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Yin T, Zhang Y, Zhao Y, Zhang X, Han S, Wang Y, Yang B. Tumor suppressor function of RBMS3 overexpression in EOC associated with immune cell infiltration. Heliyon 2024; 10:e30603. [PMID: 38726149 PMCID: PMC11079397 DOI: 10.1016/j.heliyon.2024.e30603] [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: 02/15/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Objectives Epithelial ovarian cancer (EOC) is considered to be a prevalent female malignancy with both high incidence and mortality. It is reported that RNA-binding protein 3 (RBMS3) executives a tumor suppressor function in different cancers. This investigation was designed to examine the expression of RBMS3 in epithelial ovarian cancer, the effects on EOC cells, and its connection to immune cells that infiltrate tumors in the EOC microenvironment. Methods The expression levels of RBMS3 in EOC tissues as well as their correlations with immune cell infiltration and clinical outcome were examined using bioinformatics approaches. Western blotting as well as immunohistochemistry were carried out to determine the protein levels in EOC tissues. In addition, qRT-PCR was employed to look at the expression of the mRNA. The role of RBMS3 in EOC cells was investigated, and an RBMS3 lentiviral vector was developed. The effects of RBMS3 on subcutaneous tumor development, the proliferation protein Ki-67, the tumor angiogenesis indicator CD31, and its function in controlling the tumor immune microenvironment were evaluated by in vivo tests. Results There was a considerable decrease in RBMS3 expression in EOC tissues, which was linked to a poor prognosis for patients and the infiltration of multiple immune cell. Given immunohistochemical studies, tissues with increased RBMS3 expression had decreased markers of myeloid-derived suppressor cells, regulatory T cells, and M2 macrophages, whereas M1 macrophage markers were elevated. RBMS3 appears to suppress the capabilities of proliferating, invading, and migrating in EOC cells according to in vitro tests, whereas tumors overexpressing RBMS3 developed more slowly in syngeneic mouse models. The overexpression of RBMS3 led to a decline in the levels of Ki-67 protein and CD31. Additionally, it showed a negatively correlation with markers of regulatory T cell, myeloid-derived suppressor cell, and M2 macrophage but a positive correlation with markers of M1 macrophage. Conclusions The findings revealed that elevated RBMS3 expression plays a tumor suppressor role in EOC and was connected to patient survival in EOC. The studies conducted in vitro and in vivo demonstrated a link between RBMS3 expression and the infiltration of certain immune cells, indicating a function for RBMS3 in the immunosuppressive tumor microenvironment and its promising efficiency as a novel target for immunotherapy against EOC.
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Affiliation(s)
- Tian Yin
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
- Anhui Engineering Technology Research Center of Biochemical Pharmaceutical, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Ying Zhang
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
| | - Yue Zhao
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
- Anhui Engineering Technology Research Center of Biochemical Pharmaceutical, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Xinyi Zhang
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
| | - Shuqi Han
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
| | - Yixiao Wang
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
| | - Bo Yang
- Departments of Oncology Gynecology, The First Affiliated Hospital of Bengbu Medical University, No. 287 Changhuai Road, Bengbu, 233004, China
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Li Y, Wang S, Li G, Gao C, Cui Z, Cong M, Hu J, Zhang M, Jin X, Sun H, Kong D. The RNA-binding protein RBMS3 inhibits the progression of colon cancer by regulating the stability of LIMS1 mRNA. Cancer Med 2024; 13:e7129. [PMID: 38618967 PMCID: PMC11017296 DOI: 10.1002/cam4.7129] [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: 08/06/2023] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND The RNA-binding motif single-stranded interacting protein 3 (RBMS3) is a constituent of the RNA-binding motif (RBM) protein family, which assumes a pivotal role in governing cellular biogenesis processes such as the cell cycle and apoptosis. Despite an abundance of studies elucidating RBMS3's divergent roles in the genesis and advancement of various tumors, its involvement in colon cancer remains enigmatic. METHODS The present investigation employed data analysis from TCGA and GTEx to unveil that RBMS3 expression demonstrated a diminished presence in colon cancer tissues when juxtaposed with normal colon tissues. The effect of RBMS3 and LIM zinc finger domain 1 (LIMS1) on colon cancer was substantiated via animal models and cellular experiments. The connection between RBMS3 and LIM zinc finger domain 1 (LIMS1) was verified by molecular biology methods. RESULTS The study conclusively ascertained that augmenting RBMS3 expression quells the proliferation, migration, and invasion of colon cancer cells. Furthermore, the inquiry unveiled a plausible mechanism through which RBMS3 impacts the expression of LIMS1 by modulating its mRNA stability. The investigation ascertained that RBMS3 inhibits the progression of colon cancer by regulating LIMS1. The inhibitory function of LIMS1 and RBMS3 is closely intertwined in colon cancer, with knocking down LIMS1 being able to rescue the inhibitory effect of RBMS3 overexpression on the functionality of colon cancer cell CONCLUSIONS: The discernments delineate RBMS3 as a novel suppressor of cancer via LIMS1, thereby bestowing fresh therapeutic possibilities and illuminating the intricacies of colon cancer.
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Affiliation(s)
- Yafei Li
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Shuoshuo Wang
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Guoli Li
- Department of Anus and Intestine SurgeryChifeng Municipal HospitalChifengChina
| | - Chunyang Gao
- Department of AnatomyHarbin Medical UniversityHarbinChina
| | - Zihan Cui
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Mingqi Cong
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Jie Hu
- Central Operating DepartmentThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Minghui Zhang
- Department of OncologyChifeng Municipal HospitalChifengChina
| | - Xiaoming Jin
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Haiying Sun
- Gastrointestinal Rehabilitation CenterBeijing Rehabilitation Hospital of Capital Medical UniversityBeijingChina
- Gastroenterology DepartmentFirst Hospital of DandongDandongChina
| | - Dan Kong
- Department of GynaecologyTumor Hospital of Harbin Medical UniversityHarbinChina
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3
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Gong Z, Shen P, Wang H, Zhu J, Liang K, Wang K, Mi Y, Shen S, Fang X, Liu G. A novel circular RNA circRBMS3 regulates proliferation and metastasis of osteosarcoma by targeting miR-424-eIF4B/YRDC axis. Aging (Albany NY) 2023; 15:1564-1590. [PMID: 36897170 PMCID: PMC10042691 DOI: 10.18632/aging.204567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Circular RNAs (circRNAs) have been demonstrated to have critical regulatory roles in tumorigenesis. However, the contribution of circRNAs to OS (osteosarcoma) remains largely unknown. circRNA deep sequencing was performed to the expression of circRNAs between OS and chondroma tissues. The regulatory and functional role of circRBMS3 (a circRNA derived from exons 7 to 10 of the RBMS3 gene, hsa_circ_0064644) upregulation was examined in OS and was validated in vitro and in vivo, upstream regulator and downstream target of circRBMS3 were both explored. RNA pull down, a luciferase reporter assay, biotin-coupled microRNA capture and fluorescence in situ hybridization were used to evaluate the interaction between circRBMS3 and micro (mi)-R-424-5p. For in vivo tumorigenesis experiments, Subcutaneous and Orthotopic xenograft OS mouse models were built. Expression of circRBMS3 was higher in OS tissues due to the regulation of adenosine deaminase 1-acting on RNA (ADAR1), an abundant RNA editing enzyme. Our in vitro data indicated that ShcircRBMS3 inhibits the proliferation and migration of osteosarcoma cells. Mechanistically, we showed that circRBMS3 could regulate eIF4B and YRDC, through 'sponging' miR-424-5p. Furthermore, knockdown of circRBMS3 inhibited malignant phenotypes and bone destruction of OS in vivo. Our results reveal an important role for a novel circRBMS3 in the growth and metastasis of malignant tumor cells and offer a fresh perspective on circRNAs in OS progression.
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Affiliation(s)
- Zhe Gong
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Panyang Shen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Haitao Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Jinjin Zhu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Kaiyu Liang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Kefan Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Yunfeng Mi
- Department of Orthopaedic Surgery, Ningbo First Hospital, Ningbo 315010, China
| | - Shuying Shen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Xiangqian Fang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Gang Liu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University and Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou 310016, Zhejiang Province, China
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4
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Expression of RBMS3 in Breast Cancer Progression. Int J Mol Sci 2023; 24:ijms24032866. [PMID: 36769184 PMCID: PMC9917836 DOI: 10.3390/ijms24032866] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The aim of the study was to evaluate the localization and intensity of RNA-binding motif single-stranded-interacting protein 3 (RBMS3) expression in clinical material using immunohistochemical (IHC) reactions in cases of ductal breast cancer (in vivo), and to determine the level of RBMS3 expression at both the protein and mRNA levels in breast cancer cell lines (in vitro). Moreover, the data obtained in the in vivo and in vitro studies were correlated with the clinicopathological profiles of the patients. Material for the IHC studies comprised 490 invasive ductal carcinoma (IDC) cases and 26 mastopathy tissues. Western blot and RT-qPCR were performed on four breast cancer cell lines (MCF-7, BT-474, SK-BR-3 and MDA-MB-231) and the HME1-hTERT (Me16C) normal immortalized breast epithelial cell line (control). The Kaplan-Meier plotter tool was employed to analyze the predictive value of overall survival of RBMS3 expression at the mRNA level. Cytoplasmatic RBMS3 IHC expression was observed in breast cancer cells and stromal cells. The statistical analysis revealed a significantly decreased RBMS3 expression in the cancer specimens when compared with the mastopathy tissues (p < 0.001). An increased expression of RBMS3 was corelated with HER2(+) cancer specimens (p < 0.05) and ER(-) cancer specimens (p < 0.05). In addition, a statistically significant higher expression of RBMS3 was observed in cancer stromal cells in comparison to the control and cancer cells (p < 0.0001). The statistical analysis demonstrated a significantly higher expression of RBMS3 mRNA in the SK-BR-3 cell line compared with all other cell lines (p < 0.05). A positive correlation was revealed between the expression of RBMS3, at both the mRNA and protein levels, and longer overall survival. The differences in the expression of RBMS3 in cancer cells (both in vivo and in vitro) and the stroma of breast cancer with regard to the molecular status of the tumor may indicate that RBMS3 could be a potential novel target for the development of personalized methods of treatment. RBMS3 can be an indicator of longer overall survival for potential use in breast cancer diagnostic process.
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Saikia M, Bhattacharyya DK, Kalita JK. Identification of Potential Biomarkers Using Integrative Approach: A Case Study of ESCC. SN COMPUTER SCIENCE 2023; 4:114. [PMID: 36573207 PMCID: PMC9769493 DOI: 10.1007/s42979-022-01492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
This paper presents a consensus-based approach that incorporates three microarray and three RNA-Seq methods for unbiased and integrative identification of differentially expressed genes (DEGs) as potential biomarkers for critical disease(s). The proposed method performs satisfactorily on two microarray datasets (GSE20347 and GSE23400) and one RNA-Seq dataset (GSE130078) for esophageal squamous cell carcinoma (ESCC). Based on the input dataset, our framework employs specific DE methods to detect DEGs independently. A consensus based function that first considers DEGs common to all three methods for further downstream analysis has been introduced. The consensus function employs other parameters to overcome information loss. Differential co-expression (DCE) and preservation analysis of DEGs facilitates the study of behavioral changes in interactions among DEGs under normal and diseased circumstances. Considering hub genes in biologically relevant modules and most GO and pathway enriched DEGs as candidates for potential biomarkers of ESCC, we perform further validation through biological analysis as well as literature evidence. We have identified 25 DEGs that have strong biological relevance to their respective datasets and have previous literature establishing them as potential biomarkers for ESCC. We have further identified 8 additional DEGs as probable potential biomarkers for ESCC, but recommend further in-depth analysis.
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Affiliation(s)
- Manaswita Saikia
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam 784028 India
| | - Dhruba K Bhattacharyya
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam 784028 India
| | - Jugal K Kalita
- Department of Computer Science, College of Engineering and Applied Science, University of Colorado, Colorado Springs, CO 80918 USA
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6
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Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, Van Veen JE, Murphy B, Hackett CS, Dupuy AJ, Chmura SA, van der Weyden L, Newberg JY, Liu A, Mann K, Rust AG, Weiss WA, Kinsey CG, Adams DJ, Grossmann A, Mann MB, McMahon M. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis. Cancer Res 2022; 82:4261-4273. [PMID: 36112789 PMCID: PMC9664136 DOI: 10.1158/0008-5472.can-21-3214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 01/09/2023]
Abstract
Mutationally activated BRAF is detected in approximately 7% of human lung adenocarcinomas, with BRAFT1799A serving as a predictive biomarker for treatment of patients with FDA-approved inhibitors of BRAFV600E oncoprotein signaling. In genetically engineered mouse (GEM) models, expression of BRAFV600E in the lung epithelium initiates growth of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinoma. To identify genes that cooperate with BRAFV600E for malignant progression, we used Sleeping Beauty-mediated transposon mutagenesis, which dramatically accelerated the emergence of lethal lung cancers. Among the genes identified was Rbms3, which encodes an RNA-binding protein previously implicated as a putative tumor suppressor. Silencing of RBMS3 via CRISPR/Cas9 gene editing promoted growth of BRAFV600E lung organoids and promoted development of malignant lung cancers with a distinct micropapillary architecture in BRAFV600E and EGFRL858R GEM models. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of Ctnnb1, Ccnd1, Axin2, Lgr5, and c-Myc mRNAs, suggesting that RBMS3 silencing elevates signaling through the WNT/β-catenin signaling axis. Although RBMS3 silencing rendered BRAFV600E-driven lung tumors resistant to the effects of dabrafenib plus trametinib, the tumors were sensitive to inhibition of porcupine, an acyltransferase of WNT ligands necessary for their secretion. Analysis of The Cancer Genome Atlas patient samples revealed that chromosome 3p24, which encompasses RBMS3, is frequently lost in non-small cell lung cancer and correlates with poor prognosis. Collectively, these data reveal the role of RBMS3 as a lung cancer suppressor and suggest that RBMS3 silencing may contribute to malignant NSCLC progression. SIGNIFICANCE Loss of RBMS3 cooperates with BRAFV600E to induce lung tumorigenesis, providing a deeper understanding of the molecular mechanisms underlying mutant BRAF-driven lung cancer and potential strategies to more effectively target this disease.
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Affiliation(s)
- Aria Vaishnavi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Joseph Juan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Maebh Jacob
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Eric E. Gardner
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Michael T. Scherzer
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Sophia Schuman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - J. Edward Van Veen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Brandon Murphy
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Christopher S. Hackett
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Steven A. Chmura
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Annie Liu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Karen Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Alistair G. Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - William A. Weiss
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Conan G. Kinsey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - David J. Adams
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
| | - Allie Grossmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
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7
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Górnicki T, Lambrinow J, Mrozowska M, Podhorska-Okołów M, Dzięgiel P, Grzegrzółka J. Role of RBMS3 Novel Potential Regulator of the EMT Phenomenon in Physiological and Pathological Processes. Int J Mol Sci 2022; 23:ijms231810875. [PMID: 36142783 PMCID: PMC9503485 DOI: 10.3390/ijms231810875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
RNA-binding protein 3 (RBMS3) plays a significant role in embryonic development and the pathogenesis of many diseases, especially cancer initiation and progression. The multiple roles of RBMS3 are conditioned by its numerous alternative expression products. It has been proven that the main form of RBMS3 influences the regulation of microRNA expression or stabilization. The absence of RBMS3 activates the Wnt/β-catenin pathway. The expression of c-Myc, another target of the Wnt/β-catenin pathway, is correlated with the RBMS3 expression. Numerous studies have focused solely on the interaction of RBMS3 with the epithelial-mesenchymal transition (EMT) protein machinery. EMT plays a vital role in cancer progression, in which RBMS3 is a new potential regulator. It is also significant that RBMS3 may act as a prognostic factor of overall survival (OS) in different types of cancer. This review presents the current state of knowledge about the role of RBMS3 in physiological and pathological processes, with particular emphasis on carcinogenesis. The molecular mechanisms underlying the role of RBMS3 are not fully understood; hence, a broader explanation and understanding is still needed.
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Affiliation(s)
- Tomasz Górnicki
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jakub Lambrinow
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Monika Mrozowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | | | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jędrzej Grzegrzółka
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
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8
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Wu Y, Liu Z, Wei X, Feng H, Hu B, Liu B, Luan Y, Ruan Y, Liu X, Liu Z, Wang S, Liu J, Wang T. Identification of the Functions and Prognostic Values of RNA Binding Proteins in Bladder Cancer. Front Genet 2021; 12:574196. [PMID: 34239534 PMCID: PMC8258248 DOI: 10.3389/fgene.2021.574196] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/19/2021] [Indexed: 12/01/2022] Open
Abstract
Post-transcriptional regulation plays a leading role in gene regulation and RNA binding proteins (RBPs) are the most important posttranscriptional regulatory protein. RBPs had been found to be abnormally expressed in a variety of tumors and is closely related to its occurrence and progression. However, the exact mechanism of RBPs in bladder cancer (BC) is unknown. We downloaded transcriptomic data of BC from the Cancer Genome Atlas (TCGA) database and used bioinformatics techniques for subsequent analysis. A total of 116 differentially expressed RBPs were selected, among which 61 were up-regulated and 55 were down-regulated. We then identified 12 prognostic RBPs including CTIF, CTU1, DARS2, ENOX1, IGF2BP2, LIN28A, MTG1, NOVA1, PPARGC1B, RBMS3, TDRD1, and ZNF106, and constructed a prognostic risk score model. Based on this model we found that patients in the high-risk group had poorer overall survival (P < 0.001), and the area under the receiver operator characteristic curve for this model was 0.677 for 1 year, 0.697 for 3 years, and 0.709 for 5 years. Next, we drew a nomogram based on the risk score and other clinical variables, which showed better predictive performance. Our findings contribute to a better understanding of the pathogenesis, progression and metastasis of BC. The model of these 12 genes has good predictive value and may have good prospects for improving clinical treatment regimens and patient prognosis.
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Affiliation(s)
- Yue Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xian Wei
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huan Feng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bintao Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Luan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajun Ruan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhuo Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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9
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Wang C, Wu Y, Liu Y, Pan F, Zeng H, Li X, Yu L. Tumor Suppressor Effect of RBMS3 in Breast Cancer. Technol Cancer Res Treat 2021; 20:15330338211004921. [PMID: 33910421 PMCID: PMC8107673 DOI: 10.1177/15330338211004921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: RBMS3 (RNA-binding motif, single-stranded-intervacting protein 3) acts as a tumor-suppressive gene in a number of human cancers, however, its role in breast cancer is not fully understood. This study aimed to investigate the expression and clinicopathological significance of RBMS3 in breast cancer. Methods: A total of 998 breast cancer tissue samples in The Cancer Genome Atlas (TCGA) database with survival outcomes were divided into high RBMS3 expression and low expression groups using the median as the cutoff. Clinicopathological characteristics and prognosis were compared between the 2 groups. Results: TCGA showed that RBMS3 mRNA was downregulated in breast cancer tissues, and RBMS3 downregulation was correlated with poor prognosis. Immunohistochemistry staining of 127 paraffin-embedded breast cancer tissues showed that RBMS3 protein was localized in the cytoplasm and nucleus; however, nuclear staining was present in 90.0% of normal breast tissues but only 28.3% of breast cancer tissues. Decreased RBMS3 protein expression was significantly correlated with estrogen receptor (ER)-negative status and death at final follow-up. Patients with lower RBMS3 protein expression had substantially shorter survival than those with higher RBMS3 expression. Univariate and multivariate analysis indicated that the combination of RBMS3 expression and ER status (a variable designated as “cofactor”) was an independent prognostic factor in patients with breast cancer (hazard ratio [HR] = 0.420, 95% confidence interval [CI]: 0.223-0.791, P = 0.007). Conclusion: RBMS3 downregulation was correlated with poor prognosis in breast cancer patients, and the combination of RBMS3 expression and ER status was an independent prognostic factor.
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Affiliation(s)
- Chunyang Wang
- Zhujiang New Town Dental Clinic, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Yidan Wu
- Diagnosis and Treatment Center of Breast Disease, Shantou Central Hospital, Shantou, Guangdong, China
| | - Yunqi Liu
- Department of Cardiac Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fushun Pan
- Department of Medical Ultrasonics, Institute of Diagnostic and Interventional Ultrasound, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huijuan Zeng
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoxi Li
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Yu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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10
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Aiderus A, Contreras-Sandoval AM, Meshey AL, Newberg JY, Ward JM, Swing DA, Copeland NG, Jenkins NA, Mann KM, Mann MB. Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation. Cancers (Basel) 2021; 13:E225. [PMID: 33435458 PMCID: PMC7827284 DOI: 10.3390/cancers13020225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022] Open
Abstract
A central challenge in cancer genomics is the systematic identification of single and cooperating tumor suppressor gene mutations driving cellular transformation and tumor progression in the absence of oncogenic driver mutation(s). Multiple in vitro and in vivo gene inactivation screens have enhanced our understanding of the tumor suppressor gene landscape in various cancers. However, these studies are limited to single or combination gene effects, specific organs, or require sensitizing mutations. In this study, we developed and utilized a Sleeping Beauty transposon mutagenesis system that functions only as a gene trap to exclusively inactivate tumor suppressor genes. Using whole body transposon mobilization in wild type mice, we observed that cumulative gene inactivation can drive tumorigenesis of solid cancers. We provide a quantitative landscape of the tumor suppressor genes inactivated in these cancers and show that, despite the absence of oncogenic drivers, these genes converge on key biological pathways and processes associated with cancer hallmarks.
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Affiliation(s)
- Aziz Aiderus
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Ana M. Contreras-Sandoval
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Amanda L. Meshey
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
| | - Jerrold M. Ward
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
| | - Deborah A. Swing
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Neal G. Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Nancy A. Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Karen M. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Departments of Gastrointestinal Oncology & Malignant Hematology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center, Tampa, FL 33612, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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11
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Mukherjee M, Goswami S. Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. PLoS One 2020; 15:e0237559. [PMID: 32780783 PMCID: PMC7418985 DOI: 10.1371/journal.pone.0237559] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5' and 3' untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. METHODS To have an idea of the global changes in 5' and 3'-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by 'RBPmap' and 'RNA22 v2' respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. RESULTS We identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5'-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3'UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.
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Affiliation(s)
- Moumita Mukherjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Srikanta Goswami
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
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12
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Zhang J, Bing Z, Yan P, Tian J, Shi X, Wang Y, Yang K. Identification of 17 mRNAs and a miRNA as an integrated prognostic signature for lung squamous cell carcinoma. J Gene Med 2020; 21:e3105. [PMID: 31215090 DOI: 10.1002/jgm.3105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/22/2019] [Accepted: 06/05/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gene signatures for predicting the outcome of lung squamous cell carcinoma (LUSC) have been employed for many years. However, various signatures have been applied in clinical practice. Therefore, in the present study, we aimed to filter out an effective LUSC prognostic gene signature by simultaneously integrating mRNA and microRNA (miRNA). METHODS First, based on data from the Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga), mRNAs and miRNAs that were related to overall survival of LUSC were obtained by the least absolute shrinkage and selection operator method. Subsequently, the predicting effect was tested by time-dependent receiver operating characteristic curve analysis and Kaplan-Meier survival analysis. Next, related clinical indices were added to evaluate the efficiency of the selected gene signatures. Finally, validation and comparison using three independent gene signatures were performed using data from the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo). RESULTS Our data showed that the prognostic index (PI) contained 17 mRNAs and one miRNA. According to the best normalized cut-off of PI (0.0247), the hazard ratio of the PI was 3.40 (95% confidence interval = 2.33-4.96). Moreover, when clinical factors were introduced, the PI was still the most significant index. In addition, only two Gene Ontology terms with p < 0.05 were reported. Furthermore, validation implied that, using our 18-gene signature, only hazard ratio = 1.36 (95% confidence interval = 1.01-1.83) was significant compared to the other three groups of gene biomarkers. CONCLUSIONS The 18-gene signature selected based on data from the TCGA database had an effective prognostic value for LUSC patients.
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Affiliation(s)
- Jingyun Zhang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Zhitong Bing
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Department of Computational Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Peijing Yan
- Institution of Clinical Research and Evidence Based Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Jinhui Tian
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Xiue Shi
- Gansu Rehabilitation Center Hospital, Lanzhou, China.,Gansu Evidence-Based Rehabilitation Medicine Center, Lanzhou, China
| | - Yongfeng Wang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Kehu Yang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Institution of Clinical Research and Evidence Based Medicine, Gansu Provincial Hospital, Lanzhou, China.,Gansu Evidence-Based Rehabilitation Medicine Center, Lanzhou, China
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13
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Zhang J, Luo L, Dong J, Liu M, Zhai D, Huang D, Ling L, Jia X, Luo K, Zheng G. A prognostic 11-DNA methylation signature for lung squamous cell carcinoma. J Thorac Dis 2020; 12:2569-2582. [PMID: 32642165 PMCID: PMC7330303 DOI: 10.21037/jtd.2020.03.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC), as the second frequent subtype of lung cancer, causes lots of mortalities primarily due to a lack of precise prognostic markers and timely treatment intervention. Previous studies have constructed several risk prognostic models based on DNA methylation sites in multiple tumors, whereas, DNA methylation signature of LUSC remains to be built, and its predictive value need to be evaluated. Methods The genome-wide DNA methylation data of LUSC samples was obtained from The Cancer Genome Atlas dataset. Univariate Cox analysis and the least absolute shrinkage and selection operator (LASSO) were implemented to identify DNA methylation sites related to overall survival of LUSC patients. Thus, we performed multivariate Cox regression to establish a DNA methylation signature. The Kaplan-Meier (K-M) survival curves and time-dependent receiver operating characteristic (ROC) curves were plotted to estimate the prognostic power of the signature. Comparison with other known prognostic biomarkers, our DNA methylation signature showed higher predictive specificity and sensitivity. In addition, multivariate Cox regression screened out independent prognostic factors and constructed a nomogram. Results Several statistical methods were performed to construct an 11-DNA methylation signature. LUSC patients were divided into low- and high-risk group based on risk score, and high-risk group had a shorter survival time. According to the results of K-M and ROC analyses, the 11-DNA methylation signature showed significant sensitivity and specificity in predicting the LUSC patients’ overall survival. Finally, we integrated some independent prognostic factors (risk score, metastasis stage, and tobacco smoking history) to construct a nomogram, which has excellent prognostic power and may provide guidance for the therapeutic strategies. Conclusions We constructed the first risk prognosis model based on DNA methylation site in LUSC, which showed better predictive ability. In addition, a nomogram integrating the DNA methylation signature, metastasis stage, and tobacco smoking history was developed.
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Affiliation(s)
- Jianlei Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Liyun Luo
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Jing Dong
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Meijun Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Dongfeng Zhai
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Danqing Huang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Li Ling
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Xiaoting Jia
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Kai Luo
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Guopei Zheng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
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14
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Wu Y, Meng D, You Y, Sun R, Yan Q, Bao J, Sun Y, Yun D, Li Y, Sun D. Increased expression of RBMS3 predicts a favorable prognosis in human gallbladder carcinoma. Oncol Rep 2020; 44:55-68. [PMID: 32627033 PMCID: PMC7251710 DOI: 10.3892/or.2020.7594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/22/2020] [Indexed: 01/18/2023] Open
Abstract
Multiple regions in the short arm of chromosome 3 are frequently deleted in a variety of solid tumors including gallbladder carcinoma (GBC). RNA binding motif, single‑stranded interacting protein 3 (RBMS3), a tumor suppressor gene (TSG), is located in this region. However, the role of RBMS3 in GBC remains unclear. Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) and western blotting were performed to evaluate the mRNA and protein expression levels of RBMS3 in 41 fresh frozen GBC tissues and paired normal tissues. An immunohistochemical assay was performed on a tissue microarray (TMA, consisting of 125 cases GBC and 47 normal controls). Microvessel density (MVD) counts were determined using CD34 immunohistochemical staining. Moreover, univariate and multivariate analyses were performed to determine the correlations between RBMS3 expression, MVD and patient prognosis. Cellular functions including proliferation, clonogenicity and apoptosis, were assessed to further identify in vitro roles of RBMS3. It was revealed that both mRNA and protein expression levels of RBMS3 were significantly lower in GBC tissues than in normal controls. Multivariate Cox regression analyses demonstrated cytoplasmic RBMS3 expression as an independent prognostic factor correlated with GBC angiogenesis, histopathological differentiation and TNM stage. Kaplan‑Meier curves revealed that patients with lower cytoplasmic RBMS3 levels had a significantly worse OS than patients with higher cytoplasmic RBMS3 expression. Additionally, ectopic expression of RBMS3 markedly suppressed GBC cell proliferation and clonogenicity and promoted apoptosis in vitro. These findings indicated the potential of cytoplasmic RBMS3 as a tumor prognostic biomarker and a promising therapeutic target for GBC.
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Affiliation(s)
- Youliang Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Delong Meng
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yexiang You
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ruochuan Sun
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Qiang Yan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Junjun Bao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yanjun Sun
- Department of General Surgery, The Armed Police Corps Hospital of Anhui, Hefei, Anhui 230041, P.R. China
| | - Dapeng Yun
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yongxiang Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dengqun Sun
- Department of General Surgery, The Armed Police Corps Hospital of Anhui, Hefei, Anhui 230041, P.R. China
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15
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Li X, Ma C, Luo H, Zhang J, Wang J, Guo H. Identification of the differential expression of genes and upstream microRNAs in small cell lung cancer compared with normal lung based on bioinformatics analysis. Medicine (Baltimore) 2020; 99:e19086. [PMID: 32176034 PMCID: PMC7440067 DOI: 10.1097/md.0000000000019086] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Small cell lung cancer (SCLC) is one of the most lethal cancer, mainly attributing to its high tendency to metastasis. Mounting evidence has demonstrated that genes and microRNAs (miRNAs) are related to human cancer onset and progression including invasion and metastasis.An eligible gene dataset and an eligible miRNA dataset were downloaded from the Gene Expression Omnibus (GEO) database based our screening criteria. Differentially expressed genes (DE-genes) or DE-miRNAs for each dataset obtained by the R software package. The potential target genes of the top 10 DE-miRNAs were predicted by multiple databases. For annotation, visualization and integrated discovery, Metascape 3.0 was introduced to perform enrichment analysis for the DE-genes and the predicted target genes of the selected top 10 DE-miRNAs, including Pathway and Process Enrichment Analysis or protein-protein interaction enrichment analysis. The intersection of predicted target genes and DE-genes was taken as the final DE-genes. Then apply the predicted miRNAs-targets relationship of top 10 DE-miRNAs to the final DE-genes to gain more convinced DE-miRNAs, DE-genes and their one to one relationship.GSE19945 (miRNA microarray) and GSE40275 (gene microarray) datasets were selected and downloaded. 56 DE-miRNAs and 861 DE-genes were discovered. 297 miRNAs-targets relationships (284 unique genes) were predicted as the target of top 10 upregulating DE-miRNAs. 245 miRNAs-targets relationships (238 unique genes) were identified as the target of top 10 downregulating DE-miRNAs. The key results of enrichment analysis include protein kinase B signaling, transmembrane receptor protein tyrosine kinase signaling pathway, negative regulation of cell differentiation, response to growth factor, cellular response to lipid, muscle structure development, response to growth factor, signaling by Receptor Tyrosine Kinases, epithelial cell migration, cellular response to organic cyclic compound, Cell Cycle (Mitotic), DNA conformation change, cell division, DNA replication, cell cycle phase transition, blood vessel development, inflammatory response, Staphylococcus aureus infection, leukocyte migration, and myeloid leukocyte activation. Differential expression of genes-upstream miRNAs (RBMS3-hsa-miR-7-5p, NEDD9-hsa-miR-18a-5p, CRIM1-hsa-miR-18a-5p, TGFBR2-hsa-miR-9-5p, MYO1C-hsa-miR-9-5p, KLF4-hsa-miR-7-5p, EMP2-hsa-miR-1290, TMEM2-hsa-miR-18a-5p, CTGF-hsa-miR-18a-5p, TNFAIP3-hsa-miR-18a-5p, THBS1-hsa-miR-182-5p, KPNA2-hsa-miR-144-3p, GPR137C-hsa-miR-1-3p, GRIK3-hsa-miR-144-3p, and MTHFD2-hsa-miR-30a-3p) were identified in SCLC.RBMS3, NEDD9, CRIM1, KPNA2, GPR137C, GRIK3, hsa-miR-7-5p, hsa-miR-18a-5p, hsa-miR-144-3p, hsa-miR-1-3p along with the pathways included protein kinase B signaling, muscle structure development, Cell Cycle (Mitotic) and blood vessel development may gain a high chance to play a key role in the prognosis of SCLC, but more studies should be conducted to reveal it more clearly.
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Affiliation(s)
- Xiuwei Li
- Department of Radiotherapy, Zhoukou Central Hospital, Zhoukou, China
| | | | - Huan Luo
- Department of Ophthalmology, Campus Virchow, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Jian Zhang
- Department of Radiotherapy, Zhoukou Central Hospital, Zhoukou, China
| | - Jinan Wang
- Department of Radiotherapy, Zhoukou Central Hospital, Zhoukou, China
| | - Hongtao Guo
- Department of Radiotherapy, Zhoukou Central Hospital, Zhoukou, China
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16
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Wu J, Zhang L, Song Q, Yu L, Wang S, Zhang B, Wang W, Xia P, Chen X, Xiao Y, Xu C. Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications. Brief Bioinform 2020; 22:589-600. [PMID: 32022856 DOI: 10.1093/bib/bbaa004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF) mediates transcriptional regulation and implicates epigenetic modifications in cancers. However, the systematically unveiling inverse regulatory relationship between CTCF and epigenetic modifications still remains unclear, especially the mechanism by which histone modification mediates CTCF binding. Here, we developed a systematic approach to investigate how epigenetic changes affect CTCF binding. Through integration analysis of CTCF binding in 30 cell lines, we concluded that CTCF generally binds with higher intensity in normal cell lines than that in cancers, and higher intensity in genome regions closed to transcription start sites. To facilitate the better understanding of their associations, we constructed linear mixed-effect models to analyze the effects of the epigenetic modifications on CTCF binding in four cancer cell lines and six normal cell lines, and identified seven epigenetic modifications as potential epigenetic patterns that influence CTCF binding intensity in promoter regions and six epigenetic modifications in enhancer regions. Further analysis of the effects in different locations revealed that the epigenetic regulation of CTCF binding was location-specific and cancer cell line-specific. Moreover, H3K4me2 and H3K9ac showed the potential association with immune regulation of disease. Taken together, our method can contribute to improve the understanding of the epigenetic regulation of CTCF binding and provide potential therapeutic targets for treating tumors associated with CTCF.
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Affiliation(s)
- Jie Wu
- Bioinformatics at Harbin Medical University, China
| | - Li Zhang
- Bioinformatics at Harbin Medical University, China
| | - Qian Song
- Bioinformatics at Harbin Medical University, China
| | - Lei Yu
- Bioinformatics at Harbin Medical University, China
| | - Shuyuan Wang
- Bioinformatics at Harbin Medical University, China
| | - Bo Zhang
- Bioinformatics at Harbin Medical University, China
| | - Weida Wang
- Bioinformatics at Harbin Medical University, China
| | - Peng Xia
- Bioinformatics at Harbin Medical University, China
| | - Xiaowen Chen
- Bioinformatics at Harbin Medical University, China
| | - Yun Xiao
- Bioinformatics at Harbin Medical University, China
| | - Chaohan Xu
- Bioinformatics at Harbin Medical University, China
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Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. G3-GENES GENOMES GENETICS 2020; 10:151-163. [PMID: 31694854 PMCID: PMC6945038 DOI: 10.1534/g3.119.400775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Scleroderma, or systemic sclerosis (SSc), is an autoimmune disease characterized by progressive fibrosis of the skin and internal organs. The most common cause of death in people with SSc is lung disease, but the pathogenesis of lung disease in SSc is insufficiently understood to devise specific treatment strategies. Developing targeted treatments requires not only the identification of molecular processes involved in SSc-associated lung disease, but also understanding of how these processes interact to drive pathology. One potentially powerful approach is to identify alleles that interact genetically to influence lung outcomes in patients with SSc. Analysis of interactions, rather than individual allele effects, has the potential to delineate molecular interactions that are important in SSc-related lung pathology. However, detecting genetic interactions, or epistasis, in human cohorts is challenging. Large numbers of variants with low minor allele frequencies, paired with heterogeneous disease presentation, reduce power to detect epistasis. Here we present an analysis that increases power to detect epistasis in human genome-wide association studies (GWAS). We tested for genetic interactions influencing lung function and autoantibody status in a cohort of 416 SSc patients. Using Matrix Epistasis to filter SNPs followed by the Combined Analysis of Pleiotropy and Epistasis (CAPE), we identified a network of interacting alleles influencing lung function in patients with SSc. In particular, we identified a three-gene network comprising WNT5A, RBMS3, and MSI2, which in combination influenced multiple pulmonary pathology measures. The associations of these genes with lung outcomes in SSc are novel and high-confidence. Furthermore, gene coexpression analysis suggested that the interactions we identified are tissue-specific, thus differentiating SSc-related pathogenic processes in lung from those in skin.
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Zhu L, Xi PW, Li XX, Sun X, Zhou WB, Xia TS, Shi L, Hu Y, Ding Q, Wei JF. The RNA binding protein RBMS3 inhibits the metastasis of breast cancer by regulating Twist1 expression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:105. [PMID: 30819235 PMCID: PMC6394024 DOI: 10.1186/s13046-019-1111-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/18/2019] [Indexed: 11/25/2022]
Abstract
Background Metastasis remains the biggest obstacle for breast cancer treatment. Therefore, identification of specific biomarker of metastasis is very necessary. The RNA binding protein 3 (RBMS3) acts as a tumor suppressor in various cancers. Whereas, its role and underlying molecular mechanism in breast cancer is far from elucidated. Methods Quantitative real-time PCR and western blots were carried out to determine the expression of RBMS3 in breast cancer cells and tissues. Transwell and in vivo metastasis assay were conducted to investigate the effects of RBMS3 on migration, invasion and metastasis of breast cancer cells. Transcriptome sequencing was applied to screen out the differential gene expression affected by RBMS3. RNA immunoprecipitation assay combined with luciferase reporter assay were performed to explore the direct correlation between RBMS3 and Twist1 mRNA. Results RBMS3 was downregulated in breast cancer and ectopic expression of RBMS3 contributed to inhibition of cell migration, invasion in vitro and lung metastasis in vivo. Furthermore, RBMS3 negatively regulated Twsit1 expression via directly binding to 3′-UTR of Twist1 mRNA, and thereby decreased Twist1-induced expression of matrix metalloproteinase 2 (MMP2). Additionally, Twist1-induced cell migration, invasion and lung metastasis could be reversed by the upregulation of RBMS3. Conclusions In summary, our study revealed a novel mechanism of the RBMS3/Twsit1/MMP2 axis in the regulation of invasion and metastasis of breast cancer, which may become a potential molecular marker for breast cancer treatment.
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Affiliation(s)
- Lei Zhu
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Pei-Wen Xi
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xiao-Xia Li
- Department of Critical Care Medicine, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xi Sun
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Wen-Bin Zhou
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Tian-Song Xia
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Liang Shi
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yue Hu
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Qiang Ding
- Jiangsu Breast Disease Center, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, the First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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19
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Lei X, Muscat JE, Huang Z, Chen C, Xiu G, Chen J. Differential transcriptional changes in human alveolar epithelial A549 cells exposed to airborne PM 2.5 collected from Shanghai, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:33656-33666. [PMID: 30276685 DOI: 10.1007/s11356-018-3090-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Fine particulate matters (PM2.5) are the core pollutants of haze episode, which pose a serious threat to the human health of developing countries. However, the mechanisms involved in PM2.5-induced hazard influence are not to fully elucidated. In the present study, human lung epithelial cells (A549) were exposed to various concentrations of PM2.5 samples collected from Shanghai, China. Illumina RNA-Seq method with transcriptome, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were further employed to identify the detrimental effects of PM2.5 on A549 cells in vitro. A total of 712 differentially expressed genes were obtained from global transcriptome profiling of A549 cells after PM2.5 exposure. In addition, GO function enrichment analysis revealed that major differentially expressed genes (DEGs) involved in the biological process of the immune system and the response to the stress. KEGG pathway analysis further proposes that infectious disease, cancers, cardiovascular disease, and immune disease pathway were the key human disease events that occur in A549 cells under PM2.5 stress. The data obtained here shed light on the related biological process and gene signaling pathways affected by PM2.5 exposure. This study aids our understanding of the complicated mechanisms related to PM2.5-induced health effects and is informative for the prevention and treatment of PM2.5-induced systemic diseases.
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Affiliation(s)
- Xiaoning Lei
- State Environmental Protection Key Laboratory of Risk Assessment and Control on Chemical Processes, East China University of Science and Technology (ECUST), Shanghai, 200237, China
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Penn State Hershey Medical Center, Hershey, PA, 17033, USA
| | - Joshua E Muscat
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Penn State Hershey Medical Center, Hershey, PA, 17033, USA
| | - Zhongsi Huang
- State Environmental Protection Key Laboratory of Risk Assessment and Control on Chemical Processes, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Chao Chen
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Guangli Xiu
- State Environmental Protection Key Laboratory of Risk Assessment and Control on Chemical Processes, East China University of Science and Technology (ECUST), Shanghai, 200237, China.
- Shanghai Environmental Protection Key Laboratory for Environmental Standard and Risk Management of Chemical Pollutants, East China University of Science and Technology (ECUST), Shanghai, 200237, China.
| | - Jiahui Chen
- State Environmental Protection Key Laboratory of Risk Assessment and Control on Chemical Processes, East China University of Science and Technology (ECUST), Shanghai, 200237, China
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20
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Wu G, Cao L, Zhu J, Tan Z, Tang M, Li Z, Hu Y, Yu R, Zhang S, Song L, Li J. Loss of RBMS3 Confers Platinum Resistance in Epithelial Ovarian Cancer via Activation of miR-126-5p/β-catenin/CBP signaling. Clin Cancer Res 2018; 25:1022-1035. [PMID: 30279231 DOI: 10.1158/1078-0432.ccr-18-2554] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE The development of resistance to platinum-based chemotherapy remains the unsurmountable obstacle in cancer treatment and consequently leads to tumor relapse. This study aims to investigate the mechanism by which loss of RBMS3 induced chemoresistance in epithelial ovarian cancer (EOC). EXPERIMENTAL DESIGN FISH and IHC were used to determine deletion frequency and expression of RBMS3 in 15 clinical EOC tissues and 150 clinicopathologically characterized EOC specimens. The effects of RBMS3 deletion and CBP/β-catenin antagonist PRI-724 in chemoresistance were examined by clone formation and Annexin V assays in vitro, and by intraperitoneal tumor model in vivo. The mechanism by which RBMS3 loss sustained activation of miR-126-5p/β-catenin/CBP signaling and the effects of RBMS3 and miR-126-5p competitively regulating DKK3, AXIN1, BACH1, and NFAT5 was explored using CLIP-seq, RIP, electrophoretic mobility shift, and immunoblotting and immunofluorescence assays. RESULTS Loss of RBMS3 in EOC was correlated with the overall and relapse-free survival. Genetic ablation of RBMS3 significantly enhanced, whereas restoration of RBMS3 reduced, the chemoresistance ability of EOC cells both in vitro and in vivo. RBMS3 inhibited β-catenin/CBP signaling through directly associating with and stabilizing multiple negative regulators, including DKK3, AXIN1, BACH1, and NFAT5, via competitively preventing the miR-126-5p-mediated repression of these transcripts. Importantly, cotherapy of CBP/β-catenin antagonist PRI-724 induced sensitization of RBMS3-deleted EOC to platinum therapy. CONCLUSIONS Our results demonstrate that genetic ablation of RBMS3 contributes to chemoresistance and PRI-724 may serve as a potential tailored treatment for patients with RBMS3-deleted EOC.
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Affiliation(s)
- Geyan Wu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lixue Cao
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinrong Zhu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhanyao Tan
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Miaoling Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ziwen Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yameng Hu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruyuan Yu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuxia Zhang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Libing Song
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jun Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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21
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Wu Y, Yun D, Zhao Y, Wang Y, Sun R, Yan Q, Zhang S, Lu M, Zhang Z, Lu D, Li Y. Down regulation of RNA binding motif, single-stranded interacting protein 3, along with up regulation of nuclear HIF1A correlates with poor prognosis in patients with gastric cancer. Oncotarget 2018; 8:1262-1277. [PMID: 27902480 PMCID: PMC5352053 DOI: 10.18632/oncotarget.13605] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/11/2016] [Indexed: 11/25/2022] Open
Abstract
Frequent loss of multiple regions in short arm of chromosome 3 is found in various tumors including gastric cancer (GC). RNA binding motif, single-stranded interacting protein 3 (RBMS3) is a tumor suppressor gene located in this region and mediates cancer angiogenesis. However, the role of RBMS3 in GC remains unclear. To evaluate whether RBMS3, together with HIF1A, another key regulator of angiogenesis, predicts GC prognosis, the levels of RBMS3 and HIF1A were first examined by quantitative PCR (qPCR) and western blot from 27 fresh frozen GC and paired normal gastric tissues and then tested by immunohistochemistry (IHC) from 191 GC and 46 normal controls. Moreover, uni- and multivariate analysis were employed to assess the correlations between their levels and microvessel density (MVD) and clinical prognosis. To further identify RBMS3 function in vitro, cell proliferation assay, clonogenic assay, flow cytometry analysis and endothelial cell tube formation assay were employed. We found that RBMS3 level was decreased, whereas HIF1A was elevated in GC. Furthermore, we demonstrated that RBMS3 was an independent prognostic factor and the levels of RBMS3 and HIF1A were associated with GC angiogenesis and histopathological differentiation: patients with lower RBMS3 level and higher nuclear HIF1A expression had poorer prognosis. Besides, gain- and loss-of-function study revealed RBMS3 regulation on G1/S progression, cell proliferation and the tube formation of human umbilical vein endothelial cells (HUVECs) in vitro. These findings implicated that RBMS3 and nuclear HIF1A could act as prognostic biomarkers and therapeutic targets for GC.
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Affiliation(s)
- Youliang Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Dapeng Yun
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yingjie Zhao
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yuqi Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ruochuan Sun
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Qiang Yan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Shangxin Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Mingdian Lu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Zhen Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yongxiang Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
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22
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Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data. G3-GENES GENOMES GENETICS 2018; 8:469-476. [PMID: 29187421 PMCID: PMC5919749 DOI: 10.1534/g3.117.300382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation. We employed cross-population extended haplotype homozygosity, eigenvector decomposition combined with genome-wide association studies (EigenGWAS), and efficient mixed-model association expedited methods to detect areas of the genome that are potential selected regions (PSR) in both chicken breeds, and performed gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses annotating using the Kyoto Encyclopedia of Genes and Genomes. The results of this study revealed a total of 2424 outlier loci (p-value <0.01), of which 2144 occur in the White Leghorn breed and 280 occur in the Dongxiang Blue-shelled chicken. These correspond to 327 and 94 PSRs containing 297 and 54 genes, respectively. The most significantly selected genes in Blue-shelled chicken are TMEM141 and CLIC3, while the SLCO1B3 gene, related to eggshell color, was identified via EigenGWAS. We show that the White Leghorn genes JARID2, RBMS3, GPC3, TRIB2, ROBO1, SAMSN1, OSBP2, and IGFALS are involved in immunity, reproduction, and growth, and thus might represent footprints of the selection process. In contrast, we identified six significantly enriched pathways in the Dongxiang Blue-shelled chicken that are related to amino acid and lipid metabolism as well as signal transduction. Our results also reveal the presence of a GO term associated with cell metabolism that occurs mainly in the White Leghorn breed, while the most significant QTL regions mapped to the Chicken QTL Database (GG_4.0) for the Dongxiang Blue-shelled breed are predominantly related to lesions, bone mineral content, and other related traits compared to tibia length and body weight (i.e., at 14, 28, 42, and 70 d) in the White Leghorn. The results of this study highlight differences in growth, immunity, and egg quality traits between the two breeds, and provide a foundation for the exploration of their genetic mechanisms.
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23
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Bakkar N, Kovalik T, Lorenzini I, Spangler S, Lacoste A, Sponaugle K, Ferrante P, Argentinis E, Sattler R, Bowser R. Artificial intelligence in neurodegenerative disease research: use of IBM Watson to identify additional RNA-binding proteins altered in amyotrophic lateral sclerosis. Acta Neuropathol 2018; 135:227-247. [PMID: 29134320 PMCID: PMC5773659 DOI: 10.1007/s00401-017-1785-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease with no effective treatments. Numerous RNA-binding proteins (RBPs) have been shown to be altered in ALS, with mutations in 11 RBPs causing familial forms of the disease, and 6 more RBPs showing abnormal expression/distribution in ALS albeit without any known mutations. RBP dysregulation is widely accepted as a contributing factor in ALS pathobiology. There are at least 1542 RBPs in the human genome; therefore, other unidentified RBPs may also be linked to the pathogenesis of ALS. We used IBM Watson® to sieve through all RBPs in the genome and identify new RBPs linked to ALS (ALS-RBPs). IBM Watson extracted features from published literature to create semantic similarities and identify new connections between entities of interest. IBM Watson analyzed all published abstracts of previously known ALS-RBPs, and applied that text-based knowledge to all RBPs in the genome, ranking them by semantic similarity to the known set. We then validated the Watson top-ten-ranked RBPs at the protein and RNA levels in tissues from ALS and non-neurological disease controls, as well as in patient-derived induced pluripotent stem cells. 5 RBPs previously unlinked to ALS, hnRNPU, Syncrip, RBMS3, Caprin-1 and NUPL2, showed significant alterations in ALS compared to controls. Overall, we successfully used IBM Watson to help identify additional RBPs altered in ALS, highlighting the use of artificial intelligence tools to accelerate scientific discovery in ALS and possibly other complex neurological disorders.
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Affiliation(s)
- Nadine Bakkar
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Tina Kovalik
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Ileana Lorenzini
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | | | - Kyle Sponaugle
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Philip Ferrante
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | - Rita Sattler
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.
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24
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Romney AL, Podrabsky JE. Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus. EvoDevo 2017; 8:6. [PMID: 28439397 PMCID: PMC5401559 DOI: 10.1186/s13227-017-0069-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal factors and embryonic incubation conditions. Thus, maternally packaged gene products are hypothesized to regulate developmental trajectory and perhaps the other unique developmental characters in this species. Results Using high-throughput RNA sequencing, we generated transcriptomic profiles of mRNAs, long non-coding RNAs and small non-coding RNAs (sncRNAs) in 1–2 cell stage embryos of A. limnaeus. Transcriptomic analyses suggest maternal programming of embryos through alternatively spliced mRNAs and antisense sncRNAs. Comparison of these results to those of comparable studies on zebrafish and other fishes reveals a surprisingly high abundance of transcripts involved in the cellular response to stress and a relatively lower expression of genes required for rapid transition through the cell cycle. Conclusions Maternal programming of developmental trajectory is unlikely accomplished by differential expression of diapause-specific genes. Rather, evidence suggests a role for trajectory-specific splice variants of genes expressed in both phenotypes. In addition, based on comparative studies with zebrafish, the A. limnaeus 1–2 cell stage transcriptome is unique in ways that are consistent with their unique life history. These results not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression during development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0069-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amie L Romney
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
| | - Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
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25
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Abstract
RBMS3, a gene encoding a glycine-rich RNA-binding protein, belongs to the family of c-Myc gene single-strand binding proteins (MSSP). Recently, several reports have provided evidence that RBMS3 was deregulated in a diverse range of solid tumors and played a critical role in tumor progression. However, it remains unclear whether RBMS3 inhibits the progression of human breast cancer. Thus, the aim of this study was to investigate the role of RBMS3 in breast cancer and explore the underlying mechanism in breast cancer progression. Our results showed, for the first time, that the expression of RBMS3 at both the mRNA and protein levels was significantly downregulated in human breast cancer tissues and cell lines. In addition, RBMS3 overexpression dramatically suppressed the proliferation, migration, and invasion of breast cancer cells in vitro and attenuated tumor growth in vivo. Furthermore, we observed that RBMS3 greatly inhibited the protein expression of β-catenin, cyclin D1, and c-Myc in breast cancer cells. In summary, we have shown that RBMS3 inhibited the proliferation and tumorigenesis of breast cancer cells, at least in part, through inactivation of the Wnt/β-catenin signaling pathway. Thus, RBMS3 may be a potential treatment target for breast cancer.
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Affiliation(s)
- Yuan Yang
- The Second Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Lingli Quan
- The First Department of Respiratory Medicine, Zhuzhou Central Hospital, Zhuzhou, P.R. China
| | - Ye Ling
- The Second Xiangya Hospital of Central South University, Changsha, P.R. China
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26
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Ma X, Deng J, Cao N, Guo Z, Zheng Y, Geng S, Meng M, Lin H, Duan Y, Du G. Lasting glycolytic stress governs susceptibility to urethane-induced lung carcinogenesis in vivo and in vitro. Toxicol Lett 2015; 240:130-9. [PMID: 26524634 DOI: 10.1016/j.toxlet.2015.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/02/2015] [Accepted: 10/25/2015] [Indexed: 12/15/2022]
Abstract
Urethane is a recognized genotoxic carcinogen in fermented foods and beverages. This study is to compare susceptibility of ICR mice, BALB/c mice and C57BL/6 mice to urethane-induced lung carcinogenesis. The mice were injected intraperitoneally with 600 mg/kg of urethane for three times or ten times at 7-day intervals. At week 26, lung carcinogenic incidence was found in 40% ICR mice, 20% BALB/c mice and 10% C57BL/6 mice of the 3× injection group, respectively, whereas 100% lung tumor incidence took place in three mouse strains of the 10× injection group. In the 10× injection group, urethane induced lasting glycolytic stress of lung with an increase in lactate, monocarboxylate transporter 1 (MCT-1), reactive oxygen species(ROS) and 7,8-dihydro-8-oxo-29-deoxyguanosine (8-OHdG) and a decrease in pyruvate dehydrogenase (PDH) and cytochrome C oxidase (COX). In the 3× injection group, urethane also promoted lung glycolytic stress at the end of urethane injection but it lasted no more than 7 days besides in lung tumor-bearing mice. Metformin as a glycolytic enhancer promoted urethane carcinogenic efficacy in the 3× injection group, whereas 2-deoxy-glucose (2-DG) as a glycolytic inhibitor decreased urethane carcinogenic efficacy in the 10× injection group. Further, urethane promoted tumor survival in A549 cells by inducing cancer stem-like cellular state. These data suggest that lasting glycolytic stress is sufficient for urethane-induced lung tumorigenesis, and that urethane 10× injection-induced lung cancer can serve as a valuable model for lung tumor biology and tumor prevention.
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Affiliation(s)
- Xiaofang Ma
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Jiaxiu Deng
- Department of Oncology, The First Hospital Affiliated to Henan University, Kaifeng, Henan Province 475001, China
| | - Ning Cao
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Zhenzhen Guo
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Yaqiu Zheng
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Shengnan Geng
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Mingjing Meng
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Haihong Lin
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China
| | - Yongjian Duan
- Department of Oncology, The First Hospital Affiliated to Henan University, Kaifeng, Henan Province 475001, China.
| | - Gangjun Du
- Institute of Pharmacy, Pharmacy College of Henan University, Jinming District, Kaifeng, Henan Province 475004, China.
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