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Liu P, Deng X, Zhou H, Xie J, Kong Y, Zou Y, Yang A, Li X. Multi-omics analyses unravel DNA damage repair-related clusters in breast cancer with experimental validation. Front Immunol 2023; 14:1297180. [PMID: 38022619 PMCID: PMC10644223 DOI: 10.3389/fimmu.2023.1297180] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background As one of the most common malignancies worldwide, breast cancer (BC) exhibits high heterogeneity of molecular phenotypes. The evolving view regarding DNA damage repair (DDR) is that it is context-specific and heterogeneous, but its role in BC remains unclear. Methods Multi-dimensional data of transcriptomics, genomics, and single-cell transcriptome profiling were obtained to characterize the DDR-related features of BC. We collected 276 DDR-related genes based on the Molecular Signature Database (MSigDB) database and previous studies. We acquired public datasets included the SCAN-B dataset (GEO: GSE96058), METABRIC database, and TCGA-BRCA database. Corresponding repositories such as transcriptomics, genomics, and clinical information were also downloaded. We selected scRNA-seq data from GEO: GSE176078, GSE114727, GSE161529, and GSE158724. Bulk RNA-seq data from GEO: GSE176078, GSE18728, GSE5462, GSE20181, and GSE130788 were extracted for independent analyses. Results The DDR classification was constructed in the SCAN-B dataset (GEO: GSE96058) and METABRIC database, Among BC patients, there were two clusters with distinct clinical and molecular characteristics: the DDR-suppressed cluster and the DDR-active cluster. A superior survival rate is found for tumors in the DDR-suppressed cluster, while those with the DDR-activated cluster tend to have inferior prognoses and clinically aggressive behavior. The DDR classification was validated in the TCGA-BRCA cohort and shown similar results. We also found that two clusters have different pathway activities at the genomic level. Based on the intersection of the different expressed genes among these cohorts, we found that PRAME might play a vital role in DDR. The DDR classification was then enabled by establishing a DDR score, which was verified through multilayer cohort analysis. Furthermore, our results revealed that malignant cells contributed more to the DDR score at the single-cell level than nonmalignant cells. Particularly, immune cells with immunosuppressive properties (such as FOXP3+ CD4+ T cells) displayed higher DDR scores among those with distinguishable characteristics. Conclusion Collectively, this study performs general analyses of DDR heterogeneity in BC and provides insight into the understanding of individualized molecular and clinicopathological mechanisms underlying unique DDR profiles.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huamao Zhou
- The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanan Kong
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Anli Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xing Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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Tuly KF, Hossen MB, Islam MA, Kibria MK, Alam MS, Harun-Or-Roshid M, Begum AA, Hasan S, Mahumud RA, Mollah MNH. Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1705. [PMID: 37893423 PMCID: PMC10608013 DOI: 10.3390/medicina59101705] [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: 07/21/2023] [Revised: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Breast cancer (BC) is one of the major causes of cancer-related death in women globally. Proper identification of BC-causing hub genes (HubGs) for prognosis, diagnosis, and therapies at an earlier stage may reduce such death rates. However, most of the previous studies detected HubGs through non-robust statistical approaches that are sensitive to outlying observations. Therefore, the main objectives of this study were to explore BC-causing potential HubGs from robustness viewpoints, highlighting their early prognostic, diagnostic, and therapeutic performance. Materials and Methods: Integrated robust statistics and bioinformatics methods and databases were used to obtain the required results. Results: We robustly identified 46 common differentially expressed genes (cDEGs) between BC and control samples from three microarrays (GSE26910, GSE42568, and GSE65194) and one scRNA-seq (GSE235168) dataset. Then, we identified eight cDEGs (COL11A1, COL10A1, CD36, ACACB, CD24, PLK1, UBE2C, and PDK4) as the BC-causing HubGs by the protein-protein interaction (PPI) network analysis of cDEGs. The performance of BC and survival probability prediction models with the expressions of HubGs from two independent datasets (GSE45827 and GSE54002) and the TCGA (The Cancer Genome Atlas) database showed that our proposed HubGs might be considered as diagnostic and prognostic biomarkers, where two genes, COL11A1 and CD24, exhibit better performance. The expression analysis of HubGs by Box plots with the TCGA database in different stages of BC progression indicated their early diagnosis and prognosis ability. The HubGs set enrichment analysis with GO (Gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways disclosed some BC-causing biological processes, molecular functions, and pathways. Finally, we suggested the top-ranked six drug molecules (Suramin, Rifaximin, Telmisartan, Tukysa Tucatinib, Lynparza Olaparib, and TG.02) for the treatment of BC by molecular docking analysis with the proposed HubGs-mediated receptors. Molecular docking analysis results also showed that these drug molecules may inhibit cancer-related post-translational modification (PTM) sites (Succinylation, phosphorylation, and ubiquitination) of hub proteins. Conclusions: This study's findings might be valuable resources for diagnosis, prognosis, and therapies at an earlier stage of BC.
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Affiliation(s)
- Khanis Farhana Tuly
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Md. Bayazid Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Md. Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Md. Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
- Department of Statistics, Hajee Mohammad Danesh Science & Technology University, Dinajpur 5200, Bangladesh
| | - Md. Shahin Alam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Md. Harun-Or-Roshid
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Anjuman Ara Begum
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
| | - Sohel Hasan
- Molecular and Biomedical Health Science Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (K.F.T.); (M.B.H.); (M.A.I.); (M.K.K.); (M.S.A.); (M.H.-O.-R.); (A.A.B.)
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Zhang D, Wang M, Huang X, Wang L, Liu Y, Zhou S, Tang Y, Wang Q, Li Z, Wang G. GLS as a diagnostic biomarker in breast cancer: in-silico, in-situ, and in-vitro insights. Front Oncol 2023; 13:1220038. [PMID: 37664031 PMCID: PMC10471892 DOI: 10.3389/fonc.2023.1220038] [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: 05/12/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Background Recently, a novel programmed cell death mechanism, Cuproptosis, has been discovered and found to play an important role in the development and progression of diverse tumors. In the present study, we comprehensively investigated the core gene of this mechanism, GLS, in breast cancer. Materials and methods Bulk RNA sequencing data were curated from the TCGA repository to investigate the aberrant expression of GLS over diverse cancer types. Then, we examined its efficacy as a diagnostic biomarker in breast cancer by Area Under Curve (AUC) of the Receiver Operative Characteristic (ROC) curve. Furthermore, by applying siRNA technique, we knocked down the GLS expression level in cancerous cell lines, measuring the corresponding effects on cell proliferation and metastasis. Afterward, we explored the potential implications of GLS expression in the tumor immune microenvironment quantitatively by using several R packages and algorithms, including ESTIMATE, CIBERSORT, etc. Results Pan-cancer analysis suggested that GLS was aberrantly over-expressed in many cancer types, with breast cancer being typical. More in-depth analyses revealed the expression of GLS exerted a high ROC-AUC value in breast cancer diagnosis. Through the knock-down of GLS expression, it was found that GLS expression was strongly relevant to the growth and metastasis of tumor. Furthermore, it was also found to be correlated with the immune tumor microenvironment. Conclusion We highlighted that GLS expression might be applicable as a diagnostic biomarker in breast cancer and possess significant implications in the growth and metastasis of tumor and the immune tumor microenvironment, sharing new insights into ontological and personalized medicine.
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Affiliation(s)
- Danfeng Zhang
- Departments of Breast Thyroid Vascular Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Man Wang
- Departments of Outpatient Department, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Longbin Wang
- Faculty of Life Science, Huazhong Agricultural University, Wuhan, China
| | - Ying Liu
- Department of Cardiology, Sixth Medical Center, PLA General Hospital, Beijing, China
| | - Shujing Zhou
- Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Yidan Tang
- Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Qi Wang
- Faculty of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhengrui Li
- Faculty of Dentistry, Shanghai Jiaotong University, Shanghai, China
| | - Geng Wang
- Departments of Breast Thyroid Vascular Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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Reynisdottir I, Arason A, Freysteinsdottir ES, Kristjansdottir SB, Hilmarsdottir B, Traustadottir GA, Johannsson OT, Agnarsson BA, Barkardottir RB. High Atlastin 2-2 (ATL2-2) Expression Associates with Worse Prognosis in Estrogen-Receptor-Positive Breast Cancer. Genes (Basel) 2023; 14:1559. [PMID: 37628611 PMCID: PMC10454310 DOI: 10.3390/genes14081559] [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: 06/20/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The disruption of endoplasmic reticulum (ER) homeostasis occurs in many human diseases. Atlastins (ATLs) maintain the branched network of the ER. The dysregulation of ATL2, located at ER network junctions, has been associated with cancer. ATL2 is necessary for lipid droplet formation in murine breast tissue. Thus, we analyzed whether ATL2 has a role in human breast cancer (BC) pathology. The expression of ATL2 variant ATL2-2 was analyzed in breast tumors from the BC cohorts of the TCGA, METABRIC, and two independent Icelandic cohorts, Cohort 1 and 2; its association with clinical, pathological, survival, and cellular pathways was explored. ATL2-2 mRNA and protein expression were higher in breast tumors than in normal tissue. ATL2-2 mRNA associated with tumor characteristics that indicate a worse prognosis. In METABRIC, high ATL2-2 mRNA levels were associated with shorter BC-specific survival (BCSS) in patients with estrogen-receptor-positive luminal breast tumors, which remained significant after correction for grade and tumor size (HR 1.334, CI 1.063-1.673). Tumors with high ATL2 mRNA showed an upregulation of hallmark pathways MYC targets v1, E2F targets, and G2M checkpoint genes. Taken together, the results suggest that high levels of ATL2-2 may support BC progression through key cancer driver pathways.
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Affiliation(s)
- Inga Reynisdottir
- Cell Biology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
| | - Adalgeir Arason
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Edda S. Freysteinsdottir
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Sigrun B. Kristjansdottir
- Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland; (S.B.K.); (B.A.A.)
| | - Bylgja Hilmarsdottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Gunnhildur A. Traustadottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Oskar T. Johannsson
- Department of Oncology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
| | - Bjarni A. Agnarsson
- Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland; (S.B.K.); (B.A.A.)
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Rosa B. Barkardottir
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; (A.A.); (B.H.); (G.A.T.); (R.B.B.)
- Molecular Pathology Unit, Department of Pathology, Landspitali—The National University Hospital of Iceland, 101 Reykjavik, Iceland;
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Xie J, Chen L, Wu D, Liu S, Pei S, Tang Q, Wang Y, Ou M, Zhu Z, Ruan S, Wang M, Shi J. Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis. Aging (Albany NY) 2023; 15:5592-5610. [PMID: 37338518 PMCID: PMC10333080 DOI: 10.18632/aging.204812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/27/2023] [Indexed: 06/21/2023]
Abstract
Currently, the role of liquid-liquid phase separation (LLPS) in cancer has been preliminarily explained. However, the significance of LLPS in breast cancer is unclear. In this study, single cell sequencing datasets GSE188600 and GSE198745 for breast cancer were downloaded from the GEO database. Transcriptome sequencing data for breast cancer were downloaded from UCSC database. We divided breast cancer cells into high-LLPS group and low-LLPS group by down dimension clustering analysis of single-cell sequencing data set, and obtained differentially expressed genes between the two groups. Subsequently, weighted co-expression network analysis (WGCNA) was performed on transcriptome sequencing data, and the module genes most associated with LLPS were obtained. COX regression and Lasso regression were performed and the prognostic model was constructed. Subsequently, survival analysis, principal component analysis, clinical correlation analysis, and nomogram construction were used to evaluate the significance of the prognostic model. Finally, cell experiments were used to verify the function of the model's key gene, PGAM1. We constructed a LLPS-related prognosis model consisting of nine genes: POLR3GL, PLAT, NDRG1, HMGB3, HSPH1, PSMD7, PDCD2, NONO and PGAM1. By calculating LLPS-related risk scores, breast cancer patients could be divided into high-risk and low-risk groups, with the high-risk group having a significantly worse prognosis. Cell experiments showed that the activity, proliferation, invasion and healing ability of breast cancer cell lines were significantly decreased after knockdown of the key gene PGAM1 in the model. Our study provides a new idea for prognostic stratification of breast cancer and provides a novel marker: PGAM1.
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Affiliation(s)
- Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Liang Chen
- Department of Hepatobiliary and Pancreatic Surgery, Conversion Therapy Center for Hepatobiliary and Pancreatic Tumors, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing 314001, Zhejiang, P. R. China
| | - Dan Wu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210031, Jiangsu, China
| | - Shengxuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Qikai Tang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Yue Wang
- Department of Pathology, Basic Medical School, Anhui Medical University, Hefei 230032, Anhui, China
| | - Mengmeng Ou
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Zhechen Zhu
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Shujie Ruan
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Ming Wang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
| | - Jingping Shi
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, Jiangsu, China
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Hu J, Dai C, Zhang Y, Chen W, Sun L, Zhang X, Duan M, Fu H, Long T, Kang W, Yin C, Liu X, Yu J. Effect of surgical treatment on patients with stage T3 or T4 triple-negative breast cancer: a SEER-based retrospective observational study. Front Endocrinol (Lausanne) 2023; 14:1184173. [PMID: 37305041 PMCID: PMC10250696 DOI: 10.3389/fendo.2023.1184173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Background The use of surgery is controversial in patients with stage T3 or T4 triple-negative breast cancer (TNBC). We aimed to explore the effect of surgical treatment on overall survival (OS) of these patients. Methods A total of 2,041 patients were selected and divided into the surgical and non-surgical groups based on the Surveillance, Epidemiology, and End Results database from 2010 to 2018. Propensity score matching (PSM) and inverse probability of treatment weighting (IPTW) were applied to balance covariates between different groups. The OS of the two groups were assessed by Kaplan-Meier survival curves and Cox proportional hazards regression models. Results A total of 2,041 patients were included in the study. After PSM and IPTW, baseline characteristics of the matched variables were fully balanced. Kaplan-Meier survival curves showed that the median survival time and OS of TNBC patients with stage T3 or T4 in the surgical group were significantly improved compared with those in the non-surgical group. Multivariate Cox proportional hazards regression analysis showed that surgery was a protective factor for prognosis. Conclusion Our study found that surgery prolonged the median survival and improved OS compared with the non-surgical group of TNBC patients with stage T3 or T4.
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Affiliation(s)
- Jie Hu
- Department of Tumor Radiotherapy, Taizhou Central Hospital (Affiliated Hospital of Taizhou University), Taizhou, China
| | - Changling Dai
- Department of Hematology, Taizhou Central Hospital (Affiliated Hospital of Taizhou University), Taizhou, China
| | - Yang Zhang
- College of Medical Informatics, Chongqing Medical University, Chongqing, China
| | - Weijun Chen
- Department of Tumor Radiotherapy, Taizhou Central Hospital (Affiliated Hospital of Taizhou University), Taizhou, China
| | - Lihua Sun
- Department of Tumor Radiotherapy, Taizhou Central Hospital (Affiliated Hospital of Taizhou University), Taizhou, China
| | - Xu Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Minjie Duan
- College of Medical Informatics, Chongqing Medical University, Chongqing, China
| | - Hao Fu
- Department of Infectious Disease, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Teng Long
- Department of Infectious Disease, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Kang
- Department of Mathematics, Physics and Interdisciplinary Studies, Guangzhou Laboratory, Guangzhou, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Xiaozhu Liu
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Yu
- Department of Medical Imaging, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
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Yuan K, Zhao S, Ye B, Wang Q, Liu Y, Zhang P, Xie J, Chi H, Chen Y, Cheng C, Liu J. A novel T-cell exhaustion-related feature can accurately predict the prognosis of OC patients. Front Pharmacol 2023; 14:1192777. [PMID: 37284314 PMCID: PMC10239809 DOI: 10.3389/fphar.2023.1192777] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
The phenomenon of T Cell exhaustion (TEX) entails a progressive deterioration in the functionality of T cells within the immune system during prolonged conflicts with chronic infections or tumors. In the context of ovarian cancer immunotherapy, the development, and outcome of treatment are closely linked to T-cell exhaustion. Hence, gaining an in-depth understanding of the features of TEX within the immune microenvironment of ovarian cancer is of paramount importance for the management of OC patients. To this end, we leveraged single-cell RNA data from OC to perform clustering and identify T-cell marker genes utilizing the Unified Modal Approximation and Projection (UMAP) approach. Through GSVA and WGCNA in bulk RNA-seq data, we identified 185 TEX-related genes (TEXRGs). Subsequently, we transformed ten machine learning algorithms into 80 combinations and selected the most optimal one to construct TEX-related prognostic features (TEXRPS) based on the mean C-index of the three OC cohorts. In addition, we explored the disparities in clinicopathological features, mutational status, immune cell infiltration, and immunotherapy efficacy between the high-risk (HR) and low-risk (LR) groups. Upon the integration of clinicopathological features, TEXRPS displayed robust predictive power. Notably, patients in the LR group exhibited a superior prognosis, higher tumor mutational load (TMB), greater immune cell infiltration abundance, and enhanced sensitivity to immunotherapy. Lastly, we verified the differential expression of the model gene CD44 using qRT-PCR. In conclusion, our study offers a valuable tool to guide clinical management and targeted therapy of OC.
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Affiliation(s)
- Kemiao Yuan
- Department of Oncology, Traditional Chinese Medicine Hospital of Wuxi, Wuxi, China
| | - Songyun Zhao
- Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Bicheng Ye
- School of Clinical Medicine, Yangzhou Polytechnic College, Yangzhou, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yuan Liu
- Department of General Surgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Pengpeng Zhang
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaheng Xie
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chi
- Southwest Medical University, Luzhou, China
| | - Yu Chen
- Wuxi Maternal and Child Health Care Hospital, Wuxi, China
| | - Chao Cheng
- Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Luo Y, Ye Y, Chen Y, Zhang C, Sun Y, Wang C, Ou J. A degradome-based prognostic signature that correlates with immune infiltration and tumor mutation burden in breast cancer. Front Immunol 2023; 14:1140993. [PMID: 36993976 PMCID: PMC10040797 DOI: 10.3389/fimmu.2023.1140993] [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: 01/09/2023] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionFemale breast cancer is the most common malignancy worldwide, with a high disease burden. The degradome is the most abundant class of cellular enzymes that play an essential role in regulating cellular activity. Dysregulation of the degradome may disrupt cellular homeostasis and trigger carcinogenesis. Thus we attempted to understand the prognostic role of degradome in breast cancer by means of establishing a prognostic signature based on degradome-related genes (DRGs) and assessed its clinical utility in multiple dimensions.MethodsA total of 625 DRGs were obtained for analysis. Transcriptome data and clinical information of patients with breast cancer from TCGA-BRCA, METABRIC and GSE96058 were collected. NetworkAnalyst and cBioPortal were also utilized for analysis. LASSO regression analysis was employed to construct the degradome signature. Investigations of the degradome signature concerning clinical association, functional characterization, mutation landscape, immune infiltration, immune checkpoint expression and drug priority were orchestrated. Cell phenotype assays including colony formation, CCK8, transwell and wound healing were conducted in MCF-7 and MDA-MB-435S breast cancer cell lines, respectively.ResultsA 10-gene signature was developed and verified as an independent prognostic predictor combined with other clinicopathological parameters in breast cancer. The prognostic nomogram based on risk score (calculated based on the degradome signature) showed favourable capability in survival prediction and advantage in clinical benefit. High risk scores were associated with a higher degree of clinicopathological events (T4 stage and HER2-positive) and mutation frequency. Regulation of toll-like receptors and several cell cycle promoting activities were upregulated in the high-risk group. PIK3CA and TP53 mutations were dominant in the low- and high-risk groups, respectively. A significantly positive correlation was observed between the risk score and tumor mutation burden. The infiltration levels of immune cells and the expressions of immune checkpoints were significantly influenced by the risk score. Additionally, the degradome signature adequately predicted the survival of patients undergoing endocrinotherapy or radiotherapy. Patients in the low-risk group may achieve complete response after the first round of chemotherapy with cyclophosphamide and docetaxel, whereas patients in the high-risk group may benefit from 5-flfluorouracil. Several regulators of the PI3K/AKT/mTOR signaling pathway and the CDK family/PARP family were identified as potential molecular targets in the low- and high-risk groups, respectively. In vitro experiments further revealed that the knockdown of ABHD12 and USP41 significantly inhibit the proliferation, invasion and migration of breast cancer cells.ConclusionMultidimensional evaluation verified the clinical utility of the degradome signature in predicting prognosis, risk stratification and guiding treatment for patients with breast cancer.
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Affiliation(s)
- Yulou Luo
- Department of Breast Surgery, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Yinghui Ye
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Chenguang Zhang
- Department of Breast Surgery, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Yutian Sun
- Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chengwei Wang
- Cancer Research Institute of Xinjiang Uygur Autonomous Region, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Chengwei Wang, ; Jianghua Ou,
| | - Jianghua Ou
- Department of Breast Surgery, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Chengwei Wang, ; Jianghua Ou,
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Luo Y, Tian W, Lu X, Zhang C, Xie J, Deng X, Xie Y, Yang S, Du W, He R, Wei W. Prognosis stratification in breast cancer and characterization of immunosuppressive microenvironment through a pyrimidine metabolism-related signature. Front Immunol 2022; 13:1056680. [PMID: 36524129 PMCID: PMC9745154 DOI: 10.3389/fimmu.2022.1056680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Pyrimidine metabolism is a hallmark of cancer and will soon become an essential part of cancer therapy. In the tumor microenvironment, cells reprogram pyrimidine metabolism intrinsically and extracellularly, thereby promoting tumorigenesis. Metabolites in pyrimidine metabolism have a significant impact on promoting cancer advancement and modulating immune system responses. In preclinical studies and practical clinical applications, critical targets in pyrimidine metabolism are acted upon by drugs to exert promising therapeutic effects on tumors. However, the pyrimidine metabolism in breast cancer (BC) is still largely underexplored. In this study, 163 credible pyrimidine metabolism-related genes (PMGs) were retrieved, and their somatic mutations and expression levels were determined. In addition, by using The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases, 12 PMGs related to the overall survival (OS) were determined using the univariate Cox regression analysis. Subsequently, by performing the LASSO Cox hazards regression analysis in the 12 PMGs in TCGA-BRCA dataset, we developed a prognosis nomogram using eight OS-related PMGs and then verified the same in the METABRIC, GSE96058, GSE20685, GSE42568 and GSE86166 data. Moreover, we validated relationships between the pyrimidine metabolism index (PMI) and the survival probability of patients, essential clinical parameters, including the TNM stage and the PAM50 subtypes. Next, we verified the predictive capability of the optimum model, including the signature, the PAM50 subtype, and age, using ROC analysis and calibration curve, and compared it with other single clinical factors for the predictive power of benefit using decision curve analysis. Finally, we investigated the potential effects of pyrimidine metabolism on immune checkpoints, tumor-infiltrating immune cells, and cytokine levels and determined the potential implications of pyrimidine metabolism in BC immunotherapy. In conclusion, our findings suggest that pyrimidine metabolism has underlying prognostic significance in BC and can facilitate a new management approach for patients with different prognoses and more precise immunotherapy.
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Affiliation(s)
- Yongzhou Luo
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wenwen Tian
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiuqing Lu
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Chao Zhang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jindong Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xinpei Deng
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yi Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shuhui Yang
- Surgical and Transplant Intensive Care Unit of The Third Affiliated Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Du
- Department of Pathology, The First People’s Hospital of Changde City, Changde, Hunan, China,*Correspondence: Weidong Wei, ; Rongfang He, ; Wei Du,
| | - Rongfang He
- Department of Pathology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China,*Correspondence: Weidong Wei, ; Rongfang He, ; Wei Du,
| | - Weidong Wei
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,*Correspondence: Weidong Wei, ; Rongfang He, ; Wei Du,
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Wang Y, Xu H, Han Y, Wu Y, Wang J. Comparative Efficacy of Tyrosine Kinase Inhibitors and Antibody–Drug Conjugates in HER2-Positive Metastatic Breast Cancer Patients with Brain Metastases: A Systematic Review and Network Meta-Analysis. Cancers (Basel) 2022; 14:cancers14143372. [PMID: 35884431 PMCID: PMC9321046 DOI: 10.3390/cancers14143372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Comparisons between the efficacy of tyrosine kinase inhibitors (TKIs) and antibody–drug conjugates (ADCs) in treating HER2-positive breast cancer brain metastasis (BCBM) patients have not previously been conducted. We performed a systematic review and Bayesian-based network meta-analysis to pool the estimates of progression-free survival, overall survival, and incidence of central nervous system (CNS) disease progression. The current study indicated that both T-DXd and T-DM1 presented better efficacy than TKIs regarding survival outcomes. Treatments containing neratinib or T-DM1 tended to rank the best in reducing the recurrent rate of CNS. Our study provides more evidence for the clinical decision making for patients with HER2-positive BCBM. More high-quality studies with standardized entry criteria and comparable CNS-related endpoints are warranted in the future. Abstract HER2-positive breast cancer brain metastasis (BCBM) is an important clinical problem. A systematic review and network meta-analysis were conducted to compare the efficacy of tyrosine kinase inhibitors (TKIs) and antibody–drug conjugates (ADCs), two categories of emerging agents in this field. We implemented a comprehensive literature search of PubMed, Embase, the Cochrane Library, ClinicalTrials.gov, and abstracts of oncology conferences. A network meta-analysis following Bayesian approaches was performed. Pooled hazard ratios (HRs) and odds ratios (ORs) with credible intervals (CrIs) were calculated to estimate progression-free survival (PFS), overall survival (OS), and the incidence of central nervous system (CNS) disease progression. Sixteen studies were included. Pairwise comparisons of PFS showed salient divergency between T-DXd and the physician’s choice of treatment (HR 0.17; 95% CrI 0.03–0.82) or afatinib (HR 0.14; 95% CrI 0.02–1.00). T-DXd and T-DM1 ranked first regarding PFS and OS, respectively, followed by TKI-containing regimens. The incidence of CNS disease progression was analyzed separately according to baseline BCBM status, among which neratinib-containing regimens were most likely to rank the best. In conclusion, ADCs including T-DXd and T-DM1 showed better efficacy than TKIs in the survival outcomes for HER2-positive BCBM patients. Treatments based on neratinib or T-DM1 revealed favorable results in reducing the recurrent rate of CNS.
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