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Lin L, Gong S, Deng C, Zhang G, Wu J. PTK6: An emerging biomarker for prognosis and immunotherapeutic response in clear cell renal carcinoma (KIRC). Heliyon 2024; 10:e29001. [PMID: 38596018 PMCID: PMC11002233 DOI: 10.1016/j.heliyon.2024.e29001] [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: 09/09/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Kidney renal clear cell carcinoma (KIRC), one of the most prevalent form of kidney carcinoma, is highly aggressive cancer known for significant immune infiltration and high mortality rates. The absence of sensitivity to traditional therapy has spurred the search for new treatments. Protein Tyrosine Kinase 6 (PTK6) is implicated in promoting cancer growth, spread, and metastasis. Our review of The Cancer Genome Atlas database revealed PTK6 overexpression in KIRC, though its specific role in this cancer type was unclear. We investigated PTK6's cancer-promoting roles in KIRC using the database and confirmed our findings with patient-derived tissues. Our analysis showed that elevated PTK6 expression is linked to worse outcomes and higher levels of immune infiltration. It also correlates positively with neo-antigens (NEO) and DNA ploidy changes in KIRC. This research delves into PTK6's role in KIRC development, suggesting PTK6 as a possible biomarker for prognosis and treatment in KIRC.
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Affiliation(s)
- Lizhen Lin
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siming Gong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chao Deng
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guanxiong Zhang
- The Department of Dermatology, Xiangya Hospital, Central South University, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, China
- Furong Laboratory, Changsha, Hunan, China
| | - Jing Wu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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2
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Lee S, Kim G, Lee J, Lee AC, Kwon S. Mapping cancer biology in space: applications and perspectives on spatial omics for oncology. Mol Cancer 2024; 23:26. [PMID: 38291400 PMCID: PMC10826015 DOI: 10.1186/s12943-024-01941-z] [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: 06/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell sequencing technologies, have greatly assisted novel findings in tumor biology. Recent findings in tumor biology suggest that tumors construct architectures that influence the underlying cancerous mechanisms. Increasing research has reported novel techniques to map the tissue in a spatial context or targeted sampling-based characterization and has introduced such technologies to solve oncology regarding tumor heterogeneity, tumor microenvironment, and spatially located biomarkers. In this study, we address spatial technologies that can delineate the omics profile in a spatial context, novel findings discovered via spatial technologies in oncology, and suggest perspectives regarding therapeutic approaches and further technological developments.
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Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea
| | - Gyeongjun Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario, ON, M5S 3H6, Canada
| | - Amos C Lee
- Meteor Biotech,, Co. Ltd, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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Zhu C, Sun Z, Wang J, Meng X, Ma Z, Guo R, Niu J, Tran LJ, Zhang J, Jiang T, Liu Y, Ye F, Ma B. Exploring oncogenes for renal clear cell carcinoma based on G protein-coupled receptor-associated genes. Discov Oncol 2023; 14:182. [PMID: 37816979 PMCID: PMC10564696 DOI: 10.1007/s12672-023-00795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a class of receptors on cell membranes that regulate various biological processes in cells, such as cell proliferation, differentiation, migration, apoptosis, and metabolism, by interacting with G proteins. However, the role of G protein-coupled receptors in predicting the prognosis of renal clear cell carcinoma is still unknown. The transcriptome data and clinical profiles of renal clear cell carcinoma patients, were downloaded from TCGA databases, and the validation group data were downloaded from number GSE167573, including 63 tumor samples and 14 normal samples. Single-cell RNA sequencing data were downloaded from the GEO database, No. GSE152938 and selected samples were used for GSEA enrichment analysis, WGCNA subgroup analysis, single-cell data analysis, and mutation analysis to explore the role of G protein-coupled receptor-related genes in the diagnosis and prognosis of renal clear cell carcinoma and to verify their reliability with cellular experiments. Finally, this study establishes a disease model based on G protein-coupled receptor-related genes, which may help to propose targeted therapeutic regimens in different strata of renal cell carcinoma patients.Author names: Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author: Given name [Lisa Jia] Last name [Tran].It's ok!
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Affiliation(s)
- Chengcun Zhu
- Department of Urology, The First People’s Hospital of Jiangxia District, Wuhan, 430200 Hubei China
| | - Zhou Sun
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jie Wang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
- Department of Urology, The Second People’s Hospital of Meishan City, Meishan, Sichuan China
| | - Xiangdi Meng
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Zhaosen Ma
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Rui Guo
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jiqiang Niu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, SD 57069 USA
| | - Tianxiao Jiang
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Baoluo Ma
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
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Anwaier A, Xu W, Liu W, Wei S, Tian X, Qu Y, Yang J, Zhang H, Ye D. Tumor microenvironment-based signatures distinguish intratumoral heterogeneity, prognosis, and immunogenomic features of clear cell renal cell carcinoma. JOURNAL OF THE NATIONAL CANCER CENTER 2023; 3:236-249. [PMID: 39035192 PMCID: PMC11256720 DOI: 10.1016/j.jncc.2023.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 07/23/2024] Open
Abstract
Background The tumor microenvironment (TME) performs a crucial function in the tumorigenesis and response to immunotherapies of clear cell renal cell carcinoma (ccRCC). However, a lack of recognized pre-clinical TME-based risk models poses a great challenge to investigating the risk factors correlated with prognosis and treatment responses for patients with ccRCC. Methods Stromal and immune contexture were assessed to calculate the TMErisk score of a large sample of patients with ccRCC from public and real-world cohorts using machine-learning algorithms. Next, analyses for prognostic efficacy, correlations with clinicopathological features, functional enrichment, immune cell distributions, DNA variations, immune response, and heterogeneity were performed and validated. Results Clinical hub genes, including INAFM2, SRPX, DPYSL3, VSIG4, APLNR, FHL5, A2M, SLFN11, ADAMTS4, IFITM1, NOD2, CCR4, HLA-DQB2, and PLAUR, were identified and incorporated to develop the TMErisk signature. Patients in the TMEhigh risk group (category) exhibited a considerably grim prognosis, and the TMErisk model was shown to independently function as a risk indicator for the overall survival (OS) of ccRCC patients. Expression levels of immune checkpoint genes were substantially increased in TMEhigh risk group, while those of the human leukocyte antigen (HLA) family genes were prominently decreased. In addition, tumors in the TMEhigh group showed significantly high infiltration levels of tumor-infiltrated lymphocytes, including M2 macrophages, CD8+ T cells, B cells, and CD4+ T cells. In heterogeneity analysis, more frequent somatic mutations, including pro-tumorigenic BAP1 and PBRM1, were observed in the TMEhigh group. Importantly, 19.3% of patients receiving immunotherapies in the TMEhigh group achieved complete or partial response compared with those with immune tolerance in the TMElow group, suggesting that TMErisk prominently differentiates prognosis and responses to immunotherapy for patients with ccRCC. Conclusions We first established the TMErisk score of ccRCC using machine-learning algorithms based on a large-scale population. The TMErisk score can be utilized as an innovative independent prognosis predictive marker with high sensitivity and accuracy. Our discovery also predicted the efficacy of immunotherapy in ccRCC patients, indicating the intimate link between tumor immune microenvironment and intratumoral heterogeneity.
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Affiliation(s)
- Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Wangrui Liu
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Jianfeng Yang
- Department of Surgery, ShangNan Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
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Xu S, Hu X, Chong Y, Zhu G. Investigating the Role of FoxP3 in Renal Cell Carcinoma Metastasis with BAP1 or SEDT2 Mutation. Int J Mol Sci 2023; 24:12301. [PMID: 37569676 PMCID: PMC10419232 DOI: 10.3390/ijms241512301] [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: 06/25/2023] [Revised: 07/15/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Forkhead box protein P3 (FoxP3) primarily functions as the master regulator in regulatory T cells (Tregs) differentiation, but its high level of expression has also been found in tumor cells recently. The aim of our study was to clarify the role of FoxP3 in renal cell carcinoma (RCC) progression and metastasis. We verified the FoxP3 characteristic clinicopathological data from The Cancer Genome Atlas (TCGA) database using bioinformatics tools. Meanwhile, RNA sequencing was performed to determine the FoxP3 biofunction in RCC progression. Our results showed that high expression of FoxP3 was found in BAP1- or SETD2-mutant patients with RCC, and a higher FoxP3 expression was related to worse prognosis. However, there was no statistically significant relationship between the FoxP3 IHC score and RCC malignant progression owning to the limited number of patients in our tissue microarray. Using in vitro FoxP3 loss-of-function assays, we verified that silencing FoxP3 in 786-O and ACHN cells could inhibit the cell migration/invasion capability, which was consistent with the data from RNA sequencing in 786-O cells and from the TCGA datasets. Using an in vivo nude mice orthotopic kidney cancer model, we found that silencing FoxP3 could inhibit tumor growth. In conclusion, our study demonstrated that BAP1 or SEDT2 mutation could lead to higher expression of FoxP3 in RCC patients, and FoxP3 could eventually stimulate RCC cells' invasion and metastasis, which might indicate that FoxP3 could function as a potential oncogene in RCC progression.
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Affiliation(s)
- Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
- Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an 710061, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi’an Jiaotong University, Xi’an 710061, China
| | - Xinfeng Hu
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
- Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an 710061, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi’an Jiaotong University, Xi’an 710061, China
| | - Yue Chong
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
- Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an 710061, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi’an Jiaotong University, Xi’an 710061, China
| | - Guodong Zhu
- Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
- Oncology Research Laboratory, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an 710061, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi’an Jiaotong University, Xi’an 710061, China
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Koti M, Bivalacqua T, Black PC, Cathomen T, Galsky MD, Gulley JL, Ingersoll MA, Kamat AM, Kassouf W, Siemens DR, Gao J. Adaptive Immunity in Genitourinary Cancers. Eur Urol Oncol 2023; 6:263-272. [PMID: 37069029 DOI: 10.1016/j.euo.2023.03.002] [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: 10/15/2022] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 04/19/2023]
Abstract
CONTEXT While urothelial and renal cell cancers have exhibited modest responses to novel immune checkpoint inhibitors targeting the programmed death ligand 1 and its receptor, response rates in patients with prostate cancer have remained poor. The factors underlying suboptimal outcomes observed in patients treated with novel immunotherapies are still to be resolved. OBJECTIVE To review the literature and describe the key adaptive immune physiological events associated with cancer progression and therapeutic response in genitourinary (GU) cancers. EVIDENCE ACQUISITION We performed a nonsystematic, collaborative narrative review to highlight recent advancements leading to the current state of knowledge on the critical mediators of antitumor adaptive immunity to GU cancers. Further, we discuss the findings on the pre- and post-treatment immunological events that either are unique to each of the three cancer types or exhibit overlapping clinical associations. EVIDENCE SYNTHESIS Aging-associated immune function decline is a major factor underlying poor outcomes observed in patients treated with both conventional and novel immunotherapies. Other cancer immunobiological aspects associated with suboptimal responses in GU cancers include the overall tumor mutational burden, mutations in specific tumor suppressor/DNA damage repair genes (KDM6A, PTEN, STAG2, TP53, ATM, and BRCA2), and abundance of multiple functional states of adaptive immune cells and their spatiotemporal localization within the tumor immune microenvironment. Understanding these mechanisms may potentially lead to the development of prognostic and predictive biomarkers such as immune cell infiltration profiles and tertiary lymphoid structures (TLSs) that associate with variable clinical outcomes depending on the nature of the novel immunotherapeutic approach. Implementation of newer immune-monitoring technologies and improved preclinical modeling systems will augment our understanding of the host and tumor intrinsic factors contributing to the variability of responses to immunotherapies. CONCLUSIONS Despite the tremendous progress made in the understanding of dynamic and static adaptive immune elements within the tumor immune landscape, several knowledge gaps remain. A comprehensive knowledge thus gained will lead to precision immunotherapy, improved drug sequencing, and a therapeutic response. PATIENT SUMMARY We performed a collaborative review by a diverse group of experts in the field to examine our understanding of the events and crosstalk between cancer cells and the patient's immune system that are associated with responses to novel immunotherapies. An evolving understanding of tumor-intrinsic and host-related immune alterations, both before and after therapy, will aid in the discovery of promising markers of responses to immunotherapy as well as the development of unique therapeutic approaches for the management of genitourinary cancers.
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Affiliation(s)
- Madhuri Koti
- Department of Biomedical and Molecular Sciences, Cancer Research Institute, Queen's University, Kingston, ON, Canada.
| | - Trinity Bivalacqua
- Department of Urology, Perelman Center for Advanced Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Faculty of Medicine & Medical Center - University of Freiburg, Freiburg, Germany
| | - Matthew D Galsky
- Division of Hematology/Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James L Gulley
- Center for Immuno-Oncology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Molly A Ingersoll
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, 75014, France; Mucosal Inflammation and Immunity, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Ashish M Kamat
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wassim Kassouf
- Division of Urology, McGill University Health Center, Montreal, QC, Canada
| | - D Robert Siemens
- Department of Urology, Queen's University School of Medicine, Kingston, ON, Canada
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Raghubar AM, Roberts MJ, Wood S, Healy HG, Kassianos AJ, Mallett AJ. Cellular milieu in clear cell renal cell carcinoma. Front Oncol 2022; 12:943583. [PMID: 36313721 PMCID: PMC9614096 DOI: 10.3389/fonc.2022.943583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is globally the most prevalent renal cancer. The cells of origin in ccRCC have been identified as proximal tubular epithelial cells (PTEC); however, the transcriptomic pathways resulting in the transition from normal to malignant PTEC state have remained unclear. Immunotherapy targeting checkpoints have revolutionized the management of ccRCC, but a sustained clinical response is achieved in only a minority of ccRCC patients. This indicates that our understanding of the mechanisms involved in the malignant transition and resistance to immune checkpoint therapy in ccRCC is unclear. This review examines recent single-cell transcriptomics studies of ccRCC to clarify the transition of PTEC in ccRCC development, and the immune cell types, states, and interactions that may limit the response to targeted immune therapy, and finally suggests stromal cells as key drivers in recurrent and locally invasive ccRCC. These and future single-cell transcriptomics studies will continue to clarify the cellular milieu in the ccRCC microenvironment, thus defining actional clinical, therapeutic, and prognostic characteristics of ccRCC.
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Affiliation(s)
- Arti M. Raghubar
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Matthew J. Roberts
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia
- Department of Urology, Redcliffe Hospital, Redcliffe, QLD, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Simon Wood
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Helen G. Healy
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Kassianos
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Mallett
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- *Correspondence: Andrew J. Mallett,
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Nie K, Li J, Peng L, Zhang M, Huang W. Pan-Cancer Analysis of the Characteristics of LY96 in Prognosis and Immunotherapy Across Human Cancer. Front Mol Biosci 2022; 9:837393. [PMID: 35647025 PMCID: PMC9130738 DOI: 10.3389/fmolb.2022.837393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 12/28/2022] Open
Abstract
Lymphocyte antigen 96 (LY96) is implicated in tumorigenesis by modulating host immunity. However, an integrated pan-cancer analysis of LY96 in prognosis and immunotherapy across human cancers is still lacking. Therefore, we analyzed the LY96 expression and its prognostic role in tumors by multiple databases. We also investigated the correlation between LY96 and copy number, DNA methylation, somatic mutation, microsatellite instability (MSI), tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration across human cancers. In addition, the biological processes related to LY96 across various tumors and the correlation between LY96 and 50% inhibitive concentration (IC50) of various drugs were investigated. We found that LY96 was differently expressed between tumor and normal tissues and was significantly upregulated in most types of cancers. LY96 was gradually upregulated from stages I to IV in several cancers. Moreover, we found LY96 may play a prognostic role in most cancers, and patients with high or low LY96 expression often show different clinical outcomes. LY96 was also associated with copy number, DNA methylation, somatic mutation, MSI, TMB, TME characteristics, and immune cell infiltration in cancers. LY96 may also regulate classic tumor-associated pathways in several cancers and is related to drug resistance. This article may help to elucidate the role of LY96 in tumorigenesis, which may promote the development of immunotherapy and targeted therapy in cancers.
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Affiliation(s)
- Kechao Nie
- Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Luqi Peng
- Department of Integrated Traditional Chinese and Western Internal Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Mei Zhang
- Department of Integrated Traditional Chinese and Western Internal Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Huang
- Department of Integrated Traditional Chinese and Western Internal Medicine, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Wei Huang,
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Genomics of Clear-cell Renal Cell Carcinoma: A Systematic Review and Meta-analysis. Eur Urol 2022; 81:349-361. [PMID: 34991918 DOI: 10.1016/j.eururo.2021.12.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/21/2022]
Abstract
CONTEXT Although antiangiogenic treatments and immunotherapies have significantly improved the prognosis of metastatic renal cell carcinoma (RCC), many patients will develop resistance, leading to treatment failure. Genetic tumor heterogeneity is a major cause of this resistance. OBJECTIVE To perform a meta-analysis of genomic data for clear-cell RCC obtained from primary tumors and metastases to assess the prevalence of gene mutations and copy number alterations (CNAs). EVIDENCE ACQUISITION Articles were selected from Medline and Embase libraries using the search algorithm ("Kidney Neoplasms"[Mesh] OR "Renal Cell Carcinoma") AND ("Genomics"[Mesh] OR "Mutation") from January 1999 to February 2021. A critical review was conducted according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement. Ninety-three publications were selected for inclusion in this meta-analysis. EVIDENCE SYNTHESIS Our meta-analysis included a total 14 696 patients, 14 299 primary tumor samples, and 969 metastatic samples. We evaluated the overall and subgroup prevalence of gene mutations and CNAs, including comparisons between primary tumors and metastases. In particular, for metastases we observed that the mutation prevalence was significantly more marked for ten genes compared to primary tumors, with no or little heterogeneity across studies. The VHL mutation prevalence increased significantly from 64% in primary tumors to 75% in metastases (p < 0.001). There was a significant increase in CNA prevalence from primary tumors to metastases for chromosomes 1p36.11, 9p21.3, and 18 in terms of losses, and for chromosomes 1q21.3, 7q36.3, 8q, and 20q11.21 in terms of gains. CDKN2A, also called p16 and involved in cell-cycle progression, is located at the 9p21.3 locus and was lost in 76% of metastatic samples. ASXL1, located on 20p11.21 and amplified in 50% of metastatic RCCs compared to 21% of primary tumors (p < 0.001), is closely linked to BAP1 function. CONCLUSIONS Our results underline the added value of preferential biopsies on RCC metastases to fully explore the biology of metastatic disease for therapeutic purposes. PATIENT SUMMARY We reviewed the literature on genetic mutations in primary tumors and metastatic lesions in kidney cancer. Our pooled results for all the relevant studies show a higher level of mutations in metastases than in primary tumors. This highlights the importance of taking biopsies of metastases to analyze genetic mutations and potentially guide selection of the most suitable treatment strategy.
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van Oost S, Meijer DM, Kuijjer ML, Bovée JVMG, de Miranda NFCC. Linking Immunity with Genomics in Sarcomas: Is Genomic Complexity an Immunogenic Trigger? Biomedicines 2021; 9:1048. [PMID: 34440251 PMCID: PMC8391750 DOI: 10.3390/biomedicines9081048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Sarcomas comprise a collection of highly heterogeneous malignancies that can be grossly grouped in the categories of sarcomas with simple or complex genomes. Since the outcome for most sarcoma patients has barely improved in the last decades, there is an urgent need for improved therapies. Immunotherapy, and especially T cell checkpoint blockade, has recently been a game-changer in cancer therapy as it produced significant and durable treatment responses in several cancer types. Currently, only a small fraction of sarcoma patients benefit from immunotherapy, supposedly due to a general lack of somatically mutated antigens (neoantigens) and spontaneous T cell immunity in most cancers. However, genomic events resulting from chromosomal instability are frequent in sarcomas with complex genomes and could drive immunity in those tumors. Improving our understanding of the mechanisms that shape the immune landscape of sarcomas will be crucial to overcoming the current challenges of sarcoma immunotherapy. This review focuses on what is currently known about the tumor microenvironment in sarcomas and how this relates to their genomic features. Moreover, we discuss novel therapeutic strategies that leverage the tumor microenvironment to increase the clinical efficacy of immunotherapy, and which could provide new avenues for the treatment of sarcomas.
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Affiliation(s)
- Siddh van Oost
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Debora M. Meijer
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Marieke L. Kuijjer
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
- Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
| | - Judith V. M. G. Bovée
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Noel F. C. C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
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Chen J, Zhan Y, Zhang R, Chen B, Huang J, Li C, Zhang W, Wang Y, Gao Y, Zheng J, Li Y. A New Prognostic Risk Signature of Eight Ferroptosis-Related Genes in the Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:700084. [PMID: 34249761 PMCID: PMC8267866 DOI: 10.3389/fonc.2021.700084] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common renal cell carcinoma and has poor prognosis in the locally advanced stage. Ferroptosis, a relatively new type of cell death, has gained significant attention in recent years. This study aimed to explore the prognostic value of ferroptosis-related genes (FRGs) in ccRCC. In this study, 50 differentially expressed FRGs between ccRCC and adjacent normal kidney tissues were identified, 26 of them correlated with overall survival (OS) (P <0.05). Eight optimal FRGs were selected by Lasso regression and multivariate Cox regression analysis, and used to construct a new prognostic risk signature to predict the prognosis of ccRCC patients. In addition, the signature passed the validation of prognostic survival analyses by a significant margin, and the risk score was identified as an independent prognostic marker via Cox regression analyses. Further studies indicated that the signature was significantly correlated with immune cell infiltration. Moreover, the levels of eight FRGs were examined in ccRCC. Collectively, the 8-FRG prognostic risk signature helps the clinicians predict the prognosis and OS of the patients, and standardize prognostic assessments.
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Affiliation(s)
- Ji Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yating Zhan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Junting Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chunxue Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenjie Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yajing Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxiang Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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