1
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Xu F, Yao X, Zhou N, Hu Z, Guo C, Zhou H, Yan X. Tumor hypoxia in immune infiltration and prognosis of bladder cancer. Transl Cancer Res 2024; 13:3273-3284. [PMID: 39145090 PMCID: PMC11319943 DOI: 10.21037/tcr-23-2375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 06/02/2024] [Indexed: 08/16/2024]
Abstract
Background Bladder cancer (BC) is the sixth most common cancer and the ninth leading cause of cancer death among men in the world. Previous studies have shown that tumor hypoxia plays an important role in the occurrence and development of BC, but the role of tumor hypoxia in the prognosis and immune infiltration of BC remains unclear. Our aim was to perform a bioinformatics analysis combined with a clinical analysis to explore the roles of hypoxia in BC. Methods We acquired datasets (GSE13507, GSE5287, and GSE1827) containing mRNA expression information from BC cohorts from the Gene Expression Omnibus (GEO) and measured the Hypoxia score using the Gene Set Variation Analysis (GSVA). Then we used X-tile method and log-rank test and Pearson's correlation test to analyze the relation among the Hypoxia score and the clinicopathological and immunological characteristics of BC and used stepwise Cox regression analysis to establish a Prognostic model. Results Hypoxia was found to be closely associated with tumor grade, pathological type, invasion, and prognosis of BC in our study. Moreover, we determined that hypoxia was closely related to the infiltration abundance of multiple immune cells through a correlation analysis, and the tumor immune cell infiltration was further found to be significantly associated with the tumor grade and tumor type of BC. Furthermore, we constructed several models based on the Hypoxia score and tumor immune infiltration with C-indexes ranging from 0.703 and 0.888, which showed good performance in predicting the prognosis of BC. Conclusions Our study showed that hypoxia plays an important role in the progression, prognosis, and tumor immune infiltration of BC. Our models based on hypoxia and tumor immune infiltration play a guiding role in the prognosis and treatment of BC patients.
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Affiliation(s)
- Fanghong Xu
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xinyue Yao
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Nanjing Zhou
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zuohuai Hu
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chenrui Guo
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hang Zhou
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaokai Yan
- Department of Oncology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
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2
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Diaz MJ, Quach J, Song J, Milanovic S, Tran JT, Ladehoff LC, Batchu S, Whitman P, Kaffenberger BH, Montanez-Wiscovich ME. Hypoxic transcriptomes predict survival and tumor-infiltrating immune cell composition in cutaneous melanoma. Melanoma Res 2024; 34:118-124. [PMID: 38329217 DOI: 10.1097/cmr.0000000000000938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Hypoxia has established associations with aggressive tumor phenotypes in many cancers. However, it is not currently understood whether tumor hypoxia levels map to distinct immune infiltrates in cutaneous melanoma, potentially unveiling novel therapeutic targets. To this end, we leveraged a previously identified seven-gene hypoxia signature to grade hypoxia levels of 460 cutaneous melanomas obtained from the Broad Institute GDAC Firehose portal. CIBERSORTx ( https://cibersortx.stanford.edu/ ) was employed to calculate the relative abundance of 22 mature human hematopoietic populations. Clinical outcomes and immune cell associations were assessed by computational means. Results indicated that patients with high-hypoxia tumors reported significantly worse overall survival and correlated with greater Breslow depth, validating the in-silico methodology. High-hypoxia tumors demonstrated increased infiltration of activated and resting dendritic cells, resting mast cells, neutrophils, and resting NK cells, but lower infiltration of gamma-delta T cells. These data suggest that high tumor hypoxia correlates with lower survival probability and distinct population differences of several tumor-infiltrating leukocytes in cutaneous melanomas.
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Affiliation(s)
| | - Jessica Quach
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Joanna Song
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | | | - Jasmine T Tran
- School of Medicine, Indiana University, Indianapolis, Indiana
| | - Lauren C Ladehoff
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Sai Batchu
- Cooper Medical School, Rowan University, Camden, New Jersey
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3
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Luo Q, Li X, Meng Z, Rong H, Li Y, Zhao G, Zhu H, Cen L, Liao Q. Identification of hypoxia-related gene signatures based on multi-omics analysis in lung adenocarcinoma. J Cell Mol Med 2024; 28:e18032. [PMID: 38013642 PMCID: PMC10826438 DOI: 10.1111/jcmm.18032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer and one of the malignancies with the highest incidence rate and mortality worldwide. Hypoxia is a typical feature of tumour microenvironment (TME), which affects the progression of LUAD from multiple molecular levels. However, the underlying molecular mechanisms behind LUAD hypoxia are not fully understood. In this study, we estimated the level of hypoxia by calculating a score based on 15 hypoxia genes. The hypoxia scores were relatively high in LUAD patients with poor prognosis and were bound up with tumour node metastasis (TNM) stage, tumour size, lymph node, age and gender. By comparison of high hypoxia score group and low hypoxia score group, 1820 differentially expressed genes were identified, among which up-regulated genes were mainly about cell division and proliferation while down-regulated genes were primarily involved in cilium-related biological processes. Besides, LUAD patients with high hypoxia scores had higher frequencies of gene mutations, among which TP53, TTN and MUC16 had the highest mutation rates. As for DNA methylation, 1015 differentially methylated probes-related genes were found and may play potential roles in tumour-related neurobiological processes and cell signal transduction. Finally, a prognostic model with 25 multi-omics features was constructed and showed good predictive performance. The area under curve (AUC) values of 1-, 3- and 5-year survival reached 0.863, 0.826 and 0.846, respectively. Above all, our findings are helpful in understanding the impact and molecular mechanisms of hypoxia in LUAD.
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Affiliation(s)
- Qineng Luo
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Xing Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Zixing Meng
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Hao Rong
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Yanguo Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Guofang Zhao
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Huangkai Zhu
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Lvjun Cen
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
| | - Qi Liao
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
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4
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Huang X, Gou W, Song Q, Huang Y, Wen C, Bo X, Jiang X, Feng J, Gao H. A BRAF mutation-associated gene risk model for predicting the prognosis of melanoma. Heliyon 2023; 9:e15939. [PMID: 37205993 PMCID: PMC10189240 DOI: 10.1016/j.heliyon.2023.e15939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023] Open
Abstract
BRAF mutation plays an important role in the pathogenesis and progression of melanoma and is correlated to the prognosis of melanoma patients. However, fewer studies have attempted to develop a BRAF mutation-associated gene risk model for predicting the prognosis of melanoma. The current research explores BRAF mutation-related biological features in melanoma and establishes a prognostic signature. First, we identified three significantly enriched KEGG pathways (glycosphingolipid biosynthesis - ganglio series, ether lipid metabolism, and glycosaminoglycan biosynthesis - keratan sulfate) and corresponding genes in the BRAF mutant group by gene set enrichment analysis. We then developed a prognostic signature based on 7 BRAF-associated genes (PLA2G2D, FUT8, PLA2G4E, PLA2G5, PLA2G1B, B3GNT2, and ST3GAL5) and assessed its prediction accuracy using ROC curve analysis. Finally, the nomogram was established according to the prognostic signature and independent clinical characteristics to predict the survival of melanoma patients. Furthermore, we found higher proportions of naive B cells, plasma cells, CD8 T cells, CD4 memory-activated T cells, and regulatory T cells in the low-risk group. Whereas lower proportions of M0, M1, and M2 macrophages and resting NK cells were observed in the high-risk group. The analysis also showed a significantly higher expression of immune checkpoint molecules (PD-1, PD-L1, CTLA4, BTLA, CD28, CD80, CD86, HAVCR2, ICOS, LAG3, and TIGIT) in the low-risk group. Our results provide novel insights into the effect of BRAF mutation on melanoma growth and indicate a promising direction toward immunotherapy and precision medicine in melanoma patients.
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Affiliation(s)
- Xiang Huang
- Department of Anesthesiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Wanrong Gou
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qinxian Song
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yan Huang
- Department of Dermatology, Suining First People's Hospital, Suining, 629000, Sichuan, China
| | - Chunlei Wen
- Department of Anesthesiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xue Bo
- Department of Anesthesiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xian Jiang
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jianguo Feng
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Corresponding author.
| | - Hong Gao
- Department of Anesthesiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- Corresponding author.
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5
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Barreiro K, Lay AC, Leparc G, Tran VDT, Rosler M, Dayalan L, Burdet F, Ibberson M, Coward RJM, Huber TB, Krämer BK, Delic D, Holthofer H. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles. J Extracell Vesicles 2023; 12:e12304. [PMID: 36785873 PMCID: PMC9925963 DOI: 10.1002/jev2.12304] [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: 10/18/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 02/15/2023] Open
Abstract
Extracellular vesicles (EV) are membranous particles secreted by all cells and found in body fluids. Established EV contents include a variety of RNA species, proteins, lipids and metabolites that are considered to reflect the physiological status of their parental cells. However, to date, little is known about cell-type enriched EV cargo in complex EV mixtures, especially in urine. To test whether EV secretion from distinct human kidney cells in culture differ and can recapitulate findings in normal urine, we comprehensively analysed EV components, (particularly miRNAs, long RNAs and protein) from conditionally immortalised human kidney cell lines (podocyte, glomerular endothelial, mesangial and proximal tubular cells) and compared to EV secreted in human urine. EV from cell culture media derived from immortalised kidney cells were isolated by hydrostatic filtration dialysis (HFD) and characterised by electron microscopy (EM), nanoparticle tracking analysis (NTA) and Western blotting (WB). RNA was isolated from EV and subjected to miRNA and RNA sequencing and proteins were profiled by tandem mass tag proteomics. Representative sets of EV miRNAs, RNAs and proteins were detected in each cell type and compared to human urinary EV isolates (uEV), EV cargo database, kidney biopsy bulk RNA sequencing and proteomics, and single-cell transcriptomics. This revealed that a high proportion of the in vitro EV signatures were also found in in vivo datasets. Thus, highlighting the robustness of our in vitro model and showing that this approach enables the dissection of cell type specific EV cargo in biofluids and the potential identification of cell-type specific EV biomarkers of kidney disease.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiHelsinkiFinland
| | - Abigail C. Lay
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - German Leparc
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
| | - Van Du T. Tran
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Marcel Rosler
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
| | - Lusyan Dayalan
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - Frederic Burdet
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Mark Ibberson
- Vital‐IT GroupSIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Richard J. M. Coward
- Bristol RenalBristol Medical SchoolFaculty of Health SciencesUniversity of BristolBristolUK
| | - Tobias B. Huber
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Bernhard K. Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology/Pneumology)University Medical Centre MannheimUniversity of HeidelbergMannheimGermany
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KG BiberachBiberachGermany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology/Pneumology)University Medical Centre MannheimUniversity of HeidelbergMannheimGermany
| | - Harry Holthofer
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
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6
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Chen R, Niu L, Wu L, He Y, Liu G, Hong K. Identification of an endoplasmic reticulum stress-associated gene signature to predict the immune status and prognosis of cutaneous melanoma. Medicine (Baltimore) 2022; 101:e30280. [PMID: 36086718 PMCID: PMC10980369 DOI: 10.1097/md.0000000000030280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/15/2022] [Indexed: 12/24/2022] Open
Abstract
Besides protecting normal cells from various internal and external perturbations, endoplasmic reticulum (ER) stress is also directly related to the pathogenesis of cutaneous melanoma (CM). However, due to the lack of specific molecular biomarkers, ER stress has not been considered a novel treatment target for CM. Here, we identified ER stress-related genes involved in the prognosis of CM patients and constructed an effective model for the prognostic prediction of these patients. First, gene expression data of CM and normal skin tissues from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases were retrieved to identify differentially expressed ER stress-related genes in CM. Meanwhile, an independent cohort obtained from the Gene Expression Omnibus (GEO) database was used for validation. The ER stress genes (ZBP1, DIABLO, GNLY, FASLG, AURKA, TNFRSF21, and CD40LG) that were associated with CM prognosis were incorporated into our prognostic model. The functional analyses indicated that the prognostic model was correlated with patient survival, gender, and cancer growth. Multivariate and univariate Cox regressions revealed that the constructed model could serve as an independent prognostic factor for CM patients. The pathway enrichment analysis showed that the risk model was enriched in different immunity and cancer progression-associated pathways. Moreover, the signature model was significantly connected with the immune subtypes, infiltration of immune cells, immune microenvironment, as well as tumor stem cells. The gene function analysis revealed that 7 ER stress genes were differentially expressed in CM patients and were significantly associated with prognosis and several antitumor drugs. Overall, our current model presented predictive value for the prognosis of CM patients and can be further used in the development of novel therapeutic strategies for CM.
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Affiliation(s)
- Rong Chen
- Department of Hand Plastic Surgery, The First People’s Hospital of Linping District, Hangzhou, China
| | - Linjun Niu
- Department of Oncology, Huaibei People’s Hospital, Anhui, China
| | - Liang Wu
- Department of Hand Plastic Surgery, The First People’s Hospital of Linping District, Hangzhou, China
| | - Youwu He
- Department of Hand Plastic Surgery, The First People’s Hospital of Linping District, Hangzhou, China
| | - Gang Liu
- Department of Hand Plastic Surgery, The First People’s Hospital of Linping District, Hangzhou, China
| | - Kangjie Hong
- Department of Neurology, Chun’an First People’s Hospital, Hangzhou, China
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7
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Xiao W, Tang P, Sui Z, Han Y, Zhao G, Wu X, Yang Y, Zhu N, Gong L, Yu Z, Zhang H. Establishment of a risk model by integrating hypoxia genes in predicting prognosis of esophageal squamous cell carcinoma. Cancer Med 2022; 12:2117-2133. [PMID: 35789548 PMCID: PMC9883439 DOI: 10.1002/cam4.5002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) has a dismal prognosis, and hypoxia plays a key role in metastasis and proliferation of ESCC. Thus, we aimed to develop a hypoxia-based gene signature to assist in the treatment decisions and prognosis. METHODS We performed consensus clustering analysis on samples from GSE53625 dataset from the Gene Expression Omnibus (GEO) database and used weighted gene co-expression network analysis to filter out candidate modules, which were then intersected with differentially expressed genes from clustered subgroups to obtain hypoxia-related genes (HRGs). After that, the aforementioned genes were used to construct risk score models and validated in The Cancer Genome Atlas (TCGA) database and Cox regression analysis were used to construct a nomogram. Immunohistochemical was used to detect protein expression levels of relevant genes. Moreover, the relationship between risk scores and tumor microenvironment was explored. RESULTS A hypoxia risk model containing six genes (PNPLA1, CARD18, IL-18, SLC37A2, ADAMTS18, and FAM83C) was constructed by screening key HRGs. Poorer prognosis in the high-risk group than in the low-risk group. And Cox regression analysis showed that risk score was an independent prognostic factor. The nomogram based on risk scores could well predict 1-, 3-, and 5-year survival. P53, Wnt, and hypoxia signaling pathways may be some regulatory mechanisms of hypoxia associated with the tumor microenvironment. In addition, we confirmed the high expression of BGN and low expression of IL-18 in ESCC tissues. CONCLUSIONS Our study determined the prognostic value of a 6-hypoxia gene signature and a prognostic model, providing potential prognostic predictors and therapeutic targets for ESCC.
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Affiliation(s)
- Wanyi Xiao
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Peng Tang
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Zhilin Sui
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina,Department of Thoracic SurgeryNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical CollegeShenzhenChina
| | - Youming Han
- Department of Respiratory MedicineBinhai Hospital of Tianjin Medical University General HospitalTianjinChina
| | - Gang Zhao
- Department of Gastrointestinal Cancer BiologyTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Xianxian Wu
- Department of Thoracic SurgeryNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical CollegeShenzhenChina
| | - Yueyang Yang
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Ningning Zhu
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Lei Gong
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
| | - Zhentao Yu
- Department of Thoracic SurgeryNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical CollegeShenzhenChina
| | - Hongdian Zhang
- Department of Esophageal CancerTianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinChina
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8
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Shi L, Liu X, Li Y, Li S, Wu W, Gao X, Liu B. Living Bacteria-Based Immuno-Photodynamic Therapy: Metabolic Labeling of Clostridium butyricum for Eradicating Malignant Melanoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105807. [PMID: 35277932 PMCID: PMC9108598 DOI: 10.1002/advs.202105807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/13/2022] [Indexed: 06/14/2023]
Abstract
Due to the complexity, aggressiveness, and heterogeneity of malignant melanoma, it is difficult to eradicate the whole tumor through conventional treatment. Herein, a strategy of metabolic engineering labeled anaerobic oncolytic bacteria (Clostridium butyricum) is demonstrated to achieve the ablation of melanoma. In this system, the metabolic substrate of C. butyricum d-alanine (d-Ala) is first conjugated with a photosensitizer (TPApy) showing aggregation-induced emission (AIE). The yielded metabolic substrate of d-Ala-TPAPy can be metabolically incorporated into bacterial peptidoglycan to form engineered C. Butyricum. Once the engineered C. butyricum is injected into melanoma, the bacteria can only proliferate in an anaerobic zone, stimulate the tumor immune microenvironment, and ablate the tumor hypoxia region. Following that, the relatively rich oxygen content in the peripheral area can induce the death of C. butyricum. The photosensitizer (PS) on the bacteria can subsequently exert a photodynamic effect in the oxygen-rich region and further remove the melanoma residue under light irradiation. Prominent in vivo melanoma ablation results revealed that the engineering oncolytic bacteria can provide a promising regime for solid tumor eradication.
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Affiliation(s)
- Leilei Shi
- Department of Chemical and Biomolecular EngineeringNational University of Singapore4 Engineering Drive 4Singapore117585Singapore
- The Eighth Affiliated HospitalSun Yat‐Sen University3025 Shennan Middle RoadShenzhen518033China
| | - Xiaoxiao Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)School of Basic Medical SciencesFudan University131 Dong An RoadShanghai200032China
| | - Yuzhen Li
- The Eighth Affiliated HospitalSun Yat‐Sen University3025 Shennan Middle RoadShenzhen518033China
| | - Sha Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)School of Basic Medical SciencesFudan University131 Dong An RoadShanghai200032China
| | - Wenbo Wu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore4 Engineering Drive 4Singapore117585Singapore
| | - Xihui Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)School of Basic Medical SciencesFudan University131 Dong An RoadShanghai200032China
| | - Bin Liu
- Department of Chemical and Biomolecular EngineeringNational University of Singapore4 Engineering Drive 4Singapore117585Singapore
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9
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Identification of the Pyroptosis-Related Prognosis Gene Signature and Immune Infiltration in Hepatocellular Carcinoma. DISEASE MARKERS 2022; 2022:9124216. [PMID: 35535333 PMCID: PMC9078841 DOI: 10.1155/2022/9124216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most heterogeneous malignancies worldwide with a dismal prognosis. Lack of efficient biomarkers, early detection, and prognosis is still a challenge for HCC. Pyroptosis is a new discovery inflammatory form of programmed cell death. There is growing evidence revealed that pyroptosis plays a role in physiological and pathological conditions of human cancers. However, the prognostic evaluation of these pyroptosis-related genes (PRGs) in HCC remains blank. Consensus clustering of PRGs was used to classify 374 patients with HCC from the TCGA-LIHC cohort. By applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, a 2-gene prognostic gene model (PLCG1 and GSDMC) was built and indicated the survival rate in HCC with medium-to-high accuracy. Then, the median risk score from the TCGA cohort was utilized; the prognostic gene model was also accurate in Gene Expression Omnibus (GEO) cohort. The functional enrichment analysis indicated that the oncogenic properties are associated with prominent hallmarks of cancer. The ssGSEA analyses and TIMER database indicated that immune infiltration tumor microenvironment in the HCC. In conclusion, our findings provide a foundation for further research targeting PRGs and their immune microenvironment.
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10
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Niu Z, Wang X, Xu Y, Li Y, Gong X, Zeng Q, Zhang B, Xi J, Pei X, Yue W, Han Y. Development and Validation of a Novel Survival Model for Cutaneous Melanoma Based on Necroptosis-Related Genes. Front Oncol 2022; 12:852803. [PMID: 35387121 PMCID: PMC8979066 DOI: 10.3389/fonc.2022.852803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/25/2022] [Indexed: 12/16/2022] Open
Abstract
Background Necroptosis is crucial for organismal development and pathogenesis. To date, the role of necroptosis in skin cutaneous melanoma (SKCM) is yet unveiled. In addition, the part of melanin pigmentation was largely neglected in the bioinformatic analysis. In this study, we aimed to construct a novel prognostic model based on necroptosis-related genes and analysis the pigmentation phenotype of patients to provide clinically actionable information for SKCM patients. Methods We downloaded the SKCM data from the TCGA and GEO databases in this study and identified the differently expressed and prognostic necroptosis-related genes. Patients’ pigmentation phenotype was evaluated by the GSVA method. Then, using Lasso and Cox regression analysis, a novel prognostic model was constructed based on the intersected genes. The risk score was calculated and the patients were divided into two groups. The survival differences between the two groups were compared using Kaplan-Meier analysis. The ROC analysis was performed and the area under curves was calculated to evaluate the prediction performances of the model. Then, the GO, KEGG and GSEA analyses were performed to elucidate the underlying mechanisms. Differences in the tumor microenvironment, patients’ response to immune checkpoint inhibitors (ICIs) and pigmentation phenotype were analyzed. In order to validate the mRNA expression levels of the selected genes, quantitative real-time PCR (qRT-PCR) was performed. Results Altogether, a novel prognostic model based on four genes (BOK, CD14, CYLD and FASLG) was constructed, and patients were classified into high and low-risk groups based on the median risk score. Low-risk group patients showed better survival status. The model showed high accuracy in the training and the validation cohort. Pathway and functional enrichment analysis indicated that immune-related pathways were differently activated in the two groups. In addition, immune cells infiltration patterns and sensitivity of ICIs showed a significant difference between patients from two risk groups. The pigmentation score was positively related to the risk score in pigmentation phenotype analysis. Conclusion In conclusion, this study established a novel prognostic model based on necroptosis-related genes and revealed the possible connections between necroptosis and melanin pigmentation. It is expected to provide a reference for clinical treatment.
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Affiliation(s)
- Zehao Niu
- Medical School of Chinese PLA, Beijing, China.,Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xin Wang
- Department of Ophthalmology, PLA Strategic Support Force Characteristic Medical Center, Beijing, China
| | - Yujian Xu
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yan Li
- Medical School of Chinese PLA, Beijing, China.,Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaojing Gong
- Medical School of Chinese PLA, Beijing, China.,Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Quan Zeng
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, AMMS, Beijing, China.,South China Research Center for Stem Cell and Regenerative Medicine, SCIB, Guangzhou, China
| | - Biao Zhang
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, AMMS, Beijing, China.,South China Research Center for Stem Cell and Regenerative Medicine, SCIB, Guangzhou, China
| | - Jiafei Xi
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, AMMS, Beijing, China.,South China Research Center for Stem Cell and Regenerative Medicine, SCIB, Guangzhou, China.,Academy of Military Medical Sciences (AMMS), Academy of Military Sciences, Beijing, China
| | - Xuetao Pei
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, AMMS, Beijing, China.,South China Research Center for Stem Cell and Regenerative Medicine, SCIB, Guangzhou, China.,Academy of Military Medical Sciences (AMMS), Academy of Military Sciences, Beijing, China
| | - Wen Yue
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, AMMS, Beijing, China.,South China Research Center for Stem Cell and Regenerative Medicine, SCIB, Guangzhou, China.,Academy of Military Medical Sciences (AMMS), Academy of Military Sciences, Beijing, China
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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11
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Wu G, Zhu Z, Yang Z, He M, Ren K, Dong Y, Xue Q. A Hypoxia-Related Signature for Predicting Prognosis, Cellular Processes, Immune Microenvironment and Targeted Compounds in Lung Squamous Cell Carcinoma. Int J Gen Med 2022; 15:3991-4006. [PMID: 35437352 PMCID: PMC9013258 DOI: 10.2147/ijgm.s344228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) is a malignant tumour of the lung epithelium. A hypoxic environment can promote tumour cell proliferation and invasion. Therefore, this study aims to explore hypoxia-related genes and construct reliable models to predict the prognosis, cellular processes, immune microenvironment and target compounds of lung squamous carcinoma. Methods The transcriptome data and matched clinical information of LUSC were retrieved from The Cancer Genome Atlas (TCGA) database. The GSVA algorithm calculated each LUSC patient’s hypoxia score, and all LUSC patients were divided into the high hypoxia score group and low hypoxia score group. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to screen out differentially expressed hypoxia-related genes (DE-HRGs) in LUSC microenvironment, and the underlying regulatory mechanism of DE-HRGs in LUSC was explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Hereafter, we established a prognosis-related genetic signature for DE-HRGs using univariate and multivariate Cox regression analyses. The relationship between gene signature and immune cells was further evaluated. Finally, the Comparative Toxicogenomics Database (CTD) was utilized to predict the targeted drugs for the prognostic genes. Results We obtained 376 DE-HRGs. Functional enrichment analysis indicated that the DE-HRGs were involved in the cell cycle-related regulatory processes. Next, we developed and validated 3 HRGs-based prognostic signature for LUSC, including HELLS, GPRIN1, and FAM83A. Risk score is an independent prognostic factor for LUSC. Functional enrichment analysis and immune landscape analysis suggested that the risk scoring system might be involved in altering the immune microenvironment of LUSC patients to influence patient outcomes. Ultimately, a total of 92 potential compounds were predicted for the three prognostic genes. Conclusion In summary, we developed and validated a hypoxia-related model for LUSC, reflecting the cellular processes and immune microenvironment characteristics and predicting the prognostic outcomes and targeted compounds.
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Affiliation(s)
- Gujie Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Zhenyu Zhu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Zheng Yang
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Min He
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Kuan Ren
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Yipeng Dong
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Qun Xue
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China
- Correspondence: Qun Xue, Email
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12
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Abstract
Pyroptosis is a recently identified mechanism of programmed cell death related to Caspase-1 that triggers a series of inflammatory reactions by releasing several proinflammatory factors such as IL-1β and IL-18. The process is characterised by the rupture of cell membranes and the release of cell contents through the mediation of gasdermin (GSDM) proteins. GSDMD is an important member of the GSDM family and plays a critical role in the two pathways of pyroptosis. Diabetic nephropathy (DN) is a microvascular complication of diabetes and a major cause of end-stage renal disease. Recently, it was revealed that GSDMD-mediated pyroptosis plays an important role in the occurrence and development of DN. In this review, we focus on two types of kidney cells, tubular epithelial cells and renal podocytes, to illustrate the mechanism of pyroptosis in DN and provide new ideas for the prevention, early diagnosis and molecular therapy of DN.
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13
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Identification of four hub genes in venous thromboembolism via weighted gene coexpression network analysis. BMC Cardiovasc Disord 2021; 21:577. [PMID: 34861826 PMCID: PMC8642897 DOI: 10.1186/s12872-021-02409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Background The pathogenic mechanisms of venous thromboembolism (VT) remain to be defined. This study aimed to identify differentially expressed genes (DEGs) that could serve as potential therapeutic targets for VT. Methods Two human datasets (GSE19151 and GSE48000) were analyzed by the robust rank aggregation method. Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were conducted for the DEGs. To explore potential correlations between gene sets and clinical features and to identify hub genes, we utilized weighted gene coexpression network analysis (WGCNA) to build gene coexpression networks incorporating the DEGs. Then, the levels of the hub genes were analyzed in the GSE datasets. Based on the expression of the hub genes, the possible pathways were explored by gene set enrichment analysis and gene set variation analysis. Finally, the diagnostic value of the hub genes was assessed by receiver operating characteristic (ROC) analysis in the GEO database. Results In this study, we identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples. After performing WGCNA, the magenta module was the module with the strongest negative correlation with the clinical characteristics. From the key module, FECH, GYPA, RPIA and XK were chosen for further validation. We found that these genes were upregulated in VT samples, and high expression levels were related to recurrent VT. Additionally, the four hub genes might be highly correlated with ribosomal and metabolic pathways. The ROC curves suggested a diagnostic value of the four genes for VT. Conclusions These results indicated that FECH, GYPA, RPIA and XK could be used as promising biomarkers for the prognosis and prediction of VT. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-021-02409-4.
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14
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Yan M, Hu J, Ping Y, Xu L, Liao G, Jiang Z, Pang B, Sun S, Zhang Y, Xiao Y, Li X. Single-Cell Transcriptomic Analysis Reveals a Tumor-Reactive T Cell Signature Associated With Clinical Outcome and Immunotherapy Response In Melanoma. Front Immunol 2021; 12:758288. [PMID: 34804045 PMCID: PMC8602834 DOI: 10.3389/fimmu.2021.758288] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
The infiltration of tumor-reactive T cells in the tumor site is associated with better survival and immunotherapy response. However, tumor-reactive T cells were often represented by the infiltration of total CD8+ T cells, which was confounded by the presence of bystander T cells. To identify tumor-reactive T cells at the cancer lesion, we performed integration analyses of three scRNA-seq data sets of T cells in melanoma. Extensive heterogeneous functional states of T cells were revealed in the tumor microenvironment. Among these states, we identified a subset of tumor-reactive T cells which specifically expressed tumor-reactive markers and T cell activation signature, and were strongly enriched for larger T cell receptor (TCR) clones. We further identified and validated a tumor-reactive T cell signature (TRS) to evaluate the tumor reactivity of T cells in tumor patients. Patients with high TRS scores have strong immune activity and high mutation burden in the TCGA-SKCM cohort. We also demonstrated a significant association of the TRS with the clinical outcomes of melanoma patients, with higher TRS scores representing better survival, which was validated in four external independent cohorts. Furthermore, the TRS scores exhibited greater performance on prognosis prediction than infiltration levels of CD8+ T cells and previously published prognosis-related signatures. Finally, we observed the capability of TRS to predict immunotherapy response in melanoma. Together, based on integrated analysis of single-cell RNA-sequencing, we developed and validated a tumor-reactive-related signature that demonstrated significant association with clinical outcomes and response to immunotherapy.
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Affiliation(s)
- Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangqin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of High Throughput Omics Big Data for Cold Region's Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of High Throughput Omics Big Data for Cold Region's Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
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15
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Wu Z, Chen L, Jin C, Xu J, Zhang X, Yao Y. A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma. PeerJ 2021; 9:e12304. [PMID: 34721986 PMCID: PMC8520690 DOI: 10.7717/peerj.12304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
Background Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear. Methods Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database. Results Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.
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Affiliation(s)
- Zhengyuan Wu
- Yuhang First People's Hospital, Hangzhou, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Leilei Chen
- Yuhang First People's Hospital, Hangzhou, China
| | - Chaojie Jin
- Yuhang First People's Hospital, Hangzhou, China
| | - Jing Xu
- Yuhang First People's Hospital, Hangzhou, China
| | | | - Yi Yao
- Yuhang First People's Hospital, Hangzhou, China
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16
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Zeng N, Ma L, Cheng Y, Xia Q, Li Y, Chen Y, Lu Z, Lu Q, Jiang F, Luo D. Construction of a Ferroptosis-Related Gene Signature for Predicting Survival and Immune Microenvironment in Melanoma Patients. Int J Gen Med 2021; 14:6423-6438. [PMID: 34675611 PMCID: PMC8502037 DOI: 10.2147/ijgm.s327348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
Objective In this research, we studied the genes associated with ferroptosis to develop a prognostic model and find out an association with tumor immune microenvironment in skin cutaneous melanoma (SKCM) patients. Methods To find SKCM-related ferroptosis genes, we used Cox regression and LASSO approach on 60 genes related to ferroptosis and SKCM-related RNA-seq. Following that, a ferroptosis-related gene signature was created. Time-dependent ROC curve and Kaplan–Meier analysis were calculated to determine its capability of prediction. Besides, several assessments were used to evaluate overall survival (OS), accompanied by the creation of a nomogram for the clinicopathologic factors and the ferroptosis-related gene signature we established. We also investigated the relationship between ferroptosis-related gene signature with three immune checkpoints and immune cell infiltration. Results Our prognostic model included two genes (ALOX5, CHAC1). In both TCGA and GEO cohorts, OS was lower in high-risk category. Using our gene signature, we can reliably predict OS. Additionally, our gene signature can predict immune cell infiltration and SKCM immunotherapy response. Conclusion Our gene signature has shown to be a reliable predictor of OS, reflect the immune microenvironment, and predict the effectiveness of immunotherapy for SKCM patients.
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Affiliation(s)
- Ni Zeng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China.,Department of Dermatology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, People's Republic of China
| | - Liwen Ma
- Department of Dermatology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yuxin Cheng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qingyue Xia
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yueyue Li
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yihe Chen
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Zhiyu Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qian Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, People's Republic of China
| | - Dan Luo
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
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17
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Liu Z, Tang Q, Qi T, Othmane B, Yang Z, Chen J, Hu J, Zu X. A Robust Hypoxia Risk Score Predicts the Clinical Outcomes and Tumor Microenvironment Immune Characters in Bladder Cancer. Front Immunol 2021; 12:725223. [PMID: 34484235 PMCID: PMC8415032 DOI: 10.3389/fimmu.2021.725223] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023] Open
Abstract
Background Bladder cancer (BLCA) is one of the most common urinary malignancies with poor prognosis. There is an unmet need to develop novel robust tools to predict prognosis and treatment efficacy for BLCA. Methods The hypoxia-related genes were collected from the Molecular Signatures Database. The TCGA-BLCA cohort was downloaded from the Cancer Genome Atlas and then was randomly divided into training and internal validation sets. Two external validation cohorts were gathered from Gene Expression Omnibus. Also, another independent validation cohort (Xiangya cohort) was collected from our hospital. The Cox regression model with the LASSO algorithm was applied to develop the hypoxia risk score. Then, we correlated the hypoxia risk score with the clinical outcomes, the tumor microenvironment (TME) immune characteristics, and the efficacy prediction for several treatments, which included cancer immunotherapy, chemotherapy, radiotherapy, and targeted therapies. Results Hypoxia risk score was an independent prognostic factor. A high-risk score indicated an inflamed TME based on the evidence that hypoxia risk score positively correlated with the activities of several cancer immunity cycles and the infiltration levels of many tumor-infiltrating immune cells, such as CD8 + T cells, Dendritic cells, and NK cells. Consistently, the hypoxia risk score was positively related to the expression of several immune checkpoints, such as PD-L1, PD-1, CTLA-4, and LAG-3, as well as the T cell inflamed score. Furthermore, the hypoxia risk score positively correlated with the enrichment scores of most immunotherapy-positive gene signatures. Therefore, patients with higher risk score may be more sensitive to cancer immunotherapy. Meanwhile, the hypoxia risk score was positively related to the sensitivities of several chemotherapeutic drugs, including Cisplatin, Docetaxel, Paclitaxel, Bleomycin, Camptothecin, and Vinblastine. Similarly, the enrichment scores for radiotherapy-predicted pathways and EGFR ligands were higher in the high-risk score group. Conversely, the enrichment scores of several immunosuppressive oncogenic pathways were significantly higher in the low-risk score group, such as the WNT-β-catenin network, PPARG network, and FGFR3 network. Conclusions We developed and validated a new hypoxia risk score, which could predict the clinical outcomes and the TME immune characteristics of BLCA. In general, the hypoxia risk score may aid in the precision medicine for BLCA.
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Affiliation(s)
- Zhi Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China.,Department of Urology, The Second Affiliated Hospital, Guizhou Medical University, Kaili, China
| | - Qiao Tang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Tiezheng Qi
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Belaydi Othmane
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhe Yang
- Department of Histology and Embryology, School of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jiao Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
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18
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Du T, Gao J, Li P, Wang Y, Qi Q, Liu X, Li J, Wang C, Du L. Pyroptosis, metabolism, and tumor immune microenvironment. Clin Transl Med 2021; 11:e492. [PMID: 34459122 PMCID: PMC8329701 DOI: 10.1002/ctm2.492] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
In response to a wide range of stimulations, host cells activate pyroptosis, a kind of inflammatory cell death which is provoked by the cytosolic sensing of danger signals and pathogen infection. In manipulating the cleavage of gasdermins (GSDMs), researchers have found that GSDM proteins serve as the real executors and the deterministic players in fate decisions of pyroptotic cells. Whether inflammatory characteristics induced by pyroptosis could cause damage the host or improve immune activity is largely dependent on the context, timing, and response degree. Here, we systematically review current points involved in regulatory mechanisms and the multidimensional roles of pyroptosis in several metabolic diseases and the tumor microenvironment. Targeting pyroptosis may reveal potential therapeutic avenues.
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Affiliation(s)
- Tiantian Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Jie Gao
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Peilong Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Yunshan Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Qiuchen Qi
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Xiaoyan Liu
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Juan Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Chuanxin Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| | - Lutao Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
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19
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Zhang Y, Yang F, Peng X, Li X, Luo N, Zhu W, Fu M, Li Q, Hu G. Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment. Front Cell Dev Biol 2021; 9:665364. [PMID: 33959617 PMCID: PMC8093637 DOI: 10.3389/fcell.2021.665364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/26/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Hypoxia is a common phenomenon in solid tumors, which plays an important role in tumor proliferation, apoptosis, angiogenesis, invasion and metastasis, energy metabolism and chemoradiotherapy resistance. However, comprehensive analysis of hypoxia markers in colorectal adenocarcinoma (COAD) is still lacking. And there is a need for mechanism exploration and clinical application. Methods: The gene expression, mutation and clinical data of COAD were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, respectively. Tumor samples from TCGA were randomly divided into the training and internal validation groups, while tumor samples from GEO were used as the external validation group. Univariate COX—LASSO—multivariate COX method was applied to construct the prognostic model. We clustered all TCGA tumor samples into high, medium and low hypoxia groups, evaluated the correlation between hypoxia degree and immunoactivity, and explored the combined effect of mutation for common target genes and model riskscore on survival in COAD patients. Finally, we developed a dynamic nomograph App online for direct clinical application and carried out multiple validations of the prognostic model. Results: Our hypoxia-related prognostic model for COAD patients is accurate and has been successfully validated internally and externally. Single Sample Gene Set Enrichment Analysis (ssGSEA) and Gene Set Enrichment Analysis (GSEA) results suggest that for COAD patients with higher hypoxia, the stronger the associated immunosuppressive activity, providing a possible mechanism for the lower survival rate. Finally, the dynamic nomograph App online enhances the clinical translational significance of the study. Conclusion: In this study, an accurate prognostic model for COAD patients was established and validated. In addition, our innovative findings include correlations between hypoxia levels and immune activity, as well as an in-depth exploration of common target gene mutations.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohong Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjun Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Fu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Murugesan M, Premkumar K. Systemic Multi-Omics Analysis Reveals Amplified P4HA1 Gene Associated With Prognostic and Hypoxic Regulation in Breast Cancer. Front Genet 2021; 12:632626. [PMID: 33692831 PMCID: PMC7937963 DOI: 10.3389/fgene.2021.632626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/29/2021] [Indexed: 12/19/2022] Open
Abstract
Breast cancer (BC) is a common malignant tumor in females around the world. While multimodality therapies exist, the mortality rate remains high. The hypoxic condition was one of the potent determinants in BC progression. The molecular mechanisms underpinning hypoxia and their association with BC can contribute to a better understanding of tailored therapies. In this study, two hypoxic induced BC transcriptomic cohorts (GSE27813 and GSE47533) were assessed from the GEO database. The P4HA1 gene was identified as a putative candidate and significantly regulated in hypoxic BC cells compared to normal BC cells at different time intervals (6 h, 9 h, 16 h, 32 h, and 48 h). In patients with Luminal (p < 1E-12), triple-negative subclasses (p = 1.35059E-10), Stage 1 (p = 8.8817E-16), lymph node N1 (p = 1.62436E-12), and in the 40–80 age group (p = 1.62447E-12), the expression of P4HA1 was closely associated with the clinical subtypes of BC. Furthermore, at the 10q22.1 chromosomal band, the P4HA1 gene displayed a high copy number elevation and was associated with a poor clinical regimen with overall survival, relapse-free survival, and distant metastases-free survival in BC patients. In addition, using BioGRID, the protein–protein interaction (PPI) network was built and the cellular metabolic processes, and hedgehog pathways are functionally enriched with GO and KEGG terms. This tentative result provides insight into the molecular function of the P4HA1 gene, which is likely to promote hypoxic-mediated carcinogenesis, which may favor early detection of BC and therapeutic stratification.
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Affiliation(s)
- Manikandan Murugesan
- Department of Biomedical Science, School of Biotechnology and Genetic Engineering, Bharathidasan University, Tiruchirappalli, India
| | - Kumpati Premkumar
- Department of Biomedical Science, School of Biotechnology and Genetic Engineering, Bharathidasan University, Tiruchirappalli, India
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