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Xiao Y, Gao L, Zhao X, Zhao W, Mai L, Ma C, Han Y, Li X. Novel prognostic alternative splicing events in colorectal Cancer: Impact on immune infiltration and therapy response. Int Immunopharmacol 2024; 139:112603. [PMID: 39043103 DOI: 10.1016/j.intimp.2024.112603] [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: 01/15/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024]
Abstract
OBJECTIVE This study aims to comprehensively analyze alternative splicing (AS) features in colorectal cancer (CRC) using integrative multi-omics and to elucidate their relationship with the CRC immune microenvironment. METHODS Transcriptomic data, clinical information, and Percent Spliced In (PSI) values of AS events for CRC patients were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Differentially expressed AS events were identified. Univariate Cox analysis was used to pinpoint prognosis-related AS events. A prognostic risk model was developed and validated using multivariate Cox analysis, patient survival analysis, and the area under the receiver operating characteristic (ROC) curve (AUC). Gene Set Enrichment Analysis (GSEA), immune infiltration, immunotherapy, chemotherapy sensitivity analyses, and regulatory relationships between AS events and splicing factors (SFs) were conducted. Single-cell sequencing was used to study the distribution of key factors. siRNA and overexpression vectors were utilized to silence/overexpress BCAS1 in CRC cells and evaluate their effects on cell growth, migration, and invasion. Furthermore, the interaction between BCAS1 and ANO7 pre-mRNA was investigated using RIP-PCR. RESULTS 82 prognosis-related AS events were identified in CRC patients. A 15-AS prognostic model was constructed, which correlated with immune cell infiltration and showed differences in immunotherapy and chemotherapy sensitivity. BCAS1 was identified as a potential regulator of the ANO7|58341|AT splicing event in CRC. Single-cell sequencing analysis revealed the distribution of BCAS1 and ANO7 in cancer stem cells. In vitro experiments demonstrated that overexpression of BCAS1 and silencing of ANO7 inhibit the proliferation, migration, and invasion of CRC cells. Moreover, BCAS1 suppresses the progression of CRC by modulating ANO7 alternative splicing. CONCLUSION This study provides new insights into the role of alternative splicing in colorectal cancer, particularly the potential regulatory action of BCAS1 on the ANO7|58341|AT splicing event. It also identifies the impact of alternative splicing on the tumor microenvironment and potential implications for immunotherapy, highlighting its relevance for the in-depth study and treatment of CRC.
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Affiliation(s)
- Yizhi Xiao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Liangqing Gao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Xiaojuan Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Wang Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Lei Mai
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Chengmin Ma
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Yanzhi Han
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
| | - Xiaofeng Li
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
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Zheng P, Zhang X, Ren D, Bai Q. Alternative Splicing in Glioblastoma and its Clinical Implication in Outcome Prediction. Neurol India 2024; 72:846-855. [PMID: 39216044 DOI: 10.4103/neurol-india.ni_1219_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/08/2022] [Indexed: 09/04/2024]
Abstract
BACKGROUND AND OBJECTIVE Alternative splicing (AS) offers an important mechanism to form protein polymorphism. A growing body of evidence indicates the correlation between splicing abnormality and carcinoma. Nevertheless, an overall analysis of AS signatures in glioblastoma (GBM) is absent and urgently needed. METHODS TCGA SpliceSea data was used to evaluate the AS profiles and further classified into different AS events. The survival analysis was based on these AS events, and AS-related genes were identified and performed with enrichment analysis. At last, the splicing factor-AS regulatory network was established in Cytoscape. RESULTS Eight hundred forty-two splicing events were confirmed as prognostic molecular events in GBM. Furthermore, the final prognostic signature constructed by seven AS events gave good result with an area under the curve (AUC) of receiver operating characteristic (ROC) curve up to 0.935 for five years, showing high potency in predicting patients' outcome. We built the splicing regulatory network to show the internal relationship of splicing events in GBM. PC4 and SFRS1 interacting protein 1 (PSIP1) and histone H4 acetylation may play a significant part in the prognosis induced by splicing events. CONCLUSION In our study, a high-efficiency prognostic prediction model was built for GBM patients based on AS events, which could become potential prognostic biomarkers for GBM. Meanwhile, PSIP1 may be a critical target for pharmaceutical treatment.
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Affiliation(s)
- Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, China
- Department of Key Laboratory, Shanghai Pudong New Area People's Hospital, China
| | - Xiaoxue Zhang
- Department of Key Laboratory, Shanghai Pudong New Area People's Hospital, China
| | - Dabin Ren
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, China
| | - Qingke Bai
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, China
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Ding H, Shi H, Chen W, Liu Z, Yang Z, Li X, Qiu Z, Zhuo H. Identification of Key Prognostic Alternative Splicing Events of Costimulatory Molecule-Related Genes in Colon Cancer. Comb Chem High Throughput Screen 2024; 27:1900-1912. [PMID: 37957898 DOI: 10.2174/0113862073249972231026060301] [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: 02/20/2023] [Revised: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVE This study aimed to explore the key alternative splicing events in costimulatory molecule-related genes in colon cancer and to determine their correlation with prognosis. METHODS Gene expression RNA-sequencing data, clinical data, and SpliceSeq data of colon cancer were obtained from The Cancer Genome Atlas. Differentially expressed alternative splicing events in genes were identified, Followed by correlation analysis of genes corresponding to differentially expressed alternative splicing events with costimulatory molecule-related genes. Survival analysis was conducted using differentially expressed alternative splicing events in these genes and a prognostic model was constructed. Functional enrichment, proteinprotein interaction network, and splicing factor analyses were performed. RESULTS In total, 6504 differentially expressed alternative splicing events in 3949 genes were identified between tumor and normal tissues. Correlation analysis revealed 3499 differentially expressed alternative splicing events in 2168 costimulatory molecule-related genes. Moreover, 328 differentially expressed alternative splicing events in 288 costimulatory molecule-related genes were associated with overall survival. The prognostic models constructed using these showed considerable power in predicting survival. The ubiquitin A-52 residue ribosomal protein fusion product 1 and ribosomal protein S9 were the hub nodes in the protein-protein interaction network. Furthermore, one splicing factor, splicing factor proline and glutamine-rich, was significantly associated with patient prognosis. Four splicing factor-alternative splicing pairs were obtained from four alternative splicing events in three genes: TBC1 domain family member 8 B, complement factor H, and mitochondrial fission 1. CONCLUSION The identified differentially expressed alternative splicing events of costimulatory molecule-related genes may be used to predict patient prognosis and immunotherapy responses in colon cancer.
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Affiliation(s)
- Hao Ding
- Department of General Surgery, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Huiwen Shi
- Department of General Surgery, No. 971 Hospital of PLA Navy, Shandong, China
| | - Weifeng Chen
- Department of Oncology, Huangdao District Hospital of Traditional Chinese Medicine, Shandong, China
| | - Zhisheng Liu
- Department of General Surgery, Affiliated Qingdao Hiser Hospital of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Shandong, China
| | - Zhi Yang
- The IVD Medical Marketing Department, 3D Medicines Inc., Shadong, China
| | - Xiaochuan Li
- Department of General Surgery, Qingdao Municipal Hospital, Shandong, China
| | - Zhichao Qiu
- Department of Oncology, Shunde Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongqing Zhuo
- Department of Gastrointestinal Surgery, Provincial Hospital Affiliated to Shandong First Medical University, Shadong, China
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Xie P, Batur J, An X, Yasen M, Fu X, Jia L, Luo Y. Novel, alternative splicing signature to detect lymph node metastasis in prostate adenocarcinoma with machine learning. Front Oncol 2023; 12:1084403. [PMID: 36713568 PMCID: PMC9880415 DOI: 10.3389/fonc.2022.1084403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023] Open
Abstract
Background The presence of lymph node metastasis leads to a poor prognosis for prostate cancer (Pca). Recently, many studies have indicated that gene signatures may be able to predict the status of lymph nodes. The purpose of this study is to probe and validate a new tool to predict lymph node metastasis (LNM) based on alternative splicing (AS). Methods Gene expression profiles and clinical information of prostate adenocarcinoma cohort were retrieved from The Cancer Genome Atlas (TCGA) database, and the corresponding RNA-seq splicing events profiles were obtained from the TCGA SpliceSeq. Limma package was used to identify the differentially expressed alternative splicing (DEAS) events between LNM and non-LNM groups. Eight machine learning classifiers were built to train with stratified five-fold cross-validation. SHAP values was used to explain the model. Results 333 differentially expressed alternative splicing (DEAS) events were identified. Using correlation filter and the least absolute shrinkage and selection operator (LASSO) method, a 96 AS signature was identified that had favorable discrimination in the training set and validated in the validation set. The linear discriminant analysis (LDA) was the best classifier after 100 iterations of training. The LDA classifier was able to distinguish between LNM and non-LNM with an area under the receiver operating curve of 0.962 ± 0.026 in the training set (D1 = 351) and 0.953 in the validation set (D2 = 62). The decision curve analysis plot proved the clinical application of the AS-based model. Conclusion Machine learning combined with AS data could robustly distinguish between LNM and non-LNM in Pca.
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Affiliation(s)
- Ping Xie
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China,Department of Urology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Jesur Batur
- Department of Urology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Xin An
- Department of Urology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Musha Yasen
- Department of Urology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Xuefeng Fu
- Department of Urology, The People's Hospital of Suining County, Xuzhou, Jiangsu, China
| | - Lin Jia
- Department of Urology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yun Luo
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China,*Correspondence: Yun Luo,
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [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: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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Wang Z, Wu Q, Liu Y, Li Q, Li J. Identification of prognostic alternative splicing signature in gastric cancer. Arch Public Health 2022; 80:145. [PMID: 35614517 PMCID: PMC9131537 DOI: 10.1186/s13690-022-00894-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background Aberrant alternative splicing (AS) events could be viewed as prognostic indicators in a large number of malignancies. This study aims to identify prognostic AS events, illuminate the function of the splicing variants biomarkers and provide reliable evidence for formulating public health strategies for gastric cancer (GC) surveillance. Methods RNA-Seq data, clinical information and percent spliced in (PSI) values were available in The cancer genome atlas (TCGA) and TCGA SpliceSeq data portal. A three-step regression method was conducted to identify prognostic AS events and construct multi-AS-based signatures. The associations between prognostic AS events and splicing factors were also investigated. Results We identified a total of 1,318 survival-related AS events in GC, parent genes of which were implicated in numerous oncogenic pathways. The final prognostic signatures stratified by seven types of AS events or not stratified performed well in risk prediction for GC patients. Moreover, five signatures based on AA, AD, AT, ES and RI events function as independent prognostic indicators after multivariate adjustment of other clinical variables. Splicing network also showed marked correlation between the expression of splicing factors and PSI value of AS events in GC patients. Conclusion Our findings provide a landscape of AS events and regulatory network in GC, indicating that AS events might serve as prognostic biomarkers and therapeutic targets for GC. Supplementary Information The online version contains supplementary material available at 10.1186/s13690-022-00894-3.
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Affiliation(s)
- Zhiwu Wang
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Qiong Wu
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Yankun Liu
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Qingke Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Jingwu Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China.
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Wang G, Sun L, Wang S, Guo J, Xiao R, Li W, Qi W, Qiu W. Ferroptosis‑related long non‑coding RNAs and the roles of LASTR in stomach adenocarcinoma. Mol Med Rep 2022; 25:118. [PMID: 35137922 PMCID: PMC8855154 DOI: 10.3892/mmr.2022.12634] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022] Open
Abstract
Ferroptosis is a form of programmed cell death that participates in diverse physiological processes. Increasing evidence suggests that long noncoding RNAs (lncRNAs) regulate ferroptosis in tumors, including stomach adenocarcinoma (STAD). In the present study, RNA-sequencing data from The Cancer Genome Atlas database and ferroptosis-related markers from the FerrDb data resource were analyzed to select differentially expressed lncRNAs. Univariate and multivariate Cox regression analyses were performed on these differentially expressed lncRNAs to screen 12 lncRNAs linked with overall survival (OS) and 13 associated with progression-free survival (PFS). Subsequently, two signatures for predicting OS and PFS were established based on these lncRNAs. Kaplan-Meier analyses indicated that the high-risk group of patients with STAD had relatively poor prognosis. The areas under the receiver operating characteristic curves of the two signatures indicated their excellent efficacy in predicting STAD prognosis. In addition, the effect of the lncRNA LASTR on proliferation and migration in gastric cancer was confirmed and the relationship between LASTR and ferroptosis was initially explored through experiments. These results provide potential novel targets for tumor treatment and promote personalized medicine.
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Affiliation(s)
- Gongjun Wang
- Department of Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Libin Sun
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Shasha Wang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jing Guo
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Ruoxi Xiao
- Department of Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Wenqian Li
- Department of Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Weiwei Qi
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Wensheng Qiu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
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A Novel Nomogram Combining Alternative Splicing Events and Clinical Factors for Prognosis Prediction in Head and Neck Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:4552445. [PMID: 35103061 PMCID: PMC8800633 DOI: 10.1155/2022/4552445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/18/2022]
Abstract
Due to limitations of sensitive biomarkers, the clinical prognosis of patients with head and neck squamous cell carcinoma (HNSCC) remains poor. Alternative splicing (AS) is the basis of both transcriptome and proteome richness, so more and more evidence indicates an important relationship between AS and tumor progression. The aim of this study was to offer a comprehensive analysis on AS events and then investigate its potentials as a new biomarker for patients with squamous cell carcinoma of the head and neck. In this study, univariate assays were conducted to examine the prognosis-associated AS events, and we screened 4068 survival-related AS events in 2573 genes. Then, the AS events related to survival were further determined and analyzed using LASSO regression and multivariate assays, and an eleven-AS signature was developed. Kaplan–Meier assays indicated patients with high-risk scores exhibited a shorter OS than those with low-risk scores. Multivariate assays further demonstrated that the signature’s risk score was independent of HNSCC survivals. Meanwhile, we analyzed the clinical association of AS-based prognostic signature in HNSCC patients and observed that tumor specimens with advanced stages and grades exhibited a high risk score. In addition, the results of survival nomogram revealed that predicted outcomes and actual outcomes were highly consistent. Overall, our group showed an eleven-AS signature of HNSCC, which could be regarded as a separate prognostic factor.
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He B, Wei C, Cai Q, Zhang P, Shi S, Peng X, Zhao Z, Yin W, Tu G, Peng W, Tao Y, Wang X. Switched alternative splicing events as attractive features in lung squamous cell carcinoma. Cancer Cell Int 2022; 22:5. [PMID: 34986865 PMCID: PMC8734344 DOI: 10.1186/s12935-021-02429-2] [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: 09/10/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Alternative splicing (AS) plays important roles in transcriptome and proteome diversity. Its dysregulation has a close affiliation with oncogenic processes. This study aimed to evaluate AS-based biomarkers by machine learning algorithms for lung squamous cell carcinoma (LUSC) patients. Method The Cancer Genome Atlas (TCGA) database and TCGA SpliceSeq database were utilized. After data composition balancing, Boruta feature selection and Spearman correlation analysis were used for differentially expressed AS events. Random forests and a nested fivefold cross-validation were applied for lymph node metastasis (LNM) classifier building. Random survival forest combined with Cox regression model was performed for a prognostic model, based on which a nomogram was developed. Functional enrichment analysis and Spearman correlation analysis were also conducted to explore underlying mechanisms. The expression of some switch-involved AS events along with parent genes was verified by qRT-PCR with 20 pairs of normal and LUSC tissues. Results We found 16 pairs of splicing events from same parent genes which were strongly related to the splicing switch (intrapair correlation coefficient = − 1). Next, we built a reliable LNM classifier based on 13 AS events as well as a nice prognostic model, in which switched AS events behaved prominently. The qRT-PCR presented consistent results with previous bioinformatics analysis, and some AS events like ITIH5-10715-AT and QKI-78404-AT showed remarkable detection efficiency for LUSC. Conclusion AS events, especially switched ones from the same parent genes, could provide new insights into the molecular diagnosis and therapeutic drug design of LUSC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02429-2.
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Affiliation(s)
- Boxue He
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Xiangya School of Medicine, Central South University, Changsha, 410008, China
| | - Cong Wei
- Xiangya School of Medicine, Central South University, Changsha, 410008, China
| | - Qidong Cai
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiong Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Wei Yin
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Guangxu Tu
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Weilin Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yongguang Tao
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Xiang Wang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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Zhu L, Wang Z, Sun Y, Giamas G, Stebbing J, Yu Z, Peng L. A Prediction Model Using Alternative Splicing Events and the Immune Microenvironment Signature in Lung Adenocarcinoma. Front Oncol 2021; 11:778637. [PMID: 35004299 PMCID: PMC8728792 DOI: 10.3389/fonc.2021.778637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
BackgroundAlternative splicing (AS) is a gene regulatory mechanism that drives protein diversity. Dysregulation of AS is thought to play an essential role in cancer initiation and development. This study aimed to construct a prognostic signature based on AS and explore the role in the tumor immune microenvironment (TIME) in lung adenocarcinoma.MethodsWe analyzed transcriptome profiling and clinical lung adenocarcinoma data from The Cancer Genome Atlas (TCGA) database and lists of AS-related and immune-related signatures from the SpliceSeq. Prognosis-related AS events were analyzed by univariate Cox regression analysis. Gene set enrichment analyses (GSEA) were performed for functional annotation. Prognostic signatures were identified and validated using univariate and multivariate Cox regression, LASSO regression, Kaplan–Meier survival analyses, and proportional hazards model. The context of TIME in lung adenocarcinoma was also analyzed. Gene and protein expression data of Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) were obtained from ONCOMINE and Human Protein Atlas. Splicing factor (SF) regulatory networks were visualized.ResultsA total of 19,054 survival-related AS events in lung adenocarcinoma were screened in 1,323 genes. Exon skip (ES) and mutually exclusive exons (ME) exhibited the most and fewest AS events, respectively. Based on AS subtypes, eight AS prognostic signatures were constructed. Patients with high-risk scores were associated with poor overall survival. A nomogram with good validity in prognostic prediction was generated. AUCs of risk scores at 1, 2, and 3 years were 0.775, 0.736, and 0.759, respectively. Furthermore, the prognostic signatures were significantly correlated with TIME diversity and immune checkpoint inhibitor (ICI)-related genes. Low-risk patients had a higher StromalScore, ImmuneScore, and ESTIMATEScore. AS-based risk score signature was positively associated with CD8+ T cells. CDKN2A was also found to be a prognostic factor in lung adenocarcinoma. Finally, potential functions of SFs were determined by regulatory networks.ConclusionTaken together, our findings show a clear association between AS and immune cell infiltration events and patient outcome, which could provide a basis for the identification of novel markers and therapeutic targets for lung adenocarcinoma. SF networks provide information of regulatory mechanisms.
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Affiliation(s)
- Liping Zhu
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Yilan Sun
- Department of Respiratory Disease, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Zhentao Yu
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Center, National Cancer Center, Shenzhen, China
- *Correspondence: Ling Peng, ; Zhentao Yu,
| | - Ling Peng
- Department of Respiratory Disease, Zhejiang Provincial People’s Hospital, Hangzhou, China
- *Correspondence: Ling Peng, ; Zhentao Yu,
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Wang G, Qi W, Shen L, Wang S, Xiao R, Li W, Zhang Y, Bian X, Sun L, Qiu W. The pattern of alternative splicing in lung adenocarcinoma shows novel events correlated with tumorigenesis and immune microenvironment. BMC Pulm Med 2021; 21:400. [PMID: 34872548 PMCID: PMC8647402 DOI: 10.1186/s12890-021-01776-0] [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: 10/17/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer deaths worldwide due to the lack of early diagnostic markers and specific drugs. Previous studies have shown the association of LUAD growth with aberrant alternative splicing (AS). Herein, clinical data of 535 tumor tissues and 59 normal tissues were extracted from The Cancer Genome Atlas (TCGA) database. Each sample was analyzed using the ESTIMATE algorithm; a comparison between higher and lower score groups (stromal or immune) was made to determine the overall- and progression-free survival-related differentially expressed AS (DEAS) events. We then performed unsupervised clustering of these DEASs, followed by determining their relationship with survival rate, immune cells, and the tumor microenvironment (TME). Next, two prognostic signatures were developed using bioinformatics tools to explore the prognosis of cases with LUAD. Five OS- and six PFS-associated DEAS events were implemented to establish a prognostic risk score model. When compared to the high-risk group (HRG), the PFS and OS of the low-risk group (LRG) were found to be considerable. Additionally, a better prognosis was found considerably associated with the ESTIMATE score of the patients as well as immune cells infiltration. Our analysis of AS events in LUAD not only helps to clarify the tumorigenesis mechanism of AS but also provides ideas for revealing potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Gongjun Wang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.,Department of Medcine, Qingdao University, Qingdao, China
| | - Weiwei Qi
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Liwei Shen
- Department of Oncology, Women and Children's Hospital, Qingdao University, Qingdao, Shandong, China
| | - Shasha Wang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ruoxi Xiao
- Department of Medcine, Qingdao University, Qingdao, China
| | - Wenqian Li
- Department of Medcine, Qingdao University, Qingdao, China
| | - Yuqi Zhang
- Department of Medcine, Qingdao University, Qingdao, China
| | - Xiaoqian Bian
- Department of Medcine, Qingdao University, Qingdao, China
| | - Libin Sun
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Wensheng Qiu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
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12
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Ye P, Yang Y, Zhang L, Zheng G. Prognostic Signatures of Alternative Splicing Events in Esophageal Carcinoma Based on TCGA Splice-Seq Data. Front Oncol 2021; 11:658262. [PMID: 34676158 PMCID: PMC8524056 DOI: 10.3389/fonc.2021.658262] [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: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
An alternative splicing (AS) event is a highly complex process that plays an essential role in post-transcriptional gene expression. Several studies have suggested that abnormal AS events were the primary element in the pathological process of cancer. However, few works are dedicated to the study of AS events in esophageal carcinoma (EC). In the present study, clinical information and RNA-seq data of EC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The percent spliced in (PSI) values of AS events were acquired from the TCGA Splice-seq. A total of 183 EC patients were enrolled in this study, and 2,212 AS events were found significantly associated with the overall survival of these patients by univariate Cox regression analysis. The prognostic signatures based on AS events were built by multivariate Cox analysis. Receiver operating characteristic (ROC) curves displayed that the area under the curve (AUC) of the following prognostic signatures, including exon skip (ES), alternate terminator (AT), alternate acceptor site (AA), alternate promoter (AP), alternate donor site (AD), retained intron (RI), and total events, was greater than 0.8, suggesting that these seven signatures had valuable prognosis prediction capacity. Finally, the risk score of prognostic signatures was indicated as an independent risk factor of survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the function of splicing factors (SFs) that were associated with AS events. Also, the interactive network between AS events and SFs identified several hub genes and AS events which need further study. This was a comprehensive study that explored prognosis-related AS events and established valuable prognosis signatures in EC patients. The network of interactions between AS events and SFs might offer novel insights into the fundamental mechanisms of tumorigenesis and progression of EC.
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Affiliation(s)
- Ping Ye
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Yan Yang
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Liqiang Zhang
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
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13
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Kim YM, Hong S. Controversial roles of cold‑inducible RNA‑binding protein in human cancer (Review). Int J Oncol 2021; 59:91. [PMID: 34558638 DOI: 10.3892/ijo.2021.5271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 11/05/2022] Open
Abstract
Cold‑inducible RNA‑binding protein (CIRBP) is a cold‑shock protein comprised of an RNA‑binding motif that is induced by several stressors, such as cold shock, UV radiation, nutrient deprivation, reactive oxygen species and hypoxia. CIRBP can modulate post‑transcriptional regulation of target mRNA, which is required to control DNA repair, circadian rhythms, cell growth, telomere integrity and cardiac physiology. In addition, the crucial function of CIRBP in various human diseases, including cancers and inflammatory disease, has been reported. Although CIRBP is primarily considered to be an oncogene, it may also serve a role in tumor suppression. In the present study, the controversial roles of CIRBP in various human cancers is summarized, with a focus on the interconnectivity between CIRBP and its target mRNAs involved in tumorigenesis. CIRBP may represent an important prognostic marker and therapeutic target for cancer therapy.
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Affiliation(s)
- Young-Mi Kim
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
| | - Suntaek Hong
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
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14
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Lai J, Yang H, Xu T. Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma. BMC Cancer 2021; 21:848. [PMID: 34294080 PMCID: PMC8299698 DOI: 10.1186/s12885-021-08548-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/07/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Malignant mesothelioma (MM) is a relatively rare and highly lethal tumor with few treatment options. Thus, it is important to identify prognostic markers that can help clinicians diagnose mesothelioma earlier and assess disease activity more accurately. Alternative splicing (AS) events have been recognized as critical signatures for tumor diagnosis and treatment in multiple cancers, including MM. METHODS We systematically examined the AS events and clinical information of 83 MM samples from TCGA database. Univariate Cox regression analysis was used to identify AS events associated with overall survival. LASSO analyses followed by multivariate Cox regression analyses were conducted to construct the prognostic signatures and assess the accuracy of these prognostic signatures by receiver operating characteristic (ROC) curve and Kaplan-Meier survival analyses. The ImmuCellAI and ssGSEA algorithms were used to assess the degrees of immune cell infiltration in MM samples. The survival-related splicing regulatory network was established based on the correlation between survival-related AS events and splicing factors (SFs). RESULTS A total of 3976 AS events associated with overall survival were identified by univariate Cox regression analysis, and ES events accounted for the greatest proportion. We constructed prognostic signatures based on survival-related AS events. The prognostic signatures proved to be an efficient predictor with an area under the curve (AUC) greater than 0.9. Additionally, the risk score based on 6 key AS events proved to be an independent prognostic factor, and a nomogram composed of 6 key AS events was established. We found that the risk score was significantly decreased in patients with the epithelioid subtype. In addition, unsupervised clustering clearly showed that the risk score was associated with immune cell infiltration. The abundances of cytotoxic T (Tc) cells, natural killer (NK) cells and T-helper 17 (Th17) cells were higher in the high-risk group, whereas the abundances of induced regulatory T (iTreg) cells were lower in the high-risk group. Finally, we identified 3 SFs (HSPB1, INTS1 and LUC7L2) that were significantly associated with MM patient survival and then constructed a regulatory network between the 3 SFs and survival-related AS to reveal potential regulatory mechanisms in MM. CONCLUSION Our study provided a prognostic signature based on 6 key events, representing a better effective tumor-specific diagnostic and prognostic marker than the TNM staging system. AS events that are correlated with the immune system may be potential therapeutic targets for MM.
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Affiliation(s)
- Jinzhi Lai
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Hainan Yang
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Tianwen Xu
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China.
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15
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Miao TW, Du LY, Xiao W, Mao B, Wang Y, Fu JJ. Identification of Survival-Associated Gene Signature in Lung Cancer Coexisting With COPD. Front Oncol 2021; 11:600243. [PMID: 33791201 PMCID: PMC8006292 DOI: 10.3389/fonc.2021.600243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) and lung cancer often coexist, which is associated with a worse prognosis. Thousands of biomarkers related to the survival of lung cancer have been investigated. However, those which can predict the survival of lung cancer coexisting with COPD are currently lacking. The present study aimed to identify novel gene signatures to predict the survival of patients with lung cancer coexisting COPD. Method: RNA-sequence data of lung cancer and control accompanying with matched clinical information were retrieved from the Cancer Genome Atlas (TCGA). Differently expressed genes (DEGs) associated with lung cancer coexisting COPD were screened. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed. Univariate and multivariate Cox regression analyses were applied to identify survival-associated DEGs and to construct survival-associated gene signature. Kaplan-Meier survival analysis and calibration plots of the nomogram were performed to test the predictive accuracy of the gene signature. qPCR was performed to validate the genes in the prognostic signature. Results: Sequence data from 70 patients with lung cancer coexisting COPD, 127 with lung cancer alone and 108 control tissues were included for analysis. A total of 2424 DEGs were identified when comparing lung cancer coexisting COPD with controls. The biological process was primarily associated with DNA-binding transcription activator activity, peptidase inhibitor activity, endopeptidase inhibitor activity, et al. KEGG pathways were mainly enriched in neuroactive ligand-receptor interaction, cell cycle, and Staphylococcus aureus infection. A survival-associated gene signature consisting of CEACAM5, RASAL1, CSTL1, CNGB1, and SLC4A3 was identified and represented as risk score. The high-risk score group had significantly worse survival than the low-risk score group (P < 0.001). Areas under receiver operating characteristic curves were 0.943, 0.773, 0.888 for predicting overall survival at 1-, 3-, and 5-year, respectively. The risk score was an independent predictor of survival, independent of clinical factors. High conformity of the actual survival and the nomogram–predicted probability of survival by applying the risk score. Upregulation of the five genes in patients with lung cancer coexisting COPD were confirmed by qPCR in an independent cohort. Conclusion: Our study constructed and validated a novel prognostic gene signature for predicting survival of patient with lung cancer coexisting COPD, which may contribute to the clinical treatment decisions.
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Affiliation(s)
- Ti-Wei Miao
- Respiratory Group, Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Respiratory Group, Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Xiao
- Respiratory Group, Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Bing Mao
- Respiratory Group, Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Respiratory Group, Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
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16
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Zhao Z, Cai Q, Zhang P, He B, Peng X, Tu G, Peng W, Wang L, Yu F, Wang X. N6-Methyladenosine RNA Methylation Regulator-Related Alternative Splicing (AS) Gene Signature Predicts Non-Small Cell Lung Cancer Prognosis. Front Mol Biosci 2021; 8:657087. [PMID: 34179079 PMCID: PMC8226009 DOI: 10.3389/fmolb.2021.657087] [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: 01/22/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
Aberrant N6-methyladenosine (m6A) RNA methylation regulatory genes and related gene alternative splicing (AS) could be used to predict the prognosis of non-small cell lung carcinoma. This study focused on 13 m6A regulatory genes (METTL3, METTL14, WTAP, KIAA1429, RBM15, ZC3H13, YTHDC1, YTHDC2, YTHDF1, YTHDF2, HNRNPC, FTO, and ALKBH5) and expression profiles in TCGA-LUAD (n = 504) and TCGA-LUSC (n = 479) datasets from the Cancer Genome Atlas database. The data were downloaded and bioinformatically and statistically analyzed, including the gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. There were 43,948 mRNA splicing events in lung adenocarcinoma (LUAD) and 46,020 in lung squamous cell carcinoma (LUSC), and the data suggested that m6A regulators could regulate mRNA splicing. Differential HNRNPC and RBM15 expression was associated with overall survival (OS) of LUAD and HNRNPC and METTL3 expression with the OS of LUSC patients. Furthermore, the non-small cell lung cancer prognosis-related AS events signature was constructed and divided patients into high- vs. low-risk groups using seven and 14 AS genes in LUAD and LUSC, respectively. The LUAD risk signature was associated with gender and T, N, and TNM stages, but the LUSC risk signature was not associated with any clinical features. In addition, the risk signature and TNM stage were independent prognostic predictors in LUAD and the risk signature and T stage were independent prognostic predictors in LUSC after the multivariate Cox regression and receiver operating characteristic analyses. In conclusion, this study revealed the AS prognostic signature in the prediction of LUAD and LUSC prognosis.
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Affiliation(s)
- Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Guangxu Tu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Weilin Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Xiang Wang,
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17
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Cai Q, He B, Zhang P, Zhao Z, Peng X, Zhang Y, Xie H, Wang X. Exploration of predictive and prognostic alternative splicing signatures in lung adenocarcinoma using machine learning methods. J Transl Med 2020; 18:463. [PMID: 33287830 PMCID: PMC7720605 DOI: 10.1186/s12967-020-02635-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022] Open
Abstract
Background Alternative splicing (AS) plays critical roles in generating protein diversity and complexity. Dysregulation of AS underlies the initiation and progression of tumors. Machine learning approaches have emerged as efficient tools to identify promising biomarkers. It is meaningful to explore pivotal AS events (ASEs) to deepen understanding and improve prognostic assessments of lung adenocarcinoma (LUAD) via machine learning algorithms. Method RNA sequencing data and AS data were extracted from The Cancer Genome Atlas (TCGA) database and TCGA SpliceSeq database. Using several machine learning methods, we identified 24 pairs of LUAD-related ASEs implicated in splicing switches and a random forest-based classifiers for identifying lymph node metastasis (LNM) consisting of 12 ASEs. Furthermore, we identified key prognosis-related ASEs and established a 16-ASE-based prognostic model to predict overall survival for LUAD patients using Cox regression model, random survival forest analysis, and forward selection model. Bioinformatics analyses were also applied to identify underlying mechanisms and associated upstream splicing factors (SFs). Results Each pair of ASEs was spliced from the same parent gene, and exhibited perfect inverse intrapair correlation (correlation coefficient = − 1). The 12-ASE-based classifier showed robust ability to evaluate LNM status of LUAD patients with the area under the receiver operating characteristic (ROC) curve (AUC) more than 0.7 in fivefold cross-validation. The prognostic model performed well at 1, 3, 5, and 10 years in both the training cohort and internal test cohort. Univariate and multivariate Cox regression indicated the prognostic model could be used as an independent prognostic factor for patients with LUAD. Further analysis revealed correlations between the prognostic model and American Joint Committee on Cancer stage, T stage, N stage, and living status. The splicing network constructed of survival-related SFs and ASEs depicts regulatory relationships between them. Conclusion In summary, our study provides insight into LUAD researches and managements based on these AS biomarkers.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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18
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Zhang S, Wang J, Zhang A, Zhang X, You T, Xie D, Yang W, Chen Y, Zhang X, Di C, Xie X. A SNP involved in alternative splicing of ABCB1 is associated with clopidogrel resistance in coronary heart disease in Chinese population. Aging (Albany NY) 2020; 12:25684-25699. [PMID: 33232268 PMCID: PMC7803500 DOI: 10.18632/aging.104177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 04/07/2023]
Abstract
Although many scientists are studying the association between genetic polymorphism of ABCB1 and CR in patients, the molecular mechanism has not been further studied in patients with CHD. This study investigated the relationship between SNP of the ABCB1 gene in patients with CHD and CR, and whether the polymorphism of the ABCB1 gene affects the AS of the gene. 741 patients were enrolled in the study, 316 CR cases and 425 NCR cases. The correlation between CR risk and clinical-pathological characteristics were studied. Additionally, the five SNPs were analysed by PCR and Mass Array genotyping methods. Furthermore, silicon analysis was used to predict whether the polymorphism affects the process of AS. Results showed that there was a significant correlation between rs1045642 polymorphism and CR in genotyping and allele analysis. The rs1045642 polymorphism of the ABCB1 gene of CHD patients carrying the A allele are more likely to develop CR. Silicon analysis showed that rs1045642 generated a new ESE sequence which might affect AS of ABCB1 gene. We hypothesize that the mechanism of CR might be caused by a change in the AS caused by the polymorphism of the gene. Thus, this work provides guidance for the clinical use of clopidogrel.
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Affiliation(s)
- Shasha Zhang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jing Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Anan Zhang
- The Second Hospital of Lanzhou University, Lanzhou 730000, China
| | - Xiaowei Zhang
- Department of Cardiology, The Second Hospital of Lanzhou University, Lanzhou 730000, China
| | - Tao You
- Department of Cardiac Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
- Congenital Heart Disease Diagnosis and Treatment Gansu Province International Science and Technology Cooperation Base, Lanzhou 730000, China
| | - Dingxiong Xie
- Gansu Cardiovascular Institute, Lanzhou 730050, China
| | - Wenke Yang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yuhong Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xuetian Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
- Gansu Provincial Maternity and Childcare Hospital, Lanzhou 730050, China
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19
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Wang JZ, Fu X, Fang Z, Liu H, Zong FY, Zhu H, Yu YF, Zhang XY, Wang SF, Huang Y, Hui J. QKI-5 regulates the alternative splicing of cytoskeletal gene ADD3 in lung cancer. J Mol Cell Biol 2020; 13:347-360. [PMID: 33196842 PMCID: PMC8373271 DOI: 10.1093/jmcb/mjaa063] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
Accumulating evidence indicates that the alternative splicing program undergoes extensive changes during cancer development and progression. The RNA-binding protein QKI-5 is frequently downregulated and exhibits anti-tumor activity in lung cancer. Howeve-r, little is known about the functional targets and regulatory mechanism of QKI-5. Here, we report that upregulation of exon 14 inclusion of cytoskeletal gene Adducin 3 (ADD3) significantly correlates with a poor prognosis in lung cancer. QKI-5 inhibits cell proliferation and migration in part through suppressing the splicing of ADD3 exon 14. Through genome-wide mapping of QKI-5 binding sites in vivo at nucleotide resolution by iCLIP-seq analysis, we found that QKI-5 regulates alternative splicing of its target mRNAs in a binding position-dependent manner. By binding to multiple sites in an upstream intron region, QKI-5 represses the splicing of ADD3 exon 14. We also identified several QKI mutations in tumors, which cause dysregulation of the splicing of QKI targets ADD3 and NUMB. Taken together, our results reveal that QKI-mediated alternative splicing of ADD3 is a key lung cancer-associated splicing event, which underlies in part the tumor suppressor function of QKI.
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Affiliation(s)
- Jin-Zhu Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China
| | - Zhaoyuan Fang
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Feng-Yang Zong
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan-Fei Yu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Ying Zhang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shen-Fei Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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Chang YS, Tu SJ, Chiang HS, Yen JC, Lee YT, Fang HY, Chang JG. Genome-Wide Analysis of Prognostic Alternative Splicing Signature and Splicing Factors in Lung Adenocarcinoma. Genes (Basel) 2020; 11:genes11111300. [PMID: 33142748 PMCID: PMC7693837 DOI: 10.3390/genes11111300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022] Open
Abstract
Analysis of The Cancer Genome Atlas data revealed that alternative splicing (AS) events could serve as prognostic biomarkers in various cancer types. This study examined lung adenocarcinoma (LUAD) tissues for AS and assessed AS events as potential indicators of prognosis in our cohort. RNA sequencing and bioinformatics analysis were performed. We used SUPPA2 to analyze the AS profiles. Using univariate Cox regression analysis, overall survival (OS)-related AS events were identified. Genes relating to the OS-related AS events were imported into Cytoscape, and the CytoHubba application was run. OS-related splicing factors (SFs) were explored using the log-rank test. The relationship between the percent spliced-in value of the OS-related AS events and SF expression was identified by Spearman correlation analysis. We found 1957 OS-related AS events in 1151 genes, and most were protective factors. Alternative first exon splicing was the most frequent type of splicing event. The hub genes in the gene network of the OS-related AS events were FBXW11, FBXL5, KCTD7, UBB and CDC27. The area under the curve of the MIX prediction model was 0.847 for 5-year survival based on seven OS-related AS events. Overexpression of SFs CELF2 and SRSF5 was associated with better OS. We constructed a correlation network between SFs and OS-related AS events. In conclusion, we identified prognostic predictors using AS events that stratified LUAD patients into high- and low-risk groups. The discovery of the splicing networks in this study provides an insight into the underlying mechanisms.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, 404 Taichung, Taiwan; (Y.-S.C.); (J.-C.Y.); (Y.-T.L.)
- Department of Laboratory Medicine, China Medical University Hospital, 404 Taichung, Taiwan; (S.-J.T.); (H.-S.C.)
- Center for Precision Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, China Medical University, 404 Taichung, Taiwan
| | - Siang-Jyun Tu
- Department of Laboratory Medicine, China Medical University Hospital, 404 Taichung, Taiwan; (S.-J.T.); (H.-S.C.)
| | - Hui-Shan Chiang
- Department of Laboratory Medicine, China Medical University Hospital, 404 Taichung, Taiwan; (S.-J.T.); (H.-S.C.)
| | - Ju-Chen Yen
- Epigenome Research Center, China Medical University Hospital, 404 Taichung, Taiwan; (Y.-S.C.); (J.-C.Y.); (Y.-T.L.)
| | - Ya-Ting Lee
- Epigenome Research Center, China Medical University Hospital, 404 Taichung, Taiwan; (Y.-S.C.); (J.-C.Y.); (Y.-T.L.)
| | - Hsin-Yuan Fang
- Department of Thoracic Surgery, China Medical University Hospital, 404 Taichung, Taiwan;
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, 404 Taichung, Taiwan; (Y.-S.C.); (J.-C.Y.); (Y.-T.L.)
- Department of Laboratory Medicine, China Medical University Hospital, 404 Taichung, Taiwan; (S.-J.T.); (H.-S.C.)
- Center for Precision Medicine, China Medical University Hospital, 404 Taichung, Taiwan
- School of Medicine, China Medical University, 404 Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, 413 Taichung, Taiwan
- Correspondence: ; Tel.: +886-4-22052121 (ext. 2008)
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21
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Liu Y, Jia W, Li J, Zhu H, Yu J. Identification of Survival-Associated Alternative Splicing Signatures in Lung Squamous Cell Carcinoma. Front Oncol 2020; 10:587343. [PMID: 33117720 PMCID: PMC7561379 DOI: 10.3389/fonc.2020.587343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023] Open
Abstract
Purpose: Alternative splicing (AS) is a post-transcriptional process that plays a significant role in enhancing the diversity of transcription and protein. Accumulating evidences have demonstrated that dysregulation of AS is associated with oncogenic processes. However, AS signature specifically in lung squamous cell carcinoma (LUSC) remains unknown. This study aimed to evaluate the prognostic values of AS events in LUSC patients. Methods: The RNA-seq data, AS events data and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression analysis was performed to identify survival-related AS events and survival-related parent genes were subjected to Gene Ontology enrichment analysis and gene network analysis. The least absolute shrinkage and selection operator (LASSO) method and multivariate Cox regression analysis were used to construct prognostic prediction models, and their predictive values were assessed by Kaplan-Meier analysis and receiver operating characteristic (ROC) curves. Then a nomogram was established to predict the survival of LUSC patients. And the interaction network of splicing factors (SFs) and survival-related AS events was constructed by Spearman correlation analysis and visualized by Cytoscape. Results: Totally, 467 LUSC patients were included in this study and 1,991 survival-related AS events within 1,433 genes were identified. SMAD4, FOS, POLR2L, and RNPS1 were the hub genes in the gene interaction network. Eight prognostic prediction models (seven types of AS and all AS) were constructed and all exhibited high efficiency in distinguishing good or poor survival of LUSC patients. The final integrated prediction model including all types of AS events exhibited the best prognostic power with the maximum AUC values of 0.778, 0.816, 0.814 in 1, 3, 5 years ROC curves, respectively. Meanwhile, the nomogram performed well in predicting the 1-, 3-, and 5-year survival of LUSC patients. In addition, the SF-AS regulatory network uncovered a significant correlation between SFs and survival-related AS events. Conclusion: This is the first comprehensive study to analyze the role of AS events in LUSC specifically, which improves our understanding of the prognostic value of survival-related AS events for LUSC. And these survival-related AS events might serve as novel prognostic biomarkers and drug therapeutic targets for LUSC.
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Affiliation(s)
- Yang Liu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wenxiao Jia
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Ji Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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22
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Huang R, Guo J, Yan P, Zhai S, Hu P, Zhu X, Zhang J, Qiao Y, Zhang Y, Liu H, Huang L, Zhang J, Yang D, Huang Z. The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer. Front Cell Dev Biol 2020; 8:790. [PMID: 32984314 PMCID: PMC7477087 DOI: 10.3389/fcell.2020.00790] [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] [Received: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 01/17/2023] Open
Abstract
Background Breast cancer (BRCA) ranks among the top most common female malignancies and was regarded as incurable when combined with bone and distant metastasis. Alternative splicing events (ASEs) together with splicing factors (SFs) were considered responsible for the development and progression of tumors. Methods Datasets including RNA sequencing and ASEs of BRCA samples were achieved from TCGA and TCGASpliceSeq databases. Then, a survival model was built including 15 overall-survival-associated splicing events (OS-SEs) by Cox regression and Lasso regression. The co-expressed SFs of each bone-and-distant-metastasis-related OS-SE were discovered by Pearson correlation analysis. Additionally, Gene Set Variation Analysis (GSVA) was performed to identify the downstream mechanisms of the key OS-SEs. Finally, the results were validated in different online platforms. Results A reliable survival model was established (the area under ROC = 0.856), and CIRBP was found co-expressed with FAM110B (R = 0.320, P < 0.001) associated with the fatty acid metabolism pathway. Conclusion Aberrant SF, CIRBP, regulated a specific ASE, exon skip (ES) of FAM110B, during which the fatty acid metabolism pathway played an essential part in tumorigenesis and prognosis of BRCA.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Juanru Guo
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Suna Zhai
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiayao Zhang
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Yannan Qiao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Liu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Tongji University School of Medicine, Shanghai, China
| | - Daoke Yang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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