1
|
Hu X, Zhu X, Chen Y, Zhang W, Li L, Liang H, Usmanov BB, Donadon M, Yusupbekov AA, Zheng Y. Senescence-related signatures predict prognosis and response to immunotherapy in colon cancer. J Gastrointest Oncol 2024; 15:1020-1034. [PMID: 38989417 PMCID: PMC11231866 DOI: 10.21037/jgo-24-339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers. Cellular senescence plays a vital role in carcinogenesis by activating many pathways. In this study, we aimed to identify biomarkers for predicting the survival and recurrence of CRC through cellular senescence-related genes. Methods Utilizing The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, RNA-sequencing data and clinical information for CRC were collected. A risk model for predicting overall survival was established based on five differentially expressed genes using least absolute shrinkage and selection operator-Cox regression (LASSO-Cox regression), receiver operating characteristic (ROC), and Kaplan-Meier analyses. The study also delved into both the tumor microenvironment and the response to immunotherapy. Moreover, we gathered clinical sample data from our center in order to confirm the findings of public database analysis. Results Through ROC and Kaplan-Meier analyses, a risk model was developed using five cellular senescence-related genes [i.e., CDKN2A, SERPINE1, SNAI1, CXCL1, and ETS2] to categorize patients into high- and low-risk groups. In the TCGA-colon adenocarcinoma (COAD) and GEO-COAD cohorts, the high-risk group was associated with a bleaker forecast (P<0.05), immune cell inactivation, and insensitivity to immunotherapy in IMvigor210 database (http://research-pub.gene.com/IMvigor210CoreBiologies/). Clinical samples were then used to confirm that ETS2 and CDKN2A could serve as independent prognostic biomarkers in CRC. Conclusions Gene signatures related to cellular senescence, specifically involving CDKN2A and ETS2, are emerging as promising biomarkers for predicting CRC prognosis and guiding immunotherapy.
Collapse
Affiliation(s)
- Xiaoshan Hu
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiongjie Zhu
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yifan Chen
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Wenkai Zhang
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Laiqing Li
- Guangzhou Youdi Bio-technology Co., Ltd., Guangzhou, China
| | - Huankun Liang
- Guangzhou Youdi Bio-technology Co., Ltd., Guangzhou, China
| | - Bekzod B Usmanov
- Department of Oncology and Hematology, Tashkent State Pediatric Institute, Tashkent, Uzbekistan
| | - Matteo Donadon
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
- Department of Surgery, University Maggiore Hospital della Carità, Novara, Italy
| | - Abrorjon A Yusupbekov
- Republican Specialized Scientific and Practical Medical Center of Oncology and Radiology (National Cancer Center of Uzbekistan), Tashkent, Uzbekistan
| | - Yanfang Zheng
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
2
|
Jha SK, De Rubis G, Devkota SR, Zhang Y, Adhikari R, Jha LA, Bhattacharya K, Mehndiratta S, Gupta G, Singh SK, Panth N, Dua K, Hansbro PM, Paudel KR. Cellular senescence in lung cancer: Molecular mechanisms and therapeutic interventions. Ageing Res Rev 2024; 97:102315. [PMID: 38679394 DOI: 10.1016/j.arr.2024.102315] [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: 02/25/2024] [Revised: 04/03/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Lung cancer stands as the primary contributor to cancer-related fatalities worldwide, affecting both genders. Two primary types exist where non-small cell lung cancer (NSCLC), accounts for 80-85% and SCLC accounts for 10-15% of cases. NSCLC subtypes include adenocarcinoma, squamous cell carcinoma, and large cell carcinoma. Smoking, second-hand smoke, radon gas, asbestos, and other pollutants, genetic predisposition, and COPD are lung cancer risk factors. On the other hand, stresses such as DNA damage, telomere shortening, and oncogene activation cause a prolonged cell cycle halt, known as senescence. Despite its initial role as a tumor-suppressing mechanism that slows cell growth, excessive or improper control of this process can cause age-related diseases, including cancer. Cellular senescence has two purposes in lung cancer. Researchers report that senescence slows tumor growth by constraining multiplication of impaired cells. However, senescent cells also demonstrate the pro-inflammatory senescence-associated secretory phenotype (SASP), which is widely reported to promote cancer. This review will look at the role of cellular senescence in lung cancer, describe its diagnostic markers, ask about current treatments to control it, look at case studies and clinical trials that show how senescence-targeting therapies can be used in lung cancer, and talk about problems currently being faced, and possible solutions for the same in the future.
Collapse
Affiliation(s)
- Saurav Kumar Jha
- Department of Biological Sciences and Bioengineering (BSBE), Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Shankar Raj Devkota
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Yali Zhang
- School of Chemical Engineering, University of Adelaide, Adelaide 5005, Australia
| | - Radhika Adhikari
- College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Jeonnam 58554, Republic of Korea
| | - Laxmi Akhileshwar Jha
- Naraina Vidya Peeth Group of Institutions, Faculty of Pharmacy, Dr. A. P. J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh 0208020, India
| | - Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam 781026, India; Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam 781035, India
| | - Samir Mehndiratta
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Sachin Kumar Singh
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia; School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India
| | - Nisha Panth
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia.
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia.
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia.
| |
Collapse
|
3
|
Ramoni D, Coco S, Rossi G, Dellepiane C, Bennicelli E, Santamaria S, Zinoli L, Tagliafico AS, Tagliamento M, Barletta G, Liberale L, Tirandi A, Minetti S, Bertolotto M, Montecucco F, Genova C, Carbone F. Circulating Osteopontin Predicts Clinical and Radiological Response in First-Line Treatment of Advanced Non-Small Cell Lung Cancer. Lung 2024; 202:197-210. [PMID: 38480620 PMCID: PMC11009777 DOI: 10.1007/s00408-024-00675-5] [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: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 04/13/2024]
Abstract
PURPOSE Pembrolizumab-based regimens are conditioned by the expression of PD-L1, but durable response rate is limited by innate and acquired resistance mechanisms. Here, we focus on osteopontin (OPN), an upfront biomarker of senescence, which closely associated with natural history of non-small cell lung cancer (NSCLC). METHODS Seventy-nine patients eligible to pembrolizumab regimens-alone or in combination with chemotherapy-as first-line treatment of advanced NSCLC were enrolled. Predictive value of OPN toward iRECIST progression disease (PD) was set as first outcome. Secondary ones included performance status (ECOG) at baseline, early (first and best) responses, and overall survival (OS). RESULTS High Serum OPN characterized patients with worse ECOG-PS (p = 0.015) at baseline and subjects experienced PD/death at first (OR 1.17 [1.02 to 1.35]; p = 0.030) and best responses (0.04 [0.00 to 0.81]; p = 0.035). OPN was associated with time-to-progression (B -2.74 [-4.46 to -1.01]) and time-to death (-0.13 [-0.20 to -0.05]). Cox regression models unveil a predictive value for iRECIST-PD (HR 1.01 [1.00 to 1.02]; p = -0.005), RECIST-PD (HR 1.01 [1.00 to 1.02]; p = 0.017), and OS (HR 1.02 [1.01 to 1.03]; p = 0.001). These models were internally validated through bootstrap resampling and characterized by relevant discrimination ability at ROC curve analyses. CONCLUSION Baseline levels of serum OPN is closely associated with performance status and short/long term outcomes in patients with advanced NSCLC, which are candidate to pembrolizumab-based regimens. As upfront biomarker of senescence, OPN may pave the way for future studies focusing on senescence patterns in NSCLC.
Collapse
Affiliation(s)
- Davide Ramoni
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Simona Coco
- U.O.S. Tumori Polmonari, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Giovanni Rossi
- IRCCS Ospedale Policlinico San Martino, U.O.C. Oncologia Medica 2, 16132, Genoa, Italy
- Dipartimento di Medicina, Chirurgia e Scienze Sperimentali, Università di Sassari, 07100, Sassari, Italy
| | - Chiara Dellepiane
- IRCCS Ospedale Policlinico San Martino, U.O.C. Oncologia Medica 2, 16132, Genoa, Italy
| | - Elisa Bennicelli
- IRCCS Ospedale Policlinico San Martino, U.O.C. Oncologia Medica 2, 16132, Genoa, Italy
| | - Sara Santamaria
- UOC Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Linda Zinoli
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Alberto Stefano Tagliafico
- Dipartimento di Radiodiagnostica, IRCCS-Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Health Sciences, University of Genoa, 16132, Genoa, Italy
| | - Marco Tagliamento
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Giulia Barletta
- IRCCS Ospedale Policlinico San Martino, U.O.C. Oncologia Medica 2, 16132, Genoa, Italy
| | - Luca Liberale
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa - Italian Cardiovascular Network, Genoa, Italy
| | - Amedeo Tirandi
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Silvia Minetti
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Maria Bertolotto
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
| | - Fabrizio Montecucco
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa - Italian Cardiovascular Network, Genoa, Italy
| | - Carlo Genova
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy
- UOC Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Federico Carbone
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132, Genoa, Italy.
- IRCCS Ospedale Policlinico San Martino, Genoa - Italian Cardiovascular Network, Genoa, Italy.
| |
Collapse
|
4
|
Matveeva K, Vasilieva M, Minskaia E, Rybtsov S, Shevyrev D. T-cell immunity against senescence: potential role and perspectives. Front Immunol 2024; 15:1360109. [PMID: 38504990 PMCID: PMC10948549 DOI: 10.3389/fimmu.2024.1360109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
The development of age-associated diseases is related to the accumulation of senescent cells in the body. These are old non-functional cells with impaired metabolism, which are unable to divide. Such cells are also resistant to programmed cell death and prone to spontaneous production of some inflammatory factors. The accumulation of senescent cells is related to the age-associated dysfunction of organs and tissues as well as chronic inflammation that enhances with age. In the young organism, senescent cells are removed with the innate immunity system. However, the efficiency of this process decreases with age. Nowadays, more and more evidences are accumulating to support the involvement of specific immunity and T-lymphocytes in the fight against senescent cells. It has great physiological importance since the efficient elimination of senescent cells requires a high diversity of antigen-recognizing receptors to cover the entire spectrum of senescent-associated antigens with high precision and specificity. Developing the approaches of T-cell immunity stimulation to generate or amplify a physiological immune response against senescent cells can provide new perspectives to extend active longevity. In this mini-review, the authors summarize the current understanding of the role of T-cell immunity in the fight against senescent cells and discuss the prospects of stimulating adaptive immunity for combating the accumulation of senescent cells that occurs with age.
Collapse
|
5
|
Cao T, Huang M, Huang X, Tang T. Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer. PeerJ 2024; 12:e16935. [PMID: 38435998 PMCID: PMC10909353 DOI: 10.7717/peerj.16935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
Background Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with high heterogeneity, poor prognosis, and a low 10-year survival rate of less than 50%. Although cellular senescence displays extensive effects on cancer, the comprehensions of cellular senescence-related characteristics in TNBC patients remains obscure. Method Single-cell RNA sequencing (scRNA-seq) data were analyzed by Seurat package. Scores for cellular senescence-related pathways were computed by single-sample gene set enrichment analysis (ssGSEA). Subsequently, unsupervised consensus clustering was performed for molecular cluster identification. Immune scores of patients in The Cancer Genome Atlas (TCGA) dataset and associated immune cell scores were calculated using Estimation of STromal and Immune cells in MAlignantTumours using Expression data (ESTIMATE) and Microenvironment Cell Populations-counter (MCP-counter), Tumor Immune Estimation Resource (TIMER) and Estimating the Proportion of Immune and Cancer cells (EPIC) methods, respectively. Immunotherapy scores were assessed using TIDE. Furthermore, feature genes were identified by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses; these were used to construct a risk model. Additionally, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and transwell assay were conducted for in vitro validation of hub genes. Result TNBC was classified into three subtypes based on cellular senescence-related pathways as clusters 1, 2, and 3. Specifically, cluster 1 showed the best prognosis, followed by cluster 2 and cluster 3. The levels of gene expression in cluster 2 were the lowest, whereas these were the highest in cluster 3. Moreover, clusters 1 and 3 showed a high degree of immune infiltration. TIDE scores were higher for cluster 3, suggesting that immune escape was more likely in patients with the cluster 3 subtype who were less likely to benefit from immunotherapy. Next, the TNBC risk model was constructed and validated. RT-qPCR revealed that prognostic risk genes (MMP28, ACP5 and KRT6A) were up-regulated while protective genes (CT83) were down-regulated in TNBC cell lines, validating the results of the bioinformatics analysis. Meanwhile, cellular experiments revealed that ACP5 could promote the migration and invasion abilities in two TNBC cell lines. Finally, we evaluated the validity of prognostic models for assessing TME characteristics and TNBC chemotherapy response. Conclusion In conclusion, these findings help to assess the efficacy of targeted therapies in patients with different molecular subtypes, have practical applications for subtype-specific treatment of TNBC patients, and provide information on prognostic factors, as well as guidance for the revelation of the molecular mechanisms by which senescence-associated genes influence TNBC progression.
Collapse
Affiliation(s)
- Tengfei Cao
- Department of Breast Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengjie Huang
- Department of Breast Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinyue Huang
- Department of Breast Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tian Tang
- Department of Pathology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
6
|
Haibo Z, Tianyun L, Xiaoman C, Xiaoyan H. Cell Senescence-Related Genes as Biomarkers for Prognosis and Immunotherapeutic Response in Colon Cancer. Biochem Genet 2024:10.1007/s10528-024-10690-z. [PMID: 38411939 DOI: 10.1007/s10528-024-10690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
Colon adenocarcinoma (COAD) stands out as the most prevalent malignancy diagnosed within the gastrointestinal tract, bearing substantial incidence and mortality rates. The processes of ageing and senescence intricately intertwine with tumorigenesis and immune regulation, concurrently exerting influence on the remodelling of the tumor microenvironment (TME). This phenomenon, in turn, significantly impacts the efficacy of immunotherapeutic interventions. Despite this awareness, the comprehensive understanding of the intricate interplay between cellular senescence and TME in the context of COAD remains elusive. Further inquiry is imperative to comprehensively gauge the relevance of cellular senescence-related genes (CSGs) in the realms of immune infiltration and the prognostication of COAD. Differentially expressed cell senescence-related genes (DE-CSGs) within COAD tumors and normal specimens were discerned through analysis of the TCGA-COAD dataset. Leveraging univariate, LASSO, and multivariate Cox regression analyses, we formulated a prognostic risk signature. Subsequent validation utilised two independent GEO datasets. Furthermore, a nomogram was devised to gauge the prognostic significance of this signature. Additionally, the immune landscape of the Cell Senescence-related Signature (CSS) was characterised using CIBERSORT and TIMER algorithms. The expression levels of CSGs were quantified through RT-PCR in COAD specimens. Drawing upon mRNA expression profiles of 191 DE-CSGs, we successfully established a 9-gene CSS, demonstrating its autonomy as a prognostic determinant for COAD patients. Those assigned high-risk scores exhibited an immunosuppressive phenotype, marked by elevated proportions of resting CD4+memory T cells and macrophages M0, correlating with diminished overall survival. Subsequent analyses uncovered that the amalgamation of CSS with the expression profiles of immune checkpoint key genes effectively predicted patient prognosis. Furthermore, patients with low-risk scores demonstrated a potential association with more favourable therapeutic outcomes in the context of immunotherapy. This study has culminated in the development of a prognostic risk signature grounded in cell senescence-related genes for COAD. We posit that the CSS plays a regulatory role in immune infiltration, emerging as a robust biomarker for prognosis and a predictive indicator for immunotherapeutic responsiveness within the COAD landscape.
Collapse
Affiliation(s)
- Zhang Haibo
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Lan Tianyun
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Chen Xiaoman
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Han Xiaoyan
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| |
Collapse
|
7
|
Huang Y, Jiang H, Xu G, Li X, Chen W, Lun Y, Zhang J. Comprehensive analysis of cellular senescence and immune microenvironment in papillary thyroid carcinoma. Aging (Albany NY) 2024; 16:2866-2886. [PMID: 38329430 PMCID: PMC10911381 DOI: 10.18632/aging.205520] [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: 05/11/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Senescence-induced therapy was previously considered as an effective treatment for tumors, and cellular senescence was initially regarded as an effective mechanism against cancer. However, whether cell senescence-related genes can be used to predict the prognosis of papillary thyroid carcinoma (PTC) and immunotherapy remains unclear. We developed and validated a cell senescence-related signature (CSRS) by analyzing the gene expression of 278 genes related to cellular senescence in 738 patients with PTC. Additionally, further analysis showed that CSRS was a reliable predictor of patient outcomes in combination with immune checkpoint expression and drug susceptibility, and patients with high risk scores may benefit from immunotherapy. The findings of this study demonstrate that CSRS serves as an immunotherapeutic response and prognosis biomarker affecting the tumor immune microenvironment of PTC.
Collapse
Affiliation(s)
- Yinde Huang
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
- Department of Breast and Thyroid Surgery, Chongqing General Hospital, Chongqing 401147, China
| | - Han Jiang
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| | - Guangwen Xu
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| | - Xin Li
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| | - Wenbin Chen
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| | - Yu Lun
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| | - Jian Zhang
- Department of Vascular and Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shen-Yang 110001, Liaoning, China
| |
Collapse
|
8
|
Wang Q, Shang Y, Li Y, Li X, Wang X, He Y, Ma J, Ning S, Chen H. Identification of cuproptosis-related diagnostic biomarkers in idiopathic pulmonary fibrosis. Medicine (Baltimore) 2024; 103:e36801. [PMID: 38215148 PMCID: PMC10783416 DOI: 10.1097/md.0000000000036801] [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: 09/16/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with clinical and pathological heterogeneity. Recent studies have identified cuproptosis as a novel cell death mechanism. However, the role of cuproptosis-related genes in the pathogenesis of IPF is still unclear. Two IPF datasets of the Gene Expression Omnibus database were studied. Mann-Whitney U test, correlation analysis, functional enrichment analyses, single-sample gene set enrichment analysis, CIBERSORT, unsupervised clustering, weighted gene co-expression network analysis, and receiver operating characteristic curve analysis were used to conduct our research. The dysregulated cuproptosis-related genes and immune responses were identified between IPF patients and controls. Two cuproptosis-related molecular clusters were established in IPF, the high immune score group (C1) and the low immune score group (C2). Significant heterogeneity in immunity between clusters was revealed by functional analyses results. The module genes with the strongest correlation to the 2 clusters were identified by weighted gene co-expression network analysis results. Seven hub genes were found using the Cytoscape software. Ultimately, 2 validated diagnostic biomarkers of IPF, CDKN2A and NEDD4, were obtained. Subsequently, the results were validated in GSE47460. Our investigation illustrates that CDKN2A and NEDD4 may be valid biomarkers that were useful for IPF diagnosis and copper-related clustering.
Collapse
Affiliation(s)
- Qi Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Shang
- Department of Respiration, The First Hospital of Harbin, Harbin, China
| | - Yupeng Li
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xincheng Li
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xue Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yaowu He
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Ma
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Chen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
9
|
Wang P, Zhang Y, Cai Q, Long Q, Pan S, Zhou W, Deng T, Mo W, Wang S, Zhang Y, Wang C, Chen C. Optimal combination of immune checkpoint and senescence molecule predicts adverse outcomes in patients with acute myeloid leukemia. Ann Med 2023; 55:2201507. [PMID: 37070487 PMCID: PMC10120552 DOI: 10.1080/07853890.2023.2201507] [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] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND High expression of immune checkpoints (ICs) and senescence molecules (SMs) contributes to T cell dysfunction, tumor escape, and progression, but systematic evaluation of them in co-expression patterns and prognosis in acute myeloid leukemia (AML) was lacking. METHODS Three publicly available datasets (TCGA, Beat-AML, and GSE71014) were first used to explore the effect of IC and SM combinations on prognosis and the immune microenvironment in AML, and bone marrow samples from 68 AML patients from our clinical center (GZFPH) was further used to validate the findings. RESULTS High expression of CD276, Bcl2-associated athanogene 3 (BAG3), and SRC was associated with poor overall survival (OS) of AML patients. CD276/BAG3/SRC combination, standard European Leukemia Net (ELN) risk stratification, age, and French-American-British (FAB) subtype were used to construct a nomogram model. Interestingly, the new risk stratification derived from the nomogram was better than the standard ELN risk stratification in predicting the prognosis for AML. A weighted combination of CD276 and BAG3/SRC positively corrected with TP53 mutation, p53 pathway, CD8+ T cells, activated memory CD4+ T cells, T-cell senescence score, and Tumor Immune Dysfunction and Exclusion (TIDE) score estimated by T-cell dysfunction. CONCLUSION High expression of ICs and SMs was associated with poor OS of AML patients. The co-expression patterns of CD276 and BAG3/SRC might be potential biomarkers for risk stratification and designing combinational immuno-targeted therapy in AML.Key MessagesHigh expression of CD276, BAG3, and SRC was associated with poor overall survival of AML patients.The co-expression patterns of CD276 and BAG3/SRC might be potential biomarkers for risk stratification and designing combinational immuno-targeted therapy in AML.
Collapse
Affiliation(s)
- Peipei Wang
- Department of Oncology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R. China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, P.R. China
| | - Yuling Zhang
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Qinghua Cai
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Qingqin Long
- Department of Oncology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R. China
| | - Shiyi Pan
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Wei Zhou
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Tingfen Deng
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Wenjian Mo
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Shunqing Wang
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
| | - Yuping Zhang
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
- Yuping Zhang Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou510180, P.R. China
| | - Caixia Wang
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
- Caixia Wang
| | - Cunte Chen
- Department of Hematology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, P.R.China
- CONTACT Cunte Chen
| |
Collapse
|
10
|
Tan J, Wang C, Jin Y, Xia Y, Gong B, Zhao Q. Optimal combination of MYCN differential gene and cellular senescence gene predicts adverse outcomes in patients with neuroblastoma. Front Immunol 2023; 14:1309138. [PMID: 38035110 PMCID: PMC10687280 DOI: 10.3389/fimmu.2023.1309138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Neuroblastoma (NB) is a common extracranial tumor in children and is highly heterogeneous. The factors influencing the prognosis of NB are not simple. Methods To investigate the effect of cell senescence on the prognosis of NB and tumor immune microenvironment, 498 samples of NB patients and 307 cellular senescence-related genes were used to construct a prediction signature. Results A signature based on six optimal candidate genes (TP53, IL-7, PDGFRA, S100B, DLL3, and TP63) was successfully constructed and proved to have good prognostic ability. Through verification, the signature had more advantages than the gene expression level alone in evaluating prognosis was found. Further T cell phenotype analysis displayed that exhausted phenotype PD-1 and senescence-related phenotype CD244 were highly expressed in CD8+ T cell in MYCN-amplified group with higher risk-score. Conclusion A signature constructed the six MYCN-amplified differential genes and aging-related genes can be used to predict the prognosis of NB better than using each high-risk gene individually and to evaluate immunosuppressed and aging tumor microenvironment.
Collapse
Affiliation(s)
- Jiaxiong Tan
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Chaoyu Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Yan Jin
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Yuren Xia
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Baocheng Gong
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qiang Zhao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| |
Collapse
|
11
|
Zhou X, Xu R, Lu T, Xu R, Wang C, Peng B, Chang X, Shen Z, Wang K, Shi J, Zhao J, Zhang LY. Identification of immunotherapy biomarkers for improving the clinical outcome of homologous recombination deficiency patients with lung adenocarcinoma. Aging (Albany NY) 2023; 15:8090-8112. [PMID: 37578930 PMCID: PMC10496994 DOI: 10.18632/aging.204957] [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: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023]
Abstract
Homologous recombination deficiency (HRD) is a common molecular signature of genomic instability and has been shown to be a biomarker for targeted therapies. However, there is a lack of studies on the role of HRD changes in lung adenocarcinoma (LUAD) transcriptomics. HRD scores were determined using single nucleotide polymorphism (SNP) array data from LUAD patients from The Cancer Genome Atlas (TCGA) database. Transcriptional data from patients with different scores were analyzed to identify biomarkers associated with HRD. Candidate biomarkers were validated using Gene Expression Omnibus (GEO)-sourced datasets and an immunotherapy cohort. According to the bulk transcriptome and clinical characteristics of 912 LUAD patients and Single-cell RNA-seq of 9 LUAD patients from TCGA and GEO databases, we observed increased MS4A6A expression in HRD tumors; high MS4A6A expression predicted improved survival outcomes. Furthermore, a comprehensive analysis of the tumor immune microenvironment (TIME) revealed a positive correlation between MS4A6A expression and neoantigen loading and immune cell infiltration. Additionally, the immunotherapy cohort confirmed the possibility of using MS4A6A as a biomarker. Collectively, we suggest that MS4A6A is associated with HRD and provide a new perspective toward identifying promising biomarkers for immunotherapy.
Collapse
Affiliation(s)
- Xiang Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Rongjian Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266005, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Chenghao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Xiaoyan Chang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Zhiping Shen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Kaiyu Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Jiaxin Shi
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Jiaying Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| | - Lin-You Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150084, China
| |
Collapse
|
12
|
Lin T, Wang H, Liu Y, Zhao F, He X. Gene set variation analysis-based aging and senescence score as a prognostic indicator and therapeutic guide in lung adenocarcinoma. Front Genet 2023; 14:1176292. [PMID: 37470041 PMCID: PMC10353051 DOI: 10.3389/fgene.2023.1176292] [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: 02/28/2023] [Accepted: 04/12/2023] [Indexed: 07/21/2023] Open
Abstract
Accumulating evidence suggests that aging and senescence play crucial roles in tumorigenesis, cancer progression, and treatment. However, the influence of aging and senescence-related genes (ASRGs) on clinical outcomes and treatment options in lung adenocarcinoma (LUAD) patients remains unknown. Here, we developed an aging and senescence-related scoring system, ASRS, by integrating bulk transcriptome data from 22 LUAD datasets. In 3,243 LUAD samples, higher ASRS scores were associated with poor tumor stage and pathological grade, as well as shorter overall survival, disease-free survival, and recurrence-free survival. Additionally, ASRS was associated with different immune patterns in the tumor microenvironment (TME). Importantly, ASRS was found to predict therapeutic efficacy, with patients having a low ASRS benefiting from immunotherapy and those with a high ASRS responding better to chemotherapy. Therefore, ASRS represents a previously overlooked characteristic of LUAD that can influence patient outcomes and treatment success.
Collapse
Affiliation(s)
- Tao Lin
- Department of Thoracic Surgery, Tangshan People’s Hospital, Tangshan, China
| | - Hong Wang
- Tangshan Central Blood Station, Tangshan, China
| | - Ying Liu
- Department of Neurology, Xingtai Third Hospital, Xingtai, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xi He
- Department of Thoracic Surgery, Dongguan Marina Bay Central Hospital, Dongguan, China
| |
Collapse
|
13
|
Qin RX, Yang Y, Chen JF, Huang LJ, Xu W, Qin QC, Liang XJ, Lai XY, Huang XY, Xie MS, Chen L. Transcriptomic analysis reveals the potential biological mechanism of AIS and lung adenocarcinoma. Front Neurol 2023; 14:1119160. [PMID: 37265472 PMCID: PMC10229805 DOI: 10.3389/fneur.2023.1119160] [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] [Received: 12/08/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction Acute ischemic stroke (AIS) and lung adenocarcinoma (LUAD) are associated with some of the highest morbidity and mortality rates worldwide. Despite reports on their strong correlation, the causal relationship is not fully understood. The study aimed to identify and annotate the biological functions of hub genes with clinical diagnostic efficacy in AIS and LUAD. Methods Transcriptome and single-cell datasets were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). We identified the differentially expressed genes (DEGs) upregulated in AIS and LUAD and found 372 genes intersecting both datasets. Hub genes were identified using protein-protein interaction (PPI) networks, and the diagnostic and prognostic utility of these hub genes was then investigated using receiver operating characteristic (ROC) curves, survival analysis, and univariable Cox proportional hazard regression. Single-cell analysis was used to detect whether the hub genes were expressed in tumor epithelial cells. The immune microenvironment of AIS and LUAD was assessed using the CIBERSORT algorithm. The protein expression of these hub genes was tracked using the Human Protein Atlas (HPA). We calculated the number of positive cells using the digital pathology software QuPath. Finally, we performed molecular docking after using the Enrichr database to predict possible medicines. Results We identified the molecular mechanisms underlying hub genes in AIS and LUAD and found that CCNA2, CCNB1, CDKN2A, and CDK1 were highly expressed in AIS and LUAD tissue samples compared to controls. The hub genes were mainly involved in the following pathways: the cell cycle, cellular senescence, and the HIF-1 signaling pathway. Using immunohistochemical slices from the HPA database, we confirmed that these hub genes have a high diagnostic capability for AIS and LUAD. Further, their high expression is associated with poor prognosis. Finally, curcumin was tested as a potential medication using molecular docking modeling. Discussion Our findings suggest that the hub genes we found in this study contribute to the development and progression of AIS and LUAD by altering the cellular senescence pathway. Thus, they may be promising markers for diagnosis and prognosis.
Collapse
Affiliation(s)
- Rong-Xing Qin
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yue Yang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jia-Feng Chen
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Li-Juan Huang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Wei Xu
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Qing-Chun Qin
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Jun Liang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xin-Yu Lai
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Ying Huang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Min-Shan Xie
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Li Chen
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Regenerative Medicine and Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| |
Collapse
|
14
|
Identification of Aging and Young Subtypes for Predicting Colorectal Cancer Prognosis and Immunotherapy Responses. Int J Mol Sci 2023; 24:ijms24021516. [PMID: 36675039 PMCID: PMC9862647 DOI: 10.3390/ijms24021516] [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: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is critically related to aging and severely threatens human lives. To better explore the effects of aging on CRC progression and therapy outcome, a reliable aging subtypes identification of CRC is urgently desired. Here, 28 aging-related genes associated with the CRC prognosis were selected by univariate Cox analyses. Based on these 28 genes, CRC patients were divided into the aging subtype and young subtype by non-negative matrix factorization clustering. Aging subtype and young subtype of CRC were identified with distinct molecular features and clinical prognosis. The aging subtype was characterized by upregulation of senescence-associated secretory phenotype, higher frequencies of TP53 and immune checkpoint molecules, and high sensitivity to protein kinase and angiogenesis inhibitors. Furthermore, 14 genes were selected by LASSO penalized Cox regression analyses for aging-related risk signature construction. The constructed aging risk signature exhibited good prediction and the nomogram showed robust discrimination power over the traditional CRC staging system. In conclusion, this study successfully established aging subtype and young subtype of CRC, which is helpful to identify patients with aging characteristics to evaluate prognosis and treatment outcomes. Introducing aging-based subtypes into clinical concern and patient prognostication provides new opportunities for personalized CRC treatment.
Collapse
|
15
|
Ju G, Zeng K, Lu L, Diao H, Wang H, Li X, Zhou T. Identification and validation of the cellular senescence-related molecular subtypes of triple negative breast cancer via integrating bulk and single-cell RNA sequencing data. Am J Cancer Res 2023; 13:569-588. [PMID: 36895975 PMCID: PMC9989623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
Patients with triple-negative breast cancer (TNBC) reportedly benefit from immune checkpoint blockade (ICB) therapy. However, the subtype-specific vulnerabilities of ICB in TNBC remain unclear. As the complex interplay between cellular senescence and anti-tumor immunity has been previously discussed, we aimed to identify markers related to cellular senescence that may serve as potential predictors of response to ICB in TNBC. We used three transcriptomic datasets derived from ICB-treated breast cancer samples at both scRNA-seq and bulk-RNA-seq levels to define the subtype-specific vulnerabilities of ICB in TNBC. Differences in the molecular features and immune cell infiltration among the different TNBC subtypes were further explored using two scRNA-seq, three bulk-RNA-seq, and two proteomic datasets. 18 TNBC samples were collected and utilized to verify the association between gene expression and immune cell infiltration by multiplex immunohistochemistry (mIHC). A specific type of cellular senescence was found to be significantly associated with response to ICB in TNBC. We employed the expression of four senescence-related genes, namely CDKN2A, CXCL10, CCND1, and IGF1R, to define a distinct senescence-related classifier using the non-negative matrix factorization approach. Two clusters were identified, namely the senescence-enriching cluster (C1; CDKN2A high CXCL10 high CCND1 low IGF1R low) and proliferating-enriching cluster (C2; CDKN2A low CXCL10 low CCND1 high IGF1R high). Our results indicated that the C1 cluster responds better to ICB and behaves with higher CD8+ T cell infiltration than the C2 cluster. Altogether, in this study, we developed a robust cellular senescence-related classifier of TNBC based on the expression of CDKN2A, CXCL10, CCND1, and IGF1R. This classifier act as a potential predictor of clinical outcomes and response to ICB.
Collapse
Affiliation(s)
- Gaoda Ju
- Department of Medical Oncology, Key Laboratory of Carcinogenesis & Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute Beijing 100142, China
| | - Kai Zeng
- Department of Thyroid Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University Shenzhen 518000, Guangdong, China
| | - Linlin Lu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Soochow University Suzhou 215000, Jiangsu, China
| | - Han Diao
- Department of Pathology, Affiliated Hospital of Jining Medical University Jining 272000, Shandong, China
| | - Hao Wang
- Yancheng TCM Hospital, Nanjing University of Chinese Medicine Yancheng 224002, Jiangsu, China
| | - Xiaomin Li
- Department of Radiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine Shanghai, China
| | - Tianhao Zhou
- Department of Medical Oncology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine Shanghai 200080, China
| |
Collapse
|
16
|
Domen A, Deben C, Verswyvel J, Flieswasser T, Prenen H, Peeters M, Lardon F, Wouters A. Cellular senescence in cancer: clinical detection and prognostic implications. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:360. [PMID: 36575462 PMCID: PMC9793681 DOI: 10.1186/s13046-022-02555-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/30/2022] [Indexed: 12/28/2022]
Abstract
Cellular senescence is a state of stable cell-cycle arrest with secretory features in response to cellular stress. Historically, it has been considered as an endogenous evolutionary homeostatic mechanism to eliminate damaged cells, including damaged cells which are at risk of malignant transformation, thereby protecting against cancer. However, accumulation of senescent cells can cause long-term detrimental effects, mainly through the senescence-associated secretory phenotype, and paradoxically contribute to age-related diseases including cancer. Besides its role as tumor suppressor, cellular senescence is increasingly being recognized as an in vivo response in cancer patients to various anticancer therapies. Its role in cancer is ambiguous and even controversial, and senescence has recently been promoted as an emerging hallmark of cancer because of its hallmark-promoting capabilities. In addition, the prognostic implications of cellular senescence have been underappreciated due to the challenging detection and sparse in and ex vivo evidence of cellular senescence in cancer patients, which is only now catching up. In this review, we highlight the approaches and current challenges of in and ex vivo detection of cellular senescence in cancer patients, and we discuss the prognostic implications of cellular senescence based on in and ex vivo evidence in cancer patients.
Collapse
Affiliation(s)
- Andreas Domen
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium ,grid.411414.50000 0004 0626 3418Department of Oncology, Antwerp University Hospital (UZA), 2650 Edegem (Antwerp), Belgium
| | - Christophe Deben
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium
| | - Jasper Verswyvel
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium
| | - Tal Flieswasser
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium
| | - Hans Prenen
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium ,grid.411414.50000 0004 0626 3418Department of Oncology, Antwerp University Hospital (UZA), 2650 Edegem (Antwerp), Belgium
| | - Marc Peeters
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium ,grid.411414.50000 0004 0626 3418Department of Oncology, Antwerp University Hospital (UZA), 2650 Edegem (Antwerp), Belgium
| | - Filip Lardon
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium
| | - An Wouters
- grid.5284.b0000 0001 0790 3681Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk (Antwerp), Belgium
| |
Collapse
|
17
|
Gao L, Wang X, Wang X, Wang F, Tang J, Ji J. A prognostic model and immune regulation analysis of uterine corpus endometrial carcinoma based on cellular senescence. Front Oncol 2022; 12:1054564. [PMID: 36568182 PMCID: PMC9775865 DOI: 10.3389/fonc.2022.1054564] [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: 10/04/2022] [Accepted: 10/28/2022] [Indexed: 12/13/2022] Open
Abstract
Background This study aimed to explore the clinical significance of cellular senescence in uterine corpus endometrial carcinoma (UCEC). Methods Cluster analysis was performed on GEO data and TCGA data based on cellular senescence related genes, and then performed subtype analysis on differentially expressed genes between subtypes. The prognostic model was constructed using Lasso regression. Survival analysis, microenvironment analysis, immune analysis, mutation analysis, and drug susceptibility analysis were performed to evaluate the practical relevance. Ultimately, a clinical nomogram was constructed and cellular senescence-related genes expression was investigated by qRT-PCR. Results We ultimately identified two subtypes. The prognostic model divides patients into high-risk and low-risk groups. There were notable discrepancies in prognosis, tumor microenvironment, immunity, and mutation between the two subtypes and groups. There was a notable connection between drug-sensitive and risk scores. The nomogram has good calibration with AUC values between 0.75-0.8. In addition, cellular senescence-related genes expression was investigated qRT-PCR. Conclusion Our model and nomogram may effectively forecast patient prognosis and serve as a reference for patient management.
Collapse
Affiliation(s)
- Lulu Gao
- Department of Obstetrics and Gynecology, Nantong Maternal and Child Health Hospital Affiliated to Nantong University, Nantong, China
| | - Xiangdong Wang
- Department of Integrated Traditional Chinese and Western Internal Medicine, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong, China,Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xuehai Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Fengxu Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Juan Tang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China,*Correspondence: Juan Tang, ; Jinfeng Ji,
| | - Jinfeng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong, China,*Correspondence: Juan Tang, ; Jinfeng Ji,
| |
Collapse
|
18
|
Luo Y, Liu H, Fu H, Ding GS, Teng F. A cellular senescence-related classifier based on a tumorigenesis- and immune infiltration-guided strategy can predict prognosis, immunotherapy response, and candidate drugs in hepatocellular carcinoma. Front Immunol 2022; 13:974377. [PMID: 36458010 PMCID: PMC9705748 DOI: 10.3389/fimmu.2022.974377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/25/2022] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Cellular senescence plays an irreplaceable role in tumorigenesis, progression, and tumor microenvironment (TME) remodeling. However, to date, there is limited research delineating the landscape of cellular senescence in hepatocellular carcinoma (HCC), and an improved understanding on the interaction of tumor-associated cellular senescence with HCC prognosis, TME, and response to immunotherapy is warrant. METHODS Tumorigenic and immune infiltration-associated senescence genes were determined by weighted gene co-expression network analysis (WGCNA) and the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm, and subsequently, a prognostic scoring model (named TIS) was constructed using multiple survival analysis algorithms to classify the senescence-related subtypes of HCC. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were conducted to identify the distinct hallmark pathways between high- and low-risk subtypes. Additionally, we carried out correlation analyses for TIS and clinical traits, senescence-associated secretory phenotype (SASP), immune infiltration and evasion, immune checkpoint factors, drug response, and immunotherapeutic efficacy. External experimental validation was conducted to delineate the association of CPEP3 (a TIS gene) with HCC phenotypes through assays of proliferation, colony formation, and invasion. RESULTS A five-gene TIS, composed of NET1, ATP6V0B, MMP1, GTDC1, and CPEB3, was constructed and validated using TCGA and ICGC datasets, respectively, and showed a highly robust and plausible signature for overall survival (OS) prediction of HCC in both training and validation cohorts. Patients in the TIS-high group were accompanied by worse OS, activation of carcinogenetic pathways, infiltration of immunosuppressive cells, exclusion of effector killing cells, overexpression of immunomodulatory genes and SASP, and unsatisfied response to immunotherapy. In response to anticancer drugs, patients in the TIS-high group exhibited enhanced susceptibility to several conventional chemotherapeutic agents (5-fluorouracil, docetaxel, doxorubicin, gemcitabine, and etoposide), as well as several inhibitors of pathways involved in cellular senescence (cell-cycle inhibitors, bromodomain and extraterminal domain family (BET) inhibitors, PI3K-AKT pathway inhibitors, and multikinase inhibitors). Additionally, four putative drugs (palbociclib, JAK3 inhibitor VI, floxuridine, and lestaurtinib) were identified as potential compounds for patients in the TIS-high group. Notably, in vitro functional validation showed that CPEB3 knockdown boosted the phenotypes of proliferation, clonogenicity, and invasion in HCC cells, whereas CPEB3 overexpression attenuated these phenotypes. CONCLUSIONS Our study provides comprehensive clues demonstrating the role of novel TIS in predicting HCC prognosis, immunotherapeutic response, and candidate drugs. This work highlights the significance of tumorigenesis- and immune infiltration-related cellular senescence in cancer therapy.
Collapse
Affiliation(s)
- Yi Luo
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Hao Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hong Fu
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Guo-Shan Ding
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Fei Teng
- Department of Liver Surgery and Organ Transplantation, Changzheng Hospital, Naval Medical University, Shanghai, China
| |
Collapse
|
19
|
Li J, Wang J, Liu D, Tao C, Zhao J, Wang W. Establishment and validation of a novel prognostic model for lower-grade glioma based on senescence-related genes. Front Immunol 2022; 13:1018942. [PMID: 36341390 PMCID: PMC9633681 DOI: 10.3389/fimmu.2022.1018942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/07/2022] [Indexed: 01/10/2023] Open
Abstract
Objective Increasing studies have indicated that senescence was associated with tumorigenesis and progression. Lower-grade glioma (LGG) presented a less invasive nature, however, its treatment efficacy and prognosis prediction remained challenging due to the intrinsic heterogeneity. Therefore, we established a senescence-related signature and investigated its prognostic role in LGGs. Methods The gene expression data and clinicopathologic features were from The Cancer Genome Atlas (TCGA) database. The experimentally validated senescence genes (SnGs) from the CellAge database were obtained. Then LASSO regression has been performed to build a prognostic model. Cox regression and Kaplan-Meier survival curves were performed to investigate the prognostic value of the SnG-risk score. A nomogram model has been constructed for outcome prediction. Immunological analyses were further performed. Data from the Chinese Glioma Genome Atlas (CGGA), Repository of Molecular Brain Neoplasia Data (REMBRANDT), and GSE16011 were used for validation. Results The 6-SnG signature has been established. The results showed SnG-risk score could be considered as an independent predictor for LGG patients (HR=2.763, 95%CI=1.660-4.599, P<0.001). The high SnG-risk score indicated a worse outcome in LGG (P<0.001). Immune analysis showed a positive correlation between the SnG-risk score and immune infiltration level, and the expression of immune checkpoints. The CGGA datasets confirmed the prognostic role of the SnG-risk score. And Kaplan-Meier analyses in the additional datasets (CGGA, REMBRANDT, and GSE16011) validated the prognostic role of the SnG-signature (P<0.001 for all). Conclusion The SnG-related prognostic model could predict the survival of LGG accurately. This study proposed a novel indicator for predicting the prognosis of LGG and provided potential therapeutic targets.
Collapse
Affiliation(s)
- Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Dongjing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Chuming Tao
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, China
- *Correspondence: Wen Wang, ; Jizong Zhao,
| | - Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- *Correspondence: Wen Wang, ; Jizong Zhao,
| |
Collapse
|
20
|
Gao C, Zhou G, Cheng M, Feng L, Cao P, Zhou G. Identification of senescence-associated long non-coding RNAs to predict prognosis and immune microenvironment in patients with hepatocellular carcinoma. Front Genet 2022; 13:956094. [PMID: 36330438 PMCID: PMC9624069 DOI: 10.3389/fgene.2022.956094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/30/2022] [Indexed: 02/17/2024] Open
Abstract
Background: Cellular senescence plays a complicated and vital role in cancer development because of its divergent effects on tumorigenicity. However, the long non-coding RNAs (lncRNAs) associated with tumor senescence and their prognostic value in hepatocellular carcinoma (HCC) remain unexplored. Methods: The trans-cancer oncogene-induced senescence (OIS) signature was determined by gene set variation analysis (GSVA) in the cancer genome atlas (TCGA) dataset. The OIS-related lncRNAs were identified by correlation analyses. Cox regression analyses were used to screen lncRNAs associated with prognosis, and an optimal predictive model was created by regression analysis of the least absolute shrinkage and selection operator (LASSO). The performance of the model was evaluated by Kaplan-Meier survival analyses, nomograms, stratified survival analyses, and receiver operating characteristic curve (ROC) analyses. Gene set enrichment analysis (GSEA) and cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) were carried out to explore the functional relevance and immune cell infiltration, respectively. Results: Firstly, we examined the pan-cancer OIS signature, and found several types of cancer with OIS strongly associated with the survival of patients, including HCC. Subsequently, based on the OIS signature, we identified 76 OIS-related lncRNAs with prognostic values in HCC. We then established an optimal prognostic model based on 11 (including NRAV, AC015908.3, MIR100HG, AL365203.2, AC009005.1, SNHG3, LINC01138, AC090192.2, AC008622.2, AL139423.1, and AC026356.1) of these lncRNAs by LASSO-Cox regression analysis. It was then confirmed that the risk score was an independent and potential risk indicator for overall survival (OS) (HR [95% CI] = 4.90 [2.74-8.70], p < 0.001), which outperforms those traditional clinicopathological factors. Furthermore, patients with higher risk scores also showed more advanced levels of a proinflammatory senescence-associated secretory phenotype (SASP), higher infiltration of regulatory T (Treg) cells and lower infiltration of naïve B cells, suggesting the regulatory effects of OIS on immune microenvironment. Additionally, we identified NRAV as a representative OIS-related lncRNA, which is over-expressed in HCC tumors mainly driven by DNA hypomethylation. Conclusion: Based on 11 OIS-related lncRNAs, we established a promising prognostic predictor for HCC patients, and highlighted the potential immune microenvironment-modulatory roles of OIS in HCC, providing a broad molecular perspective of tumor senescence.
Collapse
Affiliation(s)
- Chengzhi Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Guangming Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Min Cheng
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lan Feng
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Hebei University, Baoding, China
- Anhui Medical University, Hefei, China
| |
Collapse
|
21
|
Subtype Classification and Prognosis Signature Construction of Osteosarcoma Based on Cellular Senescence-Related Genes. JOURNAL OF ONCOLOGY 2022; 2022:4421952. [PMID: 36106335 PMCID: PMC9467774 DOI: 10.1155/2022/4421952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Background. Cellular senescence (CS) is an alternative procedure that replaces or reinforces inadequate apoptotic responses and is used as an influencing factor for a variety of cancers. The value of CS gene in evaluating the immunotherapy response and clinical outcome of osteosarcoma (OS) has not been reported, and an accurate risk model based on CS gene has not been developed for OS patients. Methods. 279 CS genes were obtained from CellAge. Univariate Cox regression analysis was used to screen the CS gene which was significantly related to the prognosis of OS samples in TARGET data set. The prognosis, clinicopathological features, immune infiltration, gene expression at immune checkpoints, tumor immune dysfunction and exclusion (TIDE) score, and chemotherapy resistance of OS were analyzed among clusters. Least absolute shrinkage and selection operator (Lasso) Cox regression analysis to build cellular senescence-related gene signature (CSRS). Univariate and multivariate Cox regression analysis of CSRS and clinical parameters were carried out, and the parameters with independent prognostic value were used to construct nomogram. Results. Based on 30 CS genes related to OS prognosis, OS samples were divided into three clusters: C1, C2, and C3. C3 showed the lowest survival rate and metastasis rate and the highest immune score and stromal score and was more likely to respond to immune checkpoint blockade (ICB) treatment. A CSRS scoring system including four CS genes (MYC, DLX2, EPHA3, and LIMK1) was constructed, which could distinguish the survival outcome, tumor microenvironment (TME) status, and ICB treatment response of patients with different CSRS score. Nomogram constructed by CSRS score and metastatic has a high prognostic value for OS. Conclusions. Our study identified a molecular classification determined by CS-related genes and developed a new CSRS that has potential value in OS immunotherapy response and clinical outcome prediction.
Collapse
|
22
|
Zhu ZG, Chen L, Miao DL, Jin Y, Wu Q. Integrated analysis of senescence-associated genes in pancreatic ductal adenocarcinoma. Front Genet 2022; 13:941389. [PMID: 36046234 PMCID: PMC9420911 DOI: 10.3389/fgene.2022.941389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/21/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Cellular senescence plays a critical role in the occurrence and development, and immune modulation of cancer. This research primarily investigated the role of senescence-associated genes (SAGs) in the survival and tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC). Methods: From the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database, the gene expression profiles and clinical data of PDAC samples were downloaded. SAGs in the TCGA cohort were used to build a novel prognostic model and validated in the ICGC cohort. The relationship of signature with the immune landscape, tumor mutational burden (TMB), as well as the sensitivity of different therapies, was explored. Moreover, a nomogram was developed to predict the overall survival of PDAC patients. Results: A prognostic signature was constructed on basis of three SAGs, and patients in the low-risk score group had a longer survival time. The accuracy of the signature to distinguish different score groups was confirmed through principal component analysis (PCA) and the Receiver operator curves curve. The mRNA expression of the three signature genes was also verified in normal pancreatic and PDAC cell lines by RT-qPCR. The signature could independently predict the prognosis of PDAC patients and had broad applicability. Meanwhile, the nomogram predicted that 1- and 3-years survival rates were in good agreement with the observed overall survival rates. Low-risk patients had lower tumor mutational burden, and low-TMB patients had a better prognosis. Low- and high-risk patients exhibit distinct immune cell infiltration and immune checkpoint changes. By further analyzing the risk score, patients in the low-risk group were more responsive to immunotherapy and a variety of commonly used chemotherapeutic drugs. Conclusion: The prognostic signature can well predict the prognosis and assess the possibility of immunotherapy in personalized PDAC treatment.
Collapse
|
23
|
Dai L, Wang X, Bai T, Liu J, Chen B, Li T, Yang W. Identification of a novel cellular senescence-related signature for the prediction of prognosis and immunotherapy response in colon cancer. Front Genet 2022; 13:961554. [PMID: 35991564 PMCID: PMC9386482 DOI: 10.3389/fgene.2022.961554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
The study was conducted to construct a cellular senescence-related risk score signature to predict prognosis and immunotherapy response in colon cancer. Colon cancer data were acquired from the Gene Expression Omnibus and The Cancer Genome Atlas databases. And cellular senescence-related genes were obtained from the CellAge database. The colon cancer data were classified into different clusters based on cellular senescence-related gene expression. Next, prognostic differential genes among clusters were identified with survival analysis. A cellular senescence-related risk score signature was developed by performing the LASSO regression analysis. Finally, PCA analysis, t-SNE analysis, Kaplan-Meier survival analysis, ROC analysis, univariate Cox regression analysis, multivariate Cox regression analysis, C-index analysis, meta-analysis, immune infiltration analysis, and IPS score analysis were used to evaluate the significance of the risk signature for predicting prognosis and immunotherapy response in colon cancer. The colon cancer data were classified into three clusters. The patients in cluster A and cluster B had longer survival. A cellular senescence-related risk score signature was developed. Patients in the low-risk score group showed a better prognosis. The risk score signature could predict colon cancer patients’ prognosis independently of other clinical characteristics. The risk score signature predicted the prognosis of colon cancer patients more accurately than other signatures. Patients in the low-risk score group showed a better response to immunotherapy. The opposite was true for the high-risk score group. In conclusion, the cellular senescence-related risk score signature could be used for the prediction of prognosis and immunotherapy response in colon cancer.
Collapse
|
24
|
Xing J, Jia Z, Li Y, Han Y. Construction of immunotherapy-related prognostic gene signature and small molecule drug prediction for cutaneous melanoma. Front Oncol 2022; 12:939385. [PMID: 35957907 PMCID: PMC9358033 DOI: 10.3389/fonc.2022.939385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022] Open
Abstract
Background Cutaneous melanoma (CM), a kind of skin cancer with a high rate of advanced mortality, exhibits a wide variety of driver and transmitter gene alterations in the immunological tumor microenvironment (TME) associated with tumor cell survival and proliferation. Methods We analyzed the immunological infiltration of TME cells in normal and malignant tissues using 469 CM and 556 normal skin samples. We used a single sample gene set enrichment assay (ssGSEA) to quantify the relative abundance of 28 cells, then used the LASSO COX regression model to develop a riskScore prognostic model, followed by a small molecule drug screening and molecular docking validation, which was then validated using qRT-PCR and IHC. Results We developed a prognosis model around seven essential protective genes for the first time, dramatically elevated in tumor tissues, as did immune cell infiltration. Multivariate Cox regression results indicated that riskScore is an independent and robust prognostic indicator, and its predictive value in immunotherapy was verified. Additionally, we identified Gabapentin as a possible small molecule therapeutic for CM. Conclusions A riskScore model was developed in this work to analyze patient prognosis, TME cell infiltration features, and treatment responsiveness. The development of this model not only aids in predicting patient response to immunotherapy but also has significant implications for the development of novel immunotherapeutic agents and the promotion of tailored treatment regimens.
Collapse
Affiliation(s)
- Jiahua Xing
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Ziqi Jia
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Li
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- *Correspondence: Yan Han, ; Yan Li,
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- *Correspondence: Yan Han, ; Yan Li,
| |
Collapse
|
25
|
Xing J, Guo L, Jia Z, Li Y, Han Y. The Multi-Omics Landscape and Clinical Relevance of the Immunological Signature of Phagocytosis Regulators: Implications for Risk Classification and Frontline Therapies in Skin Cutaneous Melanoma. Cancers (Basel) 2022; 14:cancers14153582. [PMID: 35892841 PMCID: PMC9331497 DOI: 10.3390/cancers14153582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary In this study, we focused on exploring phagocytosis regulators’ expression and mutational characteristics in skin cutaneous melanoma samples and delineating two molecular subtypes based on expression characteristics. We determined the relationship between phagocytosis regulators and survival by survival analysis of molecular subtypes. We then constructed a survival model (PRRS) to further quantify the criteria. Moreover, we combined pathway analysis, immune infiltration analysis, and mutation analysis to deeply explore the effects of phagocytosis regulators on skin cutaneous melanoma samples. Abstract Tumor-associated macrophages (TAMs) have gained considerable attention as therapeutic targets. Monoclonal antibody treatments directed against tumor antigens contribute significantly to cancer cell clearance by activating macrophages to phagocytose tumor cells. Due to its complicated genetic and molecular pathways, skin cutaneous melanoma (SKCM) has not yet attained the expected clinical efficacy and prognosis when compared to other skin cancers. Therefore, we chose TAMs as an entrance point. This study aimed to thoroughly assess the dysregulation and regulatory role of phagocytosis regulators in SKCM, as well as to understand their regulatory patterns in SKCM. This study subtyped prognosis-related phagocytosis regulators to investigate prognostic differences between subtypes. Then, we screened prognostic factors and constructed phagocytosis-related scoring models for survival prediction using differentially expressed genes (DEGs) between subtypes. Additionally, we investigated alternative treatment options using chemotherapeutic drug response data and clinical cohort treatment data. We first characterized and generalized phagocytosis regulators in SKCM and extensively examined the tumor immune cell infiltration. We created two phagocytosis regulator-related system (PRRS) phenotypes and derived PRRS scores using a principal component analysis (PCA) technique. We discovered that subtypes with low PRRS scores had a poor prognosis and decreased immune checkpoint-associated gene expression levels. We observed significant therapeutic and clinical improvements in patients with higher PRRS scores. Our findings imply that the PRRS scoring system can be employed as an independent and robust prognostic biomarker, serving as a critical reference point for developing novel immunotherapeutic methods.
Collapse
Affiliation(s)
- Jiahua Xing
- The First Medical Center, Department of Plastic and Reconstructive Surgery, Chinese PLA General Hospital, Beijing 100853, China; (J.X.); (L.G.); (Y.L.)
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Lingli Guo
- The First Medical Center, Department of Plastic and Reconstructive Surgery, Chinese PLA General Hospital, Beijing 100853, China; (J.X.); (L.G.); (Y.L.)
| | - Ziqi Jia
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China;
| | - Yan Li
- The First Medical Center, Department of Plastic and Reconstructive Surgery, Chinese PLA General Hospital, Beijing 100853, China; (J.X.); (L.G.); (Y.L.)
| | - Yan Han
- The First Medical Center, Department of Plastic and Reconstructive Surgery, Chinese PLA General Hospital, Beijing 100853, China; (J.X.); (L.G.); (Y.L.)
- Correspondence:
| |
Collapse
|
26
|
Zhao M, Pan B, He Y, Niu B, Gao X. Elucidating the pharmacological mechanism by which Si-Wu-Tang induces cellular senescence in breast cancer via multilevel data integration. Aging (Albany NY) 2022; 14:5812-5837. [PMID: 35859293 PMCID: PMC9365552 DOI: 10.18632/aging.204185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/27/2022] [Indexed: 01/10/2023]
Abstract
Traditional Chinese medicine (TCM) is a promising strategy for effectively treating cancer by inducing cellular senescence with minimal side effects. Si-Wu-Tang (SWT) is a TCM composed of four herbs that is commonly used in China for the treatment of gynecological diseases; SWT can prevent breast cancer (BC), but the molecular mechanism by which SWT induces cellular senescence and its clinical application value remain unknown. We identified 335 differentially expressed genes (DEGs) in SWT-treated MCF-7 cells through Gene Expression Omnibus (GEO) dataset analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the enrichment of biological processes and key signaling pathways including cellular senescence, the cell cycle, the MAPK signaling pathway, and the p53 signaling pathway. Additionally, SWT induced BC cell senescence by upregulating the expression of 33 aging/senescence-induced genes (ASIGs). According to LASSO regression analysis, NDRG1, ERRFI1, SOCS1, IRS2, IGFBP4, and BIRC3 levels were associated with BC prognosis and were used to develop risk scores. ERRFI1, SOCS1, IRS2, IGFBP4, and BIRC3 were identified as protective factors (P < 0.05, HR < 1), while NDRG1 was identified as a risk factor (P < 0.05, HR > 1). Notably, patients with low risk scores had increased senescence-associated secretory phenotypes (SASPs) and immune cell infiltration. Overall, we systematically integrated biological databases and biocomputational methods to reveal the mechanisms by which SWT induces senescence in breast cancer and its clinical value.
Collapse
Affiliation(s)
- Minhong Zhao
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan 528000, PR China
| | - Botao Pan
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan 528000, PR China
| | - Yanjun He
- Department of Emergency, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan 528000, PR China
| | - Bo Niu
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan 528000, PR China
| | - Xiuan Gao
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan 528000, PR China
| |
Collapse
|
27
|
Rodriguez JE, Naigeon M, Goldschmidt V, Roulleaux Dugage M, Seknazi L, Danlos FX, Champiat S, Marabelle A, Michot JM, Massard C, Besse B, Ferrara R, Chaput N, Baldini C. Immunosenescence, inflammaging, and cancer immunotherapy efficacy. Expert Rev Anticancer Ther 2022; 22:915-926. [PMID: 35815381 DOI: 10.1080/14737140.2022.2098718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Immunosenescence is a progressive remodeling of immune functions associated with a decreased ability of the immune system to set up an efficient immune response, both innate and adaptive, with an increase of highly differentiated T cells at the expense of naive T cells. The incidence and prevalence of most cancers increase with age, which can partly be explained by tumor escape mechanisms and decreased immunosurveillance. Aging is also associated with inflammaging, a low-grade proinflammatory state characterized by an increase in inflammatory mediators. Anti-cancer immunotherapy has profoundly changed the landscape of oncology therapy in the last 10 years. Modern T-cell targeted therapies such as bispecific T cell engagers, CAR-T cells, or immune checkpoint blockers may be theoretically affected by immunosenescence or inflammaging. AREAS COVERED A bibliographic review through PubMed and Embase was carried out using the following search terms: 'immunosenescence,' 'immunotherapy,' 'inflammaging,' 'bispecific antibodies,' 'CAR-T cells,' 'immune checkpoint blockers,' and 'older patients.' EXPERT OPINION This review explores the potential impact of immunosenescence and inflammaging on anti-cancer immunotherapy and therapeutic strategies that could counter immune senescence. A more dedicated research on immunosenescence biomarkers in future clinical trials is warranted for the development of new, more effective and safer therapies.
Collapse
Affiliation(s)
- Julieta E Rodriguez
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Marie Naigeon
- Laboratory of Immunomonitoring in Oncology, Gustave Roussy Cancer Campus, Villejuif, France.,School of Medicine, Paris-Saclay university, Kremlin Bicêtre, France.,School of Pharmacy, Paris-Saclay University, Chatenay, France
| | - Vincent Goldschmidt
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Matthieu Roulleaux Dugage
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France.,Laboratory of Immunomonitoring in Oncology, Gustave Roussy Cancer Campus, Villejuif, France.,Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Lauren Seknazi
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Francois X Danlos
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Stephane Champiat
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Aurélien Marabelle
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jean-Marie Michot
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Christophe Massard
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Benjamin Besse
- School of Medicine, Paris-Saclay university, Kremlin Bicêtre, France.,Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Roberto Ferrara
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France.,Department of Medical Oncology, Thoracic Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.,Department of Research, Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Nathalie Chaput
- Laboratory of Immunomonitoring in Oncology, Gustave Roussy Cancer Campus, Villejuif, France.,School of Pharmacy, Paris-Saclay University, Chatenay, France
| | - Capucine Baldini
- Drug Development Department, Gustave Roussy Cancer Campus, Villejuif, France.,Laboratory of Immunomonitoring in Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| |
Collapse
|