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Park H, Miyano S. Sparse spectral graph analysis and its application to gastric cancer drug resistance-specific molecular interplays identification. PLoS One 2024; 19:e0305386. [PMID: 38968283 PMCID: PMC11226138 DOI: 10.1371/journal.pone.0305386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/28/2024] [Indexed: 07/07/2024] Open
Abstract
Uncovering acquired drug resistance mechanisms has garnered considerable attention as drug resistance leads to treatment failure and death in patients with cancer. Although several bioinformatics studies developed various computational methodologies to uncover the drug resistance mechanisms in cancer chemotherapy, most studies were based on individual or differential gene expression analysis. However the single gene-based analysis is not enough, because perturbations in complex molecular networks are involved in anti-cancer drug resistance mechanisms. The main goal of this study is to reveal crucial molecular interplay that plays key roles in mechanism underlying acquired gastric cancer drug resistance. To uncover the mechanism and molecular characteristics of drug resistance, we propose a novel computational strategy that identified the differentially regulated gene networks. Our method measures dissimilarity of networks based on the eigenvalues of the Laplacian matrix. Especially, our strategy determined the networks' eigenstructure based on sparse eigen loadings, thus, the only crucial features to describe the graph structure are involved in the eigenanalysis without noise disturbance. We incorporated the network biology knowledge into eigenanalysis based on the network-constrained regularization. Therefore, we can achieve a biologically reliable interpretation of the differentially regulated gene network identification. Monte Carlo simulations show the outstanding performances of the proposed methodology for differentially regulated gene network identification. We applied our strategy to gastric cancer drug-resistant-specific molecular interplays and related markers. The identified drug resistance markers are verified through the literature. Our results suggest that the suppression and/or induction of COL4A1, PXDN and TGFBI and their molecular interplays enriched in the Extracellular-related pathways may provide crucial clues to enhance the chemosensitivity of gastric cancer. The developed strategy will be a useful tool to identify phenotype-specific molecular characteristics that can provide essential clues to uncover the complex cancer mechanism.
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Affiliation(s)
- Heewon Park
- School of Mathematics, Statistics and Data Science, Sungshin Women’s University, Seoul, Republic of Korea
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
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Suhail Y, Liu Y, Du W, Afzal J, Atiq A, Kshitiz. Oscillatory Hypoxia Induced Unfolded Protein Folding Response Gene Expression Predicts Low Survival in Human Breast Cancer Patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577274. [PMID: 38328204 PMCID: PMC10849661 DOI: 10.1101/2024.01.25.577274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Hypoxia is one of the key factors in the tumor microenvironment regulating nearly all steps in the metastatic cascade in many cancers, including in breast cancer. The hypoxic regions can however be dynamic with the availability of oxygen fluctuating or oscillating. The canonical response to hypoxia is relayed by transcription factor HIF-1, which is stabilized in hypoxia and acts as the master regulator of a large number of downstream genes. However, HIF-1 transcriptional activity can also fluctuate either due to unstable hypoxia, or by lactate mediated non-canonical degradation of HIF-1. Our understanding of how oscillatory hypoxia or HIF-1 activity specifically influence cancer malignancy is very limited. Here, using MDA-MB-231 cells as a model of triple negative breast cancer characterized by severe hypoxia, we measured the gene expression changes induced specifically by oscillatory hypoxia. We found that oscillatory hypoxia can specifically regulate gene expression differently, and at times opposite to stable hypoxia. Using The Cancer Genome Atlas (TCGA) RNAseq data of human cancer samples, we show that the oscillatory specific gene expression signature in MDA-MB-231 is enriched in most human cancers, and prognosticate low survival in breast cancer patients. In particular, we found that oscillatory hypoxia, unlike stable hypoxia, induces unfolded protein folding response (UPR) in cells resulting in gene expression predicting reduced survival.
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Affiliation(s)
- Yasir Suhail
- Department of Biomedical Engineering University of Connecticut Health, Farmington, CT, USA
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farimington, CT, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Yamin Liu
- Department of Biomedical Engineering University of Connecticut Health, Farmington, CT, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Wenqiang Du
- Department of Biomedical Engineering University of Connecticut Health, Farmington, CT, USA
| | - Junaid Afzal
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Amina Atiq
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Kshitiz
- Department of Biomedical Engineering University of Connecticut Health, Farmington, CT, USA
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farimington, CT, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
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Yu J, Gong Y, Xu Z, Chen L, Li S, Cui Y. Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling. PeerJ 2024; 12:e17629. [PMID: 38938617 PMCID: PMC11210462 DOI: 10.7717/peerj.17629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model's accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a "hot" immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment.
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Affiliation(s)
- Jinglu Yu
- PuDong Traditional Chinese Medicine Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China, Shanghai, Pudong, China
| | - Yabin Gong
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Zhenye Xu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Lei Chen
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Shuang Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongkang Cui
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Xu QT, Qiang JK, Huang ZY, Jiang WJ, Cui XM, Hu RH, Wang T, Yi XL, Li JY, Yu Z, Zhang S, Du T, Liu J, Jiang XH. Integration of machine learning for developing a prognostic signature related to programmed cell death in colorectal cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:2908-2926. [PMID: 38299230 DOI: 10.1002/tox.24157] [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: 12/08/2023] [Revised: 01/04/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) presents a significant global health burden, characterized by a heterogeneous molecular landscape and various genetic and epigenetic alterations. Programmed cell death (PCD) plays a critical role in CRC, offering potential targets for therapy by regulating cell elimination processes that can suppress tumor growth or trigger cancer cell resistance. Understanding the complex interplay between PCD mechanisms and CRC pathogenesis is crucial. This study aims to construct a PCD-related prognostic signature in CRC using machine learning integration, enhancing the precision of CRC prognosis prediction. METHOD We retrieved expression data and clinical information from the Cancer Genome Atlas and Gene Expression Omnibus (GEO) datasets. Fifteen forms of PCD were identified, and corresponding gene sets were compiled. Machine learning algorithms, including Lasso, Ridge, Enet, StepCox, survivalSVM, CoxBoost, SuperPC, plsRcox, random survival forest (RSF), and gradient boosting machine, were integrated for model construction. The models were validated using six GEO datasets, and the programmed cell death score (PCDS) was established. Further, the model's effectiveness was compared with 109 transcriptome-based CRC prognostic models. RESULT Our integrated model successfully identified differentially expressed PCD-related genes and stratified CRC samples into four subtypes with distinct prognostic implications. The optimal combination of machine learning models, RSF + Ridge, showed superior performance compared with traditional methods. The PCDS effectively stratified patients into high-risk and low-risk groups, with significant survival differences. Further analysis revealed the prognostic relevance of immune cell types and pathways associated with CRC subtypes. The model also identified hub genes and drug sensitivities relevant to CRC prognosis. CONCLUSION The current study highlights the potential of integrating machine learning models to enhance the prediction of CRC prognosis. The developed prognostic signature, which is related to PCD, holds promise for personalized and effective therapeutic interventions in CRC.
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Affiliation(s)
- Qi-Tong Xu
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jian-Kun Qiang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, China
| | - Zhi-Ye Huang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wan-Ju Jiang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xi-Mao Cui
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ren-Hao Hu
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tao Wang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, China
| | - Xiang-Lan Yi
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, China
| | - Jia-Yuan Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, China
| | - Zuoren Yu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, China
| | - Shun Zhang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tao Du
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Hua Jiang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Liu W, Luo X, Zhang Z, Chen Y, Dai Y, Deng J, Yang C, Liu H. Construction of an immune predictive model and identification of TRIP6 as a prognostic marker and therapeutic target of CRC by integration of single-cell and bulk RNA-seq data. Cancer Immunol Immunother 2024; 73:69. [PMID: 38430268 PMCID: PMC10908634 DOI: 10.1007/s00262-024-03658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Investigations elucidating the complex immunological mechanisms involved in colorectal cancer (CRC) and accurately predicting patient outcomes via bulk RNA-Seq analysis have been notably limited. This study aimed to identify the immune status of CRC patients, construct a prognostic model, and identify prognostic signatures via bulk RNA sequencing (RNA-seq) and single-cell RNA-seq (scRNA-seq). METHODS The scRNA-seq data of CRC were downloaded from Gene Expression Omnibus (GEO). The UCSC Xena database was used to obtain bulk RNA-seq data. Differentially expressed gene (DEG), functional enrichment, and random forest analyses were conducted in order to identify core genes associated with colorectal cancer (CRC) that were relevant to prognosis. A molecular immune prediction model was developed using logistic regression after screening features using the least absolute shrinkage and selection operator (LASSO). The differences in immune cell infiltration, mutation, chemotherapeutic drug sensitivity, cellular senescence, and communication between patients who were at high and low risk of CRC according to the predictive model were investigated. The prognostic genes that were closely associated with CRC were identified by random survival forest (RSF) analysis. The expression levels and clinical significance of the hub genes were analyzed in vitro. The LoVo cell line was employed to ascertain the biological role of thyroid hormone receptor-interacting protein 6 (TRIP6). RESULTS A total of seven main cell subtypes were identified by scRNA-seq analysis. A molecular immune predictive model was constructed based on the risk scores. The risk score was significantly associated with OS, stage, mutation burden, immune cell infiltration, response to immunotherapy, key pathways, and cell-cell communication. The functions of the six hub genes were determined and further utilized to establish a regulatory network. Our findings unequivocally confirmed that TRIP6 upregulation was verified in the CRC samples. After knocking down TRIP6, cell proliferation, migration, and invasion of LoVo cells were inhibited, and apoptosis was promoted. CONCLUSIONS The molecular predictive model reliably distinguished the immune status of CRC patients. We further revealed that TRIP6 may act as an oncogene in CRC, making it a promising candidate for targeted therapy and as a prognostic marker for CRC.
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Affiliation(s)
- Wenjun Liu
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Xitu Luo
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Zilang Zhang
- Department of Anorectal Surgery, The First People's Hospital of Foshan, Guangdong, 528010, China
| | - Yepeng Chen
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Yongliang Dai
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Jianzhong Deng
- Department of Anorectal Surgery, The First People's Hospital of Foshan, Guangdong, 528010, China
| | - Chengyu Yang
- The First Department of General Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Hao Liu
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510000, Guangdong, China.
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Zhou J, Dong C, Tan J, Wang G, Li Z, Li S, He Z. Promoting effect and immunologic role of secretogranin II on bladder cancer progression via regulating MAPK and NF-κB pathways. Apoptosis 2024; 29:121-141. [PMID: 37848672 DOI: 10.1007/s10495-023-01898-2] [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] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Bladder cancer (BLCA) is ranked among the top ten most prevalent cancers worldwide and is the second most common malignant tumor within the field of urology. The limited effectiveness of immune targeted therapy in treating BLCA, due to its high metastasis and recurrence rates, necessitates the identification of new therapeutic targets. Secretogranin II (SCG2), a member of the chromaffin granin/secreted granin family, plays a crucial role in the regulated release of peptides and hormones. The role of SCG2 in the tumor microenvironment (TME) of lung adenocarcinoma and colon cancer has been established, but its functional significance in BLCA remains uncertain. This study aimed to investigate SCG2 expression in 15 bladder cancer tissue samples and their corresponding adjacent control tissues. The potential involvement of SCG2 in BLCA progression was assessed using various techniques, including analysis of public databases, immunohistochemistry, Western Blotting, immunofluorescence, wound-healing assay, Transwell assay, and xenograft tumor formation experiments in nude mice. This study provided novel evidence indicating that SCG2 plays a pivotal role in facilitating the proliferation, migration, and invasion of BLCA by activating the MEK/Erk and MEK/IKK/NF-κB signaling pathways, as well as by promoting M2 macrophage polarization. These findings propose the potential of SCG2 as a molecular target for immunotherapy in human BLCA.
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Affiliation(s)
- Jiawei Zhou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Caitao Dong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Jing Tan
- Hubei Key Laboratory of Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guijun Wang
- Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Zhen Li
- Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Sheng Li
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Department of Biological Repositories, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ziqi He
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
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邓 金, 潘 腾, 周 广, 高 悦, 彭 伟, 魏 玮, 吕 纯. [High expression of secretogranin II increases oxaliplatin resistance of colorectal cancer cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:1657-1664. [PMID: 37933640 PMCID: PMC10630195 DOI: 10.12122/j.issn.1673-4254.2023.10.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVE To investigate the expression of secretogranin II (SCG2) in colorectal cancer (CRC) tissues and its impact on oxaliplatin resistance of CRC cells. METHODS We performed immunohistochemistry to detect the expression level of SCG2 on a tissue microarray containing 96 CRC and 84 adjacent tissues and analyzed the association of SCG2 expression with the clinical features of the CRC patients. SCG2 expression was also measured in DLD1 cells treated with oxaliplatin using immunoblotting and RT-qPCR analyses. The effects of SCG2 expression on oxaliplatin sensitivity and cell viability were evaluated in a DLD1 cell model of SCG2 knockout established using CRISPR-cas9 technique, and the expressions of apoptosis-related proteins were detected using Western blotting and RT-qPCR. We further examined SCG2 expression levels in an oxaliplatin-resistant DLD1 cell line and its parental DLD1 cells. RESULTS SCG2 expression was significantly increased in CRC tissues as compared with the adjacent tissues (1.932±0.816 vs 1), and the tumor tissues in advanced stages showed higher SCG2 expression levels. In DLD1 cells, treatment with oxaliplatin significantly increased SCG2 expression, and SCG2 knockout obviously increased oxaliplatin sensitivity of the cells and enhanced the expressions of apoptosis-related proteins. Compared with the parental cells, oxaliplatin-resistant DLD1 cells showed a significant increase of SCG2 expression by 3.901±0.471 folds. CONCLUSION SCG2 may serve as a risk gene in CRC, and its high expression increases oxaliplatin resistance of CRC cells.
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Affiliation(s)
- 金海 邓
- 北京大学基础医学院免疫学系;卫生部医学免疫学重点实验室;北京大学人类疾病基因研究中心,北京 100191Department of Immunology, School of Basic Medical Sciences; NHC Key Laboratory of Medical Immunology; Center for Human Disease Genomics, Peking University, Beijing 100191, China
- 湖南自兴智慧医疗科技有限公司,湖南 长沙 410221Hunan Zixing Intelligent Medical Technology Co., Ltd., Changsha 410221, China
| | - 腾 潘
- 天津医科大学肿瘤医院国家肿瘤临床医学研究中心;天津市"肿瘤防治"重点实验室;天津市恶性肿瘤临床医学研究中心,天津 300202Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Tianjin 300202, China
| | - 广林 周
- 深圳市龙岗区妇幼保健院//汕头大学医学院龙岗妇幼临床学院,广东 深圳 518172Department of Breast Surgery, Longgang District Maternity and Child Healthcare Hospital//Longgang Maternity and Child Institute of Shantou University Medical College, Shenzhen 518172, China
| | - 悦 高
- 湖南自兴智慧医疗科技有限公司,湖南 长沙 410221Hunan Zixing Intelligent Medical Technology Co., Ltd., Changsha 410221, China
| | - 伟雄 彭
- 湖南自兴智慧医疗科技有限公司,湖南 长沙 410221Hunan Zixing Intelligent Medical Technology Co., Ltd., Changsha 410221, China
| | - 玮 魏
- 上海市浦东新区浦南医院肿瘤科,上海 200120Department of Oncology, Punan Hospital of Pudong New District, Shanghai 200120, China
| | - 纯鑫 吕
- 上海市浦东新区浦南医院肿瘤科,上海 200120Department of Oncology, Punan Hospital of Pudong New District, Shanghai 200120, China
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Zhou J, Xu L, Zhou H, Wang J, Xing X. Prediction of Prognosis and Chemotherapeutic Sensitivity Based on Cuproptosis-Associated lncRNAs in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Genes (Basel) 2023; 14:1381. [PMID: 37510286 PMCID: PMC10379127 DOI: 10.3390/genes14071381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Cervical cancer is the fourth most common cancer. The 5-year survival rate for metastatic cervical cancer is less than 10%. The survival time of patients with recurrent cervical cancer is approximately 13-17 months. Cuproptosis is a novel type of cell death related to mitochondrial respiration. Accumulative studies showed that long non-coding RNAs (lncRNAs) regulated cervical cancer progression. Compressive bioinformatic analysis showed that nine cuproptosis-related lncRNAs (CRLs), including C002128.2, AC002563.1, AC009237.14, AC048337.1, AC145423.1, AL117336.1, AP001542.3, ATP2A1-AS1, and LINC00426, were independently correlated with the overall survival (OS) of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) patients. The time-dependent area under curve value reached 0.716 at 1 year, 0.718 at 3 years, and 0.719 at 5 years. Notably, CESC patients in the low-risk group had increased immune cell infiltration and expression of several immune checkpoints, which indicated that they may benefit more from immune checkpoint blockade therapy. In addition, we also used the model for drug sensitivity analysis. Several drug sensitivities were more sensitive in high-risk patients and showed significant correlations with the risk models, such as Bortezomib_1191, Luminespib_1559, and Rapamycin_1084, suggesting that these drugs may be candidate clinical drugs for patients with a high risk of CESC. In summary, this study further explored the mechanism of CRLs in CESC and provided a more optimized prognostic model and some insights into chemotherapy of CESC.
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Affiliation(s)
- Jianghong Zhou
- Department of Gynecology, Department of Obsterics and Gynecology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou 412007, China; (J.Z.); (L.X.); (H.Z.); (J.W.)
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Lili Xu
- Department of Gynecology, Department of Obsterics and Gynecology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou 412007, China; (J.Z.); (L.X.); (H.Z.); (J.W.)
| | - Hong Zhou
- Department of Gynecology, Department of Obsterics and Gynecology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou 412007, China; (J.Z.); (L.X.); (H.Z.); (J.W.)
| | - Jingjin Wang
- Department of Gynecology, Department of Obsterics and Gynecology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou 412007, China; (J.Z.); (L.X.); (H.Z.); (J.W.)
| | - Xiaoliang Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
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Cross-Talk between N6-Methyladenosine and Their Related RNAs Defined a Signature and Confirmed m6A Regulators for Diagnosis of Endometriosis. Int J Mol Sci 2023; 24:ijms24021665. [PMID: 36675186 PMCID: PMC9862014 DOI: 10.3390/ijms24021665] [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: 12/16/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
An RNA modification known as N6-methyladenosine (m6A) interacts with a range of coding and non-coding RNAs. The majority of the research has focused on identifying m6A regulators that are differentially expressed in endometriosis, but it has ignored their mechanisms that are derived from the alterations of modifications among RNAs, affecting the disease progression primarily. Here, we aimed to investigate the potential roles of m6A regulators in the diagnostic potency, immune microenvironment, and clinicopathological features of endometriosis through interacting genes. A GEO cohort was incorporated into this study. Variance expression profiling was executed via the "limma" R package. Pearson analysis was performed to investigate the correlations among 767 interacting lncRNAs, 374 interacting mRNAs, and 23 m6A regulators. K-means clustering analysis, based on patterns of mRNA modifications, was applied to perform clinical feature analysis. Infiltrating immune cells and stromal cells were calculated using the Cibersort method. An m6A-related risk model was created and supported by an independent risk assay. LASSO regression analysis and Cox analyses were implemented to determine the diagnostic genes. The diagnostic targets of endometriosis were verified using PCR and the WB method. Results: A thorough investigation of the m6A modification patterns in the GEO database was carried out, based on mRNAs and lncRNAs related to these m6A regulators. Two molecular subtypes were identified using unsupervised clustering analysis, resulting in further complex infiltration levels of immune microenvironment cells in diversified endometriosis pathology types. We identified two m6A regulators, namely METTL3 and YTHDF2, as diagnostic targets of endometriosis following the usage of overlapping genes to construct a diagnostic m6A signature of endometriosis through multivariate logistic regression, and we validated it using independent GSE86534 and GSE105764 cohorts. Finally, we found that m6A alterations might be one of the important reasons for the progression of endometriosis, especially with significant downregulation of the expressions of METTL3 and YTHDF2. Finally, m6A modification patterns have significant effects on the diversity and complexity of the progression and immune microenvironment, and might be key diagnostic markers for endometriosis.
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