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Zang Z, Yin Y, Liu C, Zhu Q, Huang X, Li H, Yang R. IL21R hypomethylation as a biomarker for distinguishing benign and malignant breast tumours. Epigenetics 2024; 19:2352683. [PMID: 38723244 PMCID: PMC11086039 DOI: 10.1080/15592294.2024.2352683] [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: 10/27/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Some benign and malignant breast tumours are similar in pathological morphology, which are difficult to be distinguished in clinical diagnosis. In this study, we intended to explore novel biomarkers for differential diagnosis of benign and malignant breast tumours. Methylation EPIC 850K beadchip and RNA-sequencing were used to analyse 29 tissue samples from patients with early-stage breast cancer (BC) and benign breast tumours for differently methylated and expressed genes. The altered methylation of IL21R was semi-quantitatively validated in an independent study with 566 tissue samples (279 BC vs. 287 benign breast tumours) using mass spectrometry. Binary logistic regression analysis was performed to evaluate the association between IL21R methylation and BC. BC-associated IL21R hypomethylation and overexpression were identified in the discovery round. In the validation round, BC patients presented significant IL21R hypomethylation compared to women with benign breast tumours (ORs ≥1.29 per-10% methylation, p-values ≤ 5.69E-14), and this hypomethylation was even enhanced in BC patients with ER-negative and PR-negative tumours as well as with triple-negative tumours. The methylation of IL21R showed efficient discriminatory power to distinguish benign breast tumours from BC (area under curve (AUC) = 0.88), and especially from ER-negative BC (AUC = 0.95), PR-negative BC (AUC = 0.93) and triple-negative BC (AUC = 0.96). We disclosed significant IL21R hypomethylation in patients with BC compared to women with benign breast tumours, and revealed the somatic change of DNA methylation could be a potential biomarker for molecular pathology of BC.
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Affiliation(s)
- Zishan Zang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifei Yin
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuandong Huang
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Hong Li
- Department of Pathology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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Wang Y, Ji B, Zhang L, Wang J, He J, Ding B, Ren M. Identification of metastasis-related genes for predicting prostate cancer diagnosis, metastasis and immunotherapy drug candidates using machine learning approaches. Biol Direct 2024; 19:50. [PMID: 38918844 PMCID: PMC11197330 DOI: 10.1186/s13062-024-00494-x] [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: 05/15/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the second leading cause of tumor-related mortality in men. Metastasis from advanced tumors is the primary cause of death among patients. Identifying novel and effective biomarkers is essential for understanding the mechanisms of metastasis in PCa patients and developing successful interventions. METHODS Using the GSE8511 and GSE27616 data sets, 21 metastasis-related genes were identified through the weighted gene co-expression network analysis (WGCNA) method. Subsequent functional analysis of these genes was conducted on the gene set cancer analysis (GSCA) website. Cluster analysis was utilized to explore the relationship between these genes, immune infiltration in PCa, and the efficacy of targeted drug IC50 scores. Machine learning algorithms were then employed to construct diagnostic and prognostic models, assessing their predictive accuracy. Additionally, multivariate COX regression analysis highlighted the significant role of POLD1 and examined its association with DNA methylation. Finally, molecular docking and immunohistochemistry experiments were carried out to assess the binding affinity of POLD1 to PCa drugs and its impact on PCa prognosis. RESULTS The study identified 21 metastasis-related genes using the WGCNA method, which were found to be associated with DNA damage, hormone AR activation, and inhibition of the RTK pathway. Cluster analysis confirmed a significant correlation between these genes and PCa metastasis, particularly in the context of immunotherapy and targeted therapy drugs. A diagnostic model combining multiple machine learning algorithms showed strong predictive capabilities for PCa diagnosis, while a transfer model using the LASSO algorithm also yielded promising results. POLD1 emerged as a key prognostic gene among the metastatic genes, showing associations with DNA methylation. Molecular docking experiments supported its high affinity with PCa-targeted drugs. Immunohistochemistry experiments further validated that increased POLD1 expression is linked to poor prognosis in PCa patients. CONCLUSIONS The developed diagnostic and metastasis models provide substantial value for patients with prostate cancer. The discovery of POLD1 as a novel biomarker related to prostate cancer metastasis offers a promising avenue for enhancing treatment of prostate cancer metastasis.
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Affiliation(s)
- YaXuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Bo Ji
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Lu Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Jinfeng Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - JiaXin He
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - BeiChen Ding
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| | - MingHua Ren
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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Yan T, Pang X, Liang B, Meng Q, Wei H, Li W, Liu D, Hu Y. Comprehensive bioinformatics analysis of human cytomegalovirus pathway genes in pan-cancer. Hum Genomics 2024; 18:65. [PMID: 38886862 PMCID: PMC11181644 DOI: 10.1186/s40246-024-00633-5] [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] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) is a herpesvirus that can infect various cell types and modulate host gene expression and immune response. It has been associated with the pathogenesis of various cancers, but its molecular mechanisms remain elusive. METHODS We comprehensively analyzed the expression of HCMV pathway genes across 26 cancer types using the Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) databases. We also used bioinformatics tools to study immune invasion and tumor microenvironment in pan-cancer. Cox regression and machine learning were used to analyze prognostic genes and their relationship with drug sensitivity. RESULTS We found that HCMV pathway genes are widely expressed in various cancers. Immune infiltration and the tumor microenvironment revealed that HCMV is involved in complex immune processes. We obtained prognostic genes for 25 cancers and significantly found 23 key genes in the HCMV pathway, which are significantly enriched in cellular chemotaxis and synaptic function and may be involved in disease progression. Notably, CaM family genes were up-regulated and AC family genes were down-regulated in most tumors. These hub genes correlate with sensitivity or resistance to various drugs, suggesting their potential as therapeutic targets. CONCLUSIONS Our study has revealed the role of the HCMV pathway in various cancers and provided insights into its molecular mechanism and therapeutic significance. It is worth noting that the key genes of the HCMV pathway may open up new doors for cancer prevention and treatment.
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Affiliation(s)
- Tengyue Yan
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xianwu Pang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028, China
| | - Boying Liang
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Qiuxia Meng
- School of Information and Managent, Guangxi Medical University, Nanning, China
| | - Huilin Wei
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Wen Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, China
| | - Dahai Liu
- School of Medicine, Foshan University, Foshan, Guangdong, 528000, People's Republic of China.
| | - Yanling Hu
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, 530021, China.
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China.
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Tang P, Zheng G, Xu C, Yu N, Du J, Hu L, Zhou Z, Zheng Y. Function of NEK2 in clear cell renal cell carcinoma and its effect on the tumor microenvironment. Medicine (Baltimore) 2024; 103:e37939. [PMID: 38758909 PMCID: PMC11098263 DOI: 10.1097/md.0000000000037939] [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: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Previous studies have revealed the critical functions of NEK2 in controlling the cell cycle which is linked to poor prognosis in multiple tumor types, but less research has been devoted to clear cell renal cell carcinoma (ccRCC). METHODS We downloaded clinical data from the gene expression omnibus (GEO) and TCGA databases together with transcriptional and mutational datasets. Strongly coexpressed genes with NEK2 were extracted from TCGA-KIRC cohort, and were submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analyses. According to NEK2 levels, the survival status, mutational characteristics, response to immunotherapy and sensitivity to drugs of the patients were studied. The potential correlations between NEK2 levels and immune cell state as well as immune cell infiltration were examined using the GEPIA, TIMER and TISIDB databases. Double immunofluorescence (IF) was performed to identify the NEK2 overexpression and relationship with CD8 in ccRCC. RESULTS The NEK2 gene was overexpressed and would enhance the nuclear division and cell cycle activities in ccRCC. ccRCC patients with high NEK2 expression had worse clinical outcomes, higher mutation burden and better therapeutic response. Moreover, NEK2 gene overexpression was positively related to various immune cell marker sets, which was also proved by validation cohort, and more infiltration of various immune cells. CONCLUSION ccRCC patients with NEK2 high expression have a poorer prognosis than those with NEK2 low expression, resulting from its function of promoting proliferation, accompanied by increased infiltration of CD8 + T cells and Tregs and T-cell exhaustion and will respond better to proper treatments.
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Affiliation(s)
- Peng Tang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Department of Urology, The First People’s Hospital of Linping District of Hangzhou, Hangzhou, China
| | - Gangfu Zheng
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Congcong Xu
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nengfeng Yu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jiaqi Du
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Liqian Hu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Zhan Zhou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of An-ti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yichun Zheng
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Sui XY, Ma XY, Hou Y, Cao SW, Wang ZQ, Jia LJ, Fan L, Shao ZM, Zhang WJ. Elongin B promotes breast cancer progression by ubiquitinating tumor suppressor p14/ARF. Cell Biol Toxicol 2024; 40:24. [PMID: 38653919 PMCID: PMC11039524 DOI: 10.1007/s10565-024-09864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
Elongin B (ELOB), a pivotal element in the ELOB/c-Cullin2/5-SOCS-box E3 ubiquitin-protein ligase complex, plays a significant role in catalyzing the ubiquitination and subsequent degradation of a broad spectrum of target proteins. Notably, it is documented to facilitate these processes. However, the regulatory role of ELOB in breast cancer remains ambiguous. In this study, through bio-informatic analysis of The Cancer Genome Atlas and Fudan University Shanghai Cancer Center database, we demonstrated that ELOB was over-expressed in breast cancer tissues and was related to unfavorable prognosis. Additionally, pathway enrichment analysis illustrated that high expression of ELOB was associated with multiple cancer promoting pathways, like cell cycle, DNA replication, proteasome and PI3K - Akt signaling pathway, indicating ELOB as a potential anticancer target. Then, we confirmed that both in vivo and in vitro, the proliferation of breast cancer cells could be significantly suppressed by the down-regulation of ELOB. Mechanically, immunoprecipitation and in vivo ubiquitination assays prompted that, as the core element of Cullin2-RBX1-ELOB E3 ligase (CRL2) complex, ELOB regulated the ubiquitination and the subsequent degradation of oncoprotein p14/ARF. Moreover, the anticancer efficacy of erasing ELOB could be rescued by simultaneous knockdown of p14/ARF. Finally, through analyzing breast cancer tissue microarrays and western blot of patient samples, we demonstrated that the expression of ELOB in tumor tissues was elevated in compared to adjacent normal tissues. In conclusion, ELOB is identified to be a promising innovative target for the drug development of breast cancer by promoting the ubiquitination and degradation of oncoprotein p14/ARF.
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Affiliation(s)
- Xin-Yi Sui
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-Yan Ma
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yujin Hou
- Department of Oncology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Shuo-Wen Cao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Qing Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li-Jun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Fan
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China.
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China.
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Wen-Juan Zhang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, P.R. China.
- Key Laboratory of Breast Cancer in Shanghai, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Xiong H, Chen Z, Li Y, Wu Z, Qian D, Chen L, Li Q, Liu H, Chen W, Lin B, Jia Y, Wang C. Pan-cancer analysis of the prognostic and immunological role of FKBP4. Heliyon 2024; 10:e29098. [PMID: 38601662 PMCID: PMC11004885 DOI: 10.1016/j.heliyon.2024.e29098] [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: 10/19/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/12/2024] Open
Abstract
Objectives Our previous studies revealed the significant roles of FK506-binding protein 4 (FKBP4) in tumorigenesis, however, there has been no pan-cancer analysis of FKBP4. Using bioinformatics, the current study reported the expression and prognostic role of FKBP4, and the correlation between FKBP4 and clinicopathological parameters, methylation, molecular network, immunological traits and drug sensitivity. Methods RNA sequencing data, somatic mutation, and related clinical information were obtained from TCGA using UCSC Xena. The association between FKBP4 expression and clinical features was assessed using TISIDB. The relationships between FKBP4 expression and tumour stage, OS, DSS, DFS, and PFS were analysed using univariate cox regression analysis. The radar plots for TMB and MSI were obtained using "Fmsb" R package. UALCAN was used to explore the effect of FKBP4 methylation on tumour and normal samples. CBioportal was used to analyse copy number mutations in FKBP4 Gene expression and drug sensitivity data were downloaded from the CellMiner database. GO analysis was performed for the high and the low expression of FKBP4 compared with the median level of FKBP4 using clusterProfiler4.0. Results FKBP4 expression is significantly upregulated in various types of cancers. Cox regression analysis showed that high FKBP4 levels were correlated with poor OS, DSS, DFS, and PFS in most patients with cancer. Methylation of FKBP4 DNA was upregulated in most cancers, and FKBP4 expression is positively associated with transmethylase expression. FKBP4 and its copy were significantly associated with the expression of immune-infiltrating cells, immune checkpoint genes, immune modulators, TMB, MMR, and MSI. FKBP4 expression levels significantly correlated with 16 different drug sensitivities (all p < 0.05). Conclusions Our pan-cancer bioinformatic analysis revealed a potential mechanism underlying the effects of FKBP4 on the prognosis and progression of various cancers.
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Affiliation(s)
- Hanchu Xiong
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zihan Chen
- Surgical Intensive Care Unit, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yucheng Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zhuazhua Wu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, The Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215000, China
| | - Long Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Qiang Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Huaxin Liu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Weijun Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Baihua Lin
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Yongshi Jia
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Cheng Wang
- Heart Center, Department of Cardiovascular Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
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Zhou X, Nie H, Wang C, Yu X, Yang X, He X, Ou C. Prognostic value and therapeutic potential of NEK family in stomach adenocarcinoma. J Cancer 2024; 15:3154-3172. [PMID: 38706902 PMCID: PMC11064251 DOI: 10.7150/jca.90197] [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: 09/15/2023] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
Never in mitosis gene A-related kinase (NEK) is an 11-membered family of serine/threonine kinases (NEK1-NEK11), which are known to play important roles in the formation and development of cancer. However, few studies have examined the roles of these kinases in the development of stomach adenocarcinoma (STAD). In this study, we conducted a comprehensive analysis of the relationships between the NEKs family members and STAD. The differential expression of the NEK genes in STAD was validated using The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER) databases, and their prognostic and diagnostic values of NEKs in STAD were assessed using the Kaplan-Meier plotter and TCGA data. The effect of NEK expression on immune cell infiltration in STAD was analysed using the TIMER and TISIDB databases. The expression levels of the majority of the NEK family members were consistently upregulated in STAD, whereas that of NEK10 was downregulated. The upregulation of NEK2/3/4/5/6/8 was closely associated with clinicopathological parameters of patients, and the overexpressed levels of these proteins had good diagnostic value for the disease. NEK1/8/9/10/11 expression correlated with poor overall survival and post-progressive survival, whereas a higher NEK1/6/9/11 level implied worse first progressive survival. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that the NEKs may be related to immunological responses. Additionally, our study confirmed that these kinases correlated with immune cell infiltration and different immune infiltration subtypes in STAD. Our results suggest that NEK9 in particular has the potential to be used as a diagnostic and prognostic biomarker of STAD development and progression and an immune target for treatment of the disease. These findings expand our understanding of the biological functions of the NEK family members in STAD.
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Affiliation(s)
- Xunjian Zhou
- Department of Pathology, The First Hospital of Changsha (The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University), Changsha 410013, Hunan, China
| | - Hui Nie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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8
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Pei L, Zhao F, Zhang Y. USP43 impairs cisplatin sensitivity in epithelial ovarian cancer through HDAC2-dependent regulation of Wnt/β-catenin signaling pathway. Apoptosis 2024; 29:210-228. [PMID: 38087046 PMCID: PMC10830728 DOI: 10.1007/s10495-023-01873-x] [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] [Accepted: 07/09/2023] [Indexed: 02/01/2024]
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of cancer death all over the world. USP43 functions as a tumor promoter in various malignant cancers. Nevertheless, the biological roles and mechanisms of USP43 in EOC remain unknown. In this study, USP43 was highly expressed in EOC tissues and cells, and high expression of USP43 were associated with a poor prognosis of EOC. USP43 overexpression promoted EOC cell proliferation, enhanced the ability of migration and invasion, decreased cisplatin sensitivity and inhibited apoptosis. Knockdown of USP43 in vitro effectively retarded above malignant progression of EOC. In vivo xenograft tumors, silencing USP43 slowed tumor growth and enhanced cisplatin sensitivity. Mechanistically, USP43 inhibited HDAC2 degradation and enhanced HDAC2 protein stability through its deubiquitylation function. USP43 diminished the sensitivity of EOC cells to cisplatin through activation of the Wnt/β-catenin signaling pathway mediated by HDAC2. Taken together, the data in this study revealed the functions of USP43 in proliferation, migration, invasion, chemoresistance of EOC cells, and the mechanism of HDAC2-mediated Wnt/β-catenin signaling pathway. Thus, USP43 might serve as a potential target for the control of ovarian cancer progression.
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Affiliation(s)
- Lipeng Pei
- Department of Obstetrics and Gynecology, General Hospital of Northern Theater Command, Shenyang, People's Republic of China
| | - Feng Zhao
- Department of Stem Cells and Regenerative Medicine, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Yi Zhang
- Department of Gynecology, The First Hospital of China Medical University, No. 155, Nanjing North Street, Shenyang, People's Republic of China.
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Gui J, Yang L, Liu J, Li Y, Zou M, Sun C, Huang L, Zhu X, Huang K. Identifying the prognosis implication, immunotherapy response prediction value, and potential targeted compound inhibitors of integrin subunit α3 (ITGA3) in human cancers. Heliyon 2024; 10:e24236. [PMID: 38293430 PMCID: PMC10825359 DOI: 10.1016/j.heliyon.2024.e24236] [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: 05/29/2023] [Revised: 11/30/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
The integrin subunit α3 (ITGA3) is a member of the integrin alpha chain protein family, which could promote progression, metastasis, and invasion in some cancers. Still, its function in the tumor microenvironment (TME), cancer prognosis, and immunotherapy remains unclear. A multifaceted analysis of ITGA3 in pan-cancer utilizing various databases and online web tools revealed ITGA3 was aberrantly expressed in tumor tissues and upregulated in most cancers, which may be related to ITGA3 genomic alterations and methylation modification. In addition, ITGA3 was significantly correlated with the poor or better prognosis of cancer patients, immune-related pathways in hallmark, immune infiltration, and immune checkpoints, revealing a biological function of ITGA3 in the tumor progression, tumor microenvironment, and tumor immunity. We also found that ITGA3 could predict the response to tumor immunotherapy based on cytokine-treated samples and immunotherapy cohorts. ITGA3 may participate in shaping and regulating the tumor microenvironment to affect the tumor immune response, which was a promising immunotherapy response predictive biomarker and potential therapeutic target to work synergistically with cancer immunotherapy to boost the response and efficacy. Finally, potential targeted compound inhibitors and sensitive drugs were screened using databases ConnectivityMap (CMap) and CellMiner, and AutoDock Tools was used for molecular docking.
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Affiliation(s)
- Jiawei Gui
- Department of Neurosurgery, The 2 Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang 330031, PR China
| | - Lufei Yang
- Department of Neurosurgery, The 2 Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Institute of Neuroscience, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, PR China
- JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, PR China
| | - Junzhe Liu
- Department of Neurosurgery, The 2 Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Institute of Neuroscience, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, PR China
- JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, PR China
| | - Yishuang Li
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, PR China
| | - Mi Zou
- The Second Clinical Medical College, Jiangxi Medical College, Nanchang University, Nanchang 330031, PR China
| | - Chengpeng Sun
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang 330031, PR China
| | - Le Huang
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang 330031, PR China
| | - Xingen Zhu
- Department of Neurosurgery, The 2 Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Institute of Neuroscience, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, PR China
- JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, PR China
| | - Kai Huang
- Department of Neurosurgery, The 2 Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Institute of Neuroscience, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, PR China
- JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, PR China
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10
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Wang Q, Wang X, Li J, Yin T, Wang Y, Cheng L. PRKCSH serves as a potential immunological and prognostic biomarker in pan-cancer. Sci Rep 2024; 14:1778. [PMID: 38245572 PMCID: PMC10799934 DOI: 10.1038/s41598-024-52153-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/15/2024] [Indexed: 01/22/2024] Open
Abstract
Protein kinase C substrate 80K-H (PRKCSH) plays a crucial role in the protein N-terminal glycosylation process, with emerging evidence implicating its involvement in tumorigenesis. To comprehensively assess PRKCSH's significance across cancers, we conducted a pan-cancer analysis using data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE). We assessed aberrant PRKCSH mRNA and protein expression, examined its prognostic implications, and identified correlations with clinical features, tumor mutational burden (TMB), microsatellite instability (MSI), and tumor immunity across cancer types. We explored PRKCSH gene alterations, DNA methylation, and their impact on patient prognosis. Gene Set Enrichment Analysis (GSEA) and single-cell analysis revealed potential biological roles. Additionally, we investigated drug susceptibility and conducted Connectivity Map (Cmap) analysis. Key findings revealed that PRKCSH exhibited overexpression in most tumors, with a significant association with poor overall survival (OS) in six cancer types. Notably, PRKCSH expression demonstrated variations across disease stages, primarily increasing in advanced stages among eleven tumor types. Moreover, PRKCSH exhibited significant correlations with TMB in five cancer categories, MSI in eight, and displayed associations with immune cell populations in pan-cancer analysis. Genetic variations in PRKCSH were identified across 26 tumor types, suggesting favorable disease-free survival. Furthermore, PRKCSH methylation displayed a significant negative correlation with its expression in 27 tumor types, with a marked decrease compared to normal tissues in ten tumors. Cmap predicted 24 potential therapeutic small molecules in over four cancer types. This study highlights that PRKCSH, as a potential oncogene, may be a promising prognostic marker and therapeutic target of immunotherapy for a range of malignancies.
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Affiliation(s)
- Qiankun Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tongxin Yin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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11
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Liu X, Yuan R, Peng J, Xu A, Nie X, Tang R, Li G. SLMO2 is a potential prognostic and immunological biomarker in human pan-cancer. Sci Rep 2024; 14:1070. [PMID: 38212657 PMCID: PMC10784594 DOI: 10.1038/s41598-024-51720-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/09/2024] [Indexed: 01/13/2024] Open
Abstract
SLMO2 is a lipid transporter that transports phosphatidylserine to the interior of mitochondria, also known as PRELID3B, which plays an important role in lipid metabolism. It has also been reported to be involved in the growth process of breast and lung tumors. However, its functions and underlying mechanisms in cancer progress remain elusive, and the potential as pan-cancer biomarker and therapeutic target remains unexplored. Using the TCGA project and GEO database, we performed pan-cancer analysis of SLMO2, which including the expression pattern, prognostic value, mutation landscape, methylation modification, protein-protein interaction network and the relationship between SLMO2 expression and immune infiltration. KEGG enrichment analysis was also performed to predict function and relevant cellular pathways of SLMO2. In addition, proliferation and migration assays were performed to detect the proliferation and metastasis capacity of breast cancer and lung cancer cells. In our study, we found that SLMO2 was overexpressed in pan-cancer and the elevated expression of SLMO2 was correlated with poorer prognosis. SLMO2 mutations were distributed in a variety of tumors and correlated with prognosis. Promoter methylation analysis showed that SLMO2 methylation levels were lower in most tumors compared with normal tissues, while a few tumors showed increased methylation levels of SLMO2. SLMO2 expression was also positively correlated with immune infiltration of MDSCs. Further pathway enrichment analysis indicated that SLMO2 was involved in regulating of cytoplasmic transport and other oncogenic processes. In vitro experiments have shown that SLMO2 promotes the proliferation and migration of breast cancer and lung cancer cells. In conclusion, our findings suggested that SLMO2 was a potential prognostic and immunological marker in pan-cancer. This study suggested a potential strategy for targeting SLMO2 to treat tumors, including manipulating tumor growth or the tumor microenvironment, especially the infiltration of MDSC.
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Affiliation(s)
- Xiong Liu
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China.
- School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Renming Yuan
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Jie Peng
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Ailei Xu
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Xiaoxia Nie
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Ruiti Tang
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China.
| | - Guangqiang Li
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, 601 W. Huangpu Ave., Guangzhou, 510632, Guangdong, China.
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12
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Xiong Y, Chen X, Yang X, Zhang H, Li X, Wang Z, Feng S, Wen W, Xiong X. miRNA transcriptomics analysis shows miR-483-5p and miR-503-5p targeted miRNA in extracellular vesicles from severe acute pancreatitis-associated lung injury patients. Int Immunopharmacol 2023; 125:111075. [PMID: 37864909 DOI: 10.1016/j.intimp.2023.111075] [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: 02/15/2023] [Revised: 09/19/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
AIM This study sought to identify potential biomarkers and miRNA-mRNA networks within extracellular vesicles (EVs) for detecting severe acute pancreatitis-associated lung injury (SAPALI). METHODS Blood-derived EVs were isolated, and their miRNA transcriptomic profiles were comprehensively analyzed using miRBase v.21 database along with miRDeep2 tool to predict novel miRNAs. DEGseq R package was deployed for the identification of differentially expressed miRNAs (DEMs). Protein-protein interaction (PPI) networks were assembled using STRING and Cytoscape. A lung injury model was established using Lipopolysaccharide (LPS)-induced BEAS-2B cells, chosen for their respiratory epithelial origin and pertinent association with lung injury. The expression levels of targeted miRNA and associated proteins, TLR4, NF-κB mRNA were quantified via RT-PCR and Western Blot. Levels of IL-6, IL-1β, TNF-α, and ROS were measured using designated kits. Dual-luciferase reporter assay was conducted to examine the interaction between miRNA and proteins. RESULTS The comparisons between the SAPALI and the control group revealed 10 DEM, including miR-503-5p and miR-483-5p. The cytoHubba plugin in Cytoscape identified three principal miRNA-mRNA interactions: miR-483-5p with PTK2 and HDAC2; miR-28-5p with MAPK1, TP53BP1, SEMA3A; and miR-503-5p with PPP1CB, SEMA6D, EPHB2, UNC5B. The SAPALI model exhibited elevated miR-503-5p, HDAC2 and inflammatory markers, with a decline UNC5B, miR-483-5p and miR-28-5p. Transfection with miR-503-5p and miR-483-5p inhibitors increased the levels of their supposed binding proteins but not miR-28-5p inhibitor. The Dual-luciferase reporter gene assay identified the interaction of miR-503-5p with UNC5B, and miR-483-5p with HDAC2, but not miR-28-5p with TP53BP1. CONCLUSIONS Our study maps miRNA-mRNA interactions in SAPALI, identifying miR-503-5p and miR-483-5p as critical regulatory miRNAs.
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Affiliation(s)
- Yicheng Xiong
- Alberta Institute, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiangyang Chen
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xiaodan Yang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Hang Zhang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xinmiao Li
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Zilu Wang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Sizhe Feng
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Wen Wen
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xiangqing Xiong
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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Zhang Z, Zhang A, Shi Y, Zhao Z, Zhao Z. An association between ATP7B expression and human cancer prognosis and immunotherapy: a pan-cancer perspective. BMC Med Genomics 2023; 16:307. [PMID: 38037104 PMCID: PMC10687837 DOI: 10.1186/s12920-023-01714-5] [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: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND ATP7B is a copper-transporting protein that contributes to the chemo-resistance of human cancer cells. It remains unclear what the molecular mechanisms behind ATP7B are in cancer, as well as its role in human pan-cancer studies. METHODS Our study evaluated the differential expression of ATP7B in cancer and paracancerous tissues based on RNA sequencing data from the GTEx and TCGA. Kaplan-Meier and Cox proportional hazards regressions were used to estimate prognostic factors associated with ATP7B.The correlations between the expression of ATP7B and immune cell infiltration, tumor mutation burden, microsatellite instability and immune checkpoint molecules were analyzed. Co-expression networks and mutations in ATP7B were analyzed using the web tools. An analysis of ATP7B expression difference on drug sensitivity on tumor cells was performed using the CTRP, GDSC and CMap database. RESULTS ATP7B expression differed significantly between cancerous and paracancerous tissues. The abnormal expression of ATP7B was linked to prognosis in LGG and KIRC. Infiltration of immune cells, tumor mutation burden, microsatellite instability and immunomodulators had all been linked to certain types of cancer. Cancer cells exhibited a correlation between ATP7B expression and drug sensitivity. CONCLUSION ATP7B might be an immunotherapeutic and prognostic biomarker based on its involvement in cancer occurrence and development.
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Affiliation(s)
- Zhanzhan Zhang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
| | - Aobo Zhang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
| | - Yunpeng Shi
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
| | - Zijun Zhao
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, No. 50, a pine in Xiangshan, Haidian District, Beijing, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China.
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, No. 12 Jiankang Road, Chang'an District, Shijiazhuang, Hebei Province, China.
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14
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Li GS, Huang ZG, Li DM, Tang YL, Zheng JH, Yang L, Feng Y, Peng JX, Li JX, Tang YX, Zeng NY, Jin MH, Tian J, Liu J, Zhou HF, Chen G, Chen F. CDK6 is a novel predictive and prognosis biomarker correlated with immune infiltrates in multiple human neoplasms, including small cell lung carcinoma. Funct Integr Genomics 2023; 23:332. [PMID: 37950078 DOI: 10.1007/s10142-023-01253-3] [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: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
Abstract
The roles of cyclin-dependent kinase 6 (CDK6) in various cancers, including small cell lung carcinoma (SCLC), remain unclear. Here, 111,54 multi-center samples were investigated to determine the expression, clinical significance, and underlying mechanisms of CDK6 in 34 cancers. The area under the curve (AUC), Cox regression analysis, and the Kaplan-Meier curves were used to explore the clinical value of CDK6 in cancers. Gene set enrichment analysis and correlation analysis were performed to detect potential CDK6 mechanisms. CDK6 expression was essential in 24 cancer cell types. Abnormal CDK6 expression was observed in 14 cancer types (e.g., downregulated in breast invasive carcinoma; p < 0.05). CDK6 allowed six cancers to be distinguished from their controls (AUC > 0.750). CDK6 expression was a prognosis marker for 13 cancers (e.g., adrenocortical carcinoma; p < 0.05). CDK6 was correlated with several immune-related signaling pathways and the infiltration levels of certain immune cells (e.g., CD8+ T cells; p < 0.05). Downregulated CDK6 mRNA and protein levels were observed in SCLC (p < 0.05, SMD = - 0.90). CDK6 allowed the identification of SCLC status (AUC = 0.91) and predicted a favorable prognosis for SCLC patients (p < 0.05). CDK6 may be a novel biomarker for the prediction and prognosis of several cancers, including SCLC.
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Affiliation(s)
- Guo-Sheng Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Jin-Hua Zheng
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, P. R. China
| | - Lin Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Yue Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Jun-Xi Peng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Jing-Xiao Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Yu-Xing Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Neng-Yong Zeng
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Qinzhou, Qinzhou, 535009, P. R. China
| | - Mei-Hua Jin
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, P. R. China
| | - Jia Tian
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, P. R. China
| | - Jun Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Feng Chen
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, P. R. China.
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15
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Lian X, Tang X. Use of a ferroptosis-related gene signature to construct diagnostic and prognostic models for assessing immune infiltration in metabolic dysfunction-associated fatty liver disease. Front Cell Dev Biol 2023; 11:1199846. [PMID: 37928903 PMCID: PMC10622674 DOI: 10.3389/fcell.2023.1199846] [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: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Metabolic dysfunction-associated fatty liver disease (MAFLD), a serious health problem worldwide, can involve ferroptosis. This study aimed to comprehensively analyze the ferroptosis-related genes associated with MAFLD. Methods: Ferroptosis-related differentially expressed genes (FRDEGs) were identified in patients with MAFLD and healthy individuals. Gene ontology functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used to analyze the relevant action pathways of the FRDEGs. The Encyclopedia of RNA Interactomes, CHIPBase, and comparative toxicogenomics databases were used to build mRNA-miRNA, mRNA-transcription factor (TF), and mRNA-drug interaction networks, respectively. A diagnostic model was constructed and bioinformatics analysis methods, such as least absolute shrinkage and selection operator regression analysis, Cox regression analysis, nomogram-based analysis, consensus clustering analysis, and single-sample GSEA, were used to systematically investigate the prognostic values and immunologic characteristics. Results: A total of 13 FRDEGs were obtained and eight were used to construct a diagnostic model and perform a prognostic analysis. Hub genes were also used to construct mRNA-miRNA and mRNA-TF interaction networks and potential drug or molecular compounds. Two MAFLD subtypes were identified: cluster2, which represents an "immunoactive" type, and cluster1, which represents an "immunosuppressive" type; a significant correlation was observed between the immune cell contents and the expression of three FRDEGs (NR4A1, FADS2, and SCD). Conclusion: A ferroptosis-related gene signature was constructed to diagnose MAFLD-associated steatohepatitis, predict the prognosis of MAFLD patients, and analyze the immunologic characteristics of MAFLD. Our findings may provide insights into developing innovative MAFLD treatment techniques.
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Affiliation(s)
- Xin Lian
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xulei Tang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
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16
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Wang CY, Xuan DTM, Ye PH, Li CY, Anuraga G, Ta HDK, Lai MD, Hsu HP. Synergistic suppressive effects on triple-negative breast cancer by the combination of JTC-801 and sodium oxamate. Am J Cancer Res 2023; 13:4661-4677. [PMID: 37970352 PMCID: PMC10636693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/13/2023] [Indexed: 11/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) poses a significant clinical challenge due to the limited targeted therapies available at present. Cancer cells preferentially use glycolysis as their primary source of energy, characterized by increased glucose uptake and lactate production. JTC-801, a nociception/orphanin FQ opioid peptide (NOP) receptor antagonist, was reported to suppress the opioid receptor-like1 (ORL1) receptor/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/nuclear factor (NF)-κB-mediated carbonic anhydrase 9 (CA9) signaling pathway. Sodium oxamate is an inhibitor of gluconeogenesis and a glycolysis inhibitor, as a competitive lactate dehydrogenase A (LDHA) inhibitor, which also produces tumor suppression due to loss of LDHA activity. However, the roles of opioid analgesic drugs (e.g., JTC-801) and glycolysis inhibitors (e.g., sodium oxamate) in TNBC have not fully been explored. Meanwhile, concurrent treatment with JTC-801 and sodium oxamate may cause synergistic anticancer effects in a TNBC model. In the present study, the combination of JTC-801 and sodium oxamate triggered cell death in the TNBC MDA MB-231 cell line. RNA-sequencing data revealed potential genes in the crosstalk between JTC-801 and sodium oxamate including ALDOC, DDIT4, DHTKD1, EIF6, ENO1, ENO3, FOXK1, FOXK2, HIF1A, MYC, PFKM, PFKP, PPARA, etc. The combination of JTC-801 and sodium oxamate provides a novel potential therapeutic strategy for TNBC patients via downregulating cell cycle- and amino acid metabolism-related pathways such as "Cell cycle-the metaphase checkpoint", "(L)-tryptophan pathways and transport", and "Glutamic acid pathway". Collectively, the present study demonstrated that the synergistic effect of co-treatment with JTC-801 and sodium oxamate significantly suppressed tumor growth and played a crucial role in tumor development, and in turn may serve as potential synergistic drugs for TNBC.
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Affiliation(s)
- Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical UniversityTaipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 11031, Taiwan
| | - Pei-Hsuan Ye
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 70101, Taiwan
| | - Chung-Yen Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 70101, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical UniversityTaipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, PGRI Adi Buana UniversityEast Java, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical UniversityTaipei 11031, Taiwan
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 70101, Taiwan
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainan 70101, Taiwan
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17
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He S, Ji Z, Zhang Q, Zhang X, Chen J, Hu J, Wang R, Ding Y. Investigation of LGALS2 expression in the TCGA database reveals its clinical relevance in breast cancer immunotherapy and drug resistance. Sci Rep 2023; 13:17445. [PMID: 37838802 PMCID: PMC10576795 DOI: 10.1038/s41598-023-44777-1] [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: 04/06/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
Breast cancer (BRCA) is known as the leading cause of death in women worldwide and has a poor prognosis. Traditional therapeutic strategies such as surgical resection, radiotherapy and chemotherapy can cause adverse reactions such as drug resistance. Immunotherapy, a new treatment approach with fewer side effects and stronger universality, can prolong the survival of BRCA patients and even achieve clinical cure. However, due to population heterogeneity and other reasons, there are still certain factors that limit the efficacy of immunotherapy. Therefore, the importance of finding new tumor immune biomarker cannot be emphasized enough. Studies have reported that LGALS2 was closely related to immunotherapy efficacy, however, it is unclear whether it can act as an immune checkpoint for BRCA immunotherapy. In the current study, changes in LGALS2 expression were analyzed in public datasets such as TCGA-BRCA. We found that LGALS2 expression was associated with immune infiltration, drug resistance and other characteristics of BRCA. Moreover, high LGALS2 expression was closely related to immunotherapy response, and was associated with methylation modifications and clinical resistance for the first time. These findings may help to elucidate the role of LGALS2 in BRCA for the development and clinical application of future immunotherapy strategies against BRCA.
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Affiliation(s)
- Song He
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Zhonghao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
- Department of Basic Medicine, Changzhi Medical College, Changzhi, 046000, Shanxi, People's Republic of China
| | - Qing Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Xiwen Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Jian Chen
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Jinping Hu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Ruiqing Wang
- The Eye Center in the Second Hospital of Jilin University, Ziqiang Street 218#, Nanguan District, Changchun, Jilin, 130041, People's Republic of China.
| | - Yu Ding
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, People's Republic of China.
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18
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Li J, Sun Y, Cao L, Wang F. Correlation of NPDC1 Expression and Perineural Invasion Status with Clinicopathological Features in Patients with Colon Cancer. Int J Gen Med 2023; 16:4549-4563. [PMID: 37822345 PMCID: PMC10563778 DOI: 10.2147/ijgm.s428590] [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: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Background Colon cancer is a prevalent gastrointestinal malignancy that often exhibits distant metastasis, hindering the effectiveness of surgical interventions. In addition to well-known hematogenous and lymphatic metastasis, perineural invasion (PNI) has emerged as a significant mode of distant metastasis in colon tumors. PNI is closely associated with oncologic pain in advanced cancer patients, but the underlying mechanisms and associated biomarkers, which might be the novel therapeutic targets, remain poorly understood. Methods In this study, we employed large databases and bioinformatics methods to identify genes strongly linked to PNI in colon cancer and investigated their involvement in tumor nerve invasion, progression mechanisms, and chemotherapy resistance. Immunohistochemical techniques were utilized to validate the expression of target genes in 384 colon cancer tissues, and their expression was correlated with clinicopathological characteristics and patient survival data in our hospital. Furthermore, we conducted a comprehensive literature review to explore the potential functions of the target genes and their associated genes. Results Our screening revealed a significant correlation between neural proliferation differentiation and control-1 (NPDC1) expression and patient prognosis, suggesting a potential association with neural infiltration in colon cancer. Additionally, NPDC1 may promote tumorigenesis, progression, and chemoresistance through various related pathways. Conclusion Our study provides novel insights into the utility of NPDC1 as a predictive marker for PNI status, disease-free survival, and overall survival in patients with colon cancer, highlighting the prevalence of NPDC1 overexpression in patients with PNI in colon cancer.
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Affiliation(s)
- Jiannan Li
- Department of Medical Microbiology, College of Basic Medical Sciences, Jilin University, Changchun, People’s Republic of China
- Department of Colorectal and Anal Surgery, Jilin University Second Hospital, Changchun, People’s Republic of China
| | - Yao Sun
- Department of Colorectal and Anal Surgery, Jilin University Second Hospital, Changchun, People’s Republic of China
| | - Lanqing Cao
- Department of Pathology, Jilin University Second Hospital, Changchun, People’s Republic of China
| | - Fang Wang
- Department of Medical Microbiology, College of Basic Medical Sciences, Jilin University, Changchun, People’s Republic of China
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Singha M, Pu L, Srivastava G, Ni X, Stanfield BA, Uche IK, Rider PJF, Kousoulas KG, Ramanujam J, Brylinski M. Unlocking the Potential of Kinase Targets in Cancer: Insights from CancerOmicsNet, an AI-Driven Approach to Drug Response Prediction in Cancer. Cancers (Basel) 2023; 15:4050. [PMID: 37627077 PMCID: PMC10452340 DOI: 10.3390/cancers15164050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/16/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Deregulated protein kinases are crucial in promoting cancer cell proliferation and driving malignant cell signaling. Although these kinases are essential targets for cancer therapy due to their involvement in cell development and proliferation, only a small part of the human kinome has been targeted by drugs. A comprehensive scoring system is needed to evaluate and prioritize clinically relevant kinases. We recently developed CancerOmicsNet, an artificial intelligence model employing graph-based algorithms to predict the cancer cell response to treatment with kinase inhibitors. The performance of this approach has been evaluated in large-scale benchmarking calculations, followed by the experimental validation of selected predictions against several cancer types. To shed light on the decision-making process of CancerOmicsNet and to better understand the role of each kinase in the model, we employed a customized saliency map with adjustable channel weights. The saliency map, functioning as an explainable AI tool, allows for the analysis of input contributions to the output of a trained deep-learning model and facilitates the identification of essential kinases involved in tumor progression. The comprehensive survey of biomedical literature for essential kinases selected by CancerOmicsNet demonstrated that it could help pinpoint potential druggable targets for further investigation in diverse cancer types.
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Affiliation(s)
- Manali Singha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Limeng Pu
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
| | - Gopal Srivastava
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Xialong Ni
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Brent A. Stanfield
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
| | - Ifeanyi K. Uche
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Paul J. F. Rider
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - J. Ramanujam
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
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Shao RN, Bai KH, Huang QQ, Chen SL, Huang X, Dai YJ. A novel prognostic prediction model of cuprotosis-related genes signature in hepatocellular carcinoma. Front Cell Dev Biol 2023; 11:1180625. [PMID: 37608927 PMCID: PMC10440422 DOI: 10.3389/fcell.2023.1180625] [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: 03/06/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
Background: Cuprotosis is a recently discovered copper-dependent cell death mechanism that relies on mitochondrial respiration. However, the role of cuprotosis-related genes (CRGs) in hepatocellular carcinoma (HCC) and their prognostic significances remain unknown. Methods: Based on the recently published CRGs, the LASSO Cox regression analysis was applied to construct a CRGs risk model using the gene expression data from the International Cancer Genome Consortium as a training set, followed by validation with datasets from The Cancer Genome Atlas and the Gene Expression Omnibus (GSE14520). Functional enrichment analysis of the CRGs was performed by single-sample gene set enrichment analysis. Results: Five of the 13 previously published CRGs were identified to be associated with prognosis in HCC. Kaplan-Meier analysis suggested that patients with high-risk scores have a shorter overall survival time than patients with low-risk scores. ROC curves indicated that the average AUC was more than 0.7, even at 4 years, and at least 0.5 at 5 years. Moreover, addition of this CRG risk score can significantly improve the efficiency of predicting overall survival compared to using traditional factors alone. Functional analysis demonstrated increased presence of Treg cells in patients with high-risk scores, suggesting a suppressed immune state in these patients. Finally, we point to the possibility that novel immunotherapies such as inhibitors of PDCD1, TIGIT, IDO1, CD274, CTLA4, and LAG3 may have potential benefits in high-risk patients. Conclusion: We constructed a better prognostic model for liver cancer by using CRGs. The CRG risk score established in this study can serve as a potentially valuable tool for predicting clinical outcome of patients with HCC.
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Affiliation(s)
- Ruo-Nan Shao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kun-Hao Bai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Endoscopy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qian-Qian Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Si-Liang Chen
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Jun Dai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
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21
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Tram VTN, Khoa Ta HD, Anuraga G, Dung PVT, Xuan DTM, Dey S, Wang CY, Liu YN. Dysbindin Domain-Containing 1 in Prostate Cancer: New Insights into Bioinformatic Validation of Molecular and Immunological Features. Int J Mol Sci 2023; 24:11930. [PMID: 37569304 PMCID: PMC10418609 DOI: 10.3390/ijms241511930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers in men, yet its pathogenic pathways remain poorly understood. Transcriptomics and high-throughput sequencing can help uncover cancer diagnostic targets and understand biological circuits. Using prostate adenocarcinoma (PRAD) datasets of various web-based applications (GEPIA, UALCAN, cBioPortal, SR Plot, hTFtarget, Genome Browser, and MetaCore), we found that upregulated dysbindin domain-containing 1 (DBNDD1) expression in primary prostate tumors was strongly correlated with pathways involving the cell cycle, mitotic in KEGG, WIKI, and REACTOME database, and transcription factor-binding sites with the DBNDD1 gene in prostate samples. DBNDD1 gene expression was influenced by sample type, cancer stage, and promoter methylation levels of different cancers, such as PRAD, liver hepatocellular carcinoma (LIHC), and lung adenocarcinoma (LUAD). Regulation of glycogen synthase kinase (GSK)-3β in bipolar disorder and ATP/ITP/GTP/XTP/TTP/CTP/UTP metabolic pathways was closely correlated with the DBNDD1 gene and its co-expressed genes in PCa. DBNDD1 gene expression was positively associated with immune infiltration of B cells, Myeloid-derived suppressor cell (MDSC), M2 macrophages, andneutrophil, whereas negatively correlated with CD8+ T cells, T follicular helper cells, M1 macrophages, and NK cells in PCa. These findings suggest that DBNDD1 may serve as a viable prognostic marker not only for early-stage PCa but also for immunotherapies.
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Affiliation(s)
- Van Thi Ngoc Tram
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Department of Medical Laboratory, University Medical Center Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Hoang Dang Khoa Ta
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan
| | - Gangga Anuraga
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Phan Vu Thuy Dung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
| | - Sanskriti Dey
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan
| | - Yen-Nien Liu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (H.D.K.T.); (G.A.); (P.V.T.D.); (D.T.M.X.); (S.D.)
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
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Yan JN, Guo LH, Zhu DP, Ye GL, Shao YF, Zhou HX. Clinical significance and potential application of cuproptosis-related genes in gastric cancer. World J Gastrointest Oncol 2023; 15:1200-1214. [PMID: 37546553 PMCID: PMC10401470 DOI: 10.4251/wjgo.v15.i7.1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 05/06/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Worldwide, gastric cancer (GC) is a common lethal solid malignancy with a poor prognosis. Cuproptosis is a novel type of cell death mediated by protein lipoylation and may be related to GC prognosis.
AIM To offer new insights to predict GC prognosis and provide multiple therapeutic targets related to cuproptosis-related genes (CRGs) for future therapy.
METHODS We collected data from several public data portals, systematically estimated the expression level and prognostic values of CRGs in GC samples, and investigated related mechanisms using public databases and bioinformatics.
RESULTS Our results revealed that FDX1, LIAS, and MTF1 were differentially expressed in GC samples and exhibited important prognostic significance in The Cancer Genome Atlas (TCGA) cohort. We constructed a nomogram model for overall survival and disease-specific survival prediction and validated it via calibration plots. Mecha-nistically, immune cell infiltration and DNA methylation prominently affected the survival time of GC patients. Moreover, protein-protein interaction network, KEGG pathway and gene ontology enrichment analyses demonstrated that FDX1, LIAS, MTF1 and related proteins play key roles in the tricarboxylic acid cycle and cuproptosis. Gene Expression Omnibus database validation showed that the expression levels of FDX1, LIAS, and MTF1 were consistent with those in the TCGA cohort. Top 10 perturbagens has been filtered by Connectivity Map.
CONCLUSION In conclusion, FDX1, LIAS, and MTF1 could serve as potential prognostic biomarkers for GC patients and provide novel targets for immunotarget therapy.
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Affiliation(s)
- Jia-Ning Yan
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Li-Hua Guo
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Dan-Ping Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Guo-Liang Ye
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Yong-Fu Shao
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Han-Xuan Zhou
- Department of Pharmacy, Yinzhou Integrated TCM and Western Medicine Hospital, Ningbo 315000, Zhejiang Province, China
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Zhu M, Sun Y, Xue H, Wu G, Wang Z, Shi J, Ma J, Gu B, Yan X. NEK6 Promotes the Progression of Osteosarcoma Through Activating STAT3 Signaling Pathway by Down-Regulation of miR-26a-5p. Int J Gen Med 2023; 16:2831-2848. [PMID: 37426517 PMCID: PMC10329465 DOI: 10.2147/ijgm.s413461] [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: 03/21/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023] Open
Abstract
Background Osteosarcoma is a malignant tumor originating from the skeletal system. There is no effective treatment other than surgery and chemotherapy, which seriously endangers the health of children and adolescents. NEK6 is a novel discovered Serine/Threonine protein kinase that can regulate cell cycle and activate several oncogenic pathways. Methods NEK6 expression in pan-cancer including sarcoma was evaluated using analysis tools of TIMER, UALCNA and GEPIA with TCGA database, and its association with overall survival in patients with sarcoma was also analyzed. TargetScan, tarbase, microT-CDS and Starbase online software were used to predict NEK6-targeted miRNAs, including miR-26a-5p. Tumor tissues from patients with osteosarcoma were collected for NEK6 and miRNA detection using RT-qPCR. NEK6 down-regulated by siRNAs or miR-26a-5p in osteosarcoma cells was detected by RT-qPCR, Western blot and Immunofluorescence staining assays. Effects of NEK6 knockdown on proliferation, migration, invasion and apoptosis of osteosarcoma cells were detected by CCK-8, wound healing, transwell and flow cytometry, respectively. The expressions of STAT3, metastasis and apoptosis-related genes were detected by Western blot. Results High expression of NEK6 and low expression of miR-26a-5p were lowly expressed in osteosarcoma and they were negative correlation. NEK6 has been confirmed as a direct target for miR-26a-5p. In addition, NEK6 down-regulated by siRNAs or miR-26a-5p led to inhibition of cell proliferation, migration and invasion while promoting cell apoptosis. The levels of phosphorylated STAT3 and metastasis genes (MMP-2, MMP-9) were inhibited, while apoptotic gene Bax was promoted and Bcl2 was inhibited by miR-26a-5p upregulation. Conclusion NEK6 can promote osteosarcoma progression via activating STAT3 signaling pathway, which is inhibited by miR-26a-5p, suggesting that NEK6 is a potential oncogene and miR-26a-5p is a suppressor of osteosarcoma. The strategy of inhibiting of NEK6 by miR-26a-5p may be an effective approach for osteosarcoma therapy.
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Affiliation(s)
- Min Zhu
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Yuyu Sun
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Huawei Xue
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Gang Wu
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Zhen Wang
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Junfeng Shi
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Jiye Ma
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Baorong Gu
- Department of Spine Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, People’s Republic of China
| | - Xiaoling Yan
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, People’s Republic of China
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Lu X, Yuan Q, Zhang C, Wang S, Wei W. Predicting the immune microenvironment and prognosis with a anoikis - related signature in breast cancer. Front Oncol 2023; 13:1149193. [PMID: 37469408 PMCID: PMC10353543 DOI: 10.3389/fonc.2023.1149193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023] Open
Abstract
Background Tumor heterogeneity is widely recognized as a crucial factor impacting the prognosis of breast cancer (BC) patients. However, there remains an insufficient understanding of the underlying impact of anoikis on the prognosis of BC patients. Methods The researchers utilized the TCGA-BRCA dataset to screen and analyze the differentially expressed genes of anoikis-related genes (ARGs) in BC and normal breast tissue. Prognostic gene signatures were established through univariate, LASSO, and multivariate Cox regression analyses. These signatures were evaluated using Kaplan-Meier curve and receiver operating characteristic (ROC) analyses, resulting in the development of an anoikis-related index (ACI). The training dataset was TCGA-BRCA, while METABRIC and GSE96058 were used for external validation. Additionally, nomograms were developed by combining risk scores and clinical parameters, enabling gene set enrichment analysis (GSEA) and tumor immunoassay. Furthermore, an exploration of small molecule compounds was conducted to identify potential therapeutic benefits. Results A six-gene anoikis-related signature was constructed, which divided BC patients into high- and low-ACI groups based on median ACI scores. The ACI accurately predicted prognosis and acted as an independent prognostic factor for BC patients. Patients in the high-ACI group exhibited poorer overall survival (OS) across all cohorts and showed more severe clinical manifestations compared to the low-ACI group. The study also explored the potential impacts of anoikis on immune cells infiltrating tumors, immune checkpoints, growth factors, and cytokine levels. Additionally, the potential implications of anoikis in BC immunotherapy were discussed, along with highlighting small molecule compounds that could offer therapeutic benefits. Conclusions Anoikis was found to hold significant prognostic value in breast cancer, providing a novel approach for managing patients with different prognoses and implementing more precise immunotherapy strategies.
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Affiliation(s)
- Xiuqing Lu
- Department of Breast Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qi Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Chao Zhang
- Department of Breast Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Sifen Wang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weidong Wei
- Department of Breast Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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Chen Y, Wen H, Li Y, Han Y, Tan J, Guo C, Cai C, Liu P, Peng Y, Liu Y, Wang X, Zeng S, Feng Z, Shen H. A multi-omics analysis reveals CLSPN is associated with prognosis, immune microenvironment and drug resistance in cancers. Biol Proced Online 2023; 25:16. [PMID: 37268895 DOI: 10.1186/s12575-023-00201-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Immunotherapy is effective only in limited patients. It is urgent to discover a novel biomarker to predict immune cells infiltration status and immunotherapy response of different cancers. CLSPN has been reported to play a pivotal role in various biological processes. However, a comprehensive analysis of CLSPN in cancers has not been conducted. METHODS To show the whole picture of CLSPN in cancers, a pan-cancer analysis was conducted in 9125 tumor samples across 33 cancer types by integrating transcriptomic, epigenomic and pharmacogenomics data. Moreover, the role of CLSPN in cancer was validated by CCK-8, EDU, colony formation and flow cytometry in vitro and tumor cell derived xenograft model in vivo. RESULTS CLSPN expression was generally upregulated in most cancer types and was significantly associated with prognosis in different tumor samples. Moreover, elevated CLSPN expression was closely correlated with immune cells infiltration, TMB (tumor mutational burden), MSI (microsatellite instability), MMR (mismatch repair), DNA methylation and stemness score across 33 cancer types. Enrichment analysis of functional genes revealed that CLSPN participated in the regulation of numerous signaling pathways involved in cell cycle and inflammatory response. The expression of CLSPN in LUAD patients were further analyzed at the single-cell level. Knockdown CLSPN significantly inhibited cancer cell proliferation and cell cycle related cyclin-dependent kinase (CDK) family and Cyclin family expression in LUAD (lung adenocarcinoma) both in vitro and in vivo experiments. Finally, we conducted structure-based virtual screening by modelling the structure of CHK1 kinase domain and Claspin phosphopeptide complex. The top five hit compounds were screened and validated by molecular docking and Connectivity Map (CMap) analysis. CONCLUSION Our multi-omics analysis offers a systematic understanding of the roles of CLSPN in pan-cancer and provides a potential target for future cancer treatment.
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Affiliation(s)
- Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Haicheng Wen
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Cao Guo
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xinwen Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Gong L, Zhong M, Gong K, Wang Z, Zhong Y, Jin Y, Chen H, Tai P, Chen X, Chen A, Cao K. Multi-Omics Analysis and Verification of the Oncogenic Value of CCT8 in Pan-Cancers. J Inflamm Res 2023; 16:2297-2315. [PMID: 37273485 PMCID: PMC10238552 DOI: 10.2147/jir.s403499] [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: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 06/06/2023] Open
Abstract
Background Chaperonin-containing TCP1 subunit 8 (CCT8) has been proved to be involved in the occurrence and development of some cancers. However, no study has reported the potential role of CCT8 in a pan-cancer manner. Methods TIMER2.0, GEPIA2, UALCAN and Sangerbox were used to explore the expression, prognosis and methylation of CCT8. We used cBioPortal, TISIDB, SangerBox, TIMER2.0 and TISMO to investigate the genetic alteration of CCT8 and the relationship of CCT8 with molecular subtype, immune subtype, immune infiltration and immunotherapy response. CCT8-related genes were screened out through GEPIA and STRING for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. CCK-8, the colony formation assay, the wound healing assay and the Transwell assay were performed to explore the influence of CCT8 on proliferation and migration. Results CCT8 was highly expressed in most cancers with a poor prognosis. The expression level of CCT8, which was affected by the promoter region methylation and genetic alteration, was related to the molecular and immune subtype of cancers. Interestingly, CCT8 was positively associated with the activated CD4 T cells and type 2 T-helper cells. CCT8 played a vital role in the cell cycle and RNA transport of cancers, and it significantly inhibited the proliferation and migration of lung adenocarcinoma cells when it was knocked down. Conclusion CCT8 plays an indispensable role in promoting the proliferation and migration of many cancers. CCT8 might be a biomarker of T-helper type 2 (Th2) cell infiltration and a promising therapeutic target for T-helper type 1(Th1)/Th2 imbalance.
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Affiliation(s)
- Lian Gong
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Ming Zhong
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Kai Gong
- Department of Clinical Medicine, Xiangnan University, Chenzhou, People’s Republic of China
| | - Zhanwang Wang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Yong Zhong
- Department of Clinical Medicine, Hubei Enshi College, Enshi, People’s Republic of China
| | - Yi Jin
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Haotian Chen
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Panpan Tai
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Xinyu Chen
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Aiyan Chen
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, 410013, People’s Republic of China
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Liu S, Wang S, Wang Z. Identification of genetic mechanisms underlying lipid metabolism-mediated tumor immunity in head and neck squamous cell carcinoma. BMC Med Genomics 2023; 16:110. [PMID: 37210507 DOI: 10.1186/s12920-023-01543-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/13/2023] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVE To identify the genetic mechanisms underlying lipid metabolism-mediated tumor immunity in head and neck squamous carcinoma (HNSC). MATERIALS AND METHODS RNA sequencing data and clinical characteristics of HNSC patients were procured from The Cancer Genome Atlas (TCGA) database. Lipid metabolism-related genes were collected from KEGG and MSigDB databases. Immune cells and immune-related genes were obtained from the TISIDB database. The differentially expressed genes (DEGs) in HNSC were identified and weighted correlation network analysis (WGCNA) was performed to identify the significant gene modules. Lasso regression analysis was performed to identify hub genes. The differential gene expression pattern, diagnostic values, relationships with clinical features, prognostic values, relationships with tumor mutation burden (TMB), and signaling pathways involved, were each investigated. RESULTS One thousand six hundred sixty-eight DEGs were identified as dysregulated between HNSC tumor samples and healthy control head and neck samples. WGCNA analysis and Lasso regression analysis identified 8 hub genes, including 3 immune-related genes (PLA2G2D, TNFAIP8L2 and CYP27A1) and 5 lipid metabolism-related genes (FOXP3, IL21R, ITGAL, TRAF1 and WIPF1). Except CYP27A1, the other hub genes were upregulated in HNSC as compared with healthy control samples, and a low expression of these hub genes indicated a higher risk of death in HNSC. Except PLA2G2D, all other hub genes were significantly and negatively related with TMB in HNSC. The hub genes were implicated in several immune-related signaling pathways including T cell receptor signaling, Th17 cell differentiation, and natural killer (NK) cell mediated cytotoxicity. CONCLUSION Three immune genes (PLA2G2D, TNFAIP8L2, and CYP27A1) and immune-related pathways (T cell receptor signaling, Th17 cell differentiation, and natural killer (NK) cell mediated cytotoxicity) were predicted to play significant roles in the lipid metabolism-mediated tumor immunity in HNSC.
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Affiliation(s)
- Shaokun Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Xuanwu Hospital Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, 100053, China
| | - Shuning Wang
- Capital Medical University, No.10 Xitou Tiao, You'an Menwai, Fengtai District, Beijing, 10069, China
| | - Zhenlin Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Xuanwu Hospital Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, 100053, China.
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Guo L, Cen H, Weng J, He Y, Guo X, He D, Liu K, Duan S, Yang J, Zhang X, Qin Z, Wan Y, Chen Z, Wu B. PER2 integrates circadian disruption and pituitary tumorigenesis. Theranostics 2023; 13:2657-2672. [PMID: 37215573 PMCID: PMC10196825 DOI: 10.7150/thno.82995] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Rationale: The role of circadian clock in pituitary tumorigenesis remains elusive. Here we investigate whether and how circadian clock modulates the development of pituitary adenomas. Methods and Results: We found altered expression of pituitary clock genes in patients with pituitary adenomas. In particular, PER2 is prominently upregulated. Further, jetlagged mice with PER2 upregulation have accelerated growth of GH3 xenograft tumor. Conversely, loss of Per2 protects mice against developing estrogen-induced pituitary adenoma. Similar antitumor effect is observed for SR8278, a chemical that can decrease pituitary PER2 expression. RNA-seq analysis suggests involvement of cell cycle disturbance in PER2 regulation of pituitary adenoma. Subsequent in vivo and cell-based experiments validate that PER2 induces pituitary expression of Ccnb2, Cdc20 and Espl1 (three cell cycle genes) to facilitate cell cycle progression and inhibit apoptosis, thereby promoting pituitary tumorigenesis. Mechanistically, PER2 regulates the transcription of Ccnb2, Cdc20 and Espl1 through enhancing the transcriptional activity of HIF-1α. HIF-1α trans-activates Ccnb2, Cdc20 and Espl1 via direct binding to its specific response element in the gene promoters. Conclusion: PER2 integrates circadian disruption and pituitary tumorigenesis. These findings advance our understanding of crosstalk between circadian clock and pituitary adenomas and highlight the relevance of clock-based approaches in disease management.
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Affiliation(s)
- Lianxia Guo
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haobin Cen
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiaxian Weng
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiting He
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaocao Guo
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Di He
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kaisheng Liu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Shuyi Duan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jing Yang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaojian Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zifei Qin
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yong Wan
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhiyong Chen
- Department of Neurosurgery, the First Affiliated Hospital of Jinan University, Guangzhou, China
- Minimally Invasive Treatment Center for Pituitary Adenoma of Jinan University, Guangzhou, China
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
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The Role of Selective Flavonoids on Triple-Negative Breast Cancer: An Update. SEPARATIONS 2023. [DOI: 10.3390/separations10030207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Among the many types of breast cancer (BC), Triple-Negative Breast Cancer (TNBC) is the most alarming. It lacks receptors for the three main biomarkers: estrogen, progesterone, and human epidermal growth factor, hence the name TNBC. This makes its treatment a challenge. Surgical procedures and chemotherapy, performed either alone or in combination, seem to be the primary therapeutic possibilities; however, they are accompanied by severe complications. Currently, the formulation of drugs using natural products has been playing an important role in the pharmaceutical industries, owing to the drugs’ increased efficacies and significantly lessened side effects. Hence, treating TNBC with chemotherapeutic drugs developed using natural products such as flavonoids in the near future is much warranted. Flavonoids are metabolic compounds largely present in all plants, vegetables, and fruits, such as blueberries, onions, (which are widely used to make red wine,) chocolates, etc. Flavonoids are known to have enormous health benefits, such as anticancer, antiviral, anti-inflammatory, and antiallergic properties. They are known to arrest the cell cycle of the tumor cells and induces apoptosis by modulating Bcl-2, Bax, and Caspase activity. They show a considerable effect on cell proliferation and viability and angiogenesis. Various studies were performed at both the biochemical and molecular levels. The importance of flavonoids in cancer treatment and its methods of extraction and purification to date have been reported as individual publications. However, this review article explains the potentiality of flavonoids against TNBC in the preclinical levels and also emphasizes their molecular mechanism of action, along with a brief introduction to its methods of extraction, isolation, and purification in general, emphasizing the fact that its quantum of yield if enhanced and its possible synergistic effects with existing chemotherapeutics may pave the way for better anticancer agents of natural origin and significantly lessened side-effects.
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Li H, Gao L, Kang X, Wang X, Yu Y, Zhang Y, Chen H. RPS24 Is Associated with a Poor Prognosis and Immune Infiltration in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24010806. [PMID: 36614249 PMCID: PMC9820840 DOI: 10.3390/ijms24010806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver malignancy, with increased mortality and morbidity. Accumulating evidence suggested that 40S ribosomal protein S24 (RPS24) is related to malignant outcomes and progression. However, the role of RPS24 remains unclear in HCC. The mRNA and protein expression pattern of RPS24 in HCC was explored and confirmed based on the bioinformatics analysis and histological examination. The correlation between RPS24 expression and clinicopathological features, diagnostic value, prognosis, methylation status, and survival were evaluated. Then, we divided the HCC cohort into two groups based on the expression of RPS24, and performed the functional enrichment and immune cells infiltration analysis of RPS24. Furthermore, in vivo and in vitro experiments were performed to investigate the effect of RPS24 on HCC cells. RPS24 was observed to be elevated in HCC samples. RPS24 overexpression or RPS24 promoter methylation contributed to an unfavorable prognosis for HCC patients. The genes in the high RPS24 expression group were mainly enriched in DNA replication, cell cycle E2F targets, and the G2M checkpoint pathway. Moreover, the expression level of RPS24 was significantly related to immune infiltration and immunotherapy response. Our experiments also demonstrated that RPS24 knockdown suppressed the growth of HCC cells and tumor proliferation of the xenograft model. Therefore, RPS24 can be a potential adverse biomarker of HCC prognosis acting through facilitating cell proliferation and the formation of an immunosuppressive microenvironment in HCC. Targeting RPS24 may offer a promising therapeutic option for HCC management.
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Affiliation(s)
- Haiyuan Li
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Lei Gao
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Xiaojuan Kang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Xueyan Wang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Yang Yu
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Yaqing Zhang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Hao Chen
- Second Clinical Medical College, Lanzhou University, Lanzhou 730000, China
- Department of Tumor Surgery, Lanzhou University Second Hospital, Lanzhou 730030, China
- Correspondence:
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Wang CC, Shen WJ, Anuraga G, Khoa Ta HD, Xuan DTM, Chen ST, Shen CF, Jiang JZ, Sun Z, Wang CY, Wang WJ. Novel Potential Therapeutic Targets of PTPN Families for Lung Cancer. J Pers Med 2022; 12:jpm12121947. [PMID: 36556168 PMCID: PMC9784538 DOI: 10.3390/jpm12121947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
Despite the treatment of lung adenocarcinoma (LUAD) having partially improved in recent years, LUAD patients still have poor prognosis rates. Therefore, it is especially important to explore effective biomarkers and exploit novel therapeutic developments. High-throughput technologies are widely used as systematic approaches to explore differences in expressions of thousands of genes for both biological and genomic systems. Recently, using big data analyses in biomedicine research by integrating several high-throughput databases and tools, including The Cancer Genome Atlas (TCGA), cBioportal, Oncomine, and Kaplan-Meier plotter, is an important strategy to identify novel biomarkers for cancer therapy. Here, we used two different comprehensive bioinformatics analysis and revealed protein tyrosine phosphatase non-receptor type (PTPN) family genes, especially PTPN1 and PTPN22, were downregulated in lung cancer tissue in comparison with normal samples. The survival curves indicated that LUAD patients with high transcription levels of PTPN5 were significantly associated with a good prognosis. Meanwhile, Gene Ontology (GO) and MetaCore analyses indicated that co-expression of the PTPN1, PTPN5, and PTPN21 genes was significantly enriched in cancer development-related pathways, including GTPase activity, regulation of small GTPase-mediated signal transduction, response to mechanical stimuli, vasculogenesis, organ morphogenesis, regulation of stress fiber assembly, mitogen-activated protein kinase (MAPK) cascade, cell migration, and angiogenesis. Collectively, this study revealed that PTPN family members are both significant prognostic biomarkers for lung cancer progression and promising clinical therapeutic targets, which provide new targets for treating LUAD patients.
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Affiliation(s)
- Chin-Chou Wang
- Divisions of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 613016, Taiwan
| | - Wan-Jou Shen
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
| | - Gangga Anuraga
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Sih-Tong Chen
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
| | - Chiu-Fan Shen
- Divisions of Pulmonary & Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Jia-Zhen Jiang
- Emergency Department, Huashan Hospital North, Fudan University, Shanghai 201508, China
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (C.-Y.W.); (W.-J.W.)
| | - Wei-Jan Wang
- Department of Biological Science and Technology, China Medical University, Taichung 40676, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
- Correspondence: (C.-Y.W.); (W.-J.W.)
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The Analysis of Relevant Gene Networks Based on Driver Genes in Breast Cancer. Diagnostics (Basel) 2022; 12:diagnostics12112882. [PMID: 36428940 PMCID: PMC9689550 DOI: 10.3390/diagnostics12112882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The occurrence and development of breast cancer has a strong correlation with a person's genetics. Therefore, it is important to analyze the genetic factors of breast cancer for future development of potential targeted therapies from the genetic level. METHODS In this study, we complete an analysis of the relevant protein-protein interaction network relating to breast cancer. This includes three steps, which are breast cancer-relevant genes selection using mutual information method, protein-protein interaction network reconstruction based on the STRING database, and vital genes calculating by nodes centrality analysis. RESULTS The 230 breast cancer-relevant genes were chosen in gene selection to reconstruct the protein-protein interaction network and some vital genes were calculated by node centrality analyses. Node centrality analyses conducted with the top 10 and top 20 values of each metric found 19 and 39 statistically vital genes, respectively. In order to prove the biological significance of these vital genes, we carried out the survival analysis and DNA methylation analysis, inquired about the prognosis in other cancer tissues and the RNA expression level in breast cancer. The results all proved the validity of the selected genes. CONCLUSIONS These genes could provide a valuable reference in clinical treatment among breast cancer patients.
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Circadian rhythm-related factors of PER and CRY family genes function as novel therapeutic targets and prognostic biomarkers in lung adenocarcinoma. Aging (Albany NY) 2022; 14:9056-9089. [PMID: 36385012 PMCID: PMC9740380 DOI: 10.18632/aging.204386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022]
Abstract
The period (PER) and cryptochrome (CRY) families play critical roles in circadian rhythms. The imbalance of circadian factors may lead to the occurrence of cancer. Expressions of PER and CRY family members decrease in various cancers. Nevertheless, expression levels, genetic variations, and molecular mechanisms of PER and CRY family members in lung adenocarcinoma (LUAD) and their correlations with prognoses and immune infiltration in LUAD patients are still unclear. In this study, to identify their biological functions in LUAD development, comprehensive high-throughput techniques were applied to analyze the relationships of expressions of PER and CRY family members with genetic variations, molecular mechanisms, and immune infiltration. The present results showed that transcription levels of PER1 and CRY2 in LUAD were significantly downregulated. High expression levels of PER2, PER3, CRY1, and CRY2 indicated longer overall survival. Some cancer signaling pathways were related to PER and CRY family members, such as cell-cycle, histidine metabolism, and progesterone-mediated oocyte maturation pathways. Expressions of PER and CRY family members significantly affected the infiltration of different immune cells. In conclusion, our findings may help better understand the molecular basis of LUAD, and provide new perspectives of PER and CRY family members as novel biomarkers for LUAD.
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A novel focal adhesion-related risk model predicts prognosis of bladder cancer —— a bioinformatic study based on TCGA and GEO database. BMC Cancer 2022; 22:1158. [PMID: 36357874 PMCID: PMC9647995 DOI: 10.1186/s12885-022-10264-5] [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: 04/22/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
Background Bladder cancer (BLCA) is the ninth most common cancer globally, as well as the fourth most common cancer in men, with an incidence of 7%. However, few effective prognostic biomarkers or models of BLCA are available at present. Methods The prognostic genes of BLCA were screened from one cohort of The Cancer Genome Atlas (TCGA) database through univariate Cox regression analysis and functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The intersecting genes of the BLCA gene set and focal adhesion-related gene were obtained and subjected to the least absolute shrinkage and selection operator regression (LASSO) to construct a prognostic model. Gene set enrichment analysis (GSEA) of high- and low-risk patients was performed to explore further the biological process related to focal adhesion genes. Univariate and multivariate Cox analysis, receiver operating characteristic (ROC) curve analysis, and Kaplan–Meier survival analysis (KM) were used to evaluate the prognostic model. DNA methylation analysis was presented to explore the relationship between prognosis and gene methylation. Furthermore, immune cell infiltration was assessed by CIBERSORT, ESTIMATE, and TIMER. The model was verified in an external GSE32894 cohort of the Gene Expression Omnibus (GEO) database, and the Prognoscan database presented further validation of genes. The HPA database validated the related protein level, and functional experiments verified significant risk factors in the model. Results VCL, COL6A1, RAC3, PDGFD, JUN, LAMA2, and ITGB6 were used to construct a prognostic model in the TCGA-BLCA cohort and validated in the GSE32894 cohort. The 7-gene model successfully stratified the patients into both cohorts’ high- and low-risk groups. The higher risk score was associated with a worse prognosis. Conclusions The 7-gene prognostic model can classify BLCA patients into high- and low-risk groups based on the risk score and predict the overall survival, which may aid clinical decision-making. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10264-5.
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Ku SC, Liu HL, Su CY, Yeh IJ, Yen MC, Anuraga G, Ta HDK, Chiao CC, Xuan DTM, Prayugo FB, Wang WJ, Wang CY. Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer. Aging (Albany NY) 2022; 14:8498-8567. [PMID: 36315446 PMCID: PMC9648792 DOI: 10.18632/aging.204357] [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: 01/22/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Breast cancer is one of the leading deaths in all kinds of malignancies; therefore, it is important for early detection. At the primary tumor site, tumor cells could take on mesenchymal properties, termed the epithelial-to-mesenchymal transition (EMT). This process is partly regulated by members of the cadherin (CDH) family of genes, and it is an essential step in the formation of metastases. There has been a lot of study of the roles of some of the CDH family genes in cancer; however, a holistic approach examining the roles of distinct CDH family genes in the development of breast cancer remains largely unexplored. In the present study, we used a bioinformatics approach to examine expression profiles of CDH family genes using the Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, MetaCore, and Tumor IMmune Estimation Resource (TIMER) platforms. We revealed that CDH1/2/4/11/12/13 messenger (m)RNA levels are overexpressed in breast cancer cells compared to normal cells and were correlated with poor prognoses in breast cancer patients’ distant metastasis-free survival. An enrichment analysis showed that high expressions of CDH1/2/4/11/12/13 were significantly correlated with cell adhesion, the extracellular matrix remodeling process, the EMT, WNT/beta-catenin, and interleukin-mediated immune responses. Collectively, CDH1/2/4/11/12/13 are thought to be potential biomarkers for breast cancer progression and metastasis.
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Affiliation(s)
- Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of General Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Hsin-Liang Liu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Che-Yu Su
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
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Hermawan A, Putri H. Bioinformatics analysis reveals the potential target of rosiglitazone as an antiangiogenic agent for breast cancer therapy. BMC Genom Data 2022; 23:72. [PMID: 36114448 PMCID: PMC9482259 DOI: 10.1186/s12863-022-01086-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Several studies have demonstrated the antitumor activity of rosiglitazone (RGZ) in cancer cells, including breast cancer cells. However, the molecular targets of RGZ in the inhibition of angiogenesis in breast cancer cells remain unclear. This study aimed to explore the potential targets of RGZ in inhibiting breast cancer angiogenesis using bioinformatics-based analysis. Results Venn diagram analysis revealed 29 TR proteins. KEGG pathway enrichment analysis demonstrated that TR regulated the adipocytokine, AMPK, and PPAR signaling pathways. Oncoprint analysis showed genetic alterations in FABP4 (14%), ADIPOQ (2.9%), PPARG (2.8%), PPARGC1A (1.5%), CD36 (1.7%), and CREBBP (11%) in patients with breast cancer in a TCGA study. The mRNA levels of FABP4, ADIPOQ, PPARG, CD36, and PPARGC1A were significantly lower in patients with breast cancer than in those without breast cancer. Analysis of gene expression using bc-GenExMiner showed that the mRNA levels of FABP, ADIPOQ, PPARG, CD36, PPARGC1A, and CREBBP were significantly lower in basal-like and triple-negative breast cancer (TNBC) cells than in non-basal-like and non-TNBC cells. In general, the protein levels of these genes were low, except for that of CREBBP. Patients with breast cancer who had low mRNA levels of FABP4, ADIPOQ, PPARG, and PPARGC1A had lower overall survival rates than those with high mRNA levels, which was supported by the overall survival related to DNA methylation. Correlation analysis of immune cell infiltration with TR showed a correlation between TR and immune cell infiltration, highlighting the potential of RGZ for immunotherapy. Conclusion This study explored the potential targets of RGZ as antiangiogenic agents in breast cancer therapy and highlighted FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP as potential targets of RGZ. These findings require further validation to explore the potential of RGZ as an antiangiogenic agent. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01086-2. Recent studies have focused on the development of indirect angiogenesis inhibitors. Bioinformatics-based identification of potential rosiglitazone target genes to inhibit breast cancer angiogenesis. FABP4, ADIPOQ, PPARG, PPARGC1A, CD36, and CREBBP are potential targets of rosiglitazone.
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Luo Q, Li J, Su X, Tan Q, Zhou F, Xie S. COL11A1 serves as a biomarker for poor prognosis and correlates with immune infiltration in breast cancer. Front Genet 2022; 13:935860. [PMID: 36160004 PMCID: PMC9500398 DOI: 10.3389/fgene.2022.935860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/26/2022] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the malignant tumor with the highest incidence rate at present, and its incidence rate ranks first in the female population. COL11A1 is an important component of collagen XI and is considered to play an important role in a variety of connective tissue diseases. Recent studies have shown that COL11A1 is associated with the occurrence and development of many kinds of malignant tumors. However, its prognostic value in breast cancer and its correlation with immune cell infiltration in tumor tissue are not clear. In this paper, we reveal the prognostic value of COL11A1 in breast cancer and its tumor immune-related function through in-depth bioinformatics analysis. The expression of COL11A1 is abnormally upregulated in breast cancer and is significantly related to the poor prognosis of breast cancer. In the analysis of the clinical characteristics of the patients, we found that the expression level of COLL11A1 was closely related to lymph node metastasis, PAM50 (Prediction Analysis of Microarray 50) expression, clinical stage and so on. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) all suggest that COL11A1 is related to tumor immunity. Further study found that the COL11A1 expression was significantly correlated with the degree of immune infiltration and the expression of a variety of immune cell markers in tumor tissue. More importantly, COL11A1 can affect the prognosis of breast cancer patients by participating in the regulation of tumor immune infiltration. Therefore, we believe that COL11A1 is a very potential target for diagnosis and treatment of breast cancer.
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Affiliation(s)
- Qi Luo
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Outpatient, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jinsui Li
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaohan Su
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Qiao Tan
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fangfang Zhou
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Anatomy, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shaoli Xie
- Department of Academician (expert) Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Biological Targeting Laboratory of Breast Cancer, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Thyroid and Breast Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- *Correspondence: Shaoli Xie, , orcid.org/0000-0003-4512-2725
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Li Q, Zhang P, Hu H, Huang H, Pan D, Mao G, Hu B. The DDR-related gene signature with cell cycle checkpoint function predicts prognosis, immune activity, and chemoradiotherapy response in lung adenocarcinoma. Respir Res 2022; 23:190. [PMID: 35840978 PMCID: PMC9288070 DOI: 10.1186/s12931-022-02110-w] [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: 06/07/2022] [Accepted: 07/09/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND As a DNA surveillance mechanism, cell cycle checkpoint has recently been discovered to be closely associated with lung adenocarcinoma (LUAD) prognosis. It is also an essential link in the process of DNA damage repair (DDR) that confers resistance to radiotherapy. Whether genes that have both functions play a more crucial role in LUAD prognosis remains unclear. METHODS In this study, DDR-related genes with cell cycle checkpoint function (DCGs) were selected to investigate their effects on the prognosis of LUAD. The TCGA-LUAD cohort and two GEO external validation cohorts (GSE31210 and GSE42171) were performed to construct a prognosis model based on the least absolute shrinkage and selection operator (LASSO) regression. Patients were divided into high-risk and low-risk groups based on the model. Subsequently, the multivariate COX regression was used to construct a prognostic nomogram. The ssGSEA, CIBERSORT algorithm, TIMER tool, CMap database, and IC50 of chemotherapeutic agents were used to analyze immune activity and responsiveness to chemoradiotherapy. RESULTS 4 DCGs were selected as prognostic signatures, and patients in the high-risk group had a lower overall survival (OS). The lower infiltration levels of immune cells and the higher expression levels of immune checkpoints appeared in the high-risk group. The damage repair pathways were upregulated, and chemotherapeutic agent sensitivity was poor in the high-risk group. CONCLUSIONS The 4-DCGs signature prognosis model we constructed could predict the survival rate, immune activity, and chemoradiotherapy responsiveness of LUAD patients.
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Affiliation(s)
- Quan Li
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Pan Zhang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Huixiao Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hang Huang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Dong Pan
- Department of Dermatology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Guangyun Mao
- Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China. .,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China. .,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.
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Li JD, Farah AA, Huang ZG, Zhai GQ, Wang RG, Liu JL, Wang QJ, Zhang GL, Lei ZL, Dang YW, Li SH. Clinical significance and potential regulatory mechanism of overexpression of pituitary tumor-transforming gene transcription factor in bladder cancer. BMC Cancer 2022; 22:713. [PMID: 35768832 PMCID: PMC9241226 DOI: 10.1186/s12885-022-09810-y] [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: 04/06/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
Background Pituitary tumor transforming gene-1 (PTTG1) transcription factor is identified as carcinogenic and associated with tumor invasiveness, but its role in bladder cancer (BLCA) remains obscure. This research is intended to analyze the aberrant expression and clinical significance of PTTG1 in BLCA, explore the relationship between PTTG1 and tumor microenvironment characteristics and predict its potential transcriptional activity in BLCA tissue. Methods We compared the expression discrepancy of PTTG1 mRNA in BLCA and normal bladder tissue, using the BLCA transcriptomic datasets from GEO, ArrayExpress, TCGA, and GTEx. In-house immunohistochemical staining was implemented to determine the PTTG1 protein intensity. The prognostic value of PTTG1 was evaluated using the Kaplan-Meier Plotter. CRISPR screen data was utilized to estimate the effect PTTG1 interference has on BLCA cell lines. We predicted the abundance of the immune cells in the BLCA tumor microenvironment using the microenvironment cell populations-counter and ESTIMATE algorithms. Single-cell RNA sequencing data was applied to identify the major cell types in BLCA, and the dynamics of BLCA progression were revealed using pseudotime analysis. PTTG1 target genes were predicted by CistromeDB. Results The elevated expression level of PTTG1 was confirmed in 1037 BLCA samples compared with 127 non-BLCA samples, with a standardized mean difference value of 1.04. Higher PTTG1 expression status exhibited a poorer BLCA prognosis. Moreover, the PTTG1 Chronos genetic effect scores were negative, indicating that PTTG1 silence may inhibit the proliferation and survival of BLCA cells. With PTTG1 mRNA expression level increasing, higher natural killer, cytotoxic lymphocyte, and monocyte lineage cell infiltration levels were observed. A total of four candidate targets containing CHEK2, OCIAD2, UBE2L3, and ZNF367 were determined ultimately. Conclusions PTTG1 mRNA over-expression may become a potential biomarker for BLCA prognosis. Additionally, PTTG1 may correlate with the BLCA tumor microenvironment and exert transcriptional activity by targeting CHEK2, OCIAD2, UBE2L3, and ZNF367 in BLCA tissue. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09810-y.
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Affiliation(s)
- Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Abdirahman Ahmed Farah
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Gao-Qiang Zhai
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Rui-Gong Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Jia-Lin Liu
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Qin-Jie Wang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Guan-Lan Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Zi-Long Lei
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China
| | - Sheng-Hua Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Rd, Guangxi Zhuang Autonomous Region, 530021, Nanning, People's Republic of China.
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Li P, Chen F, Yao C, Zhu K, Zhang B, Zheng Z. PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma. Brain Sci 2022; 12:brainsci12060763. [PMID: 35741647 PMCID: PMC9221056 DOI: 10.3390/brainsci12060763] [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: 03/17/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Glioma is one of the most common malignant tumors of the central nervous system. Immune infiltration of tumor microenvironment was associated with overall survival in low grade glioma (LGG). However, effects of Tyrosine phosphatase receptor type N (PTPRN) on the progress of LGG and its correlation with tumor infiltration are unclear. METHODS Here, datasets of LGG were from The Cancer Genome Atlas (TCGA) and normal samples were from GTEx dataset. Gepia website and Human Protein Atlas (HPA) Database were used to analyze the mRNA and protein expression of PTPRN. We evaluated the influence of PTPRN on survival of LGG patients. MethSurv was used to explore the expression and prognostic patterns of single CpG methylation of PTPRN gene in LGG. The correlations between the clinical information and PTPRN expression were analyzed using logistic regression and Multivariate Cox regression. We also explored the correlation between PTPRN expression and cancer immune infiltration by TIMER. Gene set enrichment analysis (GSEA) was formed using TCGA RNA-seq datasets. RESULTS PTPRN mRNA and protein expression decreased in LGG compared to normal brain tissue in TCGA and HPA database. Kaplan-Meier analysis showed that the high expression level of PTPRN correlated with a good overall survival (OS) of patients with LGG. The Multivariate Cox analysis demonstrated that PTPRN expression and other clinical-pathological factors (age, WHO grade, IDH status, and primary therapy outcome) significantly correlated with OS of LGG patients. The DNA methylation pattern of PTPRN with significant prognostic value were confirmed, including cg00672332, cg06971096, cg01382864, cg03970036, cg10140638, cg16166796, cg03545227, and cg25569248. Interestingly, PTPRN expression level significantly negatively correlated with infiltrating level of B cell, CD4+ T cells, Macrophages, Neutrophils, and DCs in LGG. Finally, GSEA showed that signaling pathways, mainly associated with tumor microenvironment and immune cells, were significantly enriched in PTPRN high expression. CONCLUSION PTPRN is a potential biomarker and correlates with tumor immune infiltration in LGG.
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Affiliation(s)
- Peng Li
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.)
| | - Fanfan Chen
- Neurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China; (F.C.); (C.Y.)
| | - Chen Yao
- Neurosurgical Department, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China; (F.C.); (C.Y.)
| | - Kezhou Zhu
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.)
| | - Bei Zhang
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Zelong Zheng
- Department of Neurosurgery, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Correspondence:
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Bao Z, Cheng J, Zhu J, Ji S, Gu K, Zhao Y, Yu S, Meng Y. Using Weighted Gene Co-Expression Network Analysis to Identify Increased MND1 Expression as a Predictor of Poor Breast Cancer Survival. Int J Gen Med 2022; 15:4959-4974. [PMID: 35601002 PMCID: PMC9117423 DOI: 10.2147/ijgm.s354826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/07/2022] [Indexed: 12/12/2022] Open
Abstract
Objective We used bioinformatics analysis to identify potential biomarker genes and their relationship with breast cancer (BC). Materials and Methods We used a weighted gene co-expression network analysis (WGCNA) to create a co-expression network based on the top 25% genes in the GSE24124, GSE33926, and GSE86166 datasets obtained from the Gene Expression Omnibus. We used the DAVID online platform to perform GO and KEGG pathway enrichment analyses and the Cytoscape CytoHubba plug-in to screen the potential genes. Then, we related the genes to prognostic values in BC using the Oncomine, GEPIA, and Kaplan–Meier Plotter databases. Findings were validated by immunohistochemical (IHC) staining in the Human Protein Atlas and the TCGA-BRCA cohort. LinkedOmics identified the interactive expressions of hub genes. We used UALCAN to evaluate the methylation levels of these hub genes. MethSurv and SurvivalMeth were used to assess the multilevel prognostic value. Finally, we assessed hub gene association with immune cell infiltration using TIMER. Results The mRNA levels of MKI67, UBE2C, GTSE1, CCNA2, and MND1 were significantly upregulated in BC, whereas ESR1, THSD4, TFF1, AGR2, and FOXA1 were significantly downregulated. The DNA methylation signature analysis showed a better prognosis in the low-risk group. Further subgroup analyses revealed that MND1 might serve as an independent risk factor for unfavorable BC prognosis. Additionally, MND1 expression levels positively correlate with the immune infiltration statuses of CD4+ T cells, CD8+ T cells, B cells, neutrophils, dendritic cells, and macrophages. Conclusion Our results indicate that the ten hub genes may be involved in BC’s carcinogenesis, development, or metastasis, and MND1 may be a potential biomarker and therapeutic target for BC.
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Affiliation(s)
- Zhaokang Bao
- Department of Oncology Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Jiale Cheng
- Department of Oncology Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Jiahao Zhu
- Department of Radiotherapy and Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Shengjun Ji
- Department of Radiotherapy and Oncology, The affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - Ke Gu
- Department of Radiotherapy and Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Yutian Zhao
- Department of Radiotherapy and Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Shiyou Yu
- Department of Oncology Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
| | - You Meng
- Department of Oncology Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, People’s Republic of China
- Correspondence: You Meng, Department of Oncology Surgery, The affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, 16 West Baita Road, Suzhou, Jiangsu, People’s Republic of China, Email
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Mohsenikia M, Khalighfard S, Alizadeh AM, Khori V, Ghandian Zanjan M, Zare M, Omranipour R, Patrad E, Razavi H, Malekshahi ZV, Bagheri-Hosseinabadi Z. An innovative systematic approach introduced the involved lncRNA-miR-mRNA network in cell cycle and proliferation after conventional treatments in breast cancer patients. Cell Cycle 2022; 21:1753-1774. [PMID: 35470783 PMCID: PMC9302505 DOI: 10.1080/15384101.2022.2070104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The present study aimed to explore the involved lncRNA-miRNA-mRNA network in the cell cycle and proliferation after conventional treatments in Luminal A breast cancer patients. METHODS The candidate miRNAs (miRs), lncRNAs, and mRNAs were first taken from the Gene Expression Omnibus and TCGA databases. The lncRNA-miR-mRNA network was then constructed using the high-throughput sequencing data. The expression levels of selected targets were measured in the breast cancer and healthy samples by the Real-Time PCR technique and compared with the clinical outcomes by the Kaplan-Meier method. RESULTS Our analysis revealed a group of differentially expressed 3 lncRNAs, 9 miRs, and 14 mRNAs in breast cancer patients. A significant expression decrease of the selected tumor suppressor lncRNAs, miRs, and genes and a substantial expression increase of the selected onco-lncRNAs, oncomiRs, and oncogenes were obtained in the patients compared to the healthy group. The plasma levels of the lncRNAs, miRs, and mRNAs were more significant after the operation, chemotherapy, and radiotherapy than the pre-treatment. The Kaplan-Meier analysis indicated that the patients with a high expression of miR-21, miR-20b, IGF1R, and E2F2 and a low expression of miR-125a, PDCD4, and PTEN had exhibited a shorter overall survival rate. CONCLUSION Our results suggested that the underlying mechanisms of the lncRNA, miRs, and mRNAs and relevant signaling pathways may be considered predictive and therapeutic targets for breast cancer.
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Affiliation(s)
- Maryam Mohsenikia
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Solmaz Khalighfard
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Mohammad Alizadeh
- Breast Disease Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran.,Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Khori
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maziar Ghandian Zanjan
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammadreza Zare
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ramesh Omranipour
- Breast Disease Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Patrad
- Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hengamesadat Razavi
- Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Veisi Malekshahi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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Kaur C, Sharma B, Nepali K. Switch Pocket Kinase: An Emerging Therapeutic Target for the Design of Anticancer Agents. Anticancer Agents Med Chem 2022; 22:2662-2670. [PMID: 35379129 DOI: 10.2174/1871520622666220404081302] [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: 10/18/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 11/22/2022]
Abstract
Protein kinases are amongst the most focused enzymes in current century to design, synthesize and formulate drugs ought to be effective in the treatment of various disordered and diseased states involving either overexpression or deficiency situations. The ATP pocket on the kinases is the binding active site for most of the kinase inhibitors. However, the kinase mutations prevent the binding of kinase inhibitors to ATP pocket. The switch pocket site on this enzyme when occupied by switch pocket inhibitors, the enzyme become inactive even in the mutated state. This review comprises the detailed information on various classical protein kinases and switch pocket kinase inhibitors with their mechanism of action so that new molecules can be designed to encounter mutations in the kinase enzyme.
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Affiliation(s)
- Charanjit Kaur
- Department of Pharmaceutical Chemistry, Khalsa College of Pharmacy, Amritsar, Punjab, 143002
| | - Bhargavi Sharma
- Department of Pharmaceutical Chemistry, Khalsa College of Pharmacy, Amritsar, Punjab, 143002
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei 11031, Taiwan
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Gao WL, Niu L, Chen WL, Zhang YQ, Huang WH. Integrative Analysis of the Expression Levels and Prognostic Values for NEK Family Members in Breast Cancer. Front Genet 2022; 13:798170. [PMID: 35368696 PMCID: PMC8967485 DOI: 10.3389/fgene.2022.798170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/07/2022] [Indexed: 12/29/2022] Open
Abstract
Background: In the latest rankings, breast cancer ranks first in incidence and fifth in mortality among female malignancies worldwide. Early diagnosis and treatment can improve the prognosis and prolong the survival of breast cancer (BC) patients. The NIMA-related kinase (NEK), a group of serine/threonine kinase, is a large and conserved gene family that includes NEK1–NEK11. The NEK plays a pivotal role in the cell cycle and microtubule formation. However, an integrative analysis of the effect and prognosis value of NEK family members on BC patients is still lacking. Methods: In this study, the expression profiles of NEK family members in BC and its subgroups were analyzed using UALCAN, GEPIA2, and Human Protein Atlas datasets. The prognostic values of NEK family members in BC were evaluated using the Kaplan–Meier plotter. Co-expression profiles and genetic alterations of NEK family members were analyzed using the cBioPortal database. The function and pathway enrichment analysis of the NEK family were performed using the WebGestalt database. The correlation analysis of the NEK family and immune cell infiltration in BC was conducted using the TIMER 2.0 database. Results: In this study, we compared and analyzed the prognosis values of the NEKs. We found that NEK9 was highly expressed in normal breast tissues than BC, and NEK2, NEK6, and NEK11 were significantly highly expressed in BC than adjacent normal tissues. Interestingly, the expression levels of NEK2, NEK6, and NEK10 were not only remarkably correlated with the tumor stage but also with the molecular subtype. Through multilevel research, we found that high expression levels of NEK1, NEK3, NEK8, NEK9, NEK10, and NEK11 suggested a better prognosis value in BC, while high expression levels of NEK2 and NEK6 suggested a poor prognosis value in BC. Conclusion: Our studies show the prognosis values of the NEKs in BC. Thus, we suggest that NEKs may be regarded as novel biomarkers for predicting potential prognosis values and potential therapeutic targets of BC patients.
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Affiliation(s)
- Wen-Liang Gao
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Lei Niu
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Wei-Ling Chen
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Yong-Qu Zhang
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
- *Correspondence: Yong-Qu Zhang, ; Wen-He Huang,
| | - Wen-He Huang
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
- *Correspondence: Yong-Qu Zhang, ; Wen-He Huang,
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Huang X, Zhang G, Tang T, Gao X, Liang T. One shoot, three birds: Targeting NEK2 orchestrates chemoradiotherapy, targeted therapy, and immunotherapy in cancer treatment. Biochim Biophys Acta Rev Cancer 2022; 1877:188696. [PMID: 35157980 DOI: 10.1016/j.bbcan.2022.188696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/16/2022]
Abstract
Combinational therapy has improved the cancer therapeutic landscape but is associated with a concomitant increase in adverse side reactions. Emerging evidence proposes that targeting one core target with multiple critical roles in tumors can achieve combined anti-tumor effects. This review focuses on NEK2, a member of serine/threonine kinases, with broad sequence identity to the mitotic regulator NIMA of the filamentous fungus Aspergillus nidulans. Elevated expression of NEK2 was initially found to promote tumorigeneses through abnormal regulation of the cell cycle. Subsequent studies report that NEK2 is overexpressed in a broad spectrum of tumor types and is associated with tumor progression and therapeutic resistance. Intriguingly, NEK2 has recently been revealed to mediate tumor immune escape by stabilizing the expression of PD-L1. Targeting NEK2 is thus becoming a promising approach for cancer treatment by orchestrating chemoradiotherapy, targeted therapy, and immunotherapy. It represents a novel strategy for inducing combined anti-cancer effects using a mono-agent.
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Affiliation(s)
- Xing Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou 310003, Zhejiang, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Gang Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou 310003, Zhejiang, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tianyu Tang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou 310003, Zhejiang, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiang Gao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou 310003, Zhejiang, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou 310003, Zhejiang, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, Zhejiang, China; Cancer Center, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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Chiao CC, Liu YH, Phan NN, An Ton NT, Ta HDK, Anuraga G, Minh Xuan DT, Fitriani F, Putri Hermanto EM, Athoillah M, Andriani V, Ajiningrum PS, Wu YF, Lee KH, Chuang JY, Wang CY, Kao TJ. Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer. Diagnostics (Basel) 2021; 11:diagnostics11122220. [PMID: 34943457 PMCID: PMC8699889 DOI: 10.3390/diagnostics11122220] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
The complexity of breast cancer includes many interacting biological processes, and proteasome alpha (PSMA) subunits are reported to be involved in many cancerous diseases, although the transcriptomic expression of this gene family in breast cancer still needs to be more thoroughly investigated. Consequently, we used a holistic bioinformatics approach to study the PSMA genes involved in breast cancer by integrating several well-established high-throughput databases and tools, such as cBioPortal, Oncomine, and the Kaplan–Meier plotter. Additionally, correlations of breast cancer patient survival and PSMA messenger RNA expressions were also studied. The results demonstrated that breast cancer tissues had higher expression levels of PSMA genes compared to normal breast tissues. Furthermore, PSMA2, PSMA3, PSMA4, PSMA6, and PSMA7 showed high expression levels, which were correlated with poor survival of breast cancer patients. In contrast, PSMA5 and PSMA8 had high expression levels, which were associated with good prognoses. We also found that PSMA family genes were positively correlated with the cell cycle, ubiquinone metabolism, oxidative stress, and immune response signaling, including antigen presentation by major histocompatibility class, interferon-gamma, and the cluster of differentiation signaling. Collectively, these findings suggest that PSMA genes have the potential to serve as novel biomarkers and therapeutic targets for breast cancer. Nevertheless, the bioinformatic results from the present study would be strengthened with experimental validation in the future by prospective studies on the underlying biological mechanisms of PSMA genes and breast cancer.
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Affiliation(s)
- Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan; (C.-C.C.); (H.D.K.T.); (G.A.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
| | - Yen-Hsi Liu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
| | - Nam Nhut Phan
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Nu Thuy An Ton
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan; (C.-C.C.); (H.D.K.T.); (G.A.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan; (C.-C.C.); (H.D.K.T.); (G.A.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
| | - Fenny Fitriani
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Elvira Mustikawati Putri Hermanto
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Purity Sabila Ajiningrum
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Yung-Fu Wu
- Department of Medical Research, Tri-Service General Hospital, School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Kuen-Haur Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan; (C.-C.C.); (H.D.K.T.); (G.A.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Jian-Ying Chuang
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Ph.D. Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Research Center of Neuroscience, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan; (C.-C.C.); (H.D.K.T.); (G.A.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (Y.-H.L.); (D.T.M.X.)
- Correspondence: (C.-Y.W.); (T.-J.K.)
| | - Tzu-Jen Kao
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Ph.D. Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Research Center of Neuroscience, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (C.-Y.W.); (T.-J.K.)
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