1
|
Mo C, You W, Rao Y, Lin Z, Wang S, He T, Shen H, Li X, Zhang R, Li B. Epigenetic regulation of DNA repair gene program by Hippo/YAP1-TET1 axis mediates sorafenib resistance in HCC. Cell Mol Life Sci 2024; 81:284. [PMID: 38967794 DOI: 10.1007/s00018-024-05296-y] [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: 01/25/2024] [Revised: 04/19/2024] [Accepted: 05/26/2024] [Indexed: 07/06/2024]
Abstract
Hepatocellular carcinoma (HCC) is a malignancy that occurs worldwide and is generally associated with poor prognosis. The development of resistance to targeted therapies such as sorafenib is a major challenge in clinical cancer treatment. In the present study, Ten-eleven translocation protein 1 (TET1) was found to be highly expressed in sorafenib-resistant HCC cells and knockdown of TET1 can substantially improve the therapeutic effect of sorafenib on HCC, indicating the potential important roles of TET1 in sorafenib resistance in HCC. Mechanistic studies determined that TET1 and Yes-associated protein 1 (YAP1) synergistically regulate the promoter methylation and gene expression of DNA repair-related genes in sorafenib-resistant HCC cells. RNA sequencing indicated the activation of DNA damage repair signaling was extensively suppressed by the TET1 inhibitor Bobcat339. We also identified TET1 as a direct transcriptional target of YAP1 by promoter analysis and chromatin-immunoprecipitation assays in sorafenib-resistant HCC cells. Furthermore, we showed that Bobcat339 can overcome sorafenib resistance and synergized with sorafenib to induce tumor eradication in HCC cells and mouse models. Finally, immunostaining showed a positive correlation between TET1 and YAP1 in clinical samples. Our findings have identified a previously unrecognized molecular pathway underlying HCC sorafenib resistance, thus revealing a promising strategy for cancer therapy.
Collapse
MESH Headings
- Humans
- Sorafenib/pharmacology
- Sorafenib/therapeutic use
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/drug therapy
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Drug Resistance, Neoplasm/genetics
- Epigenesis, Genetic/drug effects
- Animals
- DNA Repair/drug effects
- DNA Repair/genetics
- YAP-Signaling Proteins/metabolism
- Mice
- Proto-Oncogene Proteins/metabolism
- Proto-Oncogene Proteins/genetics
- Transcription Factors/metabolism
- Transcription Factors/genetics
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic/drug effects
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Mice, Nude
- Mixed Function Oxygenases/genetics
- Mixed Function Oxygenases/metabolism
- Hippo Signaling Pathway
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Signal Transduction/drug effects
- Xenograft Model Antitumor Assays
- Mice, Inbred BALB C
- DNA Methylation/drug effects
Collapse
Affiliation(s)
- Chunli Mo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
- The First Affiliated Hospital , of Xiamen University, Xiamen, 361100, Fujian, China
| | - Weixin You
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
| | - Yipeng Rao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
| | - Zhenping Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
| | - Shuai Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
- The First Affiliated Hospital , of Xiamen University, Xiamen, 361100, Fujian, China
| | - Ting He
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
| | - Huanming Shen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China
| | - Xun Li
- Department of Laboratory Medicine The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, 361003, Fujian, China.
- Center for Precision Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China.
| | - Rui Zhang
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, 361003, Fujian, China.
| | - Boan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361100, Fujian, China.
| |
Collapse
|
2
|
Yang M, Deng Y, Ma Y, Song C, Wu Z, Yibulayin X, Sun X, Guo Y, He D. Comprehensive pan-cancer analysis reveals that C5orf34 regulates the proliferation and mortality of lung cancer. Funct Integr Genomics 2024; 24:119. [PMID: 38951221 DOI: 10.1007/s10142-024-01397-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: 04/05/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
The gene C5orf34 exhibits evolutionary conservation among mammals, and emerging evidence suggests its potential involvement in tumor development; however, comprehensive investigations of this gene are lacking. This study aims to elucidate the functional attributes and underlying mechanisms of C5orf34 in cancer. To evaluate its clinical predictive value, we conducted an analysis of the pan-cancerous expression, clinical data, mutation, and methylation data of C5orf34. Additionally, we investigated the correlation between C5orf34 and tumor mutant load (TMB), immune cell infiltration, and microsatellite instability (MSI) through relevant analyses. Furthermore, immunohistochemical (IHC) staining was employed to validate clinical samples, while knockdown and overexpression experiments and transcriptome RNA sequencing were utilized to examine the impact of C5orf34 on LUAD cells. According to our study, C5orf34 exhibits high expression levels in the majority of malignant tumors. The upregulation of C5orf34 is governed by DNA copy number alterations and methylation patterns, and it is closely associated with patients' survival prognosis and immune characteristics, thereby holding significant clinical implications. Furthermore, IHC staining analysis, cellular experiments, and transcriptome RNA sequencing have provided evidence supporting the role of C5orf34 in modulating the cell cycle to promote LUAD proliferation, migration, and invasion. This highlights its potential as a promising therapeutic target. The findings of this investigation suggest that C5orf34 may serve as a valuable biomarker for various tumor types and represent a potential target for immunotherapy, particularly in relation to the proliferation, migration, and apoptosis of LUAD cells.
Collapse
Affiliation(s)
- Meng Yang
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China.
| | - Yuhan Deng
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Yu Ma
- Department of Clinical Laboratory, The Fourth People' Hospital of Urumqi, Urumqi, 830011, China
| | - Chunli Song
- Department of Pharmacy, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Zhenhua Wu
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Xiayimaierdan Yibulayin
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Xiaohong Sun
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Yunquan Guo
- Department of Pathology, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Dan He
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China.
| |
Collapse
|
3
|
Wang J, Yang M, Ali O, Dragland JS, Bjørås M, Farkas L. Predicting regulatory mutations and their target genes by new computational integrative analysis: A study of follicular lymphoma. Comput Biol Med 2024; 178:108787. [PMID: 38901187 DOI: 10.1016/j.compbiomed.2024.108787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Mutations in DNA regulatory regions are increasingly being recognized as important drivers of cancer and other complex diseases. These mutations can regulate gene expression by affecting DNA-protein binding and epigenetic profiles, such as DNA methylation in genome regulatory elements. However, identifying mutation hotspots associated with expression regulation and disease progression in non-coding DNA remains a challenge. Unlike most existing approaches that assign a mutation score to individual single nucleotide polymorphisms (SNP), a mutation block (MB)-based approach was introduced in this study to assess the collective impact of a cluster of SNPs on transcription factor-DNA binding affinity, differential gene expression (DEG), and nearby DNA methylation. Moreover, the long-distance target genes of functional MBs were identified using a new permutation-based algorithm that assessed the significance of correlations between DNA methylation at regulatory regions and target gene expression. Two new Python packages were developed. The Differential Methylation Region (DMR-analysis) analysis tool was used to detect DMR and map them to regulatory elements. The second tool, an integrated DMR, DEG, and SNP analysis tool (DDS-analysis), was used to combine the omics data to identify functional MBs and long-distance target genes. Both tools were validated in follicular lymphoma (FL) cohorts, where not only known functional MBs and their target genes (BCL2 and BCL6) were recovered, but also novel genes were found, including CDCA4 and JAG2, which may be associated with FL development. These genes are linked to target gene expression and are significantly correlated with the methylation of nearby DNA sequences in FL. The proposed computational integrative analysis of multiomics data holds promise for identifying regulatory mutations in cancer and other complex diseases.
Collapse
Affiliation(s)
- Junbai Wang
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, Lørenskog, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Campus AHUS/Oslo, Norway.
| | - Mingyi Yang
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Centre for Embryology and Healthy Development (CRESCO), University of Oslo, Oslo, 0373, Norway
| | - Omer Ali
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Campus AHUS/Oslo, Norway; Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway
| | - Jenny Sofie Dragland
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Centre for Embryology and Healthy Development (CRESCO), University of Oslo, Oslo, 0373, Norway
| | - Lorant Farkas
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Campus AHUS/Oslo, Norway; Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway
| |
Collapse
|
4
|
Li J, Cheng C, Zhang J. An analysis of AURKB's prognostic and immunological roles across various cancers. J Cell Mol Med 2024; 28:e18475. [PMID: 38898693 PMCID: PMC11187167 DOI: 10.1111/jcmm.18475] [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: 04/04/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Aurora kinase B (AURKB), an essential regulator in the process of mitosis, has been revealed through various studies to have a significant role in cancer development and progression. However, the specific mechanisms remain poorly understood. This study, therefore, seeks to elucidate the multifaceted role of AURKB in diverse cancer types. This study utilized bioinformatics techniques to examine the transcript, protein, promoter methylation and mutation levels of AURKB. The study further analysed associations between AURKB and factors such as prognosis, pathological stage, biological function, immune infiltration, tumour mutational burden (TMB) and microsatellite instability (MSI). In addition, immunohistochemical staining data of 50 cases of renal clear cell carcinoma and its adjacent normal tissues were collected to verify the difference in protein expression of AURKB in the two tissues. The results show that AURKB is highly expressed in most cancers, and the protein level of AURKB and the methylation level of its promoter vary among cancer types. Survival analysis showed that AURKB was associated with overall survival in 12 cancer types and progression-free survival in 11 cancer types. Elevated levels of AURKB were detected in the advanced stages of 10 different cancers. AURKB has a potential impact on cancer progression through its effects on cell cycle regulation as well as inflammatory and immune-related pathways. We observed a strong association between AURKB and immune cell infiltration, immunomodulatory factors, TMB and MSI. Importantly, we confirmed that the AURKB protein is highly expressed in kidney renal clear cell carcinoma (KIRC). Our study reveals that AURKB may be a potential biomarker for pan-cancer and KIRC.
Collapse
Affiliation(s)
- Jun Li
- Department of UrologyThe First Affiliated Hospital of Bengbu Medical UniversityBengbuChina
| | - Cui Cheng
- Department of Gynaecological OncologyThe First Affiliated Hospital of Bengbu Medical UniversityBengbuChina
| | - Jiajun Zhang
- Department of UrologyThe First Affiliated Hospital of Bengbu Medical UniversityBengbuChina
| |
Collapse
|
5
|
Huang F, Jin L, Zhang X, Wang M, Zhou C. Integrated pan-cancer analysis reveals the immunological and prognostic potential of RBFOX2 in human tumors. Front Pharmacol 2024; 15:1302134. [PMID: 38881877 PMCID: PMC11176534 DOI: 10.3389/fphar.2024.1302134] [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: 09/26/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Background The role of RNA-binding fox one homolog 2 (RBFOX2) in the progression of multiple tumors is increasingly supported by evidence. However, the unclearness pertaining to the expression of RBFOX2, its prognostic potential, and its correlation with the tumor microenvironment (TME) in pan-cancer persists. This study aims to comprehensively investigate the immunological prognostic value of RBFOX2. Methods The Cancer Genome Atlas Gene Expression Omnibus Genotype-Tissue Expression (GTEx), TIMER2.0, Kaplan-Meier (K-M) Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were utilized for a systematic analysis of RBFOX2. This analysis included studying its expression, prognostic value, DNA methylation, enrichment analysis, immune infiltration cells, and immune-related genes. Additionally, qRT-PCR, CCK-8, colony formation, transwell assays, and immunohistochemistry were employed to analyze the expression and biological function of RBFOX2 in liver cancer. Results Variations in RBFOX2 expression have been observed across diverse tumors and have been identified as indicators of unfavorable prognosis. It is closely linked to immune infiltration cells, immune checkpoints, chemokines, and chemokine receptors in the TME. Higher levels of RBFOX2 have been significantly associated with low response and poor prognosis in patients with non-small cell lung cancer (NSCLC) and melanoma who receive immunotherapy. Furthermore, the DNA methylation of RBFOX2 varies across different types of cancer and has shown better prognosis in patients with BLCA, BRCA, CESC, COAD, DLBC, HNSC, LAML, LGG, LUAD, PAAD, SKCM and THYM. Interestingly, RBFOX2 expression was found to be lower in hepatocellular carcinoma (HCC) patients' tumor tissues compared to their paired adjacent tissues. In vitro studies have shown that knockdown of RBFOX2 significantly promotes the growth and metastasis of liver cancer cells. Conclusion This study investigates the correlation between DNA methylation, prognostic value, and immune cell infiltration with the expression of RBFOX2 in pan-cancer and indicates its potential role to inhibit metastasis of liver cancer.
Collapse
Affiliation(s)
- Fengxian Huang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xinyue Zhang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, Xi'an, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Huang L, Irshad S, Sultana U, Ali S, Jamil A, Zubair A, Sultan R, Abdel-Maksoud MA, Mubarak A, Almunqedhi BM, Almanaa TN, Malik A, Alamri A, Kodous AS, Mares M, Zaky MY, Saba Sajjad S, Hameed Y. Pan-cancer analysis of HS6ST2: associations with prognosis, tumor immunity, and drug resistance. Am J Transl Res 2024; 16:873-888. [PMID: 38586106 PMCID: PMC10994782 DOI: 10.62347/ncph5416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/08/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVES In this comprehensive study spanning 33 malignancies, we explored the differential expression and prognostic significance of Heparan sulfate 6-O-sulfotransferase 2 (HS6ST2). METHODS TIMER2, UALCAN, and GEPIA2 were used for the expression analysis. cBioPortal was used for mutational analysis. CancerSEA, STRING, and DAVID, were employed for the single cell sequencing data analysis, protein-protein interaction network development, and gene enrichment analyses, respectively. GSCAlite and RT-qPCR were used for drug sensitivity and expression validation analysis. RESULTS HS6ST2 exhibited significant (P < 0.05) overexpression in multiple cancers. Prognostically, elevated HS6ST2 expression was significantly associated with poor overall survival (OS) in patients with cervical squamous cell carcinoma (CESC), kidney chromophobe (KICH), lung adenocarcinoma (LUAD), and stomach adenocarcinoma (STAD), emphasizing its potential as a prognostic indicator in these cancers. Moreover, HS6ST2 expression correlated with pathological stages in CESC, KICH, LUAD, and STAD patients. Exploration of genetic alterations using cBioPortal unveiled distinct mutational landscapes, with low mutation frequencies in CESC, KICH, LUAD, and STAD. Additionally, reduced DNA methylation in CESC, KICH, LUAD, and STAD suggested a potential link between hypomethylation and heightened HS6ST2 expression. Analysis of immune cell infiltration revealed a positive correlation between HS6ST2 expression and the infiltration of CD8+ T and CD4+ T cells in CESC, KICH, LUAD, and STAD, highlighting its involvement in the tumor immunology processes. Single-cell functional states analysis demonstrated associations between HS6ST2 and diverse cellular processes. Moreover, gene enrichment analysis revealed the involvement HS6ST2 in crucial cellular activities. GSCAlite analysis underscored the potential of HS6ST2 as a therapeutic target, showing associations with drug sensitivity. Finally, experimental validation through reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in LUAD tissues confirmed elevated HS6ST2 expression. CONCLUSION Overall, this study provides a comprehensive understanding of HS6ST2 in CESC, KICH, LUAD, and STAD, emphasizing its potential as a prognostic biomarker and therapeutic target.
Collapse
Affiliation(s)
- Luxin Huang
- Department of Gynecology, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical UniversityJinan 250000, Shandong, China
| | - Sidra Irshad
- Department of Pharmacology, Muhammad College of MedicinePeshawar 25000, Pakistan
| | - Ulfat Sultana
- Department of Pharmacology, Muhammad College of MedicinePeshawar 25000, Pakistan
| | - Saqib Ali
- Department of Computer Science, University of AgricultureFaisalabad 38000, Pakistan
| | - Ayesha Jamil
- Department of Pharmacology, Khyber Girls Medical CollegePeshawar 25000, Pakistan
| | - Ayesha Zubair
- CMH Lahore Medical College and Institute of DentistryLahore 54000, Pakistan
| | - Rizwana Sultan
- Department of Pathology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal SciencesBahawalpur 63100, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bandar M Almunqedhi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversitySaudi Arabia
| | - Abdulaziz Alamri
- Department of Biochemistry, College of Science King Saud UniversitySaudi Arabia
| | - Ahmad S Kodous
- Department of Molecular Oncology, Cancer Institute (WIA)38, Sardar Patel Road, Chennai, P.O. Box 600036, Tamilnadu, India
- Department of Radiation Biology, National Center for Radiation Research & Technology (NCRRT), Egyptian Atomic-Energy Authority (EAEA)Egypt
| | - Mohammed Mares
- Department of Zoology, College of Science King Saud UniversitySaudi Arabia
| | - Mohamed Y Zaky
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburgh, PA 15213, USA
| | | | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry Biotechnology, and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
| |
Collapse
|
8
|
Huang H, Gu J, Kuang X, Yu Y, Rao B, Fang S, Lu J, Qiu F. An integrative pan-cancer analysis of WWC family genes and functional validation in lung cancer. Cell Signal 2024; 115:111034. [PMID: 38190957 DOI: 10.1016/j.cellsig.2024.111034] [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: 09/16/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/10/2024]
Abstract
The WW and C2 domain containing (WWC) protein family functions as scaffolds regulating cell proliferation and organ growth control through the Hippo signaling pathway. However, their pan-cancer dysregulation and mechanistic roles in signaling transduction have remained unclear. We performed integrated pan-cancer analyses of WWC family gene expression using data from The Cancer Genome Atlas (TCGA) across 33 different cancer types. Prognostic relevance was evaluated by survival analyses. WWC genetic alterations, DNA methylation, pathway activities, drug response, and tumor immunology were analyzed using online databases. Furthermore, we examined the functional roles of WWCs in lung cancer cells. We observed aberrant WWC expression in various cancers, which associated with patient prognosis. WWC hypermethylation occurred in many cancers and exhibited negative correlation with expression, alongside mutations linked to poor outcomes. Pathway analysis implicated WWCs as Hippo pathway scaffolds, while drug sensitivity analysis suggested associations with diverse chemotherapies. Additionally, pan-cancer analyses elucidated vital immunomodulatory roles for WWC through heterogeneous correlations with immune cell infiltrates, checkpoint molecules, tumor mutation burden, microsatellite instability, and chemokine pathways across cancers. Experimentally, WWCs suppressed lung cancer cell proliferation, migration, and invasion while enhancing apoptosis and paclitaxel chemosensitivity. Mechanistically, WWCs bound large tumor suppressor 1 and 2 (LATS1/2) kinases to stimulate phosphorylation cascades, thereby inhibiting nuclear translocation of the Yes-associated protein (YAP) oncoprotein. Taken together, our multi-omics characterization provides comprehensive evidence for WWCs as putative tumor suppressors across cancers via Hippo pathway modulation. WWCs may serve as prognostic markers and therapeutic targets in lung cancer.
Collapse
Affiliation(s)
- Hongmei Huang
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Jiaji Gu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Xinjie Kuang
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Yonghui Yu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Boqi Rao
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Shenying Fang
- The fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510799, PR China
| | - Jiachun Lu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Fuman Qiu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China.
| |
Collapse
|
9
|
Srivastava A, Srivastava S. Multiomics data identifies RSPO2 as a prognostic biomarker in human tumors associated with pan-cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:469-499. [PMID: 38448143 DOI: 10.1016/bs.apcsb.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
RSPO2 protein may provide valuable insights into the mechanism underlying various types of tumorigenesis. The role of RSPO2 in pan-cancer has not been reported so far. Therefore, this study aimed to provide a comprehensive analysis of RSPO2 from a pan-cancer perspective employing multiomics data. The expression profile and function of RSPO2 across different tumors were investigated using various web-based tools UALCAN, GEPIA, TIMER, Human Protein Atlas, cBioPortal, TISIDB, STRING, and Metascape to interpret the expression profile, promoter methylation status, genomic alterations, survival analysis, protein-protein interaction, correlation with immune cell subtypes, tumor immune microenvironment and enrichment analysis. Comprehensive pan-cancer analysis indicated that RSPO2 was significantly downregulated in eleven and upregulated in five tumor types compared to normal tissues, validation results further suggest RSPO2 was downregulated in most of the tumors. The protein level expression of RSPO2 was mostly low in malignant tissues. We found that RSPO2 was significantly related to individual pathological stages in BLCA, COAD, LUAD and LUSC. Prognostic analysis indicates that the high RSPO2 expression was significantly correlated with the poor prognosis in BRCA, KICH, KIRP, READ, and UCES. Furthermore, RSPO2 is frequently amplified, exhibits hypermethylated promoter in most cancers, and is associated with immune subtypes, molecular subtypes and immune cell infiltration. Finally, enrichment analysis showed that RSPO2 is involved in the regulation of the canonical Wnt pathway and neuronal development. The overall comprehensive pan-cancer analysis affirms that RSPO2 could be a promising diagnostic and prognostic biomarker and latent therapy target in the future.
Collapse
Affiliation(s)
- Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India.
| |
Collapse
|
10
|
Wu Z, Li H, Wu J, Lai X, Huang S, Yu M, Liao Q, Zhang C, Zhou L, Chen X, Guo H, Chen L. The profile of genome-wide DNA methylation, transcriptome, and proteome in streptomycin-resistant Mycobacterium tuberculosis. PLoS One 2024; 19:e0297477. [PMID: 38285653 PMCID: PMC10824437 DOI: 10.1371/journal.pone.0297477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/06/2024] [Indexed: 01/31/2024] Open
Abstract
Streptomycin-resistant (SM-resistant) Mycobacterium tuberculosis (M. tuberculosis) is a major concern in tuberculosis (TB) treatment. However, the mechanisms underlying streptomycin resistance remain unclear. This study primarily aimed to perform preliminary screening of genes associated with streptomycin resistance through conjoint analysis of multiple genomics. Genome-wide methylation, transcriptome, and proteome analyses were used to elucidate the associations between specific genes and streptomycin resistance in M. tuberculosis H37Rv. Methylation analysis revealed that 188 genes were differentially methylated between the SM-resistant and normal groups, with 89 and 99 genes being hypermethylated and hypomethylated, respectively. Furthermore, functional analysis revealed that these 188 differentially methylated genes were enriched in 74 pathways, with most of them being enriched in metabolic pathways. Transcriptome analysis revealed that 516 genes were differentially expressed between the drug-resistant and normal groups, with 263 and 253 genes being significantly upregulated and downregulated, respectively. KEGG analysis indicated that these 516 genes were enriched in 79 pathways, with most of them being enriched in histidine metabolism. The methylation level was negatively related to mRNA abundance. Proteome analysis revealed 56 differentially expressed proteins, including 14 upregulated and 42 downregulated proteins. Moreover, three hub genes (coaE, fadE5, and mprA) were obtained using synthetic analysis. The findings of this study suggest that an integrated DNA methylation, transcriptome, and proteome analysis can provide important resources for epigenetic studies in SM-resistant M. tuberculosis H37Rv.
Collapse
Affiliation(s)
- Zhuhua Wu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Haicheng Li
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiawen Wu
- Institute for tuberculosis control of Zhaoqing, Zhaoqing, China
| | - Xiaoyu Lai
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Shanshan Huang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Meiling Yu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Qinghua Liao
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Xunxun Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Huixin Guo
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Liang Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| |
Collapse
|
11
|
Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.569638. [PMID: 38106096 PMCID: PMC10723383 DOI: 10.1101/2023.12.08.569638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.
Collapse
Affiliation(s)
- Zane Koch
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Adam Li
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Trey Ideker
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla California, 92093, USA
| |
Collapse
|
12
|
Guo J, Huang M, Deng S, Wang H, Wang Z, Yan B. Highly expressed RPLP2 inhibits ferroptosis to promote hepatocellular carcinoma progression and predicts poor prognosis. Cancer Cell Int 2023; 23:278. [PMID: 37980521 PMCID: PMC10656893 DOI: 10.1186/s12935-023-03140-0] [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: 09/10/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND RPLP2, an integral part of ribosomal stalk, plays an important role in the tumorigenesis of various cancers. However, its specific effect on HCC remains elusive. METHODS TCGA, GTEx, HCCDB, HPA, UALCAN, MethSurv, TISIDB, K-M plotter, FerrDb, RNAactDrug, STRING, Cytoscape and R studio were conducted for bioinformatics analysis. RPLP2 expression level in HCC was verified by IHC and western blot. IHC was used to demonstrate the immune cell infiltration. Functional experiments including CCK8, transwell and colony formation assays, and nude mice xenograft model were performed for in vitro and in vivo validation. Western blot, IHC, CCK8 assay and detection of GSH and lipid ROS were adopted to determine the effect of RPLP2 on the ferroptosis of HCC cells. RESULTS Here, we demonstrate that elevated level of RPLP2 is strongly associated with advanced clinicopathologic features, and predicts poor prognosis of HCC patients. Additionally, DNA methylation level of RPLP2 decreases in HCC, and significantly correlates with patients outcome. Moreover, high RPLP2 expression level is linked closely to the unfavorable immune infiltration. Most importantly, RPLP2 positively associates with ferroptosis suppressor GPX4, and inhibition of RPLP2 could lead to the acceleration of ferroptosis to suppress tumor progression of HCC. Last, drug sensitivity analysis predicts many drugs that potentially target RPLP2. CONCLUSION Together, our study reveals previous unrecognized role of RPLP2 in HCC, and provides new regulatory mechanism of ferroptosis, indicating RPLP2 may be a novel therapeutic target for HCC.
Collapse
Affiliation(s)
- Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Haiyan Wang
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Zuli Wang
- Center for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
| |
Collapse
|
13
|
Lu J, Liang K, Zou R, Peng Y, Wang H, Huang R, Zeng Z, Feng Z, Fan Y, Zhang S, Ji Y, Pang X, Wang Y, Zhang H, Wang Z. Comprehensive analysis of the prognostic and immunological signature of eight Tripartitemotif (TRIM) family molecules in human gliomas. Aging (Albany NY) 2023; 15:5798-5825. [PMID: 37367937 PMCID: PMC10333093 DOI: 10.18632/aging.204841] [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: 02/13/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND TRIM family molecules have been identified as being involved in the tumor progression of various cancer types. Increasingly, experimental evidence indicates that some of TRIM family molecules are implicated in glioma tumorigenesis. However, the diverse genomic changes, prognostic values and immunological landscapes of TRIM family of molecules have yet to be fully determined in glioma. METHODS In our study, employing the comprehensive bioinformatics tools, we evaluated the unique functions of 8 TRIM members including TRIM5/17/21/22/24/28/34/47 in gliomas. RESULTS The expression levels of 7 TRIM members (TRIM5/21/22/24/28/34/47) were higher in glioma as well as its diverse cancer subtypes than in normal tissues, whereas the expression level of TRIM17 was the opposite, lower in the former than in the latter. In addition, survival analysis revealed that the high expression profiles of TRIM5/21/22/24/28/34/47 were associated with poor overall survival (OS), disease-specific survival (DSS) and progress-free interval (PFI) in glioma patients, whereas TRIM17 displayed adverse outcomes. Moreover, the 8 TRIM molecules expression as well as methylation profiles remarkably correlated with different WHO grades. And genetic alterations, including mutations and copy number alterations (CNAs), in the TRIM family were correlated with longer OS, DSS and progress-free survival (PFS) in glioma patients. Furthermore, through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results of these 8 molecules and their related genes, we found that these molecules may change the immune infiltration of the tumor microenvironment and regulate the expression of immune checkpoint molecules (ICMs), affecting the occurrence and development of gliomas. The correlation analyses between the 8 TRIM molecules and TMB (tumor mutational burden)/MSI (microsatellite instability)/ICMs discovered that as the expression level of TRIM5/21/22/24/28/34/47 increased, the TMB score also increased significantly, while TRIM17 showed an opposite outcome. Further, a 6-gene signature (TRIM 5/17/21/28/34/47) for predicting overall survival (OS) in gliomas was built by using the least absolute shrinkage and selection operator (LASSO) regression, and the survival and time-dependent ROC analyses all were found to perform well in testing and validation cohorts. Results of multivariate COX regression analysis showed that TRIM5/28 are both expected to become independent risk predictors to guide clinical treatment. CONCLUSION In general, the results indicate that TRIM5/17/21/22/24/28/34/47 might exert a crucial influence on gliomas tumorigenesis and might be putative prognostic markers and therapeutic targets for glioma patients.
Collapse
Affiliation(s)
- Jiajie Lu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuecheng Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Haojian Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Rihong Huang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zhaorong Zeng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zejia Feng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Yongyang Fan
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Hongri Zhang
- Department of Neurosurgery, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| |
Collapse
|
14
|
Yan B, Guo J, Deng S, Chen D, Huang M. A pan-cancer analysis of the role of USP5 in human cancers. Sci Rep 2023; 13:8972. [PMID: 37268697 DOI: 10.1038/s41598-023-35793-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023] Open
Abstract
Posttranslational modifications (PTM) such as acetylation, deubiquitination, and phosphorylation of proteins, play important roles in various kinds of cancer progression. Ubiquitin-specific proteinase 5 (USP5), a unique member of deubiquitinating enzymes (DUBs) which recognizes unanchored polyubiquitin specifically, could regulate the stability of many tumorigenesis-associated proteins to influence cancer initiation and progression. However, the diverse biological significance of USP5 in pan-cancer has not been systematically and comprehensively studied. Here, we explored the role of USP5 in pan-cancer using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, and we also acquired and analyzed data via various software and web platforms such as R, GEPIA2.0, HPA, TISIDB, cBioPortal, UALCAN, TIMER 2.0, CancerSEA and BioGRID. USP5 expression was high in most cancers and differed significantly in different molecular and immune subtypes of cancers. In addition, USP5 had certain diagnostic value in multiple cancers, and high expression of USP5 generally predicted poor prognosis for cancer patients. We also found that the most frequent genetic alterations type of USP5 was mutation, and the DNA methylation level of USP5 decreased in various cancers. Furthermore, USP5 expression correlated with cancer-associated fibroblasts (CAFs), endothelial cells (EC) and genetic markers of immunodulators in cancers. Moreover, the result from single cell sequencing showed that USP5 could regulate several tumor biological behaviors such as apoptosis, DNA damage and metastasis. Gene enrichment analysis indicated "spliceosome" and "RNA splicing" may be the critical mechanism for USP5 to involve in cancer. Taken together, our study elucidates the biological significance of USP5 in the diagnosis, prognosis and immune in human pan-cancer.
Collapse
Affiliation(s)
- Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Dongliang Chen
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
| | - Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
| |
Collapse
|
15
|
Sun WX, Shu YP, Yang XY, Huang W, Chen J, Yu NN, Zhao M. Effects of folic acid supplementation in pregnant mice on glucose metabolism disorders in male offspring induced by lipopolysaccharide exposure during pregnancy. Sci Rep 2023; 13:7984. [PMID: 37198280 DOI: 10.1038/s41598-023-31690-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/15/2023] [Indexed: 05/19/2023] Open
Abstract
The DOHaD theory suggests that adverse environmental factors in early life may lead to the development of metabolic diseases including diabetes and hypertension in adult offspring through epigenetic mechanisms such as DNA methylation. Folic acid (FA) is an important methyl donor in vivo and participates in DNA replication and methylation. The preliminary experimental results of our group demonstrated that lipopolysaccharide (LPS, 50 µg/kg/d) exposure during pregnancy could lead to glucose metabolism disorders in male offspring, but not female offspring; however, the effect of folic acid supplementation on glucose metabolism disorders in male offspring induced by LPS exposure remains unclear. Therefore, in this study, pregnant mice were exposed to LPS on gestational day (GD) 15-17 and were given three doses of FA supplementation (2 mg/kg, 5 mg/kg, or 40 mg/kg) from mating to lactation to explore its effect on glucose metabolism in male offspring and the potential mechanism. This study confirmed that FA supplementation of 5 mg/kg in pregnant mice improved glucose metabolism in LPS-exposed offspring during pregnancy by regulating gene expression.
Collapse
Affiliation(s)
- Wan-Xiao Sun
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- Anhui Medical College, Hefei, 230601, Anhui, China
| | - Yi-Ping Shu
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Xin-Yu Yang
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Wei Huang
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jing Chen
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- Anhui Provincial Hospital, Hefei, 230022, Anhui, China
| | - Ning-Ning Yu
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Mei Zhao
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
| |
Collapse
|
16
|
Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
Collapse
Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
17
|
Bi C, Wang Z, Xiao Y, Zhao Y, Guo R, Xiong L, Ji Z, Li Y, Li Q, Qin C. I kappa B kinase interacting protein as a promising biomarker in pan-cancer: A multi-omics analysis. Front Genet 2023; 14:1138137. [PMID: 36999060 PMCID: PMC10047260 DOI: 10.3389/fgene.2023.1138137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Background: Human chromosome 12 contains I kappa B kinase interacting protein (IKBIP) is also commonly known as IKIP. The involvement of IKBIP in the growth of tumors has only been discussed in a small number of publications.Purpose: To explore the role that IKBIP plays in the development of a wide variety of neoplasms, as well as the tumor immunological microenvironment.Methods: UALCAN, HPA, Genotype Tissue Expression, Cancer Genome Maps, and other datasets were used to analyze IKBIP expression. We thoroughly investigated the predictive importance of IKBIP in pan-cancer, clinical traits, and genetic anomalies. We studied whether there is a link between IKBIP and immune-related genes, microsatellite instability (MSI), and the incidence of tumor mutational burden (TMB). The link between immune cell infiltration and IKBIP expression was examined using data on immune cell infiltration from ImmuCellAI, TIMER2, and earlier studies. Finally, gene set enrichment analysis (GSEA) was performed to determine the signaling pathways associated with IKBIP.Results: IKBIP is highly expressed in most cancers and is negatively associated with the prognosis of several major cancer types. Furthermore, IKBIP expression was linked to TMB in 13 cancers and MSI in seven cancers. Additionally, IKBIP is associated with numerous immunological and cancer-promoting pathways. Simultaneously, various cancer types have unique tumor-infiltrating immune cell profiles.Conclusion: IKBIP has the potential to act as a pan-cancer oncogene and is crucial for both carcinogenesis and cancer immunity. Elevated IKBIP expression implies an immunosuppressive environment and may be used as a prognostic biomarker and therapeutic target.
Collapse
|
18
|
KIF11 As a Potential Pan-Cancer Immunological Biomarker Encompassing the Disease Staging, Prognoses, Tumor Microenvironment, and Therapeutic Responses. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2764940. [PMID: 36742345 PMCID: PMC9893523 DOI: 10.1155/2022/2764940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022]
Abstract
KIF11 is one of the 45 family members of kinesin superfamily proteins that functions as a motor protein in mitosis. Emerging evidence revealed that KIF11 plays pivotal roles in cancer initiation, development, and progression. However, the prognostic, oncological, and immunological values of KIF11 have not been comprehensively explored in pan-cancer. In present study, we comprehensively interrogated the role of KIF11 in tumor progression, tumor stemness, genomic heterogeneity, tumor immune infiltration, immune evasion, therapy response, and prognosis of cohorts from various cancer types. In general, KIF11 was significantly upregulated in tumors compared with paired normal tissues. KIF11 showed strong relationships with pathological stage, prognosis, tumor stemness, genomic heterogeneity, neoantigens, ESTIMATE, immune checkpoint, and drug sensitivity. The methylation level of KIF11 decreased in most cancers and was correlated with the survival probability in different human cancers. The expression of KIF11 was diverse in different molecular and immune subtypes and remarkably correlated with immune cell infiltration in the tumor microenvironment. Comparative study revealed that KIF11 was a powerful biomarker and associated with immune, targeted, and chemotherapeutic outcomes in various cancers. In addition, KIF11 interaction and coexpression networks mainly participated in the regulation of cell cycle, cell division, p53 signaling pathway, DNA repair and recombination, chromatin organization, antigen processing and presentation, and drug resistance. Our pan-cancer analysis provides a comprehensive understanding of the functions of KIF11 in oncogenesis, progression, and therapy in different cancers. KIF11 may serve as a potential prognostic and immunological pan-cancer biomarker. Moreover, KIF11 could be a novel target for tumor immunotherapy.
Collapse
|
19
|
Zhang Y, Qin H, Bian J, Ma Z, Yi H. SLC2As as diagnostic markers and therapeutic targets in LUAD patients through bioinformatic analysis. Front Pharmacol 2022; 13:1045179. [PMID: 36518662 PMCID: PMC9742449 DOI: 10.3389/fphar.2022.1045179] [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: 09/15/2022] [Accepted: 11/14/2022] [Indexed: 11/05/2023] Open
Abstract
Facilitative glucose transporters (GLUTs), which are encoded by solute carrier 2A (SLC2A) genes, are responsible for mediating glucose absorption. In order to meet their higher energy demands, cancer cells are more likely than normal tissue cells to have elevated glucose transporters. Multiple pathogenic processes, such as cancer and immunological disorders, have been linked to GLUTs. Few studies, meanwhile, have been conducted on individuals with lung adenocarcinoma (LUAD) to evaluate all 14 SLC2A genes. We first identified increased protein levels of SLC2A1, SLC2A5, SLC2A6, and SLC2A9 via HPA database and downregulated mRNA levels of SLC2A3, SLC2A6, SLC2A9, and SLC2A14 by ONCOMINE and UALCAN databases in patients with LUAD. Additionally, lower levels of SLC2A3, SLC2A6, SLC2A9, SLC2A12, and SLC2A14 and higher levels of SLC2A1, SLC2A5, SLC2A10, and SLC2A11 had an association with advanced tumor stage. SLC2A1, SLC2A7, and SLC2A11 were identified as prognostic signatures for LUAD. Kaplan-Meier analysis, Univariate Cox regression, multivariate Cox regression and ROC analyses further revealed that these three genes signature was a novel and important prognostic factor. Mechanistically, the aberrant expression of these molecules was caused, in part, by the hypomethylation of SLC2A3, SLC2A10, and SLC2A14 and by the hypermethylation of SLC2A1, SLC2A2, SLC2A5, SLC2A6, SLC2A7, and SLC2A11. Additionally, SLC2A3, SLC2A5, SLC2A6, SLC2A9, and SLC2A14 contributed to LUAD by positively modulating M2 macrophage and T cell exhaustion. Finally, pathways involving SLC2A1/BUB1B/mitotic cell cycle, SLC2A5/CD86/negative regulation of immune system process, SLC2A6/PLEK/lymphocyte activation, SLC2A9/CD4/regulation of cytokine production might participate in the pathogenesis of LUAD. In summary, our results will provide the theoretical basis on SLC2As as diagnostic markers and therapeutic targets in LUAD.
Collapse
Affiliation(s)
- Yanli Zhang
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin, China
- Echocardiography Department, The First Hospital of Jilin University, Changchun, China
| | - Han Qin
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin, China
| | - Jing Bian
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin, China
| |
Collapse
|
20
|
Glycolysis-Related SLC2A1 Is a Potential Pan-Cancer Biomarker for Prognosis and Immunotherapy. Cancers (Basel) 2022; 14:cancers14215344. [PMID: 36358765 PMCID: PMC9657346 DOI: 10.3390/cancers14215344] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022] Open
Abstract
SLC2A1 plays a pivotal role in cancer glycometabolism. SLC2A1 has been proposed as a putative driver gene in various cancers. However, a pan-cancer analysis of SLC2A1 has not yet been performed. In this study, we explored the expression and prognosis of SLC2A1 in pan-cancer across multiple databases. We conducted genetic alteration, epigenetic, and functional enrichment analyses of SLC2A. We calculated the correlation between SLC2A1 and tumor microenvironment using the TCGA pan-cancer dataset. We observed high expression levels of SLC2A1 with poor prognosis in most cancers. The overall genetic alteration frequency of SLC2A1 was 1.8% in pan-cancer, and the SLC2A1 promoter was hypomethylation in several cancers. Most m6A-methylation-related genes positively correlated with the expression of SLC2A1 in 33 TCGA cancers. Moreover, SLC2A1 was mainly related to the functions including epithelial-mesenchymal transition, glycolysis, hypoxia, cell-cycle regulation, and DNA repair. Finally, SLC2A1 positively associated with neutrophils and cancer-associated fibroblasts in the tumor microenvironment of most cancers and significantly correlated with TMB and MSI in various cancers. Notably, SLC2A1 was remarkably positively correlated with PD-L1 and CTLA4 in most cancers. SLC2A1 might serve as an attractive pan-cancer biomarker for providing new insights into cancer therapeutics.
Collapse
|
21
|
Towards a better understanding of TF-DNA binding prediction from genomic features. Comput Biol Med 2022; 149:105993. [DOI: 10.1016/j.compbiomed.2022.105993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
|
22
|
Chen R, Wang X, Fu J, Liang M, Xia T. High FLT3 expression indicates favorable prognosis and correlates with clinicopathological parameters and immune infiltration in breast cancer. Front Genet 2022; 13:956869. [PMID: 36159964 PMCID: PMC9499177 DOI: 10.3389/fgene.2022.956869] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Purpose: Breast cancer is a highly heterogeneous malignancy, seriously threatening female health worldwide and inducing higher mortalities. Few have the studies evaluated Fms-like TyrosineKinase-3 (FLT3) in prognostic risk, immunotherapy or any other treatment of breast cancer. Our study focused on investigating the function of FLT3 in breast cancer. Patients and methods: Based on transcriptome and methylation data mined from The Cancer Gene Atlas (TCGA), we explored the clinical features of FLT3 expression in 1079 breast cancer samples. RT-qPCR in cell lines and tissue samples was used to verify the expression difference of FLT3. Kaplan–Meier survival analysis and cox regression models were employed for screening of FLT3 with potential prognostic capacity. Subsequently, functional analysis of the co-expressed genes was conducted using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene-set enrichment analysis (GSEA). The correlation between FLT3 expression and tumor immune infiltration was jointly analyzed with estimate, ssGSEA, TIMER, and TISIDB. Then we employed checkpoint-related molecules, immunophenoscore (IPS), and tumor mutation burden (TMB) to assess the efficacy of immuno-checkpoint inhibitors (ICIs). Pearson correlation coefficient was employed to exam the association between DNA methylation and FLT3 expression. Results: FLT3 displays an elevated expression in breast cancer than normal pairs and is significantly associated with multiple clinical characteristics like age, menopause status, histological type, pathological stage, and molecular subtype as well as increased overall survival (OS). Additionally, FLT3 is a favorable independent prognostic factor. GO, KEGG, and GSEA suggested that FLT3 was associated with diversified immune-related features. FLT3 expression is correlated with the abundance of various immune cells namely CD4+T cell, CD8+ T cell, myeloid dendritic cell, and neutrophil as well as immune inhibitors especially CTLA4, which is positively correlated with FLT3 expression. Moreover, TMB displayed a negative correlation with FLT3 expression while IPS showed adverse tendency. Ultimately, the methylation of FLT3 downregulates the gene expression and closely binds to a few clinical parameters. Conclusion: FLT3 can be used for prognostic prediction and is relevant to immune infiltration in breast cancer. FLT3 may pave the way for future novel immunotherapies.
Collapse
Affiliation(s)
- Rui Chen
- Department of Breast Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xinyang Wang
- Department of Thyroid and Breast, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Jingyue Fu
- Department of Breast Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Mengdi Liang
- Department of Breast Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Tiansong Xia
- Department of Breast Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Tiansong Xia,
| |
Collapse
|
23
|
Pancancer Analysis of the Oncogenic and Prognostic Role of NOL7: A Potential Target for Carcinogenesis and Survival. Int J Mol Sci 2022; 23:ijms23179611. [PMID: 36077008 PMCID: PMC9455868 DOI: 10.3390/ijms23179611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Despite growing evidence suggesting the critical function of NOL7 in cancer initiation and development, a systematic pancancer analysis of NOL7 is lacking. Herein, we present a comprehensive study of NOL7 which aimed to explore its potential role and detailed mechanisms across 33 human tumors based on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CATPAC) databases. As a result, both gene and protein levels of NOL7 were found to be increased in various tumor tissues, including breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), and head and neck squamous cell carcinoma (HNSC) as compared with corresponding normal tissues. Meanwhile, dysregulated NOL7 expression was found to be closely related to pathological stage and prognosis in several cancers, including LIHC, ovarian serous cystadenocarcinoma (OV), and bladder urothelial carcinoma (BLCA). The DNA methylation level of NOL7 was found to be decreased in most cancers and to be negatively associated with NOL7 expression. Furthermore, NOL7 expression was determined to be significantly associated with levels of infiltrating cells and immune checkpoint genes, including HMGB1. Analysis of NOL7-related genes revealed that RNA metabolism pathways, including “ribosome biogenesis”, “spliceosome”, and “RNA transport”, were mainly involved in the functional mechanism of NOL7 in human cancers. In summary, this pancancer study characterized the relationship between NOL7 expression and clinicopathologic features in multiple cancer types and further showed its potential regulatory network in human cancers. It represents a systemic analysis for further functional and therapeutic studies of NOL7 and highlights its predictive value with respect to the carcinogenesis and prognosis of various cancers, especially LIHC.
Collapse
|
24
|
AURKA is a prognostic potential therapeutic target in skin cutaneous melanoma modulating the tumor microenvironment, apoptosis, and hypoxia. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04164-1. [DOI: 10.1007/s00432-022-04164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/20/2022] [Indexed: 10/16/2022]
|
25
|
Zhang P, Gao H, Ye C, Yan R, Yu L, Xia C, Yang D. Large-Scale Transcriptome Data Analysis Identifies KIF2C as a Potential Therapeutic Target Associated With Immune Infiltration in Prostate Cancer. Front Immunol 2022; 13:905259. [PMID: 35720323 PMCID: PMC9203693 DOI: 10.3389/fimmu.2022.905259] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/06/2022] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers of the urinary system. In previous research, Kinesin family member 2C (KIF2C), as an oncogene, has been demonstrated to have a key role in the incidence and progression of different cancers. However, KIF2C has not been reported in PCa. We combined data from different databases, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, cBioPortal, and the Genomics of Drug Sensitivity in Cancer database, to explore the potential oncogenic role of KIF2C in PCa through a series of bioinformatics approaches, including analysis of the association between KIF2C and prognosis, clinicopathological features, gene mutations, DNA methylation, immune cell infiltration, and drug resistance. The results showed that KIF2C was significantly up-regulated in PCa. High KIF2C expression was associated with age, pathological stage, lymph node metastases, prostate-specific antigen (PSA), and Gleason score and significantly predicted an unfavorable prognosis in PCa patients. Results from Gene Set Enrichment Analysis (GSEA) suggested that KIF2C was involved in the cell cycle and immune response. KIF2C DNA methylation was reduced in PCa and was inversely linked with KIF2C expression. KIF2C was shown to have a strong relationship with the tumor microenvironment (TME), infiltrating cells, and immune checkpoint genes. Furthermore, high KIF2C expression was significantly resistant to a variety of MAPK signaling pathway-related inhibitors. Our study reveals that KIF2C may be a possible predictive biomarker for assessing prognosis in PCa patients with immune infiltration.
Collapse
Affiliation(s)
- Pingxin Zhang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hang Gao
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chunwei Ye
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruping Yan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lu Yu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengxing Xia
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Delin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| |
Collapse
|
26
|
Wang Z, Huang R, Wang H, Peng Y, Fan Y, Feng Z, Zeng Z, Ji Y, Wang Y, Lu J. Prognostic and Immunological Role of PPP1R14A as a Pan-Cancer Analysis Candidate. Front Genet 2022; 13:842975. [PMID: 35656324 PMCID: PMC9152294 DOI: 10.3389/fgene.2022.842975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
Despite emerging evidence revealing the remarkable roles of protein phosphatase 1 regulatory inhibitor subunit 14A (PPP1R14A) in cancer tumorigenesis and progression, no pan-cancer analysis is available. A comprehensive investigation of the potential carcinogenic mechanism of PPP1R14A across 33 tumors using bioinformatic techniques is reported for the first time. PPP1R14A is downregulated in major malignancies, and there is a significant correlation between the PPP1R14A expression and the prognosis of patients. The high expression of PPP1R14A in most cases was associated with poor overall survival (OS), disease-specific survival (DSS), and progress-free interval (PFI) across patients with various malignant tumors, including adrenocortical carcinoma (ACC) and bladder urothelial carcinoma (BLCA), indicated through pan-cancer survival analysis. Receiver operating characteristic (ROC) analysis subsequently exhibited that the molecule has high reference significance in diagnosing a variety of cancers. The frequency of PPP1R14A genetic changes including genetic mutations and copy number alterations (CNAs) in uterine carcinosarcoma reached 16.07%, and these alterations brought misfortune to the survival and prognosis of cancer patients. In addition, methylation within the promoter region of PPP1R14A DNA was enhanced in a majority of cancers. Downregulated phosphorylation levels of phosphorylation sites including S26, T38, and others in most cases took place in several tumors, such as breast cancer and colon cancer. PPP1R14A remarkably correlated with the levels of infiltrating cells and immune checkpoint genes. Our research on the carcinogenic effect of PPP1R14A in different tumors is comprehensively summarized and analyzed and provides a theoretical basis for future therapeutic and immunotherapy strategies.
Collapse
Affiliation(s)
- Zhaotao Wang
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rihong Huang
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Haojian Wang
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Yuecheng Peng
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Yongyang Fan
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Zejia Feng
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Zhaorong Zeng
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Yunxiang Ji
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yezhong Wang
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiajie Lu
- Department of Neurosurgery, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
27
|
Li W, Chen H, Wang Z, Liu J, Lei X, Chen W. Chromobox 4 (CBX4) promotes tumor progression and stemness via activating CDC20 in gastric cancer. J Gastrointest Oncol 2022; 13:1058-1072. [PMID: 35837165 PMCID: PMC9274029 DOI: 10.21037/jgo-22-549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The Chromobox homolog 4 (CBX4) has been found to be overexpressed in multiple malignancies. However, the associations between CBX4 and gastric cancer (GC) have remained unclear. This study aimed to determine the biological roles of CBX4 in GC and identify effective therapeutic targets. METHODS The 3-(4,5-dimethylthiazol-2-yl) (MTT) assays were used to screen CBX family members. Differential analysis was utilized to evaluate the CBX4 levels. Kaplan-Meier analysis was used to perform prognostic analysis. Western blotting assay, quantitative polymerase chain reaction (qPCR) assay and immunohistochemistry (IHC) were used to assess CBX4 expressions. Colony formation assay, Cell Counting Kit-8 (CCK-8) assay, and Transwell assay were used to assess progression features of cells. The tail vein injection model was utilized to determine the metastatic efficacy of GC cells. Tumor sphere formation assay was used to assess tumor stemness maintenance ability. Chromatin immunoprecipitation (ChIP)-qPCR assay was used to evaluate the associations between CBX4 and CDC20. A subcutaneous tumor model was used to assess the in vivo growth ability of GC. RESULTS The MTT assay revealed that only CBX4 inhibition could lead to notable restriction of GC growth, as compared to others. Differential analysis suggested that CBX4 was upregulated in tumor samples relative to normal tissues. Less favorable overall survival (OS) outcomes were noticed in GC patients with high CBX4 in comparison to those with low CBX4. High CBX4 could notably enhance cell proliferation capacity, migration ability, and in vivo metastatic efficacy. Gene set enrichment analysis (GSEA) indicated the relationships between CBX4 and GC stemness, and CBX4 overexpression could remarkably elevate self-renewal ability of GC cells. In addition, CBX4 could mainly promote CDC20 messenger RNA (mRNA) levels, and targeting CBX4 suppressed the relative CDC20 levels. The ChIP-qPCR assay further demonstrated that CBX4 coordinated with H3K4me3 to bind at the CDC20 promoter region. Additionally, CBX4 depended on CDC20 to drive GC growth. Lastly, downregulated CBX4 could notably inhibit the growth of GC in vivo. CONCLUSIONS This study highlights the oncogenic roles of CBX4 in GC. CBX4 activates CDC20 to maintain stemness features of GC, thereby creating therapeutic vulnerabilities in the treatment of GC.
Collapse
Affiliation(s)
- Wen Li
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| | - Honghui Chen
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhenggen Wang
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| | - Jingjing Liu
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| | - Xinan Lei
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| | - Wen Chen
- The Second Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, China
| |
Collapse
|
28
|
Xu H, Jiang C, Chen D, Wu Y, Lu J, Zhong L, Yao F. Analysis of Pan-Cancer Revealed the Immunological and Prognostic Potential of CBX3 in Human Tumors. Front Med (Lausanne) 2022; 9:869994. [PMID: 35573019 PMCID: PMC9096250 DOI: 10.3389/fmed.2022.869994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Chromobox protein homolog 3 (CBX3) has been recognized as a member of the heterochromatin protein 1 family and participate in transcriptional activation or inhibition, cell differentiation and growth. Despite more and more evidence shows that CBX3 has a critical function in the development of some tumors, no systematic extensive analysis of CBX3 has been reported. Thus, we intended to examine the prognostic significance of CBX3 in 33 tumors and investigate its potential immune function. We employed several bioinformatics methods to explore the potential carcinogenic impact of CBX3 premised on the data sets collected from tumor genome maps, human protein maps, cBioPortal, and genotype tissue expression. The approaches include assessing the link between CBX3 and prognosis of different tumors, immune cell infiltration, micro-satellite instability (MSI), DNA methylation, and tumor mutational burden (TMB). The outcomes illustrated that CBX3 was increasingly expressed in 29 tumors. Moreover, CBX3 exhibited a negative correlation with the prognosis of many tumors. The expression of CBX3 was linked to MSI in 12 tumors and TMB in 16 tumors. In 24 tumors, the expression of CBX3 was linked to DNA methylation. Moreover, the CBX3 expression exhibited a negative relationship with the infiltration level of the majority of immune cells, but showed a positive link to T gamma delta cells, central memory T cells, and T helper cells, especially when invading breast carcinoma, thymic carcinoma, colon carcinoma, cutaneous melanoma, endometrial carcinoma, and lung squamous carcinoma. Our research indicates that CBX3 might be used as a prognostic indicator for different malignant tumors due to its function in tumor genesis as well as tumor immunity.
Collapse
Affiliation(s)
- Haitao Xu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Caihong Jiang
- Department of Pediatric Surgery, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Dangui Chen
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Youzhi Wu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Jia Lu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Long Zhong
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Fusheng Yao
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| |
Collapse
|
29
|
Pan-Cancer Analysis of the Prognostic and Immunological Role of HSF1: A Potential Target for Survival and Immunotherapy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5551036. [PMID: 34239690 PMCID: PMC8238600 DOI: 10.1155/2021/5551036] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023]
Abstract
Emerging evidence revealed the significant roles of heat shock factor 1 (HSF1) in cancer initiation, development, and progression, but there is no pan-cancer analysis of HSF1. The present study first comprehensively investigated the expression profiles and prognostic significance of HSF1 and the relationship of HSF1 with clinicopathological parameters and immune cell infiltration using bioinformatic techniques. HSF1 is significantly upregulated in various common cancers, and it is associated with prognosis. Pan-cancer Cox regression analysis indicated that the high expression of HSF1 was associated with poor overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), head and neck squamous cell carcinoma (HNSC), and kidney renal papillary cell carcinoma (KIRP) patients. The methylation of HSF1 DNA was decreased in most cancers and negatively correlated with the HSF1 expression. Increased phosphorylation of S303, S307, and S363 in HSF1 was observed in some cancers. HSF1 remarkably correlated with the levels of infiltrating cells and immune checkpoint genes. Our pan-cancer analysis provides a deep understanding of the functions of HSF1 in oncogenesis and metastasis in different cancers.
Collapse
|