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Wang Y, Wang DY, Bu KN, Gao JD, Zhang BL. Prognosis prediction and risk stratification of breast cancer patients based on a mitochondria-related gene signature. Sci Rep 2024; 14:2859. [PMID: 38310106 PMCID: PMC10838276 DOI: 10.1038/s41598-024-52981-w] [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: 04/02/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
As the malignancy with the highest global incidence, breast cancer represents a significant threat to women's health. Recent advances have shed light on the importance of mitochondrial function in cancer, particularly in metabolic reprogramming within tumors. Recognizing this, we developed a novel risk signature based on mitochondrial-related genes to improve prognosis prediction and risk stratification in breast cancer patients. In this study, transcriptome data and clinical features of breast cancer samples were extracted from two sources: the TCGA, serving as the training set, and the METABRIC, used as the independent validation set. We developed the signature using LASSO-Cox regression and assessed its prognostic efficacy via ROC curves. Furthermore, the signature was integrated with clinical features to create a Nomogram model, whose accuracy was validated through clinical calibration curves and decision curve analysis. To further elucidate prognostic variations between high and low-risk groups, we conducted functional enrichment and immune infiltration analyses. Additionally, the study encompassed a comparison of mutation landscapes and drug sensitivity, providing a comprehensive understanding of the differing characteristics in these groups. Conclusively, we established a risk signature comprising 8 mitochondrial-related genes-ACSL1, ALDH2, MTHFD2, MRPL13, TP53AIP1, SLC1A1, ME3, and BCL2A1. This signature was identified as an independent risk predictor for breast cancer patient survival, exhibiting a significant high hazard ratio (HR = 3.028, 95%CI 2.038-4.499, P < 0.001). Patients in the low-risk group showed a more favorable prognosis, with enhanced immune infiltration, distinct mutation landscapes, and greater sensitivity to anti-tumor drugs. In contrast, the high-risk group exhibited an adverse trend in these aspects. This risk signature represents a novel and effective prognostic indicator, suggesting valuable insights for patient stratification in breast cancer.
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Affiliation(s)
- Yang Wang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ding-Yuan Wang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ke-Na Bu
- Xingyuan Hospital of Yulin City, Yulin City, 719051, Shanxi Province, China
| | - Ji-Dong Gao
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union College, Shenzhen, 518116, China.
| | - Bai-Lin Zhang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Liang Y, He S, Tan Y, Liu Q, Zhao F, Liu T, Huang C, Lu X, Zheng S. In silico analyses of pan-squamous cell carcinoma unveiled the immunological implications of MRPL13, which had previously been under-recognized. Heliyon 2024; 10:e23582. [PMID: 38187248 PMCID: PMC10770563 DOI: 10.1016/j.heliyon.2023.e23582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
The involvement of the mitochondrial ribosomal protein 13 (MRPL13) gene in the development of adenocarcinoma has been previously reported. However, the clinicopathological significance of MRPL13 in squamous cell carcinoma (SCC) remains poorly understood. To gain insight into the clinicopathological and immunological implications of MRPL13 expression in SCC, we conducted a bioinformatic analysis utilizing various available databases, including TIMER 2.0, Xiantao academic tool and TISIDB, attempting to evaluate the abnormal expression, prognosis and immunological correlation of MRPL13 in the pan-SCC setting. Subsequently, we conducted experimental verification using an esophageal squamous cell carcinoma (ESCC) tissue array subjected to multiplexed immunofluorescent (mIF) staining. The ESCC tissue array we used consists of 93 dots of ESCC and 86 dots of matched adjacent normal tissues (ANT). Data from in silico analyses showed that MRPL13 mRNA is significantly up-regulated and correlated with infiltration of CD8+ T cells in pan-SCC. However, in silico analyses did not support the prognostic role of MRPL13 in SCC. Consistently, data from the ESCC tissue array showed that MRPL13 was remarkably elevated in ESCC tissues relative to ANT in stroma, which was controlled by pan-cytokeratin (pan-CK) staining. In the epithelia, no significant difference was identified between ESCC and ANT. Furthermore, MRPL13 expression markedly correlated with the infiltration of CD8+ T cells in the stromal region but not in the epithelial region. Prognostically, no significant association was observed between MRPL13 expression and overall survival, regardless of epithelial or stromal section. Through these pan-SCC analyses, we have expanded the understanding of MRPL13 previously reported, in particular, underscoring the immunological involvement of MRPL13 in the tumor microenvironment of SCC that has been under-recognized before, suggesting that MRPL13 may regulate the infiltration of CD8+ T cells into the SCC microenvironment.
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Affiliation(s)
- Yan Liang
- Department of Pathology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830017, China
| | - Shuo He
- Department of Pathology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830017, China
| | - Yiyi Tan
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Feng Zhao
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Tao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Conggai Huang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Xiaomei Lu
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Shutao Zheng
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
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Ma X, Deng Z, Li Z, Ma T, Li G, Zhang C, Zhang W, Chang J. Leveraging a disulfidptosis/ferroptosis-based signature to predict the prognosis of lung adenocarcinoma. Cancer Cell Int 2023; 23:267. [PMID: 37946181 PMCID: PMC10634118 DOI: 10.1186/s12935-023-03125-z] [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: 07/20/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Disulfidptosis and Ferroptosis are two novel forms of cell death. Although their mechanisms differ, research has shown that there is a relationship between the two. Investigating the connection between these two forms of cell death can further deepen our understanding of the development and progression of cancer, and provide better prediction models for accurate prognosis. METHODS In this study, RNA sequencing (RNA-seq) data, clinical data, single nucleotide polymorphism (SNP) data, and single-cell sequencing data were obtained from public databases. We used weighted gene co-expression network analysis (WGCNA) and unsupervised clustering to identify new Disulfidptosis/Ferroptosis-Related Genes (DFRG), and constructed a LASSO COX prognosis model that was externally validated. To further explore this novel signature, pathway and function analysis was performed, and differences in gene mutation frequency between high- and low-risk groups were studied. Importantly, we also conducted research on immune checkpoint, immune cell infiltration levels and immune resistance indicators, in addition to analyzing real clinical immunotherapy data. RESULTS We have identified four optimal disulfidptosis/ferroptosis-related genes (ODFRGs) that are differentially expressed and associated with the prognosis of Lung Adenocarcinoma (LUAD). These genes include GMPR, MCFD2, MRPL13, and SALL2. Based on these ODFRGs, we constructed a robust prognostic model in this study, and the high-risk group showed significantly lower overall survival (OS) compared to the low-risk group. Furthermore, this model can also predict the immunotherapy outcomes of LUAD patients to some extent.
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Affiliation(s)
- Xiaoqing Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zilin Deng
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zhen Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Ting Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Guiqing Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Cuijia Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Wentao Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
| | - Jin Chang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
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王 炼, 夏 勇, 张 震, 刘 馨, 施 金, 王 月, 李 静, 张 小, 耿 志, 宋 雪, 左 芦. [High expression of MRPL13 promotes cell cycle progression and proliferation of gastric cancer cells by inhibiting p53 signaling to affect long-term prognosis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:1558-1566. [PMID: 37814870 PMCID: PMC10563107 DOI: 10.12122/j.issn.1673-4254.2023.09.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVE To determine the expression of mitochondrial ribosomal protein L13 (MRPL13) in gastric cancer and its impact on long-term prognosis and explore the possible mechanism. METHODS We analyzed MRPL13 expression level in gastric cancer and its association with the patients' prognosis based on the public cancer database the data of 100 gastric cancer patients undergoing radical gastrectomy in our hospital from January, 2014 to October, 2017. We further assessed the effects of MRPL13 overexpression and knockdown on proliferation and cell cycle of gastric cancer MGC-803 and SGC-7901 cells in vitro and on subcutaneous xenograft growth in nude mice. RESULTS Both bioinformatic analysis and the patients' data demonstrated that the expression level of MRPL13 was significantly higher in gastric cancer than in adjacent tissues (P<0.05) and positively correlated with peripheral blood Ki67, CEA and CA19-9 levels (P<0.05). High expression of MRPL13 was an independent risk factor affecting the 5-year survival rate of gastric cancer patients (HR: 3.284; 95% CI: 1.537-7.016). Gene set enrichment analysis suggested that MRPL13 was involved in cell cycle and p53 signaling. In cultured gastric cancer cells, MRPL13 overexpression significantly promoted cell proliferation, G1/S phase transition and the expressions of cyclin D1 and CDK6 (P<0.05), and MRPL13 knockdown produced the opposite effects (P<0.05). MRPL13 overexpression significantly promoted gastric cancer cell xenograft growth (P<0.05), and MRPL13 knockdown obviously inhibited tumor growth in nude mice (P<0.05). In both cultured gastric cancer cells and the xenografts in nude mice, MRPL13 overexpression significantly decreased while MRPL13 knockdown enhanced the expressions of p53 and p21 (P<0.05). CONCLUSION MRPL13 is highly expressed in gastric cancer and affects the long- term prognosis of the patients possibly by inhibiting p53 signaling to promote cancer cell proliferation and cell cycle progression.
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Affiliation(s)
- 炼 王
- 蚌埠医学院第一附属医院胃肠外科,安徽 蚌埠 233004Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
- 蚌埠医学院,安徽 蚌埠 233030Bengbu Medical College, Bengbu 233030, China
| | - 勇生 夏
- 蚌埠医学院第一附属医院胃肠外科,安徽 蚌埠 233004Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
- 蚌埠医学院,安徽 蚌埠 233030Bengbu Medical College, Bengbu 233030, China
| | - 震 张
- 蚌埠医学院第一附属医院胃肠外科,安徽 蚌埠 233004Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
- 蚌埠医学院,安徽 蚌埠 233030Bengbu Medical College, Bengbu 233030, China
| | - 馨悦 刘
- 蚌埠医学院,安徽 蚌埠 233030Bengbu Medical College, Bengbu 233030, China
- 组织移植安徽省重点实验室,安徽 蚌埠 233030Anhui Provincial Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233030, China
| | - 金冉 施
- 蚌埠医学院,安徽 蚌埠 233030Bengbu Medical College, Bengbu 233030, China
- 组织移植安徽省重点实验室,安徽 蚌埠 233030Anhui Provincial Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233030, China
| | - 月月 王
- 蚌埠医学院第一附属医院检验科,安徽 蚌埠 233004Clinical Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - 静 李
- 蚌埠医学院第一附属医院检验科,安徽 蚌埠 233004Clinical Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - 小凤 张
- 蚌埠医学院第一附属医院中心实验室,安徽 蚌埠 233004Central Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - 志军 耿
- 蚌埠医学院第一附属医院中心实验室,安徽 蚌埠 233004Central Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - 雪 宋
- 蚌埠医学院第一附属医院中心实验室,安徽 蚌埠 233004Central Laboratory, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - 芦根 左
- 蚌埠医学院第一附属医院胃肠外科,安徽 蚌埠 233004Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
- 炎症相关性疾病基础与转化研究安徽省重点实验室,安徽 蚌埠 233030Anhui Province Key Laboratory of Basic and Translational Research of Inflammation-related Diseases, Bengbu 233030, China
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Li XY, He XY, Zhao H, Qi L, Lu JJ. Identification of a novel therapeutic target for lung cancer: Mitochondrial ribosome protein L9. Pathol Res Pract 2023; 248:154625. [PMID: 37343379 DOI: 10.1016/j.prp.2023.154625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Lung cancer has a high fatality rate and incidence rate. At present, the initial and progress mechanism of lung cancer has not been completely elucidated and new therapeutic targets still need to be developed. In this study, the screening process was based on lung cancer expression profile data and survival analysis. Mitochondrial ribosome protein L9 (MRPL9) was upregulated in lung cancer tissues and related to the poor overall survival rate and recurrence-free survival rate of lung cancer patients. Knockdown of MRPL9 inhibited the proliferation, sphere-formation, and migration ability of lung cancer cells. MRPL9 was associated with the c-MYC signaling pathway, and lung cancer patients with high expression of both MRPL9 and MYC had a poor prognosis. Furthermore, c-MYC was associated with the epithelial-mesenchymal transition (EMT) regulatory protein zinc finger E-box binding homeobox 1 (ZEB1) by bioinformatics analysis. The relationship between ZEB1 and c-MYC was further confirmed by interfering with c-MYC expression. MRPL9 is a potential therapeutic target for lung cancer and exerts its biological functions by affecting the transcription factor c-MYC thereby regulating the EMT regulator ZEB1.
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Affiliation(s)
- Xin-Yuan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin-Yu He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hong Zhao
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Lu Qi
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, University of Macau, Macao, China.
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Park SW, Kang J, Kim HS, Yoon S, Kim BS, Lim C, Lee D, Kim YH. Predicting prognosis through the discovery of specific biomarkers according to colorectal cancer lymph node metastasis. Am J Cancer Res 2023; 13:3221-3233. [PMID: 37559990 PMCID: PMC10408476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/08/2023] [Indexed: 08/11/2023] Open
Abstract
Colorectal cancer (CRC) is a prevalent cancer worldwide, ranking as the third most common cancer and the second leading cause of cancer-related deaths. The presence or absence of lymph node metastases is one of the representative markers for predicting CRC prognosis, but often yields heterogeneous results. In this study, we conducted an integrative molecular analysis of CRC using publicly available data from The Cancer Genome Atlas database and NCBI's Gene Expression Omnibus. Through our analysis, we identified 372 upregulated genes that were differentially expressed in CRC patients. Additionally, Kyoto Encyclopedia of Genes and Genomes analysis revealed five significant pathways, including Hippo, FC-gamma, and forkhead box O signaling pathways, which are known to be associated with cancer. Survival analysis of 28 genes involved in these pathways led to the identification of 13 genes with prognostic significance (P < 0.05). To validate our findings, logistic regression models were generated and tested in multiple cohorts, demonstrating significant accuracy. Moreover, we identified six genes (BNIP3, CD63, RDX, RGCC, WASF1, and WASF3) whose combination predicted the best prognosis based on survival analysis. This predictive model holds promise as a potential biomarker for prognosis, survival, and treatment efficacy. In conclusion, our study provides valuable insights into the molecular characteristics of CRC and identifies prognostic biomarkers. The combination of differentially expressed genes and their involvement in cancer-related pathways enhances our understanding of CRC pathogenesis and opens avenues for personalized treatment approaches and improved patient outcomes.
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Affiliation(s)
- Sung Won Park
- Department of Convergence Medical Science, School of Medicine, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Junho Kang
- Medical Research Institute, Pusan National UniversityBusan 46241, Republic of Korea
| | - Hyung-Sik Kim
- Department of Life Science in Dentistry, School of Dentistry, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Sik Yoon
- Department of Anatomy, School of Medicine, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Byoung Soo Kim
- School of Biomedical Convergence Engineering, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Chaeseong Lim
- Occupational and Environmental Medicine, Kosin University Gospel HospitalBusan 46241, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medical Science, School of Medicine, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Yun Hak Kim
- Department of Biomedical Informatics, School of Medicine, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
- Department of Anatomy, School of Medicine, Pusan National UniversityYangsan-si, Gyeongsangnam-do 50612, Republic of Korea
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Dong T, Lu S, Li X, Yang J, Liu Y. Genetic association between ankylosing spondylitis and major depressive disorders: Shared pathways, protein networks and the key gene. Medicine (Baltimore) 2023; 102:e33985. [PMID: 37327287 PMCID: PMC10270550 DOI: 10.1097/md.0000000000033985] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023] Open
Abstract
The prevalence of ankylosing spondylitis (AS) and major depressive disorders (MDD) becomes increasingly pronounced, exerting a significant impact on the life quality of contemporary people. Although there is mounting evidence of a link between AS and major depression disorders, the specific interactions between the two have not been thoroughly investigated. To this end, this study aimed to check whether the gene expression profiles of patients with AS and major depression disorders overlapped, and whether there were any functional links between the identified genes via protein-protein interactions. Herein, the relationship between the 4 datasets (GSE73754, GSE98793, GSE25101, and GSE54564) chosen from the Gene Expression Omnibus for evaluation and validation was investigated using gene characterization and functional enrichment. Then, following Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes that explore the biological processes of common genes and demonstrate the interrelationships between common genes, hub genes were obtained using the STRING database and the application cytoHubba plugin of Cytoscape software. The correlation between the gene and 22 types of immuno-infiltrating cells was explored, and the key gene as well as the diagnostic efficiency of the key gene was obtained through verification. A total of 204 shared genes were discovered, the majority of which were functionally enriched in Ribosome, Coronavirus disease COVID19, Starch and sucrose metabolism, and Galactose metabolism. Then, efforts were made to go through STRING. Immuno-infiltration studies revealed that Neutrophils, T cells CD8, T cells CD4 naive, T cells CD4 memory resting, T cells CD4 memory activated, and T cells regulatory were associated with the pathogenesis of AS and MDD. Additionally, the receiver operating characteristic curve revealed that the key gene MRPL13 played diagnostic roles in AS and MDD after intersecting 10 hub genes with 37 differential expression genes from the 2 validation datasets. The obtained results suggest an overlapping genetic structure between AS and major depression disorders. MRPL13 may provide key insights into the relationship between AS and MDD.
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Affiliation(s)
- Tiantian Dong
- Center for External Treatment of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine Affiliated Hospital, Jinan, People’s Republic of China
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Shiyou Lu
- Center for External Treatment of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine Affiliated Hospital, Jinan, People’s Republic of China
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Xuhao Li
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Jiguo Yang
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Yuanxiang Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
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Qing L, Li Q, Yang Y, Xu W, Dong Z. A prognosis marker MUC1 correlates with metabolism and drug resistance in bladder cancer: a bioinformatics research. BMC Urol 2022; 22:114. [PMID: 35879749 PMCID: PMC9309451 DOI: 10.1186/s12894-022-01067-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/19/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
MUC1 is a type I transmembrane protein that plays an important role in tumor cell signal transduction. Although current studies have shown that MUC1 is upregulated in bladder cancer (BC), the specific mechanism is still unclear.
Methods
We performed expression analysis, gene set enrichment analysis, survival analysis, immune infiltration analysis, drug sensitivity analysis, and metabolism-related gene expression analysis on TCGA-BLCA, GES31684 and GSE13507.
Results
The expression of MUC1 in the tumor and lymphatic metastasis positive samples was significantly increased. Genes related to MUC1 expression were significantly enriched in immune response, ribosomes, exosomes, and energy metabolism. The results of the immune infiltration analysis showed that M1 macrophages in BC with high MUC1 expression were significantly decreased. Expression of MUC1 increases drug resistance in BC patients. In addition, MUC1 increases glycolysis, glucose uptake, and lactate production by inducing metabolic reprogramming.
Conclusion
MUC1 has a significant effect on the metabolism and immune cell infiltration of BC, which may be the cause of increased drug resistance, and can be used as a molecular target for the diagnosis and treatment of BC.
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Construction and Validation of a Prognostic Model Based on mRNAsi-Related Genes in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6532591. [PMID: 36267313 PMCID: PMC9578885 DOI: 10.1155/2022/6532591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
Background Breast cancer is a big threat to the women across the world with substantial morbidity and mortality. The pressing matter of our study is to establish a prognostic gene model for breast cancer based on mRNAsi for predicting patient's prognostic survival. Methods From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we downloaded the expression profiles of genes in breast cancer. On the basis of one-class logistic regression (OCLR) machine learning algorithm, mRNAsi of samples was calculated. Kaplan-Meier (K-M) and Kruskal-Wallis (K-W) tests were utilized for the assessment of the connection between mRNAsi and clinicopathological variables of the samples. As for the analysis on the correlation between mRNAsi and immune infiltration, ESTIMATE combined with Spearman test was employed. The weighted gene coexpression network analysis (WGCNA) network was established by utilizing the differentially expressed genes in breast cancer, and the target module with the most significant correlation with mRNAsi was screened. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to figure out the biological functions of the target module. As for the construction of the prognostic model, univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses were performed on genes in the module. The single sample gene set enrichment analysis (ssGSEA) and tumor mutational burden were employed for the analysis on immune infiltration and gene mutations in the high- and low-risk groups. As for the analysis on whether this model had the prognostic value, the nomogram and calibration curves of risk scores and clinical characteristics were drawn. Results Nine mRNAsi-related genes (CFB, MAL2, PSME2, MRPL13, HMGB3, DCTPP1, SHCBP1, SLC35A2, and EVA1B) comprised the prognostic model. According to the results of ssGSEA and gene mutation analysis, differences were shown in immune cell infiltration and gene mutation frequency between the high- and low-risk groups. Conclusion Nine mRNAsi-related genes screened in our research can be considered as the biomarkers to predict breast cancer patients' prognoses, and this model has a potential relationship with individual somatic gene mutations and immune regulation. This study can offer new insight into the development of diagnostic and clinical treatment strategies for breast cancer.
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Jiang N, Hu Y, Wang M, Zhao Z, Li M. The Notch Signaling Pathway Contributes to Angiogenesis and Tumor Immunity in Breast Cancer. BREAST CANCER: TARGETS AND THERAPY 2022; 14:291-309. [PMID: 36193236 PMCID: PMC9526507 DOI: 10.2147/bctt.s376873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022]
Abstract
Breast cancer in women is the first leading tumor in terms of incidence worldwide. Some subtypes of BC lack distinct molecular targets and exhibit therapeutic resistance; these patients have a poor prognosis. Thus, the search for new molecular targets is an ongoing challenge for BC therapy. The Notch signaling pathway is found in both vertebrates and invertebrates, and it is a highly conserved in the evolution of the species, controlling cellular fates such as death, proliferation, and differentiation. Numerous studies have shown that improper activation of Notch signaling may lead to excessive cell proliferation and cancer, with tumor-promoting and tumor-suppressive effects in various carcinomas. Thus, inhibitors of Notch signaling are actively being investigated for the treatment of various tumors. The role of Notch signaling in BC has been widely studied in recent years. There is a growing body of evidence suggesting that Notch signaling has a pro-oncogenic role in BC, and the tumor-promoting effect is largely a result of the diverse nature of tumor immunity. Immunological abnormality is also a factor involved in the pathogenesis of BC, suggesting that Notch signaling could be a target for BC immunotherapies. Furthermore, angiogenesis is essential for BC growth and metastasis, and the Notch signaling pathway has been implicated in angiogenesis, so studying the role of Notch signaling in BC angiogenesis will provide new prospects for the treatment of BC. We summarize the potential roles of the current Notch signaling pathway and its inhibitors in BC angiogenesis and the immune response in this review and describe the pharmacological targets of Notch signaling in BC, which may serve as a theoretical foundation for future research into exploring this pathway for novel BC therapies.
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Affiliation(s)
- Nina Jiang
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Ye Hu
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Meiling Wang
- Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Zuowei Zhao
- Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
- Correspondence: Zuowei Zhao, Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China, Tel +86-0411-84671291, Fax +86-0411-84671230, Email
| | - Man Li
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
- Man Li, Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China, Tel +86-0411-84671291, Fax +86-0411-84671230, Email
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11
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Koc EC, Koc FC, Kartal F, Tirona M, Koc H. Role of mitochondrial translation in remodeling of energy metabolism in ER/PR(+) breast cancer. Front Oncol 2022; 12:897207. [PMID: 36119536 PMCID: PMC9472243 DOI: 10.3389/fonc.2022.897207] [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: 03/15/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Remodeling of mitochondrial energy metabolism is essential for the survival of tumor cells in limited nutrient availability and hypoxic conditions. Defects in oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis also cause a switch in energy metabolism from oxidative to aerobic glycolysis contributing to the tumor heterogeneity in cancer. Specifically, the aberrant expressions of mitochondrial translation components such as ribosomal proteins (MRPs) and translation factors have been increasingly associated with many different cancers including breast cancer. The mitochondrial translation is responsible for the synthesis 13 of mitochondrial-encoded OXPHOS subunits of complexes. In this study, we investigated the contribution of mitochondrial translation in the remodeling of oxidative energy metabolism through altered expression of OXPHOS subunits in 26 ER/PR(+) breast tumors. We observed a significant correlation between the changes in the expression of mitochondrial translation-related proteins and OXPHOS subunits in the majority of the ER/PR(+) breast tumors and breast cancer cell lines. The reduced expression of OXPHOS and mitochondrial translation components also correlated well with the changes in epithelial-mesenchymal transition (EMT) markers, E-cadherin (CHD1), and vimentin (VIM) in the ER/PR(+) tumor biopsies. Data mining analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) breast cancer proteome further supported the correlation between the reduced OXPHOS subunit expression and increased EMT and metastatic marker expression in the majority of the ER/PR(+) tumors. Therefore, understanding the role of MRPs in the remodeling of energy metabolism will be essential in the characterization of heterogeneity at the molecular level and serve as diagnostic and prognostic markers in breast cancer.
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Affiliation(s)
- Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
| | - Fatih C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Funda Kartal
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Maria Tirona
- Department of Medical Oncology, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Hasan Koc
- Department of Pharmaceutical Science, School of Pharmacy, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
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Lin X, Guo L, Lin X, Wang Y, Zhang G. Expression and prognosis analysis of mitochondrial ribosomal protein family in breast cancer. Sci Rep 2022; 12:10658. [PMID: 35739158 PMCID: PMC9226049 DOI: 10.1038/s41598-022-14724-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is characterized by high morbidity. Mitochondrial ribosomal protein (MRP) family participates in mitochondrial energy metabolism, underlying BC progression. This study aims to analyze the expression and prognosis effect of the MRP genes in BC patients. GEPIA2, UALCAN, cBioPortal, and MethSurv were used to demonstrate the differential expression, genomic alteration profiles, and DNA methylation of the MRP gene family in BC. Functional enrichment analysis and protein-protein interaction network construction were performed to understand the biological function. Based on 1056 TCGA samples with the transcriptional level of MRPs, Kaplan-Meier curves, Cox, and LASSO regression were applied to explore their prognostic effects. 12 MRPs were upregulated in BC, which were associated with gene amplification and DNA methylation. MRP genetic alteration occurred in 42% of BC patients, and amplification was the most frequent variation. Functioning in its entirety, the MRP family was involved in mitochondrial translational termination, elongation, translation, and poly(A) RNA binding. High expression of MRPL1, MRPL13, MRPS6, MRPS18C, and MRPS35, as well as low levels of MRPL16, and MRPL40 significantly indicated poor prognosis in BC patients. Thus, a novel MRP-based prognostic nomogram was established and verified with favorable discrimination and calibration. We not only provided a thorough expression and prognosis analysis of the MRP family in BC patients but also constructed an MRP-based prognostic nomogram. It was suggested that MRPs acted as biomarkers in individualized risk prediction and may serve as potential therapeutic targets in BC patients.
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Affiliation(s)
- Xiaoyi Lin
- Department of Breast Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Lijuan Guo
- Department of Breast Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xin Lin
- Department of Breast Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yulei Wang
- Department of Breast Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Guochun Zhang
- Department of Breast Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
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Bao S, Wang X, Li M, Gao Z, Zheng D, Shen D, Liu L. Potential of Mitochondrial Ribosomal Genes as Cancer Biomarkers Demonstrated by Bioinformatics Results. Front Oncol 2022; 12:835549. [PMID: 35719986 PMCID: PMC9204274 DOI: 10.3389/fonc.2022.835549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/27/2022] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing and bioinformatics analyses have clearly revealed the roles of mitochondrial ribosomal genes in cancer development. Mitochondrial ribosomes are composed of three RNA components encoded by mitochondrial DNA and 82 specific protein components encoded by nuclear DNA. They synthesize mitochondrial inner membrane oxidative phosphorylation (OXPHOS)-related proteins and participate in various biological activities via the regulation of energy metabolism and apoptosis. Mitochondrial ribosomal genes are strongly associated with clinical features such as prognosis and foci metastasis in patients with cancer. Accordingly, mitochondrial ribosomes have become an important focus of cancer research. We review recent advances in bioinformatics research that have explored the link between mitochondrial ribosomes and cancer, with a focus on the potential of mitochondrial ribosomal genes as biomarkers in cancer.
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Affiliation(s)
- Shunchao Bao
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
| | - Xinyu Wang
- Department of Breast Surgery, Second Hospital of Jilin University, Changchun, China
| | - Mo Li
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
| | - Zhao Gao
- Nuclear Medicine Department, Second Hospital of Jilin University, Changchun, China
| | - Dongdong Zheng
- Department of Cardiovascular Surgery, Second Hospital of Jilin University, Changchun, China
| | - Dihan Shen
- Medical Research Center, Second Hospital of Jilin University, Changchun, China
| | - Linlin Liu
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
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Identification of the Upregulation of MRPL13 as a Novel Prognostic Marker Associated with Overall Survival Time and Immunotherapy Response in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1498924. [PMID: 34868337 PMCID: PMC8639240 DOI: 10.1155/2021/1498924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022]
Abstract
Mitochondrial ribosomal protein (MRPL) genes have been reported to participate in many cellular processes, such as cell proliferation, apoptosis, and cell cycle. Meanwhile, the occurrence rate of breast cancer (BRCA) in China steadily increased. Exploring the prognostic value of MRPL genes in BRCA could provide novel biomarkers for BRCA. In this study, to identify prognosis-related genes in breast cancer, the P value and the hazard ratio (HR) of all genes are analyzed with TCGA database. We revealed higher expression level of CEL, PGK1, WNT3A, USP41, LINC02037, PCMT1, LRP11, MCTS1, TCP1, TMEM31, STK4-AS1, STXBP5, LOC100287036, SLC16A2, MRPL13, DERL1, and TARS was correlated to shorter OS time in BRCA. However, higher expression level of JCHAIN, KLRB1, and TNFRSF14 was correlated to longer OS time in BRCA. The further analysis demonstrated MRPL13 was overexpressed in BRCA. Subtype analysis showed that MRPL13 was overexpressed in luminal, HER2-positive BRCA, and TNBC samples and was highest in TNBC samples. Moreover, we revealed higher expression of MRPL13 was significantly correlated to shorter OS time and higher TMB levels in BRCA. Pan-cancer analysis further revealed the prognostic value of MRPL13 in human cancers. MRPL13 expression was significantly increased in multiple human cancers, such as bladder cancer, colon cancer, liver cancer, and prostate cancer. Pan-cancer TMB and overall survival time showed dysregulation of MRPL13 is significantly related to the OS and TMB levels in various cancers. These results further proved that MRPL13 may be a pan-cancer biomarker for predicting prognosis and the response to immunotherapy.
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Jing C, Fu R, Wang C, Li X, Zhang W. MRPL13 Act as a Novel Therapeutic Target and Could Promote Cell Proliferation in Non-Small Cell Lung Cancer. Cancer Manag Res 2021; 13:5535-5545. [PMID: 34285575 PMCID: PMC8285246 DOI: 10.2147/cmar.s316428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 12/24/2022] Open
Abstract
Background The latent involvement of MRPL13 in non-small cell lung cancer (NSCLC) remains unclear. This study aimed to explore the role of MRPL13 in NSCLC. Methods All analyses were performed in R software 4.0, SPSS version 23, and GraphPad Prism 8. The “limma” package was used to identify differentially expressed genes. Univariate and multivariate cox analyses were used to identify prognosis-related genes. A549 and H1299 lung cancer cell lines were selected for phenotypic experiments. Results The high level of MRPL13 was correlated with poor T classification and overall survival. In vitro experiments showed that MRPL13 was highly expressed in NSCLC tissue and cell lines. MRPL13 knockdown inhibited the proliferation of lung cancer A549 and H1299 cell lines, which was further validated by in vivo experiment. Moreover, GSEA analysis suggested that the pathway of MYC target, PI3K/AKT/mTOR/ signaling, oxidative phosphorylation, and G2/M checkpoints may be the potential pathway where MRPL13 was involved. Meanwhile, MRPL13 demonstrated a negative correlation with M1 macrophage, CD8+ T cells, and CD4+ T cells, making it an underlying immunotherapy target of NSCLC. Conclusion MRPL13 may promote the proliferation of NSCLC cells and serve as an independent tumor marker and an emerging therapeutic target.
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Affiliation(s)
- Chuanqing Jing
- The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Rong Fu
- The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Can Wang
- Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Xiurong Li
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Wei Zhang
- Department of Respiratory Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, People's Republic of China
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