1
|
Ghimire P, Kinnersley B, Karami G, Arumugam P, Houlston R, Ashkan K, Modat M, Booth TC. Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic review of magnetic resonance imaging studies. Neurooncol Adv 2024; 6:vdae055. [PMID: 38680991 PMCID: PMC11046988 DOI: 10.1093/noajnl/vdae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Background Immunotherapy is an effective "precision medicine" treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunotherapy clinical trials, and if trials are beneficial, facilitate personalized neo-adjuvant treatment. The increased use of whole genome sequencing data, and the advances in bioinformatics and machine learning make such developments plausible. We performed a systematic review to determine the extent of development and validation of immune-related radiogenomic biomarkers for glioblastoma. Methods A systematic review was performed following PRISMA guidelines using the PubMed, Medline, and Embase databases. Qualitative analysis was performed by incorporating the QUADAS 2 tool and CLAIM checklist. PROSPERO registered: CRD42022340968. Extracted data were insufficiently homogenous to perform a meta-analysis. Results Nine studies, all retrospective, were included. Biomarkers extracted from magnetic resonance imaging volumes of interest included apparent diffusion coefficient values, relative cerebral blood volume values, and image-derived features. These biomarkers correlated with genomic markers from tumor cells or immune cells or with patient survival. The majority of studies had a high risk of bias and applicability concerns regarding the index test performed. Conclusions Radiogenomic immune biomarkers have the potential to provide early treatment options to patients with glioblastoma. Targeted immunotherapy, stratified by these biomarkers, has the potential to allow individualized neo-adjuvant precision treatment options in clinical trials. However, there are no prospective studies validating these biomarkers, and interpretation is limited due to study bias with little evidence of generalizability.
Collapse
Affiliation(s)
- Prajwal Ghimire
- Department of Neurosurgery, Kings College Hospital NHS Foundation Trust, London, UK
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Ben Kinnersley
- Department of Oncology, University College London, London, UK
| | | | | | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Keyoumars Ashkan
- Department of Neurosurgery, Kings College Hospital NHS Foundation Trust, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Thomas C Booth
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| |
Collapse
|
2
|
Li X, Ma W, Liu H, Wang D, Su L, Yang X. Integrative pan-cancer analysis of cuproplasia-associated genes for the genomic and clinical characterization of 33 tumors. Chin Med J (Engl) 2023; 136:2621-2631. [PMID: 37027423 PMCID: PMC10617821 DOI: 10.1097/cm9.0000000000002343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The molecular mechanisms driving tumorigenesis have continually been the focus of researchers. Cuproplasia is defined as copper-dependent cell growth and proliferation, including its primary and secondary roles in tumor formation and proliferation through signaling pathways. In this study, we analyzed the differences in the expression of cuproplasia-associated genes (CAGs) in pan-cancerous tissues and investigated their role in immune-regulation and tumor prognostication. METHODS Raw data from 11,057 cancer samples were acquired from multiple databases. Pan-cancer analysis was conducted to analyze the CAG expression, single-nucleotide variants, copy number variants, methylation signatures, and genomic signatures of micro RNA (miRNA)-messenger RNA (mRNA) interactions. The Genomics of Drug Sensitivity in Cancer and the Cancer Therapeutics Response Portal databases were used to evaluate drug sensitivity and resistance against CAGs. Using single-sample Gene Set Enrichment Analysis (ssGSEA) and Immune Cell Abundance Identifier database, immune cell infiltration was analyzed with the ssGSEA score as the standard. RESULTS Aberrantly expressed CAGs were found in multiple cancers. The frequency of single-nucleotide variations in CAGs ranged from 1% to 54% among different cancers. Furthermore, the correlation between CAG expression in the tumor microenvironment and immune cell infiltration varied among different cancers. ATP7A and ATP7B were negatively correlated with macrophages in 16 tumors including breast invasive carcinoma and esophageal carcinoma, while the converse was true for MT1A and MT2A . In addition, we established cuproplasia scores and demonstrated their strong correlation with patient prognosis, immunotherapy responsiveness, and disease progression ( P <0.05). Finally, we identified potential candidate drugs by matching gene targets with existing drugs. CONCLUSIONS This study reports the genomic characterization and clinical features of CAGs in pan-cancers. It helps clarify the relationship between CAGs and tumorigenesis, and may be helpful in the development of biomarkers and new therapeutic agents.
Collapse
Affiliation(s)
- Xinyu Li
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Weining Ma
- Department of Pediatrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Hui Liu
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200060, China
| | - Deming Wang
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Lixin Su
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Xitao Yang
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| |
Collapse
|
3
|
Larionova I, Tashireva L. Immune gene signatures as prognostic criteria for cancer patients. Ther Adv Med Oncol 2023; 15:17588359231189436. [PMID: 37547445 PMCID: PMC10399276 DOI: 10.1177/17588359231189436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Recently, the possibility of using immune gene signatures (IGSs) has been considered as a novel prognostic tool for numerous cancer types. State-of-the-art methods of genomic, transcriptomic, and protein analysis have allowed the identification of a number of immune signatures correlated to disease outcome. The major adaptive and innate immune components are the T lymphocytes and macrophages, respectively. Herein, we collected essential data on IGSs consisting of subsets of T cells and tumor-associated macrophages and indicating cancer patient outcomes. We discuss factors that can introduce errors in the recognition of immune cell types and explain why the significance of immune signatures can be interpreted with uncertainty. The unidirectional functions of cell types should be entirely addressed in the signatures constructed by the combination of innate and adaptive immune cells. The state of the antitumor immune response is the key basis for IGSs and should be considered in gene signature construction. We also analyzed immune signatures for the prediction of immunotherapy response. Finally, we attempted to explain the present-day limitations in the use of immune signatures as robust criteria for prognosis.
Collapse
Affiliation(s)
- Irina Larionova
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, 36 Lenina Av., Tomsk 634050, Russia
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Liubov Tashireva
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| |
Collapse
|
4
|
Chen J, Ye J, Lai R. A lipid metabolism-related gene signature reveals dynamic immune infiltration of the colorectal adenoma-carcinoma sequence. Lipids Health Dis 2023; 22:92. [PMID: 37403152 DOI: 10.1186/s12944-023-01866-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Lipid metabolism-related genes (LMRGs) have been reported to be correlated with the immune infiltration of colorectal cancer (CRC). This study aimed to investigate the immune infiltration characteristics along the colorectal adenoma-carcinoma sequence (ACS) based on LMRGs. METHODS Gene expression data of colorectal adenoma and carcinoma samples were obtained from the public databases. The "limma" package was applied to determine the differentially expressed LMRGs. Unsupervised consensus clustering was used to cluster colorectal samples. The features of the tumor microenvironment were analyzed by the "ESTIMATE", "GSVA", and "TIDE" algorithms. RESULTS The expression of 149 differentially expressed LMRGs was defined as the LMRG signature. Based on this signature, the adenoma and carcinoma samples were divided into three clusters. Unexpectedly, these sequential clusters showed a directional relationship and collectively constituted the progressive course of colorectal ACS. Interestingly, the LMRG signature revealed that adenoma progression was accompanied by a progressive loss of immune infiltration and a stepwise establishment of a cold microenvironment, but carcinoma progression was characterized by a progressive gain of immune infiltration and a gradual establishment of a hot microenvironment. CONCLUSIONS The LMRG signature reveals dynamic immune infiltration along the colorectal ACS, which substantially changes the understanding of the tumor microenvironment of CRC carcinogenesis and provides novel insight into the role of lipid metabolism in this process.
Collapse
Affiliation(s)
- Jie Chen
- Department of Gastroenterology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Molecular Imaging Center, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Jianfang Ye
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China
- Molecular Imaging Center, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Renxu Lai
- Department of Gastroenterology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China.
- Molecular Imaging Center, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China.
| |
Collapse
|
5
|
Xu JL. Wilms Tumor 1-Associated Protein Expression Is Linked to a T-Cell-Inflamed Phenotype in Pancreatic Cancer. Dig Dis Sci 2023; 68:831-840. [PMID: 35859262 DOI: 10.1007/s10620-022-07620-7] [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: 12/21/2021] [Accepted: 07/06/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND The molecular driving forces of anti-tumor immunity in pancreatic ductal adenocarcinoma (PDAC) remain unclear, which causing great difficulty in identifying an appropriate treatment strategy. AIMS This study aims to explore the associations between expression of Wilms tumor 1-associated protein (WTAP) and effector T-cell infiltration in PDAC. METHODS In this study, we explored the association between WTAP expression and infiltration level of CD8+ T cells in PDAC. 178 PDAC samples were selected from The Cancer Genome Atlas (TCGA) database. The associations between diverse immune-cell infiltration, Tumor Mutation Burden (TMB), immune checkpoints, and WTAP expression were performed via R software. Transcriptional hallmarks of anti-tumor immunity and known T-cell-inflamed signature of PDAC were both selected to explore the relevance to WTAP expression. Potential immune checkpoint blockade (ICB) response to different WTAP expression was predicted with tumor immune dysfunction and exclusion (TIDE) algorithm. RESULTS WTAP was closely linked to CD8+ T-cell infiltration (r ≥ 0.5, P value < 0.05) and did not show notable association with TMB in PDAC. WTAP positively linked to T-cell-inflamed gene expression profiles (GEP) (IL2RB, IL2RA, ZAP70, ITK, CD3E, CD38, CD27, CD276, CD8A, CMKLR1, CXCR6, HLA-DQA1, HLA-DRB1, HLA-E, NKG7, and STAT1), cytolytic activity (GZMA and PRF1), various immune checkpoints (IDO1, CD274, HAVCR2, PDCD1, CTLA4, LAG3, and PDCD1LG2) and 4-chemokine signature (CCL4, CCL5, CXCL9, and CXCL10). Besides, increased expression of WTAP was related to a higher TIDE score. CONCLUSIONS WTAP marks PDAC tumors with an active anti-tumor phenotype and might help the identification of PDAC patients who might benefit from immunotherapies.
Collapse
Affiliation(s)
- Ji-Li Xu
- The First Clinical Medical College, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou, Zhejiang, China.
| |
Collapse
|
6
|
Bu F, Zhao Y, Zhao Y, Yang X, Sun L, Chen Y, Zhu S, Min L. Distinct tumor microenvironment landscapes of rectal cancer for prognosis and prediction of immunotherapy response. Cell Oncol 2022; 45:1363-1381. [PMID: 36251240 DOI: 10.1007/s13402-022-00725-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Tumor microenvironment (TME) affects the progression of rectal cancer (RC), and the clinical relevance of its immune elements was widely reported. Here we aim to delineate the complete TME landscape, including non-immune features, to improve our understanding of RC heterogeneity and provide a better strategy for precision medicine. METHODS Single-cell analysis of GSE161277 using Seurat and Cellcall was performed to identify cell-cell interactions. The ssGSEA was employed to quantify the TME elements in TCGA patients, which were further clustered into subtypes by hclust. WGCNA and LASSO were combined to construct a degenerated signature for prognosis, and its performance was validated in two GEO datasets. RESULTS We proposed a subtyping strategy based on the abundance of both immune and non-immune components, which divided all RC patients into 4 subtypes (Immune-, Canonical-, Dormant- and Stem-like). Different subtypes exhibited distinct mutation landscapes, biological features, immune characteristics, immunotherapy responses and prognoses. Next, WGCNA and LASSO regression were combined to construct a 10-gene signature based on differentially expressed genes among different subtypes. Subgroups divided by this signature also exhibited different clinical parameters and responses to immune checkpoint blockades. Diverse machine learning algorithms were applied to achieve higher accuracy for survival prediction and a nomogram was further established in combination with M stage and age to provide an accurate and visual prediction of prognosis. CONCLUSIONS We identified four TME-based RC subtypes with distinct biological and clinical features. Based on those subtypes, we also proposed a degenerated 10-gene signature to predict the prognosis and immunotherapy response.
Collapse
Affiliation(s)
- Fanqin Bu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Yushan Zhao
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaohan Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Lan Sun
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing, 100071, People's Republic of China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China.
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China.
| |
Collapse
|
7
|
Liu J, Yu F, Liu Z, Wang X, Li J. A Robust Prognostic Signature of Tumor Microenvironment in Colorectal Cancer. Cancer Biother Radiopharm 2022; 37:963-975. [PMID: 34551265 DOI: 10.1089/cbr.2021.0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background: Colorectal cancer (CRC) has been a major public health problem. Tumor microenvironment (TME) greatly contributes to the heterogeneity of CRC and is crucial for the regulation of CRC progression. The authors' study aimed to develop a robust prognostic signature for CRC patients based on TME-related genes. Materials and Methods: Gene expression data and clinicopathologic information of CRC patients were collected from Gene Expression Omnibus and The Cancer Genome Atlas databases. TME-related genes with prognostic value were identified by Cox regression and bootstrap method. The authors used the prognostic genes to construct a robust prognostic model using the least absolute shrinkage and selection operator (LASSO) regression method. The immune and stromal cell abundance of CRC samples were estimated by a microenvironment cell populations-counter method. Results: Based on a training set that comprised 893 CRC samples and 4775 TME-related genes, they established a prognostic model consisting of 25 TME-related genes. With specific risk score formulae, the prognostic model divided CRC patients into high-risk and low-risk subgroups with significantly different survival, which were further confirmed in validation cohorts consisting of other 473 CRC cases or subpopulation of specific stages. The result of time-dependent receiver operating characteristic analysis demonstrated strong predictive accuracy of the prognostic model both in training and validation cohorts. Multivariate Cox regression analysis showed that the 25-gene signature was an independent prognostic factor for overall survival, which was validated through clinical subgroups analysis. Further analysis revealed that CRC samples of high-risk group was abundant of stromal-relevant processes and had a significantly higher proportion of fibroblasts and endothelial cells infiltration. Conclusion: The authors established a robust prognostic signature of 25 TME-related genes which may be an effective tool for prognostic prediction and CRC patient stratification to assist in making treatment decisions.
Collapse
Affiliation(s)
- Jingwen Liu
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fei Yu
- Emergency Department, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, P.R. China
| | - Zhao Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiaojing Wang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jianming Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| |
Collapse
|
8
|
Long non-coding RNA tumor protein 73 antisense RNA 1 influences an interaction between lysine demethylase 5A and promoter of tumor protein 73 to enhance the malignancy of colorectal cancer. Hum Cell 2022; 35:1512-1520. [PMID: 35896939 DOI: 10.1007/s13577-022-00740-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/16/2022] [Indexed: 01/23/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The aim of the present study was to explore the expression level of tumor protein 73 (TP73) in highly malignant CRC tumors and how the long non-coding RNA tumor protein 73 antisense RNA 1 (TP73-AS1) influences that transcription. We found that TP73-AS1 was highly expressed in malignant CRC samples in The Cancer Genome Atlas (TCGA) database. We also demonstrated TP73-AS1 was expressed in thirty samples of CRC tissues collected from China Medical University patients as well as in HCT116, RKO and SW480 CRC cell lines but not in HCoEpiC or CCD-18Co normal colon cells. Only wild-type TP73-AS1, but not any of its alternate splicing isoforms, was positively correlated with tumor malignancy. TP73-AS1 transcripts were shown to be located in cell nuclei especially in close proximity to the TP73 promoter in CRC cells, but not in normal colon cells. In addition, an interaction between lysine demethylase 5A (KDM5A) and TP73-AS1 in CRC cells, but not normal colon cells, and KDM5A localization on the TP73 promoter were influenced by TP73-AS1. Interestingly, the H3K4me3 level on the TP73 promoter was reduced, but was elevated by TP73-AS1 knockdown in CRC cells. In conclusion, these results suggest a novel epigenetic role of TP73-AS1 on histone demethylation that influences TP73 transcription, and shed light on malignancy in CRC.
Collapse
|
9
|
Du F, Zheng F, Han Y, Zhao J, Yuan P. Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in ER (+) and/or PR (+) and HER2 (-) Breast Cancer. Front Pharmacol 2022; 13:820437. [PMID: 35721151 PMCID: PMC9201983 DOI: 10.3389/fphar.2022.820437] [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: 11/24/2021] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Although intrinsic molecular subtype has been widely used, there remains great clinical heterogeneity of prognosis in the estrogen receptor (ER)- and/or progesterone receptor (PR)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer (BC). Methods: The transcriptome expression data of messenger RNA (mRNA) were downloaded from The Cancer Genome Atlas (TCGA), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), and the Gene Expression Omnibus (GEO) databases. Immune-related genes were acquired from the ImmPort database and additional literature search. Univariate Cox, LASSO regression, and multivariate Cox regression were used to screen prognostic immune-related genes and establish the risk signature. The correlation between the risk signature and clinical characteristics, the abundances of immune cells within the tumor microenvironment, and cancer phenotypes were further assessed. Results: Of note, 102 immune-related prognostic genes were identified in the METABRIC dataset by univariate Cox analysis. Consecutively, 7 immune-related genes (SHMT2, AGA, COL17A1, FLT3, SLC7A2, ATP6AP1, and CCL19) were selected to establish the risk signature by LASSO regression and multivariate Cox analysis. Its performance was further verified in TCGA and GSE21653 datasets. Multivariate Cox analysis showed that the risk signature was an independent prognostic factor. The 7-gene signature showed a significant correlation with intrinsic molecular subtypes and 70-gene signature. Furthermore, the CD4+ memory T cells were significantly higher in the low-risk group while a significantly higher proportion of M0-type macrophages was found in the high-risk group in both METABRIC and TCGA cohorts, which may have an influence on the prognosis. Furthermore, we found that the low-risk group may be associated with the immune-related pathway and the high-risk group was with the cell cycle-related pathway, which also showed an impact on the prognosis. Conclusion: These seven immune-related gene risk signatures provided an effective method for prognostic stratification in ER (+) and/or PR (+) and HER2 (−) BC.
Collapse
Affiliation(s)
- Feng Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), The VIPII Gastrointestinal Cancer Division of Medical Department, Peking University Cancer Hospital and Institute, Beijing, China
| | - Fangchao Zheng
- Department of Medical Oncology, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education /Beijing), Department of Palliative Care, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University, Xining, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Centre/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
10
|
Zhou M, Zhou S, Han K, Zhang J, Chen Q, Tian C, Zhu H, Jiang M, Min D. Th1 immune maturation effects of Nocardia rubra cell-wall skeleton via PI3K/Akt/PAX8 regulatory axis. Sci Prog 2022; 105:368504221092901. [PMID: 35473474 PMCID: PMC10450467 DOI: 10.1177/00368504221092901] [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] [Indexed: 11/16/2022]
Abstract
Nocardia rubra cell-wall skeleton (Nr-CWS) is reported as an external immunotherapeutic enhancer with the advantage of antitumor effect on human cancers. However, the immune regulatory role of Nr-CWS is not fully illustrated. We studied mouse CD4+ T lymphocytes isolated from mice spleen were induced by Nr-CWS and observed that the differentiation of Th1 CD4+ T cells and the cytokines of IL-2, TNF-α, IFN-γ were all enhanced by Nr-CWS. Furthermore, RNA sequencing was conducted to investigate the different mRNA profiling induced by Nr-CWS. We observed that paired box 8 (PAX8) was significantly up-regulated in Nr-CWS-treated Th1 cells compared to control. As a transcription factor, chromatin immunoprecipitation sequencing was carried out to study the genome-wide distribution of PAX8. Interestingly, we found that the binding domain of PAX8 was elevated by Nr-CWS, and the target genes associated with these binding sites showed a positive correlation between their transcription and PAX8 binding strength. Finally, we determined that Nr-CWS could enhance the activity of the PI3 K/Akt signaling pathway. Akt agonist could mimic the effect of Nr-CWS for PAX8 up-regulation, while Akt inhibitor compromised the expression of PAX8. Taken together, we determined a novel role of Nr-CWS in boosting the activity of Th1 maturation via the PI3 K/Akt/PAX8 axis.
Collapse
Affiliation(s)
- Meixiang Zhou
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Shuping Zhou
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Kun Han
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Jie Zhang
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Qingyu Chen
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Cong Tian
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Hongling Zhu
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Mengyi Jiang
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| | - Daliu Min
- Department of Oncology, Sixth People's Hospital Affiliated to Shanghai Jiaotong University, China
| |
Collapse
|
11
|
Identification of a Tumor Microenvironment-Related Gene Signature Indicative of Disease Prognosis and Treatment Response in Colon Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6290261. [PMID: 34497681 PMCID: PMC8420973 DOI: 10.1155/2021/6290261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/24/2021] [Indexed: 01/05/2023]
Abstract
Background The tumor microenvironment (TME) is associated with disease outcomes and treatment response in colon cancer. Here, we constructed a TME-related gene signature that is prognosis of disease survival and may predict response to immunotherapy in colon cancer. Methods We calculated immune and stromal scores for 385 colon cancer samples from The Cancer Genome Atlas (TCGA) database using the ESTIMATE algorithm. We identified nine TME-related prognostic genes using Cox regression analysis. We evaluated associations between protein expression, extent of immune cell infiltrate, and patient survival. We calculated risk scores and built a clinical predictive model for the TME-related gene signature. Receiver operating characteristic (ROC) curves were generated to assess the predictive power of the signature. We estimated the half-maximal inhibitory concentration (IC50) of chemotherapeutic drugs in patients using the pRRophetic algorithm. The expression of immune checkpoint genes was evaluated. Results High immune and stromal scores are significantly associated with poor overall survival (p < 0.05). We identified 773 differential TME-related prognostic genes associated with survival; these genes were enriched in immune-related pathways. Nine key prognostic genes were identified and were used to construct a TME-related prognostic signature: CADM3, LEP, CD1B, PDE1B, CCL22, ABI3BP, IGLON5, SELE, and TGFB1. This signature identified a high-risk group with worse survival outcomes, based on Kaplan-Meier analysis. A nomogram composed of clinicopathological factors and risk score exhibited good accuracy. Drug sensitivity analysis identified no difference in sensitivity between the high-risk and low-risk groups. High-risk patients had higher expression of PD-1, PDL-1, and CTLA-4 and lower expression of LAG-3 and VSIR. Infiltration of dendritic cells was higher in the high-risk group. Conclusions We identified a novel prognostic TME-related gene expression signature in colon cancer. Stratification of patients based on this gene signature could be used to improve outcomes and guide better therapy for colon cancer patients.
Collapse
|