. Here we present structures of the CAPERα UHM bound to a representative SF3b155 ULM at 1.7 Å resolution and, for comparison, in the absence of ligand at 2.2 Å resolution. The prototypical UHM/ULM interactions authenticate CAPERα as a bona fide member of the UHM family of proteins. We identify SF3b155 as the relevant ULM-containing partner of full-length CAPERα in human cell extracts. Isothermal titration calorimetry comparisons of the purified CAPERα UHM binding known ULM-containing proteins demonstrate that high affinity interactions depend on the presence of an intact, intrinsically unstructured SF3b155 domain containing seven ULM-like motifs. The interplay among bound CAPERα molecules gives rise to the appearance of two high affinity sites in the SF3b155 ULM-containing domain. In conjunction with the previously identified, UHM/ULM-mediated complexes of U2AF(65) and SPF45 with SF3b155, this work demonstrates the capacity of SF3b155 to offer a platform for coordinated recruitment of UHM-containing splicing factors.
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Affiliation(s)
- Sarah Loerch
- From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and
| | - Alexandre Maucuer
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Valérie Manceau
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Michael R Green
- the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Clara L Kielkopf
- From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and
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Preferential autoimmune response in prostate cancer to cyclin B1 in a panel of tumor-associated antigens. J Immunol Res 2014; 2014:827827. [PMID: 24860838 PMCID: PMC4016862 DOI: 10.1155/2014/827827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/28/2014] [Indexed: 12/22/2022] Open
Abstract
Previous studies have demonstrated that sera from patients with prostate cancer (PCa) contain autoantibodies that react with tumor-associated antigens (TAAs). Autoantibodies to cyclin B1 and fourteen other TAAs were detected by enzyme-linked immunosorbent assay (ELISA) and Western blotting in 464 sera from patients with PCa, benign prostatic hyperplasia (BPH), and other controls. Autoantibodies to cyclin B1 were detected in 31.0% of sera from randomly selected patients with PCa versus 4.8% in sera with BPH. In the further analysis, 31.4% of sera from PCa patients at the early stage contained anti-cyclin B1 autoantibody, and even 29.4% of patients who had normal prostate-specific antigen (PSA) levels in their serum samples were observed anti-cyclin B1 positive. The cumulative positive rate of autoantibodies against seven selected TAAs (cyclin B1, survivin, p53, DFS70/LEDGFp75, RalA, MDM2, and NPM1) in PCa reached 80.5%, significantly higher than that in normal control sera. In summary, autoantibody to cyclin B1 might be a potential biomarker for the immunodiagnosis of early stage PCa, especially useful in patients with normal PSA level. This study further supports the hypothesis that a customized TAA array can be used for enhancing anti-TAA autoantibody detection, and it may constitute a promising and powerful tool for immunodiagnosis of PCa.
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Dai L, Ren P, Liu M, Imai H, Tan EM, Zhang JY. Using immunomic approach to enhance tumor-associated autoantibody detection in diagnosis of hepatocellular carcinoma. Clin Immunol 2014; 152:127-39. [PMID: 24667685 DOI: 10.1016/j.clim.2014.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 02/19/2014] [Accepted: 03/17/2014] [Indexed: 02/09/2023]
Abstract
To explore the possibility of using a mini-array of multiple tumor-associated antigens (TAAs) as an approach to the diagnosis of hepatocellular carcinoma (HCC), 14 TAAs were selected to examine autoantibodies in sera from patients with chronic hepatitis, liver cirrhosis and HCC by immunoassays. Antibody frequency to any individual TAA in HCC varied from 6.6% to 21.1%. With the successive addition of TAAs to the panel of TAAs, there was a stepwise increase of positive antibody reactions. The sensitivity and specificity of 14 TAAs for immunodiagnosis of HCC was 69.7% and 83.0%, respectively. This TAA mini-array also identified 43.8% of HCC patients who had normal alpha-fetoprotein (AFP) levels in serum. In summary, this study further supports the hypothesis that a customized TAA array used for detecting anti-TAA autoantibodies can constitute a promising and powerful tool for immunodiagnosis of HCC and may be especially useful in patients with normal AFP levels.
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Affiliation(s)
- Liping Dai
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Pengfei Ren
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Mei Liu
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Haruhiko Imai
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eng M Tan
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jian-Ying Zhang
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA.
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Chai Y, Liu X, Dai L, Li Y, Liu M, Zhang JY. Overexpression of HCC1/CAPERα may play a role in lung cancer carcinogenesis. Tumour Biol 2014; 35:6311-7. [PMID: 24643682 DOI: 10.1007/s13277-014-1819-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/04/2014] [Indexed: 12/22/2022] Open
Abstract
HCC1/CAPERα is considered to be a novel human tumor-associated antigen, and the tumor-specific immunity of HCC1/CAPERα has been reported in several types of cancer. However, there was very limited evidence indicating its function in tumorigenesis. In the present study, to elucidate the roles and underlying molecular mechanism of HCC1/CAPERα in lung cancer, we examined the expression of HCC1/CAPERα in human non-small cell lung cancer (NSCLC) cell line and NSCLC tissue microarray (TMA). Immunohistochemistry with TMA was performed to detect HCC1/CAPERα expression in NSCLC and adjacent lung tissues. NSCLC cell line constitutively transfected by pcDNA3.1-HCC1/CAPERα, and empty pcDNA3.1 vector were used. These cells were analyzed by Western blot, MTT, immunofluorescence, wound healing assay, and transwell assays. It was found that HCC1/CAPERα was mainly localized in the nucleus of the lung cancer cells and overexpression of HCC1/CAPERα may promote lung cancer cells proliferation and increase cells migration. The frequency of HCC1/CAPERα expression in NSCLC tissues was significantly higher than that in adjacent and normal tissues (P < 0.01). Our data suggest that overexpression of HCC1/CAPERα may increase the proliferation and migration of NSCLC cells, and HCC1/CAPERα could be a promising biomarker for lung cancer.
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Affiliation(s)
- Yurong Chai
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
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Mercier I, Gonzales DM, Quann K, Pestell TG, Molchansky A, Sotgia F, Hulit J, Gandara R, Wang C, Pestell RG, Lisanti MP, Jasmin JF. CAPER, a novel regulator of human breast cancer progression. Cell Cycle 2014; 13:1256-64. [PMID: 24621503 DOI: 10.4161/cc.28156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CAPER is an estrogen receptor (ER) co-activator that was recently shown to be involved in human breast cancer pathogenesis. Indeed, we reported increased expression of CAPER in human breast cancer specimens. We demonstrated that CAPER was undetectable or expressed at relatively low levels in normal breast tissue and assumed a cytoplasmic distribution. In contrast, CAPER was expressed at higher levels in ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) specimens, where it assumed a predominantly nuclear distribution. However, the functional role of CAPER in human breast cancer initiation and progression remained unknown. Here, we used a lentiviral-mediated gene silencing approach to reduce the expression of CAPER in the ER-positive human breast cancer cell line MCF-7. The proliferation and tumorigenicity of MCF-7 cells stably expressing control or human CAPER shRNAs was then determined via both in vitro and in vivo experiments. Knockdown of CAPER expression significantly reduced the proliferation of MCF-7 cells in vitro. Importantly, nude mice injected with MCF-7 cells harboring CAPER shRNAs developed smaller tumors than mice injected with MCF-7 cells harboring control shRNAs. Mechanistically, tumors derived from mice injected with MCF-7 cells harboring CAPER shRNAs displayed reduced expression of the cell cycle regulators PCNA, MCM7, and cyclin D1, and the protein synthesis marker 4EBP1. In conclusion, knockdown of CAPER expression markedly reduced human breast cancer cell proliferation in both in vitro and in vivo settings. Mechanistically, knockdown of CAPER abrogated the activity of proliferative and protein synthesis pathways.
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Affiliation(s)
- Isabelle Mercier
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA; Department of Pharmaceutical Sciences; Philadelphia College of Pharmacy; University of the Sciences in Philadelphia; Philadelphia, PA, USA
| | - Donna M Gonzales
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Kevin Quann
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Timothy G Pestell
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Alexander Molchansky
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Federica Sotgia
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA; Breakthrough Breast Cancer Research Unit; Institute of Cancer Sciences; University of Manchester; Manchester, UK
| | - James Hulit
- Breakthrough Breast Cancer Research Unit; Institute of Cancer Sciences; University of Manchester; Manchester, UK
| | - Ricardo Gandara
- Breakthrough Breast Cancer Research Unit; Institute of Cancer Sciences; University of Manchester; Manchester, UK
| | - Chenguang Wang
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Richard G Pestell
- Department of Cancer Biology; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA
| | - Michael P Lisanti
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA; Breakthrough Breast Cancer Research Unit; Institute of Cancer Sciences; University of Manchester; Manchester, UK
| | - Jean-François Jasmin
- Department of Stem Cell Biology & Regenerative Medicine; Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA, USA; Department of Pharmaceutical Sciences; Philadelphia College of Pharmacy; University of the Sciences in Philadelphia; Philadelphia, PA, USA
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Abstract
Immunofluorescent imaging has been a powerful technique in helping to identify intracellular nuclear and cytoplasmic molecules which are target antigens of autoantibodies in systemic autoimmune disorders. Patterns of staining can be correlated with molecules engaged in specific cellular functions and distributed in distinct cellular domains. Different autoimmune disorders have different profiles of autoantibodies, and immunodiagnostics has become an important adjunct in differential diagnosis. An important finding that has eluded explanation is the presence of autoantibodies to many different antigens, manifested strikingly in systemic lupus erythematosus. In cancer, the occurrence of autoantibodies to tumor-associated antigens is not uncommon and a characteristic feature is also the presence of multiple autoantibodies. The targeted tumor-associated antigens are either oncogene or tumor suppressor gene products or their coactivators, which are altered or mutated and driving the autoimmune response. Most cancer cells have between two and eight mutated genes before oncogenic transformation occurs, initiating a process called synthetic lethality in tumorigenesis pathways. These observations beg the question of whether there are similar mechanisms in systemic lupus erythematosus and other disorders driving autoimmunity pathways. Targeting molecules that are synthetic lethal to each other is in the forefront of the search for anticancer therapy, and this could also be an objective in systemic autoimmune disorders.
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