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Sheng Y, Lei K, Sun C, Liu J, Tu Z, Zhu X, Huang K. Aberrant RBMX expression is relevant for cancer prognosis and immunotherapy response. Aging (Albany NY) 2024; 16:226-245. [PMID: 38214653 PMCID: PMC10817375 DOI: 10.18632/aging.205363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/03/2023] [Indexed: 01/13/2024]
Abstract
Cancer accounts for the highest rates of morbidity and mortality worldwide. RNA binding motif protein X-linked (RBMX) is a nuclear RNA-binding protein, associated with certain types of cancer by participating in the integration of sister chromatids and a combination of ribonucleoprotein complexes. However, the specific role of RBMX in cancer immunity remains unknown. This study presents the aberrant expression levels, single-cell distributions, effective prognostic roles, immune cell infiltration associations, and immunotherapy responses of RBMX as a biomarker in various types of cancer. Moreover, it validates the aberrant expression of RBMX in clinical cancer samples. Furthermore, we also evaluated the relationships between RBMX expression and myeloid-derived suppressor cells in clinical samples by immunofluorescent staining. The results showed that knockdown of RBMX can impair the proliferation, migration, and invasion of liver cancer cells. Finally, we indicated that RBMX may play an immunoregulatory role in cancer progression, affecting the therapeutic effects of immune checkpoint inhibitors in patients with cancer.
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Affiliation(s)
- Yilei Sheng
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- The HuanKui Medical College of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Kunjian Lei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Chengpeng Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- The HuanKui Medical College of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Jia Liu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06511, USA
| | - Zewei Tu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
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2
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Liu J, Zheng T, Chen D, Huang J, Zhao Y, Ma W, Liu H. RBMX involves in telomere stability maintenance by regulating TERRA expression. PLoS Genet 2023; 19:e1010937. [PMID: 37756323 PMCID: PMC10529574 DOI: 10.1371/journal.pgen.1010937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Telomeric repeat-containing RNA (TERRA) is a class of long noncoding RNAs (lncRNAs) that are transcribed from subtelomeric to telomeric region of chromosome ends. TERRA is prone to form R-loop structures at telomeres by invading into telomeric DNA. Excessive telomere R-loops result in telomere instability, so the TERRA level needs to be delicately modulated. However, the molecular mechanisms and factors controlling TERRA level are still largely unknown. In this study, we report that the RNA binding protein RBMX is a novel regulator of TERRA level and telomere integrity. The expression level of TERRA is significantly elevated in RBMX depleted cells, leading to enhanced telomere R-loop formation, replication stress, and telomere instability. We also found that RBMX binds to TERRA and the nuclear exosome targeting protein ZCCHC8 simultaneously, and that TERRA degradation slows down upon RBMX depletion, implying that RBMX promotes TERRA degradation by regulating its transportation to the nuclear exosome, which decays nuclear RNAs. Altogether, these findings uncover a new role of RBMX in TERRA expression regulation and telomere integrity maintenance, and raising RBMX as a potential target of cancer therapy.
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Affiliation(s)
- Jingfan Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Tian Zheng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Dandan Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
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Dragic D, Chang SL, Ennour-Idrissi K, Durocher F, Severi G, Diorio C. Association between alcohol consumption and DNA methylation in blood: a systematic review of observational studies. Epigenomics 2022; 14:793-810. [PMID: 35762294 DOI: 10.2217/epi-2022-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We systematically reviewed and evaluated current literature on alcohol consumption and DNA methylation (DNAm) at the genome-wide and probe-wise level in blood of adults. Materials & methods: Five databases (PubMed, Embase, Web of Science, CINAHL and PsycInfo) were searched until 20 December 2020. Studies assessing the effect of alcohol dependence on DNAm were not eligible. Results: 11 cross-sectional studies were included with 88 to 9643 participants. Overall, all studies had a risk of bias criteria unclear or unmet. Epigenome-wide association studies identified between 0 and 5458 differentially methylated positions, and 15 were observed in at least four studies. Conclusion: Potential methylation markers for alcohol consumption have been identified, but further validation in large cohorts is needed.
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Affiliation(s)
- Dzevka Dragic
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France
| | - Sue-Ling Chang
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada
| | - Kaoutar Ennour-Idrissi
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry & Pathology, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Francine Durocher
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France.,Department of Statistics, Computer Science & Applications "G. Parenti" (DISIA), University of Florence, Florence, 50134, Italy
| | - Caroline Diorio
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Deschênes-Fabia Center for Breast Diseases, Saint-Sacrement Hospital, Quebec, QC, G1S 4L8, Canada
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4
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Hao C, Zheng Y, Jönsson J, Cui X, Yu H, Wu C, Kajitani N, Schwartz S. hnRNP G/RBMX enhances HPV16 E2 mRNA splicing through a novel splicing enhancer and inhibits production of spliced E7 oncogene mRNAs. Nucleic Acids Res 2022; 50:3867-3891. [PMID: 35357488 PMCID: PMC9023273 DOI: 10.1093/nar/gkac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) E2 is an essential HPV16 protein. We have investigated how HPV16 E2 expression is regulated and have identifed a splicing enhancer that is required for production of HPV16 E2 mRNAs. This uridine-less splicing enhancer sequence (ACGAGGACGAGGACAAGGA) contains 84% adenosine and guanosine and 16% cytosine and consists of three ‘AC(A/G)AGG’-repeats. Mutational inactivation of the splicing enhancer reduced splicing to E2-mRNA specific splice site SA2709 and resulted in increased levels of unspliced E1-encoding mRNAs. The splicing enhancer sequence interacted with cellular RNA binding protein hnRNP G that promoted splicing to SA2709 and enhanced E2 mRNA production. The splicing-enhancing function of hnRNP G mapped to amino acids 236–286 of hnRNP G that were also shown to interact with splicing factor U2AF65. The interactions between hnRNP G and HPV16 E2 mRNAs and U2AF65 increased in response to keratinocyte differentiation as well as by the induction of the DNA damage response (DDR). The DDR reduced sumoylation of hnRNP G and pharmacological inhibition of sumoylation enhanced HPV16 E2 mRNA splicing and interactions between hnRNP G and E2 mRNAs and U2AF65. Intriguingly, hnRNP G also promoted intron retention of the HPV16 E6 coding region thereby inhibiting production of spliced E7 oncogene mRNAs.
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Affiliation(s)
- Chengyu Hao
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Yunji Zheng
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,School of Pharmacy, Binzhou Medical University, 264003 Yantai, China
| | - Johanna Jönsson
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Xiaoxu Cui
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Haoran Yu
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Liaoning IC Technology Key Lab, 116024 Dalian, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Stefan Schwartz
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
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5
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RBMX Protein Expression in T-Cell Lymphomas Predicts Chemotherapy Response and Prognosis. Cancers (Basel) 2021; 13:cancers13194788. [PMID: 34638274 PMCID: PMC8507920 DOI: 10.3390/cancers13194788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Patients with T-cell non-Hodgkin’s lymphomas (T-NHL) are often chemotherapy refractory and subsequently have poor prognosis. So far, mechanisms leading to this primary chemotherapy refractoriness and factors identifying such cases are not well established. This study investigated the prognostic relevance of the RNA binding protein X (RBMX) in 53 T-NHL cases using conventional immunohistochemistry. As shown, low RBMX expression was associated with better response to anthracycline-containing first-line treatment. Furthermore, low RBMX expression predicted an improved overall survival (OS) and progression-free survival (PFS). These results suggest that RBMX protein expression levels might be a contributing factor towards chemotherapy resistance and thus affect prognosis of patients with T-cell lymphomas. Abstract T-cell non-Hodgkin’s lymphomas (T-NHL) are a heterogeneous group of lymphomas with a mature T-cell phenotype. While in some hematological diseases the prognosis improved over the last decades, T-NHL cases often relapse early or present with an initially refractory course. Recently, it has been shown that RNA binding proteins have a crucial role for malignant tumor initiation, progression and treatment response while contributing to chemotherapy resistance. Therefore, we investigated the protein expression of the RNA binding protein X (RBMX), which has been shown to be of great relevance in disease initiation and progression in hematological diseases in 53 T-NHL cases using conventional immunohistochemistry. Low RBMX expression was associated with better response to anthracycline-containing first-line treatment. Furthermore, low RBMX expression predicted an improved overall survival and progression-free survival in univariate analysis. Multivariable Cox regression revealed RBMX as an independent prognostic marker for overall survival (p = 0.007; hazard ratio (HR) = 0.204; 95% confidence interval (CI): 0.064–0.646) and progression-free survival (p = 0.006; HR = 0.235; 95% CI: 0.083–0.666). The study identifies low RBMX expression to predict better chemotherapy response, overall survival and progression-free survival in patients with T-cell non-Hodgkin’s lymphomas. These results suggest that RBMX protein expression levels might be a contributing factor towards chemotherapy resistance and thus affect prognosis. Hence, RBMX may be a potential therapeutic target and prognostic marker in T-cell lymphomas.
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6
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Prieto C, Nguyen DTT, Liu Z, Wheat J, Perez A, Gourkanti S, Chou T, Barin E, Velleca A, Rohwetter T, Chow A, Taggart J, Savino AM, Hoskova K, Dhodapkar M, Schurer A, Barlowe TS, Vu LP, Leslie C, Steidl U, Rabadan R, Kharas MG. Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia. NATURE CANCER 2021; 2:741-757. [PMID: 34458856 PMCID: PMC8388313 DOI: 10.1038/s43018-021-00220-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/11/2021] [Indexed: 01/08/2023]
Abstract
RNA binding proteins (RBPs) are key arbiters of post-transcriptional regulation and are found to be found dysregulated in hematological malignancies. Here, we identify the RBP RBMX and its retrogene RBMXL1 to be required for murine and human myeloid leukemogenesis. RBMX/L1 are overexpressed in acute myeloid leukemia (AML) primary patients compared to healthy individuals, and RBMX/L1 loss delayed leukemia development. RBMX/L1 loss lead to significant changes in chromatin accessibility, as well as chromosomal breaks and gaps. We found that RBMX/L1 directly bind to mRNAs, affect transcription of multiple loci, including CBX5 (HP1α), and control the nascent transcription of the CBX5 locus. Forced CBX5 expression rescued the RBMX/L1 depletion effects on cell growth and apoptosis. Overall, we determine that RBMX/L1 control leukemia cell survival by regulating chromatin state through their downstream target CBX5. These findings identify a mechanism for RBPs directly promoting transcription and suggest RBMX/L1, as well as CBX5, as potential therapeutic targets in myeloid malignancies.
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Affiliation(s)
- Camila Prieto
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diu T T Nguyen
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Department of Systems Biology, Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Justin Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Alexendar Perez
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy Chou
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony Velleca
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas Rohwetter
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Chow
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James Taggart
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela M Savino
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katerina Hoskova
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Dhodapkar
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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7
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RBMX suppresses tumorigenicity and progression of bladder cancer by interacting with the hnRNP A1 protein to regulate PKM alternative splicing. Oncogene 2021; 40:2635-2650. [PMID: 33564070 PMCID: PMC8049873 DOI: 10.1038/s41388-021-01666-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/23/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
The prognosis for patients with metastatic bladder cancer (BCa) is poor, and it is not improved by current treatments. RNA-binding motif protein X-linked (RBMX) are involved in the regulation of the malignant progression of various tumors. However, the role of RBMX in BCa tumorigenicity and progression remains unclear. In this study, we found that RBMX was significantly downregulated in BCa tissues, especially in muscle-invasive BCa tissues. RBMX expression was negatively correlated with tumor stage, histological grade and poor patient prognosis. Functional assays demonstrated that RBMX inhibited BCa cell proliferation, colony formation, migration, and invasion in vitro and suppressed tumor growth and metastasis in vivo. Mechanistic investigations revealed that hnRNP A1 was an RBMX-binding protein. RBMX competitively inhibited the combination of the RGG motif in hnRNP A1 and the sequences flanking PKM exon 9, leading to the formation of lower PKM2 and higher PKM1 levels, which attenuated the tumorigenicity and progression of BCa. Moreover, RBMX inhibited aerobic glycolysis through hnRNP A1-dependent PKM alternative splicing and counteracted the PKM2 overexpression-induced aggressive phenotype of the BCa cells. In conclusion, our findings indicate that RBMX suppresses BCa tumorigenicity and progression via an hnRNP A1-mediated PKM alternative splicing mechanism. RBMX may serve as a novel prognostic biomarker for clinical intervention in BCa.
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8
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Gao L, Xie ZC, Pang JS, Li TT, Chen G. A novel alternative splicing-based prediction model for uteri corpus endometrial carcinoma. Aging (Albany NY) 2020; 11:263-283. [PMID: 30640723 PMCID: PMC6339785 DOI: 10.18632/aging.101753] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Alternative splicing (AS) is crucial a mechanism by which the complexity of mammalian and viral proteom increased overwhelmingly. There lacks systematic and comprehensive analysis of the prognostic significance of AS profiling landscape for uteri corpus endometrial carcinoma (UCEC). In this study, univariate and multivariate Cox regression analyses were conducted to identify candidate survival-associated AS events curated from SpliceSeq for the construction of prognostic index (PI) models. A correlation network between splicing factor-related AS events and significant survival-associated AS events were constructed using Cytoscape 3.5. As consequence, 28281 AS events from 8137 genes were detected from 506 UCEC patients, including 2630 survival-associated AS events. Kaplan Meier survival analysis revealed that six of the seven PI models (AD, AP, AT, ME, RI and ALL) exhibited good performance in stratifying the prognosis of low risk and high risk group (P<0.05). Among the six PI models, PI-AT performed best with an area under curves (AUC) value of 0.758 from time-dependent receiver operating characteristic. Correlation network implicated potential regulatory mechanism of AS events in UCEC. PI models based on survival-associated AS events for UCEC in this study showed preferable prognosis-predicting ability and may be promising prognostic indicators for UCEC patients. Summary: This is the first study to systematically investigate the prognostic value of AS in UCEC. Findings in the presents study supported the clinical potential of AS for UCEC and shed light on the potential AS-associated molecular basis of UCEC.
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Affiliation(s)
- Li Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Zu-Cheng Xie
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Jin-Shu Pang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Tian-Tian Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
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9
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Hernández JE, González-Montiel A, Allos-Villalva JCC, Cantú D, Barquet S, Olivares-Mundo A, Herrera LA, Prada D. Prognostic molecular biomarkers in endometrial cancer: A review. ACTA ACUST UNITED AC 2019; 7:17-28. [PMID: 34322276 PMCID: PMC8315102 DOI: 10.14312/2052-4994.2019-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background: Endometrial cancer (EC) is the fourth most common malignancy in women worldwide and the most common gynecological cancer in developed countries. The endometrioid subtype has an excellent prognosis with conventional treatment; however, recurrence reduces overall survival. Objective: Describe the most relevant evidence regarding selected potential molecular biomarkers that may predict overall survival (OS), relapse-free survival (RFS), and cancer-specific survival (CSS) in EC. Methods: An exhaustive search was performed in PUBMED with the search terms endometrial cancer, molecular biomarker, and survival. We selected original articles written in English about endometrial cancer, molecular biomarkers, and that included survival analysis published between January 2000 and December 2016. Results: Several molecular prognostic biomarkers have been studied in terms of survival and therapeutic response in women with endometrial cancer; hormone receptors, microRNAs, and other molecules have emerged as potentially useful biomarkers, including HER2, p21, HE4, PTEN, p27, ANCCA, and ANXA2. Conclusions: The use of biomarkers in the assessment of OS, RFS, and CSS requires large trials to expand our understanding of endometrial carcinogenesis. Several molecular markers are significantly associated with a high tumor grade and advanced clinical stage in EC and, therefore, could have additive effects when combined.
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Affiliation(s)
- J Edgardo Hernández
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Ailyn González-Montiel
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Jesús C Ceb Allos-Villalva
- Department of Biomedical Informatics, Faculty of Medicine, National Autonomous University of Mexico, C.U., Av. Universidad 3000, Mexico City, Mexico, 04510
| | - David Cantú
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Salim Barquet
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Anny Olivares-Mundo
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Luis A Herrera
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080
| | - Diddier Prada
- Unit of Biomedical Research, National Cancer Institute- Biomedical Research Institute, National Autonomous University of Mexico. San Fernando 22, Colonia Sección XVI, Delegatión Tlalpan, Mexico City, Mexico, 14080.,Department of Biomedical Informatics, Faculty of Medicine, National Autonomous University of Mexico, C.U., Av. Universidad 3000, Mexico City, Mexico, 04510
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10
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Prognostic Potential of Alternative Splicing Markers in Endometrial Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:1039-1048. [PMID: 31785579 PMCID: PMC6889075 DOI: 10.1016/j.omtn.2019.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/09/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
Alternative splicing (AS), an important post-transcriptional regulatory mechanism that regulates the translation of mRNA isoforms and generates protein diversity, has been widely demonstrated to be associated with oncogenic processes. In this study, we systematically analyzed genome-wide AS patterns to explore the prognostic implications of AS in endometrial cancer (EC). A total of 2,324 AS events were identified as being associated with the overall survival of EC patients, and eleven of these events were further selected using a random forest algorithm. With the implementation of a generalized, boosted regression model, a prognostic AS model that aggregated these eleven markers was ultimately established with high performance for risk stratification in EC patients. Functional analysis of these eleven AS markers revealed various potential signaling pathways implicated in the progression of EC. Splicing network analysis demonstrated the notable correlation between the expression of splicing factors and AS markers in EC and further determined eight candidate splicing factors that could be therapeutic targets for EC. Taken together, the results of this study present the utility of AS profiling in identifying biomarkers for the prognosis of EC and provide comprehensive insight into the molecular mechanisms involved in EC processes.
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11
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Elliott DJ, Dalgliesh C, Hysenaj G, Ehrmann I. RBMX family proteins connect the fields of nuclear RNA processing, disease and sex chromosome biology. Int J Biochem Cell Biol 2018; 108:1-6. [PMID: 30593955 DOI: 10.1016/j.biocel.2018.12.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
RBMX is a ubiquitously expressed nuclear RNA binding protein that is encoded by a gene on the X chromosome. RBMX belongs to a small protein family with additional members encoded by paralogs on the mammalian Y chromosome and other chromosomes. These RNA binding proteins are important for normal development, and also implicated in cancer and viral infection. At the molecular level RBMX family proteins contribute to splicing control, transcription and genome integrity. Establishing what endogenous genes and pathways are controlled by RBMX and its paralogs will have important implications for understanding chromosome biology, DNA repair and mammalian development. Here we review what is known about this family of RNA binding proteins, and identify important current questions about their functions.
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Affiliation(s)
- David J Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK.
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Gerald Hysenaj
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
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12
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Knocking down the expression of TRA2β inhibits the proliferation and migration of human glioma cells. Pathol Res Pract 2015; 211:731-9. [DOI: 10.1016/j.prp.2015.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/04/2015] [Accepted: 04/29/2015] [Indexed: 01/08/2023]
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13
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Hirschfeld M, Ouyang YQ, Jaeger M, Erbes T, Orlowska-Volk M, Zur Hausen A, Stickeler E. HNRNP G and HTRA2-BETA1 regulate estrogen receptor alpha expression with potential impact on endometrial cancer. BMC Cancer 2015; 15:86. [PMID: 25884434 PMCID: PMC4355463 DOI: 10.1186/s12885-015-1088-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/19/2015] [Indexed: 01/11/2023] Open
Abstract
Background Estrogen receptor alpha (ERa/ESR1) expression is regulated by alternative splicing. Its most frequently detectable exon7 skipping isoform (ERaD7) is a dominant negative variant. Elevated expression of ERaD7 was already detected in endometrial cancer (EC), while its potential prognostic significance has not been characterized so far. Exon7 contains potential binding sites for the two functional splicing regulatory opponents, HNRNPG and HTRA2-BETA1 known to trigger opposite effects on EC outcome. This study served to elucidate the influence of HNRNPG and HTRA2-BETA1 on ERa exon7 splicing regulation and the impact of ERaD7 concentration on type 1 EC outcome. Methods Functional in vitro experiments for HNRNPG and HTRA2-BETA1 in regard to the regulatory impact on endogenous and exogenous ERaD7 splicing were performed. Additionally, real-time PCR determined mRNA levels of ERaD7, HNRNPG and HTRA2-BETA1 in 116 type 1 EC patients. Results HNRNPG and HTRA2-BETA1 were found to be specific regulators of ERa exon7 splicing. While HTRA2-BETA1 promoted exon7 inclusion, HNRNPG antagonized this effect by inducing exon7 skipping (p = 0.004). ERaD7 was detected in 71 out of 116 type 1 EC specimens. Statistical analyses revealed an inverse correlation between ERaD7 mRNA levels and tumor grading (p = 0.029), FIGO stage (p = 0.033) as well as lymph node metastases (p = 0.032), respectively. Furthermore, higher ERaD7 expression could be correlated to an improved disease-specific survival (p = 0.034). Conclusions Our study demonstrates antagonistic regulatory effects of HNRNPG and HTRA2-BETA1 on ERa exon7 splicing with potential impact on type 1 EC clinical outcome due to the consecutively variable expression levels of the ERa isoform D7. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1088-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc Hirschfeld
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, Hugstetterstr 55, 79106, Freiburg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Yi Qin Ouyang
- Department of Obstetrics and Gynecology, Tongji Hospital of Tongji University, Shanghai, China.
| | - Markus Jaeger
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, Hugstetterstr 55, 79106, Freiburg, Germany.
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, Hugstetterstr 55, 79106, Freiburg, Germany.
| | | | - Axel Zur Hausen
- Institute of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Elmar Stickeler
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, Hugstetterstr 55, 79106, Freiburg, Germany.
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Zhu L, Hu Z, Liu J, Gao J, Lin B. Gene expression profile analysis identifies metastasis and chemoresistance-associated genes in epithelial ovarian carcinoma cells. Med Oncol 2014; 32:426. [PMID: 25502083 PMCID: PMC4262766 DOI: 10.1007/s12032-014-0426-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022]
Abstract
The purpose of this study was to identify genes that associated with higher ability of metastasis and chemotherapic resistance in epithelial ovarian carcinoma (EOC) cells. An oligonucleotide microarray with probe sets complementary to 41,000+ unique human genes and transcripts was used to determine whether gene expression profile may differentiate three epithelial ovarian cell lines (RMG-I-C, COC1 and HO8910) from their sub-lines (RMG-I-H, COCI/DDP and HO8910/PM) with higher ability of metastasis and chemotherapic resistance. Quantitative real-time PCR and immunohistochemical staining validated the microarray results. Hierarchic cluster analysis of gene expression identified 49 genes that exhibited ≥2.0-fold change and P value ≤0.05. Highly differential expression of GCET2, NLRP4, FOXP1 and SNX29 genes was validated by quantitative PCR in all cell line samples. Finally, FOXP1 was validated at the protein level by immunohistochemistry in paraffin embedded ovarian tissues (i.e., for metastasis, 15 primary EOC and 10 omental metastasis [OM]; for chemoresistance, 13 sensitive and 13 resistant EOC). The identification of higher ability of metastasis and chemotherapic resistance-associated genes may provide a foundation for the development of new type-specific diagnostic strategies and treatment for metastasis and chemotherapic resistance in epithelial ovarian cancer.
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Affiliation(s)
- Liancheng Zhu
- Department of Obstetrics and Gynecology, Shengjing Hospital Affiliated to China Medical University, Shenyang, 110004, Liaoning Province, China,
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15
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Mao G, Lv L, Liu Y, Chen B, Li M, Ni T, Yang D, Zhu H, Xue Q, Ni R. The expression levels and prognostic value of high temperature required A2 (HtrA2) in NSCLC. Pathol Res Pract 2014; 210:939-43. [DOI: 10.1016/j.prp.2014.06.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 04/06/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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16
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Transformer 2β (Tra2β/SFRS10) positively regulates the progression of NSCLC via promoting cell proliferation. J Mol Histol 2014; 45:573-82. [DOI: 10.1007/s10735-014-9582-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
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17
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Moursy A, Allain FHT, Cléry A. Characterization of the RNA recognition mode of hnRNP G extends its role in SMN2 splicing regulation. Nucleic Acids Res 2014; 42:6659-72. [PMID: 24692659 PMCID: PMC4041419 DOI: 10.1093/nar/gku244] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Regulation of SMN2 exon 7 splicing is crucial for the production of active SMN protein and the survival of Spinal Muscular Atrophy (SMA) patients. One of the most efficient activators of exon 7 inclusion is hnRNP G, which is recruited to the exon by Tra2-β1. We report that in addition to the C-terminal region of hnRNP G, the RNA Recognition Motif (RRM) and the middle part of the protein containing the Arg–Gly–Gly (RGG) box are important for this function. To better understand the mode of action of hnRNP G in this context we determined the structure of its RRM bound to an SMN2 derived RNA. The RRM interacts with a 5′-AAN-3′ motif and specifically recognizes the two consecutive adenines. By testing the effect of mutations in hnRNP G RRM and in its putative binding sites on the splicing of SMN2 exon 7, we show that it specifically binds to exon 7. This interaction is required for hnRNP G splicing activity and we propose its recruitment to a polyA tract located upstream of the Tra2-β1 binding site. Finally, our data suggest that hnRNP G plays a major role in the recruitment of the Tra2-β1/hnRNP G/SRSF9 trimeric complex to SMN2 exon 7.
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Affiliation(s)
- Ahmed Moursy
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH), 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH), 8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH), 8093 Zürich, Switzerland
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Dubrez L, Berthelet J, Glorian V. IAP proteins as targets for drug development in oncology. Onco Targets Ther 2013; 9:1285-304. [PMID: 24092992 PMCID: PMC3787928 DOI: 10.2147/ott.s33375] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The inhibitors of apoptosis (IAPs) constitute a family of proteins involved in the regulation of
various cellular processes, including cell death, immune and inflammatory responses, cell
proliferation, cell differentiation, and cell motility. There is accumulating evidence supporting
IAP-targeting in tumors: IAPs regulate various cellular processes that contribute to tumor
development, such as cell death, cell proliferation, and cell migration; their expression is
increased in a number of human tumor samples, and IAP overexpression has been correlated with tumor
growth, and poor prognosis or low response to treatment; and IAP expression can be rapidly induced
in response to chemotherapy or radiotherapy because of the presence of an internal ribosome entry
site (IRES)-dependent mechanism of translation initiation, which could contribute to resistance to
antitumor therapy. The development of IAP antagonists is an important challenge and was subject to
intense research over the past decade. Six molecules are currently in clinical trials. This review
focuses on the role of IAPs in tumors and the development of IAP-targeting molecules for anticancer
therapy.
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Affiliation(s)
- Laurence Dubrez
- Institut National de la Santé et de la Recherche Médicale (Inserm), Dijon, France ; Université de Bourgogne, Dijon, France
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Bidkhori G, Narimani Z, Hosseini Ashtiani S, Moeini A, Nowzari-Dalini A, Masoudi-Nejad A. Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. PLoS One 2013; 8:e67552. [PMID: 23874428 PMCID: PMC3708931 DOI: 10.1371/journal.pone.0067552] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 05/18/2013] [Indexed: 02/04/2023] Open
Abstract
Our goal of this study was to reconstruct a “genome-scale co-expression network” and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named “genome-scale co-expression network”. As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules.
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Affiliation(s)
- Gholamreza Bidkhori
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Zahra Narimani
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Saman Hosseini Ashtiani
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Moeini
- Department of Algorithms and Computation, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- * E-mail:
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