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Zhang S, Wang Y, Zhang X, Wang M, Wu H, Tao Y, Fan W, Liu L, Wang B, Gao W. ATP6AP1 as a potential prognostic biomarker in CRC by comprehensive analysis and verification. Sci Rep 2024; 14:4018. [PMID: 38369634 PMCID: PMC10874971 DOI: 10.1038/s41598-024-54437-7] [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: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
The role of ATP6AP1 in colorectal cancer (CRC) remains elusive despite its observed upregulation in pan-cancer. Therefore, the current study aimed to assess the clinical significance of ATP6AP1 and its relationship with the immune infiltration in CRC. Transcriptome data of CRC were obtained from The Cancer Genome Atlas (TCGA) database and analyzed using the combination of R packages and tumor-related databases, including TIMER2, TISIDB, cBioPortal, and MethSurv. The tissue arrays and immunohistochemical staining were performed to verify the expression and clinical characteristics of ATP6AP1. The results revealed that ATP6AP1 expression was significantly elevated in CRC and associated with poor clinicopathological characteristics and prognosis. Furthermore, the analysis demonstrated ATP6AP1 expression was correlated with the infiltration of immune cells and cancer-associated fibroblasts in the microenvironment of CRC. Moreover, ATP6AP1 was found to be linked to various immune checkpoints and chemokines, with enrichment of cytoplasmic vesicle lumen, endopeptidase regulator activity, and endopeptidase inhibitor activity observed in the high ATP6AP1 expressional group. In conclusion, the findings of this study suggest that ATP6AP1 upregulation may serve as a biomarker for poor diagnosis in CRC and offer a potential target for immunotherapy in CRC.
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Affiliation(s)
- Shijie Zhang
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, China
| | - Yan Wang
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, China
| | - Xiaodong Zhang
- Department of Cardiology, The Affiliated Hospital of Jiangnan University, No.1000, He Feng Road, Wuxi, 214122, Jiangsu Province, China
| | - Min Wang
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Hao Wu
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Yuwen Tao
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Wentao Fan
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Li Liu
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Bangting Wang
- Digestive Endoscopy Department, The First Affiliated Hospital with Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China.
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, China.
| | - Wenqing Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
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Xiong YM, Zhou F, Zhou JW, Liu F, Zhou SQ, Li B, Liu ZJ, Qin Y. Aberrant Expressions of PSMD14 in Tumor Tissue are the Potential Prognostic Biomarkers for Hepatocellular Carcinoma after Curative Resection. Curr Genomics 2023; 24:368-384. [PMID: 38327651 PMCID: PMC10845065 DOI: 10.2174/0113892029277262231108105441] [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: 08/14/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) has a high mortality rate, with curative resection being the primary treatment. However, HCC patients have a large possibility of recurrence within 5 years after curative resection. Methods Thus, identifying biomarkers to predict recurrence is crucial. In our study, we analyzed data from CCLE, GEO, and TCGA, identifying eight oncogenes associated with HCC. Subsequently, the expression of 8 genes was tested in 5 cases of tumor tissues and the adjacent non-tumor tissues. Then ATP6AP1, PSMD14 and HSP90AB1 were selected to verify the expression in 63 cases of tumor tissues and the adjacent non-tumor tissues. The results showed that ATP6AP1, PSMD14, HSP90AB1 were generally highly expressed in tumor tissues. A five-year follow-up of the 63 clinical cases, combined with Kaplan-Meier Plotter's relapse-free survival (RFS) analysis, found a significant correlation between PSMD14 expression and recurrence in HCC patients. Subsequently, we analyzed the PSMD14 mutations and found that the PSMD14 gene mutations can lead to a shorter disease-free survival time for HCC patients. Results The results of enrichment analysis indicated that the differentially expressed genes related to PSMD14 are mainly enriched in the signal release pathway. Conclusion In conclusion, our research showed that PSMD14 might be related to recurrence in HCC patients, and the expression of PSMD14 in tumor tissue might be a potential prognostic biomarker after tumor resection in HCC patients.
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Affiliation(s)
- Yi-Mei Xiong
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Fang Zhou
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Jia-Wen Zhou
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Fei Liu
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Si-Qi Zhou
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Bo Li
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Zhong-Jian Liu
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Yang Qin
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
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Su H, Chen Y, Lin F, Li W, Gu X, Zeng W, Liu D, Li M, Zhong S, Chen Q, Chen Q. Establishment of a lysosome-related prognostic signature in breast cancer to predict immune infiltration and therapy response. Front Oncol 2023; 13:1325452. [PMID: 38162504 PMCID: PMC10757638 DOI: 10.3389/fonc.2023.1325452] [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: 10/21/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Background Lysosomes are instrumental in intracellular degradation and recycling, with their functional alterations holding significance in tumor growth. Nevertheless, the precise role of lysosome-related genes (LRGs) in breast cancer (BC) remains elucidated. This study aimed to establish a prognostic model for BC based on LRGs. Methods Employing The Cancer Genome Atlas (TCGA) BC cohort as a training dataset, this study identified differentially expressed lysosome-related genes (DLRGs) through intersecting LRGs with differential expression genes (DEGs) between tumor and normal samples. A prognostic model of BC was subsequently developed using Cox regression analysis and validated within two Gene Expression Omnibus (GEO) external validation sets. Further analyses explored functional pathways, the immune microenvironment, immunotherapeutic responses, and sensitivity to chemotherapeutic drugs in different risk groups. Additionally, the mRNA and protein expression levels of genes within the risk model were examined by utilizing the Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases. Clinical tissue specimens obtained from patients were gathered to validate the expression of the model genes via Real-Time Polymerase Chain Reaction (RT-PCR). Results We developed a risk model of BC based on five specific genes (ATP6AP1, SLC7A5, EPDR1, SDC1, and PIGR). The model was validated for overall survival (OS) in two GEO validation sets (p=0.00034 for GSE20685 and p=0.0095 for GSE58812). In addition, the nomogram incorporating clinical factors showed better predictive performance. Compared to the low-risk group, the high-risk group had a higher level of certain immune cell infiltration, including regulatory T cells (Tregs) and type 2 T helper cells (Th2). The high-risk patients appeared to respond less well to general immunotherapy and chemotherapeutic drugs, according to the Tumor Immune Dysfunction and Exclusion (TIDE), Immunophenotype Score (IPS), and drug sensitivity scores. The RT-PCR results validated the expression trends of some prognostic-related genes in agreement with the previous differential expression analysis. Conclusion Our innovative lysosome-associated signature can predict the prognosis for BC patients, offering insights for guiding subsequent immunotherapeutic and chemotherapeutic interventions. Furthermore, it has the potential to provide a scientific foundation for identifying prospective therapeutic targets.
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Affiliation(s)
- Hairong Su
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Chen
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengye Lin
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wanhua Li
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiangyu Gu
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weijie Zeng
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Breast, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dan Liu
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Breast, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Man Li
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaowen Zhong
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Breast, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qianjun Chen
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Breast, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qubo Chen
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Tan YW, Teo FMS, Ler SG, Alli-Shaik A, Nyo M, Chong CY, Tan NWH, Wang RYL, Gunaratne J, Chu JJH. Potential relevance of salivary legumain for the clinical diagnostic of hand, foot, and mouth disease. J Med Virol 2023; 95:e29243. [PMID: 38009231 DOI: 10.1002/jmv.29243] [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: 06/21/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
The fight against hand, foot, and mouth disease (HFMD) remains an arduous challenge without existing point-of-care (POC) diagnostic platforms for accurate diagnosis and prompt case quarantine. Hence, the purpose of this salivary biomarker discovery study is to set the fundamentals for the realization of POC diagnostics for HFMD. Whole salivary proteome profiling was performed on the saliva obtained from children with HFMD and healthy children, using a reductive dimethylation chemical labeling method coupled with high-resolution mass spectrometry-based quantitative proteomics technology. We identified 19 upregulated (fold change = 1.5-5.8) and 51 downregulated proteins (fold change = 0.1-0.6) in the saliva samples of HFMD patients in comparison to that of healthy volunteers. Four upregulated protein candidates were selected for dot blot-based validation assay, based on novelty as biomarkers and exclusions in oral diseases and cancers. Salivary legumain was validated in the Singapore (n = 43 healthy, 28 HFMD cases) and Taiwan (n = 60 healthy, 47 HFMD cases) cohorts with an area under the receiver operating characteristic curve of 0.7583 and 0.8028, respectively. This study demonstrates the feasibility of a broad-spectrum HFMD POC diagnostic test based on legumain, a virus-specific host systemic signature, in saliva.
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Affiliation(s)
- Yong Wah Tan
- Collaborative and Translation Unit for Hand, Foot and Mouth Disease (HFMD), Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fiona Mei Shan Teo
- Collaborative and Translation Unit for Hand, Foot and Mouth Disease (HFMD), Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siok Ghee Ler
- Translational Biomedical Proteomics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Asfa Alli-Shaik
- Translational Biomedical Proteomics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Min Nyo
- Infectious Disease Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chia Yin Chong
- Infectious Disease Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Natalie Woon Hui Tan
- Infectious Disease Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Robert Y L Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Kidney Research Center and Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial and Children's Hospital, Linkou, Taiwan
| | - Jayantha Gunaratne
- Translational Biomedical Proteomics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Collaborative and Translation Unit for Hand, Foot and Mouth Disease (HFMD), Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Infectious Disease Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Li M, Jiang F, Xue L, Peng C, Shi Z, Zhang Z, Li J, Pan Y, Wang X, Feng C, Qiao D, Chen Z, Luo Q, Chen X. Recent Progress in Biosensors for Detection of Tumor Biomarkers. Molecules 2022; 27:7327. [PMID: 36364157 PMCID: PMC9658374 DOI: 10.3390/molecules27217327] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 10/07/2023] Open
Abstract
Cancer is a leading cause of death worldwide, with an increasing mortality rate over the past years. The early detection of cancer contributes to early diagnosis and subsequent treatment. How to detect early cancer has become one of the hot research directions of cancer. Tumor biomarkers, biochemical parameters for reflecting cancer occurrence and progression have caused much attention in cancer early detection. Due to high sensitivity, convenience and low cost, biosensors have been largely developed to detect tumor biomarkers. This review describes the application of various biosensors in detecting tumor markers. Firstly, several typical tumor makers, such as neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), prostate-specific antigen (PSA), squamous cell carcinoma antigen (SCCA), carbohydrate, antigen19-9 (CA19-9) and tumor suppressor p53 (TP53), which may be helpful for early cancer detection in the clinic, are briefly described. Then, various biosensors, mainly focusing on electrochemical biosensors, optical biosensors, photoelectrochemical biosensors, piezoelectric biosensors and aptamer sensors, are discussed. Specifically, the operation principles of biosensors, nanomaterials used in biosensors and the application of biosensors in tumor marker detection have been comprehensively reviewed and provided. Lastly, the challenges and prospects for developing effective biosensors for early cancer diagnosis are discussed.
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Affiliation(s)
- Mantong Li
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Feng Jiang
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Liangyi Xue
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Cheng Peng
- Guangzhou Institute of Food Inspection, Guangzhou 510080, China
| | - Zhengzheng Shi
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zheng Zhang
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jia Li
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yupeng Pan
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xinya Wang
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Chunqiong Feng
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Dongfang Qiao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhenzhong Chen
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qizhi Luo
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xuncai Chen
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
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Mei Y, Zhao L, Jiang M, Yang F, Zhang X, Jia Y, Zhou N. Characterization of glucose metabolism in breast cancer to guide clinical therapy. Front Surg 2022; 9:973410. [PMID: 36277284 PMCID: PMC9580338 DOI: 10.3389/fsurg.2022.973410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background Breast cancer (BRCA) ranks as a leading cause of cancer death in women worldwide. Glucose metabolism is a noticeable characteristic of the occurrence of malignant tumors. In this study, we aimed to construct a novel glycometabolism-related gene (GRG) signature to predict overall survival (OS), immune infiltration and therapeutic response in BRCA patients. Materials and methods The mRNA sequencing and corresponding clinical data of BRCA patients were obtained from public cohorts. Lasso regression was applied to establish a GRG signature. The immune infiltration was evaluated with the ESTIMATE and CIBERSORT algorithms. The drug sensitivity was estimated using the value of IC50, and further forecasted the therapeutic response of each patient. The candidate target was selected in Cytoscape. A nomogram was constructed via the R package of “rms”. Results We constructed a six-GRG signature based on CACNA1H, CHPF, IRS2, NT5E, SDC1 and ATP6AP1, and the high-risk patients were correlated with poorer OS (P = 2.515 × 10−7). M2 macrophage infiltration was considerably superior in high-risk patients, and CD8+ T cell infiltration was significantly higher in low-risk patients. Additionally, the high-risk group was more sensitive to Lapatinib. Fortunately, SDC1 was recognized as candidate target and patients had a better OS in the low-SDC1 group. A nomogram integrating the GRG signature was developed, and calibration curves were consistent between the actual and predicted OS. Conclusions We identified a novel GRG signature complementing the present understanding of the targeted therapy and immune biomarker in breast cancer. The GRGs may provide fresh insights for individualized management of BRCA patients.
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Affiliation(s)
- Yingying Mei
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lantao Zhao
- Department of Anesthesiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Man Jiang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fangfang Yang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xiaochun Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yizhen Jia
- Core Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Correspondence: Na Zhou Yizhen Jia
| | - Na Zhou
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Correspondence: Na Zhou Yizhen Jia
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Tian Y, Gao M, Huang L, Zhou H, Wang J. ATP6AP1 is a potential prognostic biomarker and is associated with iron metabolism in breast cancer. Front Genet 2022; 13:958290. [PMID: 36147483 PMCID: PMC9486317 DOI: 10.3389/fgene.2022.958290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer occurrence and progression may be facilitated by aberrant expression of ATPase H+ transporting accessory protein 1 (ATP6AP1). However, the clinical relevance of ATP6AP1 in breast cancer remains unclear. In this study, we investigated the association between ATP6AP1 and breast cancer. Data collected from patients with breast cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were used in this study. To determine the relationship between ATP6AP1 and breast cancer survival rates, Kaplan-Meier analysis was used. To determine the prognostic value of ATP6AP1, a receiver operating characteristic (ROC) curve was constructed. To identify the major pathways involving ATP6AP1, we performed functional enrichment analysis using gene set enrichment analysis (GSEA). We analyzed the association between ATP6AP1 expression and tumor immunity using the ESTIMATE algorithm and single-sample GSEA (ssGSEA). A nomogram based on a Cox regression analysis was constructed to predict the impact of ATP6AP1 on prognosis. ATP6AP1 expression was significantly upregulated in breast cancer tissues. Moreover, patients with elevated ATP6AP1 expression had shorter total survival rates than those with lower expression levels (p = 0.032). The area under the receiver operating characteristic curve for ATP6AP1 was 0.939. Gene set enrichment analysis revealed that reaction iron uptake and transport, proteasome degradation, glutathione metabolism, and pyruvate metabolism were enriched in the ATP6AP1 high expression phenotype. The relationship between immune infiltration cells and ATP6AP1 expression, including macrophages, B cells, dendritic cells, cytotoxic cells, NK cells, and T cells, was found to be negative, suggesting that ATP6AP1 overexpression results in immunosuppression. Based on the Cox regression analyses, the calibration plot of the nomogram demonstrated effective performance in predicting breast cancer patients. ATP6AP1 may facilitate breast cancer progression by inhibiting antitumor immunity and promoting iron metabolism and may be a biomarker for breast cancer prognosis.
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Affiliation(s)
- Ye Tian
- Department of Thyroid and Breast Surgery, Wuhan No, 1 Hospital, Wuhan, China
| | - Ming Gao
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Huang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hu Zhou
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Wang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Juan Wang,
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Xu J, Qin S, Yi Y, Gao H, Liu X, Ma F, Guan M. Delving into the Heterogeneity of Different Breast Cancer Subtypes and the Prognostic Models Utilizing scRNA-Seq and Bulk RNA-Seq. Int J Mol Sci 2022; 23:ijms23179936. [PMID: 36077333 PMCID: PMC9456551 DOI: 10.3390/ijms23179936] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Breast cancer (BC) is the most common malignancy in women with high heterogeneity. The heterogeneity of cancer cells from different BC subtypes has not been thoroughly characterized and there is still no valid biomarker for predicting the prognosis of BC patients in clinical practice. Methods: Cancer cells were identified by calculating single cell copy number variation using the inferCNV algorithm. SCENIC was utilized to infer gene regulatory networks. CellPhoneDB software was used to analyze the intercellular communications in different cell types. Survival analysis, univariate Cox, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analysis were used to construct subtype specific prognostic models. Results: Triple-negative breast cancer (TNBC) has a higher proportion of cancer cells than subtypes of HER2+ BC and luminal BC, and the specifically upregulated genes of the TNBC subtype are associated with antioxidant and chemical stress resistance. Key transcription factors (TFs) of tumor cells for three subtypes varied, and most of the TF-target genes are specifically upregulated in corresponding BC subtypes. The intercellular communications mediated by different receptor–ligand pairs lead to an inflammatory response with different degrees in the three BC subtypes. We establish a prognostic model containing 10 genes (risk genes: ATP6AP1, RNF139, BASP1, ESR1 and TSKU; protective genes: RPL31, PAK1, STARD10, TFPI2 and SIAH2) for luminal BC, seven genes (risk genes: ACTR6 and C2orf76; protective genes: DIO2, DCXR, NDUFA8, SULT1A2 and AQP3) for HER2+ BC, and seven genes (risk genes: HPGD, CDC42 and PGK1; protective genes: SMYD3, LMO4, FABP7 and PRKRA) for TNBC. Three prognostic models can distinguish high-risk patients from low-risk patients and accurately predict patient prognosis. Conclusions: Comparative analysis of the three BC subtypes based on cancer cell heterogeneity in this study will be of great clinical significance for the diagnosis, prognosis and targeted therapy for BC patients.
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Gokhale M, Mohanty SK, Ojha A. A stacked autoencoder based gene selection and cancer classification framework. Biomed Signal Process Control 2022. [DOI: 10.1016/j.bspc.2022.103999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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