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Zeng X, Du S, Geng L, Ma J. Nc-RNA-mediated low expression of AZIN1 correlated with unfavorable prognosis in kidney renal clear cell carcinoma. Cancer Med 2024; 13:e70105. [PMID: 39140420 PMCID: PMC11322861 DOI: 10.1002/cam4.70105] [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: 01/17/2024] [Revised: 06/19/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024] Open
Abstract
OBJECTIVE Kidney renal clear cell carcinoma (KIRC, ccRCC) is the most common type of renal cancer with high recurrence and mortality. It has long been recognized that Antizyme inhibitor 1 (AZIN1) serves as a pro-oncogenic molecule in multiple cancers. However, the clinicopathological features of AZIN1 in KIRC remain unexplored. MATERIALS AND METHODS The Cancer Genome Atlas (TCGA, TIMER, and GEPIA) were employed for pan-cancer expression and survival analysis of AZIN1, indicating the unique anti-tumor role of AZIN1 in KIRC. The expression and clinical characteristics of AZIN1 in KIRC were further proven via Human Protein Atlas and TCGA. single-sample GSEA was employed to investigate the immune infiltration of AZIN1. Then the downstream pathways were illustrated via the LinkedOmics, Metascape, and Cytoscape databases. The possible upper regulating noncoding RNAs (ncRNAs) were analyzed from five programs-TargetScan, StarBase, miRanda, PITA, and miRmap. RESULTS AZIN1 is downregulated in KIRC patients. Lower levels of AZIN1 were linked with unfavorable outcomes in KIRC patients. The AZIN1 expression was positively related to immune cell infiltration in KIRC. We also elucidated a possible upstream regulatory ncRNA of AZIN1 in KIRC namely STK4-AS1/AC068338.2-miR-106b-5p-AZIN1 axis as well as the downstream signaling pathways. CONCLUSION This study illustrated the unique anti-tumor role of AZIN1 in KIRC and provided potential value for guiding immunotherapy and targeted therapy.
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Affiliation(s)
- Xinyi Zeng
- Department of HematologyHuadong Hospital Affiliated with Fudan UniversityShanghaiChina
| | - Shen Du
- Department of Nuclear Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Lou Geng
- Department of Hematology, Institute of Hematology, Shanghai Changhai HospitalNaval Medical UniversityShanghaiChina
| | - Jiexian Ma
- Department of HematologyHuadong Hospital Affiliated with Fudan UniversityShanghaiChina
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Zakari S, Niels NK, Olagunju GV, Nnaji PC, Ogunniyi O, Tebamifor M, Israel EN, Atawodi SE, Ogunlana OO. Emerging biomarkers for non-invasive diagnosis and treatment of cancer: a systematic review. Front Oncol 2024; 14:1405267. [PMID: 39132504 PMCID: PMC11313249 DOI: 10.3389/fonc.2024.1405267] [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: 03/22/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cancer remains a global health challenge, necessitating continuous advancements in diagnostic and treatment strategies. This review focuses on the utility of non-invasive biomarkers in cancer diagnosis and treatment, their role in early detection, disease monitoring, and personalized therapeutic interventions. Through a systematic review of the literature, we identified 45 relevant studies that highlight the potential of these biomarkers across various cancer types, such as breast, prostate, lung, and colorectal cancers. The non-invasive biomarkers discussed include liquid biopsies, epigenetic markers, non-coding RNAs, exosomal cargo, and metabolites. Notably, liquid biopsies, particularly those based on circulating tumour DNA (ctDNA), have emerged as the most promising method for early, non-invasive cancer detection due to their ability to provide comprehensive genetic and epigenetic information from easily accessible blood samples. This review demonstrates how non-invasive biomarkers can facilitate early cancer detection, accurate subtyping, and tailored treatment strategies, thereby improving patient outcomes. It underscores the transformative potential of non-invasive biomarkers in oncology, highlighting their application for enhancing early detection, survival rates, and treatment precision in cancer care. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023474749 PROSPERO, identifier CRD42023474749.
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Affiliation(s)
- Suleiman Zakari
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, College of Medicine, Federal University of Health Sciences Otukpo, Otukpo, Benue State, Nigeria
| | - Nguedia K. Niels
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Biotechnology Centre, University of Yaounde I, Yaounde, Cameroon
| | - Grace V. Olagunju
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, United States
| | - Precious C. Nnaji
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Oluwabusayo Ogunniyi
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Mercy Tebamifor
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
| | - Emmanuel N. Israel
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
| | - Sunday E. Atawodi
- Department of Biochemistry, Federal University Lokoja, Lokoja, Kogi State, Nigeria
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communication - Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
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Zhao J, Pan X, Wang Z, Chen Y, Liu D, Shen Y, Wei X, Xu C, Zhang X, Hu X, Chen J, Zhao J, Tang B, Sun G, Shen P, Liu Z, Zeng H, Liang J. Epigenetic modification of PHLDA2 is associated with tumor microenvironment and unfavorable outcome of immune checkpoint inhibitor-based therapies in clear cell renal cell carcinoma. Eur J Med Res 2024; 29:378. [PMID: 39033192 PMCID: PMC11264912 DOI: 10.1186/s40001-024-01939-9] [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: 04/20/2024] [Accepted: 06/15/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND A substantial proportion of patients with metastatic clear cell renal cell carcinoma (ccRCC) cannot derive benefit from immune checkpoint inhibitor (ICI) plus anti-angiogenic agent combination therapy, making identification of predictive biomarkers an urgent need. The members of pleckstrin homology-like domain family A (PHLDA) play critical roles in multiple cancers, whereas their roles in ccRCC remain unknown. METHODS Transcriptomic, clinical, genetic alteration and DNA methylation data were obtained for integrated analyses from TCGA database. RNA sequencing was performed on 117 primary tumors and 79 normal kidney tissues from our center. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis, gene set enrichment analysis were performed to explore transcriptomic features. Data from three randomized controlled trials (RCT), including CheckMate025, IMmotion151, JAVELIN101, were obtained for validation. RESULTS Members of PHLDA family were dysregulated in pan-cancer. Elevated PHLDA2 expression was associated with adverse clinicopathologic parameters and worse prognosis in ccRCC. Aberrant DNA hypomethylation contributed to up-regulation of PHLDA2. An immunosuppressive microenvironment featured by high infiltrates of Tregs and cancer-associated fibroblasts, was observed in ccRCC with higher PHLDA2 expression. Utilizing data from three RCTs, the association of elevated PHLDA2 expression with poor therapeutic efficacy of ICI plus anti-angiogenic combination therapy was confirmed. CONCLUSIONS Our study revealed that elevated PHLDA2 expression regulated by DNA hypomethylation was correlated with poor prognosis and immunosuppressive microenvironment, and highlighted the role of PHLDA2 as a robust biomarker for predicting therapeutic efficacy of ICI plus anti-angiogenic agent combination therapy in ccRCC, which expand the dimension of precision medicine.
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Affiliation(s)
- Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Yuntian Chen
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Dingbang Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Yu Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Xinyuan Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Chenhao Xu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Xu Hu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Pengfei Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China.
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China.
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, Sichuan, China.
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Chen J, Liu JS, Liu JY, She L, Zou T, Yang F, Li XP, Wang Z, Liu Z. Plasma metabolomics of immune-related adverse events for patients with lung cancer treated with PD-1/PD-L1 inhibitors. J Immunother Cancer 2024; 12:e009399. [PMID: 38991728 PMCID: PMC11243122 DOI: 10.1136/jitc-2024-009399] [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] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Metabolomics has the characteristics of terminal effects and reflects the physiological state of biological diseases more directly. Several current biomarkers of multiple omics were revealed to be associated with immune-related adverse events (irAEs) occurrence. However, there is a lack of reliable metabolic biomarkers to predict irAEs. This study aims to explore the potential metabolic biomarkers to predict risk of irAEs and to investigate the association of plasma metabolites level with survival in patients with lung cancer receiving PD-1/PD-L1 inhibitor treatment. METHODS The study collected 170 plasmas of 85 patients with lung cancer who received immune checkpoint inhibitors (ICIs) treatment. 58 plasma samples of 29 patients with irAEs were collected before ICIs treatment and at the onset of irAEs. 112 plasma samples of 56 patients who did not develop irAEs were collected before ICIs treatment and plasma matched by treatment cycles to onset of irAEs patients. Untargeted metabolomics analysis was used to identify the differential metabolites before initiating ICIs treatment and during the process that development of irAEs. Kaplan-Meier curves analysis was used to detect the associations of plasma metabolites level with survival of patients with lung cancer. RESULTS A total of 24 differential metabolites were identified to predict the occurrence of irAEs. Baseline acylcarnitines and steroids levels are significantly higher in patients with irAEs, and the model of eight acylcarnitine and six steroid metabolites baseline level predicts irAEs occurrence with area under the curve of 0.91. Patients with lower concentration of baseline decenoylcarnitine(AcCa(10:1) 2, decenoylcarnitine(AcCa(10:1) 3 and hexanoylcarnitine(AcCa(6:0) in plasma would have better overall survival (OS). Moreover, 52 differential metabolites were identified related to irAEs during ICIs treatment, dehydroepiandrosterone sulfate, corticoserone, cortisol, thyroxine and sphinganine 1-phaosphate were significantly decreased in irAEs group while oxoglutaric acid and taurocholic acid were significantly increased in irAEs group. CONCLUSIONS High levels of acylcarnitines and steroid hormone metabolites might be risk factor to development of irAEs, and levels of decenoylcarnitine (AcCa(10:1) 2, decenoylcarnitine (AcCa(10:1) 3 and hexanoylcarnitine (AcCa(6:0) could be used to predict OS for patients with lung cancer received ICIs treatment.
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Affiliation(s)
- Juan Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jia-Si Liu
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Jun-Yan Liu
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Lei She
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Ting Zou
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Fan Yang
- Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiang-Ping Li
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, Hunan, People's Republic of China
| | - Zhan Wang
- Lung Cancer and Gastrointestinal Unit, Department of Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, Hunan, People's Republic of China
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Du L, Zhang N, Wang B, Cheng W, Wen J. Establishment and validation of a novel disulfidptosis-related immune checkpoint gene signature in clear cell renal cell carcinoma. Discov Oncol 2024; 15:236. [PMID: 38904744 PMCID: PMC11192710 DOI: 10.1007/s12672-024-01105-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal tumors and is associated with a unfavorable prognosis. Disulfidptosis is a recently identified form of cell death mediated by disulfide bonds. Numerous studies have highlighted the significance of immune checkpoint genes (ICGs) in ccRCC. Nevertheless, the involvement of disulfidptosis-related immune checkpoint genes (DRICGs) in ccRCC remains poorly understood. METHODS The mRNA expression profiles and clinicopathological data of ccRCC patients were obtained from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases. The associations between disulfidptosis-related genes (DRGs) and immune checkpoint genes (ICGs) were assessed to identify DRICGs. Cox regression analysis and least absolute shrinkage and selection operator (LASSO) analysis were conducted to construct a risk signature. RESULTS A total of 39 differentially expressed immune-related candidate genes were identified. A prognostic signature was constructed utilizing nine DRICGs (CD276, CD80, CD86, HLA-E, LAG3, PDCD1LG2, PVR, TIGIT, and TNFRSF4) and validated using GEO data. The risk model functioned as an independent prognostic indicator for ccRCC, while the associated nomogram provided a reliable scoring system for ccRCC. Gene set enrichment analysis indicated enrichment of phospholipase D, antigen processing and presentation, and ascorbate and aldarate metabolism-related signaling pathways in the high-risk group. Furthermore, the DRICGs exhibited correlations with the infiltration of various immune cells. It is noteworthy that patients with ccRCC categorized into distinct risk groups based on this model displayed varying sensitivities to potential therapeutic agents. CONCLUSIONS The novel DRICG-based risk signature is a reliable indicator for the prognosis of ccRCC patients. Moreover, it also aids in drug selection and correlates with the tumour immune microenvironment in ccRCC.
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Affiliation(s)
- Lihuan Du
- Department of Urology, The Second Affiliated Hospital of Zhejiang University, NO. 88 Jiefang Road, Hangzhou, 310009, China.
| | - Nan Zhang
- Department of Urology, The Second Affiliated Hospital of Zhejiang University, NO. 88 Jiefang Road, Hangzhou, 310009, China
| | - Bohan Wang
- Department of Urology, The Second Affiliated Hospital of Zhejiang University, NO. 88 Jiefang Road, Hangzhou, 310009, China
| | - Wei Cheng
- Department of Urology, Traditional Chinese Medicine Hospital of Longyou, Longyou, 324400, Quzhou, China
| | - Jiaming Wen
- Department of Urology, The Second Affiliated Hospital of Zhejiang University, NO. 88 Jiefang Road, Hangzhou, 310009, China
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Gao J, Zhang P, Nie X, Tang M, Yuan Y, He L, Wang X, Ma J, Li L. Proteomic and metabolomic profiling of plasma predicts immune-related adverse events in older patients with advanced non-small cell lung cancer. iScience 2024; 27:109946. [PMID: 38827402 PMCID: PMC11141140 DOI: 10.1016/j.isci.2024.109946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/12/2023] [Accepted: 05/06/2024] [Indexed: 06/04/2024] Open
Abstract
The clinical success of immune checkpoint inhibitors is compromised by the fact of immune-related adverse events (irAEs), especially for older patients. To identify predictive biomarkers for older patients with irAEs, we used multiplex immunoassay and flow cytometry and liquid chromatography-tandem mass spectrometry to test immune factors and plasma protein and metabolites levels in non-small cell lung cancer (NSCLC) patients. The results showed that older patients with irAEs displayed lower CD28, CD4+ T cell, and B cell and higher interleukin (IL)-10 and CCL2 levels at baseline. Besides, lower aldolase, fructose-bisphosphate B (ALDOB), higher ST6GAL1, and lower lactate/pyruvate ratio at baseline were found in older patients with irAEs. Based on metabolomic markers, predictive models were developed to distinguish patients with grade 2-4 irAEs from grade 0-1 (Area under curve, AUC = 0.831) and to distinguish patients with grade 3-4 irAEs from grade 2 (AUC = 1). Our results confirmed the predictive value of plasma metabolites for irAEs in older patients with NSCLC.
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Affiliation(s)
- Jiayi Gao
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
- Graduate School Peking Union Medical College, Beijing 100730, China
| | - Ping Zhang
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Xin Nie
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Yue Yuan
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Liuer He
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Xue Wang
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Junling Ma
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Lin Li
- Department of Oncology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
- Graduate School Peking Union Medical College, Beijing 100730, China
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Hazra R, Chattopadhyay S, Mallick A, Gayen S, Roy S. Revealing the therapeutic properties of gut microbiota: transforming cancer immunotherapy from basic to clinical approaches. Med Oncol 2024; 41:175. [PMID: 38874788 DOI: 10.1007/s12032-024-02416-3] [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: 04/11/2024] [Accepted: 05/25/2024] [Indexed: 06/15/2024]
Abstract
The immune system plays a pivotal role in the battle against cancer, serving as a formidable guardian in the ongoing fight against malignant cells. To combat these malignant cells, immunotherapy has emerged as a prevalent approach leveraging antibodies and peptides such as anti-PD-1, anti-PD-L1, and anti-CTLA-4 to inhibit immune checkpoints and activate T lymphocytes. The optimization of gut microbiota plays a significant role in modulating the defense system in the body. This study explores the potential of certain gut-resident bacteria to amplify the impact of immunotherapy. Contemporary antibiotic treatments, which can impair gut flora, may diminish the efficacy of immune checkpoint blockers. Conversely, probiotics or fecal microbiota transplantation can help re-establish intestinal microflora equilibrium. Additionally, the gut microbiome has been implicated in various strategies to counteract immune resistance, thereby enhancing the success of cancer immunotherapy. This paper also acknowledges cutting-edge technologies such as nanotechnology, CAR-T therapy, ACT therapy, and oncolytic viruses in modulating gut microbiota. Thus, an exhaustive review of literature was performed to uncover the elusive link that could potentiate the gut microbiome's role in augmenting the success of cancer immunotherapy.
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Affiliation(s)
- Rudradeep Hazra
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Soumyadeep Chattopadhyay
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Arijit Mallick
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Sakuntala Gayen
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Souvik Roy
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India.
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Deng J, Tu S, Li L, Li G, Zhang Y. Diagnostic, predictive and prognostic molecular biomarkers in clear cell renal cell carcinoma: A retrospective study. Cancer Rep (Hoboken) 2024; 7:e2116. [PMID: 38837683 PMCID: PMC11150078 DOI: 10.1002/cnr2.2116] [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: 10/28/2023] [Revised: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common and aggressive subtype of kidney cancer. Many patients are diagnosed at advanced stages, making early detection crucial. Unfortunately, there are currently no noninvasive tests for ccRCC, emphasizing the need for new biomarkers. Additionally, ccRCC often develops resistance to treatments like radiotherapy and chemotherapy. Identifying biomarkers that predict treatment outcomes is vital for personalized care. The integration of artificial intelligence (AI), multi-omics analysis, and computational biology holds promise in bolstering detection precision and resilience, opening avenues for future investigations. The amalgamation of radiogenomics and biomaterial-basedimmunomodulation signifies a revolutionary breakthrough in diagnostic medicine. This review summarizes existing literature and highlights emerging biomarkers that enhance diagnostic, predictive, and prognostic capabilities for ccRCC, setting the stage for future clinical research.
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Affiliation(s)
- Jian Deng
- Department of OncologyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
- School of Basic Medical SciencesSouthwest Medical UniversityLuzhouPeople's Republic of China
| | - ShengYuan Tu
- School of Basic Medical SciencesSouthwest Medical UniversityLuzhouPeople's Republic of China
| | - Lin Li
- School of StomatologySouthwest Medical UniversityLuzhouPeople's Republic of China
| | - GangLi Li
- Department of OncologyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
| | - YinHui Zhang
- Department of PharmacyThe Affiliated Hospital of Southwest Medical UniversityLuzhouPeople's Republic of China
- Department of AnesthesiologyHospital (T.C.M) Affiliated to Southwest Medical UniversityLuzhouPeople's Republic of China
- Department of PharmacyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
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Alosaimi ME, Alotaibi BS, Abduljabbar MH, Alnemari RM, Almalki AH, Serag A. Unveiling the altered metabolic pathways induced by nivolumab in non-small cell lung cancer via GC-MS metabolomics approach coupled with multivariate analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1240:124144. [PMID: 38703714 DOI: 10.1016/j.jchromb.2024.124144] [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: 02/16/2024] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
This research investigates the effects of the immunotherapeutic agent nivolumab on the metabolism of lung cancer cells (NCI-H1975) using GC-MS metabolomic profiling. Multivariate analysis such as unsupervised PCA and supervised OPLS-DA along with univariate analysis and pathway analysis were employed to explore the metabolomic data and identify altered metabolic pathways induced by nivolumab treatment. The study revealed distinct metabolic alterations in cancer cells, linked to proliferative and survival advantages, such as enhanced glycolysis, increased glutaminolysis, and modified amino acid metabolism. Key findings indicate elevated levels of glycolysis-related metabolites (glycine, alanine, pyruvate, and lactate) and TCA cycle intermediates (succinate, fumarate, malate) in cancer cells, with a significant decrease following nivolumab treatment. Additionally, lower levels of aspartic acid and citrate in cancer cells imply altered nucleotide synthesis and fatty acid production essential for tumor growth. Treatment with nivolumab also reduced oleic acid levels, indicative of its effect on disrupted lipid metabolism. Our research shows nivolumab's potential to modify metabolic pathways involved in lung cancer progression, suggesting its dual role in cancer therapy: as an immune response modulator and a metabolic pathway disruptor.
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Affiliation(s)
- Manal E Alosaimi
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Badriyah S Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Maram H Abduljabbar
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Reem M Alnemari
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11751, Cairo, Egypt.
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10
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Mao X, Huang W, Xue Q, Zhang X. Prognostic impact and immunotherapeutic implications of NETosis-related prognostic model in clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2024; 150:278. [PMID: 38801430 PMCID: PMC11129999 DOI: 10.1007/s00432-024-05761-y] [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: 03/11/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND The ramifications of necroptosis on the prognostication of clear cell renal cell carcinoma (ccRCC) remain inadequately expounded. METHODS A prognostic model delineating the facets of necroptosis in ccRCC was constructed, employing a compendium of algorithms. External validation was effectuated using the E-MTAB-1980 dataset. The exploration of immune infiltration scores was undertaken through the exploitation of multiple algorithms. Single-cell RNA sequencing data were procured from the GSE171306 dataset. Real-time quantitative PCR (RT-qPCR) was engaged to scrutinize the differential expression of SLC25A37 across cancer and paracancer tissues, as well as diverse cell lines. Assessments of proliferative and metastatic alterations in 769-P and 786-O cells were accomplished through Cell Counting Kit-8 (CCK8) and wound healing assays. RESULTS The necroptosis-related signature (NRS) emerges as a discerning metric, delineating patients' immune attributes, tumor mutation burden, immunotherapy response, and drug susceptibility. Single-cell RNA sequencing analysis unveils the marked enrichment of SLC25A37 in tumor cells. Concurrently, RT-qPCR discloses the overexpression of SLC25A37 in both ccRCC tissues and cell lines. SLC25A37 knockdown mitigates the proliferative and metastatic propensities of 769-P and 786-O cells, as evidenced by CCK8 and wound healing assays. CONCLUSION The NRS assumes a pivotal role in ascertaining the prognosis, tumor mutation burden, immunotherapy response, drug susceptibility, and immune cell infiltration features of ccRCC patients. SLC25A37 emerges as a putative player in immunosuppressive microenvironments, thereby providing a prospective avenue for the design of innovative immunotherapeutic targets for ccRCC.
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Affiliation(s)
- Xingjun Mao
- Department of Urology, Baoying People's Hospital, Xincheng Road, Baoying, Yangzhou, 225800, Jiangsu, China
| | - Wen Huang
- Department of Good Clinical Practice Office, Nanjing First Hospital, Nanjing Medical University, ChangLe Road 68, Qinhuai District, Nanjing, Jiangsu, China
| | - Qing Xue
- Department of Urology, Baoying People's Hospital, Xincheng Road, Baoying, Yangzhou, 225800, Jiangsu, China.
| | - Xiaolei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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11
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Liu Y, Zeng D, Gao Y. ZNF692 promotes the migration and response to immunotherapy of clear cell renal cell carcinoma cells by targeting metabolic pathway. Discov Oncol 2024; 15:158. [PMID: 38735008 PMCID: PMC11089031 DOI: 10.1007/s12672-024-01005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), with high mortality and poor prognosis, is the most common type of renal malignancy. It is necessary to identify new biomarkers that can serve as indicators for the detection of ccRCC at its early stages. In this study, we analyzed the role of classical zinc finger protein 692 (ZNF692) in ccRCC using datasets from The Cancer Genome Atlas (TCGA) and Single Cell Portal and immunohistochemical (IHC) staining of a tissue-microarray, and analyzed the function of ZNF692 in ccRCC cells. The analyses indicated that ZNF692 was upregulated in ccRCC samples compared with normal or paracancerous control samples (P < 0.001) and that the expression of this gene was linked to poor overall survival (HR = 2.1, P < 0.0001). The knockdown of ZNF692 inhibited the proliferation and migration of ccRCC cells by target GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2), and transmembrane 9 superfamily member 2 (TM9SF2)). T, B, proximal, and collecting tubule cells are the dominant cell types in normal kidney tissue where ZNF692 is expressed. In addition, immune checkpoint blockade (ICB) therapy dramatically changed the expression patterns of ZNF692. Collectively, these data indicate that ZNF692 may serve as prognosis, and as a potential indicator of the response to ICB therapy, a possibility needs to be verified by a case‒control study.
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Affiliation(s)
- Yuming Liu
- Department of Anesthesiology, MengChao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Dehua Zeng
- Department of Pathology, The 900, Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Yunzhen Gao
- The Institute of Psychiatry and Neurology Medicine, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China.
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12
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Augustin RC, Cai WL, Luke JJ, Bao R. Facts and Hopes in Using Omics to Advance Combined Immunotherapy Strategies. Clin Cancer Res 2024; 30:1724-1732. [PMID: 38236069 PMCID: PMC11062841 DOI: 10.1158/1078-0432.ccr-22-2241] [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: 07/22/2023] [Revised: 09/28/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024]
Abstract
The field of oncology has been transformed by immune checkpoint inhibitors (ICI) and other immune-based agents; however, many patients do not receive a durable benefit. While biomarker assessments from pivotal ICI trials have uncovered certain mechanisms of resistance, results thus far have only scraped the surface. Mechanisms of resistance are as complex as the tumor microenvironment (TME) itself, and the development of effective therapeutic strategies will only be possible by building accurate models of the tumor-immune interface. With advancement of multi-omic technologies, high-resolution characterization of the TME is now possible. In addition to sequencing of bulk tumor, single-cell transcriptomic, proteomic, and epigenomic data as well as T-cell receptor profiling can now be simultaneously measured and compared between responders and nonresponders to ICI. Spatial sequencing and imaging platforms have further expanded the dimensionality of existing technologies. Rapid advancements in computation and data sharing strategies enable development of biologically interpretable machine learning models to integrate data from high-resolution, multi-omic platforms. These models catalyze the identification of resistance mechanisms and predictors of benefit in ICI-treated patients, providing scientific foundation for novel clinical trials. Moving forward, we propose a framework by which in silico screening, functional validation, and clinical trial biomarker assessment can be used for the advancement of combined immunotherapy strategies.
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Affiliation(s)
- Ryan C. Augustin
- UPMC Hillman Cancer Center, Pittsburgh, PA
- University of Pittsburgh, Department of Medicine, Pittsburgh, PA
- Mayo Clinic, Department of Medical Oncology, Rochester, MN
| | - Wesley L. Cai
- University of Pittsburgh, Department of Medicine, Pittsburgh, PA
| | - Jason J. Luke
- UPMC Hillman Cancer Center, Pittsburgh, PA
- University of Pittsburgh, Department of Medicine, Pittsburgh, PA
| | - Riyue Bao
- UPMC Hillman Cancer Center, Pittsburgh, PA
- University of Pittsburgh, Department of Medicine, Pittsburgh, PA
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13
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Augustin RC, Luke JJ. Rapidly Evolving Pre- and Post-surgical Systemic Treatment of Melanoma. Am J Clin Dermatol 2024; 25:421-434. [PMID: 38409643 DOI: 10.1007/s40257-024-00852-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
With the development of effective BRAF-targeted and immune-checkpoint immunotherapies for metastatic melanoma, clinical trials are moving these treatments into earlier adjuvant and perioperative settings. BRAF-targeted therapy is a standard of care in resected stage III-IV melanoma, while anti-programmed death-1 (PD1) immunotherapy is now a standard of care option in resected stage IIB through IV disease. With both modalities, recurrence-free survival and distant-metastasis-free survival are improved by a relative 35-50%, yet no improvement in overall survival has been demonstrated. Neoadjuvant anti-PD1 therapy improves event-free survival by approximately an absolute 23%, although improvements in overall survival have yet to be demonstrated. Understanding which patients are most likely to recur and which are most likely to benefit from treatment is now the highest priority question in the field. Biomarker analyses, such as gene expression profiling of the primary lesion and circulating DNA, are preliminarily exciting as potential biomarkers, though each has drawbacks. As in the setting of metastatic disease, markers that inform positive outcomes include interferon-γ gene expression, PD-L1, and high tumor mutational burden, while negative predictors of outcome include circulating factors such as lactate dehydrogenase, interleukin-8, and C-reactive protein. Integrating and validating these markers into clinically relevant models is thus a high priority. Melanoma therapeutics continues to advance with combination adjuvant approaches now investigating anti-PD1 with lymphocyte activation gene 3 (LAG3), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), and individualized neoantigen therapies. How this progress will be integrated into the management of a unique patient to reduce recurrence, limit toxicity, and avoid over-treatment will dominate clinical research and patient care over the next decade.
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Affiliation(s)
- Ryan C Augustin
- UPMC Hillman Cancer Center, 5150 Centre Ave. Room 1.27C, Pittsburgh, PA, 15232, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jason J Luke
- UPMC Hillman Cancer Center, 5150 Centre Ave. Room 1.27C, Pittsburgh, PA, 15232, USA.
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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14
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Wang X, Shi A, Liu J, Kong W, Huang Y, Xue W, Yang F, Huang J. CDCA5-EEF1A1 interaction promotes progression of clear cell renal cell carcinoma by regulating mTOR signaling. Cancer Cell Int 2024; 24:147. [PMID: 38658931 PMCID: PMC11044369 DOI: 10.1186/s12935-024-03330-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Cell division cycle associated 5 (CDCA5) plays ontogenetic role in various human cancers. However, its specific function and regulatory mechanism in ccRCC remain uncertain. METHODS Immunohistochemistry and western blots were performed to investigate the expression of CDCA5 in ccRCC tissues. Genetic knockdown and upregulation of CDCA5 were performed to investigate its functional roles in ccRCC proliferation, migration, apoptosis and sunitinib resistance. Furthermore, Co-IP assay and LC-MS/MS were performed to investigate the underlying mechanisms. RESULTS We found that CDCA5 expression is frequently upregulated in ccRCC tumors and is associated with poor prognosis of ccRCC patients. Functionally, CDCA5 promotes proliferation, migration, and sunitinib resistance, while inhibiting apoptosis in ccRCC cells. In vivo mouse xenograft model confirms that silencing of CDCA5 drastically inhibits the growth of ccRCC. Mechanistically, we discovered that CDCA5 interacts with Eukaryotic Translation Elongation Factor 1 Alpha 1 (EEF1A1) to regulate mTOR signaling pathway, thereby promoting ccRCC progression. CONCLUSIONS Taken together, our results demonstrate the significant role of CDCA5 in ccRCC progression. The findings may provide insights for the development of new treatment strategies targeting CDCA5 for ccRCC patients.
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Affiliation(s)
- Xun Wang
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - An Shi
- Department of Critical Care Medicine, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Jie Liu
- Department of Pharmacy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Wen Kong
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Yiran Huang
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Wei Xue
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Fan Yang
- Department of Pharmacy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Jiwei Huang
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
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15
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Kang X, Lau HCH, Yu J. Modulating gut microbiome in cancer immunotherapy: Harnessing microbes to enhance treatment efficacy. Cell Rep Med 2024; 5:101478. [PMID: 38631285 PMCID: PMC11031381 DOI: 10.1016/j.xcrm.2024.101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/15/2024] [Accepted: 02/22/2024] [Indexed: 04/19/2024]
Abstract
Immunotherapy has emerged as a robust approach against cancer, yet its efficacy has varied among individuals, accompanied by the occurrence of immune-related adverse events. As a result, the efficacy of immunotherapy is far from satisfactory, and enormous efforts have been invested to develop strategies to improve patient outcomes. The gut microbiome is now well acknowledged for its critical role in immunotherapy, with better understanding on host-microbes interaction in the context of cancer treatment. Also, an increasing number of trials have been conducted to evaluate the potential and feasibility of microbiome-targeting approaches to enhance efficacy of cancer treatment in patients. Here, the role of the gut microbiome and metabolites (e.g., short-chain fatty acids, tryptophan metabolites) in immunotherapy and the underlying mechanisms are explored. The application of microbiome-targeting approaches that aim to improve immunotherapy efficacy (e.g., fecal microbiota transplantation, probiotics, dietary intervention) is also elaborated, with further discussion on current challenges and suggestions for future research.
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Affiliation(s)
- Xing Kang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong.
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16
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Lu Z, Pan Y, Wang S, Wu J, Miao C, Wang Z. Multi-omics and immunogenomics analysis revealed PFKFB3 as a targetable hallmark and mediates sunitinib resistance in papillary renal cell carcinoma: in silico study with laboratory verification. Eur J Med Res 2024; 29:236. [PMID: 38622715 PMCID: PMC11017615 DOI: 10.1186/s40001-024-01808-5] [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: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Glycolysis-related metabolic reprogramming is a central hallmark of human cancers, especially in renal cell carcinoma. However, the regulatory function of glycolytic signature in papillary RCC has not been well elucidated. In the present study, the glycolysis-immune predictive signature was constructed and validated using WGCNA, glycolysis-immune clustering analysis. PPI network of DEGs was constructed and visualized. Functional enrichments and patients' overall survival were analyzed. QRT-PCR experiments were performed to detect hub genes' expression and distribution, siRNA technology was used to silence targeted genes; cell proliferation and migration assays were applied to evaluate the biological function. Glucose concentration, lactate secretion, and ATP production were measured. Glycolysis-Immune Related Prognostic Index (GIRPI) was constructed and combined analyzed with single-cell RNA-seq. High-GIRPI signature predicted significantly poorer outcomes and relevant clinical features of pRCC patients. Moreover, GIRPI also participated in several pathways, which affected tumor immune microenvironment and provided potential therapeutic strategy. As a key glycolysis regulator, PFKFB3 could promote renal cancer cell proliferation and migration in vitro. Blocking of PFKFB3 by selective inhibitor PFK-015 or glycolytic inhibitor 2-DG significantly restrained renal cancer cells' neoplastic potential. PFK-015 and sunitinib could synergistically inhibit pRCC cells proliferation. Glycolysis-Immune Risk Signature is closely associated with pRCC prognosis, progression, immune infiltration, and therapeutic response. PFKFB3 may serve as a pivotal glycolysis regulator and mediates Sunitinib resistance in pRCC patients.
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Affiliation(s)
- Zhongwen Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China
| | - Yongsheng Pan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Songbo Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China
| | - Jiajin Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China.
| | - Chenkui Miao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China.
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, China.
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17
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Silva RVN, Berzotti LA, Laia MG, Araújo LS, Silva CA, Ribeiro KB, Brandão M, Michelleti AMR, Machado JR, Lira RCP. Implications of MTHFD2 expression in renal cell carcinoma aggressiveness. PLoS One 2024; 19:e0299353. [PMID: 38422037 PMCID: PMC10903874 DOI: 10.1371/journal.pone.0299353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Renal cell carcinoma (RCC) is the most common type of cancer in kidney and is often diagnosed in advanced stages. Until now, there is no reliable biomarker to assess tumor prognosis during histopathological diagnosis. The Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) overexpression has been suggested as prognostic indicator for RCC, however, its protein profile needs to be clarified. This study investigated the MTHFD2 expression in different RCC cohorts, associating it with tumor characteristics and prognostic factors. Gene expression comparisons between non-neoplastic (NN) and tumor samples, as well as patients' survival analysis, were assessed using KM-Plotter tool. MTHFD2 protein pattern was evaluated in 117 RCC by immunohistochemistry and associations with prognosis, clinical and pathological data were investigated. The tumors exhibited higher MTHFD2 transcript levels than NN, being even higher in the metastatic group. Opposite gene expression patterns were found among clear cell renal cell carcinoma (ccRCC) and pappilary renal cell carcinoma (pRCC) subtypes, showing higher and lower expressions compared to NN samples respectively. Overexpression was associated with shorter overall survival for ccRCC and pRCC subtypes, and shorter recurrence-free survival for pRCC. The immunolabeling profile varied according to tumor subtypes, with lower intensity and expression scores in ccRCC compared to pRCC and to chromophobe renal cell carcinoma (chRCC). MTHFD2 protein expression was associated with larger tumors and higher Fuhrman grades. Although prognostic value of protein immunostaining was not confirmed, patients with higher MTHFD2 tended to have lower survival rates in the pRCC group. The results highlight MTHFD2 different patterns according to RCC histological subtypes, revealing marked variations at both the genetic and protein levels. The mRNA indicated tumor prognosis, and greater expression in the tumor samples. Although MTHFD2 immunolabeling suggests tumor aggressiveness, it needs to be validated in other cohorts as potential prognostic factor.
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Affiliation(s)
- Rafaela V. N. Silva
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Lucas A. Berzotti
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marcella G. Laia
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Liliane S. Araújo
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Crislaine A. Silva
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Karen B. Ribeiro
- Clinics Hospital, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Millena Brandão
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Adilha M. R. Michelleti
- Department of Clinical Surgery, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Juliana R. Machado
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Régia C. P. Lira
- Department of Pathology, Genetics and Evolution, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
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18
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Jing X, Qin X, Liu H, Liu H, Wang H, Qin J, Zhang Y, Cao S, Fan X. DNA damage response alterations in clear cell renal cell carcinoma: clinical, molecular, and prognostic implications. Eur J Med Res 2024; 29:107. [PMID: 38326910 PMCID: PMC10848511 DOI: 10.1186/s40001-024-01678-x] [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: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic responses. Nonetheless, the characteristics and significance of DDR alterations in clear cell renal cell carcinoma (ccRCC) remain undefined. This study aimed to explore the predictive role, molecular mechanism, and tumor immune profile of DDR genes in ccRCC. METHODS We prospectively sequenced 757 tumors and matched blood DNA samples from Chinese patients with ccRCC using next-generation sequencing (NGS) and analyzed data from 537 patients from The Cancer Genome Atlas (TCGA). A comprehensive analysis was performed. RESULTS Fifty-two percent of Chinese patients with ccRCC harbored DDR gene mutations and 57% of TCGA patients. The immunotherapy treatment prognosis of patients with DDR gene mutations was superior to that of patients without DDR gene mutations (p = 0.047). DDR gene mutations were associated with more gene mutations and a higher tumor mutation load (TMB, p < 0.001). Moreover, patients with DDR gene mutations have a distinct mutational signature compared with those with wild-type DDR. Furthermore, the DDR-mut group had elevated neoantigen load (including single-nucleotide variants (SNV) and indel neoantigen load, p = 0.037 and p = 0.002, respectively), TCR Shannon (p = 0.025), and neutrophils (p = 0.010). DDR gene mutations exhibited a distinct immune profile with significantly higher expression levels of TNFSF9, CD70, ICAM1, and indoleamine-2,3-dioxygenase (IDO) and lower expression levels of VTCN1 and IL12A. CONCLUSIONS Our data suggest that the detection of somatic mutations in DDR genes can predict the efficacy of immunotherapy in patients with ccRCC. Furthermore, we revealed the unique molecular and immune mechanisms underlying ccRCC with DDR gene mutations.
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Affiliation(s)
- Xiao Jing
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangcheng Qin
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China
| | - Hao Liu
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Liu
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Jiayue Qin
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Yanui Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Xiaodong Fan
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China.
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19
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Yu H, Zhang C, Bai X, Yin H, Li X, Zhou X, He W, Kuang Y, Gou X, Li J. Identifying endoplasmic reticulum stress-related genes as new diagnostic and prognostic biomarkers in clear cell renal cell carcinoma. Transl Androl Urol 2024; 13:1-24. [PMID: 38404554 PMCID: PMC10891384 DOI: 10.21037/tau-23-374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/22/2023] [Indexed: 02/27/2024] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most common cancers worldwide, and its incidence is increasing every year. Endoplasmic reticulum stress (ERS) caused by protein misfolding has broad and profound effects on the progression and metastasis of various cancers. Accumulating evidence suggests that ERS is closely related to the occurrence and progression of ccRCC. This study aimed to identify ERS-related genes for evaluating the prognosis of ccRCC. Methods Transcriptomic expression profiles were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), and clinical data were downloaded from the TCGA. First, the differentially expressed genes (DEGs) were analyzed using the limma package, and the DEGs related to ERS (ERS-DEGs) were identified from the GeneCards database. Second, a function and pathway enrichment analysis and a Gene Set Enrichment Analysis (GSEA) were performed. Third, a protein-protein interaction (PPI) network was constructed to identify the hub genes, and a gene-micro RNA (miRNA) network and gene-transcription factor (TF) network were established using the hub genes. Finally, a least absolute shrinkage and selection operator (LASSO) regression analysis was conducted to establish a diagnostic model, and a Cox analysis was used to analyze the correlations between the expression of the characteristic genes and the clinical characteristics. Results We identified 11 signature genes and established a diagnostic model. Further, the Cox analysis results revealed a correlation between the expression levels of the signature genes and the clinical characteristics. Ultimately, five signature genes (i.e., TNFSF13B, APOL1, COL5A3, and CDH5) were found to be associated with a poor prognosis. Conclusions This study suggests that TNFSF13B, APOL1, COL5A3, and CDH5 may have potential as prognostic biomarkers in ccRCC and may provide new evidence to support targeted therapy in ccRCC.
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Affiliation(s)
- Haitao Yu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunlin Zhang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuesong Bai
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hubin Yin
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinyuan Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyang He
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Youlin Kuang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhang J, Zhao Q, Huang H, Lin X. Establishment and validation of a novel peroxisome-related gene prognostic risk model in kidney clear cell carcinoma. BMC Urol 2024; 24:26. [PMID: 38297313 PMCID: PMC10829319 DOI: 10.1186/s12894-024-01404-z] [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: 06/12/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Kidney clear cell carcinoma (KIRC) is the most common subtype of renal cell carcinoma. Peroxisomes play a role in the regulation of tumorigenesis and cancer progression, yet the prognostic significance of peroxisome-related genes (PRGs) remains rarely studied. The study aimed to establish a novel prognostic risk model and identify potential biomarkers in KIRC. METHODS The significant prognostic PRGs were screened through differential and Cox regression analyses, and LASSO Cox regression analysis was performed to establish a prognostic risk model in the training cohort, which was validated internally in the testing and entire cohorts, and further assessed in the GSE22541 cohort. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the function and pathway differences between the high-risk and low-risk groups. The relationship between risk score and immune cell infiltration levels was evaluated in the CIBERSORT, ESTIMATE and TIMER databases. Finally, potential biomarkers were identified and validated from model genes, using immunohistochemistry. RESULTS Fourteen significant prognostic PRGs were identified using multiple analyses, and 9 genes (ABCD1, ACAD11, ACAT1, AGXT, DAO, EPHX2, FNDC5, HAO1, and HNGCLL1) were obtained to establish a prognostic model via LASSO Cox regression analysis. Combining the risk score with clinical factors to construct a nomogram, which provided support for personalized treatment protocols for KIRC patients. GO and KEGG analyses highlighted associations with substance metabolism, transport, and the PPAR signaling pathways. Tumor immune infiltration indicated immune suppression in the high-risk group, accompanied by higher tumor purity and the expression of 9 model genes was positively correlated with the level of immune cell infiltration. ACAT1 has superior prognostic capabilities in predicting the outcomes of KIRC patients. CONCLUSIONS The peroxisome-related prognostic risk model could better predict prognosis in KIRC patients.
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Affiliation(s)
- Jing Zhang
- School of Stomatology, Henan University, Jinming Road, Kaifeng, Henan, 475000, China
| | - Qian Zhao
- School of Stomatology, Henan University, Jinming Road, Kaifeng, Henan, 475000, China
| | - Hongwei Huang
- Department of Pediatric General Surgery, The Third Affiliated Hospital of Zhengzhou University, No. 7 Kangfu Qian Street, Zhengzhou, Henan, 450052, China
| | - Xuhong Lin
- Department of Clinical Laboratory, Huaihe Hospital of Henan University, No.115 Ximen Street, Kaifeng, Henan, 475000, China.
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21
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Yao Q, Zhang X, Wang Y, Wang C, Wei C, Chen J, Chen D. Comprehensive analysis of a tryptophan metabolism-related model in the prognostic prediction and immune status for clear cell renal carcinoma. Eur J Med Res 2024; 29:22. [PMID: 38183155 PMCID: PMC10768089 DOI: 10.1186/s40001-023-01619-0] [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: 11/30/2023] [Accepted: 12/24/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is characterized as one of the most common types of urological cancer with high degrees of malignancy and mortality. Due to the limited effectiveness of existing traditional therapeutic methods and poor prognosis, the treatment and therapy of advanced ccRCC patients remain challenging. Tryptophan metabolism has been widely investigated because it significantly participates in the malignant traits of multiple cancers. The functions and prognostic values of tryptophan metabolism-related genes (TMR) in ccRCC remain virtually obscure. METHODS We employed the expression levels of 40 TMR genes to identify the subtypes of ccRCC and explored the clinical characteristics, prognosis, immune features, and immunotherapy response in the subtypes. Then, a model was constructed for the prediction of prognosis based on the differentially expressed genes (DEGs) in the subtypes from the TCGA database and verified using the ICGC database. The prediction performance of this model was confirmed by the receiver operating characteristic (ROC) curves. The relationship of Risk Score with the infiltration of distinct tumor microenvironment cells, the expression profiles of immune checkpoint genes, and the treatment benefits of immunotherapy and chemotherapy drugs were also investigated. RESULTS The two subtypes revealed dramatic differences in terms of clinical characteristics, prognosis, immune features, and immunotherapy response. The constructed 6-gene-based model showed that the high Risk Score was significantly connected to poor overall survival (OS) and advanced tumor stages. Furthermore, increased expression of CYP1B1, KMO, and TDO2 was observed in ccRCC tissues at the translation levels, and an unfavorable prognosis for these patients was also found. CONCLUSION We identified 2 molecular subtypes of ccRCC based on the expression of TMR genes and constructed a prognosis-related model that may be used as a powerful tool to guide the prediction of ccRCC prognosis and personalized therapy. In addition, CYP1B1, KMO, and TDO2 can be regarded as the risk prognostic genes for ccRCC.
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Affiliation(s)
- Qinfan Yao
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Xiuyuan Zhang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Yucheng Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Cuili Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Chunchun Wei
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China.
- Institute of Nephropathy, Zhejiang University, Hangzhou, China.
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China.
| | - Dajin Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory of Kidney Disease Prevention and Control Technology, Zhejiang Province, Hangzhou, China.
- Institute of Nephropathy, Zhejiang University, Hangzhou, China.
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China.
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Anbiyaee O, Moalemnia A, Ghaedrahmati F, Shooshtari MK, Khoshnam SE, Kempisty B, Halili SA, Farzaneh M, Morenikeji OB. The functions of long non-coding RNA (lncRNA)-MALAT-1 in the pathogenesis of renal cell carcinoma. BMC Nephrol 2023; 24:380. [PMID: 38124072 PMCID: PMC10731893 DOI: 10.1186/s12882-023-03438-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Renal cell carcinoma (RCC), a prevalent form of renal malignancy, is distinguished by its proclivity for robust tumor proliferation and metastatic dissemination. Long non-coding RNAs (lncRNAs) have emerged as pivotal modulators of gene expression, exerting substantial influence over diverse biological processes, encompassing the intricate landscape of cancer development. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), an exemplar among lncRNAs, has been discovered to assume functional responsibilities within the context of RCC. The conspicuous expression of MALAT-1 in RCC cells has been closely linked to the advancement of tumors and an unfavorable prognosis. Experimental evidence has demonstrated the pronounced ability of MALAT-1 to stimulate RCC cell proliferation, migration, and invasion, thereby underscoring its active participation in facilitating the metastatic cascade. Furthermore, MALAT-1 has been implicated in orchestrating angiogenesis, an indispensable process for tumor expansion and metastatic dissemination, through its regulatory influence on pro-angiogenic factor expression. MALAT-1 has also been linked to the evasion of immune surveillance in RCC, as it can regulate the expression of immune checkpoint molecules and modulate the tumor microenvironment. Hence, the potential utility of MALAT-1 as a diagnostic and prognostic biomarker in RCC emerges, warranting further investigation and validation of its clinical significance. This comprehensive review provides an overview of the diverse functional roles exhibited by MALAT-1 in RCC.
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Affiliation(s)
- Omid Anbiyaee
- Cardiovascular Research Center, School of Medicine, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Moalemnia
- Faculty of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Khombi Shooshtari
- Chronic Renal Failure Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology Division of Anatomy, Wrocław Medical University, Wrocław, Poland
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
- Physiology Graduate Faculty North, Carolina State University, Raleigh, NC, 27695, US
- Center of Assisted Reproduction Department of Obstetrics and Gynecology, University Hospital and Masaryk University, Brno, Czech Republic
| | - Shahla Ahmadi Halili
- Department of Internal Medicine, School of Science, Chronic Renal Failure Research Center, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, USA.
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23
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Zhang L, Li Y, Cai B, Chen J, Zhao K, Li M, Lang J, Wang K, Pan S, Zhu K. A Notch signaling-related lncRNA signature for predicting prognosis and therapeutic response in clear cell renal cell carcinoma. Sci Rep 2023; 13:21141. [PMID: 38036719 PMCID: PMC10689792 DOI: 10.1038/s41598-023-48596-2] [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: 08/29/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
Increasing evidence has confirmed the vital role of Notch signaling in the tumorigenesis of clear cell renal cell carcinoma (ccRCC). The underlying function of long non-coding RNA (lncRNA) related to Notch signaling in ccRCC remains unclear. In present study, the prognostic value and therapeutic strategy of Notch signaling-related lncRNA are comprehensively explored in ccRCC. In total, we acquired 1422 NSRlncRNAs, of which 41 lncRNAs were identified the key NSRlncRNAs associated with the occurrence of ccRCC. The prognostic signature containing five NSRlncRNAs (AC092611.2, NNT-AS1, AGAP2-AS1, AC147651.3, and AC007406.3) was established and validated, and the ccRCC patients were clustered into the high- and low-risk groups. The overall survival of patients in the low-risk group were much more favorable than those in the high-risk group. Multivariate Cox regression analysis indicated that the risk score was an independent prognostic biomarker. Based on the risk score and clinical variables, a nomogram for predicting prognosis of ccRCC patients was constructed, and the calibration curves and DCA curves showed the superior predictive ability of nomogram. The risk score was correlated with immune cell infiltration, targeted therapy or chemotherapy sensitivity, and multiple oncogenic pathways. Additionally, consensus clustering analysis stratified the ccRCC patients into four clusters with obvious different outcomes, immune microenvironments, and expression of immune checkpoints. The constructed NSRlncRNA-based signature might serve as a potential biomarker for predicting prognosis and response to immunotherapy or targeted therapy in patients with ccRCC.
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Affiliation(s)
- Lulu Zhang
- Department of Medical Research Center, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Yulei Li
- Department of Urology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Bin Cai
- Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Jiajun Chen
- Department of Urology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Keyuan Zhao
- Department of Urology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Mengyao Li
- Department of Pathology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Juan Lang
- Department of Pathology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China
| | - Kaifang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Shouhua Pan
- Department of Urology, Shaoxing People's Hospital, No.568, Zhongxing North Road, Shaoxing, 312000, Zhejiang Province, China.
| | - Ke Zhu
- Nanchang People's Hospital, No.1268 Jiuzhou Street, Xihu District, Nanchang City, China.
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24
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Madama D, Carrageta DF, Guerra-Carvalho B, Botelho MF, Oliveira PF, Cordeiro CR, Alves MG, Abrantes AM. Impact of Different Treatment Regimens and Timeframes in the Plasmatic Metabolic Profiling of Patients with Lung Adenocarcinoma. Metabolites 2023; 13:1180. [PMID: 38132862 PMCID: PMC10744969 DOI: 10.3390/metabo13121180] [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: 10/27/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, the treatment of advanced non-small cell lung cancer (NSCLC) has suffered a variety of alterations. Chemotherapy (CTX), immunotherapy (IT) and tyrosine kinase inhibitors (TKI) have shown remarkable results. However, not all patients with NSCLC respond to these drug treatments or receive durable benefits. In this framework, metabolomics has been applied to improve the diagnosis, treatment, and prognosis of lung cancer and particularly lung adenocarcinoma (AdC). In our study, metabolomics was used to analyze plasma samples from 18 patients with AdC treated with CTX or IT via 1H-NMR spectroscopy. Relevant clinical information was gathered, and several biochemical parameters were also evaluated throughout the treatments. During the follow-up of patients undergoing CTX or IT, imaging control is recommended in order to assess the effectiveness of the therapy. This evaluation is usually performed every three treatments. Based on this procedure, all the samples were collected before the beginning of the treatment and after three and six treatments. The identified and quantified metabolites in the analyzed plasma samples were the following: isoleucine, valine, alanine, acetate, lactate, glucose, tyrosine, and formate. Multivariate/univariate statistical analyses were performed. Our data are in accordance with previous published results, suggesting that the plasma glucose levels of patients under CTX become higher throughout the course of treatment, which we hypothesize could be related to the tumor response to the therapy. It was also found that alanine levels become lower during treatment with CTX regimens, a fact that could be associated with frailty. NMR spectra of long responders' profiles also showed similar results. Based on the results of the study, metabolomics can represent a potential option for future studies, in order to facilitate patient selection and the monitoring of therapy efficacy in treated patients with AdC. Further studies are needed to improve the prospective identification of predictive markers, particularly glucose and alanine levels, as well as confer guidance to NSCLC treatment and patient stratification, thus avoiding ineffective therapeutic strategies.
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Affiliation(s)
- Daniela Madama
- Clinical Academic Centre of Coimbra (CACC), Department of Pulmonology, Faculty of Medicine, University Hospitals of Coimbra, University of Coimbra, 3004-504 Coimbra, Portugal
| | - David F. Carrageta
- Clinical and Experimental Endocrinology, UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal (M.G.A.)
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
| | - Bárbara Guerra-Carvalho
- Clinical and Experimental Endocrinology, UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal (M.G.A.)
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Maria F. Botelho
- Clinical Academic Centre of Coimbra (CACC), Centre for Innovative Biomedicine and Biotechnology (CIBB), Coimbra Institute for Clinical and Biomedical Research (iCBR), Biophysics Institute of Faculty of Medicine of University of Coimbra, Area of Environmental Genetics and Oncobiology (CIMAGO), 3000-548 Coimbra, Portugal
| | - Pedro F. Oliveira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Carlos R. Cordeiro
- Clinical Academic Centre of Coimbra (CACC), Department of Pulmonology, Faculty of Medicine, University Hospitals of Coimbra, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Marco G. Alves
- Clinical and Experimental Endocrinology, UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal (M.G.A.)
| | - Ana M. Abrantes
- Clinical Academic Centre of Coimbra (CACC), Centre for Innovative Biomedicine and Biotechnology (CIBB), Coimbra Institute for Clinical and Biomedical Research (iCBR), Biophysics Institute of Faculty of Medicine of University of Coimbra, Area of Environmental Genetics and Oncobiology (CIMAGO), 3000-548 Coimbra, Portugal
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25
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Rushing BR, Thessen AE, Soliman GA, Ramesh A, Sumner SCJ. The Exposome and Nutritional Pharmacology and Toxicology: A New Application for Metabolomics. EXPOSOME 2023; 3:osad008. [PMID: 38766521 PMCID: PMC11101153 DOI: 10.1093/exposome/osad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The exposome refers to all of the internal and external life-long exposures that an individual experiences. These exposures, either acute or chronic, are associated with changes in metabolism that will positively or negatively influence the health and well-being of individuals. Nutrients and other dietary compounds modulate similar biochemical processes and have the potential in some cases to counteract the negative effects of exposures or enhance their beneficial effects. We present herein the concept of Nutritional Pharmacology/Toxicology which uses high-information metabolomics workflows to identify metabolic targets associated with exposures. Using this information, nutritional interventions can be designed toward those targets to mitigate adverse effects or enhance positive effects. We also discuss the potential for this approach in precision nutrition where nutrients/diet can be used to target gene-environment interactions and other subpopulation characteristics. Deriving these "nutrient cocktails" presents an opportunity to modify the effects of exposures for more beneficial outcomes in public health.
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Affiliation(s)
- Blake R. Rushing
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne E Thessen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ghada A. Soliman
- Department of Environmental, Occupational and Geospatial Health Sciences, City University of New York-Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Aramandla Ramesh
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, Meharry Medical College, Nashville, TN, USA
| | - Susan CJ Sumner
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Tian L, Wang Y, Zhang Z, Feng X, Xiao F, Zong M. CD72, a new immune checkpoint molecule, is a novel prognostic biomarker for kidney renal clear cell carcinoma. Eur J Med Res 2023; 28:531. [PMID: 37980541 PMCID: PMC10656955 DOI: 10.1186/s40001-023-01487-8] [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: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND The incidence and mortality of clear cell carcinoma of the kidney increases yearly. There are limited screening methods and advances in treating kidney renal clear cell carcinoma (KIRC). It is important to find new biomarkers to screen, diagnose and predict the prognosis of KIRC. Some studies have shown that CD72 influences the development and progression of colorectal cancer, nasopharyngeal cancer, and acute lymphoid leukemia. However, there is a lack of research on the role of CD72 in the pathogenesis of KIRC. This study aimed to determine whether CD72 is associated with the prognosis and immune infiltration of KIRC, providing an essential molecular basis for the early non-invasive diagnosis and immunotherapy of KIRC. METHODS Using TCGA, GTE, GEO, and ImmPort databases, we obtained the differentially expressed mRNA (DEmRNA) associated with the prognosis and immunity of KIRC patients. We used the Kruskal-Wallis test to identify clinicopathological parameters associated with target gene expression. We performed univariate and multivariate COX regression analyses to determine the effect of target gene expression and clinicopathological parameters on survival. We analyzed the target genes' relevant functions and signaling pathways through enrichment analysis. Finally, the correlation of target genes with tumor immune infiltration was explored by ssGSEA and Spearman correlation analysis. RESULTS The results revealed that patients with KIRC with higher expression of CD72 have a poorer prognosis. CD72 was associated with the Pathologic T stage, Pathologic stage, Pathologic M stage, Pathologic N stage, Histologic grade in KIRC patients, Laterality, and OS event. It was an independent predictor of the overall survival of KIRC patients. Functional enrichment analysis showed that CD72 was significantly enriched in oncogenic and immune-related pathways. According to ssGSEA and Spearman correlation analysis, CD72 expression was significantly associated with tumor immune cells and immune checkpoints. CONCLUSION Our study suggests that CD72 is associated with tumor immunity and may be a biomarker relevant to the diagnosis and prognosis of KIRC patients.
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Affiliation(s)
- Lv Tian
- Department of Rehabilitation, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
- School of Nursing, Jilin University, Changchun, China
| | - Yiming Wang
- School of Nursing, Jilin University, Changchun, China
| | - Zhiyuan Zhang
- School of Nursing, Jilin University, Changchun, China
| | - Xuechao Feng
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - Fengjun Xiao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Minru Zong
- Department of Rehabilitation, China-Japan Union Hospital of Jilin University, Changchun, 130033, China.
- School of Nursing, Jilin University, Changchun, China.
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27
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Wu HF, Liu H, Zhang ZW, Chen JM. CENPE and LDHA were potential prognostic biomarkers of chromophobe renal cell carcinoma. Eur J Med Res 2023; 28:481. [PMID: 37925501 PMCID: PMC10625266 DOI: 10.1186/s40001-023-01449-0] [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: 08/31/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Most sarcomatoid differentiated renal cell carcinoma was differentiated from Chromophobe renal cell carcinoma (KICH) and related to a bad prognosis. Thus, finding biomarkers is important for the therapy of KICH. METHODS The UCSC was used for determining the expression of mRNA and miRNA and clinical data in KICH and normal samples. KEGG and GO were used for predicting potential function of differently expressed genes (DEGs). Optimal prognostic markers were determined by Lasso regression. Kaplan-Meier survival, ROC, and cox regression were used for assessing prognosis value. GSEA was used for predicting potential function of markers. The relations between markers and immune cell infiltration were determined by Pearson method. The upstream miRNA of markers was predicted in TargetScan and DIANA. RESULTS The 6162 upregulated and 13,903 downregulated DEGs were identified in KICH. Further CENPE and LDHA were screened out as optimal prognostic risk signatures. CENPE was highly expressed while LDHA was lowly expressed in KICH samples, and the high expressions of 2 genes contributed to bad prognosis. The functions of CENPE and LDHA were mainly enriched in proliferation related pathways such as cell cycle and DNA replication. In addition, the correlation of 2 genes with immune infiltrates in KICH was also observed. Finally, we found that has-miR-577 was the common upstream of 2 genes and the binding sites can be predicted. CONCLUSION CENPE and LDHA were identified as the important prognostic biomarkers in KICH, and they might be involved in the proliferation of cancer cell.
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Affiliation(s)
- Hui-Feng Wu
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
| | - Hao Liu
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China.
| | - Zhe-Wei Zhang
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
| | - Ji-Min Chen
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China
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28
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Ding W, Zhang M, Zhang P, Zhang X, Sun J, Lin B. Identification of anoikis-related subtypes and immune landscape in kidney renal clear cell carcinoma. Sci Rep 2023; 13:18069. [PMID: 37872217 PMCID: PMC10593771 DOI: 10.1038/s41598-023-45069-4] [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: 06/20/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023] Open
Abstract
Anoikis is a specific form of programmed cell death induced by the loss of cell contact with the extracellular matrix and other cells, and plays an important role in organism development, tissue homeostasis, disease development and tumor metastasis. We comprehensively investigated the expression patterns of anoikis-related genes (ARGs) in kidney renal clear cell carcinoma (KIRC) from public databases. Anoikis-related prognostic signatures were established based on four ARGs expression, in which KIRC patients were assigned different risk scores and divided into two different risk groups. In addition, four ARGs expression was validated by qRT-PCR. A better prognosis was observed in the low-risk group, but with lower immune activity (including immune cells and immune-related functions) in the tumor microenvironment. Combined with the relevant clinical characteristics, a nomogram for clinical application was established. Receiver operating characteristics (ROC) and calibration curves were constructed to demonstrate the predictive power of this risk signature. In addition, higher risk scores were significantly and positively correlated with higher gene expression of tumor mutation load (TMB), immune checkpoints (ICPs) and mismatch repair (MMR)-related proteins in general. The results also suggested that the high-risk group was more sensitive to immunotherapy and certain chemotherapeutic agents. Anoikis-related prognostic signatures may provide a better understanding of the roles of ARGs and offer new perspectives for clinical prognosis and individualized treatment.
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Affiliation(s)
- Wencong Ding
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Min Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Ping Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Xianghong Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Junwei Sun
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Biying Lin
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China.
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Almalki AH. Recent Analytical Advances for Decoding Metabolic Reprogramming in Lung Cancer. Metabolites 2023; 13:1037. [PMID: 37887362 PMCID: PMC10609104 DOI: 10.3390/metabo13101037] [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: 08/24/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Metabolic reprogramming is a fundamental trait associated with lung cancer development that fuels tumor proliferation and survival. Monitoring such metabolic pathways and their intermediate metabolites can provide new avenues concerning treatment strategies, and the identification of prognostic biomarkers that could be utilized to monitor drug responses in clinical practice. In this review, recent trends in the analytical techniques used for metabolome mapping of lung cancer are capitalized. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and imaging mass spectrometry (MSI). The advantages and limitations of the application of each technique for monitoring the metabolite class or type are also highlighted. Moreover, their potential applications in the analysis of many biological samples will be evaluated.
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Affiliation(s)
- Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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30
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Li C, Wu J, Zhang L, Wang F, Xu L, Zhao Y, Xiao Y, Zhuang F, Hou L, Zhao D, She Y, Xie D, Chen C. Brief Report: Acetaminophen Reduces Neoadjuvant Chemoimmunotherapy Efficacy in Patients With NSCLC by Promoting Neutrophil Extracellular Trap Formation: Analysis From a Phase 2 Clinical Trial. JTO Clin Res Rep 2023; 4:100556. [PMID: 37654895 PMCID: PMC10466912 DOI: 10.1016/j.jtocrr.2023.100556] [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: 04/24/2023] [Revised: 06/26/2023] [Accepted: 07/15/2023] [Indexed: 09/02/2023] Open
Abstract
Introduction Neoadjuvant chemoimmunotherapy has recently been the standard of care for resectable locally advanced NSCLC. Factors affecting the neoadjuvant immunotherapy efficacy, however, remain elusive. Metabolites have been found to modulate immunity and associate with immunotherapeutic efficacy in advanced tumors. Therefore, we aimed to investigate the impact of plasma metabolites on the pathologic response after neoadjuvant chemoimmunotherapy. Methods Patients with stage IIIA (N2) NSCLC who underwent neoadjuvant chemoimmunotherapy in a prospective phase 2 clinical trial (NCT04422392) were enrolled. Metabolomic profiling of the plasma before treatment was performed using liquid chromatography-mass spectrometry. A Lewis lung carcinoma mouse model was further used to investigate the underlying mechanisms. Proteomics and multiplexed immunofluorescence of the mice tumor were performed. Results A total of 39 patients who underwent three cycles of anti-programmed cell death-protein 1 (anti-PD-1) (sintilimab) and chemotherapy were included. The level of acetaminophen (APAP) was found to be significantly elevated in patients who did not achieve major pathologic response. The level of APAP remained an independent predictor for major pathologic response in multivariate logistic analysis. In the Lewis lung carcinoma mouse model, combination of APAP and anti-PD-1 treatment significantly reduced the treatment efficacy compared with anti-PD-1 treatment alone. Proteomics of the tumor revealed that myeloid leukocyte activation and neutrophil activation pathways were enriched after APAP treatment. Tumor microenvironment featuring analysis also revealed that the combination treatment group was characterized with more abundant neutrophil signature. Further multiplexed immunofluorescence confirmed that more neutrophil extracellular trap formation was observed in the combination treatment group. Conclusions APAP could impair neoadjuvant chemoimmunotherapy efficacy in patients with NSCLC by promoting neutrophil activation and neutrophil extracellular trap formation.
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Affiliation(s)
- Chongwu Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Lei Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Fang Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Long Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Yue Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Yun Xiao
- DeepKinase Co, Ltd., Beijing, People’s Republic of China
| | - Fenghui Zhuang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Deping Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Yunlang She
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
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Deng L, Jiang H. Decreased Expression of GLYATL1 Predicts Poor Prognosis in Patients with Clear Cell Renal Cell Carcinoma. Int J Gen Med 2023; 16:3757-3768. [PMID: 37649851 PMCID: PMC10464902 DOI: 10.2147/ijgm.s419301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023] Open
Abstract
Background GLYATL1 is a member of the glycine-N-acyltransferase family, which catalyses acyl group transfer. The role of GLYATL1 in cancer is largely unknown; therefore, the potential value of GLYATL1 in clear cell renal cell carcinoma (ccRCC) was explored. Methods The ccRCC gene expression profiles and clinical data were obtained from the University of California Santa Cruz Xena platform. Differential expression and survival analysis were performed using R software. Samples from the TIMER public database and real-world were used for validation. The potential molecular mechanism of GLYATL1 in ccRCC was explored using gene set enrichment analysis (GSEA). Results GLYATL1 was downregulated, indicating a poor prognosis in ccRCC. Low expression of GLYATL1 was significantly associated with advanced stage and higher histological grade ccRCC. The differential expression of GLYATL1 was validated at the protein level using clinical samples and tissue microarray. The results of GSEA showed that multiple crucial signalling pathways including fatty acid metabolism, adipogenesis, oxidative phosphorylation and epithelial-mesenchymal transition were enriched. Conclusion This study demonstrated that GLYATL1 downregulation has an unfavourable impact on the survival of patients with ccRCC. The resulting data indicated that GLYATL1 could be a potential new target for ccRCC therapy, which may be helpful for the personalized treatment of such individuals.
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Affiliation(s)
- Limin Deng
- Department of Urology, Meizhou Academy of Medical Sciences, Meizhou People’s Hospital, Guangdong Medical University, Meizhou, Guangdong Province, People’s Republic of China
| | - Huiming Jiang
- Department of Urology, Meizhou Academy of Medical Sciences, Meizhou People’s Hospital, Meizhou, Guangdong Province, People's Republic of China
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Limeta A, Gatto F, Herrgård MJ, Ji B, Nielsen J. Leveraging high-resolution omics data for predicting responses and adverse events to immune checkpoint inhibitors. Comput Struct Biotechnol J 2023; 21:3912-3919. [PMID: 37602228 PMCID: PMC10432706 DOI: 10.1016/j.csbj.2023.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/22/2023] Open
Abstract
A long-standing goal of personalized and precision medicine is to enable accurate prediction of the outcomes of a given treatment regimen for patients harboring a disease. Currently, many clinical trials fail to meet their endpoints due to underlying factors in the patient population that contribute to either poor responses to the drug of interest or to treatment-related adverse events. Identifying these factors beforehand and correcting for them can lead to an increased success of clinical trials. Comprehensive and large-scale data gathering efforts in biomedicine by omics profiling of the healthy and diseased individuals has led to a treasure-trove of host, disease and environmental factors that contribute to the effectiveness of drugs aiming to treat disease. With increasing omics data, artificial intelligence allows an in-depth analysis of big data and offers a wide range of applications for real-world clinical use, including improved patient selection and identification of actionable targets for companion therapeutics for improved translatability across more patients. As a blueprint for complex drug-disease-host interactions, we here discuss the challenges of utilizing omics data for predicting responses and adverse events in cancer immunotherapy with immune checkpoint inhibitors (ICIs). The omics-based methodologies for improving patient outcomes as in the ICI case have also been applied across a wide-range of complex disease settings, exemplifying the use of omics for in-depth disease profiling and clinical use.
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Affiliation(s)
- Angelo Limeta
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Francesco Gatto
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
- Department of Oncology-Pathology, Karolinska Institute, 171 64 Stockholm, Sweden
| | | | - Boyang Ji
- BioInnovation Institute, 2200 Copenhagen N, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
- BioInnovation Institute, 2200 Copenhagen N, Denmark
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Zhu M, Li Y, Wang Y, Lin P, Mi J, Zhong W. Multi-omics analysis uncovers clinical, immunological, and pharmacogenomic implications of cuproptosis in clear cell renal cell carcinoma. Eur J Med Res 2023; 28:248. [PMID: 37481601 PMCID: PMC10362584 DOI: 10.1186/s40001-023-01221-4] [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: 03/06/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVE The latest research proposed a novel copper-dependent programmed cell death named cuproptosis. We aimed to elucidate the influence of cuproptosis in clear cell renal cell carcinoma (ccRCC) from a multi-omic perspective. METHODS This study systematically assessed mRNA expression, methylation, and genetic alterations of cuproptosis genes in TCGA ccRCC samples. Through unsupervised clustering analysis, the samples were classified as different cuproptosis subtypes, which were verified through NTP method in the E-MTAB-1980 dataset. Next, the cuproptosis score (Cuscore) was computed based on cuproptosis-related genes via PCA. We also evaluated clinical and immunogenomic features, drug sensitivity, immunotherapeutic response, and post-transcriptional regulation. RESULTS Cuproptosis genes presented multi-layer alterations in ccRCC, and were linked with patients' survival and immune microenvironment. We defined three cuproptosis subtypes [C1 (moderate cuproptosis), C2 (low cuproptosis), and C3 (high cuproptosis)], and the robustness and reproducibility of this classification was further proven. Overall survival was best in C3, moderate in C1, and worst in C2. C1 had the highest sensitivity to pazopanib, and sorafenib, while C2 was most sensitive to sunitinib. Furthermore, C1 patients benefited more from anti-PD-1 immunotherapy. Patients with high Cuscore presented the notable survival advantage. Cuscore was highly linked with immunogenomic features, and post-transcriptional events that contributed to ccRCC development. Finally, several potential compounds and druggable targets (NMU, RARRES1) were selected for low Cuscore group. CONCLUSION Overall, our study revealed the non-negligible role of cuproptosis in ccRCC development. Evaluation of the cuproptosis subtypes improves our cognition of immunogenomic features and better guides personalized prognostication and precision therapy.
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Affiliation(s)
- Maoshu Zhu
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Yongsheng Li
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Yun Wang
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Pingli Lin
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Jun Mi
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Weimin Zhong
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China.
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Ždralević M, Pouysségur J. Editorial: Immunometabolism and therapeutic targeting of aggressive cancers. Front Oncol 2023; 13:1226078. [PMID: 37377913 PMCID: PMC10291691 DOI: 10.3389/fonc.2023.1226078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Affiliation(s)
- Maša Ždralević
- Institute for Advanced Studies, University of Montenegro, Podgorica, Montenegro
| | - Jacques Pouysségur
- Medical Biology Department, Centre Scientifique de Monaco (CSM), Monaco, Monaco
- Centre A. Lacassagne, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France
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Allegra A, Murdaca G, Mirabile G, Gangemi S. Redox Signaling Modulates Activity of Immune Checkpoint Inhibitors in Cancer Patients. Biomedicines 2023; 11:biomedicines11051325. [PMID: 37238995 DOI: 10.3390/biomedicines11051325] [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: 04/06/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Although immunotherapy is already a staple of cancer care, many patients may not benefit from these cutting-edge treatments. A crucial field of research now focuses on figuring out how to improve treatment efficacy and assess the resistance mechanisms underlying this uneven response. For a good response, immune-based treatments, in particular immune checkpoint inhibitors, rely on a strong infiltration of T cells into the tumour microenvironment. The severe metabolic environment that immune cells must endure can drastically reduce effector activity. These immune dysregulation-related tumour-mediated perturbations include oxidative stress, which can encourage lipid peroxidation, ER stress, and T regulatory cells dysfunction. In this review, we have made an effort to characterize the status of immunological checkpoints, the degree of oxidative stress, and the part that latter plays in determining the therapeutic impact of immunological check point inhibitors in different neoplastic diseases. In the second section of the review, we will make an effort to assess new therapeutic possibilities that, by affecting redox signalling, may modify the effectiveness of immunological treatment.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy
| | - Giuseppe Murdaca
- Department of Internal Medicine, Ospedale Policlinico San Martino IRCCS, University of Genova, Viale Benedetto XV, n. 6, 16132 Genova, Italy
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
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Zheng J, Li YZ, Ni WJ, Hou SM, Lu KQ, Yan Y, Ren LQ, Liu BC, Wang B. Comprehensive Analysis of the Roles of Fatty Acid Transport Related Proteins in Clear Cell Renal Cell Carcinoma. Prostaglandins Other Lipid Mediat 2023; 167:106732. [PMID: 37044156 DOI: 10.1016/j.prostaglandins.2023.106732] [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: 04/14/2023]
Abstract
OBJECTIVE This study aimed to explore the clinical significance of fatty acid transport-related protein (FATRP) in patients with clear cell renal cell carcinoma(ccRCC). METHODS RNA-seq data and corresponding clinical data of ccRCC were obtained from TCGA data portal. Seventeen key FATRP genes were comprehensively investigated using bioinformatics approaches to systematically investigate their expression patterns in ccRCC. In addition, the correlation between the expression levels of these genes and clinicopathological features in ccRCC was further explored. RESULTS Among the 17 key FATRP genes, only FABP5, FABP6, and FABP7 could be regarded as ideal biomarkers for ccRCC, as they were highly expressed in ccRCC tumor tissues, and positively correlates with tumor progression and poor prognosis. FABP6 had the highest copy number variations (CNV) events (63.07%), and ccRCC patients with FABP6 amplification had a better prognosis than the unaltered group. DNA methylation levels of FABP6 and FABP7 were downregulated in ccRCC tumor tissues compared to those in normal tissues. FABP5 showed the opposite results. Moreover, a novel four FATRP gene (FABP1, FABP5, FABP7, FATP2) and three clinical parameter (age, stage, and grade) prediction model was constructed and that comprised a significant independent prognostic signature. CONCLUSIONS Only a few FATRP genes are upregulated in ccRCC tumor tissue, and positively correlate with tumor progression and poor prognosis. The accuracy of a single gene of these FATRP genes as predictors of progression and prognosis of ccRCC is limited. The performance of the novel prediction model proposed by this study was much better than that of any single gene.
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Affiliation(s)
- Jing Zheng
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China; Department of Gerontology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yan-Zhi Li
- Department of Gerontology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Shi-Mei Hou
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Ke-Qi Lu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yu Yan
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Li-Qun Ren
- Department of Gerontology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
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Derveaux E, Geubbelmans M, Criel M, Demedts I, Himpe U, Tournoy K, Vercauter P, Johansson E, Valkenborg D, Vanhove K, Mesotten L, Adriaensens P, Thomeer M. NMR-Metabolomics Reveals a Metabolic Shift after Surgical Resection of Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15072127. [PMID: 37046788 PMCID: PMC10093525 DOI: 10.3390/cancers15072127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Background: Lung cancer can be detected by measuring the patient’s plasma metabolomic profile using nuclear magnetic resonance (NMR) spectroscopy. This NMR-based plasma metabolomic profile is patient-specific and represents a snapshot of the patient’s metabolite concentrations. The onset of non-small cell lung cancer (NSCLC) causes a change in the metabolite profile. However, the level of metabolic changes after complete NSCLC removal is currently unknown. Patients and methods: Fasted pre- and postoperative plasma samples of 74 patients diagnosed with resectable stage I-IIIA NSCLC were analyzed using 1H-NMR spectroscopy. NMR spectra (s = 222) representing two preoperative and one postoperative plasma metabolite profile at three months after surgical resection were obtained for all patients. In total, 228 predictors, i.e., 228 variables representing plasma metabolite concentrations, were extracted from each NMR spectrum. Two types of supervised multivariate discriminant analyses were used to train classifiers presenting a strong differentiation between the pre- and postoperative plasma metabolite profiles. The validation of these trained classification models was obtained by using an independent dataset. Results: A trained multivariate discriminant classification model shows a strong differentiation between the pre- and postoperative NSCLC profiles with a specificity of 96% (95% CI [86–100]) and a sensitivity of 92% (95% CI [81–98]). Validation of this model results in an excellent predictive accuracy of 90% (95% CI [77–97]) and an AUC value of 0.97 (95% CI [0.93–1]). The validation of a second trained model using an additional preoperative control sample dataset confirms the separation of the pre- and postoperative profiles with a predictive accuracy of 93% (95% CI [82–99]) and an AUC value of 0.97 (95% CI [0.93–1]). Metabolite analysis reveals significantly increased lactate, cysteine, asparagine and decreased acetate levels in the postoperative plasma metabolite profile. Conclusions: The results of this paper demonstrate that surgical removal of NSCLC generates a detectable metabolic shift in blood plasma. The observed metabolic shift indicates that the NSCLC metabolite profile is determined by the tumor’s presence rather than donor-specific features. Furthermore, the ability to detect the metabolic difference before and after surgical tumor resection strongly supports the prospect that NMR-generated metabolite profiles via blood samples advance towards early detection of NSCLC recurrence.
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Affiliation(s)
- Elien Derveaux
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, B-3500 Hasselt, Belgium
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Agoralaan 1—Building D, B-3590 Diepenbeek, Belgium
| | - Melvin Geubbelmans
- Data Science Institute, Hasselt University, Agoralaan 1, B-3590 Diepenbeek, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, B-3590 Diepenbeek, Belgium
| | - Maarten Criel
- Department of Respiratory Medicine, Ziekenhuis Oost-Limburg, Schiepse Bos 6, B-3600 Genk, Belgium
| | - Ingel Demedts
- Department of Respiratory Medicine, AZ Delta, Deltalaan 1, B-8800 Roeselare, Belgium
| | - Ulrike Himpe
- Department of Respiratory Medicine, AZ Delta, Deltalaan 1, B-8800 Roeselare, Belgium
| | - Kurt Tournoy
- Department of Respiratory Medicine, Onze-Lieve-Vrouw Ziekenhuis, Moorselbaan 164, B-9300 Aalst, Belgium
- Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 85, B-9000 Ghent, Belgium
| | - Piet Vercauter
- Department of Respiratory Medicine, Onze-Lieve-Vrouw Ziekenhuis, Moorselbaan 164, B-9300 Aalst, Belgium
| | - Erik Johansson
- Sartorius Stedim Data Analytics AB, Östra Strandgatan 24, 903 33 Umeå, Sweden
| | - Dirk Valkenborg
- Data Science Institute, Hasselt University, Agoralaan 1, B-3590 Diepenbeek, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, B-3590 Diepenbeek, Belgium
| | - Karolien Vanhove
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Agoralaan 1—Building D, B-3590 Diepenbeek, Belgium
- Department of Respiratory Medicine, AZ Vesalius, Hazelereik 51, B-3700 Tongeren, Belgium
| | - Liesbet Mesotten
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, B-3500 Hasselt, Belgium
- Department of Nuclear Medicine, Ziekenhuis Oost-Limburg, Schiepse Bos 6, B-3600 Genk, Belgium
| | - Peter Adriaensens
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Agoralaan 1—Building D, B-3590 Diepenbeek, Belgium
| | - Michiel Thomeer
- Faculty of Medicine and Life Sciences, Hasselt University, Martelarenlaan 42, B-3500 Hasselt, Belgium
- Department of Respiratory Medicine, Ziekenhuis Oost-Limburg, Schiepse Bos 6, B-3600 Genk, Belgium
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Endoplasmic Reticulum Stress in Renal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24054914. [PMID: 36902344 PMCID: PMC10003093 DOI: 10.3390/ijms24054914] [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: 01/18/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
The endoplasmic reticulum is an organelle exerting crucial functions in protein production, metabolism homeostasis and cell signaling. Endoplasmic reticulum stress occurs when cells are damaged and the capacity of this organelle to perform its normal functions is reduced. Subsequently, specific signaling cascades, together forming the so-called unfolded protein response, are activated and deeply impact cell fate. In normal renal cells, these molecular pathways strive to either resolve cell injury or activate cell death, depending on the extent of cell damage. Therefore, the activation of the endoplasmic reticulum stress pathway was suggested as an interesting therapeutic strategy for pathologies such as cancer. However, renal cancer cells are known to hijack these stress mechanisms and exploit them to their advantage in order to promote their survival through rewiring of their metabolism, activation of oxidative stress responses, autophagy, inhibition of apoptosis and senescence. Recent data strongly suggest that a certain threshold of endoplasmic reticulum stress activation needs to be attained in cancer cells in order to shift endoplasmic reticulum stress responses from a pro-survival to a pro-apoptotic outcome. Several endoplasmic reticulum stress pharmacological modulators of interest for therapeutic purposes are already available, but only a handful were tested in the case of renal carcinoma, and their effects in an in vivo setting remain poorly known. This review discusses the relevance of endoplasmic reticulum stress activation or suppression in renal cancer cell progression and the therapeutic potential of targeting this cellular process for this cancer.
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Mei L, Zhang Z, Li X, Yang Y, Qi R. Metabolomics profiling in prediction of chemo-immunotherapy efficiency in advanced non-small cell lung cancer. Front Oncol 2023; 12:1025046. [PMID: 36733356 PMCID: PMC9887290 DOI: 10.3389/fonc.2022.1025046] [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: 08/22/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Background To explore potential metabolomics biomarker in predicting the efficiency of the chemo-immunotherapy in patients with advanced non-small cell lung cancer (NSCLC). Methods A total of 83 eligible patients were assigned to receive chemo-immunotherapy. Serum samples were prospectively collected before the treatment to perform metabolomics profiling analyses under the application of gas chromatography mass spectrometry (GC-MS). The key metabolites were identified using projection to latent structures discriminant analysis (PLS-DA). The key metabolites were used for predicting the chemo-immunotherapy efficiency in advanced NSCLC patients. Results Seven metabolites including pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate were identified as the key metabolites to the chemo-immunotherapy response. The receiver operating characteristic curves (AUC) were 0.79 (95% CI: 0.69-0.90), 0.60 (95% CI: 0.48-0.73), 0.69 (95% CI: 0.57-0.80), 0.63 (95% CI: 0.51-0.75), 0.60 (95% CI: 0.48-0.72), 0.56 (95% CI: 0.43-0.67), and 0.67 (95% CI: 0.55-0.80) for the key metabolites, respectively. A binary logistic regression was used to construct a combined biomarker model to improve the discriminating efficiency. The AUC was 0.86 (95% CI: 0.77-0.94) for the combined biomarker model. Pathway analyses showed that urea cycle, glucose-alanine cycle, glycine and serine metabolism, alanine metabolism, and glutamate metabolism were the key metabolic pathway to the chemo-immunotherapy response in patients with advanced NSCLC. Conclusion Metabolomics analyses of key metabolites and pathways revealed that GC-MS could be used to predict the efficiency of chemo-immunotherapy. Pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate played a central role in the metabolic of PD patients with advanced NSCLC.
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Affiliation(s)
- Lihong Mei
- Department of Dermatology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Zhihua Zhang
- Department of Echocardiography, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xushuo Li
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Ying Yang
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Ruixue Qi
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China,*Correspondence: Ruixue Qi,
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Vignoli A, Meoni G, Ghini V, Di Cesare F, Tenori L, Luchinat C, Turano P. NMR-Based Metabolomics to Evaluate Individual Response to Treatments. Handb Exp Pharmacol 2023; 277:209-245. [PMID: 36318327 DOI: 10.1007/164_2022_618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological stimuli may cause individuals to lose their position and then regain it, or move irreversibly to other positions. By way of examples, mostly selected from our own work using 1H NMR on biological fluids, we describe the effects on the individual metabolomic fingerprint of mild external interventions, such as diet or probiotic administration. Then we move to pathologies (such as celiac disease, various types of cancer, viral infections, and other diseases), each characterized by a well-defined metabolomic fingerprint. We describe the effects of drugs on the disease fingerprint and on its reversal to a healthy metabolomic status. Drug toxicity can be also monitored by metabolomics. We also show how the individual metabolomic fingerprint at the onset of a disease may discriminate responders from non-responders to a given drug, or how it may be prognostic of e.g., cancer recurrence after many years. In parallel with fingerprinting, profiling (i.e., the identification and quantification of many metabolites and, in the case of selected biofluids, of the lipoprotein components that contribute to the 1H NMR spectral features) can provide hints on the metabolic pathways that are altered by a disease and assess their restoration after treatment.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy.
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Villemin C, Six A, Neville BA, Lawley TD, Robinson MJ, Bakdash G. The heightened importance of the microbiome in cancer immunotherapy. Trends Immunol 2023; 44:44-59. [PMID: 36464584 DOI: 10.1016/j.it.2022.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022]
Abstract
The human microbiome is recognized as a key factor in health and disease. This has been further corroborated by identifying changes in microbiome composition and function as a novel hallmark in cancer. These effects are exerted through microbiome interactions with host cells, impacting a wide variety of developmental and physiological processes. In this review, we discuss some of the latest findings on how the bacterial component of the microbiome can influence outcomes for different cancer immunotherapy modalities, highlighting identified mechanisms of action. We also address the clinical efforts to utilize this knowledge to achieve better responses to immunotherapy. A refined understanding of microbiome variations in patients and microbiome-host interactions with cancer therapies is essential to realize optimal clinical responses.
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Affiliation(s)
| | - Anne Six
- Microbiotica Ltd., Cambridge, UK
| | | | - Trevor D Lawley
- Microbiotica Ltd., Cambridge, UK; Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
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Qin J, Yang Y, Du W, Li G, Wu Y, Luo R, Liu S, Fan J. The potential value of LC-MS non-targeted metabonomics in the diagnosis of follicular thyroid carcinoma. Front Oncol 2022; 12:1076548. [PMID: 36620583 PMCID: PMC9814718 DOI: 10.3389/fonc.2022.1076548] [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: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background To explore the metabolic differences of follicular thyroid carcinoma (FTC) by metabonomics, to find potential biomarkers for the diagnosis of FTC, and to explore the pathogenesis and diagnosis and treatment strategies of FTC. Method The metabonomics of 15 patients with FTC and 15 patients with follicular thyroid nodules(FTN) treated in Henan Cancer Hospital were analyzed by liquid chromatography-mass spectrometry (LC-MS). Results The analysis showed that the metabolite profiles of FTC tissues could be well distinguished from those of control tissues, and 6 kinds of lipids were identified respectively, including lysophosphatidic acid(LysoPA) [LysoPA(0:0/18:0),LysoPA(0:0/18:2(9Z,12Z)],LysoPA[20:4(8Z,11Z,14Z,17Z)/0:0)]; phosphatidic acid(PA) [PA(20:3(8Z,11Z,14Z)/0:0),PA(20:4(5Z,8Z,11Z,14Z)/0:0),PA(20:5(5Z,8Z,11Z,14Z,17Z)/0:0)]; lysophosphatidylcholine(LPC) [LPC(18:1),LPC(16:0),LPC[16:1(9Z)/0:0],LPC(17:0),LPC[22:4(7Z,10Z,13Z,16Z),LPC(20:2(11Z,14Z); phosphatidylcholine(PC)(PC(14:0/0:0),PC(16:0/0:0); sphingomyelin(SM) (d18:0/12:0); fatty acid(FA)(18:1(OH3)]. There are 2 kinds of amino acids, including L-glutamate,L-glutamine.There are 3 other metabolites, including retinol,flavin adenine dinucleotide,androsterone glucuronide.Lipid metabolites are the main metabolites in these metabolites.The metabolic pathways related to FTC were analyzed by KEGG and HMDB, and 9 metabolic pathways were found, including 4 amino acid related metabolic pathways, 1 lipid metabolic pathways and 4 other related pathways. Conclusion There are significant differences in many metabonomic characteristics between FTC and FTN, suggesting that these metabolites can be used as potential biomarkers. Further study found that LysoPA and its analogues can be used as biomarkers in the early diagnosis of FTC.It may be related to the abnormal metabolism of phospholipase D (PLD), the key enzyme of LysoPA synthesis caused by RAS pathway. At the same time, it was found that the metabolic pathway of amino acids and lipids was the main metabolic pathway of FTC. The abnormality of LysoPA may be the cause of follicular tumor carcinogenesis caused by lipid metabolic pathway.
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Affiliation(s)
- Jiali Qin
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Yang Yang
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Wei Du
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China,Department of Anatomy, Zhengzhou University, Zhengzhou, Henan, China
| | - Gang Li
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Yao Wu
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Ruihua Luo
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China,*Correspondence: Jie Fan, ; Shanting Liu, ; Ruihua Luo,
| | - Shanting Liu
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China,*Correspondence: Jie Fan, ; Shanting Liu, ; Ruihua Luo,
| | - Jie Fan
- Department of Head Neck and Thyroid Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China,*Correspondence: Jie Fan, ; Shanting Liu, ; Ruihua Luo,
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Contemporary Clinical Definitions, Differential Diagnosis, and Novel Predictive Tools for Renal Cell Carcinoma. Biomedicines 2022; 10:biomedicines10112926. [PMID: 36428491 PMCID: PMC9687297 DOI: 10.3390/biomedicines10112926] [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: 09/20/2022] [Revised: 10/26/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Despite significant progress regarding clinical detection/imaging evaluation modalities and genetic/molecular characterization of pathogenesis, advanced renal cell carcinoma (RCC) remains an incurable disease and overall RCC mortality has been steadily rising for decades. Concomitantly, clinical definitions have been greatly nuanced and refined. RCCs are currently viewed as a heterogeneous series of cancers, with the same anatomical origin, but fundamentally different metabolisms and clinical behaviors. Thus, RCC pathological diagnosis/subtyping guidelines have become increasingly intricate and cumbersome, routinely requiring ancillary studies, mainly immunohistochemistry. Meanwhile, RCC-associated-antigen targeted systemic therapy has been greatly diversified and emerging, novel clinical applications for RCC immunotherapy have already reported significant survival benefits, at least in the adjuvant setting. Even so, systemically disseminated RCCs still associate very poor clinical outcomes, with currently available therapeutic modalities only being able to prolong survival. In lack of a definitive cure for advanced RCCs, integration of the amounting scientific knowledge regarding RCC pathogenesis into RCC clinical management has been paramount for improving patient outcomes. The current review aims to offer an integrative perspective regarding contemporary RCC clinical definitions, proper RCC clinical work-up at initial diagnosis (semiology and multimodal imaging), RCC pathological evaluation, differential diagnosis/subtyping protocols, and novel clinical tools for RCC screening, risk stratification and therapeutic response prediction.
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Systematic Review of NMR-Based Metabolomics Practices in Human Disease Research. Metabolites 2022; 12:metabo12100963. [PMID: 36295865 PMCID: PMC9609461 DOI: 10.3390/metabo12100963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 12/02/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the principal analytical techniques for metabolomics. It has the advantages of minimal sample preparation and high reproducibility, making it an ideal technique for generating large amounts of metabolomics data for biobanks and large-scale studies. Metabolomics is a popular “omics” technology and has established itself as a comprehensive exploratory biomarker tool; however, it has yet to reach its collaborative potential in data collation due to the lack of standardisation of the metabolomics workflow seen across small-scale studies. This systematic review compiles the different NMR metabolomics methods used for serum, plasma, and urine studies, from sample collection to data analysis, that were most popularly employed over a two-year period in 2019 and 2020. It also outlines how these methods influence the raw data and the downstream interpretations, and the importance of reporting for reproducibility and result validation. This review can act as a valuable summary of NMR metabolomic workflows that are actively used in human biofluid research and will help guide the workflow choice for future research.
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Yan C, Wu D, Gan L, Wang J, Yang W, Xu B. Significant metabolic alterations in non-small cell lung cancer patients by epidermal growth factor receptor-targeted therapy and PD-1/PD-L1 immunotherapy. Front Pharmacol 2022; 13:949745. [PMID: 36034789 PMCID: PMC9403486 DOI: 10.3389/fphar.2022.949745] [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: 05/21/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Cancer-related deaths are primarily attributable to lung cancer, of which non-small cell lung cancer (NSCLC) is the most common type. Molecular targeting therapy and antitumor immunotherapy have both made great strides in the treatment of NSCLC, but their underlying mechanisms remain unclear, especially from a metabolic perspective. Methods: Herein, we used a nontargeted metabolomics approach based on liquid chromatography-mass spectrometry to analyze the metabolic response of NSCLC patients to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) or PD-1/PD-L1 inhibitors. Multiple analyses, including principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA) and pathway analysis, were used for metabolic data analysis. Additionally, differential metabolites were analysed and identified by publically available and integrated databases. Results: After treatment with EGFR-TKIs or PD-1/PD-L1 inhibitors, glutamate/glutamine, phenylalanine, n-acetyl-l-leucine, n-acetyl-d-tryptophan, D-n-valine, arachidonic acid, and linoleic acid levels were significantly increased in patients with NSCLC, whereas carnitine, stearyl carnitine, palmitoyl carnitine, linoleic carnitine, and palmitic acid levels were markedly decreased. Compared with newly diagnosed, untreated patients, there were three shared metabolic pathways (phenylalanine metabolism, glycerophospholipid metabolism, and D-glutamine and D-glutamate metabolism) in the EGFR-TKIs or PD-1/PD-L1 inhibitor-treated groups, all of which were related to lipid and amino acid metabolism. Moreover, there were significant differences in lipid metabolism (glycerophospholipid metabolism and phosphatidylinositol signaling) and amino acid metabolism (tryptophan metabolism) between the EGFR-TKI and PD-1/PD-L1 inhibitor groups. Conclusion: Our results show that EGFR-TKIs and PD-1/PD-L1 inhibitors induce changes in carnitine, amino acids, fatty acids, and lipids and alter related metabolic pathways in NSCLC patients. Endogenous metabolism changes occur due to drug action and might be indicative of antitumor therapeutic effect. These findings will provide new clues for identifying the antitumor mechanism of these two treatments from the perspective of metabolism.
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Affiliation(s)
- Chen Yan
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Wu
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Lingling Gan
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Jun Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenyu Yang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Bei Xu
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
- *Correspondence: Bei Xu,
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Gong WJ, Cao P, Zhang QL, Han XY, Wang SW, Huang YF, Wu SL, Li Q, Zhang R, Xu SB, Liu YN, Shi SJ, Zhang Y. Prediction of response and adverse drug reaction of pemetrexed plus platinum-based chemotherapy in lung adenocarcinoma by serum metabolomic profiling. Transl Oncol 2022; 19:101393. [PMID: 35290920 PMCID: PMC8918859 DOI: 10.1016/j.tranon.2022.101393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 12/02/2022] Open
Abstract
Oncologists need effective tools to predict and improve their treatment outcome. We assessed the performance of a metabolomics approach to predict the response and toxicity to pemetrexed plus platinum-based chemotherapy in lung adenocarcinoma. We established effective and convenient models that can predict the efficacy and toxicity of pemetrexed plus platinum chemotherapy in lung adenocarcinoma patients before treatment delivery.
Background Pemetrexed plus platinum doublet chemotherapy regimen remains to be the standard first-line treatment for lung adenocarcinoma patients. However, few biomarkers can be used to identify potential beneficiaries with maximal efficacy and minimal toxicity. This study aimed to explore potential biomarker models predictive of efficacy and toxicity after pemetrexed plus platinum chemotherapy based on metabolomics profiling. Methods A total of 144 patients who received at least two cycles of pemetrexed plus platinum chemotherapy were enroled in the study. Serum samples were collected before initial treatment to perform metabolomics profiling analysis. Logistic regression analysis was performed to establish prediction models. Results 157 metabolites were found to be differentially expressed between the response group and the nonresponse group. A panel of Phosphatidylserine 20:4/20:1, Sphingomyelin d18:1/18:0, and Phosphatidic Acid 18:1/20:0 could predict pemetrexed and platinum chemotherapy response with an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.7968. 76 metabolites were associated with hematological toxicity of pemetrexed plus platinum chemotherapy. A panel incorporating triglyceride 14:0/22:3/22:5, 3-(3-Hydroxyphenyl) Propionate Acid, and Carnitine C18:0 was the best predictive ability of hematological toxicity with an AUROC of 0.7954. 54 differential expressed metabolites were found to be associated with hepatotoxicity of pemetrexed plus platinum chemotherapy. A model incorporating stearidonic acid, Thromboxane B3, l-Homocitrulline, and phosphoinositide 20:3/18:0 showed the best predictive ability of hepatotoxicity with an AUROC of 0.8186. Conclusions This study established effective and convenient models that can predict the efficacy and toxicity of pemetrexed plus platinum chemotherapy in lung adenocarcinoma patients before treatment delivery.
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Prognostic impact of prognostic nutritional index on renal cell carcinoma: A meta-analysis of 7,629 patients. PLoS One 2022; 17:e0265119. [PMID: 35312690 PMCID: PMC8936492 DOI: 10.1371/journal.pone.0265119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/23/2022] [Indexed: 12/03/2022] Open
Abstract
Background Prognostic nutritional index (PNI) is a parameter which reflects nutritional and inflammatory status. The prognostic value of PNI in renal cell carcinoma (RCC) remains in debate. The aim of this study is to evaluate the prognostic value and clinicopathological features of PNI in RCC. Methods A literature search was performed in the databases of PubMed, Embase, Web of Science, and Cochrane Library. Hazard ratios (HRs), odds ratios (ORs), and 95% confidence intervals (CIs) were extracted for meta-analysis. The association between PNI and overall survival (OS), cancer-specific survival (CSS), disease-free survival (DFS), progression-free survival (PFS), recurrence-free survival (RFS), and clinicopathological factors were evaluated. Results Eleven studies involving 7,629 patients were included for meta-analysis. A decreased PNI was shown to be a significant predictor of worse OS (HR = 2.00, 95%CI = 1.64–2.42, p<0.001), CSS (HR = 2.54, 95%CI = 1.61–4.00, p<0.001), and DFS/PFS/RFS (HR = 2.12, 95%CI = 1.82–2.46, p<0.001) in RCC. Furthermore, a low PNI was correlated with Fuhrman grade III-IV (OR = 1.96, 95%CI = 1.27–3.02, p = 0.002), T stage T3-T4 (OR = 2.21, 95%CI = 1.27–3.87, p = 0.005), presence of sarcomatoid differentiation (OR = 5.00, 95%CI = 2.52–9.92, p<0.001), and presence of tumor necrosis (OR = 3.63, 95%CI = 2.54–5.19, p<0.001). Conclusion PNI is an independent prognostic indicator of survival and associated with Fuhrman grade, T stage, sarcomatoid differentiation, and tumor necrosis in patients with RCC.
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Leigh SJ, Lynch CMK, Bird BRH, Griffin BT, Cryan JF, Clarke G. Gut microbiota-drug interactions in cancer pharmacotherapies: implications for efficacy and adverse effects. Expert Opin Drug Metab Toxicol 2022; 18:5-26. [PMID: 35176217 DOI: 10.1080/17425255.2022.2043849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The gut microbiota is involved in host physiology and health. Reciprocal microbiota-drug interactions are increasingly recognized as underlying some individual differences in therapy response and adverse events. Cancer pharmacotherapies are characterized by a high degree of interpatient variability in efficacy and side effect profile and recently, the microbiota has emerged as a factor that may underlie these differences. AREAS COVERED The effects of cancer pharmacotherapy on microbiota composition and function are reviewed with consideration of the relationship between baseline microbiota composition, microbiota modification, antibiotics exposure and cancer therapy efficacy. We assess the evidence implicating the microbiota in cancer therapy-related adverse events including impaired gut function, cognition and pain perception. Finally, potential mechanisms underlying microbiota-cancer drug interactions are described, including direct microbial metabolism, and microbial modulation of liver metabolism and immune function. This review focused on preclinical and clinical studies conducted in the last 5 years. EXPERT OPINION Preclinical and clinical research supports a role for baseline microbiota in cancer therapy efficacy, with emerging evidence that the microbiota modification may assist in side effect management. Future efforts should focus on exploiting this knowledge towards the development of microbiota-targeted therapies. Finally, a focus on specific drug-microbiota-cancer interactions is warranted.
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Affiliation(s)
| | | | | | | | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Machine Learning for Prediction of Immunotherapy Efficacy in Non-Small Cell Lung Cancer from Simple Clinical and Biological Data. Cancers (Basel) 2021; 13:cancers13246210. [PMID: 34944830 PMCID: PMC8699503 DOI: 10.3390/cancers13246210] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are now a therapeutic standard in advanced non-small cell lung cancer (NSCLC), but strong predictive markers for ICIs efficacy are still lacking. We evaluated machine learning models built on simple clinical and biological data to individually predict response to ICIs. METHODS Patients with metastatic NSCLC who received ICI in second line or later were included. We collected clinical and hematological data and studied the association of this data with disease control rate (DCR), progression free survival (PFS) and overall survival (OS). Multiple machine learning (ML) algorithms were assessed for their ability to predict response. RESULTS Overall, 298 patients were enrolled. The overall response rate and DCR were 15.3% and 53%, respectively. Median PFS and OS were 3.3 and 11.4 months, respectively. In multivariable analysis, DCR was significantly associated with performance status (PS) and hemoglobin level (OR 0.58, p < 0.0001; OR 1.8, p < 0.001). These variables were also associated with PFS and OS and ranked top in random forest-based feature importance. Neutrophil-to-lymphocyte ratio was also associated with DCR, PFS and OS. The best ML algorithm was a random forest. It could predict DCR with satisfactory efficacy based on these three variables. Ten-fold cross-validated performances were: accuracy 0.68 ± 0.04, sensitivity 0.58 ± 0.08; specificity 0.78 ± 0.06; positive predictive value 0.70 ± 0.08; negative predictive value 0.68 ± 0.06; AUC 0.74 ± 0.03. CONCLUSION Combination of simple clinical and biological data could accurately predict disease control rate at the individual level.
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Gómez-Cebrián N, Vázquez Ferreiro P, Carrera Hueso FJ, Poveda Andrés JL, Puchades-Carrasco L, Pineda-Lucena A. Pharmacometabolomics by NMR in Oncology: A Systematic Review. Pharmaceuticals (Basel) 2021; 14:ph14101015. [PMID: 34681239 PMCID: PMC8539252 DOI: 10.3390/ph14101015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacometabolomics (PMx) studies aim to predict individual differences in treatment response and in the development of adverse effects associated with specific drug treatments. Overall, these studies inform us about how individuals will respond to a drug treatment based on their metabolic profiles obtained before, during, or after the therapeutic intervention. In the era of precision medicine, metabolic profiles hold great potential to guide patient selection and stratification in clinical trials, with a focus on improving drug efficacy and safety. Metabolomics is closely related to the phenotype as alterations in metabolism reflect changes in the preceding cascade of genomics, transcriptomics, and proteomics changes, thus providing a significant advance over other omics approaches. Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical platforms in metabolomics studies. In fact, since the introduction of PMx studies in 2006, the number of NMR-based PMx studies has been continuously growing and has provided novel insights into the specific metabolic changes associated with different mechanisms of action and/or toxic effects. This review presents an up-to-date summary of NMR-based PMx studies performed over the last 10 years. Our main objective is to discuss the experimental approaches used for the characterization of the metabolic changes associated with specific therapeutic interventions, the most relevant results obtained so far, and some of the remaining challenges in this area.
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Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
| | | | | | | | - Leonor Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain;
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
| | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, 31008 Navarra, Spain
- Correspondence: (L.P.-C.); (A.P.-L.); Tel.: +34-963246713 (L.P.-C.)
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