1
|
Ma Q, Gao J, Hui Y, Zhang ZM, Qiao YJ, Yang BF, Gong T, Zhao DM, Huang BR. Single-cell RNA-sequencing and genome-wide Mendelian randomisation along with abundant machine learning methods identify a novel B cells signature in gastric cancer. Discov Oncol 2025; 16:11. [PMID: 39760915 PMCID: PMC11703799 DOI: 10.1007/s12672-025-01759-1] [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: 10/28/2024] [Accepted: 01/02/2025] [Indexed: 01/07/2025] Open
Abstract
BACKGROUND Gastric cancer (GC) has a poor prognosis, considerable cellular heterogeneity, and ranks fifth among malignant tumours. Understanding the tumour microenvironment (TME) and intra-tumor heterogeneity (ITH) may lead to the development of novel GC treatments. METHODS The single-cell RNA sequencing (scRNA-seq) dataset was obtained from the Gene Expression Omnibus (GEO) database, where diverse immune cells were isolated and re-annotated based on cell markers established in the original study to ascertain their individual characteristics. We conducted a weighted gene co-expression network analysis (WGCNA) to identify genes with a significant correlation to GC. Utilising bulk RNA sequencing data, we employed machine learning integration methods to train specific biomarkers for the development of novel diagnostic combinations. A two-sample Mendelian randomisation study was performed to investigate the causal effect of biomarkers on gastric cancer (GC). Ultimately, we utilised the DSigDB database to acquire associations between signature genes and pharmaceuticals. RESULTS The 18 genes that made up the signature were as follows: ZFAND2A, PBX4, RAMP2, NNMT, RNASE1, CD93, CDH5, NFKBIE, VWF, DAB2, FAAH2, VAT1, MRAS, TSPAN4, EPAS1, AFAP1L1, DNM3. Patients were categorised into high-risk and low-risk groups according to their risk scores. Individuals in the high-risk cohort exhibited a dismal outlook. The Mendelian randomisation study demonstrated that individuals with a genetic predisposition for elevated NFKBIE levels exhibited a heightened likelihood of acquiring GC. Molecular docking indicates that gemcitabine and chloropyramine may serve as effective therapeutics against NFKBIE. CONCLUSIONS We developed and validated a signature utilising scRNA-seq and bulk sequencing data from gastric cancer patients. NFKBIE may function as a novel biomarker and therapeutic target for GC.
Collapse
Affiliation(s)
- Qi Ma
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Jie Gao
- Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Yuan Hui
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Zhi-Ming Zhang
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Yu-Jie Qiao
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Bin-Feng Yang
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Ting Gong
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Duo-Ming Zhao
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China
| | - Bang-Rong Huang
- Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730050, China.
| |
Collapse
|
2
|
Zeng X, Shapaer T, Tian J, Abudoukelimu A, Zhao Z, Shayimu P, Ma B. Identifying a CD8T cell signature in the tumor microenvironment to forecast gastric cancer outcomes from sequencing data. J Gastrointest Oncol 2024; 15:2067-2078. [PMID: 39554559 PMCID: PMC11565103 DOI: 10.21037/jgo-24-603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 10/14/2024] [Indexed: 11/19/2024] Open
Abstract
Background The tumor microenvironment (TME) could be critical in carcinogenesis, immune evasion, and treatment response. TME-related genes are limited in their ability to predict gastric cancer (GC) outcomes. We utilized data from The Cancer Genome Atlas (TCGA) to investigate the functional roles of TME-related genes in GC. Methods We acquired single-cell data, bulk sequencing data, and clinical characteristics of GC patients from the TCGA database. The CD8T cell genes associated with the TME were selected for bioinformatic analysis in GC. Tumor classification of GC was established through consistent cluster analysis. We then evaluated the prognosis and immune cell infiltration in connection with a CD8T cell-related model for GC. Results The single-cell messenger RNA (mRNA) sequencing (scRNA-Seq) dataset of GSE134520 was utilized to investigate the pathogenesis and disease-specific cell types in GC. Interestingly, compared to healthy tissue, the proportions of CD8Tex cells, malignant cells, and gland mucous increased in GC, whereas the proportion of pit mucous decreased in GC. Since CD8Tex cells may play a vital role in pancreatic adenocarcinoma (PAAD), based on the 612 differentially expressed genes (DEGs) involved in CD8Tex cells, TCGA-GC patients were stratified into low- and high-risk groups. The downregulated DEGs in the low-risk G1 group were associated with proteoglycans in cancer, the cGMP-PKG signaling pathway, focal adhesion, and cell adhesion molecules (CAMs), whereas the upregulated DEGs were associated with viral protein interaction with cytokine and cytokine receptors, the tumor necrosis factor (TNF) signaling pathway, the interleukin (IL)-17 signaling pathway, and the chemokine signaling pathway. Combined with univariate Cox analysis, we ultimately identified 23 CD8T cell-related prognostic genes: TCIM, AADAC, SLC2A3, ZNF331, TSC22D3, CMTM3, ZFP36, VIM, CLDND1, GABARAPL1, SOCS3, RGS1, TCEAL9, RGS2, CD59, SPRY1, EMP3, ZEB2, PDE4B, GLIPR1, ERRFI1, and LBH. Using the Cox regression model to prioritize the 23 CD8T cell-related genes, we finally selected 7 genes: CXCR4, AADAC, SLC2A3, CMTM3, RGS2, CD59, and ZEB2. Conclusions CD8T cell-related genes have a strong association with tumor classification and immune response in GC patients. A CD8T cell-related signature demonstrated robust prognostic predictive performance for GC. Our findings may reveal novel insights into the diagnosis and treatment of GC.
Collapse
Affiliation(s)
- Xiangyue Zeng
- Gastrointestinal Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| | - Tiannake Shapaer
- Gastrointestinal Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| | - Jianguo Tian
- General Surgery Department, Emin County People’s Hospital in Tacheng District, Urumqi, China
| | - Abulajiang Abudoukelimu
- Gastrointestinal Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| | - Zeliang Zhao
- Gastrointestinal Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| | - Paerhati Shayimu
- Gastrointestinal Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| | - Binlin Ma
- Department of Breast and Thyroid Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Xinjiang Medical University, Urumqi, China
| |
Collapse
|
3
|
Gong T, Liu X, Li Q, Branch DR, Loriamini M, Wen W, Shi Y, Tan Q, Fan B, Zhou Z, Li Y, Yang C, Li S, Duan X, Chen L. Oncolytic Virus Senecavirus A Inhibits Hepatocellular Carcinoma Proliferation and Growth by Inducing Cell Cycle Arrest and Apoptosis. J Clin Transl Hepatol 2024; 12:713-725. [PMID: 39130624 PMCID: PMC11310753 DOI: 10.14218/jcth.2024.00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 08/13/2024] Open
Abstract
Background and Aims Hepatocellular carcinoma (HCC) is a highly aggressive tumor with limited treatment options and high mortality. Senecavirus A (SVA) has shown potential in selectively targeting tumors while sparing healthy tissues. This study aimed to investigate the effects of SVA on HCC cells in vitro and in vivo and to elucidate its mechanisms of action. Methods The cell counting kit-8 assay and colony formation assay were conducted to examine cell proliferation. Flow cytometry and nuclear staining were employed to analyze cell cycle distribution and apoptosis occurrence. A subcutaneous tumor xenograft HCC mouse model was created in vivo using HepG2 cells, and Ki67 expression in the tumor tissues was assessed. The terminal deoxynucleotidyl transferase dUTP nick end labeling assay and hematoxylin and eosin staining were employed to evaluate HCC apoptosis and the toxicity of SVA on mouse organs. Results In vitro, SVA effectively suppressed the growth of tumor cells by inducing apoptosis and cell cycle arrest. However, it did not have a notable effect on normal hepatocytes (MIHA cells). In an in vivo setting, SVA effectively suppressed the growth of HCC in a mouse model. SVA treatment resulted in a significant decrease in Ki67 expression and an increase in apoptosis of tumor cells. No notable histopathological alterations were observed in the organs of mice during SVA administration. Conclusions SVA inhibits the growth of HCC cells by inducing cell cycle arrest and apoptosis. It does not cause any noticeable toxicity to vital organs.
Collapse
Affiliation(s)
- Tao Gong
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Xiao Liu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qingyuan Li
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Donald R. Branch
- Departments of Medicine and Laboratory Medicine and Pathobiology, Centre for Innovation, Canadian Blood Services, Hamilton, Ontario, Canada
| | - Melika Loriamini
- Departments of Medicine and Laboratory Medicine and Pathobiology, Centre for Innovation, Canadian Blood Services, Hamilton, Ontario, Canada
| | - Wenxian Wen
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Yaoqiang Shi
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Qi Tan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Bin Fan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Zhonghui Zhou
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yujia Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Chunhui Yang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan, China
- The Hospital of Xidian Group, Xi’an, Shaanxi, China
- The Joint-Laboratory on Transfusion-Transmitted Diseases (TTDs) between Institute of Blood Transfusion and Nanning Blood Center, Nanning Blood Center, Nanning, Guangxi, China
| |
Collapse
|
4
|
Bintintan V, Burz C, Pintea I, Muntean A, Deleanu D, Lupan I, Samasca G. Predictive Factors of Immunotherapy in Gastric Cancer: A 2024 Update. Diagnostics (Basel) 2024; 14:1247. [PMID: 38928662 PMCID: PMC11202567 DOI: 10.3390/diagnostics14121247] [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: 05/24/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Many studies on gastric cancer treatment have identified predictors of immunotherapy benefits. This article provides an update on the major developments in research related to predictive factors of immunotherapy for gastric cancer. We used the search term "predictive factors, immunotherapy, gastric cancer" to find the most current publications in the PubMed database related to predictive factors of immunotherapy in gastric cancer. Programmed cell death, genetic, and immunological factors are the main study topics of immunotherapy's predictive factors in gastric cancer. Other preventive factors for immunotherapy in gastric cancer were also found, including clinical factors, tumor microenvironment factors, imaging factors, and extracellular factors. Since there is currently no effective treatment for gastric cancer, we strongly propose that these studies be prioritized.
Collapse
Affiliation(s)
- Vasile Bintintan
- Department of Surgery 1, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania;
| | - Claudia Burz
- Institute of Oncology, “Prof. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
- Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (I.P.); (A.M.); (D.D.)
| | - Irena Pintea
- Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (I.P.); (A.M.); (D.D.)
| | - Adriana Muntean
- Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (I.P.); (A.M.); (D.D.)
| | - Diana Deleanu
- Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (I.P.); (A.M.); (D.D.)
| | - Iulia Lupan
- Department of Molecular Biology, Babes-Bolyai University, 400084 Cluj-Napoca, Romania;
| | - Gabriel Samasca
- Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (I.P.); (A.M.); (D.D.)
| |
Collapse
|
5
|
Li J, Chen G, Luo Y, Xu J, He J. The molecular subtypes and clinical prognosis characteristic of tertiary lymphoid structures-related gene of cutaneous melanoma. Sci Rep 2023; 13:23097. [PMID: 38155221 PMCID: PMC10754817 DOI: 10.1038/s41598-023-50327-6] [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: 08/28/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Despite the remarkable efficacy of PD-1-associated immune checkpoint inhibitors in treating cutaneous melanoma (CM), the inconsistency in the expression of PD-1 and its ligand PD-L1, and resulting variability in the effectiveness of immunotherapy, present significant challenges for clinical application. Therefore, further research is necessary to identify tumor-related biomarkers that can predict the prognosis of immunotherapy. Tertiary lymphoid structures (TLSs) have been recognized as a crucial factor in predicting the response of immune checkpoint inhibitors in solid tumors, including CM. However, the study of TLSs in CM is not yet comprehensive. Gene expression profiles have been shown to correlate with CM risk stratification and patient outcomes. In this study, we identified TLS-related genes that can be used for prognostic purposes and developed a corresponding risk model. The impact of TLS-related genes on clinicopathological characteristics, immune infiltration and drug susceptibility was also explored. Our biological function enrichment analysis provided preliminary evidence of related signaling pathways. Our findings provide a new perspective on risk stratification and individualized precision therapy for CM.
Collapse
Affiliation(s)
- Juan Li
- Chongqing Academy of Chinese Materia Medica, Chongqing, People's Republic of China
- Chonging College of Traditional Chinese Medicine, Bishan District, 61 Puguoba Road, Bicheng Street, Chongqing, 402760, People's Republic of China
| | - Gang Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, People's Republic of China
| | - Yang Luo
- Chongqing Academy of Chinese Materia Medica, Chongqing, People's Republic of China
| | - Jin Xu
- Chongqing Academy of Chinese Materia Medica, Chongqing, People's Republic of China
| | - Jun He
- Chonging College of Traditional Chinese Medicine, Bishan District, 61 Puguoba Road, Bicheng Street, Chongqing, 402760, People's Republic of China.
| |
Collapse
|