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Xudong X, Heng L, Benchao C, Wenjie C, Bao L, Gaofeng L. Integrated RNA expression and alternative polyadenylation analysis identified CPSF1- CCDC137 oncogenic axis in lung adenocarcinoma. Environ Toxicol 2024; 39:2405-2416. [PMID: 38174951 DOI: 10.1002/tox.24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024]
Abstract
This study aims to analyze the RNA expression and alternative polyadenylation (APA) events and identify APA tuned genes with prognostic significance in lung adenocarcinoma (LUAD). Genome-wide RNA expression profile and APA events were acquired in LUAD cancer and normal samples in GSE197346. Comparative analysis screened common deregulated genes and transcripts. All 11 and 19 transcripts were up and down expressed and polyadenylated in cancer samples, respectively. Clinical analysis found eight genes with prognostic significance, such as coiled-coil domain containing 137 (CCDC137). Role of CCDC137 in LUAD was first reported in this study. The cellular and animal experiments indicated that downregulated CCDC137 suppressed the malignant tumor phenotype and tumor growth in LUAD. Then, to identify APA regulators for elevated CCDC137, we analyzed the expression of 26 APA regulators in GSE197346 and The Cancer Genome Atlas (TCGA), and found 4 differential regulators: CPSF1, CELF2, NUDT21, and ELAVL1. At last, the correlation of eight genes with four differential APA regulators was analyzed, and CPSF1 showed a strong positive correlation with CCDC137. Based on the above results, we propose an oncogenic axis of CPSF1-CCDC137 in LUAD. This study first constructed a polyadenylation tuned RNA expression map in LUAD, and the proposed oncogenic axis of CPSF1-CCDC137 would shed light on the pathogenesis of LUAD.
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Affiliation(s)
- Xiang Xudong
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Heng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Benchao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Wenjie
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lei Bao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Gaofeng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
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Dai W, Wu J, Peng X, Hou W, Huang H, Cheng Q, Liu Z, Luyten W, Schoofs L, Zhou J, Liu S. CDK12 orchestrates super-enhancer-associated CCDC137 transcription to direct hepatic metastasis in colorectal cancer. Clin Transl Med 2022; 12:e1087. [PMID: 36254394 PMCID: PMC9577262 DOI: 10.1002/ctm2.1087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatic metastasis is the primary and direct cause of death in individuals with colorectal cancer (CRC) attribute to lack of effective therapeutic targets. The present study aimed to identify potential druggable candidate targets for patients with liver metastatic CRC. METHODS The transcriptional profiles of super-enhancers (SEs) in primary and liver metastatic CRC were evaluated in publicly accessible CRC datasets. Immunohistochemistry of human CRC tissues was conducted to determine the expression level of CDK12. Cellular proliferation, survival and stemness were examined upon CDK12 inhibition by shCDK12 or a selective CDK12 inhibitor named SR-4835 with multiple in vitro and in vivo assays. RNA sequencing and bioinformatics analyses were carried out to investigate the mechanisms of CDK12 inhibition in CRC cells. RESULTS We identified CDK12 as a driver gene for direct hepatic metastasis in CRC. Suppression of CDK12 led to robust inhibition of proliferation, survival and stemness. Mechanistically, CDK12 intervention preferentially repressed the transcription of SE-associated genes. Integration of the SE landscape and RNA sequencing, BCL2L1 and CCDC137 were identified as SE-associated oncogenic genes to strengthen the abilities of cellular survival, proliferation and stemness, eventually increasing liver metastasis of CRC. CONCLUSIONS Our data highlight the potential of CDK12 and SE-associated oncogenic transcripts as therapeutic targets for patients with liver metastatic CRC.
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Affiliation(s)
- Wei Dai
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Junhong Wu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Xiaopeng Peng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Wen Hou
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Hao Huang
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Qilai Cheng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Zhiping Liu
- Center for ImmunologyGannan Medical UniversityGanzhouJiangxiChina
| | | | | | - Jingfeng Zhou
- Department of Hematology and OncologyInternational Cancer CenterShenzhen Key LaboratoryShenzhen University General HospitalShenzhen University Clinical Medical AcademyShenzhen University Health Science CenterShenzhenChina
| | - Shenglan Liu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
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Guo L, Li B, Lu Z, Liang H, Yang H, Chen Y, Zhu S, Zeng M, Wei Y, Liu T, Jiang T, Xuan M, Tang H. CCDC137 Is a Prognostic Biomarker and Correlates With Immunosuppressive Tumor Microenvironment Based on Pan-Cancer Analysis. Front Mol Biosci 2021; 8:674863. [PMID: 34055889 PMCID: PMC8155610 DOI: 10.3389/fmolb.2021.674863] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Background The coiled-coil domain containing (CCDC) family proteins have important biological functions in various diseases. However, the coiled-coil domain containing 137 (CCDC137) was rarely studied. We aim to investigate the role of CCDC137 in pan-cancer. Methods CCDC137 expression was evaluated in RNA sequence expression profilers of pan-cancer and normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. The influence of CCDC137 on the prognosis of tumor patients was analyzed using clinical survival data from TCGA. Function and pathway enrichment analysis was performed to explore the role of CCDC137 using the R package “clusterProfiler.” We further analyzed the correlation of immune cell infiltration score of TCGA samples and CCDC137 expression using TIMER2 online database. Results CCDC137 was over-expressed and associated with worse survival status in various tumor types. CCDC137 expression was positively correlated with tumor associated macrophages (TAMs) and cancer associated fibroblasts (CAFs) in Lower Grade Glioma (LGG) and Uveal Melanoma (UVM). In addition, high CCDC137 expression was positively correlated with most immunosuppressive genes, including TGFB1, PD-L1, and IL10RB in LGG and UVM. Conclusions Our study identified CCDC137 as an oncogene and predictor of worse survival in most tumor types. High CCDC137 may contribute to elevated infiltration of TAMs and CAFs and be associated with tumor immunosuppressive status.
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Affiliation(s)
- Lihao Guo
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Boxin Li
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Zhaohong Lu
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Hairong Liang
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Hui Yang
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yuting Chen
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Shiheng Zhu
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Minjuan Zeng
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yixian Wei
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Tonggong Liu
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Tikeng Jiang
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Mei Xuan
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Huanwen Tang
- Dongguan Key Laboratory of Environmental Medicine, Department of Environmental and Occupational Health, School of Public Health, Guangdong Medical University, Dongguan, China
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Zhang F, Bieniasz PD. HIV-1 Vpr induces cell cycle arrest and enhances viral gene expression by depleting CCDC137. eLife 2020; 9:55806. [PMID: 32538781 PMCID: PMC7295576 DOI: 10.7554/elife.55806] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
The HIV-1 Vpr accessory protein induces ubiquitin/proteasome-dependent degradation of many cellular proteins by recruiting them to a cullin4A-DDB1-DCAF1 complex. In so doing, Vpr enhances HIV-1 gene expression and induces (G2/M) cell cycle arrest. However, the identities of Vpr target proteins through which these biological effects are exerted are unknown. We show that a chromosome periphery protein, CCDC137/cPERP-B, is targeted for depletion by HIV-1 Vpr, in a cullin4A-DDB1-DCAF1 dependent manner. CCDC137 depletion caused G2/M cellcycle arrest, while Vpr-resistant CCDC137 mutants conferred resistance to Vpr-induced G2/M arrest. CCDC137 depletion also recapitulated the ability of Vpr to enhance HIV-1 gene expression, particularly in macrophages. Our findings indicate that Vpr promotes cell-cycle arrest and HIV-1 gene expression through depletion of CCDC137.
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Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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