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Cao L, Ba Y, Chen F, Zhang S, Zhang H. Exploration of bacterial lipopolysaccharide-related genes signature based on T cells for predicting prognosis in colorectal cancer. Aging (Albany NY) 2024; 16:11606-11625. [PMID: 39115879 PMCID: PMC11346792 DOI: 10.18632/aging.206041] [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: 04/03/2024] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
PURPOSE The intratumoral microorganisms participates in the progression and immunotherapy of colorectal cancer (CRC). However, due to technical limitations, the impact of microorganisms on CRC has not been fully understood. Therefore, we conducted a systematic analysis of relationship between bacterial lipopolysaccharide (LPS)-associated genes and immune cells to explore new biomarkers for predicting the prognosis of CRC. METHODS The single-cell RNA sequencing data and the Comparative Toxicogenomics Database were used to screen T cells-associated LPS-related genes (TALRGs). Then, we established and validated the TALRGs risk signature in The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) cohort and GSE39582 cohort. Besides, we compared the differences in tumor-infiltrating immune cell types, immunotherapeutic response, somatic mutation profiles, and tumor mutation burden (TMB) between high-risk group and low-risk group. In addition, the immunotherapeutic cohort (Imvigor210) treated with an anti-PD-L1 agent was performed to explore the potential value of the TALRGs signature on immunotherapy. RESULTS Five prognostic TALRGs were identified and selected to build the prognostic model. The high-risk group had poor prognosis in both TCGA-COAD cohort (P < 0.0001) and GSE39582 cohort (P = 0.00019). The areas under the curves (AUCs) of TALRGs signature were calculated (TCGA-COAD cohort: 0.624 at 1 years, 0.639 at 3 years, 0.648 at 5 years; anti-PD-L1 cohort was 0.59). The high-risk group had advanced pathological stages and higher TMN stages in both TCGA-COAD cohort and GSE39582 cohort. The high-risk group had the higher infiltration of immunosuppressive cells, the expressions of immune checkpoint molecules, the IC50 values of chemotherapy drugs, and TP53 mutation rate (P < 0.05). In addition, patients with high TMB had worse prognosis (P < 0.05). Furthermore, the Imvigor210 also showed patients with high-risk scores had poor prognosis (platinum-treated cohort: P = 0.0032; non-platinum-treated cohort: P = 0.00017). CONCLUSIONS Microorganisms are closely related to the tumor microenvironment to influence the progression and immune response of CRC via stimulating T cells through LPS-related genes. The TALRGs signature contributed to predict the prognosis and immunotherapy of CRC, and became new therapeutic targets and biomarkers of CRC.
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Affiliation(s)
- Lichao Cao
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Ying Ba
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Fang Chen
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Shenrui Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Hezi Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
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Liu L, Yang S, Lin K, Yu X, Meng J, Ma C, Wu Z, Hao Y, Chen N, Ge Q, Gao W, Wang X, Lam EWF, Zhang L, Li F, Jin B, Jin D. Sp1 induced gene TIMP1 is related to immune cell infiltration in glioblastoma. Sci Rep 2022; 12:11181. [PMID: 35778451 PMCID: PMC9249770 DOI: 10.1038/s41598-022-14751-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Tumor immune microenvironment exerts a profound effect on the population of infiltrating immune cells. Tissue inhibitor of matrix metalloproteinase 1 (TIMP1) is frequently overexpressed in a variety of cells, particularly during inflammation and tissue injury. However, its function in cancer and immunity remains enigmatic. In this study, we find that TIMP1 is substantially up-regulated during tumorigenesis through analyzing cancer bioinformatics databases, which is further confirmed by IHC tissue microarrays of clinical samples. The TIMP1 level is significantly increased in lymphocytes infiltrating the tumors and correlated with cancer progression, particularly in GBM. Notably, we find that the transcriptional factor Sp1 binds to the promoter of TIMP1 and triggers its expression in GBM. Together, our findings suggest that the Sp1-TIMP1 axis can be a potent biomarker for evaluating immune cell infiltration at the tumor sites and therefore, the malignant progression of GBM.
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Affiliation(s)
- Lu Liu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Shuyao Yang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Kefeng Lin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xiaoman Yu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, People's Republic of China
| | - Jiaqi Meng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Chao Ma
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Zheng Wu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Ning Chen
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Qi Ge
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Wenli Gao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Eric W-F Lam
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Lin Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Fangcheng Li
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, Guangdong, People's Republic of China.
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
| | - Di Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
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Wan D, Feng J, Wang P, Yang Z, Sun T. Hypoxia- and Inflammation-Related Transcription Factor SP3 May Be Involved in Platelet Activation and Inflammation in Intracranial Hemorrhage. Front Neurol 2022; 13:886329. [PMID: 35720085 PMCID: PMC9201407 DOI: 10.3389/fneur.2022.886329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 12/05/2022] Open
Abstract
The purpose of this study was to identify the biomarkers implicated in the development of intracranial hemorrhage (ICH) and potential regulatory pathways. In the transcriptomic data for patients with ICH, we identified DEmiRNAs and DEmRNAs related to hypoxia, inflammation, and their transcription factors (TFs). An ICH-based miRNA-TF-mRNA regulatory network was thus constructed, and four biomarkers (TIMP1, PLAUR, DDIT3, and CD40) were screened for their association with inflammation or hypoxia by machine learning. Following this, SP3 was found to be a transcription factor involved in hypoxia and inflammation, which regulates TIMP1 and PLAUR. From the constructed miRNA-TF-mRNA regulatory network, we identified three axes, hsa-miR-940/RUNX1/TIMP1, hsa-miR-571/SP3/TIMP1, and hsa-miR-571/SP3/PLAUR, which may be involved in the development of ICH. Upregulated TIMP1 and PLAUR were validated in an independent clinical cohort 3 days after ICH onset. According to Gene Set Enrichment Analysis (GSEA), SP3 was discovered to be important in interleukin signaling and platelet activation for hemostasis. Transcription factor SP3 associated with hypoxia or inflammation plays an important role in development of ICH. This study provides potential targets for monitoring the severity of inflammation and hypoxia in patients with ICH.
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Affiliation(s)
- Ding Wan
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
- Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Jin Feng
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Peng Wang
- Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Zhenxing Yang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Tao Sun
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
- Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
- *Correspondence: Tao Sun
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Auma AWN, Kowal C, Shive CL, Lange A, Damjanovska S, Zebrowski E, Reyes E, Calabrese L, Kostadinova L, Falck-Ytter Y, Mattar M, Anthony DD. Transient elastography score is elevated during rheumatoid factor-positive chronic hepatitis C virus infection and rheumatoid factor decline is highly variable over the course of direct-acting antiviral therapy. PLoS One 2022; 17:e0267512. [PMID: 35482664 PMCID: PMC9049346 DOI: 10.1371/journal.pone.0267512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/09/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Elevated rheumatoid factor (RF) levels and systemic immune activation are highly prevalent during chronic hepatitis C virus (HCV) infection. Direct-acting antiviral (DAA) therapy has been associated with normalization of various soluble immune activation parameters. Whether the RF levels relate to soluble immune activation markers during chronic HCV infection, and over what time frame RF levels normalize during and after DAA treatment is unknown and was investigated here. METHODS In a longitudinal study, plasma and serum was obtained from HCV infected RF positive (RF+) and RF negative (RF-) participants. The levels of RF, HCV RNA and soluble markers of inflammation were determined before (week 0), during (weeks 4, 8 and 12) and after (week 24) treatment with HCV DAA therapy. In a subset of RF+ participants, the analysis was extended to over 70 weeks after therapy initiation. Hepatic and other clinical parameters were determined at baseline (week 0) in all participants. RESULTS Before therapy, transient elastography (TE) score was greater in RF+ compared to RF- HCV infected participants, while the systemic levels of soluble inflammatory markers were comparable. Following DAA therapy initiation, HCV RNA levels became undetectable within 4 weeks in both the RF+ and RF- groups. RF levels declined in the first 6 months in most RF+ persons but most commonly remained positive. The levels of some soluble inflammatory markers declined, mainly within 4 weeks of DAA therapy start, in both the RF+ and RF- groups. The baseline (week 0) TE score correlated with RF levels before, during and after DAA therapy, while plasma IL-18 levels correlated with RF level after DAA therapy. CONCLUSION During chronic HCV infection, TE score is elevated in RF+ HCV infected individuals and factors other than HCV viremia (including liver stiffness or fibrosis and select markers of inflammation) likely contribute to persistence of RF after treatment of HCV with DAA.
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Affiliation(s)
- Ann W. N. Auma
- Department of Pathology, Department of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Corinne Kowal
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Carey L. Shive
- Department of Pathology, Department of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Alyssa Lange
- Department of Pathology, Department of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Sofi Damjanovska
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Elizabeth Zebrowski
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Elane Reyes
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Leonard Calabrese
- Department of Rheumatologic and Immunologic Disease, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Lenche Kostadinova
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Yngve Falck-Ytter
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Maya Mattar
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
| | - Donald D. Anthony
- Department of Pathology, Department of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland VA Medical Center and VA GRECC, Cleveland, Ohio, United States of America
- Division of Rheumatology, MetroHealth Medical Center, Cleveland, Ohio, United States of America
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Moran CA, Collins LF, Beydoun N, Mehta PK, Fatade Y, Isiadinso I, Lewis TT, Weber B, Goldstein J, Ofotokun I, Quyyumi A, Choi MY, Titanji K, Lahiri CD. Cardiovascular Implications of Immune Disorders in Women. Circ Res 2022; 130:593-610. [PMID: 35175848 PMCID: PMC8869407 DOI: 10.1161/circresaha.121.319877] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Immune responses differ between men and women, with women at higher risk of developing chronic autoimmune diseases and having more robust immune responses to many viruses, including HIV and hepatitis C virus. Although immune dysregulation plays a prominent role in chronic systemic inflammation, a key driver in the development of atherosclerotic cardiovascular disease (ASCVD), standard ASCVD risk prediction scores underestimate risk in populations with immune disorders, particularly women. This review focuses on the ASCVD implications of immune dysregulation due to disorders with varying global prevalence by sex: autoimmune disorders (female predominant), HIV (male-female equivalent), and hepatitis C virus (male predominant). Factors contributing to ASCVD in women with immune disorders, including traditional risk factors, dysregulated innate and adaptive immunity, sex hormones, and treatment modalities, are discussed. Finally, the need to develop new ASCVD risk stratification tools that incorporate variables specific to populations with chronic immune disorders, particularly in women, is emphasized.
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Affiliation(s)
- Caitlin A. Moran
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA
| | - Lauren F. Collins
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA
| | - Nour Beydoun
- Emory University School of Medicine, Department of Medicine, Center for Heart Disease Prevention, Division of Cardiology and Emory Women’s Heart Center, Atlanta, GA, USA
| | - Puja K. Mehta
- Emory University School of Medicine, Department of Medicine, Center for Heart Disease Prevention, Division of Cardiology and Emory Women’s Heart Center, Atlanta, GA, USA
| | - Yetunde Fatade
- Emory University School of Medicine, Department of Medicine, Atlanta, GA, USA
| | - Ijeoma Isiadinso
- Emory University School of Medicine, Department of Medicine, Center for Heart Disease Prevention, Division of Cardiology and Emory Women’s Heart Center, Atlanta, GA, USA
| | - Tené T Lewis
- Emory University, Rollins School of Public Health, Department of Epidemiology, Atlanta, GA, USA
| | - Brittany Weber
- Harvard Medical School, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jill Goldstein
- Massachusetts General Hospital, Department of Psychiatry, and Harvard Medical School, Departments of Psychiatry and Medicine, Boston, MA, USA
| | - Igho Ofotokun
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA
| | - Arshed Quyyumi
- Emory University School of Medicine, Department of Medicine, Center for Heart Disease Prevention, Division of Cardiology and Emory Women’s Heart Center, Atlanta, GA, USA
| | - May Y. Choi
- Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Kehmia Titanji
- Emory University, Department of Medicine, Division of Endocrinology, Metabolism, and Lipids, Atlanta, GA, USA
| | - Cecile D. Lahiri
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA
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Heart Failure in Chronic Infectious and Inflammatory Conditions: Mechanistic Insights from Clinical Heterogeneity. Curr Heart Fail Rep 2022; 19:267-278. [PMID: 35838874 PMCID: PMC9283814 DOI: 10.1007/s11897-022-00560-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 01/21/2023]
Abstract
PURPOSE OF REVIEW The balance between inflammation and its resolution plays an important and increasingly appreciated role in heart failure (HF) pathogenesis. In humans, different chronic inflammatory conditions and immune-inflammatory responses to infection can lead to diverse HF manifestations. Reviewing the phenotypic and mechanistic diversity of these HF presentations offers useful clinical and scientific insights. RECENT FINDINGS HF risk is increased in patients with chronic inflammatory and autoimmune disorders and relates to disease severity. Inflammatory condition-specific HF manifestations exist and underlying pathophysiologic causes may differ across conditions. Although inflammatory disease-specific presentations of HF differ, chronic excess in inflammation and auto-inflammation relative to resolution of this inflammation is a common underlying contributor to HF. Further studies are needed to phenotypically refine inflammatory condition-specific HF pathophysiologies and prognoses, as well as potential targets for intervention.
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Gao Y, Nepal N, Jin SZ. Toll-like receptors and hepatitis C virus infection. Hepatobiliary Pancreat Dis Int 2021; 20:521-529. [PMID: 34419367 DOI: 10.1016/j.hbpd.2021.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a worldwide issue. However, the current treatment for hepatitis C has many shortcomings. Toll-like receptors (TLRs) are pattern recognition receptors involved in HCV infection, and an increasing number of studies are focusing on the role of TLRs in the progression of hepatitis C. DATA SOURCES We performed a PubMed search up to January 2021 with the following keywords: hepatitis C, toll-like receptors, interferons, inflammation, and immune evasion. We also used terms such as single-nucleotide polymorphisms (SNPs), susceptibility, fibrosis, cirrhosis, direct-acting antiviral agents, agonists, and antagonists to supplement the query results. We reviewed relevant publications analyzing the correlation between hepatitis C and TLRs and the role of TLRs in HCV infection. RESULTS TLRs 1-4 and 6-9 are involved in the process of HCV infection. When the host is exposed to the HCV, TLRs, as important participants in HCV immune evasion, trigger innate immunity to remove the virus and also promote inflammation and liver fibrosis. TLR gene SNPs affect hepatitis C susceptibility, treatment, and prognosis. The contribution of each TLR to HCV is different. Drugs targeting various TLRs are developed and validated, and TLRs can synergize with classic hepatitis C drugs, including interferon and direct-acting antiviral agents, constituting a new direction for the treatment of hepatitis C. CONCLUSIONS TLRs are important receptors in HCV infection. Different TLRs induce different mechanisms of virus clearance and inflammatory response. Although TLR-related antiviral therapy strategies exist, more studies are needed to explore the clinical application of TLR-related drugs.
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Affiliation(s)
- Yang Gao
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Narayan Nepal
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Shi-Zhu Jin
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China.
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The molecular feature of macrophages in tumor immune microenvironment of glioma patients. Comput Struct Biotechnol J 2021; 19:4603-4618. [PMID: 34471502 PMCID: PMC8383063 DOI: 10.1016/j.csbj.2021.08.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background Gliomas are one of the most common types of primary tumors in central nervous system. Previous studies have found that macrophages actively participate in tumor growth. Methods Weighted gene co-expression network analysis was used to identify meaningful macrophage-related gene genes for clustering. Pamr, SVM, and neural network were applied for validating clustering results. Somatic mutation and methylation were used for defining the features of identified clusters. Differentially expressed genes (DEGs) between the stratified groups after performing elastic regression and principal component analyses were used for the construction of MScores. The expression of macrophage-specific genes were evaluated in tumor microenvironment based on single cell sequencing analysis. A total of 2365 samples from 15 glioma datasets and 5842 pan-cancer samples were used for external validation of MScore. Results Macrophages were identified to be negatively associated with the survival of glioma patients. Twenty-six macrophage-specific DEGs obtained by elastic regression and PCA were highly expressed in macrophages at single-cell level. The prognostic value of MScores in glioma was validated by the active proinflammatory and metabolic profile of infiltrating microenvironment and response to immunotherapies of samples with this signature. MScores managed to stratify patient survival probabilities in 15 external glioma datasets and pan-cancer datasets, which predicted worse survival outcome. Sequencing data and immunohistochemistry of Xiangya glioma cohort confirmed the prognostic value of MScores. A prognostic model based on MScores demonstrated high accuracy rate. Conclusion Our findings strongly support a modulatory role of macrophages, especially M2 macrophages in glioma progression and warrants further experimental studies.
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Key Words
- ACC, Adrenocortical carcinoma
- BBB, brain blood barrier
- BLCA, Bladder Urothelial Carcinoma
- BRCA, Breast invasive carcinoma
- CDF, cumulative distribution function
- CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma
- CGGA, Chinese Glioma Genome Atlas
- CHOL, Cholangiocarcinoma
- CNA, copy number alternations
- CNV, copy number variation
- COAD, Colon adenocarcinoma
- CSF-1, colony-stimulating factor-1
- DLBC, Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
- DMP, differentially methylated position
- ESCA, Esophageal carcinoma
- GBM, glioblastoma
- GEO, Gene Expression Omnibus
- GO, gene ontology
- GSEA, gene set enrichment analysis
- GSVA, gene set variation analysis
- Glioma microenvironment
- HNSC, Head and Neck squamous cell carcinoma
- IGR, intergenic region
- IHC, immunohistochemistry
- IL, interleukin
- Immunotherapy
- KEGG, Kyoto Encyclopaedia of Genes and Genomes
- KICH, Kidney Chromophobe
- KIRC, Kidney renal clear cell carcinoma
- KIRP, Kidney renal papillary cell carcinoma
- LGG, low grade glioma
- LIHC, Liver hepatocellular carcinoma
- LUAD, Lung adenocarcinoma
- LUSC, Lung squamous cell carcinoma
- MMP-2, matrix metalloproteinase-2
- MT1, MMP membrane type 1 matrix metalloprotease
- Machine learning
- Macrophage
- OV, Ovarian serous cystadenocarcinoma
- PAAD, Pancreatic adenocarcinoma
- PAM, partition around medoids
- PCA, principal component analysis
- PCPG, Pheochromocytoma and Paraganglioma
- PRAD, Prostate adenocarcinoma
- Prognostic model
- READ, Rectum adenocarcinoma
- SARC, Sarcoma
- SKCM, Skin Cutaneous Melanoma
- SNP, single-nucleotide polymorphism
- SNV, single-nucleotide variant
- STAD, Stomach adenocarcinoma
- SVM, Support Vector Machines
- TAM, tumor associated macrophage
- TCGA, The Cancer Genome Atlas
- TGF-β, tumor growth factor-β
- THCA, Thyroid carcinoma
- THYM, Thymoma
- TIMP-2, tissue inhibitor of metalloproteinase-2
- TLR2, toll-like receptor 2
- TME, tumor microenvironment
- TNFα, tumor necrosis factor α
- TSS, transcription start site
- UCEC, Uterine Corpus Endometrial Carcinoma
- UCS, Uterine Carcinosarcoma
- WGCNA, weighted gene co-expression network analysis
- pamr, prediction analysis for microarrays
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