1
|
Liu C, Han X, Zhang S, Huang M, Guo B, Zhao Z, Yang S, Jin J, Pu W, Yu H. The role of NCAPH in cancer treatment. Cell Signal 2024; 121:111262. [PMID: 38901722 DOI: 10.1016/j.cellsig.2024.111262] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Many solid tumors frequently overexpress Non-SMC Condensin I Complex Subunit H (NCAPH), and new studies suggest that NCAPH may be a target gene for clinical cancer therapy. Numerous investigations have shown that a variety of transcription factors, including as MYBL2, FOXP3, GATA3, and OTC1, can stimulate the transcription of NCAPH. Additionally, NCAPH stimulates many oncogenic signaling pathways, such as β-Catenin/PD-L1, PI3K/AKT/SGK3, MEK/ERK, AURKB/AKT/mTOR, PI3K/PDK1/AKT, and Chk1/Chk2. Tumor immune microenvironment modification and tumor growth, apoptosis, metastasis, stemness, and treatment resistance all depend on these signals. NCAPH has the ability to form complexes with other proteins that are involved in glycolysis, DNA damage repair, and chromatin remodeling. This review indicates that NCAPH expression in most malignant tumors is associated with poor prognosis and low recurrence-free survival.
Collapse
Affiliation(s)
- Caiyan Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiao Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Siqi Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Manru Huang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bin Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zixuan Zhao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shenshen Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jun Jin
- International Education College, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Weiling Pu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Haiyang Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| |
Collapse
|
2
|
Qian Z, Wu F, Feng G, Lin W, Cai X, Wu J, Ke K, Ye Z, Xu G. A prognostic risk model based on lactate metabolism and transport-related lncRNAs for gastric adenocarcinoma. Biomarkers 2024; 29:211-221. [PMID: 38629165 DOI: 10.1080/1354750x.2024.2341411] [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: 09/17/2023] [Accepted: 04/04/2024] [Indexed: 05/15/2024]
Abstract
BACKGROUND Increased lactate levels and metastasis in tumours are strongly associated with dismal outcomes. But prognostic value of lactate metabolism and transport-related lncRNAs in gastric adenocarcinoma (GA) patients remains unaddressed. METHODS Gene expression data of GA were provided by The Cancer Genome Atlas. Lactate metabolism and transport-related gene data were accessed from GSEA. LncRNAs related to lactate metabolism and transport were identified by correlation analysis. A prognostic model was built by regression analysis. Validity of prognostic model was confirmed through survival analysis and receiver operating characteristic (ROC) curve. Immunity of each risk group was evaluated by immune correlation analysis .LncRNA-mRNA network was built by correlation analysis using Cytoscape software. RESULTS A 12-gene prognostic model based on lactate metabolism and transport-related lncRNAs was built in GA. Median riskscore was utilized to classify GA samples into high- and low-risk groups. Survival analysis and ROC curves demonstrated validity of prognostic model. Most immune checkpoint molecules and TIDE scores were lower in the low-risk group. LINC01303 and LINC01545 may be the key prognostic factors in patients with GA. CONCLUSION This study successfully built a prognostic model of lactate metabolism and transport-related lncRNAs in GA. The findings guide prognostic management of GA patients.
Collapse
Affiliation(s)
- Zhenyuan Qian
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Fang Wu
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Guoqing Feng
- Department of General Surgery, Haining Traditional Chinese Medicine Hospital, Haining, Jiaxing, Zhejiang, China
| | - Wenfa Lin
- Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Xufan Cai
- Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Jianzhang Wu
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Kun Ke
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zaiyuan Ye
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Guoxi Xu
- Department of Gastrointestinal Surgery, Jinjiang Municipal Hospital, Jinjiang, Quanzhou, Fujian, China
| |
Collapse
|
3
|
Li R, Wang D, Yang H, Pu L, Li X, Yang F, Zhu R. Important role and underlying mechanism of non‑SMC condensin I complex subunit G in tumours (Review). Oncol Rep 2024; 51:77. [PMID: 38639175 DOI: 10.3892/or.2024.8736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
At present, the incidence of tumours is increasing on a yearly basis, and tumourigenesis is usually associated with chromosomal instability and cell cycle dysregulation. Moreover, abnormalities in the chromosomal structure often lead to DNA damage, further exacerbating gene mutations and chromosomal rearrangements. However, the non‑SMC condensin I complex subunit G (NCAPG) of the structural maintenance of chromosomes family is known to exert a key role in tumour development. It has been shown that high expression of NCAPG is closely associated with tumour development and progression. Overexpression of NCAPG variously affects chromosome condensation and segregation during cell mitosis, influences cell cycle regulation, promotes tumour cell proliferation and invasion, and inhibits apoptosis. In addition, NCAPG has been associated with tumour cell stemness, tumour resistance and recurrence. The aim of the present review was to explore the underlying mechanisms of NCAPG during tumour development, with a view towards providing novel targets and strategies for tumour therapy, and through the elucidation of the mechanisms involved, to lay the foundation for future developments in health.
Collapse
Affiliation(s)
- Ruobing Li
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Dechun Wang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Hong Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Leilei Pu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Xiaohong Li
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Fumei Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Rong Zhu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| |
Collapse
|
4
|
Song J, Chen J, Chen Y, Wang Y, Zheng L, Yu H, Chen C. Colorectal cancer subtyping and prognostic model construction based on interleukin-related genes. Physiol Genomics 2024; 56:367-383. [PMID: 38073490 DOI: 10.1152/physiolgenomics.00099.2023] [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: 08/29/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 04/20/2024] Open
Abstract
Members of the interleukin (IL) family are closely linked to cancer development and progression. However, research on the prognosis of colorectal cancer (CRC) related to IL is still lacking. This study investigated new CRC prognostic markers and offered new insights for CRC prognosis and treatment. CRC-related data and IL gene data were collected from public databases. Sample clustering was done with the NMF package to divide samples into different subtypes. Differential, enrichment, survival, and immune analyses were conducted on subtypes. A prognostic model was constructed using regression analysis. Drug sensitivity analysis was performed using GDSC database. Western blot analysis was performed to assess the effect of IL-7 on the JAK/STAT signaling pathway. Flow cytometry was used to examine the impact of IL-7 on CD8+ T cell apoptosis. Two CRC subtypes based on IL-associated genes were obtained. Cluster 1 had a higher survival rate than cluster 2, and they showed differences in some immune levels. The two clusters were mainly enriched in the JAK-STAT signaling pathway, T helper 17 cell differentiation, and the IL-17 signaling pathway. An 11-gene signature was built, and risk score was an independent prognosticator for CRC. The low-risk group showed a higher sensitivity to nine common targeted anticancer drugs. Western blot and flow cytometry results demonstrated that IL-7 could phosphorylate STAT5 and promote survival of CD8+ T cells. In conclusion, this study divided CRC samples into two IL-associated subtypes and obtained an 11-gene signature. In addition, targeted drugs that may improve the prognosis of patients with CRC were identified. These findings are of paramount importance for patient prognosis and CRC treatment.NEW & NOTEWORTHY We identified two clusters with significant survival differences in colorectal cancer (CRC) based on interleukin-related genes, constructed an 11-gene risk score model that can independently predict the prognosis of CRC, and explored some targeted drugs that may improve the prognosis of patients with CRC. The results of this study have important implications for the prognosis and treatment of CRC.
Collapse
Affiliation(s)
- Jintian Song
- Department of Abdominal Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Jianbin Chen
- Department of Oncology and Vascular Interventional Therapy, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Yigui Chen
- Department of Abdominal Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Yi Wang
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Liang Zheng
- Department of Abdominal Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Hui Yu
- Department of Pharmacy, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Changjiang Chen
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, People's Republic of China
| |
Collapse
|
5
|
Wu W, Huang T, Li S, Gong G, Zhao D, Qiu Y. Subtyping and prognostic model construction based on vesicle-mediated transport-related genes in colorectal cancer. Hum Mol Genet 2024; 33:478-490. [PMID: 37971354 DOI: 10.1093/hmg/ddad197] [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: 09/18/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is impacted by various environmental and genetic variables. Dysregulation of vesicle-mediated transport-related genes (VMTRGs) has been observed in many malignancies, but their effect on prognosis in CRC remains unclear. METHODS CRC samples were clustered into varying subtypes per differential expression of VMTRGs. R package was utilized to explore differences in survival, immune, and drug sensitivity among different disease subtypes. According to differentially expressed genes (DEGs) between subtypes, regression analysis was employed to build a riskscore model and identify independent prognostic factors. The model was validated through a Gene Expression Omnibus (GEO) dataset. Immune landscape, immunophenoscore (IPS), and Tumor Immune Dysfunction and Exclusion (TIDE) scores for different risk groups were calculated. RESULTS Two subtypes of CRC were identified based on VMTRGs, which showed significant differences in survival rates, immune cell infiltration abundance, immune functional activation levels, and immune checkpoint expression levels. Cluster2 exhibited higher sensitivity to anti-tumor drugs such as Nilotinib, Cisplatin, and Oxaliplatin compared to Cluster1. DEGs were mainly enriched in biological processes such as epidermis development, epidermal cell differentiation, and receptor-ligand activity, and signaling pathways like pancreatic secretion. The constructed 13-gene riskscore model demonstrated good predictive ability for CRC patients' prognosis. Furthermore, differences in immune landscape, IPS, and TIDE scores were observed among different risk groups. CONCLUSION This study successfully obtained two CRC subtypes with distinct survival statuses and immune levels based on differential expression of VMTRGs. A 13-gene risk model was constructed. The findings had important implications for prognosis and treatment of CRC.
Collapse
Affiliation(s)
- Wei Wu
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| | - Tong Huang
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| | - Shengwen Li
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| | - Guangwei Gong
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| | - Dan Zhao
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| | - Yue Qiu
- Department of General Surgery, The Central Hospital of Xiaogan, 6 Guangchang Road, Xiaogan City, Hubei Province 432000, China
| |
Collapse
|
6
|
Limbu S, McCloskey KE. Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma. PLoS One 2023; 18:e0294171. [PMID: 37948380 PMCID: PMC10637681 DOI: 10.1371/journal.pone.0294171] [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: 02/27/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
Lung cancer makes up one-fourth of all cancer-related mortality with the highest mortality rate among all cancers. Despite recent scientific advancements in cancer therapeutics, the 5-year survival rate of lung adenocarcinoma (LUAD) cancer patients remains below 15 percent. It has been suggested that the high mortality rate of LUAD is linked to the acquisition of progenitor-like cells with stem-like characteristics that assist the whole tumor in regulating immune cell infiltration. To examine this hypothesis further, this study mined several databases to explore the presence of stemness-related genes and miRNAs in LUAD cancers. We examine their association with immune and accessory cell infiltration rates and patient survival. We found 3 stem cell-related genes, ORC1L, KIF20A, and DLGAP5, present in LUAD that also correlate with changes in immune infiltration rates and reduced patient survival rates. Additionally, the modulation in myeloid-derived suppressor cell (MDSC) infiltration and miRNA hsa-mir-1247-3p mediated targeting of tumor suppressor SLC24A4 and oncogenes RAB3B and HJURP appears to primarily regulate LUAD patient survival. Given these findings, hsa-mir-1247-3p and/or its associated gene targets may offer a promising avenue to enhance patient survivability.
Collapse
Affiliation(s)
- Shiwani Limbu
- Quantitative and System Biology Program, University of California, Merced, Merced, CA, United States of America
| | - Kara E. McCloskey
- Quantitative and System Biology Program, University of California, Merced, Merced, CA, United States of America
- Materials Science and Engineering Department, University of California, Merced, Merced, CA, United States of America
| |
Collapse
|
7
|
Guo Q, Huang Y, Zhan X. Hepatocellular Carcinoma Subtyping and Prognostic Model Construction Based on Chemokine-Related Genes. Med Princ Pract 2023; 32:332-342. [PMID: 37848003 PMCID: PMC10727522 DOI: 10.1159/000534537] [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: 06/06/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Chemokines not only regulate immune cells but also play significant roles in development and treatment of tumors and patient prognoses. However, these effects have not been fully explained in hepatocellular carcinoma (HCC). MATERIALS AND METHODS We conducted a clustering analysis of chemokine-related genes. We then examined the differences in survival rates and analyzed immune levels using single-sample Gene Set Enrichment Analysis (ssGSEA) for each subtype. Based on chemokine-related genes of different subtypes, we built a prognostic model in The Cancer Genome Atlas (TCGA) dataset using the survival package and glmnet package and validated it in the Gene Expression Omnibus (GEO) dataset. We used univariate and multivariate regression analyses to select independent prognostic factors and used R package rms to draw a nomogram reflecting patient survival rates at 1, 3, and 5 years. RESULTS We identified two chemokine subtypes and, after screening, found that Cluster1 had higher survival rates than Cluster2. In addition, in terms of immune evaluation, stromal evaluation, ESTIMATE evaluation, immune abundance, immune function, and expressions of various immune checkpoints, immune levels of Cluster1 were significantly better than those of Cluster2. The immunophenoscore (IPS) of HCC patients in Cluster1 was significantly higher than that in Cluster2. Furthermore, we established a prognostic model consisting of 9 genes, which correlated with chemokines. Through testing, Riskscore was revealed as an independent prognostic factor, and the model could effectively predict HCC patients' prognoses in both TCGA and GEO datasets. CONCLUSION This study resulted in the development of a novel prognostic model related to chemokine genes, providing new targets and theoretical support for HCC patients.
Collapse
Affiliation(s)
- Qiusheng Guo
- Department of Medical Oncology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China,
| | - Yangyang Huang
- Pharmacy Department, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, China
| | - Xiaoan Zhan
- Department of Oncology Surgery, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, China
| |
Collapse
|
8
|
Ishikawa A, Yasumatsu R, Fukui T, Kido A, Katsuya N, Sentani K, Kuraoka K, Oue N, Suzuki T, Oka S, Kotachi T, Tanabe K, Ohdan H, Ashktorab H, Smoot D, Yasui W. Kinesin Family Member B18 Is Related to Gastric Mucin Phenotype and Contributes to Gastric Cancer Progression by Regulating Epithelial-Mesenchymal Transition. Oncology 2023; 102:354-365. [PMID: 37812924 DOI: 10.1159/000533791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/08/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Gastric cancer (GC) remains a common health concern worldwide and is the third leading cause of death in Japan. It can be broadly classified into gastric and intestinal mucin phenotypes using immunohistochemistry. We previously reported numerous associations of kinesin family member (KIF) genes and mucin phenotypes with GC. However, no previous studies have reported on the importance of KIF18B in GC using immunostaining. Thus, in this study, we investigated the expression and functions of KIF18B, which is highly expressed in gastric mucin phenotype GC. METHODS We performed RNA-seq of gastric and intestinal mucin type GCs, and clinicopathological studies of the KIF18B we found were performed using 96 GC cases. We also performed functional analysis using GC-derived cell lines. RESULT RNA-seq showed the upregulation of matrisome-associated genes in gastric mucin phenotype GC and a high expression of KIF18B. KIF18B was detected in 52 of the 96 GC cases (54%) through immunohistochemistry. Low KIF18B expression was significantly associated with poor overall survival (p < 0.01). Other molecules that were significantly associated with KIF18B were MUC5AC and claudin 18; these were also significantly associated with the gastric mucin phenotype. KIF18B small interfering RNA (siRNA)-transfected GC cells showed greater growth and spheroid colony formation than the negative control siRNA-transfected cells. Furthermore, expression of snail family transcriptional repressor 1 and cadherin 2 was significantly increased and that of cadherin 1 was significantly decreased in KIF18B siRNA-transfected GC cells. CONCLUSION These findings not only suggest that KIF18B may be a useful prognostic marker, but also provide insight into the pathogenesis of the GC phenotype.
Collapse
Affiliation(s)
- Akira Ishikawa
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryo Yasumatsu
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takafumi Fukui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Aya Kido
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Narutaka Katsuya
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuya Kuraoka
- Department of Diagnostic Pathology, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takahisa Suzuki
- Department of Surgery, National Hospital Organization, Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Shiro Oka
- Department of Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takahiro Kotachi
- Department of Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Tanabe
- Department of Perioperative and Critical Care Management, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hideki Ohdan
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University College of Medicine, Washington, District of Columbia, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Medical Corporation Hiroshima Health Association, Hiroshima, Japan
| |
Collapse
|
9
|
Zhou Y, Dai X, Lyu J, Li Y, Bao X, Deng F, Liu K, Cui L, Cheng L. Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs. Medicine (Baltimore) 2022; 101:e31075. [PMID: 36281116 PMCID: PMC9592387 DOI: 10.1097/md.0000000000031075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND To construct and verify a novel prognostic model for thyroid cancer (THCA) based on N7-methylguanosine modification-related lncRNAs (m7G-lncRNAs) and their association with immune cell infiltration. METHODS In this study, we identified m7G-lncRNAs using co-expression analysis and performed differential expression analysis of m7G-lncRNAs between groups. We then constructed a THCA prognostic model, performed survival analysis and risk assessment for the THCA prognostic model, and performed independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, analysis of the regulatory relationship between prognostic differentially expressed m7G-related lncRNAs (PDEm7G-lncRNAs) and mRNAs and correlation analysis of immune cells and risk scores in THCA patients were carried out. RESULTS We identified 29 N7-methylguanosine modification-related mRNAs and 116 differentially expressed m7G-related lncRNAs, including 87 downregulated and 29 upregulated lncRNAs. Next, we obtained 8 PDEm7G-lncRNAs. A final optimized model was constructed consisting of 5 PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, TMEM105, SMG7-AS1 and HMGA2-AS1). Six PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, HMGA2-AS1, LINC01976, MID1IP1-AS1, and SMG7-AS1) had positive regulatory relationships with 10 PDEm7G-mRNAs, while 2 PDEm7G-lncRNAs (LINC02026 and TMEM105) had negative regulatory relationships with 2 PDEm7G-mRNAs. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with THCA. Forest maps and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Finally, we demonstrated a correlation between different immune cells and risk scores. CONCLUSION Our results will help identify high-risk or low-risk patients with THCA and facilitate early prediction and clinical intervention in patients with high risk and poor prognosis.
Collapse
Affiliation(s)
- Yang Zhou
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xuezhong Dai
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jianhong Lyu
- Department of Anesthesiology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yingyue Li
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xueyu Bao
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Fang Deng
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Kun Liu
- Department of Otorhinolaryngology, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Liming Cui
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Li Cheng
- Department of Endocrinology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- * Correspondence: Li Cheng, The Third People’s Hospital of Yunnan Province, 292 Beijing Road, Guandu District, Kunming City, Yunnan Province 650011, China (e-mail: )
| |
Collapse
|
10
|
Yang H, Xiong B, Xiong T, Wang D, Yu W, Liu B, She Q. Identification of key genes and mechanisms of epicardial adipose tissue in patients with diabetes through bioinformatic analysis. Front Cardiovasc Med 2022; 9:927397. [PMID: 36158806 PMCID: PMC9500152 DOI: 10.3389/fcvm.2022.927397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundIn recent years, peri-organ fat has emerged as a diagnostic and therapeutic target in metabolic diseases, including diabetes mellitus. Here, we performed a comprehensive analysis of epicardial adipose tissue (EAT) transcriptome expression differences between diabetic and non-diabetic participants and explored the possible mechanisms using various bioinformatic tools.MethodsRNA-seq datasets GSE108971 and GSE179455 for EAT between diabetic and non-diabetic patients were obtained from the public functional genomics database Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) were identified using the R package DESeq2, then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were analyzed. Next, a PPI (protein–protein interaction) network was constructed, and hub genes were mined using STRING and Cytoscape. Additionally, CIBERSORT was used to analyze the immune cell infiltration, and key transcription factors were predicted based on ChEA3.ResultsBy comparing EAT samples between diabetic and non-diabetic patients, a total of 238 DEGs were identified, including 161 upregulated genes and 77 downregulated genes. A total of 10 genes (IL-1β, CD274, PDCD1, ITGAX, PRDM1, LAG3, TNFRSF18, CCL20, IL1RN, and SPP1) were selected as hub genes. GO and KEGG analysis showed that DEGs were mainly enriched in the inflammatory response and cytokine activity. Immune cell infiltration analysis indicated that macrophage M2 and T cells CD4 memory resting accounted for the largest proportion of these immune cells. CSRNP1, RELB, NFKB2, SNAI1, and FOSB were detected as potential transcription factors.ConclusionComprehensive bioinformatic analysis was used to compare the difference in EAT between diabetic and non-diabetic patients. Several hub genes, transcription factors, and immune cell infiltration were identified. Diabetic EAT is significantly different in the inflammatory response and cytokine activity. These findings may provide new targets for the diagnosis and treatment of diabetes, as well as reduce potential cardiovascular complications in diabetic patients through EAT modification.
Collapse
|
11
|
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
|
12
|
Blocker SJ, Cook J, Everitt JI, Austin WM, Watts TL, Mowery YM. Automated Nuclear Segmentation in Head and Neck Squamous Cell Carcinoma Pathology Reveals Relationships between Cytometric Features and ESTIMATE Stromal and Immune Scores. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1305-1320. [PMID: 35718057 PMCID: PMC9484476 DOI: 10.1016/j.ajpath.2022.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 04/09/2023]
Abstract
The tumor microenvironment (TME) plays an important role in the progression of head and neck squamous cell carcinoma (HNSCC). Currently, pathologic assessment of TME is nonstandardized and subject to observer bias. Genome-wide transcriptomic approaches to understanding the TME, while less subject to bias, are expensive and not currently a part of the standard of care for HNSCC. To identify pathology-based biomarkers that correlate with genomic and transcriptomic signatures of TME in HNSCC, cytometric feature maps were generated in a publicly available data set from a cohort of patients with HNSCC, including whole-slide tissue images and genomic and transcriptomic phenotyping (N = 49). Cytometric feature maps were generated based on whole-slide nuclear detection, using a deep-learning algorithm trained for StarDist nuclear segmentation. Cytometric features in each patient were compared to transcriptomic measurements, including Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data (ESTIMATE) scores and stemness scores. With correction for multiple comparisons, one feature (nuclear circularity) demonstrated a significant linear correlation with ESTIMATE stromal score. Two features (nuclear maximum and minimum diameter) correlated significantly with ESTIMATE immune score. Three features (nuclear solidity, nuclear minimum diameter, and nuclear circularity) correlated significantly with transcriptomic stemness score. This study provides preliminary evidence that observer-independent, automated tissue-slide analysis can provide insights into the HNSCC TME which correlate with genomic and transcriptomic assessments.
Collapse
Affiliation(s)
- Stephanie J Blocker
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina.
| | - James Cook
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina
| | | | - Wyatt M Austin
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina
| | - Tammara L Watts
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Yvonne M Mowery
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, North Carolina; Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| |
Collapse
|
13
|
Li Y, Wang H, Liao L, Tang P, He H, Liu L, Yan J, Peng Q. Systemic Analysis of the Anticancer Effects of Sijunzi Decoction on Gastric Cancer Based on Network Pharmacology. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221109418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objective: Sijunzi decoction (SJZD) has been used for alleviating peptic ulcer or gastric discomfort, and treating spleen disorders since the Song Dynasty, but its pharmacological effect on human gastric cancer (GC) is still unclear. In this research, a network pharmacology-based strategy was applied to explore active ingredients, potential targets, and molecular mechanisms of SJZD against GC. Methods: The active compounds and potential targets of SJZD, as well as GC-associated gene targets, were retrieved from publicly available databases. Bioinformatics approaches were used to assess the network interaction, functional regulation, and signaling pathways between SJZD ingredients and GC targets. The anticancer effects of SJZD against GC were verified in vivo by a mouse subcutaneous model. Results: The results of network analysis showed that quercetin was the most active ingredient in SJZD. Several prominent target genes of SJZD were identified, such as AKT1 and STAT3. Gene ontology analysis revealed that the core anti-GC targets of SJZD included transcription factor activity and kinase activity. Pathway enrichment analysis indicated that GC patients could be benefited from SJZD treatment via modulation of signaling pathways related to endocrine system, cancer, and infectious disease. Furthermore, in vivo experiments showed that high-dose SJZD could inhibit GC xenograft tumor growth, reduce GC cell proliferation, induce GC cell apoptosis, and decrease the expression of p-AKT1 and p-STAT3. Conclusions: Taken together, our results suggest that SJZD can serve as an effective adjuvant therapeutic agent for GC patients.
Collapse
Affiliation(s)
- Yuejun Li
- Department of Oncology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou City, P. R. China
- Department of Oncology, The First Affiliated Hospital of Hunan College of Traditional Chinese Medicine, Zhuzhou City, P. R. China
| | - Hong Wang
- Department of Oncology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou City, P. R. China
- Department of Oncology, The First Affiliated Hospital of Hunan College of Traditional Chinese Medicine, Zhuzhou City, P. R. China
| | - Linli Liao
- Hunan Provincial Key Laboratory for the Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha City, P. R. China
| | - Ping Tang
- Department of Oncology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou City, P. R. China
- Department of Oncology, The First Affiliated Hospital of Hunan College of Traditional Chinese Medicine, Zhuzhou City, P. R. China
| | - Haihui He
- Department of Oncology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou City, P. R. China
- Department of Oncology, The First Affiliated Hospital of Hunan College of Traditional Chinese Medicine, Zhuzhou City, P. R. China
| | - Lingzhi Liu
- Department of Oncology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou City, P. R. China
- Department of Oncology, The First Affiliated Hospital of Hunan College of Traditional Chinese Medicine, Zhuzhou City, P. R. China
| | - Junfeng Yan
- School of Informatics, Hunan University of Chinese Medicine, Changsha City, P. R. China
| | - Qinghua Peng
- Hunan Provincial Key Laboratory for the Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha City, P. R. China
| |
Collapse
|