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Chinchilla-Tábora LM, Montero JC, Corchete LA, González-Morais I, del Barco Morillo E, Olivares-Hernández A, Rodríguez González M, Sayagués JM, Ludeña MD. Differentially Expressed Genes Involved in Primary Resistance to Immunotherapy in Patients with Advanced-Stage Pulmonary Cancer. Int J Mol Sci 2024; 25:2048. [PMID: 38396726 PMCID: PMC10889097 DOI: 10.3390/ijms25042048] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In the last few years, nivolumab has become the standard of care for advanced-stage lung cancer patients. Unfortunately, up to 60% of patients do not respond to this treatment. In our study, we identified variations in gene expression related to primary resistance to immunotherapy. Bronchoscopy biopsies were obtained from advanced non-small cell lung cancer (NSCLC) patients previously characterized as responders or non-responders after nivolumab treatment. Ten tumor biopsies (from three responders and seven non-responders) were analyzed by the differential expression of 760 genes using the NanoString nCounter platform. These genes are known to be involved in the response to anti-PD1/PD-L1 therapy. All the patients were treated with nivolumab. Examining the dysregulated expression of 24 genes made it possible to predict the response to nivolumab treatment. Supervised analysis of the gene expression profile (GEP) revealed that responder patients had significantly higher levels of expression of CXCL11, NT5E, KLRK1, CD3G, GZMA, IDO1, LCK, CXCL9, GNLY, ITGAL, HLA-DRB1, CXCR6, IFNG, CD8A, ITK, B2M, HLA-B, and HLA-A than did non-responder patients. In contrast, PNOC, CD19, TP73, ARG1, FCRL2, and PTGER1 genes had significantly lower expression levels than non-responder patients. These findings were validated as predictive biomarkers in an independent series of 201 patients treated with nivolumab (22 hepatocellular carcinomas, 14 non-squamous cell lung carcinomas, 5 head and neck squamous cell carcinomas, 1 ureter/renal pelvis carcinoma, 120 melanomas, 4 bladder carcinomas, 31 renal cell carcinomas, and 4 squamous cell lung carcinomas). ROC curve analysis showed that the expression levels of ITK, NT5E, ITGAL, and CD8A were the best predictors of response to nivolumab. Further, 13/24 genes showed an adverse impact on overall survival (OS) in an independent, large series of patients with NSCLC (2166 cases). In summary, we found a strong association between the global GEP of advanced NSCLC and the response to nivolumab. The classification of NSCLC patients based on GEP enabled us to identify those patients who genuinely benefited from treatment with immune checkpoint inhibitors (ICIs). We also demonstrated that abnormal expression of most of the markers comprising the genomic signature has an adverse influence on OS, making them significant markers for therapeutic decision-making. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these biomarkers.
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Affiliation(s)
- Luis Miguel Chinchilla-Tábora
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
| | - Juan Carlos Montero
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | | | - Idalia González-Morais
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
| | - Edel del Barco Morillo
- Department of Medical Oncology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (A.O.-H.)
| | - Alejandro Olivares-Hernández
- Department of Medical Oncology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (E.d.B.M.); (A.O.-H.)
| | - Marta Rodríguez González
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
| | - José María Sayagués
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
- Biomedical Research Networking Centers-Oncology (CIBERONC), 28029 Madrid, Spain
| | - María Dolores Ludeña
- Department of Pathology, Institute for Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca, 37007 Salamanca, Spain; (L.M.C.-T.); (J.C.M.); (I.G.-M.); (M.R.G.)
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Shen J, Wang Y, Deng X, Sana SRGL. Combining bioinformatics and machine learning algorithms to identify and analyze shared biomarkers and pathways in COVID-19 convalescence and diabetes mellitus. Front Endocrinol (Lausanne) 2023; 14:1306325. [PMID: 38169604 PMCID: PMC10758397 DOI: 10.3389/fendo.2023.1306325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Background Most patients who had coronavirus disease 2019 (COVID-19) fully recovered, but many others experienced acute sequelae or persistent symptoms. It is possible that acute COVID-19 recovery is just the beginning of a chronic condition. Even after COVID-19 recovery, it may lead to the exacerbation of hyperglycemia process or a new onset of diabetes mellitus (DM). In this study, we used a combination of bioinformatics and machine learning algorithms to investigate shared pathways and biomarkers in DM and COVID-19 convalescence. Methods Gene transcriptome datasets of COVID-19 convalescence and diabetes mellitus from Gene Expression Omnibus (GEO) were integrated using bioinformatics methods and differentially expressed genes (DEGs) were found using the R programme. These genes were also subjected to Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to find potential pathways. The hub DEGs genes were then identified by combining protein-protein interaction (PPI) networks and machine learning algorithms. And transcription factors (TFs) and miRNAs were predicted for DM after COVID-19 convalescence. In addition, the inflammatory and immune status of diabetes after COVID-19 convalescence was assessed by single-sample gene set enrichment analysis (ssGSEA). Results In this study, we developed genetic diagnostic models for 6 core DEGs beteen type 1 DM (T1DM) and COVID-19 convalescence and 2 core DEGs between type 2 DM (T2DM) and COVID-19 convalescence and demonstrated statistically significant differences (p<0.05) and diagnostic validity in the validation set. Analysis of immune cell infiltration suggests that a variety of immune cells may be involved in the development of DM after COVID-19 convalescence. Conclusion We identified a genetic diagnostic model for COVID-19 convalescence and DM containing 8 core DEGs and constructed a nomogram for the diagnosis of COVID-19 convalescence DM.
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Affiliation(s)
- Jinru Shen
- The First Clinical Medical School, Harbin Medical University, Harbin, China
| | - Yaolou Wang
- The First Clinical Medical School, Harbin Medical University, Harbin, China
| | - Xijin Deng
- Department of Anaesthesiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si Ri Gu Leng Sana
- Department of Anaesthesiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Yuan K, Zhao S, Ye B, Wang Q, Liu Y, Zhang P, Xie J, Chi H, Chen Y, Cheng C, Liu J. A novel T-cell exhaustion-related feature can accurately predict the prognosis of OC patients. Front Pharmacol 2023; 14:1192777. [PMID: 37284314 PMCID: PMC10239809 DOI: 10.3389/fphar.2023.1192777] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
The phenomenon of T Cell exhaustion (TEX) entails a progressive deterioration in the functionality of T cells within the immune system during prolonged conflicts with chronic infections or tumors. In the context of ovarian cancer immunotherapy, the development, and outcome of treatment are closely linked to T-cell exhaustion. Hence, gaining an in-depth understanding of the features of TEX within the immune microenvironment of ovarian cancer is of paramount importance for the management of OC patients. To this end, we leveraged single-cell RNA data from OC to perform clustering and identify T-cell marker genes utilizing the Unified Modal Approximation and Projection (UMAP) approach. Through GSVA and WGCNA in bulk RNA-seq data, we identified 185 TEX-related genes (TEXRGs). Subsequently, we transformed ten machine learning algorithms into 80 combinations and selected the most optimal one to construct TEX-related prognostic features (TEXRPS) based on the mean C-index of the three OC cohorts. In addition, we explored the disparities in clinicopathological features, mutational status, immune cell infiltration, and immunotherapy efficacy between the high-risk (HR) and low-risk (LR) groups. Upon the integration of clinicopathological features, TEXRPS displayed robust predictive power. Notably, patients in the LR group exhibited a superior prognosis, higher tumor mutational load (TMB), greater immune cell infiltration abundance, and enhanced sensitivity to immunotherapy. Lastly, we verified the differential expression of the model gene CD44 using qRT-PCR. In conclusion, our study offers a valuable tool to guide clinical management and targeted therapy of OC.
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Affiliation(s)
- Kemiao Yuan
- Department of Oncology, Traditional Chinese Medicine Hospital of Wuxi, Wuxi, China
| | - Songyun Zhao
- Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Bicheng Ye
- School of Clinical Medicine, Yangzhou Polytechnic College, Yangzhou, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yuan Liu
- Department of General Surgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Pengpeng Zhang
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaheng Xie
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chi
- Southwest Medical University, Luzhou, China
| | - Yu Chen
- Wuxi Maternal and Child Health Care Hospital, Wuxi, China
| | - Chao Cheng
- Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Liu S, Chen H, Zheng Z, He Y, Yao X. Development of a Molecular-Subtype-Associated Immune Prognostic Signature That Can Be Recognized by MRI Radiomics Features in Bladder Cancer. Bioengineering (Basel) 2023; 10:bioengineering10030318. [PMID: 36978709 PMCID: PMC10045524 DOI: 10.3390/bioengineering10030318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/04/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Background: Bladder cancer (BLCA) is highly heterogeneous with distinct molecular subtypes. This research aimed to investigate the heterogeneity of different molecular subtypes from a tumor microenvironment perspective and develop a molecular-subtype-associated immune prognostic signature that can be recognized by MRI radiomics features. Methods: Individuals with BLCA in The Cancer Genome Atlas (TCGA) and IMvigor210 were classified into luminal and basal subtypes according to the UNC classification. The proportions of tumor-infiltrating immune cells (TIICs) were examined using The Cell Type Identification by Estimating Relative Subsets of RNA Transcripts algorithm. Immune-linked genes that were expressed differentially between luminal and basal subtypes and associated with prognosis were selected to develop the immune prognostic signature (IPS) and utilized for the classification of the selected individuals into low- and high-risk groups. Functional enrichment analysis (GSEA) was performed on the IPS. The data from RNA-sequencing and MRI images of 111 BLCA samples in our center were utilized to construct a least absolute shrinkage and selection operator (LASSO) model for the prediction of patients’ IPSs. Results: Half of the TIICs showed differential distributions between the luminal and basal subtypes. IPS was highly associated with molecular subtypes, critical immune checkpoint gene expression, prognoses, and immunotherapy response. The prognostic value of the IPS was further verified through several validation data sets (GSE32894, GSE31684, GSE13507, and GSE48277) and meta-analysis. GSEA revealed that some oncogenic pathways were co-enriched in the group at high risk. A novel performance of a LASSO model developed as per ten radiomics features was achieved in terms of IPS prediction in both the validation (area under the curve (AUC): 0.810) and the training (AUC: 0.839) sets. Conclusions: Dysregulation of TIICs contributed to the heterogeneity between the luminal and basal subtypes. The IPS can facilitate molecular subtyping, prognostic evaluation, and personalized immunotherapy. A LASSO model developed as per the MRI radiomics features can predict the IPSs of affected individuals.
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Affiliation(s)
- Shenghua Liu
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai 200072, China
| | - Haotian Chen
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai 200072, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai 200072, China
| | - Zongtai Zheng
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai 200072, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yanyan He
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai 200072, China
- Correspondence: (Y.H.); (X.Y.)
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai 200072, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai 200072, China
- Correspondence: (Y.H.); (X.Y.)
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