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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. ENVIRONMENTAL TOXICOLOGY 2024; 39:2405-2416. [PMID: 38174951 DOI: 10.1002/tox.24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Shao T, Li J, Su M, Yang C, Ma Y, Lv C, Wang W, Xie Y, Xu G, Shi C, Zhou X, Fan H, Li Y, Xu J. A machine learning model identifies M3-like subtype in AML based on PML/RARα targets. iScience 2024; 27:108947. [PMID: 38322990 PMCID: PMC10844831 DOI: 10.1016/j.isci.2024.108947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/25/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Abstract
The typical genomic feature of acute myeloid leukemia (AML) M3 subtype is the fusion event of PML/RARα, and ATRA/ATO-based combination therapy is current standard treatment regimen for M3 subtype. Here, a machine-learning model based on expressions of PML/RARα targets was developed to identify M3 patients by analyzing 1228 AML patients. Our model exhibited high accuracy. To enable more non-M3 AML patients to potentially benefit from ATRA/ATO therapy, M3-like patients were further identified. We found that M3-like patients had strong GMP features, including the expression patterns of M3 subtype marker genes, the proportion of myeloid progenitor cells, and deconvolution of AML constituent cell populations. M3-like patients exhibited distinct genomic features, low immune activity and better clinical survival. The initiative identification of patients similar to M3 subtype may help to identify more patients that would benefit from ATO/ATRA treatment and deepen our understanding of the molecular mechanism of AML pathogenesis.
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Affiliation(s)
- Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jianing Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Minghai Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Changbo Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yingying Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Chongwen Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Wei Wang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yunjin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Gang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Ce Shi
- Key Laboratory of Hepatosplenic Surgery of Ministry of Education, NHC Key Laboratory of Cell Transplantation, the First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Xinying Zhou
- Key Laboratory of Hepatosplenic Surgery of Ministry of Education, NHC Key Laboratory of Cell Transplantation, the First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Huitao Fan
- Key Laboratory of Hepatosplenic Surgery of Ministry of Education, NHC Key Laboratory of Cell Transplantation, the First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150001, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province 150001, China
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Wang Y, Wang Y, Zhou J, Ying P, Wang Z, Wu Y, Hao M, Qiu S, Jin H, Wang X. A novel coiled-coil domain containing-related gene signature for predicting prognosis and treatment effect of breast cancer. J Cancer Res Clin Oncol 2023; 149:14205-14225. [PMID: 37558766 DOI: 10.1007/s00432-023-05222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
PURPOSE Breast cancer (BRCA) is a prevalent tumor worldwide. The association between the coiled-coil domain-containing (CCDC) protein family and different tumors has been established. However, the prognostic significance of this protein family in breast cancer remains uncertain. METHODS Gene expression and clinical data were obtained from the TCGA, METABRIC, and GEO databases. Prognosis genes were identified using univariate Cox and LASSO Cox regression, leading to the establishment of a prognostic signature. Subsequently, the risk model was conducted based on survival and clinical feature analyses, and a nomogram for prognosis prediction was developed. Furthermore, analyses of biological function, immune characteristics, and drug sensitivity were performed. Finally, single-cell sequencing data were utilized to uncover the expression patterns of genes in the risk model. RESULTS Five genes were identified and utilized for risk modeling. The model demonstrated excellent prognostic value as indicated by ROC and Kaplan-Meier analysis. The high-risk group exhibited shorter survival time and higher likelihood of recurrence. Functional annotation indicated a correlation between the risk score and immune pathways. Conversely, the low-risk group displayed a greater enrichment in immune pathways and exhibited more active immune microenvironment characteristics. Additionally, drug sensitivity analysis using both public and our sequencing data revealed that the risk model possessed a broad range of predictive values. CONCLUSIONS We have developed a gene signature and have verified that patients with low-risk are more likely to have better prognosis and respond positively to therapy. This finding offers a valuable point of reference for BRCA individualized treatment.
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Affiliation(s)
- Yufei Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanmei Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Pingting Ying
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhuo Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Wu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Minyan Hao
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuying Qiu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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