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Zhang Y, Cheng F, Ma J, Shi G, Deng H. Development of cancer-associated fibroblast-related gene signature for predicting the survival and immunotherapy response in lung adenocarcinoma. Aging (Albany NY) 2023; 15:204774. [PMID: 37280069 PMCID: PMC10292873 DOI: 10.18632/aging.204774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
The present study aims to construct a predictive model for prognosis and immunotherapy response in lung adenocarcinoma (LUAD). Transcriptome data were extracted from the Cancer Genome Atlas (TCGA), GSE41271, and IMvigor210. The weighted gene correlation network analysis was utilized to identify the hub modules related to immune/stromal cells. Then, univariate, LASSO, and multivariate Cox regression analyses were employed to develop a predictive signature based on genes of the hub module. Moreover, the association between the predictive signature and immunotherapy response was also investigated. As a result, seven genes (FGF10, SERINE2, LSAMP, STXBP5, PDE5A, GLI2, FRMD6) were screened to develop the cancer associated fibroblasts (CAFs)-related risk signature (CAFRS). LUAD patients with high-risk score underwent shortened Overall survival (OS). A strong correlation was found between CAFRS and immune infiltrations/functions. The gene set variation analysis showed that G2/M checkpoint, epithelial-mesenchymal transition, hypoxia, glycolysis, and PI3K-Akt-mTOR pathways were greatly enriched in the high-risk subgroup. Moreover, patients with higher risk score were less likely to respond to immunotherapy. A nomogram based on CAFRS and Stage presented a stronger predictive performance for OS than the single indicator. In conclusion, the CAFRS exhibited a potent predictive value for OS and immunotherapy response in LUAD.
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Affiliation(s)
- Yong Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fuyi Cheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jinhu Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Gang Shi
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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Zhang W, Cao J, Liu K, Qu Z, Zheng Y, Yu J, Yu Y, Wang Y, Wu W. Non-invasive plasma testing for CD274 UTR structural variations by next-generation sequencing in cancer. Cell Death Dis 2023; 9:35. [PMID: 36717553 PMCID: PMC9887064 DOI: 10.1038/s41420-023-01316-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Immunotherapy is now the main choice of systemic therapy for many cancer patients, while current biomarkers for tumor immunotherapy may be limited by the accessibility of patient tumor tissue or tumor neoplastic content. Rare mutation in the 5' and 3'-untranslated region (UTR) of CD274 gene (Protein name: PD-L1) has been recently reported in hematologic and solid tumors as a potential biomarker for assessing efficacy during immunotherapy. However, multi-omics analysis for CD274 UTR region, especially circulating tumor DNA (ctDNA), have been little explored in the pan-cancer perspective. We developed a cSMART2.0 technology featured with higher capture efficiency and homogeneity to detect this rare structural variant in 2249 Chinese patients' cohort with multiple cancers. An incidence of 0.36% was detected in this cohort, consistent with TCGA (The Cancer Genome Atlas), while the prevalence of SV in CD274 UTR region in liver and breast cancer were significantly higher than TCGA. The liquid biopsy result from ctDNA was 100% concordance with gDNA result getting from tumor tissue detection, and further validated by immunohistochemistry (IHC) and multiplex immunofluorescence (mIF) experiments. Patients carrying this SV in CD274 UTR region without driver gene mutation responded to immune checkpoint inhibitors (ICIs). This study proves that rare structural variants in CD274 UTR region exist in various cancer in Chinese population for the first time, which can induce immune escape and be used for prediction of response to ICIs. Liquid biopsy based cSMART 2.0 technology could offer more sensitive and accurate detection to navigate potential ICIs patients and to benefit patients with advanced disease when tissue samples are not available.
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Affiliation(s)
| | - Jian Cao
- Berry Oncology Corporation, Beijing, China
| | - Ke Liu
- Berry Oncology Corporation, Beijing, China
| | - Ziwei Qu
- Berry Oncology Corporation, Beijing, China
| | - Ying Zheng
- Berry Oncology Corporation, Beijing, China
| | - Jun Yu
- Berry Oncology Corporation, Beijing, China
| | - Yishan Yu
- grid.410587.fDepartment of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yongsheng Wang
- grid.13291.380000 0001 0807 1581Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wendy Wu
- Berry Oncology Corporation, Beijing, China
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Cavalieri S, Serafini MS, Carenzo A, Canevari S, Lenoci D, Pistore F, Miceli R, Vecchio S, Ferrari D, Moro C, Sponghini A, Caldara A, Rocca MC, Secondino S, Moretti G, Denaro N, Caponigro F, Vaccher E, Rinaldi G, Ferraù F, Bossi P, Licitra L, De Cecco L. An Inflammatory Signature to Predict the Clinical Benefit of First-Line Cetuximab Plus Platinum-Based Chemotherapy in Recurrent/Metastatic Head and Neck Cancer. Cells 2022; 11:cells11193176. [PMID: 36231138 PMCID: PMC9563947 DOI: 10.3390/cells11193176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) pathway has been shown to play a crucial role in several inflammatory conditions and host immune-inflammation status is related to tumor prognosis. This study aims to evaluate the prognostic significance of a four-gene inflammatory signature in recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) patients treated with the EGFR inhibitor cetuximab plus chemotherapy. The inflammatory signature was assessed on 123 R/M HNSCC patients, enrolled in the multicenter trial B490 receiving first-line cetuximab plus platinum-based chemotherapy. The primary endpoint of the study was progression free survival (PFS), while secondary endpoints were overall survival (OS) and objective response rate (ORR). The patient population was subdivided into 3 groups according to the signature score groups. The four-genes-signature proved a significant prognostic value, resulting in a median PFS of 9.2 months in patients with high vs. 6.2 months for intermediate vs. 3.9 months for low values (p = 0.0016). The same findings were confirmed for OS, with median time of 18.4, 13.4, and 7.5 months for high, intermediate, and low values of the score, respectively (p = 0.0001). When ORR was considered, the signature was significantly higher in responders than in non-responders (p = 0.0092), reaching an area under the curve (AUC) of 0.65 (95% CI: 0.55–0.75). Our findings highlight the role of inflammation in the response to cetuximab and chemotherapy in R/M-HNSCC and may have translational implications for improving treatment selection.
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Affiliation(s)
- Stefano Cavalieri
- Head and Neck Medical Oncology Department, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori, 20133 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mara Serena Serafini
- Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Carenzo
- Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Silvana Canevari
- Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Deborah Lenoci
- Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Federico Pistore
- Head and Neck Medical Oncology Department, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Rosalba Miceli
- Clinical Epidemiology and Trial Organization, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Stefania Vecchio
- Medical Oncology, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Daris Ferrari
- Medical Oncology, Ospedali Santi Paolo e Carlo, 20142 Milan, Italy
| | - Cecilia Moro
- Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Andrea Sponghini
- Medical Oncology, A.O. Universitaria Maggiore della Carità, 28100 Novara, Italy
| | - Alessia Caldara
- Medical Oncology, Ospedale Santa Chiara, 38122 Trento, Italy
| | - Maria Cossu Rocca
- Division of Urogenital and Head and Neck Medical Oncology, European Institute of Oncology IRCCS, 20133 Milan, Italy
| | - Simona Secondino
- Medical Oncology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | | | - Nerina Denaro
- Medical Oncology, St. Croce e Carle University Teaching Hospital and ARCO Foundation, 12045 Cuneo, Italy
| | - Francesco Caponigro
- Medical Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione Pascale, 80131 Naples, Italy
| | - Emanuela Vaccher
- Medical Oncology and Immune-Related Tumours, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Gaetana Rinaldi
- Medical Oncology, AOU Policlinico "Paolo Giaccone", 90127 Palermo, Italy
| | | | - Paolo Bossi
- Head and Neck Medical Oncology Department, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Lisa Licitra
- Head and Neck Medical Oncology Department, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori, 20133 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Loris De Cecco
- Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
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Xu M, Gong J, Pan J. Prognostic Signature, Immune Features, and Therapeutic Responses of a Novel Ubiquitination-Related Gene Signature in Lung Adenocarcinoma. Journal of Oncology 2022; 2022:1-13. [PMID: 36016582 PMCID: PMC9398812 DOI: 10.1155/2022/2524649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Growing studies have implicated the association of ubiquitination-related genes (UbRGs) with the cancer progression and the long-term survival of patients. However, the prognostic values of UbRGs in lung adenocarcinoma (LUAD) have not been investigated. Our study aimed to establish a ubiquitination-related model for prognosis prediction and internal mechanism investigation. The transcriptome expression profiles and corresponding clinical information of LUAD were obtained from TCGA and GEO datasets. Differentially expressed genes (DEGs) were screened between LUAD specimens and nontumor specimens. Kaplan–Meier analysis and univariate assays were carried out on DEGs to preliminarily screen survival-related UbRGs. Then, the LASSO Cox regression model was applied to develop a multigene signature, which was then demonstrated in two GEO datasets by the use of Kaplan-Meier, ROC, and Cox analyses. We estimated the immune cell infiltration in tumor microenvironment via CIBERSORT and immunotherapy response through the TIDE algorithm. In this study, a total of 71 ubiquitination-related DEGs were identified. Nine UbRGs, including TUBA4A, TRIM2, PLK1, ARRB1, TRIM58, PLK1, ARRB1, CCNB1, TRIM6, PTTG1, and CCT2, were included to establish a risk model, which was validated in TCGA and GEO datasets. The multivariate assays demonstrated that the 9-UbRGs signature was a robust independent prognostic factor in the overall survival of LUAD patients. The abundance of CD8 T cells, activated CD4 T memory cells, resting NK cells and macrophages was higher in the high-risk group, and the TMB of high-risk group was statistically higher than the low-risk group. Multiple drugs approved by FAD, targeting UbRGs, were available for the treatment of LUAD. Overall, we identified a nine ubiquitination-related gene signature, and the signature may be applied to be a potential biomarker for CD8 T cells response and clinical responses to immune checkpoint inhibitors for LUAD.
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