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Chang L, Ding J, Pu J, Zhu J, Zhou X, Luo Q, Li J, Qian M, Lin S, Li J, Wang K. A novel lncRNA LOC101928222 promotes colorectal cancer angiogenesis by stabilizing HMGCS2 mRNA and increasing cholesterol synthesis. J Exp Clin Cancer Res 2024; 43:185. [PMID: 38965575 PMCID: PMC11223299 DOI: 10.1186/s13046-024-03095-8] [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: 12/11/2023] [Accepted: 06/07/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Metastasis is the leading cause of mortality in patients with colorectal cancer (CRC) and angiogenesis is a crucial factor in tumor invasion and metastasis. Long noncoding RNAs (lncRNAs) play regulatory functions in various biological processes in tumor cells, however, the roles of lncRNAs in CRC-associated angiogenesis remain to be elucidated in CRC, as do the underlying mechanisms. METHODS We used bioinformatics to screen differentially expressed lncRNAs from TCGA database. LOC101928222 expression was assessed by qRT-PCR. The impact of LOC101928222 in CRC tumor development was assessed both in vitro and in vivo. The regulatory mechanisms of LOC101928222 in CRC were investigated by cellular fractionation, RNA-sequencing, mass spectrometric, RNA pull-down, RNA immunoprecipitation, RNA stability, and gene-specific m6A assays. RESULTS LOC101928222 expression was upregulated in CRC and was correlated with a worse outcome. Moreover, LOC101928222 was shown to promote migration, invasion, and angiogenesis in CRC. Mechanistically, LOC101928222 synergized with IGF2BP1 to stabilize HMGCS2 mRNA through an m6A-dependent pathway, leading to increased cholesterol synthesis and, ultimately, the promotion of CRC development. CONCLUSIONS In summary, these findings demonstrate a novel, LOC101928222-based mechanism involved in the regulation of cholesterol synthesis and the metastatic potential of CRC. The LOC101928222-HMGCS2-cholesterol synthesis pathway may be an effective target for diagnosing and managing CRC metastasis.
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Affiliation(s)
- Lisha Chang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Ding
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juan Pu
- Department of Oncology, Lianshui County People's Hospital, Affiliated Hospital of Kangda college, Nanjing Medical University, Huaian, Jiangsu, China
| | - Jing Zhu
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiang Zhou
- Head and neck surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qian Luo
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Li
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mengsen Qian
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuhui Lin
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juan Li
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Keming Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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Pan W, Liu X, Liu S. ALYREF m5C RNA methylation reader predicts bladder cancer prognosis by regulating the tumor immune microenvironment. Medicine (Baltimore) 2024; 103:e37590. [PMID: 38579085 PMCID: PMC10994465 DOI: 10.1097/md.0000000000037590] [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: 08/16/2023] [Accepted: 02/22/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND 5-Methylcytidine (m5C) methylation is a recently emerging epigenetic modification that is closely related to tumor proliferation, occurrence, and metastasis. This study aimed to investigate the clinicopathological characteristics and prognostic value of m5C regulators in bladder cancer (BLCA), and their correlation with the tumor immune microenvironment. METHODS Thirteen m5C RNA methylation regulators were analyzed using RNA-sequencing and corresponding clinical information obtained from the TCGA database. The Cluster Profiler package was used to analyze the gene ontology function of potential targets and enriched the Kyoto Encyclopedia of Genes and Genomes pathway. Kaplan-Meier survival analysis was used to compare survival differences using the log-rank test and univariate Cox proportional hazards regression. The correlation between signature prognostic m5C regulators and various immune cells was analyzed. Univariate and multivariate Cox regression analyses identified independence of the ALYREF gene signature. RESULTS Nine out of the 13 m5C RNA methylation regulators were differentially expressed in BLCA and normal samples and were co-expressed. These 9 regulators were associated with clinicopathological tumor characteristics, particularly high or low tumor risk, pT or pTNM stage, and migration. Consensus clustering analysis divides the BLCA samples into 4 clusters. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment annotation and gene ontology function analysis identified 273 upregulated and 594 downregulated genes in BLCA. Notably, only ALYREF was significantly correlated with OS (P < .05). ALYREF exhibited significant infiltration levels in macrophage cells. Therefore, we constructed a nomogram for ALYREF as an independent prognostic factor. Additionally, we observed that both the mRNA and protein levels of ALYREF were upregulated, and immunofluorescence showed that ALYREF was mainly distributed in nuclear speckles. ALYREF overexpression was significantly associated with poor OS. CONCLUSION Our findings demonstrated the potential of ALYREF to predict clinical prognostic risks in BLCA patients and regulate the tumor immune microenvironment. As such, ALYREF may serve as a novel prognostic indicator in BLCA patients.
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Affiliation(s)
- Wengu Pan
- Kidney Transplantation of The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Kidney Transplantation, Multidisciplinary Innovation Center for Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Xiaoli Liu
- Kidney Transplantation of The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Kidney Transplantation, Multidisciplinary Innovation Center for Nephrology, The Second Hospital of Shandong University, Jinan, China
| | - Shuangde Liu
- Kidney Transplantation of The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Kidney Transplantation, Multidisciplinary Innovation Center for Nephrology, The Second Hospital of Shandong University, Jinan, China
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Lu F, Gao G, Zhang H, Zhang W. The relationship between polymorphism of IGF2BP2 gene rs4402960 and risk of pan-cancer: a meta-analysis and a bioinformatics analysis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-17. [PMID: 38555596 DOI: 10.1080/15257770.2024.2333036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
Abstract
OBJECTIVE To conduct a meta-analysis and a bioinformatics analysis to assess the relationship between IGF2BP2 gene polymorphism and pan-cancer risk. METHODS PubMed, EMBASE, and Web of Science were conducted to literature searches. The heterogeneity test was used in five genetic models. Odds ratios (OR), 95% confidence intervals (CI), and p-values were used to evaluate the combined effects of various genetic models. Subgroup analysis and Meta-regression analysis were used to analyze the characteristics of heterogeneity. Sensitivity analysis and publication bias were also performed. Transcriptomic information on IGF2BP2 was downloaded and analyzed from the TCGA and GTEx databases. GEPIA (http://gepia.cancer-pku.cn/) was performed to analyze the relationship between IGF2BP2 expression and cancer tissue. RESULTS This meta-analysis contained 7 case-control studies, with 5,908 cases and 7,890 controls. There were significant differences in the heterozygous genetic model of IGF2BP2 gene rs4402960 polymorphism (OR = 1.080, 95% CI = 1.003-1.163, p = 0.041). In subgroup analysis based on ethnicity, There was a statistical significant association in Chinese (heterozygous: OR = 1.110, 95% CI = 1.010-1.220, p = 0.030). Bioinformatics analysis found that IGF2BP2 was over-expressed in pan-cancer (p < 0.01). In addition, the Kaplan-Meier estimate showed that there is statistical significance of OS between the low and high IGF2BP2 TPM groups in Lung adenocarcinoma (p <0.001). CONCLUSIONS To sum up, IGF2BP2 gene polymorphism may be related to cancer risk. IGF2BP2 has diagnostic value in the diagnosis and treatment of pan-cancer.
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Affiliation(s)
- Fengke Lu
- Department of Blood Transfusion, Liuzhou Hospital, Guangzhou Women and Children's Medical Center, Liuzhou, Guangxi, China
| | - Gan Gao
- Department of Clinical Laboratory, Liuzhou Hospital, Guangzhou Women and Children's Medical Center, Liuzhou, Guangxi, China
| | - Hongyu Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou Traditional Chinese Medical Hospital, The Third Clinical Faculty of Guangxi University of Chinese Medicine, Liuzhou, Guangxi, China
| | - Wei Zhang
- Department of Clinical Laboratory, Guilin TCM Hospital Affiliated to Guangxi University of Chinese Medicine, Guilin, Guangxi, China
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Tong M, Luo S, Gu L, Wang X, Zhang Z, Liang C, Huang H, Lin Y, Huang J. SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer. Comput Biol Med 2024; 171:108113. [PMID: 38368754 DOI: 10.1016/j.compbiomed.2024.108113] [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: 10/11/2023] [Revised: 01/09/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND The emergence of single-cell technology offers a unique opportunity to explore cellular similarity and heterogeneity between precancerous diseases and solid tumors. However, there is lacking a systematic study for identifying and characterizing similarities at single-cell resolution. METHODS We developed SIMarker, a computational framework to detect cellular similarities between precancerous diseases and solid tumors based on gene expression at single-cell resolution. Taking hepatocellular carcinoma (HCC) as a case study, we quantified the cellular and molecular connections between HCC and cirrhosis. Core analysis modules of SIMarker is publicly available at https://github.com/xmuhuanglab/SIMarker ("SIM" means "similarity" and "Marker" means "biomarkers). RESULTS We found PGA5+ hepatocytes in HCC showed cirrhosis-like characteristics, including similar transcriptional programs and gene regulatory networks. Consequently, the genes constituting the gene expression program of these cirrhosis-like subpopulations were designated as cirrhosis-like signatures (CLS). Strikingly, our utilization of CLS enabled the development of diagnosis and prognosis biomarkers based on within-sample relative expression orderings of gene pairs. These biomarkers achieved high precision and concordance compared with previous studies. CONCLUSIONS Our work provides a systematic method to investigate the clinical translational significance of cellular similarities between HCC and cirrhosis, which opens avenues for identifying similar paradigms in other categories of cancers and diseases.
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Affiliation(s)
- Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China.
| | - Shijie Luo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China
| | - Lin Gu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xinkang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China
| | - Chenyu Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China
| | - Huaqiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 316005, China.
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Zheng J, Tang H, Yang Y, Yang K. Comprehensive analysis of the prognosis and biological significance of ROR β in head and neck squamous cell carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:487-508. [PMID: 37278231 DOI: 10.1002/tox.23859] [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: 03/28/2023] [Revised: 05/10/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
Recent studies have shown that abnormal expression of the core circadian clock gene, retinoic acid-related orphan receptor β (RORβ ), is closely associated with the occurrence and progression of various malignant tumors. However, the expression and function of RORβ in head and neck squamous cell carcinoma (HNSCC) remains unclear. Here, we comprehensively investigated the altered expression, clinical significance, prognostic value, and biological functions of RORβ in HNSC, as well as its correlation with changes in the tumor immune microenvironment. We found that RORβ expression was decreased in HNSC and 19 other cancers. Low RORβ expression was significantly associated with tumor size, clinical stage, and survival time in HNSC patients, indicating that it may have diagnostic and prognostic value in HNSCC. Epigenetic analysis showed that the promoter methylation level of RORβ was significantly higher in HNSCC compared to adjacent noncancerous tissues. Furthermore, RORβ hypermethylation was significantly associated with low expression levels of RORβ and poor prognosis in HNSCC patients (p < 0.05). Enrichment analysis found that RORβ was involved in immune system regulation and T-cell activation, as well as the PI3K/AKT and ECM receptors interaction pathways. In vitro assays revealed that RORβ regulated the proliferation, migration and invasion ability of HNSCC cells. Additionally, we found that RORβ expression was significantly correlated with changes in the tumor immune microenvironment, suggesting it may affect prognosis by regulating immune infiltration in HNSC patients. Therefore, RORβ may serve as a potential prognostic biomarker and therapeutic target for HNSCC patients.
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Affiliation(s)
- Jiawen Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Tang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yixin Yang
- Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, China
| | - Kai Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Li X, Wang J, Guo Z, Ma Y, Xu D, Fan D, Dai P, Chen Y, Liu Q, Jiao J, Fan J, Wu N, Li X, Li G. Copper metabolism-related risk score identifies hepatocellular carcinoma subtypes and SLC27A5 as a potential regulator of cuproptosis. Aging (Albany NY) 2023; 15:15084-15113. [PMID: 38157255 PMCID: PMC10781498 DOI: 10.18632/aging.205334] [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: 05/24/2023] [Accepted: 11/10/2023] [Indexed: 01/03/2024]
Abstract
AIMS Dysregulated copper metabolism has been noticed in many types of cancer including hepatocellular carcinoma (HCC); however, a comprehensive understanding about this dysregulation still remains unclear in HCC. METHODS A set of bioinformatic tools was integrated to analyze the expression and prognostic significance of copper metabolism-related genes. A related risk score, termed as CMscore, was developed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression. Pathway enrichment analyses and tumor immune cell infiltration were further investigated in CMscore stratified HCC patients. Weighted correlation network analysis (WGCNA) was used to identify potential regulator of cuproptosis. RESULTS Copper metabolism was dysregulated in HCC. HCC patients in the high-CMscore group showed a significantly lower overall survival (OS) and enriched in most cancer-related pathways. Besides, HCC patients with high CMscore had higher expression of pro-tumor immune infiltrates and immune checkpoints. Moreover, cancer patients with high CMscore from two large cohorts exhibited significantly prolonged survival time after immunotherapy. WGCNA and subsequently correlation analysis revealed that SLC27A5 might be a potential regulator of cuproptosis in HCC. In vitro experiments revealed that SLC27A5 inhibited cell proliferation and migration of HCC cells and could upregulate FDX1, the key regulator of cuproptosis. SIGNIFICANCE The CMscore is helpful in clustering HCC patients with distinct prognosis, gene mutation signatures, and sensitivity to immunotherapy. SLC27A5 might serve as a potential target in the induction of cuproptosis in HCC.
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Affiliation(s)
- Xiaoyan Li
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
- Department of Central Laboratory, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jinping Wang
- Department of Ultrasound, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zongliang Guo
- Department of General Surgery, Shanxi Province Cancer Hospital, Affiliated of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yong Ma
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital, Affiliated of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Dawei Xu
- Department of Blood Transfusion, Shanxi Provincial People’s Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Daguang Fan
- Department of Hepatobiliary and Pancreatic Surgery, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Peng Dai
- Department of Hepatobiliary and Pancreatic Surgery, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yifan Chen
- College of Management, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Qiongwen Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinke Jiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jinhan Fan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ningxue Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Xin Li
- Department of Geriatric Medicine, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- MOE Key Laboratory of Modern Teaching Technology, Center for Teacher Professional Ability Development, Shaanxi Normal University, Xi’an, Shannxi, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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Cai Z, Duan Y, Li W, Liu Z, Gong Z, Hong S, He X, Xuanyuan X, Chen Y, Bi X, Wang W. FANCI serve as a prognostic biomarker correlated with immune infiltrates in skin cutaneous melanoma. Front Immunol 2023; 14:1295831. [PMID: 38077326 PMCID: PMC10703153 DOI: 10.3389/fimmu.2023.1295831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background As a member of tumor, Skin cutaneous melanoma (SKCM) poses a serious threat to people's health because of its strong malignancy. Unfortunately, effective treatment methods for SKCM remain lacking. FANCI plays a vital role in the occurrence and metastasis of various tumor types. However, its regulatory role in SKCM is unclear. The purpose of this study was to explore the association of FANCI with SKCM. Methods This study investigated the expression of FANCI in GSE46517, GSE15605, and GSE114445 from the Gene Expression Omnibus database and The Cancer Genome Atlas (TCGA)-SKCM datasets using the package "limma" or "DESeq2" in R environment and also investigated the prognostic significance of FANCI by utilizing the GEPIA database. Additionally, our research made use of real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression between SKCM and normal tissues and developed the knockdown of FANCI in A375 and A875 cells to further analyze the function of FANCI. Finally, this study analyzed the correlation of FANCI and tumor-infiltrating immune cells by CIBERSORT, ESTIMATE, and ssGSEA algorithms. Results The FANCI level was increasing in SKCM tissues from GSE46517, GSE15605, GSE114445, and TCGA-SKCM. However, high FANCI expression correlated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinformatics. Knocking down FANCI suppresses A375 and A875 cell proliferation, migration, and invasion. FANCI could be involved in the immunological milieu of SKCM by regulating immune responses and infiltrating numerous immune cells, particularly neutrophils, CD8+ T cells, and B cells. Furthermore, patients with SKCM who have a high FANCI expression level are reported to exhibit immunosuppression, whereas those with a low FANCI expression level are more likely to experience positive outcomes from immunotherapy. Conclusions The increased FANCI expression in SKCM can be a prognostic biomarker. Knockdown FANCI can reduce the occurrence and progression of SKCM. The FANCI expression provides a foundation for predicting the immune status and treatment of SKCM.
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Affiliation(s)
- Zhenguo Cai
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yanjuan Duan
- Department of Dermatology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wen Li
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhuohang Liu
- Department of Neurology, Minhang Hospital, Fudan University/Central Hospital of Minhang District, Shanghai, China
| | - Zijun Gong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sheng Hong
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xu He
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xinyang Xuanyuan
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Youdong Chen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinling Bi
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wuqing Wang
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Xu L, Yang H, Yan M, Li W. Matrix metalloproteinase 1 is a poor prognostic biomarker for patients with hepatocellular carcinoma. Clin Exp Med 2023; 23:2065-2083. [PMID: 36169759 DOI: 10.1007/s10238-022-00897-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/08/2022] [Indexed: 02/01/2023]
Abstract
Hepatocellular carcinoma (HCC) remains an incurable malignancy despite the treatment methods being continually updated. Matrix metalloproteinases (MMPs) promote the progression of HCC; however, no consensus exists on which MMP plays the predominant role in HCCs. In the present study, we analyzed differentially expressed genes in HCCs, especially MMPs, compared with adjacent tissues using the Cancer Genome Atlas database. The KEGG enrichment pathway using differentially expressed genes included extracellular matrix-receptor interaction, which was correlated with MMPs. We found that among the MMP family, only MMP1, MMP3, MMP8, MMP9, MMP11, MMP12, MMP14, MMP15, MMP20, MMP21, and MMP24 significantly increased in HCCs compared with adjacent tissues. Crucially, survival and univariate analyses indicated that only MMPs 1, 9, 12, and 14 predict poor overall survival; however, multivariate Cox analysis and a nomogram demonstrated that only MMP1 is a poor prognostic biomarker for HCCs. In addition, we observed significant enrichment of uncharacterized cells but decreased macrophages in HCC tissues. Consistent with decreased macrophages in HCCs, MMP1 was negatively associated with macrophages but positively correlated with uncharacterized cells, indicating that the main producer of MMP1 is uncharacterized cells. Furthermore, MMP1 expression was negatively correlated with immune responses of HCCs. Taken together, our findings indicated that MMP1 is a poor and predominant prognostic biomarker for patients with HCC and that anti-MMP1 may be a novel therapy that is worth studying in depth.
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Affiliation(s)
- Linping Xu
- Department of Research and Foreign Affairs, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China.
| | - Hui Yang
- Department of Gastroenterology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Meimei Yan
- Department of Research and Foreign Affairs, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Wei Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Du R, Li J, Li F, Mi L, Dionigi G, Sun H, Liang N. Estimating disease-free survival of thyroid cancer based on novel cuprotosis-related gene model. Front Endocrinol (Lausanne) 2023; 14:1209172. [PMID: 37745716 PMCID: PMC10515282 DOI: 10.3389/fendo.2023.1209172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Background Cuprotosis is a newly discovered form of cell death that differs from other types of cell death. The aim of this study was to investigate the functional role and a possible prognostic model for thyroid cancer. Methods TCGA and GEO were used to investigate the differential expression of CRGs in THCA. KEGG and GO enrichment analyses were applied to investigate the possible molecular functions. The features of CRGs were selected by LASSO regression. 20 pairs of samples were randomly collected from the hospital to compare expression between tumor and normal. Results Among the 19 CRGs related to thyroid cancer recurrence, 16 genes were differentially expressed in thyroid cancer. KEGG analysis showed that the 19 CRGs were mainly enriched in cell death, cell cycle and ribosomal pathways. K-M survival analysis and subsequent multiple logistic regression revealed that the expression of BUB1 and GINS2 were potential risk factors for disease-free survival (DFS) of thyroid cancer. In addition, further LASSO-regression selected the following three DFS-related CRGs: FDX1, BUB1 and RPL3. A novel prognostic prediction model was constructed by nomogram, and the prediction probability for 1-, 3- and 5-year survival approached the actual time. As for the possible mechanisms, FDX1, BUB1 and RPL3 were associated with immune infiltration. The cell model experiment illustrated that the ATM signaling pathway might be involved in thyroid cancer cell death. Conclusion Three CRG models (FDX1, BUB1, RPL3) could better predict the prognosis of thyroid cancer. Immune cell infiltration and the ATM pathway were the possible mechanisms.
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Affiliation(s)
- Rui Du
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Jingting Li
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Fang Li
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Lusi Mi
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Gianlorenzo Dionigi
- Department of Pathophysiology and Transplantation, Division of Surgery, Istituto Auxologico Italiano IRCCS (Istituto di Ricovero e Cura a Carattere Scientifco), University of Milan, Milan, Italy
| | - Hui Sun
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
| | - Nan Liang
- Division of Thyroid Surgery, The China-Japan Union Hospital of Jilin University, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, Changchun, China
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10
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Yuan L, Xiao Z, Lu R. Hypoxanthine guanine phosphoribosyltransferase 1, a target of miR-125b-5p, promotes cell proliferation and invasion in head and neck squamous cell carcinoma. Heliyon 2023; 9:e20174. [PMID: 37810145 PMCID: PMC10559962 DOI: 10.1016/j.heliyon.2023.e20174] [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: 02/03/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
The mechanism of hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) upregulation and its function in head and neck squamous cell carcinoma (HNSCC) remains obscure. Herein, the expression and function of HPRT1 and the mechanism underlying its upregulation in HNSCC were explored. Firstly, the expression of HPRT1 and its prognostic values were simultaneously validated using bioinformatic analysis and quantitative real-time PCR (qRT-PCR), and immunohistochemistry staining with local HNSCC samples. The effects of HPRT1 knockdown on proliferation and invasion of HNSCC cells were detected using cell counting kit-8 (CCK-8), plate clone formation, Transwell invasion, nude mouse xenograft model assays. Moreover, the miRNA targeting HPRT1 was validated using dual-luciferase report assay, qRT-PCR and Western blot analysis. The functions of miRNA targeting HPRT1 and its dependence on HPRT1 were further investigated in HNSCC. The results indicated that HPRT1 was highly expressed in HNSCC tissues and cells, which positively correlated with advanced tumor progression and predicted poor prognosis in patients with HNSCC. HPRT1 knockdown markedly inhibited proliferation and invasion of HNSCC cells both in vitro and in vivo. MiR-125b-5p, which was downregulated and positively correlated with a favorable outcome for patients, directly targeted and downregulated HPRT1 expression, and subsequently suppressed cell proliferation and invasion in HNSCC. Collectively, the present study demonstrates that HPRT1 upregulation, at least partially caused by miR-125b-5p downregulation, could promote the malignant progression of HNSCC, highlighting the potential application of the miR-125b-5p/HPRT1 axis as a novel indicator and target in the diagnosis and treatment of HNSCC.
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Affiliation(s)
- Li Yuan
- Department of Nuclear Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiqiang Xiao
- The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruohuang Lu
- Department of Stomatology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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11
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Liang K, Ke Z, Huang J, Zhang X. Expression and clinical value of NLRP1 and NLRC4 inflammasomes in prostate cancer. Oncol Lett 2023; 26:385. [PMID: 37559581 PMCID: PMC10407840 DOI: 10.3892/ol.2023.13971] [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: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 08/11/2023] Open
Abstract
The present study explored the clinical value of the protein expression levels of nucleotide binding oligomerization-like receptor family pyrin domain containing 1 (NLRP1) and nucleotide-binding oligomerization domain leucine-rich repeat and caspase recruitment domain-containing 4 (NLRC4) inflammasomes in the diagnosis and treatment of prostate cancer. A total of 54 patients with prostatic hyperplasia and 58 patients with prostate cancer were recruited at The First People's Hospital of Pinghu between January and May 2022. Immunohistochemical staining was used to determine the protein expression levels of the NLRP1 and NLRC4 inflammasomes in addition to the proinflammatory cytokines IL-18 and IL-1β in the two groups of patients. The protein expression levels of NLRP1 and NLRC4 inflammasome were significantly increased in patients with prostate cancer compared with patients with prostate hyperplasia. The differences in expression of NLRP1 and NLRC4 inflammatory vesicles in prostate cancer of different stages were also compared based on data from The Cancer Genome Atlas. The protein expression level of NLRP1 demonstrated a significant positive correlation with IL-1β and IL-18 expression, and the protein expression level of the NLRC4 inflammasome was significantly positively correlated with IL-18 expression. The protein expression levels of both NLRP1 and NLRC4 demonstrated a significant positive correlation with the Gleason score of prostate cancer. The expression of NLRP1 in tumor (T)3/T4 was significantly higher compared with T1 and expression of the NLRC4 inflammasome in T2 and T3/T4 was significantly higher compared with T1. Expression of the NLRP1 and NLRC4 inflammasomes was significantly higher in patients with prostate cancer, compared with patients with prostatic hyperplasia. Therefore, expression of NLRP1 and NLRC4 may promote tumorigenesis by promoting the maturation and release of proinflammatory cytokines IL-1β and IL-18. Expression of the NLRP1 and NLRC4 inflammasomes demonstrated a significant positive correlation with the risk of prostate cancer. Expression of the NLRP1 and NLRC4 inflammasomes in middle- and advanced-stage tumors was higher compared with early-stage tumors. These results suggested that inflammasome expression may serve a significant role in the progression of tumors and could provide a fixed value for the risk assessment and prognosis prediction of prostate cancer.
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Affiliation(s)
- Ke Liang
- Department of Urology, The First People's Hospital of Pinghu, Pinghu, Zhejiang 314200, P.R. China
| | - Zunjin Ke
- Department of Urology, The First People's Hospital of Pinghu, Pinghu, Zhejiang 314200, P.R. China
| | - Jianhong Huang
- Department of Urology, The First People's Hospital of Pinghu, Pinghu, Zhejiang 314200, P.R. China
| | - Xijiong Zhang
- Department of Pathology, The First People's Hospital of Pinghu, Pinghu, Zhejiang 314200, P.R. China
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12
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Wang X, Zhao M, Zhang C, Chen H, Liu X, An Y, Zhang L, Guo X. Establishment and Clinical Application of the Nomogram Related to Risk or Prognosis of Hepatocellular Carcinoma: A Review. J Hepatocell Carcinoma 2023; 10:1389-1398. [PMID: 37637500 PMCID: PMC10460189 DOI: 10.2147/jhc.s417123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent primary liver malignancy, accounting for approximately 90% of all primary liver cancers, with high mortality and a poor prognosis. A large number of predictive models have been applied that integrate multiple clinical factors and biomarkers to predict the prognosis of HCC. Nomograms, as easy-to-use prognostic predictive models, are widely used to predict the probability of clinical outcomes. We searched PubMed with the keywords "hepatocellular carcinoma" and "nomogram", and 974 relative literatures were retrieved. According to the construction methodology and the real validity of the nomograms, in this study, 97 nomograms for HCC were selected in 77 publications. These 97 nomograms were established based on more than 100,000 patients, covering seven main prognostic outcomes. The research data of 56 articles are from hospital-based HCC patients, and 13 articles provided external validation results of the nomogram. In addition to AFP, tumor size, tumor number, stage, vascular invasion, age, and other common prognostic risk factors are included in the HCC-related nomogram, more and more biomarkers, including gene mRNA expression, gene polymorphisms, and gene signature, etc. were also included in the nomograms. The establishment, assessment and validation of these nomograms are also discussed in depth. This study would help clinicians construct and select appropriate nomograms to guide precise judgment and appropriate treatments.
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Affiliation(s)
- Xiangze Wang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Minghui Zhao
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Chensheng Zhang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Haobo Chen
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Xingyu Liu
- School of Computer and Information Engineering, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Yang An
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Lu Zhang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, People’s Republic of China
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13
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Yang S, Zhou P, Qi L, Wang Y, Li Y, Wang X. Promoting proliferation and tumorigenesis of breast cancer: KCND2's significance as a prognostic factor. Funct Integr Genomics 2023; 23:257. [PMID: 37522982 DOI: 10.1007/s10142-023-01183-0] [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: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
In recent years, the potassium voltage-gated channel subfamily D (KCND) channels, particularly KCND2 (also known as Kv4.2), have been suggested to play a role in a variety of cancers, but their role in breast cancer has not yet been revealed. We analyzed RNA sequencing data from The Cancer Genome Atlas database and the Genotype-Tissue Expression database to investigate the differential expression of KCND2 in breast cancer and normal breast tissue. In addition, we leveraged GO and KEGG analysis techniques to gain a better understanding of the potential functional enrichment of 500 genes related to KCND2. Our findings were validated using collected tissue samples and clinical data from hospitals showed that KCND2 is a crucial independent factor in the prognosis of breast cancer patients. The higher the expression of KCND2, the shorter the survival time of breast cancer patients. Colony formation assay confirmed that KCND2 promotes the proliferation of breast cancer cells, whereas transwell assay and wound healing assay verified that KCND2 promoted breast cancer invasion and migration. In addition, 5-Ethynyl-2'-deoxyuridine (EdU) and flow cytometry revealed that KCND2 affected the cycle changes of breast cancer cells and contributed to the G1/S phase transition of breast cancer cells. Overall, our study demonstrates that KCND2 holds a promising potential as a significant target for breast cancer diagnosis and therapy.
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Affiliation(s)
- Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Pengpeng Zhou
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
- Department of Minimally Invasive Interventional Radiology, Shandong Second Provincial General Hospital, Jinan, 250117, China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yu Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yang Li
- Clinical Laboratory, Zhangqiu People's Hospital, Jinan, 250200, China
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
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14
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Liu T, Li C, Zhang J, Hu H, Li C. Unveiling efferocytosis-related signatures through the integration of single-cell analysis and machine learning: a predictive framework for prognosis and immunotherapy response in hepatocellular carcinoma. Front Immunol 2023; 14:1237350. [PMID: 37575252 PMCID: PMC10414188 DOI: 10.3389/fimmu.2023.1237350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 08/15/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) represents a prominent gastrointestinal malignancy with a grim clinical outlook. In this regard, the discovery of novel early biomarkers holds substantial promise for ameliorating HCC-associated mortality. Efferocytosis, a vital immunological process, assumes a central position in the elimination of apoptotic cells. However, comprehensive investigations exploring the role of efferocytosis-related genes (EFRGs) in HCC are sparse, and their regulatory influence on HCC immunotherapy and targeted drug interventions remain poorly understood. Methods RNA sequencing data and clinical characteristics of HCC patients were acquired from the TCGA database. To identify prognostically significant genes in HCC, we performed the limma package and conducted univariate Cox regression analysis. Subsequently, machine learning algorithms were employed to identify hub genes. To assess the immunological landscape of different HCC subtypes, we employed the CIBERSORT algorithm. Furthermore, single-cell RNA sequencing (scRNA-seq) was utilized to investigate the expression levels of ERFGs in immune cells and to explore intercellular communication within HCC tissues. The migratory capacity of HCC cells was evaluated using CCK-8 assays, while drug sensitivity prediction reliability was determined through wound-healing assays. Results We have successfully identified a set of nine genes, termed EFRGs, that hold significant potential for the establishment of a hepatocellular carcinoma-specific prognostic model. Furthermore, leveraging the individual risk scores derived from this model, we were able to stratify patients into two distinct risk groups, unveiling notable disparities in terms of immune infiltration patterns and response to immunotherapy. Notably, the model's capacity to accurately predict drug responses was substantiated through comprehensive experimental investigations, encompassing wound-healing assay, and CCK8 experiments conducted on the HepG2 and Huh7 cell lines. Conclusions We constructed an EFRGs model that serves as valuable tools for prognostic assessment and decision-making support in the context of immunotherapy and chemotherapy.
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Affiliation(s)
- Tao Liu
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Chao Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians University, Munich, Germany
| | - Jiantao Zhang
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Han Hu
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Chenyao Li
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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15
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Zheng Z, Li H, Yang R, Guo H. Role of the membrane-spanning 4A gene family in lung adenocarcinoma. Front Genet 2023; 14:1162787. [PMID: 37533433 PMCID: PMC10390740 DOI: 10.3389/fgene.2023.1162787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.
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16
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Zhao W, Chang Y, Wu Z, Jiang X, Li Y, Xie R, Fu D, Sun C, Gao J. Identification of PIMREG as a novel prognostic signature in breast cancer via integrated bioinformatics analysis and experimental validation. PeerJ 2023; 11:e15703. [PMID: 37483962 PMCID: PMC10358341 DOI: 10.7717/peerj.15703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023] Open
Abstract
Background Phosphatidylinositol binding clathrin assembly protein interacting mitotic regulator (PIMREG) expression is upregulated in a variety of cancers. However, its potential role in breast cancer (BC) remains uncertain. Methods The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to gather relevant information. The expression of PIMREG and its clinical implication in BC were assessed by using Wilcoxon rank-sum test. The prognostic value of PIMREG in BC was evaluated through the Cox regression model and nomogram, and visualized by Kaplan-Meier survival curves. Genes/proteins that interact with PIMREG in BC were also identified through GeneMANIA and MaxLink. Gene set enrichment analysis (GSEA) was then performed. The correlations of the immune cell infiltration and immune checkpoints with the expression of PIMREG in BC were explored via TIMER, TISIDB, and GEPIA. Potential drugs that interact with PIMREG in BC were explored via Q-omic. The siRNA transfection, CCK-8, and transwell migration assay were conducted to explore the function of PIMREG in cell proliferation and migration. Results PIMREG expression was significantly higher in infiltrating ductal carcinoma, estrogen receptor negative BC, and progestin receptor negative BC. High expression of PIMREG was associated with poor overall survival, disease-specific survival, and progression-free interval. A nomogram based on PIMREG was developed with a satisfactory prognostic value. PIMREG also had a high diagnostic ability, with an area under the curve of 0.940. Its correlations with several immunomodulators were also observed. Immune checkpoint CTLA-4 was significantly positively associated with PIMREG. HDAC2 was found as a potentially critical link between PIMREG and BRCA1/2. In addition, PIMREG knockdown could inhibit cell proliferation and migration in BC. Conclusions The high expression of PIMREG is associated with poor prognosis and immune checkpoints in BC. HDAC2 may be a critical link between PIMREG and BRCA1/2, potentially a therapeutic target.
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Affiliation(s)
- Wenjing Zhao
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuanjin Chang
- School of Medicine, Jiangnan College, WuXi, JiangSu, China
| | - Zhaoye Wu
- School of Medicine, Jiangnan College, WuXi, JiangSu, China
| | - Xiaofan Jiang
- School of Medicine, Jiangnan College, WuXi, JiangSu, China
| | - Yong Li
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruijin Xie
- School of Medicine, Jiangnan College, WuXi, JiangSu, China
| | - Deyuan Fu
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chenyu Sun
- Department of General Surgery, The second Affiliated Hospital of Anhui Medical University, Anhui, China
- Department of Medicine, AMITA Health Saint Joseph Hospital, Chicago, IL, USA
| | - Ju Gao
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
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17
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Lv X, Wang W, Liu X, Liu Y, Guo L, Wang C. Low expression of acyl-CoA thioesterase 13 is associated with poor prognosis in ovarian serous cystadenocarcinoma. Front Genet 2023; 14:1213022. [PMID: 37424730 PMCID: PMC10323136 DOI: 10.3389/fgene.2023.1213022] [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: 04/27/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
Objective: Acyl-CoA thioesterase 13 (ACOT13) encodes a member of the thioesterase superfamily. It has not been reported in ovarian cancer. This research aimed at evaluating the expression and prognostic value of ACOT13 in ovarian serous cystadenocarcinoma (OSC). Methods: We extracted and analyzed TCGA, GEPIA, THPA, GTEx, miRWalk, and GDSC databases to investigate the potential carcinogenic mechanism of ACOT13 in OSC, including the correlation of ACOT13 with prognosis, immune checkpoint, tumor mutational burden (TMB), and 50% inhibition concentration (IC50) score. The incidence of endpoint events was compared with Kaplan-Meier survival analysis. Independent prognostic factors for OSC were evaluated with univariate and multivariate Cox regression analyses, and a nomogram was established. Results: The expression of ACOT13 was increased in OSC and correlated with tumor stage, with higher expression in stages I and II than in stages III and IV. Besides, it was observed that low expression of ACOT13 is correlated with poor overall survival (OS), progression-free survival (PFS), and disease-specific survival (DSS) in patients with OSC. There was a positive correlation between ACOT13 expression and immune checkpoint sialic acid-binding Ig-like lectin (SIGLEC) 15 and TMB. Patients with low ACOT13 expression had higher cisplatin IC50 scores. Conclusion: ACOT13 is an independent prognostic factor and a promising clinical target for OSC. In the future, the carcinogenic mechanism and clinical application value of ACOT13 in ovarian cancer need to be further studied.
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Affiliation(s)
- Xiaofeng Lv
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weijiao Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhuan Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Changyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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18
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Xu K, Liu Y, Luo H, Wang T. Efferocytosis signatures as prognostic markers for revealing immune landscape and predicting immunotherapy response in hepatocellular carcinoma. Front Pharmacol 2023; 14:1218244. [PMID: 37383726 PMCID: PMC10294713 DOI: 10.3389/fphar.2023.1218244] [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: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly lethal liver cancer with late diagnosis; therefore, the identification of new early biomarkers could help reduce mortality. Efferocytosis, a process in which one cell engulfs another cell, including macrophages, dendritic cells, NK cells, etc., plays a complex role in tumorigenesis, sometimes promoting and sometimes inhibiting tumor development. However, the role of efferocytosis-related genes (ERGs) in HCC progression has been poorly studied, and their regulatory effects in HCC immunotherapy and drug targeting have not been reported. Methods: We downloaded efferocytosis-related genes from the Genecards database and screened for ERGs that showed significant expression changes between HCC and normal tissues and were associated with HCC prognosis. Machine learning algorithms were used to study prognostic gene features. CIBERSORT and pRRophetic R packages were used to evaluate the immune environment of HCC subtypes and predict treatment response. CCK-8 experiments conducted on HCC cells were used to assess the reliability of drug sensitivity prediction. Results: We constructed a prognostic prediction model composed of six genes, and the ROC curve showed good predictive accuracy of the risk model. In addition, two ERG-related subgroups in HCC showed significant differences in tumor immune landscape, immune response, and prognostic stratification. The CCK-8 experiment conducted on HCC cells confirmed the reliability of drug sensitivity prediction. Conclusion: Our study emphasizes the importance of efferocytosis in HCC progression. The risk model based on efferocytosis-related genes developed in our study provides a novel precision medicine approach for HCC patients, allowing clinicians to customize treatment plans based on unique patient characteristics. The results of our investigation carry noteworthy implications for the development of individualized treatment approaches involving immunotherapy and chemotherapy, thereby potentially facilitating the realization of personalized and more efficacious therapeutic interventions for HCC.
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Affiliation(s)
- Ke Xu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Yu Liu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Huiyan Luo
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Tengfei Wang
- Department of Equipment, Bishan Hospital of Chongqing, Chongqing, China
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19
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Song T, Hu Z, Zeng C, Luo H, Liu J. FLOT1, stabilized by WTAP/IGF2BP2 mediated N6-methyladenosine modification, predicts poor prognosis and promotes growth and invasion in gliomas. Heliyon 2023; 9:e16280. [PMID: 37260902 PMCID: PMC10227343 DOI: 10.1016/j.heliyon.2023.e16280] [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: 12/16/2022] [Revised: 05/06/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
The expression, function, and mechanism of FLOT1 (flotillin-1) remains unknown in gliomas. Here, the expression and clinical value of FLOT1 in gliomas was bioinformatically and experimentally analyzed via online omics data and local tissues. Moreover, the effects of FLOT1 depletion on cell proliferation and invasion were also detected. Besides, the underlying roles of N6-methyladenosine modification (m6A) in FLOT1 upregulation was further explored. The results demonstrated that FLOT1 was significantly upregulated in gliomas and positively correlated with advanced progression and poor prognosis of patients. FLOT1 silencing notably suppressed the cell proliferation and invasion in gliomas. The expression of WTAP and IGF2BP2was positively correlated with FLOT1 expression and served as the writer and reader of FLOT1 m6A, respectively, which stabilized FLOT1 mRNA and maintained its upregulation in gliomas. Lastly, ectopic expression of FLOT1 could notably restore the inhibitory effects caused by WTAP and IGF2BP2 depletion in glioma cells. Collectively, our results originally confirmed the upregulation and oncogenic roles of FLOT1, and revealed that WTAP/IGF2BP2 mediated m6A contributed to the upregulation of FLOT1 in gliomas, highlighting the promising application of WTAP/IGF2BP2/FLOT1 axis in target treatment of gliomas.
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Affiliation(s)
- Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurosurgery, Xiangya Jiangxi Hospital, Central South University, Nanchang, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhongxu Hu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chong Zeng
- Department of Medicine, The Seventh Affiliated Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Haijun Luo
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Jie Liu
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
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Ji S, Xu M, Cai C, He X. MESP1-knockdown inhibits the proliferation and epithelial mesenchymal transition of hepatocellular carcinoma and enhances the tumor-suppressive effect of 5-fluorouracil. Biochem Biophys Res Commun 2023; 670:1-11. [PMID: 37271034 DOI: 10.1016/j.bbrc.2023.05.036] [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: 04/17/2023] [Revised: 05/03/2023] [Accepted: 05/12/2023] [Indexed: 06/06/2023]
Abstract
Primary liver hepatocellular carcinoma (HCC) is the third most deadly malignancy worldwide,in part, because it is often diagnosed at an advanced stage. Thus, molecular markers are needed to aid in the early diagnosis and treatment of HCC. Expression of abnormal mesoderm posterior-1 (MESP1) promotes tumorigenesis; however,its role in the regulation of HCC proliferation, apoptosis,and invasion is unknown. Here,we analyzed data in The Cancer Genome Atlas (TCGA)and Genotype Tissue Expression (GTEx) databases on the pan-cancer expression of MESP1 and its relationship with clinical characteristics and prognosis of patients with HCC. The expression of MESP1 was measured in 48 HCC tissues using immunohistochemical staining,and the results were correlated with clinical stage, tumor differentiation, tumor size,and metastasis. MESP1 expression was downregulated using small interfering RNA (siRNA) in the HCC cell lines HepG2 and Hep3B,and cell viability, proliferation,cell cycle, apoptosis,and invasion were analyzed. Finally,we also evaluated the tumor suppression effect of MESP1 downregulation combined with 5-fluorouracil (5-FU) treatment. Our results showed that MESP1 is a pan-oncogene associated with poor prognosis in patients with HCC. siRNA-induced downregulation of MESP1 expression in HepG2 and Hep3B cells exhibited downregulation of β-catenin and GSK3β expression 48h after transfection, along with an increase in apoptosis rate, arrest in the G1-S phase,and a decrease in mitochondrial membrane potential. Moreover,the expression levels of c-Myc, PARP1, bcl2, Snail1, MMP9, and immune checkpoint genes (TIGIT, CTLA4,LAG3,CD274,and PDCD1) were downregulated, while those of caspase3 and E-cadherin were upregulated. Tumor cells also showed decreased migration ability. Furthermore, siRNA interference of MESP1 expression combined with 5-FU-treatment of HCC cells significantly enhanced the G1-S phase block and apoptosis. MESP1 showed an aberrant high expression in HCC and was associated with poor clinical outcomes; therefore, MESP1 may be a potential target for the diagnosis and treatment of HCC.
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Affiliation(s)
- Shuqin Ji
- Department of Pathology, Chongqing Medical University, 400016, China; Pathological Diagnosis Center of Chongqing Medical University, 400016, China
| | - Man Xu
- Department of Pathology, Chongqing Medical University, 400016, China; Pathological Diagnosis Center of Chongqing Medical University, 400016, China.
| | - Chenyu Cai
- Department of Pathology, Chongqing Medical University, 400016, China; Pathological Diagnosis Center of Chongqing Medical University, 400016, China
| | - Xinyue He
- Department of Pathology, Chongqing Medical University, 400016, China; Pathological Diagnosis Center of Chongqing Medical University, 400016, China
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Wang H, Yang C, Li D, Wang R, Li Y, Lv L. Bioinformatics analysis and experimental validation of a novel autophagy-related signature relevant to immune infiltration for recurrence prediction after curative hepatectomy. Aging (Albany NY) 2023; 15:2610-2630. [PMID: 37014321 PMCID: PMC10120910 DOI: 10.18632/aging.204632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/05/2023]
Abstract
Hepatocellular carcinoma (HCC) remains imposing an enormous economic and healthcare burden worldwide. In this present study, we constructed and validated a novel autophagy-related gene signature to predict the recurrence of HCC patients. A total of 29 autophagy-related differentially expressed genes were identified. A five-gene signature (CLN3, HGF, TRIM22, SNRPD1, and SNRPE) was constructed for HCC recurrence prediction. Patients in high-risk groups exhibited a significantly poor prognosis compared with low-risk patients both in the training set (GSE14520 dataset) and the validation set (TCGA and GSE76427 dataset). Multivariate cox regression analysis demonstrated that the 5-gene signature was an independent risk factor for recurrence-free survival (RFS) in HCC patients. The nomograms incorporating 5-gene signature and clinical prognostic risk factors were able to effectively predict RFS. KEGG and GSEA analysis revealed that the high-risk group was enriched with multiple oncology characteristics and invasive-related pathways. Besides, the high-risk group had a higher level of immune cells and higher levels of immune checkpoint-related gene expression in the tumor microenvironment, suggesting that they might be more likely to benefit from immunotherapy. Finally, the immunohistochemistry and cell experiments confirmed the role of SNRPE, the most significant gene in the gene signature. SNRPE was significantly overexpressed in HCC. After SNRPE knockdown, the proliferation, migration and invasion ability of the HepG2 cell line were significantly inhibited. Our study established a novel five-gene signature and nomogram to predict RFS of HCC, which may help in clinical decision-making for individual treatment.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Chengkai Yang
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
| | - Dong Li
- Department of Anesthesiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei 430061, China
| | - Ruling Wang
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Yanbing Li
- Department of Hepatobiliary and pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Lizhi Lv
- Department of Hepatobiliary Surgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, China
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistic Team, Fuzhou, Fujian 350025, China
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Peng Q, Jiang X, Tan S, Xu X, Xia L, Wu N, Lin J, Oyang L, Tang Y, Peng M, Su M, Luo X, Han Y, Liao Q, Zhou Y. Clinical significance and integrative analysis of the cuproptosis-associated genes in head and neck squamous cell carcinoma. Aging (Albany NY) 2023; 15:1964-1976. [PMID: 36947706 PMCID: PMC10085596 DOI: 10.18632/aging.204579] [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: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023]
Abstract
Head and neck squamous cell carcinoma (HNSC) is a kind of malignant tumor originating from the oropharynx, larynx, nasopharynx and oral cavity. The incidence of HNSC is increasing and it is the sixth malignant tumor in the world at present. "Cuprotosis" is a novel cuper-dependent cell death mode that is closely related to mitochondrial respiration. Tumorigenesis is closely related to the dysregulation of cell death. However, the relationship between cuprotosis and HNSC remains unclear. Here, we investigated the association between 10 cuprotosis-associated genes (CAGs) and HNSC using multi-omics public data. We found that CAGs had abnormal expression and significant genetic changes in HNSC, especially CDKN2A with 54% mutation rate. Expression of CAGs significantly correlates with the prognosis of HNSC patients. Moreover, the CAGs expression is correlated with the immune checkpoints expression and immune cells infiltration. These CAGs expression was associated with multiple drugs sensitivity of cancer cells, such as cisplatin and docetaxel. These findings indicate that CAGs are likely to serve an essential role in the diagnosis, prognosis, immunotherapy and drug therapy prediction of HNSC.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xuemeng Xu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Mingjing Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China
- Public Service Platform of Tumor Organoids Technology, Changsha 410013, Hunan, China
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Zhong Y, Zheng C, Zhang W, Wu H, Wang M, Zhang Q, Feng H, Wang G. Pan-Cancer analysis and experimental validation identify the oncogenic nature of ESPL1: Potential therapeutic target in colorectal cancer. Front Immunol 2023; 14:1138077. [PMID: 37006282 PMCID: PMC10060535 DOI: 10.3389/fimmu.2023.1138077] [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: 01/05/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionExtra spindle pole bodies like 1 (ESPL1) are required to continue the cell cycle, and its primary role is to initiate the final segregation of sister chromatids. Although prior research has revealed a link between ESPL1 and the development of cancer, no systematic pan-cancer analysis has been conducted. Combining multi-omics data with bioinformatics, we have thoroughly described the function of ESPL1 in cancer. In addition, we examined the impact of ESPL1 on the proliferation of numerous cancer cell lines. In addition, the connection between ESPL1 and medication sensitivity was verified using organoids obtained from colorectal cancer patients. All these results confirm the oncogene nature of ESPL1.MethodsHerein, we downloaded raw data from numerous publicly available databases and then applied R software and online tools to explore the association of ESPL1 expression with prognosis, survival, tumor microenvironment, tumor heterogeneity, and mutational profiles. To validate the oncogene nature of ESPL1, we have performed a knockdown of the target gene in various cancer cell lines to verify the effect of ESPL1 on proliferation and migration. In addition, patients’ derived organoids were used to verify drug sensitivity.ResultsThe study found that ESPL1 expression was markedly upregulated in tumorous tissues compared to normal tissues, and high expression of ESPL1 was significantly associated with poor prognosis in a range of cancers. Furthermore, the study revealed that tumors with high ESPL1 expression tended to be more heterogeneous based on various tumor heterogeneity indicators. Enrichment analysis showed that ESPL1 is involved in mediating multiple cancer-related pathways. Notably, the study found that interference with ESPL1 expression significantly inhibited the proliferation of tumor cells. Additionally, the higher the expression of ESPL1 in organoids, the greater the sensitivity to PHA-793887, PAC-1, and AZD7762.DiscussionTaken together, our study provides evidence that ESPL1 may implicate tumorigenesis and disease progression across multiple cancer types, highlighting its potential utility as both a prognostic indicator and therapeutic target.
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Affiliation(s)
- Yuchen Zhong
- Cancer Center/Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Department of Colorectal Cancer Surgery, The Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Science, Hangzhou, Zhejiang, China
| | - Chaojing Zheng
- Cancer Center/Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Weiyuan Zhang
- Cancer Center/Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongyu Wu
- Department of Colorectal Cancer Surgery, The Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Science, Hangzhou, Zhejiang, China
| | - Meng Wang
- Department of Colorectal Cancer Surgery, The Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Science, Hangzhou, Zhejiang, China
| | - Qian Zhang
- Department of Colorectal Cancer Surgery, The Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Science, Hangzhou, Zhejiang, China
| | - Haiyang Feng
- Department of Colorectal Cancer Surgery, The Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Science, Hangzhou, Zhejiang, China
- *Correspondence: Haiyang Feng, ; Guiyu Wang,
| | - Guiyu Wang
- Cancer Center/Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Haiyang Feng, ; Guiyu Wang,
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Xu X, Ju Y, Zhao X, Yang P, Zhu F, Fang B. SMG7-AS1 as a prognostic biomarker and predictor of immunotherapy responses for skin cutaneous melanoma. Genomics 2023; 115:110614. [PMID: 36931476 DOI: 10.1016/j.ygeno.2023.110614] [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: 11/04/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the most life-threatening skin cancer and lacks early detection and effective treatment strategies. Many long noncoding RNAs are associated with the development of tumors and may serve as potential immunotherapeutic targets. In this study, microarray analysis was performed to screen for differentially expressed lncRNAs between SKCM and normal tissues, and SMG7-AS1 was identified as an upregulated lncRNA in SKCM. Subsequently, bioinformatic analysis revealed that dysregulation of SMG7-AS1 influences metastasis and immune infiltration. qRT-PCR of clinical samples demonstrated that the expression of SMG7-AS1 was higher in melanoma tissues. Flow cytometry showed that SMG7-AS1 plays a vital role in the cell cycle. Additionally, SMG7-AS1 was found to be associated with immunotherapy responses. To the best of our knowledge, this study is the first to report that SMG7-AS1 is associated with SKCM and may serve as a prognostic biomarker and predictor of immunotherapy responses in SKCM.
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Affiliation(s)
- Xuezheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xueheng Zhao
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Pu Yang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Fang Zhu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410078, People's Republic of China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China.
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Zhou H, Zeng C, Liu J, Luo H, Huang W. F-Box Protein 43, Stabilized by N6-Methyladenosine Methylation, Enhances Hepatocellular Carcinoma Cell Growth and Invasion via Promoting p53 Degradation in a Ubiquitin Conjugating Enzyme E2 C-Dependent Manner. Cancers (Basel) 2023; 15:cancers15030957. [PMID: 36765911 PMCID: PMC9913344 DOI: 10.3390/cancers15030957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The roles of F-box protein 43 (FBXO43) in carcinogenesis have been rarely revealed. The present study investigates the expression, function, and underlying mechanism of FBXO43 in hepatocellular carcinoma (HCC). Firstly, the expression and clinical significance of FBXO43 in HCC were investigated bioinformatically and experimentally using online omics data and local tissue samples. The role of N6-methyladenosine modification (m6A) of mRNA in regulating FBXO43 expression and the effects of m6A/FBXO43 axis alteration on cell proliferation and invasion were investigated further. Moreover, the underlying mechanism of the oncogenic FBXO43 was also explored. The results demonstrated that FBXO43 was significantly upregulated in HCC and was positively correlated with advanced progression and poor prognosis in patients. METTL3 and IGF2BP2 expressions were positively correlated with FBXO43 expression and served as the writer and reader of FBXO43 m6A, respectively, which stabilized and upregulated FBXO43 mRNA in HCC. FBXO43 silencing significantly reduced cell proliferation and invasion, and ectopic expression of FBXO43 could significantly restore the inhibitory effects caused by METTL3 and IGF2BP2 depletion in HCC cells. Mechanistically, FBXO43 depletion reduced the expression of UBE2C, a p53 ubiquitin-conjugating enzyme, suppressed proteasomal degradation of p53, and thus inhibited cell proliferation and invasion in HCC. In summary, the present study revealed that METTL3/IGF2BP2 mediated m6A contributed to the upregulation of FBXO43 that promoted the malignant progression of HCC by stimulating p53 degradation in a UBE2C-dependent manner, highlighting the promising application of FBXO43 as a target in HCC treatment.
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Affiliation(s)
- Huijun Zhou
- Department of Gastroenterology and Urology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410083, China
| | - Chong Zeng
- Department of Medicine, The Seventh Affiliated Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Jie Liu
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Haijun Luo
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Wei Huang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410083, China
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha 410083, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-18773187433
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Wu H, He H, Huang J, Wang C, Dong Y, Lin R, Cheng Z, Qiu Q, Hong L. Identification and validation of transferrin receptor protein 1 for predicting prognosis and immune infiltration in lower grade glioma. Front Mol Neurosci 2022; 15:972308. [PMID: 36483569 PMCID: PMC9723399 DOI: 10.3389/fnmol.2022.972308] [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: 06/18/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Transferrin receptor protein 1 (TFRC), an ananda molecule associated with ferroptosis, has been identified as affecting a wide spectrum of pathological processes in various cancers, but the prognostic value correlates with the tumor microenvironment of TFRC in lower-grade glioma (LGG) is still unclear. MATERIALS AND METHODS Clinical pathological information and gene expression data of patients with LGG come from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), GTEx, Oncomine, UCSC Xena, and GEO databases. We then used various bioinformatics methods and mathematical models to analyze those data, aiming to investigate the clinical significance of TFRC in LGG and illustrate its association with tumor immunity. In addition, the molecular function and mechanisms of TFRC were revealed by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). Immunohistochemical experiments and single-cell analysis have been performed. RESULTS TFRC expression was highly expressed in many tumors and showed a poor prognosis. Including gliomas, it was significantly associated with several poor clinical prognostic variables, tumor immune microenvironment, tumor mutational burden (TMB), m6a modification, and ferroptosis in LGG. TFRC as a key factor was further used to build a prediction nomogram. The C-index, calibration curve, and decision curve analysis showed the nomogram was clinically useful and calibration was accurate. At the same time, we also demonstrated that promoter hypomethylation of DNA upstream of TFRC could lead to high TFRC expression and poor overall survival. There is a significant correlation between TFRC and CD8 + T cell, macrophage cell infiltration, and several immune checkpoints, such as PD-L1(cd274), CTLA4, and PD1, suggesting a novel direction for future clinical application. Functional and molecular mechanism analysis showed an association of TFRC expression with immune-related pathways through GSEA, GO, and KEGG analysis. Finally, immunohistochemical experiments and single-cell analysis confirmed the expression of TFRC in glioma. CONCLUSION TFRC may be a potential prognostic biomarker and an immunotherapeutic target for glioma.
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Affiliation(s)
- Hongrong Wu
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Haoyang He
- The First Clinical Medical College of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jiexiong Huang
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Chuan Wang
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuejiao Dong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ruilin Lin
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhuofeng Cheng
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Qiancheng Qiu
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - LiangLi Hong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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Wei Z, Gan J, Feng X, Zhang M, Chen Z, Zhao H, Du Y. APOBEC3B is overexpressed in cervical cancer and promotes the proliferation of cervical cancer cells through apoptosis, cell cycle, and p53 pathway. Front Oncol 2022; 12:864889. [PMID: 36249021 PMCID: PMC9556651 DOI: 10.3389/fonc.2022.864889] [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: 01/29/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
Objective APOBEC3B (A3B), a member of the APOBEC family of cytidine deaminases, has been gradually regarded as a key cancerous regulator. However, its expression and mechanism in cervical cancer (CC) have not been fully elucidated. This study was to investigate its expression pattern and potential mechanism on the cell cycle, as well as HPV oncogenes in CC. Methods Data from The Cancer Genome Atlas (TCGA) and Gene Expression (GEO) were used to indicate the mRNA expression pattern of A3B in cervical cancer. Western blot assay was used to detect A3B levels in SiHa and Hela cell lines. Immunohistochemistry (IHC) was used to explore A3B protein abundance and sublocation in cervical cancer as well as normal cervical tissues. Based on the Protein atlas (www.proteinatlas.org), A3B expression in the SiHa cell line is lower than in the HeLa cell line. Therefore, the SiHa cell line was used for A3B gene overexpression experiments while the HeLa cell line was used for knockdown experiments. Flow cytometry analysis was used to detect cell apoptosis. Biological function and cancer-related pathways of A3B were conducted using bioinformatics analysis. Results A3B mRNA was significantly overexpressed in cervical cancer in TCGA-cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), GSE67522, and GSE7803. A3B was more highly expressed in cervical cancers than in high-grade squamous intraepithelial lesions and normal controls. A3B expression was found to be progressively activated during cervical cancer development. IHC results showed that A3B was significantly higher in cervical cancer tissues than in normal cervical tissues. A3B plasmid-mediated overexpression experiments and A3B siRNA-mediated knockdown experiments showed that A3B significantly promotes cell proliferation, migration, cell cycle, and chemoresistance in cervical cancer cells by the p53 pathway. GO and KEGG analyses showed that A3B expression was strikingly associated with cell proliferation, apoptosis, and immune-associated pathways. Conclusions Taken together, our study implies that A3B promotes cell proliferation, migration, and cell cycle and inhibits cancer cell apoptosis through the p53-mediated signaling pathway. Moreover, A3B could also contribute to chemoresistance in cervical cancer cells. It may be a potential diagnostic biomarker and therapeutic target for chemoresistant cervical cancers.
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Affiliation(s)
- Zhi Wei
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
| | - Jianfeng Gan
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
| | - Xuan Feng
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
| | - Mo Zhang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
- Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Zhixian Chen
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
| | - Hongbo Zhao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
- *Correspondence: Yan Du, ; Hongbo Zhao,
| | - Yan Du
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai, China
- Institutes of Integrative Medicine, Fudan University, Shanghai, China
- *Correspondence: Yan Du, ; Hongbo Zhao,
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He S, Qiao J, Wang L, Yu L. A novel immune-related gene signature predicts the prognosis of hepatocellular carcinoma. Front Oncol 2022; 12:955192. [PMID: 36185203 PMCID: PMC9520462 DOI: 10.3389/fonc.2022.955192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
Immune-related genes play a key role in regulating the cancer immune microenvironment, influencing the overall survival of patients with hepatocellular carcinoma (HCC). Along with the rapid development of immunotherapy, identifying immune-related genes with prognostic value in HCC has attracted increasing attention. Here, we aimed to develop a prognostic signature based on immune-related genes. By investigating the transcriptome landscape of 374 HCC and 160 non-HCC samples in silico, a total of 2251 differentially expressed genes were identified. Among which, 183 differentially expressed immune-related genes were subjected to a univariate Cox proportional hazard model to screen for genes with possible prognostic significance. A 10-gene prognostic signature, including HLA-G, S100A9, S100A10, DCK, CCL14, NRAS, EPO, IL1RN, GHR and RHOA, was generated employing a multivariate Cox proportional hazard model. Kaplan–Meier and Receiver Operator Characteristic (ROC) curves were used to evaluate the prognostic utility of the 10-gene signature. Moreover, the underlying mechanisms of these genes were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. According to the Tumor Immune Estimation Resource (TIMER) database, our prognostic signature was significantly associated with tumor-infiltrating B cells, CD4 T cells, dendritic cells, macrophages and neutrophils. Our study provides a novel prognostic signature based on immune-related genes associated with clinical outco mes of HCC.
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Huan S, Chen M, Sun S, Zhong Y, Chen Y, Ji Y, Yin G. Identification of a 5-lncRNA-Based Signature for Immune Characteristics and Prognosis of Lung Squamous Cell Carcinoma and Verification of the Function of lncRNA SPATA41. Front Genet 2022; 13:905353. [PMID: 36105081 PMCID: PMC9465393 DOI: 10.3389/fgene.2022.905353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the most lethal cancers worldwide. Traditional tumor-node-metastasis (TNM) staging system has many insufficiencies in predicting immune characteristics, overall survival (OS), and prognosis of LUSC. LncRNA is currently found involved in tumor development and effectively predicts tumor prognosis. We screened potential tumor-related lncRNAs for immune characteristics and constructed a nomogram combining lncRNA and traditional clinical indicators for prognosis prediction. We obtained the large-scale gene expression profiles of samples from 492 LUSC patients in The Cancer Genome Atlas database. SPATA41, AL034550.2, AP003721.2, AC106786.1, and AC078889.1 were finally screened to construct a 5-lncRNA-based signature. The risk score of the signature divided patients into subgroups of high-risk and low-risk with significant differences in OS. Their area under the curve (AUC) reached more than 0.70 in 1, 3, and 5 years. In addition, compared with the high-risk subgroup, the low-risk subgroup exhibited a remarkably favorable prognosis and TME score, along with a higher immune infiltration score and lower TIDE score. The signature also significantly related to chemotherapy response, especially in cisplatin, vinorelbine, and paclitaxel. Importantly, the nomogram we constructed had good reliability with the assessment of the calibration chart and consistency index (c-index). GO and KEGG enrichment analysis indicated that co-expression mRNAs of the 5 lncRNAs were mainly focused on RNA splicing, DNA replication, and protein serine/threonine kinase activity. Functional assays demonstrated that SPATA41, one of the five OS-related lncRNAs, regulated invasion, migration, proliferation, and programmed death in vitro. In summary, our 5-lncRNA-based signature has a good performance in predicting immune characteristics and prognosis of LUSC patients.
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Affiliation(s)
- Sheng Huan
- Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Department of Anesthesiology, Nanjing Second Hospital, Nanjing, China
| | - Miao Chen
- Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Department of Surgery, Nanjing Second Hospital, Nanjing, China
| | - Sumin Sun
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Yanling Zhong
- Department of Anesthesiology, Nanjing Second Hospital, Nanjing, China
| | - Yu Chen
- Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Yihao Ji
- Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Department of Critical Medicine, Nanjing Second Hospital, Nanjing, China
| | - Guoping Yin
- Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Department of Anesthesiology, Nanjing Second Hospital, Nanjing, China
- *Correspondence: Guoping Yin,
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Zhang H, Huang T, Ren X, Fang X, Chen X, Wei H, Sun W, Wang Y. Integrated pan-cancer analysis of CSMD2 as a potential prognostic, diagnostic, and immune biomarker. Front Genet 2022; 13:918486. [PMID: 36061177 PMCID: PMC9428318 DOI: 10.3389/fgene.2022.918486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
The protein encoded by CUB and Sushi Multiple Domains 2 (CSMD2) is likely involved in regulating the complement cascade reaction of the immune system. However, current scientific evidence on the comprehensive roles of CSMD2 in pan-cancer is relatively scarce. Therefore, in this study, we explored the transcriptional level of CSMD2 in pan-caner using TCGA, GEO, and International Cancer Genome Consortium databases. Receiver operating characteristic curve analysis was used to investigate the diagnostic efficacy of CSMD2. The Kaplan-Meier Plotter and Oncolnc were used to investigate the correlation between CSMD2 expression and prognosis. Additionally, we analyzed the correlation between epigenetic methylation and CSMD2 expression in various cancers based on UALCAN, as well as, the correlation between CSMD2 and tumor mutational burden (TMB), microsatellite instability (MSI), and tumor neoantigen burden (TNB) in tumors. TIMER2.0 database was employed to investigate the correlation between CSMD2 and immune cells in the tumor microenvironment and immune checkpoints. Based on TISIDB, the correlation between CSMD2 and MHC molecules and immunostimulators was analyzed. Ultimately, we observed with a pan-cancer analysis that CSMD2 was upregulated in most tumors and had moderate to high diagnostic efficiency, and that high expression was closely associated with poor prognosis in patients with tumors. Moreover, hypermethylation of CSMD2 promoter and high levels of m6A methylation regulators were also observed in most cancers. CSMD2 expression was negatively correlated with TMB and MSI in stomach adenocarcinoma (STAD) and stomach and esophageal carcinoma (STES), as well as with tumor mutational burden, microsatellite instability, and TNB in head-neck squamous cell carcinoma (HNSC). In most cancers, CSMD2 might be associated with immune evasion or immunosuppression, as deficient anti-tumor immunity and upregulation of immune checkpoints were also observed in this study. In conclusion, CSMD2 could serve as a promising prognostic, diagnostic and immune biomarker in pan-cancer.
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Affiliation(s)
- Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Taobi Huang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiangqing Ren
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xia Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Hui Wei
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Weiming Sun
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Yuping Wang,
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Meng Q, Xu Y, Ling X, Liu H, Ding S, Wu H, Yan D, Fang X, Li T, Liu Q. Role of ferroptosis-related genes in coronary atherosclerosis and identification of key genes: integration of bioinformatics analysis and experimental validation. BMC Cardiovasc Disord 2022; 22:339. [PMID: 35906548 PMCID: PMC9338511 DOI: 10.1186/s12872-022-02747-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background Coronary atherosclerosis (CA) is the most common type of atherosclerosis. However, the inherent pathogenesis and mechanisms of CA are unclear, and the relationship with ferroptosis-related genes (FRGs) has not been reported. The purpose of this study was to use bioinformatics techniques to evaluate potential therapeutic targets for CA.Please provide the given name for author “Dingshun”.Please provide the given name for author “Dingshun”.
Methods First, the GSE132651 dataset was acquired from the Gene Expression Omnibus database. Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Protein–Protein interaction network were successively conducted. Next, overlapping genes between hub genes and CA genes were found. FRGs were found when comparing the CA group with the normal group. The correlation between overlapping genes and FRGs was further analyzed. At last, we performed Elisa to validate the expression of these genes in human blood specimens. Mice aortic tissues were used for western blot to detect the expression of proteins. Results Based on the GSE132651 dataset, 102 differentially expressed genes were identified. Five overlapping genes between hub genes and CA genes were found (CCNA2, RRM2, PBK, PCNA, CDK1). TFRC and GPX4 were found to be FRGs. TFRC was positively correlated with CCNA2, PBK, PCNA, CDK1, RRM2, with CDK1 being the strongest correlation. GPX4 was negatively correlated with these genes, among which CCNA2 was the strongest correlation. The ELISA results showed that CCNA2, CDK1, and TFRC expression were markedly increased in serum of the CA samples compared with controls, while GPX4 expression was markedly decreased in the CA samples. The western blot results show that GPX4 expression was lower in the model group, TFRC, CDK1, and CCNA2 protein expression were high in the model group. Conclusions Ferroptosis-related genes GPX4 and TFRC were closely correlated with the identified overlapping genes CCNA2 and CDK1, which may serve as targeted therapies for the treatment of CA. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02747-x.
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Affiliation(s)
- Qingwen Meng
- Deparment of Cardiology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China.,Hainan Provincial Key Laboratory of Tropical Brain Research and Transformation, Hainan Medical University, Haikou, 570100, China
| | - Yiqian Xu
- Department of Pharmacology, Hainan Medical University, Haikou, 570100, China
| | - Xuebin Ling
- Deparment of Cardiology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China
| | - Huajiang Liu
- Deparment of Cardiology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China
| | - Shun Ding
- Department of Pharmacology, Hainan Medical University, Haikou, 570100, China
| | - Haolin Wu
- Department of Pharmacology, Hainan Medical University, Haikou, 570100, China
| | - Dongming Yan
- Department of Pharmacology, Hainan Medical University, Haikou, 570100, China
| | - Xingyue Fang
- Deparment of Cardiology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China
| | - Tianfa Li
- Deparment of Cardiology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China.
| | - Qibing Liu
- Department of Pharmacology, Hainan Medical University, Haikou, 570100, China. .,Department of Pharmacy, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China.
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Pan D, Wu W, Zuo G, Xie X, Li H, Ren X, Kong C, Zhou W, Zhang Z, Waterfall M, Chen S. Sphingosine 1-phosphate receptor 2 promotes erythrocyte clearance by vascular smooth muscle cells in intraplaque hemorrhage through MFG-E8 production. Cell Signal 2022; 98:110419. [PMID: 35905868 DOI: 10.1016/j.cellsig.2022.110419] [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: 06/07/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 11/03/2022]
Abstract
Intraplaque hemorrhage (IPH) accelerates atherosclerosis progression. To scavenge excessive red blood cells (RBCs), vascular smooth muscle cells (VSMCs) with great plasticity may function as phagocytes. Here, we investigated the erythrophagocytosis function of VSMCs and possible regulations involved. Based on transcriptional microarray analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that genes up-regulated in human carotid atheroma with IPH were enriched in functions of phagocytic activities, while those down-regulated were enriched in VSMCs contraction function. Transcriptional expression of Milk fat globule-epidermal growth factor 8 (MFG-E8) was also down-regulated in atheroma with IPH. In high-fat diet-fed apolipoprotein E-deficient mice, erythrocytes were present in cells expressing VSMC markers αSMA in the brachiocephalic artery, suggesting VSMCs play a role in erythrophagocytosis. Using immunofluorescence and flow cytometry, we also found that eryptotic RBCs were bound to and internalized by VSMCs in a phosphatidylserine/MFG-E8/integrin αVβ3 dependent manner in vitro. Inhibiting S1PR2 signaling with specific inhibitor JTE-013 or siRNA decreased Mfge8 expression and impaired the erythrophagocytosis of VSMCs in vitro. Partial ligation was performed in the left common carotid artery (LCA) followed by intra-intimal injection of isolated erythrocytes to observe their clearance in vivo. Interfering S1PR2 expression in VSMCs with Adeno-associated virus 9 inhibited MFG-E8 expression inside LCA plaques receiving RBCs injection and attenuated erythrocytes clearance. Erythrophagocytosis by VSMCs increased vascular endothelial growth factor-a secretion and promoted angiogenesis. The present study revealed that VSMCs act as phagocytes for RBC clearance through S1PR2 activation induced MFG-E8 release.
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Affiliation(s)
- Daorong Pan
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Wen Wu
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Guangfeng Zuo
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xiangrong Xie
- Department of Cardiology, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
| | - Hui Li
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xiaomin Ren
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Chaohua Kong
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Wenying Zhou
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Zihan Zhang
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Martin Waterfall
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Shaoliang Chen
- Department of Cardiology, Nanjing First Hospital, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210006, Jiangsu, China.
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Guo J, Zhao C, Zhang X, Wan Z, Chen T, Miao J, Cai J, Xie W, Chen H, Huang M, Zhao X, Wei W, Shen Q. A novel 8-gene panel for prediction of early biochemical recurrence in patients with prostate cancer after radical prostatectomy. Am J Cancer Res 2022; 12:3318-3332. [PMID: 35968320 PMCID: PMC9360249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
Approximately 25% of prostate cancer (PCa) cases experience biochemical recurrence (BCR) following radical prostatectomy (RP). The patients with BCR, especially with BCR ≤2 year after RP (early BCR), are more likely to develop clinical metastasis and castration resistance. Now decision-making regarding BCR after RP relies solely on clinical parameters. We thus attempted to establish an early BCR-risk prediction model by combining a molecular signature with clinicopathological features for guiding clinical decision-making. In this study, an 8-gene signature was derived, and these eight genes were SPTBN2, LGI3, TGM3, LENG9, HAS3, SLC25A27, PCDHGA1, and ADPRHL1. The Kaplan-Meier analysis revealed a significantly prolonged BCR-free survival in the patients with low-risk scores compared to those with high-risk scores in both training and validation datasets. Harrell's concordance index and time-dependent receiver operating characteristic analysis demonstrated that this gene signature tended to outperform three commercial panels at early BCR prediction. Moreover, this signature was also proven as an independent predictor of BCR-free survival. A nomogram, incorporating the gene signature and clinicopathologic features, was constructed and excellently predicted 1-, 2- and 3-year BCR-free survival of localized PCa patients after RP. Gene set enrichment analysis, tumor immunity, and mRNA expression profiling analysis showed that the high-risk group was more prone to the immunosuppressive microenvironment and impaired DNA damage response than the low-risk group. Collectively, we successfully developed a novel 8-gene signature as a powerful predictor for early BCR after RP and created a prognostic nomogram, which may help inform the clinical management of PCa.
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Affiliation(s)
- Jinan Guo
- Department of Urology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
- Shenzhen Urology Minimally Invasive Engineering CenterShenzhen, China
| | - Chenhui Zhao
- Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xinzhou Zhang
- Department of Nephrology, Shenzhen key Laboratory of Kindey Diseases, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
| | - Zhong Wan
- Shuguang Hospital, Shanghai University of Traditional Chinese MedicineShanghai, China
| | | | | | | | | | - Hao Chen
- 3D Medicines, IncShanghai, China
| | | | | | - Wei Wei
- Department of Urology, Hwa Mei Hospital, University of Chinese Academy of SciencesNingbo, China
| | - Qi Shen
- Department of Hematology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
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Peng L, Zhu N, Wang D, Zhou Y, Liu Y. Comprehensive Analysis of Prognostic Value and Immune Infiltration of NLRC4 and CASP1 in Colorectal Cancer. Int J Gen Med 2022; 15:5425-5440. [PMID: 35692355 PMCID: PMC9174061 DOI: 10.2147/ijgm.s353380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 05/16/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction Nod-like receptor C4 (NLRC4) is a member of the Nod-like receptor (NLR) family, and its expression mediates the activation of caspase-1 (CASP1). Abnormal expression of NLRC4 and CASP1 is associated with multiple tumors. However, the expression differences, prognostic value and immune correlation of NLRC4 and CASP1 in colorectal cancer (CRC) remain to be determined. Methods In this study, TCGA, CCLE, HPA, PrognoScan, STRING and GeneMANIA databases were used to analyze differences in expression, prognostic value, genetic alterations and immune cell infiltration of NLRC4 and CASP1 in CRC patients. Then, we further validated the expression of NLRC4 and CASP1 in CRC using immunohistochemistry (IHC). Results NLRC4 and CASP1 were expressed low in CRC tissues and CRC cell lines. The expression of NLRC4 was significantly related to the patient’s gender and lymph node metastasis. NLRC4 and CASP1 down-regulated expression was observably correlated with poor survival and diverse immune cells infiltration in CRC patients. NLRC4 and CASP1 have a gene mutation alteration. NLRC4 and CASP1 had a significant positive correlation in CRC. Conclusion This study will provide new ideas for the prognosis and treatment in CRC. NLRC4 and CASP1 are expected to be novel biomarkers and potential immunotherapy targets in CRC patients.
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Affiliation(s)
- Li Peng
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People’s Republic of China
| | - Ni Zhu
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People’s Republic of China
| | - Dan Wang
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People’s Republic of China
| | - Yanhong Zhou
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People’s Republic of China
- Correspondence: Yanhong Zhou; Yifei Liu, Email ;
| | - Yifei Liu
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People’s Republic of China
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Zheng D, Wang X, Cheng L, Qin L, Jiang Z, Zhao R, Li Y, Shi J, Wu Q, Long Y, Wang S, Tang Z, Wei W, Yang J, Li Y, Zhou H, Liu Q, Liu P, Chen X, Yao Y, Yang L, Li P. The Chemokine Receptor CCR8 Is a Target of Chimeric Antigen T Cells for Treating T Cell Malignancies. Front Immunol 2022; 13:808347. [PMID: 35693763 PMCID: PMC9182403 DOI: 10.3389/fimmu.2022.808347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells have been successfully used in the therapy of B cell leukemia and lymphoma, but still have many challenges in their use for treating T cell malignancies, such as the lack of unique tumor antigens, their limitation of T cell expansion, and the need for third party donors or genome editing. Therefore, we need to find novel targets for CAR T cell therapy to overcome these challenges. Here, we found that both adult T-cell leukemia/lymphoma (ATLL) patients and ATLL cells had increased CCR8 expression but did not express CD7. Moreover, targeting CCR8 in T cells did not impair T cell expansion in vitro. Importantly, anti-CCR8 CAR T cells exhibited antitumor effects on ATLL- and other CCR8-expressing T-ALL cells in vitro and in vivo, and prolonged the survival of ATLL and Jurkat tumor-bearing mouse models. In conclusion, these collective results show that anti-CCR8 CAR T cells possess strong antitumor activity and represent a promising therapeutic approach for ATLL and CCR8+ tumors.
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Affiliation(s)
- Diwei Zheng
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xindong Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Lin Cheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Le Qin
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiwu Jiang
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruocong Zhao
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, Hong Kong SAR, China
| | - Yao Li
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingxuan Shi
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiting Wu
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Youguo Long
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Suna Wang
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhaoyang Tang
- Guangdong Zhaotai In vivo Biomedicine Ltd., Guangzhou, China
- Guangdong Zhaotai Cell Biology Technology Ltd., Foshan, China
| | - Wei Wei
- Guangdong Cord Blood Bank, Guangzhou, China
| | - Jie Yang
- Guangdong Women and Children Hospital, Guangzhou, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pentao Liu
- School of Biomedical Sciences, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Xinwen Chen
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yao Yao
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - LiHua Yang
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Li
- China-New Zealand Joint Laboratory of Biomedine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, Hong Kong SAR, China
- *Correspondence: Peng Li,
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Wang H, Yang C, Jiang Y, Hu H, Fang J, Yang F. A novel ferroptosis-related gene signature for clinically predicting recurrence after hepatectomy of hepatocellular carcinoma patients. Am J Cancer Res 2022; 12:1995-2011. [PMID: 35693077 PMCID: PMC9185608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
High recurrence rate in HCC is the primary cause of the poor prognosis after hepatectomy. Therefore, in this study, we aimed to construct a gene signature for predicting the recurrence rate in HCC. The mRNA expression profiles and clinical information of HCC patients from GEO and TCGA databases were used, and ferroptosis-related gene list was obtained from the FerrDb database. We identified 39 ferroptosis-related genes (FDEGs) that were differentially expressed between HCC samples and normal tissues from the GSE14520 dataset. The univariate and multivariate Cox regression analyses were employed to construct a prognostic signature. Seven FDEGs (MAPK9, SLC1A4, PCK2, ACSL3, STMN1, CDO1, and CXCL2) were included to construct a risk model, which was validated in the TCGA dataset. Patients in high-risk groups exhibited a significantly poor prognosis compared with patients in low-risk groups in both the training set (GSE14520 cohort) and the validation set (TCGA cohort). Multivariate cox regression analyses demonstrated that the 7-gene signature was an independent risk factor for RFS in HCC patients. KEGG analysis showed that FDEGs were mainly enriched in Ferroptosis, Hepatocellular carcinoma pathway, and MAPK signaling pathway. GSEA analysis suggested that the high-risk group was correlated with multiple oncogenic signatures and invasive-related pathways. These results indicated that this risk model can accurately predict recurrence after hepatectomy and offer novel research directions for personalized treatment in HCC patients.
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Affiliation(s)
- Huaxiang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of MedicineShiyan, Hubei 442000, China
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Chengkai Yang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
| | - Yi Jiang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
| | - Huanzhang Hu
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third People’s Hospital of Fujian University of Traditional Chinese MedicineFuzhou 350108, Fujian, China
| | - Fang Yang
- The Fuzong Clinical Medical College of Fujian Medical UniversityFuzhou 350025, Fujian, China
- Department of Hepatobiliary Surgery, 900 Hospital of The Joint Logistics TeamFuzhou 350025, Fujian, China
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Hu W, Shi Y, Han T, Liu C, Cao X, Shi G, Zhu W. A Panel of E2F Target Gene Signature Predicting the Prognosis of Hepatocellular Carcinoma. Front Genet 2022; 13:879299. [PMID: 35591857 PMCID: PMC9110819 DOI: 10.3389/fgene.2022.879299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/18/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatocellular carcinoma is one of the most malignant tumors, and the therapeutic effects of traditional treatments are poor. It is urgent to explore and identify new biomarkers and therapeutic targets to develop novel treatments which are individualized and effective. Three hallmarks, including E2F targets, G2M checkpoint and DNA repair, were collected by GSEA analysis. The panel of E2F-related gene signature consisted of five genes: HN1, KIF4A, CDCA3, CDCA8 and SSRP1. They had various mutation rates ranging from 0.8 to 5% in hepatocellular carcinoma, and patients with gene mutation had poorer prognosis. Among these genes, HN1 has the greatest mutation rate, and SSRP1 has the greatest impact on the model with a B (COX) value of 0.8842. Patients with higher expression of these genes had poorer prognosis. Kaplan-Meier curves in stratified survival analysis confirmed that patients with high risk scores had poor prognosis (p < 0.05). The results of univariate and multivariate COX survival analysis showed that risk score was closely related to the overall survival of patients with hepatocellular carcinoma. For clinical validation, we found that all the genes in the model were upregulated in hepatocellular carcinoma tissues compared to normal liver tissues, which was consistent with the previous results we obtained. Our study demonstrated that a panel of E2F target genes signature including five genes could predict the prognosis of hepatocellular carcinoma. This panel gene signature can facilitate the development of individualized and effective treatment for hepatocellular carcinoma.
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Affiliation(s)
- Wenmin Hu
- School of Medicine and Pharmacy, Ocean University of China, Department of Pulmonary and Critical Care Medicine, Qingdao Municipal Hospital, Qingdao, China
| | - Yongmei Shi
- Department of Gynecology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Tongqin Han
- Department of General Practice, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China
| | - Caiyun Liu
- Department of Hepatobiliary Surgery, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Xipeng Cao
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Guangjun Shi
- Department of Hepatobiliary Surgery, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- *Correspondence: Guangjun Shi, ; Wenjing Zhu,
| | - Wenjing Zhu
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- Respiratory Disease Key Laboratory of Qingdao, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
- *Correspondence: Guangjun Shi, ; Wenjing Zhu,
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Zhang YF, Ma C, Qian XP. Development and external validation of a novel nomogram for predicting cancer-specific survival in patients with ascending colon adenocarcinoma after surgery: a population-based study. World J Surg Oncol 2022; 20:126. [PMID: 35439983 PMCID: PMC9020108 DOI: 10.1186/s12957-022-02576-4] [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: 12/25/2021] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
Background This study aimed to develop and validate a novel nomogram to predict the cancer-specific survival (CSS) of patients with ascending colon adenocarcinoma after surgery. Methods Patients with ascending colon adenocarcinoma were enrolled from the Surveillance, Epidemiology, and End Results (SEER) database from 1973 to 2015 and randomly divided into a training set (5930) and a validation set (2540). The cut-off values for age, tumour size and lymph node ratio (LNR) were calculated via X-tile software. In the training set, independent prognostic factors were identified using univariate and multivariate Cox analyses, and a nomogram incorporating these factors was subsequently built. Data from the validation set were used to assess the reliability and accuracy of the nomogram and then compared with the 8th edition of the American Joint Committee on Cancer (AJCC) tumour-node-metastasis (TNM) staging system. Furthermore, external validation was performed from a single institution in China. Results A total of 8470 patients were enrolled from the SEER database, 5930 patients were allocated to the training set, 2540 were allocated to the internal validation set and a separate set of 473 patients was allocated to the external validation set. The optimal cut-off values of age, tumour size and lymph node ratio were 73 and 85, 33 and 75 and 4.9 and 32.8, respectively. Univariate and multivariate Cox multivariate regression revealed that age, AJCC 8th edition T, N and M stage, carcinoembryonic antigen (CEA), tumour differentiation, chemotherapy, perineural invasion and LNR were independent risk factors for patient CSS. The nomogram showed good predictive ability, as indicated by discriminative ability and calibration, with C statistics of 0.835 (95% CI, 0.823–0.847) and 0.848 (95% CI, 0.830–0.866) in the training and validation sets and 0.732 (95% CI, 0.664–0.799) in the external validation set. The nomogram showed favourable discrimination and calibration abilities and performed better than the AJCC TNM staging system. Conclusions A novel validated nomogram could effectively predict patients with ascending colon adenocarcinoma after surgery, and this predictive power may guide clinicians in accurate prognostic judgement.
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Affiliation(s)
- Yi Fan Zhang
- Department of Radiotherapy, The Xuzhou School of Clinical Medicine of Nanjing Medical University, Xuzhou, 221000, China.,Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - Cheng Ma
- Department of Gastrointestinal Surgery, The Xuzhou School of Clinical Medicine of Nanjing Medical University, Xuzhou, 221000, China
| | - Xiao Ping Qian
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210000, China. .,Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, 210000, China.
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He Q, Fan B, Du P, Jin Y. Construction and Validation of Two Hepatocellular Carcinoma-Progression Prognostic Scores Based on Gene Set Variation Analysis. Front Cell Dev Biol 2022; 10:806989. [PMID: 35356272 PMCID: PMC8959467 DOI: 10.3389/fcell.2022.806989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Liver hepatocellular carcinoma (LIHC) remains a global health challenge with a low early diagnosis rate and high mortality. Therefore, finding new biomarkers for diagnosis and prognosis is still one of the current research priorities. Methods: Based on the variation of gene expression patterns in different stages, the LIHC-development genes (LDGs) were identified by differential expression analysis. Then, prognosis-related LDGs were screened out to construct the LIHC-unfavorable gene set (LUGs) and LIHC-favorable gene set (LFGs). Gene set variation analysis (GSVA) was conducted to build prognostic scoring models based on the LUGs and LFGs. ROC curve analysis and univariate and multivariate Cox regression analysis were carried out to verify the diagnostic and prognostic utility of the two GSVA scores in two independent datasets. Additionally, the key LCGs were identified by the intersection analysis of the PPI network and univariate Cox regression and further evaluated their performance in expression level and prognosis prediction. Single-sample GSEA (ssGSEA) was performed to understand the correlation between the two GSVA enrichment scores and immune activity. Result: With the development of LIHC, 83 LDGs were gradually upregulated and 247 LDGs were gradually downregulated. Combining with LIHC survival analysis, 31 LUGs and 32 LFGs were identified and used to establish the LIHC-unfavorable GSVA score (LUG score) and LIHC-favorable GSVA score (LFG score). ROC curve analysis and univariate/multivariate Cox regression analysis suggested the LUG score and LFG score could be great indicators for the early diagnosis and prognosis prediction. Four genes (ESR1, EHHADH, CYP3A4, and ACADL) were considered as the key LCGs and closely related to good prognosis. The frequency of TP53 mutation and copy number variation (CNV) were high in some LCGs. Low-LFG score patients have active metabolic activity and a more robust immune response. The high-LFG score patients characterized immune activation with the higher infiltration abundance of type I T helper cells, DC, eosinophils, and neutrophils, while the high-LUG score patients characterized immunosuppression with the higher infiltration abundance of type II T helper cells, TRegs, and iDC. The high- and low-LFG score groups differed significantly in immunotherapy response scores, immune checkpoints expression, and IC50 values of common drugs. Conclusion: Overall, the LIHC-progression characteristic genes can be great diagnostic and prognostic signatures and the two GSVA score systems may become promising indices for guiding the tumor treatment of LIHC patients.
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Zhang W, Feng J, Zeng W, He Z, Yang W, Lu H. Integrated analysis of the prognostic and oncogenic roles of OPN3 in human cancers. BMC Cancer 2022; 22:187. [PMID: 35180853 PMCID: PMC8857800 DOI: 10.1186/s12885-022-09219-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background Emerging cell- or tissue-based evidence has demonstrated that opsin 3 (OPN3) mediates a variety of pathological processes affecting tumorigenesis, clinical prognosis, and treatment resistance in some cancers. However, a comprehensive analysis of OPN3 across human cancers is unavailable. Therefore, a pancancer analysis of OPN3 expression was performed and its potential oncogenic roles were explored. Methods The expression and characterization of OPN3 were evaluated among 33 tumour types using The Cancer Genome Atlas (TCGA) dataset. Additionally, the OPN3 RNA level and overall survival (OS) in relation to its expression level in 33 cancer types were estimated. Based on the analysis above, 347 samples from 5 types of tumours were collected and detected for the protein expression of OPN3 by immunohistochemical assay. Furthermore, the biological role of OPN3 in cancers was evaluated via gene set enrichment analysis (GSEA). Results The OPN3 expression level was heterogeneous across cancers, yet a remarkable difference existed between OPN3 expression and patient overall survival among the 7 types of these 33 cancers. Consistently, a high immunohistochemical score of OPN3 was significantly associated with a poor prognosis among patients with 5 types of tumours. Additionally, OPN3 expression was involved in cancer-associated fibroblast infiltration in 5 types of tumours, and promoter hypomethylation of OPN3 was observed in 3 tumour types. Additionally, OPN3 protein phosphorylation sites of Tyr140 and Ser380 were identified via posttranscriptional modification analysis, suggesting the potential function of Tyr140 and Ser380 phosphorylation in tumorigenesis. Furthermore, the enrichment analysis was mainly concentrated in C7orf70, C7orf25 and the “ribosome” pathway by GSEA in 5 types of cancers, indicating that OPN3 might affect tumorigenesis and progression by regulating gene expression and ribosome biogenesis. Conclusions High expression of OPN3 was significantly associated with a poor clinical prognosis in five types of cancers. Its molecular function was closely associated with the ribosomal pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09219-7.
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Affiliation(s)
- Wei Zhang
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, No.28 Guiyi Road, Guiyang, Guizhou, 550001, P.R. China
| | - Jianglong Feng
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, No.28 Guiyi Road, Guiyang, Guizhou, 550001, P.R. China.,Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Wen Zeng
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, No.28 Guiyi Road, Guiyang, Guizhou, 550001, P.R. China
| | - Zhi He
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, No.28 Guiyi Road, Guiyang, Guizhou, 550001, P.R. China
| | - Wenxiu Yang
- Department of Pathology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongguang Lu
- Department of Dermatology, Affiliated Hospital of Guizhou Medical University, No.28 Guiyi Road, Guiyang, Guizhou, 550001, P.R. China.
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Tong X, Zhao X, Dang X, Kou Y, Kou J. Predicting Diagnostic Gene Biomarkers Associated With Immune Checkpoints, N6-Methyladenosine, and Ferroptosis in Patients With Acute Myocardial Infarction. Front Cardiovasc Med 2022; 9:836067. [PMID: 35224064 PMCID: PMC8873927 DOI: 10.3389/fcvm.2022.836067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
This study aimed to determine early diagnosis genes of acute myocardial infarction (AMI) and then validate their association with ferroptosis, immune checkpoints, and N6-methyladenosine (m6A), which may provide a potential method for the early diagnosis of AMI. Firstly, we downloaded microarray data from NCBI (GSE61144, GSE60993, and GSE42148) and identified differentially expressed genes (DEGs) in samples from healthy subjects and patients with AMI. Also, we performed systematic gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and used STRING to predict protein interactions. Moreover, MCC and MCODE algorithms in the cytoHubba plug-in were used to screen nine key genes in the network. We then determined the diagnostic significance of the nine obtained DEGs by plotting receiver operating characteristic curves using a multiscale curvature classification algorithm. Meanwhile, we investigated the relationship between AMI and immune checkpoints, ferroptosis, and m6A. In addition, we further validated the key genes through the GSE66360 dataset and consequently obtained nine specific genes that can be used as early diagnosis biomarkers for AMI. Through screening, we identified 210 DEGs, including 53 downregulated and 157 upregulated genes. According to GO, KEGG, and key gene screening results, FPR1, CXCR1, ELANE, TLR2, S100A12, TLR4, CXCL8, FPR2 and CAMP could be used for early prediction of AMI. Finally, we found that AMI was associated with ferroptosis, immune checkpoints, and m6A and FPR1, CXCR1, ELANE, TLR2, S100A12, TLR4, CXCL8, FPR2 and CAMP are effective markers for the diagnosis of AMI, which can provide new prospects for future studies on the pathogenesis of AMI.
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Affiliation(s)
- Xiao Tong
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xinyi Zhao
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xuan Dang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yan Kou
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
- *Correspondence: Yan Kou
| | - Junjie Kou
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
- Junjie Kou
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Wang D, Zhou Y, Hua L, Li J, Zhu N, Liu Y. CDK3, CDK5 and CDK8 Proteins as Prognostic and Potential Biomarkers in Colorectal Cancer Patients. Int J Gen Med 2022; 15:2233-2245. [PMID: 35250301 PMCID: PMC8893271 DOI: 10.2147/ijgm.s349576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 12/26/2022] Open
Abstract
Introduction Methods Results Conclusion
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Affiliation(s)
- Dan Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
| | - Yanhong Zhou
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
| | - Li Hua
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
| | - Jiaxiang Li
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
| | - Ni Zhu
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
| | - Yifei Liu
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China
- Correspondence: Yifei Liu, School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, HuBei, People’s Republic of China, Tel +86-715-8266030, Email
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Wang D, Peng L, Hua L, Li J, Liu Y, Zhou Y. Mapk14 is a Prognostic Biomarker and Correlates with the Clinicopathological Features and Immune Infiltration of Colorectal Cancer. Front Cell Dev Biol 2022; 10:817800. [PMID: 35141222 PMCID: PMC8818961 DOI: 10.3389/fcell.2022.817800] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most common gastrointestinal tumors, ranking in the top 5 of all common tumors in terms of incidence and mortality. However, the mechanisms driving the evolution of colorectal cancer remain unclear. Therefore, we investigated the association between Mapk14 expression and clinicopathological and tumor-infiltrating immune cells. Methods: In this study, we collected CRC patient data from The Cancer Genome Atlas (TCGA), compared the expression level in CRC and normal colorectal tissue using the Wilcoxon rank sum test and assessed the relationship between Mapk14 and clinicopathological features using the Welch one-way ANOVA test. Kaplan-Meier and timeROC GSE17537 datasets were obtained from the Gene Expression Omnibus (GEO) dataset to assess the prognostic impact of the Mapk14 gene on colorectal cancer. Second, we further explored the methylation level of Mapk14 and its influencing factors. Single-cell sequencing of Mapk14 in the tumor immune microenvironment (TIME) was analyzed using the GSE108989 dataset. Further analyses based on the TIMER method were performed to assess the correlation between Mapk14 and tumor immune infiltration, immune checkpoints, tumor mutational load and microsatellite instability. Finally, the results of the bioinformatics analysis were verified by an immunohistochemical analysis. Results: The results showed that the expression of Mapk14 was upregulated in CRC tumor tissues compared with normal colorectal tissues and the high expression of Mapk14 was associated with poor clinicopathological features and poor prognoses in the CRC array. In addition, cg05798012 and cg25375420 of Mapk14 are the main DNA methylation sites affecting OS. Single-cell sequencing of the tumor immune microenvironment showed that the abundance and cell state of dysfunctional T cells changed greatly. Importantly, the abnormal overexpression of Mapk14 in colorectal cancer is related to the level of immune infiltration of immune cells (including CD8+ T cells, neutrophils, dendritic cells, B cells, CD4+ T cells, and macrophages). The high expression of Mapk14 was significantly correlated with immune checkpoints (including SIGLEC15, TIGIT, LAG3, CTLA4 and PDCDILG2), while the high expression of Mapk14 was negatively correlated with TMB and MSI but mostly positively correlated with drug sensitivity. Finally, the immunohistochemical results confirmed that the clinical stage (Ⅰ, Ⅱ, Ⅲ and Ⅳ) and M stage (M0 and M1) affected the abnormally high expression of Mapk14. Conclusion: A comprehensive bioinformatics study and experimental validation revealed that Mapk14 could serve as a novel prognostic biomarker associated with immune infiltration and pharmacotherapy and may represent a potential therapeutic target for the treatment of CRC.
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Affiliation(s)
| | | | | | | | - Yifei Liu
- *Correspondence: Yifei Liu, ; Yanhong Zhou,
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Shi T, Iwama H, Fujita K, Kobara H, Nishiyama N, Fujihara S, Goda Y, Yoneyama H, Morishita A, Tani J, Yamada M, Nakahara M, Takuma K, Masaki T. Evaluating the Effect of Lenvatinib on Sorafenib-Resistant Hepatocellular Carcinoma Cells. Int J Mol Sci 2021; 22:13071. [PMID: 34884875 PMCID: PMC8657692 DOI: 10.3390/ijms222313071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related deaths worldwide. Sorafenib has been used as a first-line systemic treatment for over a decade. However, resistance to sorafenib limits patient response and presents a major hurdle during HCC treatment. Lenvatinib has been approved as a first-line systemic treatment for advanced HCC and is the first agent to achieve non-inferiority against sorafenib. Therefore, in the present study, we evaluated the inhibition efficacy of lenvatinib in sorafenib-resistant HCC cells. Only a few studies have been conducted on this topic. Two human HCC cell lines, Huh-7 and Hep-3B, were used to establish sorafenib resistance, and in vitro and in vivo studies were employed. Lenvatinib suppressed sorafenib-resistant HCC cell proliferation mainly by inducing G1 cell cycle arrest through ERK signaling. Hep-3B sorafenib-resistant cells showed partial cross-resistance to lenvatinib, possibly due to the contribution of poor autophagic responsiveness. Overall, the findings suggest that the underlying mechanism of lenvatinib in overcoming sorafenib resistance in HCC involves FGFR4-ERK signaling. Lenvatinib may be a suitable second-line therapy for unresectable HCC patients who have developed sorafenib resistance and express FGFR4.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Carcinoma, Hepatocellular/blood supply
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/drug effects
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Liver Neoplasms/blood supply
- Liver Neoplasms/drug therapy
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Mice, Inbred BALB C
- MicroRNAs/genetics
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/genetics
- Phenylurea Compounds/pharmacology
- Quinolines/pharmacology
- Sorafenib/pharmacology
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Tingting Shi
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hisakazu Iwama
- Life Science Research Center, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan;
| | - Koji Fujita
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Noriko Nishiyama
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Shintaro Fujihara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Yasuhiro Goda
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hirohito Yoneyama
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Asahiro Morishita
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Joji Tani
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Mari Yamada
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Mai Nakahara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Kei Takuma
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Tsutomu Masaki
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
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Qiu D, Hu J, Hu J, Yu A, Othmane B, He T, Ding J, Cheng X, Ren W, Tan X, Yu Q, Chen J, Zu X. PMEPA1 Is a Prognostic Biomarker That Correlates With Cell Malignancy and the Tumor Microenvironment in Bladder Cancer. Front Immunol 2021; 12:705086. [PMID: 34777336 PMCID: PMC8582246 DOI: 10.3389/fimmu.2021.705086] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023] Open
Abstract
Prostate transmembrane protein androgen induced 1 (PMEPA1) has been reported to promote cancer progression, but the potential role of PMEPA1 in bladder cancer (BLCA) remains elusive. We assess the role of PMEPA1 in BLCA, via a publicly available database and in vitro study. PMEPA1 was identified from 107 differentially expressed genes (DEGs) to have prognostic value. GO, KEGG, and GSEA analysis indicated that PMEPA1 was involved in cancer progression and the tumor microenvironment (TME). Then bioinformatical analysis in TCGA, GEO, TIMER, and TISIDB show a positive correlation with the inflammation and infiltration levels of three tumor-infiltrating immune cells (TAMs, CAFs, and MDSCs) and immune/stromal scores in TME. Moreover, in vitro study revealed that PMEPA1 promotes bladder cancer cell malignancy. Immunohistochemistry and survival analysis shed light on PMEPA1 potential to be a novel biomarker in predicting tumor progression and prognosis. At last, we also analyzed the role of PMEPA1 in predicting the molecular subtype and the response to several treatment options in BLCA. We found that PMEPA1 may be a novel potential biomarker to predict the progression, prognosis, and molecular subtype of BLCA.
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Affiliation(s)
- Dongxu Qiu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,Department of Urology, Central People's Hospital of Zhanjiang, Zhanjiang, China
| | - Jiao Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Anze Yu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,Immunobiology & Transplant Science Center, Houston Methodist Research Institute, Texas Medical Center, Houston, TX, United States
| | - Belaydi Othmane
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Tongchen He
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Ding
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xu Cheng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,Institute for Infection Prevention and Hospital Epidemiology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Wenbiao Ren
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,George Whipple Lab for Cancer Research, Departments of Pathology and Urology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Xiyan Tan
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Qiaoyan Yu
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
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46
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Cui M, Qu F, Wang L, Liu X, Yu J, Tang Z, Cheng D. m5C RNA methyltransferase-related gene NSUN4 stimulates malignant progression of hepatocellular carcinoma and can be a prognostic marker. Cancer Biomark 2021; 33:389-400. [PMID: 34744073 DOI: 10.3233/cbm-210154] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a cancer with relatively high mortality, yet little attention has been devoted for related prognostic biomarkers. This study analyzed differential expression of m5C RNA methyltransferase-related genes in normal samples and tumors samples in TCGA-LIHC using Wilcoxon test. K-means consensus clustering analysis was implemented to subdivide samples. Independent prognostic factors were screened by univariate and multivariate Cox regression analyses. KEGG pathway enrichment analysis was performed on the screened independent prognostic factor using GSEA tools. qPCR was conducted to test mRNA expression of key m5C RNA methyltransferase-related genes in tissues and cells. There were 7 m5C RNA methyltransferase-related genes (NOP2, NSUN4, etc.) differentially expressed in HCC tumor tissues. HCC samples were classified into 3 subgroups through clustering analysis according to the expression mode of m5C RNA methyltransferase-related genes. It was also discovered that patients in different subgroups presented significant differences in survival rate and distribution of grade. Additionally, NOP2, NSUN4 and NSUN5 expression notable varied in different grades. Through regression analyses combined with various clinical pathological factors, it was displayed that NSUN4 could work as an independent prognostic factor. KEGG analysis showed that NSUN4 mainly enriched in signaling pathways involved in ADHERENS JUNCTION, RNA DEGRADATION, MTOR SIGNALING PATHWAY, COMPLEMENT and COAGULATION CASCADES. As examined by qPCR, NSUN4 was conspicuously upregulated in HCC patient's tissues and cells. Altogether, our study preliminarily developed a novel biomarker that could be independently used in prognosis of HCC, which may provide a new direction for the study of related molecular mechanism or treatment regimen.
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Feng X, Mu S, Ma Y, Wang W. Development and Verification of an Immune-Related Gene Pairs Prognostic Signature in Hepatocellular Carcinoma. Front Mol Biosci 2021; 8:715728. [PMID: 34660693 PMCID: PMC8517445 DOI: 10.3389/fmolb.2021.715728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
With the increasing prevalence of Hepatocellular carcinoma (HCC) and the poor prognosis of immunotherapy, reliable immune-related gene pairs (IRGPs) prognostic signature is required for personalized management and treatment of patients. Gene expression profiles and clinical information of HCC patients were obtained from the TCGA and ICGC databases. The IRGPs are constructed using immune-related genes (IRGs) with large variations. The least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct IRGPs signature. The IRGPs signature was verified through the ICGC cohort. 1,309 IRGPs were constructed from 90 IRGs with high variability. We obtained 50 IRGPs that were significantly connected to the prognosis and constructed a signature that included 17 IRGPs. In the TCGA and ICGC cohorts, patients were divided into high and low-risk patients by the IRGPs signature. The overall survival time of low-risk patients is longer than that of high-risk patients. After adjustment for clinical and pathological factors, multivariate analysis showed that the IRGPs signature is an independent prognostic factor. The Receiver operating characteristic (ROC) curve confirmed the accuracy of the signature. Besides, gene set enrichment analysis (GSEA) revealed that the signature is related to immune biological processes, and the immune microenvironment status is distinct in different risk patients. The proposed IRGPs signature can effectively assess the overall survival of HCC, and provide the relationship between the signature and the reactivity of immune checkpoint therapy and the sensitivity of targeted drugs, thereby providing new ideas for the diagnosis and treatment of the disease.
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Affiliation(s)
- Xiaofei Feng
- Department of Orthopedics, Lanzhou University First Affiliated Hospital, Lanzhou, China
| | - Shanshan Mu
- Pediatric Rheumatism Immunology Department, Lanzhou University Second Hospital, Lanzhou, China
| | - Yao Ma
- Clinical Laboratory Center, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - Wenji Wang
- Department of Orthopedics, Lanzhou University First Affiliated Hospital, Lanzhou, China
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Wang J, Zhang Q, Shi F, Yadav DK, Hong Z, Wang J, Liang T, Bai X. A Seven-Gene Signature to Predict Prognosis of Patients With Hepatocellular Carcinoma. Front Genet 2021; 12:728476. [PMID: 34603388 PMCID: PMC8481951 DOI: 10.3389/fgene.2021.728476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 01/27/2023] Open
Abstract
Purpose: Hepatocellular carcinoma (HCC) is one of the most prevalent malignant diseases worldwide and has a poor prognosis. Gene-based prognostic models have been reported to predict the overall survival of patients with HCC. Unfortunately, most of the genes used in earlier prognostic models lack prospective validation and, thus, cannot be used in clinical practice. Methods: Candidate genes were selected from GEPIA (Gene Expression Profiling Interactive Analysis), and their associations with patients’ survival were confirmed by RT-PCR using cDNA tissue microarrays established from patients with HCC after radical resection. A multivariate Cox proportion model was used to calculate the coefficient of corresponding gene. The expression of seven genes of interest (MKI67, AR, PLG, DNASE1L3, PTTG1, PPP1R1A, and TTR) with two reference genes was defined to calculate a risk score which determined groups of different risks. Results: Our risk scoring efficiently classified patients (n = 129) with HCC into a low-, intermediate-, and high-risk group. The three groups showed meaningful distinction of 3-year overall survival rate, i.e., 88.9, 74.5, and 20.6% for the low-, intermediate-, and high-risk group, respectively. The prognostic prediction model of risk scores was subsequently verified using an independent prospective cohort (n = 77) and showed high accuracy. Conclusion: Our seven-gene signature model performed excellent long-term prediction power and provided crucially guiding therapy for patients who are not a candidate for surgery.
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Affiliation(s)
- Junli Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Fukang Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dipesh Kumar Yadav
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengtao Hong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianing Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
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Wu Y, Fu Y, He K, Song H. Pan-cancer analysis of nemo-like kinase (NLK) expression convergence to pancreatic adenocarcinoma that has diagnostic, prognostic and treatment value. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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50
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Chen B, Zhu Y, Chen J, Feng Y, Xu Y. Activation of TC10-Like Transcription by Lysine Demethylase KDM4B in Colorectal Cancer Cells. Front Cell Dev Biol 2021; 9:617549. [PMID: 34249900 PMCID: PMC8260841 DOI: 10.3389/fcell.2021.617549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Malignant colorectal cancers (CRCs) are characterized by enhanced migration and invasion thus acquiring the ability to metastasize. We have previously shown that the small GTPase TC10-like (TCL) contributes to aggressive migration and invasion in malignant CRC cells. TCL expression is differentially expressed in CRC cells and can be upregulated by hypoxia although the underlying epigenetic mechanism is not fully appreciated. Here, we report that differential TCL expression in CRC cells appeared to be associated with histone H3K9 methylation. RNAi screening revealed that the lysine demethylase KDM4B was essential for TCL transcription in CRC cells. KDM4B interacted with and was recruited by the sequence-specific transcription factor ETS-related gene 1 (ERG1) to the TCL promoter to activate transcription. Mechanistically, KDM4B mediated H3K9 demethylase facilitated the assembly of pre-initiation complex (PIC) on the TCL promoter. KDM4B knockdown attenuated migration and invasion of CRC cells. Importantly, KDM4B expression was upregulated in human CRC specimens of advanced stages compared to those of lower grades and associated with poor prognosis. Together, these data uncover a novel epigenetic mechanism underlying malignant transformation of CRC cells and suggest that KDM4B may be considered as a therapeutic target in CRC intervention.
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Affiliation(s)
- Baoyu Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Junliang Chen
- Department of Pathophysiology, Wuxi Medical School, Jiangnan University, Wuxi, China
| | - Yifei Feng
- Department of Colorectal Surgery, The First Hospital Affiliated With Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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