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Yao Z, Lu L, Xu Q, Hua S, Wang H, Jiang H. Integrated Analysis Reveals COL4A3 as a Novel Diagnostic and Therapeutic Target in UV-Related Skin Cutaneous Melanoma. Clin Cosmet Investig Dermatol 2024; 17:1429-1446. [PMID: 38911338 PMCID: PMC11192641 DOI: 10.2147/ccid.s461959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/07/2024] [Indexed: 06/25/2024]
Abstract
Background High levels of UV exposure are a significant factor that can trigger the onset and progression of SKCM. Moreover, this exposure is closely linked to the malignancy of the tumor and the prognosis of patients. Our objective is to identify a tumor biomarker database associated with UV exposure, which can be utilized for prognostic analysis and diagnosis and treatment of SKCM. Methods This study used the weighted gene co-expression network analyses (WGCNA) and gene mutation frequency analyses to screen for UV-related target genes using the GSE59455 and the cancer genome atlas databases (TCGA). The prognostic model was created using Cox regression and least absolute shrinkage and selection operator analyses (LASSCO). Furthermore, in vitro experiments further validated that the overexpression or knockdown of COL4A3 could regulate the proliferation and migration abilities of SKMEL28 and A357 melanoma cells. Results A prognostic model was created that included six genes with a high UV-related mutation in SKCM: COL4A3, CHRM2, DSC3, GIMAP5, LAMC2, and PSG7. The model had a strong patient survival correlation (P˂0.001, hazard ratio (HR) = 1.57) and significant predictor (P˂0.001, HR = 3.050). Furthermore, the model negatively correlated with immune cells, including CD8+ T cells (Cor=-0.408, P˂0.001), and M1-type macrophages (Cor=-0.385, P˂0.001), and immune checkpoints, including programmed cell death ligand-1. Moreover, we identified COL4A3 as a molecule with significant predictive functionality. Overexpression of COL4A3 significantly inhibited the proliferation, migration, and invasion abilities of SKMEL28 and A357 melanoma cells, while knockdown of COL4A3 yielded the opposite results. And overexpression of COL4A3 enhanced the inhibitory effects of imatinib on the proliferation, migration, and invasion abilities of SKMEL28 and A357 cells. Conclusion The efficacy of the prognostic model was validated by analyzing the prognosis, immune infiltration, and immune checkpoint profiles. COL4A3 stands out as a novel diagnostic and therapeutic target for SKCM, offering new strategies for small-molecule targeted drug therapies.
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Affiliation(s)
- Zuochao Yao
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
| | - Lu Lu
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
| | - Qianhui Xu
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
| | - Shan Hua
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
| | - Hui Wang
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
| | - Hua Jiang
- Department of Plastic and Reconstructive Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, People’s Republic of China
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Xia B, Zeng P, Xue Y, Li Q, Xie J, Xu J, Wu W, Yang X. Identification of potential shared gene signatures between gastric cancer and type 2 diabetes: a data-driven analysis. Front Med (Lausanne) 2024; 11:1382004. [PMID: 38903804 PMCID: PMC11187270 DOI: 10.3389/fmed.2024.1382004] [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: 02/04/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Background Gastric cancer (GC) and type 2 diabetes (T2D) contribute to each other, but the interaction mechanisms remain undiscovered. The goal of this research was to explore shared genes as well as crosstalk mechanisms between GC and T2D. Methods The Gene Expression Omnibus (GEO) database served as the source of the GC and T2D datasets. The differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA) were utilized to identify representative genes. In addition, overlapping genes between the representative genes of the two diseases were used for functional enrichment analysis and protein-protein interaction (PPI) network. Next, hub genes were filtered through two machine learning algorithms. Finally, external validation was undertaken with data from the Cancer Genome Atlas (TCGA) database. Results A total of 292 and 541 DEGs were obtained from the GC (GSE29272) and T2D (GSE164416) datasets, respectively. In addition, 2,704 and 336 module genes were identified in GC and T2D. Following their intersection, 104 crosstalk genes were identified. Enrichment analysis indicated that "ECM-receptor interaction," "AGE-RAGE signaling pathway in diabetic complications," "aging," and "cellular response to copper ion" were mutual pathways. Through the PPI network, 10 genes were identified as candidate hub genes. Machine learning further selected BGN, VCAN, FN1, FBLN1, COL4A5, COL1A1, and COL6A3 as hub genes. Conclusion "ECM-receptor interaction," "AGE-RAGE signaling pathway in diabetic complications," "aging," and "cellular response to copper ion" were revealed as possible crosstalk mechanisms. BGN, VCAN, FN1, FBLN1, COL4A5, COL1A1, and COL6A3 were identified as shared genes and potential therapeutic targets for people suffering from GC and T2D.
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Affiliation(s)
- Bingqing Xia
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ping Zeng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuling Xue
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Jianhui Xie
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Jiamin Xu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Wenzhen Wu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Xiaobo Yang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
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Zheng T, Zheng Z, Zhou H, Guo Y, Li S. The multifaceted roles of COL4A4 in lung adenocarcinoma: An integrated bioinformatics and experimental study. Comput Biol Med 2024; 170:107896. [PMID: 38217972 DOI: 10.1016/j.compbiomed.2023.107896] [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: 11/05/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Abnormal expression of collagen IV subunits has been reported in cancers, but the significance is not clear. No study has reported the significance of COL4A4 in lung adenocarcinoma (LUAD). METHODS COL4A4 expression data, single-cell sequencing data and clinical data were downloaded from public databases. A range of bioinformatics and experimental methods were adopted to analyze the association of COL4A4 expression with clinical parameters, tumor microenvironment (TME), drug resistance and immunotherapy response, and to investigate the roles and underlying mechanism of COL4A4 in LUAD. RESULTS COL4A4 is differentially expressed in most of cancers analyzed, being associated with prognosis, tumor stemness, immune checkpoint gene expression and TME parameters. In LUAD, COL4A4 expression is down-regulated and associated with various TME parameters, response to immunotherapy and drug resistance. LUAD patients with lower COL4A4 have worse prognosis. Knockdown of COL4A4 significantly inhibited the expression of cell-cycle associated genes, and the expression and activation of signaling pathways including JAK/STAT3, p38, and ERK pathways, and induced quiescence in LUAD cells. Besides, it significantly induced the expression of a range of bioactive molecule genes that have been shown to have critical roles in TME remodeling and immune regulation. CONCLUSIONS COL4A4 is implicated in the pathogenesis of cancers including LUAD. Its function may be multifaceted. It can modulate the activity of LUAD cells, TME remodeling and tumor stemness, thus affecting the pathological process of LUAD. COL4A4 may be a prognostic molecular marker and a potential therapeutic target.
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Affiliation(s)
- Tiaozhan Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Zhiwen Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Hanxi Zhou
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Yiqing Guo
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Shikang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China.
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Wang T, Chen P, Li T, Li J, Zhao D, Meng F, Zhao Y, Zheng Z, Liu X. A Five-gene Signature based on MicroRNA for Predicting Prognosis and Immunotherapy in Stomach Adenocarcinoma. Curr Med Chem 2024; 31:2378-2399. [PMID: 38310388 DOI: 10.2174/0109298673281631231127051017] [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: 09/27/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 02/05/2024]
Abstract
AIMS We aimed to classify molecular subtypes and establish a prognostic gene signature based on miRNAs for the prognostic prediction and therapeutic response in Stomach adenocarcinoma (STAD). BACKGROUND STAD is a common diagnosed gastrointestinal malignancy and its heterogeneity is a big challenge that influences prognosis and precision therapies. Present study was designed to classify molecular subtypes and construct a prognostic gene signature based on miRNAs for the prognostic prediction and therapeutic response in STAD. OBJECTIVE The objective of this study is to investigate the molecular subtypes and prognostic model for STAD. METHODS A STAD specific miRNA-messenger RNA (mRNA) competing endogenous RNA (ceRNA) network was generated using the RNA-Seq and miRNA expression profiles from The Cancer Genome Atlas (TCGA) database, in which miRNA-related mRNAs were screened. Molecular subtypes were then determined using miRNA-related genes. Through univariate Cox analysis and multivariate regression analysis, a prognostic model was established in GSE84437 Train dataset and validated in GSE84437 Test, TCGA, GSE84437 and GSE66229 datasets. Immunotherapy datasets were employed for assessing the performance of the risk model. Finally, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was applied to validate the expression of hub genes used for the risk score signature. RESULTS We constructed a ceRNA network containing 84 miRNAs and 907 mRNAs and determined two molecular subtypes based on 26 genes from the intersection of TCGASTAD and GSE84437 datasets. Subtype S2 had poor prognosis, lower tumor mutational burden, higher immune score and lower response to immunotherapy. Subtype S1 was more sensitive to Sorafenib, Pyrimethamine, Salubrinal, Gemcitabine, Vinorelbine and AKT inhibitor VIII. Next, a five-gene signature was generated and its robustness was validated in Test and external datasets. This risk model also had a good prediction performance in immunotherapy datasets. CONCLUSION This study promotes the underlying mechanisms of miRNA-based genes in STAD and offers directions for classification. A five-gene signature accurately predicts the prognosis and helps therapeutic options.
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Affiliation(s)
- Tianwei Wang
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, 13000, China
| | - Piji Chen
- Department of Clinical Laboratory, Yantian People's Hospital of Southern University of Science and Technology, Shenzhen, 518083, China
| | - Tingting Li
- Department of Oncology, Northern Theater Command General Hospital, Shenyang, 110015, China
| | - Jianong Li
- Department of Oncology, Northern Theater Command General Hospital, Shenyang, 110015, China
| | - Dong Zhao
- Department of Oncology, Northern Theater Command General Hospital, Shenyang, 110015, China
| | - Fanfei Meng
- Department of Translational Medicine, YuceBio Technology Co., Ltd, Shenzhen, 518035, China
| | - Yujie Zhao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis, YuceBio Technology Co., Ltd, Shenzhen, 518035, China
| | - Zhendong Zheng
- Department of Oncology, Northern Theater Command General Hospital, Shenyang, 110015, China
- People's Hospital of Huzhu Tu Autonomous County, Haidong, Qinghai Province, 810500, China
| | - Xuefei Liu
- Department of Oncology, Northern Theater Command General Hospital, Shenyang, 110015, China
- People's Hospital of Huzhu Tu Autonomous County, Haidong, Qinghai Province, 810500, China
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Wang S, Yang X, Liu C, Hu J, Yan M, Ding C, Fu Y. Identification of key genes associated with poor prognosis and neoplasm staging in gastric cancer. Medicine (Baltimore) 2023; 102:e35111. [PMID: 37800754 PMCID: PMC10553055 DOI: 10.1097/md.0000000000035111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/16/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is highly biologically and genetically heterogeneous disease with poor prognosis. Increasing evidence indicates that biomarkers can serve as prediction and clinical intervention. Therefore, it is vital to identify core molecules and pathways participating in the development of GC. METHODS In this study, GSE54129, GSE56807, GSE63089, and GSE118916 were used for identified overlapped 75 DEGs. GO and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed DEGs mainly enriched in biological process about collagen-containing extracellular matrix and collagen metabolic. Next, protein-protein interaction network was built and the hub gene was excavated. Clinicopathological features and prognostic value were also evaluated. RESULTS Hub genes were shown as below, FN1, COL1A2, COL1A1, COL3A1, COL4A1, COL6A3, COL5A2, SPARC, PDGFRB, COL12A1. Those genes were upregulation in GC and related to the poor prognosis (except COL5A2, P = .73). What is more, high expression indicated worse T stage and tumor, node, metastasis stage in GC patients. Later, the results of 25 GC tumor specimens and 34 normal tissues showed that FN1, COL3A1, COL4A1, SPARC, COL5A2, and COL12A1 were significantly upregulated in cancer samples. CONCLUSION Our study systematically explored the core genes and crucial pathways in GC, providing insights into clinical management and individual treatment.
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Affiliation(s)
- Shuoshan Wang
- Department of General Medicine, The First People’s Hospital of Foshan, The Affiliated Foshan Hospital of Sun Yat-Sen University, Guangdong, China
| | - Xiansheng Yang
- Second Department of Gastrointestinal Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, GuangZhou, China
| | - Chang Liu
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, China
| | - Jinlun Hu
- Department of General Medicine, The First People’s Hospital of Foshan, The Affiliated Foshan Hospital of Sun Yat-Sen University, Guangdong, China
| | - Mei Yan
- Department of General Medicine, The First People’s Hospital of Foshan, The Affiliated Foshan Hospital of Sun Yat-Sen University, Guangdong, China
| | - Chan Ding
- Department of General Medicine, The First People’s Hospital of Foshan, The Affiliated Foshan Hospital of Sun Yat-Sen University, Guangdong, China
| | - Yue Fu
- Department of General Medicine, The First People’s Hospital of Foshan, The Affiliated Foshan Hospital of Sun Yat-Sen University, Guangdong, China
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Liu Y, Chen Y, Wang F, Lin J, Tan X, Chen C, Wu LL, Zhang X, Wang Y, Shi Y, Yan X, Zhao K. Caveolin-1 promotes glioma progression and maintains its mitochondrial inhibition resistance. Discov Oncol 2023; 14:161. [PMID: 37642765 PMCID: PMC10465474 DOI: 10.1007/s12672-023-00765-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Glioma is a lethal brain cancer and lacking effective therapies. Challenges include no effective therapeutic target, intra- and intertumoral heterogeneity, inadequate effective drugs, and an immunosuppressive microenvironment, etc. Deciphering the pathogenesis of gliomas and finding out the working mechanisms are urgent and necessary for glioma treatment. Identification of prognostic biomarkers and targeting the biomarker genes will be a promising therapy. METHODS From our RNA-sequencing data of the oxidative phosphorylation (OXPHOS)-inhibition sensitive and OXPHOS-resistant cell lines, we found that the scaffolding protein caveolin 1 (CAV1) is highly expressed in the resistant group but not in the sensitive group. By comprehensive analysis of our RNA sequencing data, Whole Genome Bisulfite Sequencing (WGBS) data and public databases, we found that CAV1 is highly expressed in gliomas and its expression is positively related with pathological processes, higher CAV1 predicts shorter overall survival. RESULTS Further analysis indicated that (1) the differentiated genes in CAV1-high groups are enriched in immune infiltration and immune response; (2) CAV1 is positively correlated with tumor metastasis markers; (3) the methylation level of CAV1 promoters in glioma group is lower in higher stage than that in lower stage; (4) CAV1 is positively correlated with glioma stemness; (5) higher expression of CAV1 renders the glioma cells' resistant to oxidative phosphorylation inhibitors. CONCLUSION Therefore, we identified a key gene CAV1 and deciphered its function in glioma progression and prognosis, proposing that CAV1 may be a therapeutic target for gliomas.
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Affiliation(s)
- Yu'e Liu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Yi Chen
- The China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Fei Wang
- Shanghai Pudong Hospital, Pudong Medical Center, Fudan University, Shanghai, 201399, China
| | - Jianghua Lin
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Xiao Tan
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, No. 168 Changhai Road, Shanghai, 200433, China
| | - Lei-Lei Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Xiaoling Zhang
- National Joint Engineering Laboratory for Human Disease Animal Models, First Affiliated Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, First Hospital of Jilin University, Changchun, China
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200092, China
| | - Xiaoli Yan
- Laboratory of Immunology and Pathogen Biology, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Kaijun Zhao
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
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Al-Rawi NH, Hachim IY, Hachim MY, Salmeh A, Uthman AT, Marei H. Anatomical landscape of oral squamous cell carcinoma: A single cancer center study in UAE. Heliyon 2023; 9:e15884. [PMID: 37206025 PMCID: PMC10189390 DOI: 10.1016/j.heliyon.2023.e15884] [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: 12/30/2022] [Revised: 03/12/2023] [Accepted: 04/25/2023] [Indexed: 05/21/2023] Open
Abstract
Objectives This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma using the Cancer Genome Atlas's cBioPortal database (http://cbioportal.org). Material and methods Histological examination of all hematoxylin and eosin-stained slides and assessment of all demographic and clinical information from laboratory records were performed on all OSCC diagnosed between 2005 and 2018. Results Males made up 71.4% of the sample of 231 OSCCs that were evaluated. The patients' average age was 55.38 years. The two most prevalent afflicted sites were the anterior two-thirds of the tongue (57.6%) and the cheek (28.1%). The most prevalent site among smokers were the floor of mouth, cheek, and jaw bones. There was a link between tumor size and numerous anatomical subsites that was shown to be highly significant. OSCC in the FOM was associated with a 25% mortality rate. Patients with OSCC of the anterior tongue and cheek had the best prognosis, with only 15.7% and 15.3% of patients dying during follow-up. Conclusion The present investigation found a correlation between the diverse clinicopathological characteristics of the various anatomical subsites in OSCC. Different anatomical subsites also displayed varying degrees of gene mutation.
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Affiliation(s)
- Natheer H. Al-Rawi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Dental Medicine, University of Sharjah, United Arab Emirates
- Corresponding author. Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
| | - Ibrahim Y. Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mahmood Y. Hachim
- College of Medicine, Mohammed bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Asmaa T. Uthman
- College of Dentistry, Gulf Medical University, Ajman, United Arab Emirates
| | - Hesham Marei
- College of Dentistry, Gulf Medical University, Ajman, United Arab Emirates
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Tous C, Muñoz-Redondo C, Bravo-Gil N, Gavilan A, Fernández RM, Antiñolo J, Navarro-González E, Antiñolo G, Borrego S. Identification of Novel Candidate Genes for Familial Thyroid Cancer by Whole Exome Sequencing. Int J Mol Sci 2023; 24:ijms24097843. [PMID: 37175550 PMCID: PMC10178269 DOI: 10.3390/ijms24097843] [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: 03/31/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Thyroid carcinoma (TC) can be classified as medullary (MTC) and non-medullary (NMTC). While most TCs are sporadic, familial forms of MTC and NMTC also exist (less than 1% and 3-9% of all TC cases, respectively). Germline mutations in RET are found in more than 95% of familial MTC, whereas familial NMTC shows a high degree of genetic heterogeneity. Herein, we aimed to identify susceptibility genes for familial NMTC and non-RET MTC by whole exome sequencing in 58 individuals belonging to 18 Spanish families with these carcinomas. After data analysis, 53 rare candidate segregating variants were identified in 12 of the families, 7 of them located in previously TC-associated genes. Although no common mutated genes were detected, biological processes regulating functions such as cell proliferation, differentiation, survival and adhesion were enriched. The reported functions of the identified genes together with pathogenicity and structural predictions, reinforced the candidacy of 36 of them, suggesting new loci related to TC and novel genotype-phenotype correlations. Therefore, our strategy provides clues to possible molecular mechanisms underlying familial forms of MTC and NMTC. These new molecular findings and clinical data of patients may be helpful for the early detection, development of tailored therapies and optimizing patient management.
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Affiliation(s)
- Cristina Tous
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Carmen Muñoz-Redondo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Angela Gavilan
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Juan Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Elena Navarro-González
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
- Department of Endocrinology and Nutrition, University Hospital Virgen del Rocío, 41013 Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
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Zheng T, Zhou H, Zheng Z, Guo Y, Liu J, Zhang J, Li S. The pathological significance and potential mechanism of ARHGEF6 in lung adenocarcinoma. Comput Biol Med 2023; 158:106894. [PMID: 37058762 DOI: 10.1016/j.compbiomed.2023.106894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/19/2023] [Accepted: 04/09/2023] [Indexed: 04/16/2023]
Abstract
BACKGROUND Emerging evidences suggest that ARHGEF6 is involved in cancers but the exact significance and underlying mechanism are unclear. This study aimed to elucidate the pathological significance and potential mechanism of ARHGEF6 in lung adenocarcinoma (LUAD). METHODS Bioinformatics and experimental methods were used to analyze the expression, the clinical significance, the cellular function and potential mechanisms of ARHGEF6 in LUAD. RESULTS ARHGEF6 was downregulated in LUAD tumor tissues and correlated negatively with poor prognosis and tumor stemness, positively with the Stromal score, the Immune score and the ESTIMATE score. The expression level of ARHGEF6 was also associated with drug sensitivity, the abundance of immune cells, the expression levels of Immune checkpoint genes and immunotherapy response. Mast cells, T cells and NK cells were the first three cells with the highest expression of ARHGEF6 in LUAD tissues. Overexpression of ARHGEF6 reduced proliferation and migration of LUAD cells and the growth of xenografted tumors, which could be reversed by re-knockdown of ARHGEF6. Results of RNA sequencing revealed that ARHGEF6 overexpression induced significant changes in the expression profile of LUAD cells, and genes encoding uridine 5'-diphosphate-glucuronic acid transferases (UGTs) and extracellular matrix (ECM) components were downregulated. CONCLUSIONS ARHGEF6 functions as a tumor suppressor in LUAD and may serve as a new prognostic marker and potential therapeutic target. Regulating tumor microenvironment and immunity, inhibiting the expression of UGTs and ECM components in the cancer cells, and decreasing the stemness of the tumors may among the mechanisms underlying the function of ARHGEF6 in LUAD.
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Affiliation(s)
- Tiaozhan Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Hanxi Zhou
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Zhiwen Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Yiqing Guo
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Junfei Liu
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Jingmin Zhang
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Shikang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China.
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Wang Q, Zhang W, Guo Y, Shi F, Li Y, Kong Y, Lyu J, Wang S. A mutational signature and significantly mutated driver genes associated with immune checkpoint inhibitor response across multiple cancers. Int Immunopharmacol 2023; 116:109821. [PMID: 36753986 DOI: 10.1016/j.intimp.2023.109821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/08/2023]
Abstract
Immune checkpoint inhibitor (ICI) treatments dramatically prolong the survival outcomes of several advanced cancers. However, as multiple studies reported, only a subset of patients could benefit from the ICI treatment. In this study, we aim to uncover novel molecular biomarkers predictive of immunotherapy efficacy across multiple cancers. Pre-treatment somatic mutational profiles and immunotherapy clinical information were obtained from 1097 samples of multiple cancers, including melanoma, non-small cell lung cancer (NSCLC), clear cell renal cell carcinoma (ccRCC), bladder carcinoma (BLCA), and head and neck squamous cell carcinoma (HNSCC). Mutational signatures, molecular subtypes, and significantly mutated genes (SMGs) were determined, and their connections with ICI response and outcome were also evaluated. We extracted a total of six mutational signatures across all samples. Among, a mutational signature featured by T > C substitutions was identified to associate with an ICI resistance. A molecular subtype determined based on mutational activities was connected with a significantly improved ICI response rate and outcome. Totaling 50 SMGs were identified, and we observed that patients with COL11A1 or COL4A6 mutations exhibited a superior ICI treatment efficacy than those without such mutations. In this study, we uncovered several novel molecular determinants of cancer immunotherapy response under a multiple-cancer setting, which provides clues for enrolling patients to receive immunotherapy and customizing personalized treatment strategies.
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Affiliation(s)
- Qinghua Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China.
| | - Wenjing Zhang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuxian Guo
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Fuyan Shi
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yuting Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yujia Kong
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Juncheng Lyu
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
| | - Suzhen Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, Shandong 261053, China
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11
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The involvement of collagen family genes in tumor enlargement of gastric cancer. Sci Rep 2023; 13:100. [PMID: 36596829 PMCID: PMC9810739 DOI: 10.1038/s41598-022-25061-0] [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: 01/23/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023] Open
Abstract
Extracellular matrix (ECM) not only serves as a support for tumor cell but also regulates cell-cell or cell-matrix cross-talks. Collagens are the most abundant proteins in ECM. Several studies have found that certain collagen genes were overexpressed in gastric cancer (GC) tissues and might serve as potential biomarkers and therapeutic targets in GC patients. However, the expression patterns of all collagen family genes in GC tissue and their functions are still not clear. With RNA sequencing (RNA-Seq) data, microarray data, and corresponding clinical data obtained from TCGA, GTEx, and GEO databases, bioinformatics analyses were performed to investigate the correlation between the expression patterns of collagen family genes and GC progression. We found that quite many of the collagen family genes were overexpressed in GC tissues. The increase in mRNA expression of most of these overexpressed collagen genes happened between T1 and T2 stage, which indicates the significance of collagens in tumor enlargement of GC. Notably, the mRNA expressions of these differentially expressed collagens genes were highly positively correlated. The elevated expression of a large number of collagen genes in early T stage might greatly change the composition and structure organization of ECM, contributing to ECM remodeling in GC progression.
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12
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MALDI-MSI: A Powerful Approach to Understand Primary Pancreatic Ductal Adenocarcinoma and Metastases. Molecules 2022; 27:molecules27154811. [PMID: 35956764 PMCID: PMC9369872 DOI: 10.3390/molecules27154811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer-related deaths are very commonly attributed to complications from metastases to neighboring as well as distant organs. Dissociate response in the treatment of pancreatic adenocarcinoma is one of the main causes of low treatment success and low survival rates. This behavior could not be explained by transcriptomics or genomics; however, differences in the composition at the protein level could be observed. We have characterized the proteomic composition of primary pancreatic adenocarcinoma and distant metastasis directly in human tissue samples, utilizing mass spectrometry imaging. The mass spectrometry data was used to train and validate machine learning models that could distinguish both tissue entities with an accuracy above 90%. Model validation on samples from another collection yielded a correct classification of both entities. Tentative identification of the discriminative molecular features showed that collagen fragments (COL1A1, COL1A2, and COL3A1) play a fundamental role in tumor development. From the analysis of the receiver operating characteristic, we could further advance some potential targets, such as histone and histone variations, that could provide a better understanding of tumor development, and consequently, more effective treatments.
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13
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Zeng Z, Zuo Y, Jin Y, Peng Y, Zhu X. Identification of Extracellular Matrix Signatures as Novel Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2022; 13:872380. [PMID: 35711936 PMCID: PMC9197387 DOI: 10.3389/fgene.2022.872380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/03/2022] [Indexed: 02/05/2023] Open
Abstract
The extracellular matrix (ECM) is vital to normal cellular function and has emerged as a key factor in cancer initiation and metastasis. However, the prognostic and oncological values of ECM organization-related genes have not been comprehensively explored in lung adenocarcinoma (LUAD) patients. In this study, we included LUAD samples from The Cancer Genome Atlas (TCGA, training set) and other three validation sets (GSE87340, GSE140343 and GSE115002), then we constructed a three-gene prognostic signature based on ECM organization-related genes. The prognostic signature involving COL4A6, FGA and FSCN1 was powerful and robust in both the training and validation datasets. We further constructed a composite prognostic nomogram to facilitate clinical practice by integrating an ECM organization-related signature with clinical characteristics, including age and TNM stage. Patients with higher risk scores were characterized by proliferation, metastasis and immune hallmarks. It is worth noting that high-risk group showed higher fibroblast infiltration in tumor tissue. Accordingly, factors (IGFBP5, CLCF1 and IL6) reported to be secreted by cancer-associated fibroblasts (CAFs) showed higher expression level in the high-risk group. Our findings highlight the prognostic value of the ECM organization signature in LUAD and provide insights into the specific clinical and molecular features underlying the ECM organization-related signature, which may be important for patient treatment.
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Affiliation(s)
- Zhen Zeng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaofeng Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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