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Zhang L, Zhu Q, Zhao Q, Lin X, Song H, Liu H, Zhu G, Lu S, Cao B. Tumor-infiltrating immune cell score as an independent prognostic predictor for endometrial carcinoma: Insights from a comprehensive analysis of the immune landscape. Cancer Rep (Hoboken) 2024; 7:e1939. [PMID: 38017652 PMCID: PMC10809205 DOI: 10.1002/cnr2.1939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/20/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Immune cells are crucial components in the tumor microenvironment and have a significant impact on the outcomes of patients. AIMS Here, we aimed to establish a prognostic score based on different types of tumor-infiltrating immune cells for Endometrial Carcinoma (EC). METHODS AND RESULTS We enrolled and analyzed 516 EC patients from The Cancer Genome Atlas. The relative abundance of 22 immune cells were estimated by using the CIBERSORTx algorithm. Cox regression was performed to identify potential prognostic immune cells, which were used to develop a Tumor-infiltrating Immune Cell Score (TICS). The prognostic and incremental value of TICS for overall survival were compared with traditional prognostic factors using the C-index and decision curves. Clustering analysis using all immune cells identified three immune landscape subtypes, which had weak correlation with survival. A TICS was constructed using CD8T cells, resting memory CD4 T cells, activated NK and activated DCs, and classified patients as low-, moderate- and high-risk subgroups. The low-risk subgroup had higher tumor mutation burden and activation of IL2/STAT5, IL2/STAT3 and IFN-gamma response pathways. Conversely, the high-risk subgroup was associated with DNA copy number variation, hypoxia and EMT process. The TICS subgroups significantly predicted overall survival, which was independent of patient age, tumor stage, grade and molecular classification. Moreover, we developed a nomogram incorporating TICS and clinicopathologic factors, which significantly improved the predictive accuracy compared to the clinicopathologic model alone. CONCLUSION The TICS is an effective and independent prognostic predictor for EC patients and may serve as a useful supplement to clinicopathological factors and molecular subtyping.
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Affiliation(s)
- Liping Zhang
- Department of Clinical Laboratory, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengdu Medical CollegeChengduChina
| | - Qiaoying Zhu
- Department of Clinical Laboratory, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengdu Medical CollegeChengduChina
| | - Qi Zhao
- Department of Biobank, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xueping Lin
- Department of Clinical Laboratory, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengdu Medical CollegeChengduChina
| | - Hui Song
- Department of Clinical Laboratory, Sichuan Provincial Maternity and Child Health Care Hospital, Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengdu Medical CollegeChengduChina
| | - Hong Liu
- Department of Gynecologic Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Guiquan Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Shun Lu
- Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Bangrong Cao
- Department of Biobank, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterUniversity of Electronic Science and Technology of ChinaChengduChina
- Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer CenterUniversity of Electronic Science and Technology of ChinaChengduChina
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Nevalainen T, Autio A, Hurme M. Human endogenous retroviruses of the HERV-K (HML-2) family are expressed in the brain of healthy individuals and modify the composition of the brain-infiltrating immune cells. Heliyon 2023; 9:e21283. [PMID: 37920490 PMCID: PMC10618496 DOI: 10.1016/j.heliyon.2023.e21283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/10/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the human genome. RNA expression of individual HERVs has frequently been observed in various pathologic conditions, but some activity can also be seen in healthy individuals, e.g. in the blood. To quantitate the basal expression levels of HERVs in the brain, we now used high-throughput sequencing-based metagenomic analysis to characterize the expression profiles of the HERV-K (HML-2) family proviruses in different brain regions of healthy brain tissue. To this end, RNA-seq data from the Genotype-Tissue Expression (GTEx) project was used. The GTEx project is a public resource to study tissue-specific gene expression and regulation, consisting of a large selection of sequenced samples from different tissues. The GTEx data used in this study consisted of 378 samples taken from 13 brain regions from 55 individuals. The data demonstrated that out of 99 intact proviruses in the family 58 were expressed, but the expression profiles were highly divergent and there were no significant differences in the expression profiles between the various anatomic regions of the brain. It is known that the brain contains a variety of infiltrating immune cells, which are probably of great importance both in the normal defense mechanisms as well as in the various pathogenic processes. Digital cytometry (CIBERSORTx) was used to quantify the proportions of the infiltrating immune cells in the same brain samples. Six most abundant (>5 % of the total population) cell types were observed to be CD4 memory resting T cells, M0 macrophages, plasma cells, CD8 T cells, CD4 memory activated T cells, and monocytes. Analysis of the correlations between the individual HERVs and infiltrating cell types indicated that a cluster of 6 HERVs had a notable correlation signature between T cell type infiltrating cell proportions and HERV RNA expression intensity. The correlations between inflammatory type infiltrating cells were negative or weak. Taken together, these data indicate that the expression of HERVs is associated with a T cell type immunity.
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Affiliation(s)
- Tapio Nevalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
| | - Arttu Autio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
| | - Mikko Hurme
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
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Barak O, Lovelace T, Chu T, Cao Z, Sadovsky E, Mouillet JF, Ouyang Y, Benos PV, Sadovsky Y. Defining trophoblast injury patterns in the transcriptomes of dysfunctional placentas. Placenta 2023; 143:87-90. [PMID: 37866321 PMCID: PMC10842313 DOI: 10.1016/j.placenta.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Trophoblast injury is central to clinically relevant placenta dysfunction. We hypothesized that the mRNA of primary human trophoblasts, exposed to distinct injuries in vitro, capture transcriptome patterns of placental biopsies obtained from common obstetrical syndromes. We deployed a CIBERSORTx deconvolution method to correlate trophoblastic RNAseq-based expression matrices with the transcriptome of omics-defined placental dysfunction patterns in vivo. We found distinct trophoblast injury patterns in placental biopsies from women with fetal growth restriction and a hypertensive disorder, or in biopsies clustered by their omics analysis. Our RNAseq data are useful for defining the contribution of trophoblast injuries to placental dysfunction syndromes.
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Affiliation(s)
- Oren Barak
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tyler Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhishen Cao
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | | | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA; Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
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Gu J, Zhang LN, Gu X, Zhu Y. Identification of hub genes associated with oxidative stress in heart failure and their correlation with immune infiltration using bioinformatics analysis. PeerJ 2023; 11:e15893. [PMID: 37609434 PMCID: PMC10441528 DOI: 10.7717/peerj.15893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/23/2023] [Indexed: 08/24/2023] Open
Abstract
Both oxidative stress and the immune response are associated with heart failure (HF). In this study, our aim was to identify the hub genes associated with oxidative stress andimmune infiltration of HF by bioinformatics analysis and experimental verification. The expression profile of GSE36074 was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened by GEO2R. The genes related to oxidative stress were extracted from GeneCards websites. Then, the functional enrichment analysis of oxidative stress-related DEGs (OSRDEGs) was performed using DAVID. In addition, we constructed a protein-protein interaction (PPI) network using the STRING database and screened for hub genes with Cytoscape software. We also used CIBERSORTx to analyze immune infiltration in mice heart tissues between the TAC and Sham groups and explored the correlation between immune cells and hub genes. Finally, the hub genes were carried out using reverse transcription quantitative PCR (RT-qPCR), immunohistochemistry (IHC) and western blot. A total of 136 OSRDEGs were found in GSE36074. Enrichment analysis revealed that these OSRDEGs were enriched in the mitochondrion, HIF-1, FoxO, MAPK and TNF signaling pathway. The five hub genes (Mapk14, Hif1a, Myc, Hsp90ab1, and Hsp90aa1) were screened by the cytoHubba plugin. The correlation analysis between immune cells and hub genes showed that Mapk14 was positively correlated with Th2 Cells, while Hif1a and Hsp90ab1exhibited a negative correlation with Th2 Cells; Myc exhibited a negative correlation with Monocytes; whereas, Hsp90aa1 was negatively correlated with NK Resting. Finally, five hub genes were validated by RT-qPCR, IHC and western blot. Mapk14, Hif1a, Myc, Hsp90ab1, and Hsp90aa1 are hub genes of HF and may play a critical role in the oxidative stress of HF. This study may provide new targets for the treatment of HF, and the potential immunotherapies are worthy of further study.
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Affiliation(s)
- Jianjun Gu
- Department of Cardiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Cardiology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Li Na Zhang
- Department of Cardiology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiang Gu
- Department of Cardiology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Ye Zhu
- Department of Cardiology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
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Xie S, Cai Y, Chen D, Xiang Y, Cai W, Mao J, Ye J. Single-cell transcriptome analysis reveals heterogeneity and convergence of the tumor microenvironment in colorectal cancer. Front Immunol 2023; 13:1003419. [PMID: 36685571 PMCID: PMC9845924 DOI: 10.3389/fimmu.2022.1003419] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Colorectal cancer (CRC) ranks second for mortality and third for morbidity among the most commonly diagnosed cancers worldwide. We aimed to investigate the heterogeneity and convergence of tumor microenvironment (TME) in CRC. Methods We analyzed the single-cell RNA sequencing data obtained from the Gene Expression Omnibus (GEO) database and identified 8 major cell types and 25 subgroups derived from tumor, para-tumor and peripheral blood. Results In this study, we found that there were significant differences in metabolic patterns, immunophenotypes and transcription factor (TF) regulatory patterns among different subgroups of each major cell type. However, subgroups manifested similar lipid metabolic patterns, immunosuppressive functions and TFs module at the end of the differentiation trajectory in CD8+ T cells, myeloid cells and Fibroblasts. Meanwhile, TFs regulated lipid metabolism and immunosuppressive ligand-receptor pairs were detected by tracing the differentiation trajectory. Based on the cell subgroup fractions calculated by CIBERSORTx and bulk RNA-sequencing data from The Cancer Genome Atlas (TCGA), we constructed an immune risk model and clinical risk model of CRC which presented excellent prognostic value. Conclusion This study identified that the differentiation was accompanied by remodeling of lipid metabolism and suppression of immune function, which suggest that lipid remodeling may be an important trigger of immunosuppression. More importantly, our work provides a new perspective for understanding the heterogeneity and convergence of the TME and will aid the development of prognosis and immunotherapies of CRC patients.
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Affiliation(s)
- Siyuan Xie
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yangke Cai
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Delong Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Xiang
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Gastroenterology, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Wen Cai
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianshan Mao
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Ye
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Teh RQ, Liu GS, Wang JH. Bioinformatics Tools for Bulk Gene Expression Deconvolution in Diabetic Retinopathy. Methods Mol Biol 2023; 2678:107-115. [PMID: 37326707 DOI: 10.1007/978-1-0716-3255-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Retinal neovascularization is one of the leading causes of vision loss and a hallmark of proliferative diabetic retinopathy (PDR). The immune system is observed to be involved in the pathogenesis of diabetic retinopathy (DR). The specific immune cell type that contributes to retinal neovascularization can be identified via a bioinformatics analysis of RNA sequencing (RNA-seq) data, known as deconvolution analysis. Previous study has identified the infiltration of macrophages in the retina of rats with hypoxia-induced retinal neovascularization and patients with PDR through a deconvolution algorithm, known as CIBERSORTx. Here, we describe the protocols of using CIBERSORTx to perform the deconvolution analysis and downstream analysis of RNA-seq data.
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Affiliation(s)
- Ru Qi Teh
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Guei-Sheung Liu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia.
| | - Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.
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Liu H, Yu B, Deng Z, Zhao H, Zeng A, Li R, Fu M. Role of immune cell infiltration and small molecule drugs in adhesive capsulitis: Novel exploration based on bioinformatics analyses. Front Immunol 2023; 14:1075395. [PMID: 36875119 PMCID: PMC9976580 DOI: 10.3389/fimmu.2023.1075395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Background Adhesive capsulitis (AC) is a type of arthritis that causes shoulder joint pain, stiffness, and limited mobility. The pathogenesis of AC is still controversial. This study aims to explore the role of immune related factors in the occurrence and development of AC. Methods The AC dataset was downloaded from Gene Expression Omnibus (GEO) data repository. Differentially expressed immune-related genes (DEIRGs) were obtained based on R package "DESeq2" and Immport database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to explore the functional correlation of DEIRGs. MCC method and Least Absolute Shrinkage and Selection Operator (LASSO) regression were conducted to identify the hub genes. The immune cell infiltration in shoulder joint capsule between AC and control was evaluated by CIBERSORTx, and the relationship between hub genes and infiltrating immune cells was analyzed by Spearman's rank correlation. Finally, potential small molecule drugs for AC were screened by the Connectivity Map database (CMap) and further verified by molecular docking. Results A total of 137 DEIRGs and eight significantly different types of infiltrating immune cells (M0 macrophages, M1 macrophages, regulatory T cells, Tfh cells, monocytes, activated NK cells, memory resting CD4+T cells and resting dendritic cells) were screened between AC and control tissues. MMP9, FOS, SOCS3, and EGF were identified as potential targets for AC. MMP9 was negatively correlated with memory resting CD4+T cells and activated NK cells, but positively correlated with M0 macrophages. SOCS3 was positively correlated with M1 macrophages. FOS was positively correlated with M1 macrophages. EGF was positively correlated with monocytes. Additionally, dactolisib (ranked first) was identified as a potential small-molecule drug for the targeted therapy of AC. Conclusions This is the first study on immune cell infiltration analysis in AC, and these findings may provide a new idea for the diagnosis and treatment of AC.
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Affiliation(s)
- Hailong Liu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baoxi Yu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zengfa Deng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hang Zhao
- China-Japan Friendship School of Clinical Medicine, Peking University, Beijing, China
| | - Anyu Zeng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruiyun Li
- Department of Anesthesiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Ming Fu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Lv M, He F, Guo J, Zheng Z, Wang W, Xie J. Identification of hub genes correlated with tumor-associated M1-like macrophage infiltration in soft tissue sarcomas. Front Genet 2022; 13:999966. [PMID: 36561315 PMCID: PMC9763622 DOI: 10.3389/fgene.2022.999966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Soft tissue sarcomas (STS) are a heterogeneous series of tumors that might result in severe disability and death. Tumor-associated M1-like macrophage infiltration plays a critical role in tumor development and progression. This study aimed at identifying the hub genes associated with M1-like macrophage infiltration in STS cells. First, the expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were imported to calculate the level of M1-like macrophage infiltration by CIBERSORTx. Afterward, the Kaplan-Meier survival analysis was performed to evaluate the correlation between macrophage infiltration and prognosis. Then, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction analysis of GEO data were applied to identify the key gene related to M1-like macrophage infiltration, followed by the functional analysis using TCGA cohort to validate downstream signaling associated with the gene. Finally, pan-cancer analysis was conducted to investigate the gene function in other types of tumors. We found LCK expression positively related to the M1-like macrophage infiltration level, and it positively regulated the expression level of genes regulated to macrophage polarization, and chemotaxis, including interferon-γ (INF-γ), interleukin-12 (IL12), tumor necrosis factor (TNF), PI3K, NF-κB, and CXCL9, 10, and 11. In summary, an 'LCK-INF-γ/IL-12-TNF/PI3K-NF-κB' axis might exist in STS cells that regulate M1-like macrophage infiltration.
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Cai W, Song W, Liu Z, Maharjan DT, Liang J, Lin GN. An Integrative Analysis of Identified Schizophrenia-Associated Brain Cell Types and Gene Expression Changes. Int J Mol Sci 2022; 23. [PMID: 36232882 DOI: 10.3390/ijms231911581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Schizophrenia (SCZ) is a severe mental disorder that may result in hallucinations, delusions, and extremely disordered thinking. How each cell type in the brain contributes to SCZ occurrence is still unclear. Here, we leveraged the human dorsolateral prefrontal cortex bulk RNA-seq data, then used the RNA-seq deconvolution algorithm CIBERSORTx to generate SCZ brain single-cell RNA-seq data for a comprehensive analysis to understand SCZ-associated brain cell types and gene expression changes. Firstly, we observed that the proportions of brain cell types in SCZ differed from normal samples. Among these cell types, astrocyte, pericyte, and PAX6 cells were found to have a higher proportion in SCZ patients (astrocyte: SCZ = 0.163, control = 0.145, P.adj = 4.9 × 10-4, effect size = 0.478; pericyte: SCZ = 0.057, control = 0.066, P.adj = 1.1 × 10-4, effect size = 0.519; PAX6: SCZ = 0.014, control = 0.011, P.adj = 0.014, effect size = 0.377), while the L5/6_IT_CAR3 cells and LAMP5 cells are the exact opposite (L5/6_IT_Car3: SCZ = 0.102, control = 0.108, P.adj = 0.016, effect size = 0.369; LAMP5: SCZ = 0.057, control = 0.066, P.adj = 2.2 × 10-6, effect size = 0.617). Next, we investigated gene expression in cell types and functional pathways in SCZ. We observed chemical synaptic transmission dysregulation in two types of GABAergic neurons (PVALB and LAMP5), and immune reaction involvement in GABAergic neurons (SST) and non-neuronal cell types (endothelial and oligodendrocyte). Furthermore, we observed that some differential expression genes from bulk RNA-seq displayed cell-type-specific abnormalities in the expression of molecules in SCZ. Finally, the cell types with the SCZ-related transcriptomic changes could be considered to belong to the same module since we observed two major similar coordinated transcriptomic changes across these cell types. Together, our results offer novel insights into cellular heterogeneity and the molecular mechanisms underlying SCZ.
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Manella G, Ezagouri S, Champigneulle B, Gaucher J, Mendelson M, Lemarie E, Stauffer E, Pichon A, Howe CA, Doutreleau S, Golik M, Verges S, Asher G. The human blood transcriptome exhibits time-of-day-dependent response to hypoxia: Lessons from the highest city in the world. Cell Rep 2022; 40:111213. [PMID: 35977481 PMCID: PMC9396531 DOI: 10.1016/j.celrep.2022.111213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
High altitude exposes humans to hypobaric hypoxia, which induces various physiological and molecular changes. Recent studies point toward interaction between circadian rhythms and the hypoxic response, yet their human relevance is lacking. Here, we examine the effect of different high altitudes in conjunction with time of day on human whole-blood transcriptome upon an expedition to the highest city in the world, La Rinconada, Peru, which is 5,100 m above sea level. We find that high altitude vastly affects the blood transcriptome and, unexpectedly, does not necessarily follow a monotonic response to altitude elevation. Importantly, we observe daily variance in gene expression, especially immune-related genes, which is largely altitude dependent. Moreover, using a digital cytometry approach, we estimate relative changes in abundance of different cell types and find that the response of several immune cell types is time- and altitude dependent. Taken together, our data provide evidence for interaction between the transcriptional response to hypoxia and the time of day in humans. Low oxygen availability upon high altitude vastly affects human blood transcriptome The transcriptomic changes upon altitude elevation are not necessarily monotonic The daily variance in gene expression is dependent on altitude The response of several immune cell types is time- and altitude dependent
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Affiliation(s)
- Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Saar Ezagouri
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Benoit Champigneulle
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Jonathan Gaucher
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Monique Mendelson
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Emeline Lemarie
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Emeric Stauffer
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Team "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, Université de Lyon, France; Laboratoire d'Excellence du Globule Rouge (Labex GR-Ex), PRES Sorbonne, Paris, France
| | - Aurélien Pichon
- Laboratoire MOVE, STAPS, Université de Poitiers, Poitiers, France
| | - Connor A Howe
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia - Okanagan, Kelowna, BC, Canada
| | - Stéphane Doutreleau
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Samuel Verges
- HP2 Laboratory, INSERM U1300, Grenoble Alpes University, CHU Grenoble Alpes, Grenoble, France.
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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11
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Mehani B, Asanigari S, Chung HJ, Dazelle K, Singh A, Hannenhalli S, Aldape K. Immune cell gene expression signatures in diffuse glioma are associated with IDH mutation status, patient outcome and malignant cell state, and highlight the importance of specific cell subsets in glioma biology. Acta Neuropathol Commun 2022; 10:19. [PMID: 35144680 PMCID: PMC8830123 DOI: 10.1186/s40478-022-01323-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 12/17/2022] Open
Abstract
The tumor micro-environment (TME) plays an important role in various cancers, including gliomas. We estimated immune cell type-specific gene expression profiles in 3 large clinically annotated glioma datasets using CIBERSORTx and LM22/LM10 blood-based immune signatures and found that the proportions and estimated gene expression patterns of specific immune cells significantly varied according to IDH mutation status. When IDH-WT and IDH-MUT tumors were considered separately, cluster-of-cluster analyses of immune cell gene expression identified groups with distinct survival outcomes. We confirmed and extended these findings by applying a signature matrix derived from single-cell RNA-sequencing data derived from 19 glioma tumor samples to the bulk profiling data, validating findings from the LM22/LM10 results. To link immune cell signatures with outcomes in checkpoint therapy, we then showed a significant association of monocytic lineage cell gene expression clusters with patient survival and with mesenchymal gene expression scores. Integrating immune cell-based gene expression with previously described malignant cell states in glioma demonstrated that macrophage M0 abundance significantly correlated with mesenchymal state in IDH-WT gliomas, with evidence of a previously implicated role of the Oncostatin-M receptor and macrophages in the mesenchymal state. Among IDH-WT tumors that were enriched for the mesenchymal cell state, the estimated M0 macrophage expression signature coordinately also trended to a mesenchymal signature. We also examined IDH-MUT tumors stratified by 1p/19q status, showing that a mesenchymal gene expression signature the M0 macrophage fraction was enriched in IDH-MUT, non-codeleted tumors. Overall, these results highlight the biological and clinical significance of the immune cell environment related to IDH mutation status, patient prognosis and the mesenchymal state in diffuse gliomas.
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Abstract
Kawasaki disease (KD) is a systemic vasculitis that predominantly damages medium- and small-sized vessels, and mainly causes coronary artery lesions (CALs). The diagnostic criterion of KD mainly depends on clinical features, so children could be easily misdiagnosed and could suffer from CALs. Through analysis, a total of 14 immune-related DEGs were obtained, of which IL1B, ADM, PDGFC, and TGFA were identified as diagnostic markers of KD. Compared with the non-KD group, KD patients contained a higher proportion of naive B cells, activated memory CD4 T cells, gamma delta T cells, and neutrophils, while the proportions of memory B cells, CD8 T cells, activated memory CD4 T cells, and activated NK cells were relatively lower. In conclusion, immune-related genes can be used as diagnostic markers of KD, and the difference in immune cells between KD and non-KD might provide new insight into understanding the pathogenesis of KD.
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Affiliation(s)
- Dong Liu
- Department of Cardiovascular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pediatrics, Sichuan Clinical Research Center for Birth Defects, The Affliated Hospital of Southwest Medical University, Luzhou, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Meixuan Song
- Department of Gastrointestinal Surgery, The Affliated Hospital of Southwest Medical University, Luzhou, China
| | - Fengchuan Jing
- Department of Cardiovascular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Bin Liu
- Department of Pediatrics, Sichuan Clinical Research Center for Birth Defects, The Affliated Hospital of Southwest Medical University, Luzhou, China
| | - Qijian Yi
- Department of Cardiovascular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
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13
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Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell 2021; 184:5482-5496.e28. [PMID: 34597583 DOI: 10.1016/j.cell.2021.09.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/21/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.
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Affiliation(s)
- Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Chloé B Steen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Armon Azizi
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Joanna Przybyl
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
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14
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Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell 2021; 39:1422-1437.e10. [PMID: 34597589 PMCID: PMC9205168 DOI: 10.1016/j.ccell.2021.08.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).
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Affiliation(s)
- Chloé B Steen
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mohammad S Esfahani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Armon Azizi
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - David M Kurtz
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Farnaz Khameneh
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
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15
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Yu K, Li D, Xu F, Guo H, Feng F, Ding Y, Wan X, Sun N, Zhang Y, Fan J, Liu L, Yang H, Yang X. IDO1 as a new immune biomarker for diabetic nephropathy and its correlation with immune cell infiltration. Int Immunopharmacol 2021; 94:107446. [PMID: 33581581 DOI: 10.1016/j.intimp.2021.107446] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Indoleamine 2,3-dioxygenase 1(IDO1) has complicated roles in immune-inflammatory response regulation, but its correlation with immune cell infiltration in diabetic nephropathy (DN) remains unknown. METHODS Gene expression data were extracted from the GEO database. Differentially expressed genes (DEGs) were identified and functional correlation analysis was performed. The immune hub gene was screened using Maximal Clique Centrality, and verified in DN model mice via western blotting, immunohistochemistry, and immunofluorescence analysis. CIBERSORTx was used to assign values to immune cell infiltration in DN and determine a correlation with the hub gene. The prognostic significance of the hub gene was then validated. RESULTS The 330 screened DEGs from the GEO dataset were most enriched in GO functions and KEGG pathways associated with immune inflammation. IDO1 was identified as a hub immune gene, with upregulated expression in DN model mice. IDO1 expression was positively correlated with M1 macrophages (R = 0.58, P < 0.001) and monocytes (R = 0.44, P = 0.049), and was negatively correlated with resting memory CD4 T cells (R = -0.51, P = 0.019). IDO1 expression was upregulated in peritoneal macrophages after high glucose stimulation, and inflammatory factor production was reversed by IDO1 inhibition. Higher IDO1 expression was associated with worse prognosis in DN patients via multivariate survival analysis (P < 0.001). CONCLUSIONS IDO1 was identified as a diagnostic and prognostic biomarker for DN and shown to play a vital role in immune cell infiltration in DN, ascertained using microarray data and CIBERSORTx for the first time.
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Affiliation(s)
- Kuipeng Yu
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China; Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China; NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Dengren Li
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Fuping Xu
- Neurology Department, Zibo Central Hospital, Shandong University, Zibo 255036, Shandong, China
| | - Hao Guo
- High-tech Zone Branch Hospital, Qilu Hospital of Shandong University, Jinan 250101, Shandong, China
| | - Feng Feng
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China; NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Yu Ding
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Xiang Wan
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Nan Sun
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Yang Zhang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Jiahui Fan
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Lei Liu
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China
| | - Huimin Yang
- Department of General Practice, Qilu Hospital of Shandong University, Jinan 250012 Shandong, China
| | - Xiangdong Yang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong, China.
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16
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Ran T, Chen Z, Zhao L, Ran W, Fan J, Hong S, Yang Z. LAMB1 Is Related to the T Stage and Indicates Poor Prognosis in Gastric Cancer. Technol Cancer Res Treat 2021; 20:15330338211004944. [PMID: 33784890 PMCID: PMC8020091 DOI: 10.1177/15330338211004944] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Gastric cancer (GC) is a common tumor malignancy with high incidence and poor prognosis. Laminin is an indispensable component of basement membrane and extracellular matrix, which is responsible for bridging the internal and external environment of cells and transmitting signals. This study mainly explored the association of the LAMB1 expression with clinicopathological characteristics and prognosis in gastric cancer. METHODS The expression data and clinical information of gastric cancer patients were downloaded from The Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG). And we analyzed the relationship between LAMB1 expression and clinical characteristics through R. CIBERSORTx was used to calculate the absolute score of immune cells in gastric tumor tissues. Then COX proportional hazard models and Kaplan-Meier curves were performed to evaluate the role of LAMB1 and its influence on prognosis in gastric cancer patients. Finally, GO and KEGG analysis were applied for LAMB1-related genes in gastric cancer, and PPI network was constructed in Cytoscape software. RESULTS In the TCGA cohort, patients with gastric cancer frequently generated LAMB1 gene copy number variation, but had little effect on mRNA expression. Both in the TCGA and ACRG cohorts, the mRNA expression of LAMB1 in gastric cancer tissues was higher than it in normal tissues. All patients were divided into high expression group and low expression group according to the median expression level of LAMB1. The elevated expression group obviously had more advanced cases and higher infiltration levels of M2 macrophages. COX proportional hazard models and Kaplan-Meier curves revealed that patients with enhanced expression of LAMB1 have a worse prognosis. GO/KEGG analysis showed that LAMB1-related genes were enriched in PI3K-Akt signaling pathway, focal adhesion, ECM-receptor interaction, etc. CONCLUSIONS The high expression of LAMB1 in gastric cancer is related to the poor prognosis of patients, and it may be related to microenvironmental changes in tumors.
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Affiliation(s)
- Tao Ran
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - ZhiJi Chen
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - LiWen Zhao
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Wei Ran
- The Fourth Department of Infectious Disease, Chongqing Public Health Center, Chongqing, China
| | - JinYu Fan
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - SiYa Hong
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - ZhaoXia Yang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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17
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Su H, Cai T, Zhang S, Yan X, Zhou L, He Z, Xue P, Li J, Zheng M, Yang X, Feng B. Identification of hub genes associated with neutrophils infiltration in colorectal cancer. J Cell Mol Med 2021; 25:3371-3380. [PMID: 33666342 PMCID: PMC8034475 DOI: 10.1111/jcmm.16414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the leading cause of cancer‐related mortality in the world. Accumulating evidence indicate that tumour infiltrating immune cells participated in cancer progression. Among them, tumour infiltrating neutrophils (TINs) are reported to play crucial role in various cancers. In this study, we used CIBERSORTx, a digital cytometry tool to evaluate the neutrophils infiltration in CRC based on gene expression data of CRC tissues from GSE39582 data set and The Cancer Genome Atlas data set (TCGA‐COAD and TCGA‐READ). Weighted gene co‐expression network analysis (WGCNA) was conducted in GSE39582 data set to identify hub genes associated with neutrophil infiltration. The association of hub gene and neutrophils was then validated in TCGA cohorts and an independent RJ cohort. Functional analysis was performed to investigate the molecular mechanisms of the interested hub gene. We found that neutrophil infiltration is elevated in CRC tissues, and it is related to a poorer prognosis. A total of 18 gene modules are identified by WGCNA in GSE39582 data set, among which lightcyan module is significantly correlated with neutrophils infiltration. Furthermore, Superoxide Dismutase 2 (SOD2) in lightcyan module was proved to correlated with neutrophils infiltration in various cancer types. In addition, SOD2 expression is highly associated with several chemokines, including CXCL8, a neutrophils‐related attractant, and functional analysis revealed that SOD2 is involved in neutrophils recruitment biological process. These results indicate that an ‘SOD2‐CXCL8‐neutrophil recruitment’ axis plays a potential role in colorectal cancer progression.
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Affiliation(s)
- Hao Su
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyi Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sen Zhang
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xialin Yan
- Department of General Surgery, Tongji University Tenth People's Hospital, Shanghai, China
| | - Leqi Zhou
- Department of General Surgery, Changhai Hospital, Shanghai, China
| | - Zirui He
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pei Xue
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianwen Li
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minhua Zheng
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Feng
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Zhang L, Zhang M, Chen X, He Y, Chen R, Zhang J, Huang J, Ouyang C, Shi G. Identification of the tubulointerstitial infiltrating immune cell landscape and immune marker related molecular patterns in lupus nephritis using bioinformatics analysis. Ann Transl Med 2021; 8:1596. [PMID: 33437795 PMCID: PMC7791250 DOI: 10.21037/atm-20-7507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease that commonly affects the kidneys. Research into markers that can predict the prognosis of tubulointerstitial lupus nephritis (LN) has been impeded by the lack of well-designed studies. Methods In this study, we selected and merged 3 sets of renal biopsy tubulointerstitial data from GSE32591, GSE69438, and GSE127797, including 95 LN and 15 living healthy donors. CIBERSORTx was utilized for differentially infiltrating immune cell (DIIC) analysis. Weighted Gene Co-Expression network analysis (WGCNA) was employed to explore differentially expressed gene (DEG) related modules. Combined WGCNA hub genes and protein-protein interaction (PPI) validation was used for immune marker identification. Lastly, unsupervised clustering was carried out to validate the correlation between these markers and clinical characteristics. Results Our findings unveiled TYROBP, C1QB, LAPTM5, CTSS, PTPRC as the 5 immune markers, which were negatively correlated with glomerular filtration rate (GFR). Specifically, the expression levels of TYROBP and C1QB were significantly different between proliferative LN (PLN) and membranous LN (MLN). Unsupervised clustering could aggregate LN by these immune marker expression spectrums. Conclusions This study is the first to identify infiltrating immune cells and associated molecular patterns in the tubulointerstitium of LN by utilizing bioinformatics methods. These findings contribute to a better understanding of the mechanisms behind LN, and promote more precise diagnosis.
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Affiliation(s)
- Lu Zhang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,The Fifth Hospital of Xiamen, Xiang'an Branch, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Mengqin Zhang
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xing Chen
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,The Fifth Hospital of Xiamen, Xiang'an Branch, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yan He
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Rongjuan Chen
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jun Zhang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,The Fifth Hospital of Xiamen, Xiang'an Branch, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiyi Huang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,The Fifth Hospital of Xiamen, Xiang'an Branch, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Chun Ouyang
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guixiu Shi
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, Xiamen, China
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19
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Li L, Shen L, Ma J, Zhou Q, Li M, Wu H, Wei M, Zhang D, Wang T, Qin S, Xing T. Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx. Front Med (Lausanne) 2020; 7:451. [PMID: 33043022 PMCID: PMC7527443 DOI: 10.3389/fmed.2020.00451] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/07/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a commonly diagnosed cancer with high mortality rates. The immune response plays an important role in the progression of HCC. Immunotherapies are becoming an increasingly promising tool for treating cancers. Advancements in scRNA-seq (single-cell RNA sequencing) have allowed us to identify new subsets in the immune microenvironment of HCC. Yet, distribution of these new cell types and their potential prognostic value in bulk samples from large cohorts remained unclear. This study aimed to investigate the tumor-infiltration and prognostic value of new cell subsets identified by a previous scRNA-seq study in a TCGA HCC cohort using CIBERSORTx, a machine learning method to estimate cell proportion and infer cell-type-specific gene expression profiles. We observed different distributions of tumor-infiltrating lymphocytes between tumor and normal cells. Among these, the CD4-GZMA cell subset showed association with prognosis (log-rank test, p < 0.05). We further analyzed CD4-GZMA cell specific gene expression with CIBERSORTx, and found 19 prognostic genes (univariable cox regression, p < 0.05). Finally, we applied Least absolute shrinkage and selection operator (LASSO) Cox regression to construct an immune risk score model and performed a prognostic assessment of our model in TCGA and ICGC cohorts. Taken together, the immune landscape in HCC bulk samples may be more complex than assumed, with heterogeneity and different tumor-infiltration relative to scRNA-seq results. Additionally, CD4-GZMA cells and their characteristics may yield therapeutic benefits in the immune treatment of HCC.
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Affiliation(s)
- Lixing Li
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Shen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingsong Ma
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Mo Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Muyun Wei
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Di Zhang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Tonghai Xing
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
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20
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Lu H, Dai W, Guo J, Wang D, Wen S, Yang L, Lin D, Xie W, Wen L, Fang J, Wang Z. High Abundance of Intratumoral γδ T Cells Favors a Better Prognosis in Head and Neck Squamous Cell Carcinoma: A Bioinformatic Analysis. Front Immunol 2020; 11:573920. [PMID: 33101298 PMCID: PMC7555127 DOI: 10.3389/fimmu.2020.573920] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/01/2020] [Indexed: 01/08/2023] Open
Abstract
γδ T cells are a small subset of unconventional T cells that are enriched in the mucosal areas, and are responsible for pathogen clearance and maintaining integrity. However, the role of γδ T cells in head and neck squamous cell carcinoma (HNSCC) is largely unknown. Here, by using RNA-seq data from The Cancer Genome Atlas (TCGA), we discovered that HNSCC patients with higher levels of γδ T cells were positively associated with lower clinical stages and better overall survival, and high abundance of γδ T cells was positively correlated with CD8+/CD4+ T cell infiltration. Gene ontology and pathway analyses showed that genes associated with T cell activation, proliferation, effector functions, cytotoxicity, and chemokine production were enriched in the group with a higher γδ T cell abundance. Furthermore, we found that the abundance of γδ T cells was positively associated with the expression of the butyrophilin (BTN) family proteins BTN3A1/BTN3A2/BTN3A3 and BTN2A1, but only MICB, one of the ligands of NKG2D, was involved in the activation of γδ T cells, indicating that the BTN family proteins might be involved in the activation and proliferation of γδ T cells in the tumor microenvironment of HNSCC. Our results indicated that γδ T cells, along with their ligands, are promising targets in HNSCC with great prognostic values and treatment potentials.
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Affiliation(s)
- Huanzi Lu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Wenxiao Dai
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Junyi Guo
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Dikan Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Shuqiong Wen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lisa Yang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Dongjia Lin
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Wenqiang Xie
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Liling Wen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Juan Fang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Zhi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
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21
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Chen H, Chen C, Yuan X, Xu W, Yang MQ, Li Q, Shen Z, Yin L. Identification of Immune Cell Landscape and Construction of a Novel Diagnostic Nomogram for Crohn's Disease. Front Genet 2020; 11:423. [PMID: 32425988 PMCID: PMC7212409 DOI: 10.3389/fgene.2020.00423] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Crohn’s disease (CD) has an increasing incidence and prevalence worldwide. The etiology of CD remains unclear and there is no gold standard for diagnosis. The dysregulated immune response and different infiltration status of immune cells are critical for CD pathogenesis; therefore, it is important to provide an overview of immune-cell alterations in CD and explore a novel method for auxiliary diagnosis. Here we analyzed microarray datasets from Gene Expression Omnibus (GEO), and an extended version of Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORTx) was utilized to estimate the fraction of 22 types of immune cells. Differentially expressed genes (DEGs) and a protein-protein interaction (PPI) network were identified, and we performed gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) to identify differentially regulated pathways in CD. Least absolute shrinkage and selection operator (LASSO) regression was conducted to filter features, and a diagnostic nomogram based on logistic regression was built and validated in an independent validation cohort. In the derivation cohort, we found a proportion of 17 immune-cell types to be significantly altered between CD and healthy controls and a total of 150 DEGs were identified, which were mostly related to the immune response. Among the 15 hub genes based on the PPI network, C-X-C chemokine ligand 8 (CXCL8) and interleukin-1B (IL-1B) showed the highest degree of interaction. Additionally, GSEA and GSVA identified five significantly enriched pathways, among which the nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway was critical in the CD development. Furthermore, six variables comprising of CXCL8, IL-1B, M1 macrophages, regulatory T cells, CD8+ T cells, and plasma cells were identified by LASSO regression and incorporated into a logistic regression model. The nomogram displayed a good prediction, with a 0.915 area under the receiver operating curve (AUC) and a C-index of 0.915 [95% confidence interval (CI): 0.875–0.955]. Similar results were found in the validation cohort, with an AUC of 0.884 and a 0.884 C-index (95% CI: 0.843–0.924). These results provide novel in silico insight into cellular and molecular characteristics of CD and potential biomarkers for diagnosis and targeted therapy.
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Affiliation(s)
- Hong Chen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunqiu Chen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoqi Yuan
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weiwei Xu
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Mu-Qing Yang
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiwei Li
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhenyu Shen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lu Yin
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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22
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Yuan Y, Zhou Y, Li Y, Hill C, Ewing RM, Jones MG, Davies DE, Jiang Z, Wang Y. Deconvolution of RNA-Seq Analysis of Hyperbaric Oxygen-Treated Mice Lungs Reveals Mesenchymal Cell Subtype Changes. Int J Mol Sci 2020; 21:E1371. [PMID: 32085618 PMCID: PMC7039706 DOI: 10.3390/ijms21041371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023] Open
Abstract
Hyperbaric oxygen (HBO) is widely applied to treat several hypoxia-related diseases. Previous studies have focused on the immediate effect of HBO-exposure induced oxidative stress on the lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive HBO exposure did not alter the morphology of murine lungs. However, by deconvolution of RNA-seq from those mice lungs using CIBERSORTx and the expression profile matrices of 8 mesenchymal cell subtypes obtained from bleomycin-treated mouse lungs, we identify several mesenchymal cell subtype changes. These include increases in Col13a1 matrix fibroblasts, mesenchymal progenitors and mesothelial cell populations and decreases in lipofibroblasts, endothelial and Pdgfrb high cell populations. Our data suggest that repetitive HBO exposure may affect biological processes in the lungs such as response to wounding, extracellular matrix, vasculature development and immune response.
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Affiliation(s)
- Yuan Yuan
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu, China
| | - Yilu Zhou
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Yali Li
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu, China
| | - Charlotte Hill
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Rob M Ewing
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark G Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Donna E Davies
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
| | - Zhenglin Jiang
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu, China
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK
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