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Zhou R, Zhou J, Deng S, Zhu Y, Muhuitijiang B, Wu J, Tan W. Developing and experimental validating a B cell exhaustion-related gene signature to assess prognosis and immunotherapeutic response in bladder cancer. Gene 2024; 927:148634. [PMID: 38848880 DOI: 10.1016/j.gene.2024.148634] [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: 08/29/2023] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND B cell exhaustion (BEX) refers to the impairment of normal B cell functions and decreased proliferation capability. However, the prognostic value of BEX-related genes in bladder cancer (BLCA) remains unclear. METHODS BLCA cases from TCGA were used for training, while GSE5287, GSE13507, GSE31684, and GSE32894 cohorts from GEO were used for external validation. BEX-related genes were identified through literature retrieval, unsupervised clustering, and genomic difference detection. Gene pairing, LASSO, random forest, and Cox regression were employed to construct a predictive model. B cell samples from scRNAseqDB, GSE111636, and IMvigor210 were utilized to explore immunoprofiles and the predictive ability of the model in immunotherapeutic response. Additionally, 21 pairs of BLCA and paracarcinoma samples from Nanfang Hospital were used to re-confirm our findings through RT-qPCR, immunofluorescence, and flow cytometry. RESULTS 39 BEX-related genes were identified. A 4-gene-pair signature was constructed and served as a reliable prognostic predictor across multiple datasets (pooled HR = 2.32; 95 % CI = 1.81-2.98). The signature reflected the BEX statuses of B cells (FDR < 0.05) and showed promise in evaluating immunotherapeutic sensitivity (P < 0.001). In the local cohort, CD52, TUBB6, and CAV1 were down-regulated in BLCA tissues, while TGFBI, UBE2L6, TINAGL1, and IL32 were up-regulated (all P < 0.05). Furthermore, the infiltration levels of CD19 + CD52 + and CD19 + TUBB6 + B cells in paracarcinoma samples were higher than those in BLCA samples (all P < 0.05). CONCLUSION A BEX-related gene signature was developed to predict prognosis and immunotherapeutic sensitivity in BLCA, providing valuable guidance for personalized treatment.
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Affiliation(s)
- Ranran Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Jiawei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China
| | - Shikai Deng
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Bahaerguli Muhuitijiang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Jiaxu Wu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510080, Guangdong, China.
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510080, Guangdong, China; The First Clinical Medical College, Southern Medical University, Guangzhou 510080, Guangdong, China.
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2
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Lobo A, Collins K, Kaushal S, Acosta AM, Akgul M, Adhya AK, Al-Ahmadie HA, Al-Obaidy KI, Amin A, Amin MB, Aron M, Balzer BL, Biswal R, Mohanty S, Browning L, Chakrabarti I, Cima L, Cimadamore A, Desai S, Dhillon J, Deshwal A, Diego GG, Diwaker P, Galea LA, Magi-Galluzzi C, Giannico GA, Gupta NS, Haider A, Hirsch MS, Iczkowski KA, Arora S, Jain E, Jain D, Jha S, Kandukuri S, Kao CS, Kryvenko ON, Kumar RM, Kumari N, Kunju LP, Kuthi L, Lobo J, Lopez JI, Luthringer DJ, Maclean F, Manini C, Mannan R, Martos MG, Mehra R, Menon S, Mishra P, Moch H, Montironi R, Baisakh MR, Netto GJ, Nigam LK, Osunkoya AO, Pagliuca F, Paner GP, Panizo A, Parwani AV, Picken MM, Prendeville S, Przybycin CG, Purkait S, Queipo FJ, Rao BV, Rao P, Reuter VE, Sancheti S, Sangoi AR, Sardana R, Satturwar S, Shah RB, Sharma S, Dixit M, Verma M, Sirohi D, Smith SC, Soni S, Sundaram S, Swain M, Tretiakova M, Trpkov K, MuñizUnamunzaga G, Zhou M, Williamson SR, Lopez-Beltran A, Cheng L, Mohanty SK. Advances, recognition, and interpretation of molecular heterogeneity among conventional and subtype histology of urothelial carcinoma (UC): a survey among urologic pathologists and comprehensive review of the literature. Histopathology 2024; 85:748-759. [PMID: 39075659 DOI: 10.1111/his.15287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024]
Abstract
AIMS Urothelial carcinoma (UC) demonstrates significant molecular and histologic heterogeneity. The WHO 2022 classification has hinted at adding molecular signatures to the morphologic diagnosis. As morphology and associated molecular repertoire may potentially translate to choices of and response to therapy and relapse rate, broader acceptability of recognizing these key features among uropathologists is needed. This prompted an international survey to ascertain the practice patterns in classical/subtype UC among uropathologists across the globe. METHODS AND RESULTS A survey instrument was shared among 98 uropathologists using SurveyMonkey software. Anonymized respondent data were analysed. The response rate was 85%. A majority were in concordance with the profiles of luminal (93%) and basal (82%) types. Opinion on the FGFR3 testing platform was variable. While 95% concurred that TERT promoter mutation is the key driver in UC, 72% had the opinion that APOBEC mutagenesis is the main signature in muscle invasive bladder cancer (MIBC). Uropathologists have divergent opinions on MIBC and ERCC2 mutations. Among the participants, 94% would quantify aggressive micropapillary and sarcomatoid histology, while 88% would reevaluate another transurethral resection of the bladder tumour specimen in nonmuscle invasive tumour with micropapillary, small cell, or sarcomatoid histology. A leading number agreed to specific molecular signatures of micropapillary (93%), plasmacytoid (97%), and small cell (86%) subtypes. Ninety-six percent of participants agreed that a small-cell component portends a more aggressive course and should be treated with neoadjuvant chemotherapy and 63% would perform HER2/neu testing only on oncologist's request in advanced tumours. Ninety percent agreed that microsatellite instability testing, although not a standard protocol, should be considered in young patients with upper tract UC. Eighty-six percent agreed that UC with high tumour mutational burden would be a better candidate for immunotherapy. CONCLUSION In the era of precision medicine, enhanced understanding of molecular heterogeneity of UC will contribute to better therapeutic options, novel biomarker discovery, innovative management protocols, and outcomes. Our survey provides a broad perspective of pathologists' perceptions and experience regarding incorporation of histomolecular approaches to "personalize" therapy. Due to variable clinical adoption, there is a need for additional data using uniform study criteria. This will drive generation of best practice guidelines in this area for widespread and consistent clinical utility.
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Affiliation(s)
- Anandi Lobo
- Department of Pathology, Kapoor Centre of Urology and Pathology, Raipur, India
| | - Katrina Collins
- Department of Pathology, Indiana University Health, Indiana, USA
| | - Seema Kaushal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Andres M Acosta
- Department of Pathology, Indiana University Health, Indiana, USA
| | - Mahmut Akgul
- Department of Pathology, Albany Medical Center, Albany, USA
| | - Amit K Adhya
- Department of Pathology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | | | - Ali Amin
- Department of Pathology, Alpert Medical School of Brown University, Providence, USA
| | - Mahul B Amin
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, USA
| | - Manju Aron
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, USA
| | - Bonnie L Balzer
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Rupanita Biswal
- Department of Pathology, Bagchi Sri Shankara Cancer Hospital, Bhubaneswar, India
| | - Subashish Mohanty
- Department of Pathology, SUM Ultimate Medicare Hospital, Bhubaneswar, India
| | - Lisa Browning
- Department of Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Indranil Chakrabarti
- Department of Pathology, All India Institute of Medical Sciences, Kalyani, India
| | - Luca Cima
- Department of Pathology, Santa Chiara Hospital of Trento, Trento, Italy
| | - Alessia Cimadamore
- Department of Pathology, Molecular Medicine and Cell Therapy Foundation, c/o Polytechnic University of the Marche Region, Ancona, Italy
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | | | | | - Guillermo G Diego
- Department of Pathology, University Gregorio Marañon Hospital, Madrid, Spain
| | - Preeti Diwaker
- Department of Pathology, University College of Medical Sciences, New Delhi, India
| | - Laurence A Galea
- Department of Pathology, Melbourne Pathology, Melbourne, Australia
| | | | | | - Nilesh S Gupta
- Department of Pathology, Henry Ford Health System, Detroit, USA
| | - Aiman Haider
- Department of Pathology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Samriti Arora
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Ekta Jain
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Deepika Jain
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Shilpy Jha
- Department of Pathology, Advanced Medical and Research Institute, Bhubaneswar, India
| | - Shivani Kandukuri
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, USA
| | - Chia-Sui Kao
- Department of Pathology, Cleveland Clinic, Cleveland, USA
| | - Oleksandr N Kryvenko
- Department of Pathology, University of Miami Miller School of Medicine, Miami, USA
| | - Ramani M Kumar
- Department of Pathology, Dane Diagnostics, Palakkad, India
| | - Niraj Kumari
- Department of Pathology, All India Institute of Medical Sciences, Raebareli, India
| | - Lakshmi P Kunju
- Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Levente Kuthi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - João Lobo
- Department of Pathology, Portuguese Oncology Institute - Porto, Porto, Portugal
| | - Jose I Lopez
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | | | - Fiona Maclean
- Department of Pathology, Douglass Hanly Moir Pathology, Sydney, Australia
| | - Claudia Manini
- Department of Pathology, University of Turin, Turin, Italy
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, USA
| | - María G Martos
- Department of Pathology, University Gregorio Marañon Hospital, Madrid, Spain
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, USA
| | - Santosh Menon
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Pritinanda Mishra
- Department of Pathology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Holger Moch
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Rodolfo Montironi
- Department of Pathology, Molecular Medicine and Cell Therapy Foundation, c/o Polytechnic University of the Marche Region, Ancona, Italy
| | - Manas R Baisakh
- Department of Pathology, Prolife Diagnostics, Bhubaneswar, India
| | - George J Netto
- Department of Pathology, University of Pennsylvania, Philadelphia, USA
| | - Lovelesh K Nigam
- Department of Pathology, Institute of Kidney Diseases and Research Center, Ahmedabad, India
| | - Adeboye O Osunkoya
- Department of Pathology, Emory University School of Medicine, Atlanta, USA
| | - Francesca Pagliuca
- Department of Pathology, Università degliStudidella Campania Luigi Vanvitelli, Caserta, Italy
| | - Gladell P Paner
- Department of Pathology, University of Chicago, Chicago, USA
| | - Angel Panizo
- Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Anil V Parwani
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, USA
| | - Maria M Picken
- Department of Pathology, Loyola University Medical Center, Hines, USA
| | - Susan Prendeville
- Department of Pathology, University Health Network, University of Toronto, Toronto, Canada
| | | | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Francisco J Queipo
- Department of Pathology, Hospital Universitario de A Coruna, A Coruna, Spain
| | - B Vishal Rao
- Department of Pathology, Basavatarakam Indo-American Cancer Hospital and Research Institute, Hyderabad, India
| | - Priya Rao
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Sankalp Sancheti
- Department of Pathology, Homi Bhabha Cancer Hospital, Punjab, India
| | - Ankur R Sangoi
- Department of Pathology, Stanford University, Stanford, USA
| | - Rohan Sardana
- Department of Pathology, Sardana Laboratories, Jalandhar, India
| | - Swati Satturwar
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, USA
| | - Rajal B Shah
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Shivani Sharma
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Mallika Dixit
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Monica Verma
- Department of Pathology, CORE Diagnostics, Gurgaon, India
| | - Deepika Sirohi
- Department of Pathology, University of California, San Francisco, USA
| | - Steven C Smith
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, USA
| | - Shailesh Soni
- Department of Pathology, Muljibhai Patel Urological Hospital, Nadiad, India
| | - Sandhya Sundaram
- Department of Pathology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | | | | | - Kiril Trpkov
- Department of Pathology, University of Calgary, Calgary, Canada
| | | | - Ming Zhou
- Department of Pathology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | | | - Antonio Lopez-Beltran
- Department of Pathology, Unit of Anatomical Pathology, Faculty of Medicine, Cordoba University, Cordoba, Spain
| | - Liang Cheng
- Department of Pathology, Alpert Medical School of Brown University, Providence, USA
| | - Sambit K Mohanty
- Department of Pathology, CORE Diagnostics, Gurgaon, India
- Department of Pathology, Advanced Medical and Research Institute, Bhubaneswar, India
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3
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Holmsten K, Sjödahl G, Abrahamsson J, Bernardo C, Eriksson P, Höglund M, Liedberg F, Ullén A. Molecular Subtypes Are Associated With Clinical Benefit in Cisplatin-Treated Metastatic Urothelial Cancer Patients. JCO Precis Oncol 2024; 8:e2400209. [PMID: 39348658 PMCID: PMC11446528 DOI: 10.1200/po.24.00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/10/2024] [Accepted: 08/15/2024] [Indexed: 10/02/2024] Open
Abstract
PURPOSE Cisplatin-based combination chemotherapy (CHT) is standard of care in metastatic urothelial cancer (mUC); however, no predictive molecular biomarkers are available for clinical use. The aim of this study was to investigate the impact of molecular subtypes in relation to treatment response and survival in patients with mUC treated with first-line CHT. PATIENTS AND METHODS Molecular subtype classification according to the Lund Taxonomy (LundTax) was performed by tumor transcriptomic profiling and immunostaining in a retrospective cohort. Molecular subtypes were investigated in relation to the primary end point overall response rate (ORR) and secondary end points progression-free survival (PFS) and overall survival (OS). Differential gene expression and association to treatment response were explored. RESULTS Ninety-five patients with mUC were classified into urothelial-like (Uro, 43%), genomically unstable (GU, 26%), basal squamous-like (Ba/Sq, 20%), mesenchymal-like (Mes-like, 8%), and small cell neuroendocrine-like (Sc/NE, 3%) subtypes. Patients with Mes-like tumors had lower ORR (14%) compared with Uro (70%), GU (77%), Ba/Sq (75%), and Sc/NE (67%; odds ratio, 0.06 [95% CI, 0.01 to 0.54], P = .012). Furthermore, patients with Mes-like tumors had significantly shorter PFS (hazard ratio [HR], 5.18 [95% CI, 2.28 to 11.76], P < .001) and OS (HR, 3.19 [95% CI, 1.45 to 7.03], P = .004). Patients with Uro and GU showed the longest survival. In responders, an enrichment of downregulated stromal- and immune-related genes was seen. Downregulation of interferon-induced transmembrane protein 2 was associated with increased ORR and improved OS. CONCLUSION This study identifies different CHT responses by LundTax molecular subtypes in patients with mUC, where the Mes-like subtype was associated with lower response rate and shorter survival.
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Affiliation(s)
- Karin Holmsten
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Oncology, Capio S:t Görans Hospital, Stockholm, Sweden
| | - Gottfrid Sjödahl
- Department of Translational Medicine, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Johan Abrahamsson
- Department of Translational Medicine, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Carina Bernardo
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Mattias Höglund
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Fredrik Liedberg
- Department of Translational Medicine, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Anders Ullén
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Pelvic Cancer, Genitourinary Oncology and Urology Unit, Karolinska University Hospital, Stockholm, Sweden
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4
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Cotillas EA, Bernardo C, Veerla S, Liedberg F, Sjödahl G, Eriksson P. A versatile and upgraded version of the LundTax classification algorithm applied to independent cohorts. J Mol Diagn 2024:S1525-1578(24)00207-1. [PMID: 39326668 DOI: 10.1016/j.jmoldx.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 06/10/2024] [Accepted: 08/28/2024] [Indexed: 09/28/2024] Open
Abstract
Stratification of cancer into biologically and molecularly similar subgroups is a cornerstone of precision medicine. The Lund Taxonomy classification system for urothelial carcinoma (UC) aims to be applicable across the whole disease spectrum including both non-muscle invasive and invasive bladder cancer. For a classification system to be useful it is of critical importance that it can be applied robustly and reproducibly to new samples. However, transcriptomic methods used for subtype classification are affected by analytic platform, data preprocessing, cohort composition, and tumor purity. Furthermore, only limited data has been published evaluating the transferability of existing classification algorithms to external datasets. In the present investigation a single sample classifier was developed based on in-house microarray and RNA-sequencing data, intended to be broadly applicable across studies and platforms. The new classification algorithm was applied to 10 published external bladder cancer cohorts (n=2560 cases) to evaluate its ability to capture characteristic subtype-associated gene expression signatures and complementary data such as mutations, clinical outcomes, treatment response, or histological subtypes. The effect of sample purity on the classification results was evaluated by generating low-purity versions of samples in silico. The classifier was robustly applicable across different gene expression profiling platforms and preprocessing methods and was less sensitive to variations in sample purity.
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Affiliation(s)
- Elena Aramendía Cotillas
- Department of Translational Medicine, Lund University, Malmö, Sweden; Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Carina Bernardo
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Fredrik Liedberg
- Department of Translational Medicine, Lund University, Malmö, Sweden; Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Gottfrid Sjödahl
- Department of Translational Medicine, Lund University, Malmö, Sweden; Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Pontus Eriksson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.
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5
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Meireles S, Dias C, Martins D, Marques A, Dias N, Pacheco-Figueiredo L, Silva J, Silva CM, Barbosa M, Costa L, Lopes JM, Soares P. Biomarker Profiling of Upper Tract Urothelial Carcinoma Only and with Synchronous or Metachronous Bladder Cancer. Biomedicines 2024; 12:2154. [PMID: 39335667 PMCID: PMC11429062 DOI: 10.3390/biomedicines12092154] [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: 08/05/2024] [Revised: 09/09/2024] [Accepted: 09/14/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Molecular profiling in upper tract urothelial carcinoma (UTUC) with synchronous or metachronous urothelial bladder cancer (UBC) is scarce. We intended to assess immunohistochemical (IHC) and genetic differences between UTUC-only and UTUC with synchronous or metachronous UBC (UTUC + UBC) and evaluate the effect of subsequent UBC on the outcome of UTUC patients stratified by luminal-basal subtypes. METHODS A retrospective cohort of UTUC was divided into UTUC-only (n = 71) and UTUC + UBC (n = 43). IHC expression of cytokeratin 5/6 (CK5/6), CK20, GATA3, and p53 was evaluated to assess relevant subtypes. Genetic characterization comprised TERTp, FGFR3, RAS, and TP53 status. Kaplan-Meier and Cox regression analyses estimated the effect of clinicopathological variables and molecular profiles on progression-free survival (PFS) and overall survival (OS) of UTUC patients. RESULTS No meaningful differences were detected among both subgroups according to luminal-basal stratification and genetic analysis. UTUC + UBC was independently associated with a worse PFS when stratified by luminal-basal phenotype (HR 3.570, CI 95% 1.508-8.453, p = 0.004) but with no impact in OS (HR 1.279, CI 95% 0.513-3.190, p = 0.597). CONCLUSIONS This study reveals that both subgroups exhibited equivalent genomic features and luminal-basal subtypes. The involvement of the bladder relates to shorter PFS but does not seem to influence the survival outcome of UTUC, independently of the IHC phenotype.
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Affiliation(s)
- Sara Meireles
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Medical Oncology Department, Centro Hospitalar Universitário de São João (CHUSJ), Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carolina Dias
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Diana Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Pathology Department, Centro Hospitalar Universitário de São João, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ana Marques
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Pathology Department, Centro Hospitalar Universitário de São João, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno Dias
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Urology Department, Centro Hospitalar Universitário de São João (CHUSJ), Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Luís Pacheco-Figueiredo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- Department of Urology, Trofa Saúde Private Hospitals, 4785-409 Trofa, Portugal
| | - João Silva
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Urology Department, Centro Hospitalar Universitário de São João (CHUSJ), Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carlos Martins Silva
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Urology Department, Centro Hospitalar Universitário de São João (CHUSJ), Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Miguel Barbosa
- Medical Oncology Department, Centro Hospitalar Universitário de São João (CHUSJ), Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Luís Costa
- Medical Oncology Department, Centro Hospitalar Universitário Lisboa Norte, Avenida Professor Egas Moniz MB, 1649-028 Lisboa, Portugal
- Institute of Molecular Medicine-João Lobo Antunes, Faculty of Medicine, University of Lisbon, Avenida Professor Egas Moniz MB, 1649-028 Lisboa, Portugal
| | - José Manuel Lopes
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Pathology Department, Centro Hospitalar Universitário de São João, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Paula Soares
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
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6
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Kim B, Kim K, Yang S, Moon KC. Immunophenotypic and molecular changes during progression of papillary urothelial carcinoma. Investig Clin Urol 2024; 65:501-510. [PMID: 39249924 PMCID: PMC11390262 DOI: 10.4111/icu.20230318] [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: 09/22/2023] [Revised: 01/11/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024] Open
Abstract
PURPOSE Urothelial carcinoma has various molecular subtypes, each with different tumor characteristics. Although it is known that molecular changes occur during tumor progression, little is known about the specifics of these changes. In this study, we performed transcriptional analysis to understand the molecular changes during tumor progression. MATERIALS AND METHODS Formalin-fixed, paraffin-embedded tumor tissues were obtained from 12 patients with muscle-invasive bladder cancer (MIBC). The invasive and non-invasive papillary areas were identified in papillary urothelial carcinoma specimens. Immunohistochemistry (IHC) and mRNA sequencing were performed for each tumor area. RESULTS Patients with CK5/6-negative and CK20-positive non-invasive papillary areas were selected and classified into the IHC switch subgroup (CK5/6-positive and CK20-negative in the invasive area) and the IHC unchanged subgroup (CK5/6-negative and CK20-positive in the invasive area) according to the IHC results of the invasive area. We identified differences in the mRNA expression between the non-invasive papillary and invasive areas of the papillary MIBC tissue samples. In both the non-invasive papillary and invasive areas, the IHC switch subgroup showed basal subtype gene expression, while the IHC unchanged subgroup demonstrated luminal subtype gene expression. CONCLUSIONS The non-invasive papillary area showed a gene expression pattern similar to that of the invasive area. Therefore, even if the non-invasive papillary area exhibits a luminal phenotype on IHC, it can have a basal subtype gene expression depending on the invasive area.
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Affiliation(s)
- Bohyun Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Sunah Yang
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
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Jung M, Kim B, Lee JS, Kim JY, Han D, Kim K, Yang S, Kim EN, Kim H, Nikas IP, Yang S, Moon KC, Lee H, Ryu HS. KRT18 as a Novel Biomarker of Urothelial Papilloma while Evaluating Low-Grade Papillary Urothelial Neoplasms: Bi-Center Analysis. Pathobiology 2024:1-12. [PMID: 39191209 DOI: 10.1159/000540926] [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: 06/11/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
INTRODUCTION Although urothelial papilloma (UP) is an indolent papillary neoplasm that can mimic the morphology of low-grade papillary urothelial carcinoma (PUC), there is no immunomarker to differentiate reliably these two entities. In addition, the molecular characteristics of UP are not fully understood. METHODS We conducted an in-depth proteomic analysis of papillary urothelial lesions (n = 31), including UP and PUC along with normal urothelium. Protein markers distinguishing UP and PUC were selected with machine learning analysis, followed by internal and external validation using immunohistochemistry. RESULTS In the proteomic analysis, UP and PUC showed overlapping proteomic profiles. We identified EHD4 and KRT18 as candidate diagnostic biomarkers of UP. Through immunohistochemical validation in two independent cohorts (n = 120), KRT18 was suggested as a novel UP diagnostic marker, able to differentiate UP from low-grade PUC. We also found that 3.5% of patients with UP developed urothelial carcinoma in subsequent resections, supporting the malignant potential of UP. KRT18 downregulation was significantly associated with UPs subsequently progressing to urothelial carcinoma, following their initial diagnosis. CONCLUSION This is the first study that successfully revealed UPs comprehensive proteomic landscape, while it also identified KRT18 as a potential diagnostic biomarker of UP.
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Affiliation(s)
- Minsun Jung
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Bohyun Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Jae Seok Lee
- Department of Pathology, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Jun Yong Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dohyun Han
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sunah Yang
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun Na Kim
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeyooon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ilias P Nikas
- Medical School, University of Cyprus, Nicosia, Cyprus
| | - Sohyeon Yang
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyebin Lee
- Department of Radiation Oncology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
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8
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Zeng X, Lu Z, Dai C, Su H, Liu Z, Cheng S. Establish TIIC signature score based the machine learning fusion in bladder cancer. Discov Oncol 2024; 15:368. [PMID: 39186114 PMCID: PMC11347539 DOI: 10.1007/s12672-024-01187-7] [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: 05/26/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Bladder cancer is a prevalent malignant tumor with high heterogeneity. Current treatments, such as transurethral resection of bladder tumor (TURBT) and intravesical Bacillus Calmette-Guérin (BCG) therapy, still have limitations, with approximately 30% of non-muscle-invasive bladder cancer (NMIBC) progressing to muscle-invasive bladder cancer (MIBC), and a substantial number of MIBC patients experiencing recurrence after surgery. Immunotherapy has shown potential benefits, but accurate prediction of its prognostic effects remains challenging. METHODS We analyzed bladder cancer RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and used various machine learning algorithms to screen for feature RNAs related to tumor-infiltrating immune cells (TIICs) from single-cell data. Based on these RNAs, we established a TIIC signature score and evaluated its relationship with overall survival (OS) and immunotherapy response in bladder cancer patients. RESULTS The study identified 171 TIIC-RNAs and selected 11 TIIC-RNAs with prognostic value through survival analysis. The TIIC signature score established using a machine learning fusion method was significantly associated with OS and showed good predictive performance in different datasets. Additionally, the signature score was negatively correlated with immunotherapy response, with patients with low TIIC feature scores showing better survival outcomes after immunotherapy. Further biological functional analysis revealed a close association between the TIIC signature score and immune regulation processes, cellular metabolism, and genetic variations. CONCLUSION This study successfully constructed and validated an RNA signature scoring system based on tumor-infiltrating immune cell (TIIC) features, which can effectively predict OS and the effectiveness of immunotherapy in bladder cancer patients.
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Affiliation(s)
- Xiangju Zeng
- Department of Outpatient, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Zhijie Lu
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Caixia Dai
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Hao Su
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Ziqi Liu
- Department of Acupuncture and Moxibustion, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Shunhua Cheng
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
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9
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Lin G, Lin J, Wang H, Wang L, Zhan F, Wu L, Xue L, Dong Y, Wei W, Liu L. Characterization of the stem cell landscape and identification of a stemness-associated prognostic signature in bladder cancer. Cancer Cell Int 2024; 24:299. [PMID: 39182054 PMCID: PMC11344935 DOI: 10.1186/s12935-024-03465-4] [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: 05/09/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
It is accepted that cancer stem cells (CSCs) are key to the occurrence, progression, drug resistance, and recurrence of bladder cancer (BLCA). Here, we aimed to characterize the landscapes of CSCs and investigate the biological and clinical signatures based on a prognostic model constructed by genes associated with CSCs. The malignant epithelial cells were discovered and sorted into six clusters through single cell analysis. C2 was identified as the CSCs. The signaling involved in the interactions between C2, cancer-associated fibroblasts (CAFs), and immune cells mainly consisted of MK, THBS, ANGPTL, VISFATIN, JAM, and ncWNT pathways. The CSC-like prognostic index (CSCLPI) constructed by the random survival forest was a reliable risk factor for BLCA and had a stable and powerful effect on predicting the overall survival of patients with BLCA. The level of CAFs was higher among patients with higher CSCLPI scores, suggesting that CAFs play a significant role in regulating biological characteristics. The CSCLPI-developed survival prediction nomogram has the potential to be applied clinically to predict the 1-, 2-, 3-, and 5-year overall survival of patients with BLCA. The CSCLPI can be used for prognostic prediction and drug treatment evaluation in the clinic.
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Affiliation(s)
- Gaoteng Lin
- Department of Urology, The 900th Hospital of Joint Logistic Support Force, Fuzhou, China
| | - Jiamei Lin
- Burn Plastic Surgery And Wound Repair Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory of Molecular Pathology in Tumors, Baise, Guangxi, China
| | - Hao Wang
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Liucheng Wang
- Department of Urology, Lianshui People's Hospital of Kangda College Affiliated to Nanjing Medical University, Nanjing, Jiangsu, 223400, China
| | - Fangfang Zhan
- Department of Rehabilitation, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350000, China
- Department of Rehabilitation, Binhai Campus of the First Affiliated Hospital, National Regional Medical Center, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Liqian Wu
- Department of Urology, The 900th Hospital of Joint Logistic Support Force, Fuzhou, China
| | - Liang Xue
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
| | - Yang Dong
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China
- Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, 221009, China
| | - Wanqing Wei
- Department of Urology, Lianshui People's Hospital of Kangda College Affiliated to Nanjing Medical University, Nanjing, Jiangsu, 223400, China.
| | - Lin Liu
- Department of Urology, Xuzhou Central Hospital, Jiefang South Road, No. 199, Xuzhou, Jiangsu, China.
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10
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Chen Z, Hu J, Ou Y, Ye F, Li W, Liu S, Jiang H. Integrating single-cell transcriptomics to reveal the ferroptosis regulators in the tumor microenvironment that contribute to bladder urothelial carcinoma progression and immunotherapy. Front Immunol 2024; 15:1427124. [PMID: 39238647 PMCID: PMC11375220 DOI: 10.3389/fimmu.2024.1427124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024] Open
Abstract
Background Ferroptosis, as a novel form of programmed cell death, plays a crucial role in the occurrence and development of bladder cancer (BCa). However, the regulatory mechanisms of ferroptosis in the tumor microenvironment (TME) of BCa remain to be elucidated. Methods Based on single-cell RNA (scRNA) transcriptomic data of BCa, we employed non-negative matrix factorization (NMF) dimensionality reduction clustering to identify novel ferroptosis-related cell subtypes within the BCa TME, aiming to explore the biological characteristics of these TME cell subtypes. Subsequently, we conducted survival analysis and univariate Cox regression analysis to explore the prognostic significance of these cell subtypes. We investigated the relationship between specific subtypes and immune infiltration, as well as their implications for immunotherapy. Finally, we discovered a valuable and novel biomarker for BCa, supported by a series of in vitro experiments. Results We subdivided cancer-associated fibroblasts (CAFs), macrophages, and T cells into 3-5 small subpopulations through NMF and further explored the biological features. We found that ferroptosis played an important role in the BCa TME. Through bulk RNA-seq analysis, we further verified that ferroptosis affected the progression, prognosis, and immunotherapy response of BCa by regulating the TME. Especially ACSL4+CAFs, we found that high-level infiltration of this CAF subtype predicted worse prognosis, more complex immune infiltration, and less response for immunotherapy. Additionally, we found that this type of CAF was associated with cancer cells through the PTN-SDC1 axis, suggesting that SDC1 may be crucial in regulating CAFs in cancer cells. A series of in vitro experiments confirmed these inferences: SDC1 promoted the progression of BCa. Interestingly, we also discovered FTH1+ macrophages, which were closely related to SPP1+ macrophages and may also be involved in the regulation of BCa TME. Conclusion This study revealed the significant impact of ferroptosis on bladder cancer TME and identified novel ferroptosis-related TME cell subpopulations, ACSL4+CAFs, and important BCa biomarker SDC1.
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Affiliation(s)
- Ziang Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jia Hu
- Department of Anesthesiology, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, Anhui, China
| | - Yuxi Ou
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Weijian Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shenghua Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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11
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Chen D, Cao H, Zheng X, Wang H, Han Z, Wang W. Immune checkpoint gene signature assesses immune infiltration profiles in bladder cancer and identifies KRT23 as an immunotherapeutic target. BMC Cancer 2024; 24:1024. [PMID: 39160525 PMCID: PMC11331755 DOI: 10.1186/s12885-024-12790-w] [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: 06/04/2024] [Accepted: 08/09/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND In the past few decades, researchers have made promising progress, including the development of immune checkpoint inhibitors (ICIs) in the therapy of bladder cancer (BLCA). Existing studies mainly focus on single immune checkpoint inhibitors but lack relevant studies on the gene expression profiles of multiple immune checkpoints. METHODS RNA-sequencing profiling data and clinical information of BLCA patients and normal human bladder samples were acquired from the Cancer Genome Atlas and Gene Expression Omnibus databases and analyzed to identify different expression profiles of immune checkpoint genes (ICGs) after consensus clustering analysis. Based on the 526 intersecting differentially expressed genes, the LASSO Cox regression analysis was utilized to construct the ICG signature. RESULTS According to the expression of ICGs, BLCA patients were divided into three subtypes with different phenotypic and mechanistic characteristics. Furthermore, the developed ICG signature were independent predictors of outcome in BLCA patients, and was correlated with the immune infiltration, the expression of ICGs and chemotherapeutic effect. CONCLUSIONS This study systematically and comprehensively analyzed the expression profile of immune checkpoint genes, and established the ICG signature to investigate the differences in ICGs expression and tumor immune microenvironment, which will help risk stratification and accelerate precision medicine. Finally, we identified KRT23 as the most critical model gene, and highlighted KRT23 as a potential target to enhance immunotherapy against BLCA.
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Affiliation(s)
- Dongshan Chen
- Department of Urology, Beijing Chaoyang Hospital Affiliated Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
- Department of Urology, Qilu Hospital of Shandong University, Wenhuaxi Road #107, Jinan, 250012, China
| | - Haoyuan Cao
- Department of Urology, Beijing Chaoyang Hospital Affiliated Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Xiang Zheng
- Department of Urology, Beijing Chaoyang Hospital Affiliated Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Haojun Wang
- Department of Urology, Beijing Chaoyang Hospital Affiliated Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Zengchi Han
- Department of Urology, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, NO.1 Jingba Road, Shizhong District, Jinan, 250001, China.
| | - Wei Wang
- Department of Urology, Beijing Chaoyang Hospital Affiliated Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China.
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12
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Kim JY, Lee JS, Han D, Nikas IP, Kim H, Jung M, Ryu HS. Quantitative proteomics and immunohistochemistry uncover NT5DC2 as a diagnostic biomarker for papillary urothelial carcinoma. Heliyon 2024; 10:e35475. [PMID: 39165948 PMCID: PMC11334882 DOI: 10.1016/j.heliyon.2024.e35475] [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: 04/23/2024] [Revised: 06/27/2024] [Accepted: 07/29/2024] [Indexed: 08/22/2024] Open
Abstract
The accurate diagnosis of papillary urothelial carcinoma (PUC) is frequently challenging due to benign mimickers. Other than morphology-based diagnostic criteria, reliable biomarkers for differentiating benign and malignant papillary urothelial neoplasms remain elusive, so we sought to discover new markers to address this challenge. We first performed tandem mass spectrometry-based quantitative proteomics using diverse papillary urothelial lesions, including PUC, urothelial papilloma (UP), inverted urothelial papilloma, and cystitis cystica. We prioritized potential diagnostic biomarkers using machine learning, and subsequently validated through immunohistochemistry (IHC) in two independent cohorts. Metabolism, transport, cell cycle, development, and immune response functions were differentially enriched between malignant and benign papillary neoplasms. RhoB and NT5DC2 were shortlisted as optimal candidate markers for PUC diagnosis. In our pilot study using IHC, NT5DC2 was subsequently selected as its expression consistently differed in PUC (p = 0.007). Further validation of NT5DC2 using 49 low-grade (LG) urothelial lesions, including 15 LG-PUCs and 17 UPs, which are the most common mimickers, concordantly revealed lower IHC expression levels in LG-PUC (p = 0.0298). Independent external validation with eight LG-PUCs and eight UPs confirmed the significant downregulation of NT5DC2 in LG-PUC (p = 0.0104). We suggest that NT5DC2 is a potential IHC biomarker for differentiating LG-PUC from its benign mimickers, especially UP.
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Affiliation(s)
- Jun Yong Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jae Seok Lee
- Department of Pathology, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, 51353, Republic of Korea
| | - Dohyun Han
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Ilias P. Nikas
- Medical School, University of Cyprus, Nicosia, 2029, Cyprus
| | - Hyeyoon Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Minsun Jung
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Han Suk Ryu
- Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
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13
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Hao S, Yang Z, Wang G, Cai G, Qin Y. Development of prognostic model incorporating a ferroptosis/cuproptosis-related signature and mutational landscape analysis in muscle-invasive bladder cancer. BMC Cancer 2024; 24:958. [PMID: 39107713 PMCID: PMC11302292 DOI: 10.1186/s12885-024-12741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) is a prevalent and aggressive malignancy. Ferroptosis and cuproptosis are recently discovered forms of programmed cell death (PCD) that have attracted much attention. However, their interactions and impacts on MIBC overall survival (OS) and treatment outcomes remain unclear. METHODS Data from the TCGA-BLCA project (as the training set), cBioPortal database, and GEO datasets (GSE13507 and GSE32894, as the test sets) were utilized to identify hub ferroptosis/cuproptosis-related genes (FRGs and CRGs) and develop a prognostic signature. Differential expression analysis (DEA) was conducted, followed by univariate and multivariate Cox's regression analyses and multiple machine learning (ML) techniques to select genetic features. The performance of the ferroptosis/cuproptosis-related signature was evaluated using Kaplan-Meier (K-M) survival analysis and receiver-operating characteristics (ROC) curves. Mutational and tumour immune microenvironment landscapes were also explored. Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) experiments confirmed the expression patterns of the hub genes, and functional assays assessed the effects of SCD knockdown on cell viability, proliferation, and migration. RESULTS DEA revealed dysregulated FRGs and CRGs in the TCGA MIBC cohort. SCD, DDR2, and MT1A were identified as hub genes. A prognostic signature based on the sum of the weighted expression of these genes demonstrated strong predictive efficacy in the training and test sets. Nomogram incorporating this signature accurately predicted 1-, 3-, and 5-year survival probabilities in the TCGA cohort and GSE13507 dataset. Copy number variation (CNV) and tumour immune microenvironment analysis revealed that high risk score level groups were associated with immunosuppression and lower tumour purity. The associations of risk scores with immunotherapy and chemical drugs were also explored, indicating their potential for guiding treatment for MIBC patients. The dysregulated expression patterns of three hub genes were validated by RT-qPCR experiments. CONCLUSIONS Targeting hub FRGs and CRGs could be a promising therapeutic approach for MIBC. Our prognostic model offers a new framework for MIBC subtyping and can inform personalized therapeutic strategies.
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Affiliation(s)
- Sida Hao
- Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003Zhejiang , China
| | - Zitong Yang
- Department of Urology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Gang Wang
- Department of Urology, Affiliated Hangzhou First People's Hospital, Xihu University School of Medicine, Hangzhou, Zhejiang, China
| | - Guofeng Cai
- Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003Zhejiang , China
| | - Yong Qin
- Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003Zhejiang , China.
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14
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Olislagers M, de Jong FC, Rutten VC, Boormans JL, Mahmoudi T, Zuiverloon TCM. Molecular biomarkers of progression in non-muscle-invasive bladder cancer - beyond conventional risk stratification. Nat Rev Urol 2024:10.1038/s41585-024-00914-7. [PMID: 39095581 DOI: 10.1038/s41585-024-00914-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2024] [Indexed: 08/04/2024]
Abstract
The global incidence of bladder cancer is more than half a million diagnoses each year. Bladder cancer can be categorized into non-muscle-invasive bladder cancer (NMIBC), which accounts for ~75% of diagnoses, and muscle-invasive bladder cancer (MIBC). Up to 45% of patients with NMIBC develop disease progression to MIBC, which is associated with a poor outcome, highlighting a clinical need to identify these patients. Current risk stratification has a prognostic value, but relies solely on clinicopathological parameters that might not fully capture the complexity of disease progression. Molecular research has led to identification of multiple crucial players involved in NMIBC progression. Identified biomarkers of progression are related to cell cycle, MAPK pathways, apoptosis, tumour microenvironment, chromatin stability and DNA-damage response. However, none of these biomarkers has been prospectively validated. Reported gene signatures of progression do not improve NMIBC risk stratification. Molecular subtypes of NMIBC have improved our understanding of NMIBC progression, but these subtypes are currently unsuitable for clinical implementation owing to a lack of prospective validation, limited predictive value as a result of intratumour subtype heterogeneity, technical challenges, costs and turnaround time. Future steps include the development of consensus molecular NMIBC subtypes that might improve conventional clinicopathological risk stratification. Prospective implementation studies of biomarkers and the design of biomarker-guided clinical trials are required for the integration of molecular biomarkers into clinical practice.
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Affiliation(s)
- Mitchell Olislagers
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Florus C de Jong
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Vera C Rutten
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tokameh Mahmoudi
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tahlita C M Zuiverloon
- Department of Urology, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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15
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Huang X, Du G, Yang Y, Su P, Chen S, Cai C, Huang T, Zeng Y, Tao Y, Tian D, Zhang N. Advancing bladder cancer management: development of a prognostic model and personalized therapy. Front Immunol 2024; 15:1430792. [PMID: 39104534 PMCID: PMC11298345 DOI: 10.3389/fimmu.2024.1430792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Background Bladder cancer (BLCA) was recognized as a significant public health challenge due to its high incidence and mortality rates. The influence of molecular subtypes on treatment outcomes was well-acknowledged, necessitating further exploration of their characterization and application. This study was aimed at enhancing the understanding of BLCA by mapping its molecular heterogeneity and developing a robust prognostic model using single-cell and bulk RNA sequencing data. Additionally, immunological characteristics and personalized treatment strategies were investigated through the risk score. Methods Single-cell RNA sequencing (scRNA-seq) data from GSE135337 and bulk RNA-seq data from several sources, including GSE13507, GSE31684, GSE32894, GSE69795, and TCGA-BLCA, were utilized. Molecular subtypes, particularly the basal-squamous (Ba/Sq) subtype associated with poor prognosis, were identified. A prognostic model was constructed using LASSO and Cox regression analyses focused on genes linked with the Ba/Sq subtype. this model was validated across internal and external datasets to ensure predictive accuracy. High- and low-risk groups based on the risk score derived from TCGA-BLCA data were analyzed to examine their immune-related molecular profiles and treatment responses. Results Six molecular subtypes were identified, with the Ba/Sq subtype being consistently associated with poor prognosis. The prognostic model, based on basal-squamous subtype-related genes (BSSRGs), was shown to have strong predictive performance across diverse clinical settings with AUC values at 1, 3, and 5 years indicating robust predictability in training, testing, and entire datasets. Analysis of the different risk groups revealed distinct immune infiltration and microenvironments. Generally higher tumor mutation burden (TMB) scores and lower tumor immune dysfunction and exclusion (TIDE) scores were exhibited by the low-risk group, suggesting varied potentials for systemic drug response between the groups. Finally, significant differences in potential systemic drug response rates were also observed between risk groups. Conclusions The study introduced and validated a new prognostic model for BLCA based on BSSRGs, which was proven effective in prognosis prediction. The potential for personalized therapy, optimized by patient stratification and immune profiling, was highlighted by our risk score, aiming to improve treatment efficacy. This approach was promised to offer significant advancements in managing BLCA, tailoring treatments based on detailed molecular and immunological insights.
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Affiliation(s)
- Xiang Huang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guotu Du
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ying Yang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Peng Su
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shicheng Chen
- Department of Urology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chongjiong Cai
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Urology, Renhuai People’s Hospital, Zunyi, China
| | - Tianyu Huang
- Department of Nursing, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yu Zeng
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yonggang Tao
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Demei Tian
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Neng Zhang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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16
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Lin H, Fu L, Zhou X, Yu A, Chen Y, Liao W, Shu G, Zhang L, Tan L, Liang H, Wang Z, Deng Q, Wang J, Jin M, Chen Z, Wei J, Cao J, Chen W, Li X, Li P, Lu J, Luo J. LRP1 induces anti-PD-1 resistance by modulating the DLL4-NOTCH2-CCL2 axis and redirecting M2-like macrophage polarisation in bladder cancer. Cancer Lett 2024; 593:216807. [PMID: 38462037 DOI: 10.1016/j.canlet.2024.216807] [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: 10/31/2023] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
The tumour microenvironment (TME) drives bladder cancer (BLCA) progression. Targeting the TME has emerged as a promising strategy for BLCA treatment in recent years. Furthermore, checkpoint blockade therapies are only beneficial for a minority of patients with BLCA, and drug resistance is a barrier to achieving significant clinical effects of anti-programmed cell death protein-1 (PD-1)/programmed death protein ligand-1 (PD-L1) therapy. In this study, higher low-density lipoprotein receptor-related protein 1 (LRP1) levels were related to a poorer prognosis for patients with various cancers, including those with higher grades and later stages of BLCA. Enrichment analysis demonstrated that LRP1 plays a role in the epithelial-mesenchymal transition (EMT), NOTCH signalling pathway, and ubiquitination. LRP1 knockdown in BLCA cells delayed BLCA progression both in vivo and in vitro. Furthermore, LRP1 knockdown suppressed EMT, reduced DLL4-NOTCH2 signalling activity, and downregulated M2-like macrophage polarisation. Patients with BLCA and higher LRP1 levels responded weakly to anti-PD-1 therapy in the IMvigor210 cohort. Moreover, LRP1 knockdown enhanced the therapeutic effects of anti-PD-1 in mice. Taken together, our findings suggest that LRP1 is a potential target for improving the efficacy of anti-PD-1/PD-L1 therapy by preventing EMT and M2-like macrophage polarisation by blocking the DLL4-NOTCH2 axis.
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Affiliation(s)
- Hansen Lin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liangmin Fu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xinwei Zhou
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Anze Yu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuhang Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wuyuan Liao
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guannan Shu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Lizhen Zhang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lei Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Zhu Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Qiong Deng
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Jieyan Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Meiyu Jin
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Zhenhua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jinhuan Wei
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiazheng Cao
- Department of Urology, Jiangmen Central Hospital, Haibang Street 23, Pengjiang District, Jiangmen, 529030, Guangdong Province, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaofei Li
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Pengju Li
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Jun Lu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Junhang Luo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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17
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Guo CC, Lee S, Lee JG, Chen H, Zaleski M, Choi W, McConkey DJ, Wei P, Czerniak B. Molecular profile of bladder cancer progression to clinically aggressive subtypes. Nat Rev Urol 2024; 21:391-405. [PMID: 38321289 DOI: 10.1038/s41585-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
Bladder cancer is a histologically and clinically heterogenous disease. Most bladder cancers are urothelial carcinomas, which frequently develop distinct histological subtypes. Several urothelial carcinoma histological subtypes, such as micropapillary, plasmacytoid, small-cell carcinoma and sarcomatoid, show highly aggressive behaviour and pose unique challenges in diagnosis and treatment. Comprehensive genomic characterizations of the urothelial carcinoma subtypes have revealed that they probably arise from a precursor subset of conventional urothelial carcinomas that belong to different molecular subtypes - micropapillary and plasmacytoid subtypes develop along the luminal pathway, whereas small-cell and sarcomatoid subtypes evolve along the basal pathway. The subtypes exhibit distinct genomic alterations, but in most cases their biological properties seem to be primarily determined by specific gene expression profiles, including epithelial-mesenchymal transition, urothelial-to-neural lineage plasticity, and immune infiltration with distinct upregulation of immune regulatory genes. These breakthrough studies have transformed our view of bladder cancer histological subtype biology, generated new hypotheses for therapy and chemoresistance, and facilitated the discovery of new therapeutic targets.
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Affiliation(s)
- Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June G Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Zaleski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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18
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Yan Z, Liu Y, Wang M, Wang L, Chen Z, Liu X. A novel signature constructed by mitochondrial function and cell death-related gene for the prediction of prognosis in bladder cancer. Sci Rep 2024; 14:14667. [PMID: 38918587 PMCID: PMC11199696 DOI: 10.1038/s41598-024-65594-0] [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: 04/06/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
Bladder urothelial carcinoma (BLCA) presents a persistent challenge in clinical management. Despite recent advancements demonstrating the BLCA efficacy of immune checkpoint inhibitors (ICI) in BLCA patients, there remains a critical need to identify and expand the subset of individuals who benefit from this treatment. Mitochondria, as pivotal regulators of various cell death pathways in eukaryotic cells, exert significant influence over tumor cell fate and survival. In this study, our objective was to investigate biomarkers centered around mitochondrial function and cell death mechanisms to facilitate prognostic prediction and guide therapeutic decision-making in BLCA. Utilizing ssGSEA and LASSO regression, we developed a prognostic signature termed mitochondrial function and cell death (mtPCD). Subsequently, we evaluated the associations between mtPCD score and diverse clinical outcomes, including prognosis, functional pathway enrichment, immune cell infiltration, immunotherapy response analysis and drug sensitivity, within high- and low-risk subgroups. Additionally, we employed single-cell level functional assays, RT-qPCR, and immunohistochemistry to validate the differential expression of genes comprising the mtPCD signature. The mtPCD signature comprises a panel of 10 highly influential genes, strongly correlated with survival outcomes in BLCA patients and exhibiting robust predictive capabilities. Importantly, individuals classified as high-risk according to mtPCD score displayed a subdued overall immune response, characterized by diminished immunotherapeutic efficacy. In summary, our findings highlight the development of a novel prognostic signature, which not only holds promise as a biomarker for BLCA prognosis but also offers insights into the immune landscape of BLCA. This paradigm may pave the way for personalized treatment strategies in BLCA management.
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Affiliation(s)
- Zhiwei Yan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yunxun Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Minghui Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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19
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Wu J, Zhang F, Zheng X, Chen D, Li Z, Bi Q, Qiu X, Sun Z, Wang W. Identification of bladder cancer subtypes and predictive signature for prognosis, immune features, and immunotherapy based on immune checkpoint genes. Sci Rep 2024; 14:14431. [PMID: 38910160 PMCID: PMC11194261 DOI: 10.1038/s41598-024-65198-8] [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: 12/08/2023] [Accepted: 06/18/2024] [Indexed: 06/25/2024] Open
Abstract
Immunotherapy based on immune checkpoint genes (ICGs) has recently made significant progress in the treatment of bladder cancer patients, but many patients still cannot benefit from it. In the present study, we aimed to perform a comprehensive analysis of ICGs in bladder cancer tissues with the aim of evaluating patient responsiveness to immunotherapy and prognosis. We scored ICGs in each BLCA patient from TCGA and GEO databases by using ssGSEA and selected genes that were significantly associated with ICGs scores by using the WCGNA algorithm. NMF clustering analysis was performed to identify different bladder cancer molecular subtypes based on the expression of ICGs-related genes. Based on the immune related genes differentially expressed among subgroups, we further constructed a novel stratified model containing nine genes by uni-COX regression, LASSO regression, SVM algorithm and multi-COX regression. The model and the nomogram constructed based on the model can accurately predict the prognosis of bladder cancer patients. Besides, the patients classified based on this model have large differences in sensitivity to immunotherapy and chemotherapy, which can provide a reference for individualized treatment of bladder cancer.
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Affiliation(s)
- Jiyue Wu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Feilong Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Xiang Zheng
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Dongshan Chen
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Zhen Li
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Qing Bi
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Xuemeng Qiu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China
| | - Zejia Sun
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China.
| | - Wei Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gong Ti Nan Road, Chaoyang District, Beijing, 100020, China.
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20
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Al-Ahmadie H, Netto GJ. Molecular Pathology of Urothelial Carcinoma. Clin Lab Med 2024; 44:181-198. [PMID: 38821640 DOI: 10.1016/j.cll.2023.08.010] [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] [Indexed: 06/02/2024]
Abstract
Urothelial carcinoma is characterized by the presence of a wide spectrum of histopathologic features and molecular alterations that contribute to its morphologic and genomic heterogeneity. It typically harbors high rates of somatic mutations with considerable genomic and transcriptional complexity and heterogeneity that is reflective of its varied histomorphologic and clinical features. This review provides an update on the recent advances in the molecular characterization and novel molecular taxonomy of urothelial carcinoma and variant histologies.
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Affiliation(s)
- Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NW 10065, USA.
| | - George J Netto
- Department of Pathology, University of Alabama at Birmingham, University of Alabama at Birmingham School of Medicine, WP Building, Suite P230, 619 19th Street South, Birmingham, AL 35249-7331, USA.
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21
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Reike MJ, de Jong JJ, Bismar TA, Boorjian SA, Mian OY, Wright JL, Dall'Era MA, Kaimakliotis HZ, Lotan Y, Boormans JL, Black PC, Gibb EA. Alignment of molecular subtypes across multiple bladder cancer subtyping classifiers. Urol Oncol 2024; 42:177.e5-177.e14. [PMID: 38480079 DOI: 10.1016/j.urolonc.2024.01.027] [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: 10/01/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Treatment of patients with muscle-invasive bladder cancer (MIBC) includes cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC). Molecular subtypes have been associated with patient outcomes after NAC and RC, but the reported results have been highly inconsistent. OBJECTIVE To evaluate the association of molecular subtypes from different classifiers with overall survival (OS) among patients with MIBC who underwent RC. MATERIALS AND METHODS We analyzed gene expression data generated from transurethral resection of MIBC from a previously assembled and published meta-cohort, NACmeta (N = 601, 247 treated with NAC+RC and 354 RC without NAC), where extended follow-up was available. Molecular subtypes were assigned using the Genomic Subtyping Classifier (GSC), the Consensus Classifier, The Cancer Genome Atlas (TCGA) Classifier, and the Lund Classifier. For survival analysis, inverse probability weighting was used to balance the clinical NAC and non-NAC patient groups. RESULTS A high consistency in gene expression patterns and nomenclature was observed between luminal-like subtypes, defined as GSC-Luminal, Consensus-Luminal Papillary (LumP), TCGA Luminal-Papillary (LumP) and Lund-UroA, but not for basal-like subtypes such GSC-Basal, Consensus Basal/Squamous, TCGA-Basal/Squamous and Lund-Basal/Squamous. Patients with luminal-like subtypes demonstrated no difference in 3-year OS when treated with or without NAC (P = 0.7 for GSC, P = 0.94 for Consensus, P = 0.87 for TCGA and P = 0.66 for Lund-UroA, respectively). CONCLUSION Luminal-like molecular subtypes identify a subgroup of MIBC patients who do not appear to benefit from current NAC regimens, even for locally advanced disease. In addition, we were able to illustrate differences in subtyping nomenclature that are not reflected in the underlying biological definition of the subtypes. PATIENT SUMMARY Muscle-invasive bladder cancer exhibits molecular diversity, and various classifications identify different groups who do not benefit from chemotherapy. On the other hand, there is a high inconsistency in the way cancer groupings are named.
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Affiliation(s)
- Moritz J Reike
- Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany.
| | - Joep J de Jong
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Tarek A Bismar
- Department of Pathology and Laboratory Medicine, University of Calgary, Cumming School of Medicine, Calgary, Alberta, Canada
| | | | - Omar Y Mian
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA
| | - Jonathan L Wright
- Division of Oncology, Department of Medicine, University of Washington School of Medicine, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Marc A Dall'Era
- Department of Urology, University of Texas Health San Antonio, San Antonio, USA
| | | | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
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22
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Zheng L, Chen H, Zhao J, Roy-Chowdhuri S, Kamat AM, Alhalabi O, Gao J, Siefker-Radtke A, Hansel DE, Czerniak B, Guo CC. Plasmacytoid urothelial carcinoma of the urinary bladder-A clinicopathological and molecular analysis of 52 cases. Hum Pathol 2024; 148:1-6. [PMID: 38679207 DOI: 10.1016/j.humpath.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Plasmacytoid urothelial carcinoma (UC) is a rare histologic subtype of bladder cancer that is associated with an aggressive clinical behavior. We analyzed the clinicopathologic and molecular features of plasmacytoid UC in 52 patients from a single institute. The patients included 44 men and 8 women, with a mean age of 64 years (range, 41-91 years). All bladder cancers were high-grade UC, and plasmacytoid component accounted for a mean of 47% of bladder tumors (range, 5-100%). Distinct gene mutations were found in most plasmacytoid UCs (n = 49); the most common mutations were TP53 (n = 30), followed by TERT (n = 20), and CDH1 (n = 18). Copy number analysis was performed in 34 patients, and 13 of them showed copy number variations. Expression of HER2 was analyzed in 18 patients by immunohistochemistry, and 3 of them showed HER2 overexpression, which was confirmed by fluorescence in situ hybridization analysis. Thirty-two patients died of disease in a median of 15 months (range, 1-45 months). No individual gene mutations were significantly associated with clinical outcome, but mutations in the mammalian target of rapamycin (mTOR) pathway, including PICK3CA and PIK3R1 mutations, were associated with a significantly shorter survival duration (p < 0.05). Plasmacytoid UC is an aggressive histologic subtype that demonstrates frequent somatic gene mutations and CNVs, which may underlie its oncogenesis and progression. Gene mutations of the mTOR pathway are associated with poor outcome in a subset of patients with plasmacytoid UC.
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Affiliation(s)
- Lan Zheng
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Hui Chen
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Jianping Zhao
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Ashish M Kamat
- The University of Texas MD Anderson Cancer Center, Department of Urology, Houston, TX, USA
| | - Omar Alhalabi
- The University of Texas MD Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Jianjun Gao
- The University of Texas MD Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Arlene Siefker-Radtke
- The University of Texas MD Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Donna E Hansel
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Bogdan Czerniak
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA
| | - Charles C Guo
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX, USA.
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23
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Hemenway G, Anker JF, Riviere P, Rose BS, Galsky MD, Ghatalia P. Advancements in Urothelial Cancer Care: Optimizing Treatment for Your Patient. Am Soc Clin Oncol Educ Book 2024; 44:e432054. [PMID: 38771987 DOI: 10.1200/edbk_432054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The standard treatment paradigm for muscle invasive bladder cancer has been neoadjuvant cisplatin-based chemotherapy followed by radical cystectomy. However, efforts are ongoing to personalize treatment by incorporating biomarkers to better guide treatment selection. In addition, bladder preservation strategies are aimed at avoiding cystectomy in well-selected patients. Similarly, in the metastatic urothelial cancer space, the standard frontline treatment option of platinum-based chemotherapy has changed with the availability of data from EV-302 trial, making the combination of enfortumab vedotin (EV) and pembrolizumab the preferred first-line treatment option. Here, we examine the optimization of treatment intensity and sequencing, focusing on the challenges and opportunities associated with EV/pembrolizumab therapy, including managing toxicities and exploring alternative dosing approaches. Together, these articles provide a comprehensive overview of contemporary strategies in bladder cancer management, highlighting the importance of individualized treatment approaches, ongoing research, and multidisciplinary collaboration to improve patient outcomes in this complex disease landscape.
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Affiliation(s)
| | - Jonathan F Anker
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Paul Riviere
- UCSD Radiation Medicine and Applied Sciences, San Diego, CA
| | - Brent S Rose
- UCSD Radiation Medicine and Applied Sciences, San Diego, CA
| | - Matthew D Galsky
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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24
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Peng X, Liu C, Zhang L, Chen Y, Mao L, Gao S, Shi X, Zuo L. IL4I1: a novel molecular biomarker represents an inflamed tumor microenvironment and precisely predicts the molecular subtype and immunotherapy response of bladder cancer. Front Pharmacol 2024; 15:1365683. [PMID: 38873416 PMCID: PMC11169701 DOI: 10.3389/fphar.2024.1365683] [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: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction: IL4I1, also known as Interleukin-4-induced gene 1, is an enzyme that can modulate the immune system by acting as a L-amino acid oxidase. Nevertheless, a precise understanding of the correlation of IL4I1 with immunological features and immunotherapy efficacy in bladder cancer (BLCA) remains incomplete. Methods: We analyzed RNA sequencing data from the Cancer Genome Atlas (TCGA) to investigate the immune function and prognostic importance of IL4I1 across different cancer types. We further examined the TCGA-BLCA cohort for correlations between IL4I1 and various immunological characteristics of tumor microenvironment (TME), such as cancer immune cycle, immune cell infiltration, immune checkpoint expression and T cell inflamed score. Validation was conducted using two independent cohort, GSE48075 and E-MTAB-4321. Finally, RNA sequencing data from the IMvigor210 cohort and immunohistochemistry assays were employed to validate the predictive value of IL4I1 for the TME and immunotherapy efficacy. Results: In our findings, a positive correlation was observed between IL4I1 expression and immunomodulators expression, immune cell infiltration, the cancer immune cycle, and T cell inflamed score in BLCA, suggesting a significant link to the inflamed TME. In addition, studies have shown that IL4I1 elevated levels of individuals tend to be more performance for basal subtype and exhibit enhanced response rates to diverse treatment modalities, specifically immunotherapy. Clinical data from the IMvigor 210 cohort confirmed a higher rate of response to immunotherapy and better survival benefits in patients with high IL4I1 expression. Discussion: To summarize, our research showed that elevated IL4I1 levels are indicative of an inflamed TME, the basal subtype, and a more favorable response to various treatment methods, especially immune checkpoint blockade therapy in BLCA.
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Affiliation(s)
- Xiangrong Peng
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Chuan Liu
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Li Zhang
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Yin Chen
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Lixin Mao
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Shenglin Gao
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
- Department of Urology, Gonghe County Hospital of Traditional Chinese Medicine, Hainan Tibetan Autonomous Prefecture, Qinghai, China
| | - Xiaokai Shi
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Li Zuo
- Department of Urology, ChangZhou No.2 people’s Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
- Laboratory of Urology, ChangZhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
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25
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Lee S, Bondaruk J, Wang Y, Chen H, Lee JG, Majewski T, Mullen RD, Cogdell D, Chen J, Wang Z, Yao H, Kus P, Jeong J, Lee I, Choi W, Navai N, Guo C, Dinney C, Baggerly K, Mendelsohn C, McConkey D, Behringer RR, Kimmel M, Wei P, Czerniak B. Loss of LPAR6 and CAB39L dysregulates the basal-to-luminal urothelial differentiation program, contributing to bladder carcinogenesis. Cell Rep 2024; 43:114146. [PMID: 38676926 PMCID: PMC11265536 DOI: 10.1016/j.celrep.2024.114146] [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: 11/02/2023] [Revised: 02/19/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
We describe a strategy that combines histologic and molecular mapping that permits interrogation of the chronology of changes associated with cancer development on a whole-organ scale. Using this approach, we present the sequence of alterations around RB1 in the development of bladder cancer. We show that RB1 is not involved in initial expansion of the preneoplastic clone. Instead, we found a set of contiguous genes that we term "forerunner" genes whose silencing is associated with the development of plaque-like field effects initiating carcinogenesis. Specifically, we identified five candidate forerunner genes (ITM2B, LPAR6, MLNR, CAB39L, and ARL11) mapping near RB1. Two of these genes, LPAR6 and CAB39L, are preferentially downregulated in the luminal and basal subtypes of bladder cancer, respectively. Their loss of function dysregulates urothelial differentiation, sensitizing the urothelium to N-butyl-N-(4-hydroxybutyl)nitrosamine-induced cancers, which recapitulate the luminal and basal subtypes of human bladder cancer.
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Affiliation(s)
- Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yishan Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rachel D Mullen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Cogdell
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiansong Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ziqiao Wang
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui Yao
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pawel Kus
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Joon Jeong
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ilkyun Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Neema Navai
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Charles Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keith Baggerly
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cathy Mendelsohn
- Department of Urology, Genetics & Development and Pathology, Columbia University, New York, NY 10032, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Richard R Behringer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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26
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Sincic V, Arlenhold KF, Richtmann S, Lilljebjörn H, Eriksson P, Sjödahl G, Wokander M, Hägerbrand K, Ellmark P, Fioretos T, Borrebaeck CAK, Liedberg F, Lundberg K. Distinct Infiltration of T Cell Populations in Bladder Cancer Molecular Subtypes. Cells 2024; 13:926. [PMID: 38891058 PMCID: PMC11171717 DOI: 10.3390/cells13110926] [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: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
Bladder cancer is a heterogenous disease, and molecular subtyping is a promising method to capture this variability. Currently, the immune compartment in relation to subtypes is poorly characterized. Here, we analyzed the immune compartment in bladder tumors and normal bladder urothelium with a focus on T cell subpopulations using flow cytometry and RNA sequencing. The results were investigated in relation to tumor invasiveness (NMIBC/MIBC) and molecular subtypes according to the Lund Taxonomy system. Whereas the NMIBC/MIBC differed in the overall immune infiltration only, the molecular subtypes differed both in terms of immune infiltration and immune compartment compositions. The Basal/Squamous (Ba/Sq) and genomically unstable (GU) tumors displayed increased immune infiltration compared to urothelial-like (Uro) tumors. Additionally, the GU tumors had a higher proportion of regulatory T cells within the immune compartment compared to Uro tumors. Furthermore, sequencing showed higher levels of exhaustion in CD8+ T cells from GU tumors compared to both Uro tumors and the control. Although no such difference was detected at the transcriptomic level in Uro tumors compared to the controls, CD8+ T cells in Uro tumors showed higher expression of several exhaustion markers at the protein level. Taken together, our findings indicate that depending on the molecular subtype, different immunotherapeutic interventions might be warranted.
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Affiliation(s)
- Viktor Sincic
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- CREATE Health Cancer Center, Lund University, 223 81 Lund, Sweden
| | - Ken F. Arlenhold
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- CREATE Health Cancer Center, Lund University, 223 81 Lund, Sweden
| | - Sarah Richtmann
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- CREATE Health Cancer Center, Lund University, 223 81 Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 221 84 Lund, Sweden
| | - Gottfrid Sjödahl
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden
| | - Mats Wokander
- Department of Urology, Skåne University Hospital, 205 02 Malmö, Sweden
| | | | - Peter Ellmark
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- Alligator Bioscience AB, Medicon Village, 223 63 Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
- Department of Clinical Genetics, University and Regional Laboratories Region Skåne, 221 85 Lund, Sweden
| | - Carl A. K. Borrebaeck
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- CREATE Health Cancer Center, Lund University, 223 81 Lund, Sweden
| | - Fredrik Liedberg
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden
- Department of Urology, Skåne University Hospital, 205 02 Malmö, Sweden
| | - Kristina Lundberg
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
- CREATE Health Cancer Center, Lund University, 223 81 Lund, Sweden
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27
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Dressler FF, Diedrichs F, Sabtan D, Hinrichs S, Krisp C, Gemoll T, Hennig M, Mackedanz P, Schlotfeldt M, Voß H, Offermann A, Kirfel J, Roesch MC, Struck JP, Kramer MW, Merseburger AS, Gratzke C, Schoeb DS, Miernik A, Schlüter H, Wetterauer U, Zubarev R, Perner S, Wolf P, Végvári Á. Proteomic analysis of the urothelial cancer landscape. Nat Commun 2024; 15:4513. [PMID: 38802361 PMCID: PMC11130393 DOI: 10.1038/s41467-024-48096-5] [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: 09/02/2023] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Urothelial bladder cancer (UC) has a wide tumor biological spectrum with challenging prognostic stratification and relevant therapy-associated morbidity. Most molecular classifications relate only indirectly to the therapeutically relevant protein level. We improve the pre-analytics of clinical samples for proteome analyses and characterize a cohort of 434 samples with 242 tumors and 192 paired normal mucosae covering the full range of UC. We evaluate sample-wise tumor specificity and rank biomarkers by target relevance. We identify robust proteomic subtypes with prognostic information independent from histopathological groups. In silico drug prediction suggests efficacy of several compounds hitherto not in clinical use. Both in silico and in vitro data indicate predictive value of the proteomic clusters for these drugs. We underline that proteomics is relevant for personalized oncology and provide abundance and tumor specificity data for a large part of the UC proteome ( www.cancerproteins.org ).
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Affiliation(s)
- Franz F Dressler
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.
| | - Falk Diedrichs
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Deema Sabtan
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sofie Hinrichs
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christoph Krisp
- Section Mass Spectrometry and Proteomics, Campus Forschung N27 00.008, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Martin Hennig
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Paulina Mackedanz
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Mareile Schlotfeldt
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Hannah Voß
- Section Mass Spectrometry and Proteomics, Campus Forschung N27 00.008, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Offermann
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jutta Kirfel
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Marie C Roesch
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Julian P Struck
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Department of Urology, Faculty of Health Sciences Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Mario W Kramer
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Axel S Merseburger
- Department of Urology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christian Gratzke
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik S Schoeb
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arkadiusz Miernik
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Campus Forschung N27 00.008, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Wetterauer
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University, 3500, Krems, Austria
| | - Roman Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- The National Medical Research Center for Endocrinology, Moscow, Russia
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sven Perner
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Institute of Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Center for Precision Oncology, Tuebingen, Germany
| | - Philipp Wolf
- Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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28
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Matye D, Leak J, Woolbright BL, Taylor JA. Preclinical models of bladder cancer: BBN and beyond. Nat Rev Urol 2024:10.1038/s41585-024-00885-9. [PMID: 38769130 DOI: 10.1038/s41585-024-00885-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Preclinical modelling is a crucial component of advancing the understanding of cancer biology and therapeutic development. Several models exist for understanding the pathobiology of bladder cancer and evaluating therapeutics. N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN)-induced bladder cancer is a commonly used model that recapitulates many of the features of human disease. Particularly in mice, BBN is a preferred laboratory model owing to a high level of reproducibility, high genetic fidelity to the human condition, and its relative ease of use. However, important aspects of the model are often overlooked in laboratory studies. Moreover, the advent of new models has yielded a variety of methodologies that complement the use of BBN. Toxicokinetics, histopathology, molecular genetics and sex can differ between available models and are important factors to consider in bladder cancer modelling.
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Affiliation(s)
- David Matye
- School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Juliann Leak
- School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Benjamin L Woolbright
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - John A Taylor
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
- Department of Urology, University of Kansas Medical Center, Kansas City, KS, USA.
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29
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Warrick J. Molecular Subtypes of Bladder Cancer: Component Signatures and Potential Value in Clinical Decision-making. Adv Anat Pathol 2024; 31:178-187. [PMID: 38231156 DOI: 10.1097/pap.0000000000000430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Bladder cancer may be classified into "molecular subtypes" based on gene expression. These are associated with treatment response and patient outcomes. The gene expression signatures that define these subtypes are diverse, including signatures of epithelial differentiation, stromal involvement, cell cycle activity, and immune cell infiltration. Multiple different systems are described. While earlier studies considered molecular subtypes to be intrinsic properties of cancer, recent data have shown molecular subtypes change as tumors progress and evolve, and often differ between histologically distinct regions of a tumor. The data also indicate that some signatures that define molecular subtypes may be treated as independent continuous variables, rather than categorical subtypes, and these individual signatures may be more clinically informative. This review describes molecular subtypes of urothelial carcinoma, including histologic subtypes and tumors with divergent differentiation, and explores potential future uses in patient management.
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Affiliation(s)
- Joshua Warrick
- Departments of Pathology and Urology, Penn State College of Medicine, Hershey, PA
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30
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Li DX, Wu RC, Wang J, Yu QX, Tuo ZT, Ye LX, Feng DC, Deng S. An endothelial-related prognostic index for bladder cancer patients. Discov Oncol 2024; 15:128. [PMID: 38662077 PMCID: PMC11045713 DOI: 10.1007/s12672-024-00992-4] [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: 11/25/2023] [Accepted: 04/22/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Within the tumor microenvironment, endothelial cells hold substantial sway over bladder cancer (BC) prognosis. Herein, we aim to elucidate the impact of endothelial cells on BC patient outcomes by employing an integration of single-cell and bulk RNA sequencing data. METHODS All data utilized in this study were procured from online databases. R version 3.6.3 and relevant packages were harnessed for the development and validation of an endothelial-associated prognostic index (EPI). RESULTS EPI was formulated, incorporating six genes (CYTL1, FAM43A, GSN, HSPG2, RBP7, and SLC2A3). EPI demonstrated significant prognostic value in both The Cancer Genome Atlas (TCGA) and externally validated dataset. Functional results revealed a profound association between EPI and endothelial cell functionality, as well as immune-related processes. Our findings suggest that patients with low-risk EPI scores are more likely to respond positively to immunotherapy, as indicated by immune checkpoint activity, immune infiltration, tumor mutational burden, stemness index, TIDE, and IMvigor210 analyses. Conversely, individuals with high-risk EPI scores exhibited heightened sensitivity to cisplatin, docetaxel, and gemcitabine treatment regimens. CONCLUSION We have effectively discerned pivotal genes from the endothelial cell perspective and constructed an EPI for BC patients, thereby offering promising prospects for precision medicine.
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Affiliation(s)
- Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Rui-Cheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qing-Xin Yu
- Department of Pathology, Ningbo Clinical Pathology Diagnosis Center, Ningbo, China
| | - Zhou-Ting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Lu-Xia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Shi Deng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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31
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Zheng K, Hai Y, Chen H, Zhang Y, Hu X, Ni K. Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model. J Transl Med 2024; 22:365. [PMID: 38632658 PMCID: PMC11025237 DOI: 10.1186/s12967-024-05186-8] [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: 12/31/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Molecular subtyping is expected to enable precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE), we aimed to develop a novel TIDE-based subtyping strategy to guide personalized immunotherapy in the bladder cancer (BC). METHODS Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. Subsequently, consensus clustering was applied to classify BC patients based on TIDE marker-genes. Patients' clinicopathological, molecular features and signaling pathways of the different TIDE subtypes were well characterized. We also utilize the deconvolution algorithms to analyze the tumor microenvironment, and further explore the sensitivity and mechanisms of each subtype to immunotherapy. Furthermore, BC patient clinical information, real-world BC samples and urine samples were collected for the validation of our findings, which were used for RNA-seq analysis, H&E staining, immunohistochemistry and immunofluorescence staining, and enzyme-linked immunosorbent assay. Finally, we also explored the conservation of our novel TIDE subtypes in pan-cancers. RESULTS We identified 69 TIDE biomarker genes and classified BC samples into three subtypes using consensus clustering. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples and collected patient clinical data. This subtyping method was proved to be more efficient than previous known methods in identifying non-responders to immunotherapy. We also propose that combining our TIDE subtypes with known biomarkers can potentially improve the sensitivity and specificity of these biomarkers. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, we confirmed that the TIDE subtypes are conserved across the pan-tumors. CONCLUSIONS Our novel TIDE-based subtyping method can serve as a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized therapy decisions for selecting potential beneficiaries and excluding resistant patients of ICB therapy.
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Affiliation(s)
- Kun Zheng
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Youlong Hai
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Hongqi Chen
- Department of Urology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, 215200, Jiangsu, China
| | - Yukun Zhang
- Beijing University of Chinese Medicine East Hospital, Zaozhuang Hospital, Zaozhuang, 277000, Shandong, China
| | - Xiaoyong Hu
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Kai Ni
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
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32
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Cai T, Feng T, Li G, Wang J, Jin S, Ye D, Zhu Y. Deciphering the prognostic features of bladder cancer through gemcitabine resistance and immune-related gene analysis and identifying potential small molecular drug PIK-75. Cancer Cell Int 2024; 24:125. [PMID: 38570787 PMCID: PMC10993528 DOI: 10.1186/s12935-024-03258-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Bladder cancer (BCa) stands out as a prevalent and highly lethal malignancy worldwide. Chemoresistance significantly contributes to cancer recurrence and progression. Traditional Tumor Node Metastasis (TNM) stage and molecular subtypes often fail to promptly identify treatment preferences based on sensitivity. METHODS In this study, we developed a prognostic signature for BCa with uni-Cox + LASSO + multi-Cox survival analysis in multiple independent cohorts. Six machine learning algorithms were adopted to screen out the hub gene, RAC3. IHC staining was used to validate the expression of RAC3 in BCa tumor tissue. RT-qPCR and Western blot were performed to detect and quantify the mRNA and protein levels of RAC3. CCK8, colony formation, wound healing, and flow cytometry analysis of apoptosis were employed to determine cell proliferation, migration, and apoptosis. Molecular docking was used to find small target drugs, PIK-75. 3D cell viability assay was applied to evaluate the ATP viability of bladder cancer organoids before and after PIK-75 treated. RESULTS The established clinical prognostic model, GIRS, comprises 13 genes associated with gemcitabine resistance and immunology. This model has demonstrated robust predictive capabilities for survival outcomes across various independent public cohorts. Additionally, the GIRS signature shows significant correlations with responses to both immunotherapy and chemotherapy. Leveraging machine learning algorithms, the hub gene, RAC3, was identified, and potential upstream transcription factors were screened through database analysis. IHC results showed that RAC3 was higher expressed in GEM-resistant BCa patients. Employing molecular docking, the small molecule drug PIK-75, as binding to RAC3, was identified. Experiments on cell lines, organoids and animals validated the biological effects of PIK-75 in bladder cancer. CONCLUSIONS The GIRS signature offers a valuable complement to the conventional anatomic TNM staging system and molecular subtype stratification in bladder cancer. The hub gene, RAC3, plays a crucial role in BCa and is significantly associated with resistance to gemcitabine. The small molecular drug, PIK-75 having the potential as a therapeutic agent in the context of gemcitabine-resistant and immune-related pathways.
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Affiliation(s)
- Tingting Cai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tao Feng
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guangren Li
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University, Shandong, China
- Shandong Provincial Qianfoshan Hospital, Shandong, China
| | - Shengming Jin
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yiping Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Zhou J, Zhou R, Zhu Y, Deng S, Muhuitijiang B, Li C, Shi X, Zhang L, Tan W. Investigating the impact of regulatory B cells and regulatory B cell-related genes on bladder cancer progression and immunotherapeutic sensitivity. J Exp Clin Cancer Res 2024; 43:101. [PMID: 38566204 PMCID: PMC10985985 DOI: 10.1186/s13046-024-03017-8] [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: 11/27/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Regulatory B cells (Bregs), a specialized subset of B cells that modulate immune responses and maintain immune tolerance in malignant tumors, have not been extensively investigated in the context of bladder cancer (BLCA). This study aims to elucidate the roles of Bregs and Breg-related genes in BLCA. METHODS We assessed Breg infiltration levels in 34 pairs of BLCA and corresponding paracancerous tissues using immunohistochemical staining. We conducted transwell and wound healing assays to evaluate the impact of Bregs on the malignant phenotype of SW780 and T24 cells. Breg-related genes were identified through gene sets and transcriptional analysis. The TCGA-BLCA cohort served as the training set, while the IMvigor210 and 5 GEO cohorts were used as external validation sets. We employed LASSO regression and random forest for feature selection and developed a risk signature using Cox regression. Primary validation of the risk signature was performed through immunohistochemical staining and RT-qPCR experiments using the 34 local BLCA samples. Additionally, we employed transfection assays and flow cytometry to investigate Breg expansion ability and immunosuppressive functions. RESULTS Breg levels in BLCA tissues were significantly elevated compared to paracancerous tissues (P < 0.05) and positively correlated with tumor malignancy (P < 0.05). Co-incubation of SW780 and T24 cells with Bregs resulted in enhanced invasion and migration abilities (all P < 0.05). We identified 27 Breg-related genes, including CD96, OAS1, and CSH1, which were integrated into the risk signature. This signature demonstrated robust prognostic classification across the 6 cohorts (pooled HR = 2.25, 95% CI = 1.52-3.33). Moreover, the signature exhibited positive associations with advanced tumor stage (P < 0.001) and Breg infiltration ratios (P < 0.05) in the local samples. Furthermore, the signature successfully predicted immunotherapeutic sensitivity in three cohorts (all P < 0.05). Knockdown of CSH1 in B cells increased Breg phenotype and enhanced suppressive ability against CD8 + T cells (all P < 0.05). CONCLUSIONS Bregs play a pro-tumor role in the development of BLCA. The Breg-related gene signature established in this study holds great potential as a valuable tool for evaluating prognosis and predicting immunotherapeutic response in BLCA patients.
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Affiliation(s)
- Jiawei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Ranran Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Shikai Deng
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China
| | - Bahaerguli Muhuitijiang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Chengyao Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China
| | - Xiaojun Shi
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Ling Zhang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China.
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China.
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China.
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Hashemi Gheinani A, Kim J, You S, Adam RM. Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nat Rev Urol 2024; 21:214-242. [PMID: 37604982 DOI: 10.1038/s41585-023-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/23/2023]
Abstract
The application of bioinformatics has revolutionized the practice of medicine in the past 20 years. From early studies that uncovered subtypes of cancer to broad efforts spearheaded by the Cancer Genome Atlas initiative, the use of bioinformatics strategies to analyse high-dimensional data has provided unprecedented insights into the molecular basis of disease. In addition to the identification of disease subtypes - which enables risk stratification - informatics analysis has facilitated the identification of novel risk factors and drivers of disease, biomarkers of progression and treatment response, as well as possibilities for drug repurposing or repositioning; moreover, bioinformatics has guided research towards precision and personalized medicine. Implementation of specific computational approaches such as artificial intelligence, machine learning and molecular subtyping has yet to become widespread in urology clinical practice for reasons of cost, disruption of clinical workflow and need for prospective validation of informatics approaches in independent patient cohorts. Solving these challenges might accelerate routine integration of bioinformatics into clinical settings.
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Affiliation(s)
- Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Urology, Inselspital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Jina Kim
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Liu G, Jin K, Liu Z, Su X, Xu Z, Li B, Xu J, Liu H, Chang Y, Zhu Y, Xu L, Wang Z, Wang Y, Zhang W. Integration of CD4 + T cells and molecular subtype predicts benefit from PD-L1 blockade in muscle-invasive bladder cancer. Cancer Sci 2024; 115:1306-1316. [PMID: 38402640 PMCID: PMC11007017 DOI: 10.1111/cas.16119] [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: 11/23/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
Muscle-invasive bladder cancer (MIBC) is a disease characterized by molecular and clinical heterogeneity, posing challenges in selecting the most appropriate treatment in clinical settings. Considering the significant role of CD4+ T cells, there is an emerging need to integrate CD4+ T cells with molecular subtypes to refine classification. We conducted a comprehensive study involving 895 MIBC patients from four independent cohorts. The Zhongshan Hospital (ZSHS) and The Cancer Genome Atlas (TCGA) cohorts were included to investigate chemotherapeutic response. The IMvigor210 cohort was included to assess the immunotherapeutic response. NCT03179943 was used to evaluate the clinical response to a combination of immune checkpoint blockade (ICB) and chemotherapy. Additionally, we evaluated genomic characteristics and the immune microenvironment to gain deeper insights into the distinctive features of each subtype. We unveiled four immune-molecular subtypes, each exhibiting distinct clinical outcomes and molecular characteristics. These subtypes include luminal CD4+ Thigh, which demonstrated benefits from both immunotherapy and chemotherapy; luminal CD4+ Tlow, characterized by the highest level of fibroblast growth factor receptor 3 (FGFR3) mutation, thus indicating potential responsiveness to FGFR inhibitors; basal CD4+ Thigh, which could benefit from a combination of ICB and chemotherapy; and basal CD4+ Tlow, characterized by an immune suppression microenvironment and likely to benefit from transforming growth factor-β (TGF-β) inhibition. This immune-molecular classification offers new possibilities for optimizing therapeutic interventions in MIBC.
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Affiliation(s)
- Ge Liu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Kaifeng Jin
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Urology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Zhaopei Liu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Xiaohe Su
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Ziyue Xu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Bingyu Li
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Jingtong Xu
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Hailong Liu
- Department of Urology, Xinhua HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuan Chang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yu Zhu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Le Xu
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zewei Wang
- Department of Urology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical SciencesFudan UniversityShanghaiChina
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Zheng X, Qiu L, Huang Y, Cheng R, Huang S, Xu K, Cai W, Deng Y, Wang W, Zhong X, Cui F, Hao Z, Liu J. Exploring the molecular and immune-landscape of lung cancer associated with cystic airspaces. Mol Immunol 2024; 168:75-88. [PMID: 38430689 DOI: 10.1016/j.molimm.2024.01.007] [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: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024]
Abstract
To explore the molecular biological characteristics of lung cancer associated with cystic airspaces (LCCA) and its potential roles on prognosis. A total of 165 LCCAs and 201 non-LCCAs were enrolled in this study. Bulk RNA sequencing was implemented in eight LCCAs and nine non-LCCAs to explore the differentially expressed genes. TCGA data were used to analyze LCCA-specific genes that associated with overall survival (OS). The median age was 60 (IQR 53 to 65) years in LCCA cohort. We found LCCA were predominant in men and had less visceral pleura invasion (VPI) or lympho-vascular invasion (LVI). Moreover, LCCA presented with higher histological heterogeneity. Kaplan-Meier analysis showed that patients of age more than 60 and positive VPI had significantly less PFS in LCCA. Cox regression suggested that LCCA, micropapillary subtype proportion and VPI were the independent risk factors for PFS. LCCA had up-regulated pathways associated with EMT, angiogenesis and cell migration. In addition, LCCA displayed higher levels of immunosuppressor infiltration (M2 macrophages, CAFs and MDSCs) and distinct cell death and metabolic patterns. BCR/TCR repertoire analysis revealed less BCR richness, clonality and high-abundance shared clonotypes in LCCA. Finally, Cox regression analysis identified that four cystic-specific genes, KCNK3, NRN1, PARVB and TRHDE-AS1, were associated with OS of lung adenocarcinoma (LUAD). And cystic-specific risk scores (CSRSs) were calculated to construct a nomogram, which performance well. Our study for the first time indicated significantly distinct molecular biological and immune characteristics between LCCA and non-LCCA, which provide complementary prognostic values in early-stage non-small cell lung cancer (NSCLC).
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Affiliation(s)
- Xiang Zheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China; Department of Oncology, The First Clinical Medical College of Henan University, Kaifeng, China
| | - Li Qiu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ying Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ran Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Sihe Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ke Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weipeng Cai
- Department of Thoracic Surgery, Shantou Central Hospital, Shantou, China
| | - Yu Deng
- Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xi Zhong
- Department of Medical Imaging, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Fei Cui
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhexue Hao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China.
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Baek SW, Leem SH. A Multi-Gene Signature of Non-Muscle-Invasive Bladder Cancer Identifies Patients Who Respond to Immunotherapies Including Bacillus Calmette-Guérin and Immune Checkpoint Inhibitors. Int J Mol Sci 2024; 25:3800. [PMID: 38612609 PMCID: PMC11012101 DOI: 10.3390/ijms25073800] [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: 03/05/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Approximately 75% of bladder cancer cases originate as non-muscle-invasive bladder cancer (NMIBC). Despite initial diagnosis, NMIBC commonly recurs, with up to 45% advancing to muscle-invasive bladder cancer (MIBC) and metastatic disease. Treatment for high-risk NMIBC typically includes procedures like transurethral resection and, depending on recurrence risk, intravesical chemotherapy or immunotherapy such as Bacillus Calmette-Guérin (BCG). However, persistent shortages of BCG necessitate alternative first-line treatments. We aim to use a multi-gene signature in high-risk NMIBC patients to determine whether patients may benefit from immune checkpoint inhibitors (ICIs) as an alternative to BCG and to evaluate their clinical utility. The multi-gene signature obtained from the three independent NMIBC cohorts was applied to stratify the UROMOL2016 cohort (n = 476) using consensus clustering. Each subtype was distinguished by biological pathway analysis. Validation analysis using a machine learning algorithm was performed in six independent cohorts including the BRS (n = 283) cohort treated with BCG and the IMvigor210 (n = 298) clinical trials treated with PD-L1 inhibitors. Based on consensus cluster analysis, NMIBC patients in the UROMOL2016 cohort were classified into three classes exhibiting distinguished characteristics, including DNA damage repair (DDR). Survival analysis showed that the NMIBC-DDR class had the highest rates of disease progression (progression-free survival, p = 0.002 by log-rank test) in the UROMOL cohort and benefited from BCG and ICIs (respectively, p = 0.02 and p = 0.03 by log-rank test). This study suggests that the multi-gene signature may have a role in identifying high-risk NMIBC patients and improving the responsiveness of ICIs. Additionally, we propose immunotherapy as a new first-line treatment for patients with high-risk NMIBC because of the shortage of BCG supply. It is important to help more patients prioritize cancer immunotherapy.
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Affiliation(s)
- Seung-Woo Baek
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea;
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Health Sciences, The Graduate School of Dong-A University, Busan 49315, Republic of Korea
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Lv L, Wei Q, Zhang J, Dong Y, Shan Z, Chang N, Zhao Y, Bian P, Yi Q. IGF2BP3 prevent HMGB1 mRNA decay in bladder cancer and development. Cell Mol Biol Lett 2024; 29:39. [PMID: 38504159 PMCID: PMC10949762 DOI: 10.1186/s11658-024-00545-1] [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: 02/05/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND IGF2BP3 functions as an RNA-binding protein (RBP) and plays a role in the posttranscriptional control of mRNA localization, stability, and translation. Its dysregulation is frequently associated with tumorigenesis across various cancer types. Nonetheless, our understanding of how the expression of the IGF2BP3 gene is regulated remains limited. The specific functions and underlying mechanisms of IGF2BP3, as well as the potential benefits of targeting it for therapeutic purposes in bladder cancer, are not yet well comprehended. METHODS The mRNA and protein expression were examined by RT-qPCR and western blotting, respectively. The methylation level of CpG sites was detected by Bisulfite sequencing PCR (BSP). The regulation of IGF2BP3 expression by miR-320a-3p was analyzed by luciferase reporter assay. The functional role of IGF2BP3 was determined through proliferation, colony formation, wound healing, invasion assays, and xenograft mouse model. The regulation of HMGB1 by IGF2BP3 was investigated by RNA immunoprecipitation (RIP) and mRNA stability assays. RESULTS We observed a significant elevation in IGF2BP3 levels within bladder cancer samples, correlating with more advanced stages and grades, as well as an unfavorable prognosis. Subsequent investigations revealed that the upregulation of IGF2BP3 expression is triggered by copy number gain/amplification and promoter hypomethylation in various tumor types, including bladder cancer. Furthermore, miR-320a-3p was identified as another negative regulator in bladder cancer. Functionally, the upregulation of IGF2BP3 expression exacerbated bladder cancer progression, including the proliferation, migration, and invasion of bladder cancer. Conversely, IGF2BP3 silencing produced the opposite effects. Moreover, IGF2BP3 expression positively correlated with inflammation and immune infiltration in bladder cancer. Mechanistically, IGF2BP3 enhanced mRNA stability and promoted the expression of HMGB1 by binding to its mRNA, which is a factor that promotes inflammation and orchestrates tumorigenesis in many cancers. Importantly, pharmacological inhibition of HMGB1 with glycyrrhizin, a specific HMGB1 inhibitor, effectively reversed the cancer-promoting effects of IGF2BP3 overexpression in bladder cancer. Furthermore, the relationship between HMGB1 mRNA and IGF2PB3 is also observed in mammalian embryonic development, with the expression of both genes gradually decreasing as embryonic development progresses. CONCLUSIONS Our present study sheds light on the genetic and epigenetic mechanisms governing IGF2BP3 expression, underscoring the critical involvement of the IGF2BP3-HMGB1 axis in driving bladder cancer progression. Additionally, it advocates for the investigation of inhibiting IGF2BP3-HMGB1 as a viable therapeutic approach for treating bladder cancer.
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Affiliation(s)
- Lei Lv
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, Anhui, China
| | - Qinqin Wei
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Jianxiao Zhang
- Medical Consulting Center, Hebei Children's Hospital, Shijiazhuang, 050030, Hebei, China
| | - Yitong Dong
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Zhenglei Shan
- The Second Clinical College, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Na Chang
- Department of Radiation Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, Anhui, People's Republic of China
| | - Ye Zhao
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Po Bian
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Qiyi Yi
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
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Chen X, Yin Y, He Y, Meng F, Zhao J, Liu F, Xu Y, Wang G, Zhu X, Ma S, Lu H, Cai S, Song Y, Dai J. The prognostic significance and clinical relevance of stem cell characteristic in bladder cancer. Heliyon 2024; 10:e24858. [PMID: 38333832 PMCID: PMC10850424 DOI: 10.1016/j.heliyon.2024.e24858] [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: 05/15/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Background Bladder cancer (BLCA) is a common malignant tumor of urinary system and prognostic biomarkers are needed for better clinical decision-making and patient management. Cancer stem cells (CSCs) are involved in carcinogenesis, development, metastasis and recurrence of BLCA. This study explored the prognostic and predictive value of CSCs-related genes and laid the groundwork for precision treatment development in BLCA. Methods The mRNA data and corresponding clinical information obtained from TCGA-BLCA cohort was used to discover biomarkers and develop CSCs-related prognostic model, which was further validated in GSE32548 and GSE32894 datasets. In addition, the association between CSCs-related risk score and therapeutic efficacy was analyzed to explore the potential predictive value of the prognostic model. Results We identified four CSCs-related subtypes and 900 differentially expressed genes (DEGs) among subtypes. Then the CSCs-related prognostic model was built based on 16 CSCs-related DEGs with the most significant prognostic value. Patients in the low-risk group had better overall survival than those in high-risk group (P < 0.001; HR, 0.42; 95 %CI, 0.31-0.57). Multivariable Cox analysis in training and test sets confirmed the independence of CSCs-related risk score as a prognostic factor (P < 0.05). The difference of survival between two risk groups were probably due to the significantly varied immune microenvironment based on the analysis of infiltrated immune cells. Additionally, the risk score was significantly associated with chemotherapy sensitivity and the response to anti-PD-L1 therapy (P < 0.05) which suggested a potential predictive value of CSCs-related risk model. Conclusion We established a risk classifier based on 16 CSCs-related genes for predicting survival in patients with BLCA. The CSCs-related risk model has both prognostic value and potential predictive value for therapeutic efficacy, which brings us closer to understanding the important role of CSCs in BLCA and may provide guidance for clinical treatment decision-making and patient management. The clinical utility of the CSCs-related risk classifier warrants further studies.
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Affiliation(s)
- Xia Chen
- Clinical Research Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Yuanyuan Yin
- Clinical Research Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Yuming He
- Burning Rock Biotech, Guangzhou, China
| | | | - Jing Zhao
- Burning Rock Biotech, Guangzhou, China
| | - Fang Liu
- Burning Rock Biotech, Guangzhou, China
| | - Yu Xu
- Burning Rock Biotech, Guangzhou, China
| | | | - Xin Zhu
- Burning Rock Biotech, Guangzhou, China
| | - Sijia Ma
- Burning Rock Biotech, Guangzhou, China
| | - Huafei Lu
- Burning Rock Biotech, Guangzhou, China
| | | | - Yanping Song
- Department of Urological Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Junyong Dai
- Department of Urological Oncology, Chongqing University Cancer Hospital, Chongqing, China
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Tripathi N, Fortuna GG, Gebrael G, Dal E, Mathew Thomas V, Gupta S, Swami U. Predictors of response to neoadjuvant therapy in urothelial cancer. Crit Rev Oncol Hematol 2024; 194:104236. [PMID: 38128631 DOI: 10.1016/j.critrevonc.2023.104236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Neoadjuvant cisplatin-based chemotherapy (NACC) followed by radical cystectomy is the standard treatment for localized muscle-invasive bladder cancer (MIBC). Patients who achieve a complete pathological response following NACC have better overall survival than those with residual disease. However, a subset of patients does not derive benefit from NACC while experiencing chemotherapy-related side effects that may delay cystectomy, which can be detrimental. There is a need for predictive and prognostic biomarkers to better stratify patients who will derive benefits from NACC. This review summarizes the currently available literature on various predictors of response to neoadjuvant chemotherapy. Covered predictors include clinical factors, treatment regimens (including chemotherapy and immunotherapy), histological predictors, and molecular predictors such as DNA repair genes, p53, FGFR3, ERBB2, Bcl-2, EMMPRIN, survivin, choline-phosphate cytidylyltransferase-α, epigenetic markers, immunological markers, other molecular predictors and gene expression profiling. Further, we elaborate on the potential role of neoadjuvant immunotherapy and the correlative biomarkers of response.
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Affiliation(s)
- Nishita Tripathi
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Gliceida Galarza Fortuna
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Georges Gebrael
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Emre Dal
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Vinay Mathew Thomas
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sumati Gupta
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Umang Swami
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Gill E, Perks CM. Mini-Review: Current Bladder Cancer Treatment-The Need for Improvement. Int J Mol Sci 2024; 25:1557. [PMID: 38338835 PMCID: PMC10855537 DOI: 10.3390/ijms25031557] [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: 12/03/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Bladder cancer is the tenth most common cancer and is a significant burden on health care services worldwide, as it is one of the most costly cancers to treat per patient. This expense is due to the extensive treatment and follow-ups that occur with costly and invasive procedures. Improvement in both treatment options and the quality of life these interventions offer has not progressed at the rates of other cancers, and new alternatives are desperately needed to ease the burden. A more modern approach needs to be taken, with urinary biomarkers being a positive step in making treatments more patient-friendly, but there is still a long way to go to make these widely available and of a comparable standard to the current treatment options. New targets to hit the major signalling pathways that are upregulated in bladder cancer, such as the PI3K/AkT/mTOR pathway, are urgently needed, with only one drug approved so far, Erdafitinib. Immune checkpoint inhibitors also hold promise, with both PD-1 and CDLA-4 antibody therapies approved for use. They effectively block ligand/receptor binding to block the immune checkpoint used by tumour cells. Other avenues must be explored, including drug repurposing and novel biomarkers, which have revolutionised this area in other cancers.
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Affiliation(s)
| | - Claire M. Perks
- Cancer Endocrinology Group, Learning & Research Building, Southmead Hospital, Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK;
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42
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Lerner SP, McConkey DJ, Tangen CM, Meeks JJ, Flaig TW, Hua X, Daneshmand S, Alva AS, Lucia MS, Theodorescu D, Goldkorn A, Milowsky MI, Choi W, Bangs R, Gustafson DL, Plets M, Thompson IM. Association of Molecular Subtypes with Pathologic Response, PFS, and OS in a Phase II Study of COXEN with Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer. Clin Cancer Res 2024; 30:444-449. [PMID: 37966367 PMCID: PMC10824507 DOI: 10.1158/1078-0432.ccr-23-0602] [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: 02/28/2023] [Revised: 04/25/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
PURPOSE The Coexpression Extrapolation (COXEN) gene expression model with chemotherapy-specific scores [for methotrexate, vinblastine, adriamycin, cisplatin (ddMVAC) and gemcitabine/cisplatin (GC)] was developed to identify responders to neoadjuvant chemotherapy (NAC). We investigated RNA-based molecular subtypes as additional predictive biomarkers for NAC response, progression-free survival (PFS), and overall survival (OS) in patients treated in S1314. EXPERIMENTAL DESIGN A total of 237 patients were randomized between four cycles of ddMVAC (51%) and GC (49%). On the basis of Affymetrix transcriptomic data, we determined subtypes using three classifiers: TCGA (k = 5), Consensus (k = 6), and MD Anderson (MDA; k = 3) and assessed subtype association with path response to NAC and determined associations with COXEN. We also tested whether each classifier contributed additional predictive power when added to a model based on predefined stratification (strat) factors (PS 0 vs. 1; T2 vs. T3, T4a). RESULTS A total of 155 patients had gene expression results, received at least three of four cycles of NAC, and had pT-N response based on radical cystectomy. TCGA three-group classifier basal-squamous (BS)/neuronal, luminal (Lum), Lum infiltrated, and GC COXEN score yielded the largest AUCs for pT0 (0.59, P = 0.28; 0.60, P = 0.18, respectively). For downstaging ( CONCLUSIONS The Consensus classifier, based in part on the TCGA and MDA classifiers, modestly improved prediction for pathologic downstaging but subtypes were not associated with PFS or OS.
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Affiliation(s)
| | | | | | - Joshua J Meeks
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Thomas W Flaig
- University of Colorado, School of Medicine, Aurora, Colorado
| | - Xing Hua
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Siamak Daneshmand
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | - M Scott Lucia
- University of Colorado, School of Medicine, Aurora, Colorado
| | | | - Amir Goldkorn
- University of Southern California, Los Angeles, California
| | - Matthew I Milowsky
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | | | - Rick Bangs
- SWOG Cancer Research Network, Portland, Oregon
| | | | - Melissa Plets
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ian M Thompson
- CHRISTUS Medical Center Hospital, University of Texas Health Science Center at San Antonio, San Antonio, Texas
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43
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Okato A, Utsumi T, Ranieri M, Zheng X, Zhou M, Pereira LD, Chen T, Kita Y, Wu D, Hyun H, Lee H, Gdowski AS, Raupp JD, Clark-Garvey S, Manocha U, Chafitz A, Sherman F, Stephens J, Rose TL, Milowsky MI, Wobker SE, Serody JS, Damrauer JS, Wong KK, Kim WY. FGFR inhibition augments anti-PD-1 efficacy in murine FGFR3-mutant bladder cancer by abrogating immunosuppression. J Clin Invest 2024; 134:e169241. [PMID: 38226620 PMCID: PMC10786699 DOI: 10.1172/jci169241] [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: 01/30/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
The combination of targeted therapy with immune checkpoint inhibition (ICI) is an area of intense interest. We studied the interaction of fibroblast growth factor receptor (FGFR) inhibition with ICI in urothelial carcinoma (UC) of the bladder, in which FGFR3 is altered in 50% of cases. Using an FGFR3-driven, Trp53-mutant genetically engineered murine model (UPFL), we demonstrate that UPFL tumors recapitulate the histology and molecular subtype of their FGFR3-altered human counterparts. Additionally, UPFL1 allografts exhibit hyperprogression to ICI associated with an expansion of T regulatory cells (Tregs). Erdafitinib blocked Treg proliferation in vitro, while in vivo ICI-induced Treg expansion was fully abrogated by FGFR inhibition. Combined erdafitinib and ICI resulted in high therapeutic efficacy. In aggregate, our work establishes that, in mice, co-alteration of FGFR3 and Trp53 results in high-grade, non-muscle-invasive UC and presents a previously underappreciated role for FGFR inhibition in blocking ICI-induced Treg expansion.
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Affiliation(s)
- Atsushi Okato
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Takanobu Utsumi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michela Ranieri
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Xingnan Zheng
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Luiza D. Pereira
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Ting Chen
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Yuki Kita
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Di Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyesun Hyun
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyojin Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Andrew S. Gdowski
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - John D. Raupp
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sean Clark-Garvey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alison Chafitz
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Fiona Sherman
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Janaye Stephens
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Tracy L. Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Matthew I. Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Sara E. Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine
| | - Jonathan S. Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Pathology and Laboratory Medicine
- Department of Microbiology and Immunology
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - William Y. Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Genetics, and
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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44
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Wang Y, Tang Y, Liu Z, Tan X, Zou Y, Luo S, Yao K. Identification of an inflammation-related risk signature for prognosis and immunotherapeutic response prediction in bladder cancer. Sci Rep 2024; 14:1216. [PMID: 38216619 PMCID: PMC10786915 DOI: 10.1038/s41598-024-51158-9] [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: 10/24/2023] [Accepted: 01/01/2024] [Indexed: 01/14/2024] Open
Abstract
Tumor inflammation is one of the hallmarks of tumors and is closely related to tumor occurrence and development, providing individualized prognostic prediction. However, few studies have evaluated the relationship between inflammation and the prognosis of bladder urothelial carcinoma (BLCA) patients. Therefore, we constructed a novel inflammation-related prognostic model that included six inflammation-related genes (IRGs) that can precisely predict the survival outcomes of BLCA patients. RNA-seq expression and corresponding clinical data from BLCA patients were downloaded from The Cancer Genome Atlas database. Enrichment analysis was subsequently performed to determine the enrichment of GO terms and KEGG pathways. K‒M analysis was used to compare overall survival (OS). Cox regression and LASSO regression were used to identify prognostic factors and construct the model. Finally, this prognostic model was used to evaluate cell infiltration in the BLCA tumor microenvironment and analyze the effect of immunotherapy in high- and low-risk patients. We established an IRG signature-based prognostic model with 6 IRGs (TNFRSF12A, NR1H3, ITIH4, IL1R1, ELN and CYP26B1), among which TNFRSF12A, IL1R1, ELN and CYP26B1 were unfavorable prognostic factors and NR1H3 and ITIH4 were protective indicators. High-risk score patients in the prognostic model had significantly poorer OS. Additionally, high-risk score patients were associated with an inhibitory immune tumor microenvironment and poor immunotherapy response. We also found a correlation between IRS-related genes and bladder cancer chemotherapy drugs in the drug sensitivity data. The IRG signature-based prognostic model we constructed can predict the prognosis of BLCA patients, providing additional information for individualized prognostic judgment and treatment selection.
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Affiliation(s)
- Yanjun Wang
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Yi Tang
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Zhicheng Liu
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Xingliang Tan
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Yuantao Zou
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Sihao Luo
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Kai Yao
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China.
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China.
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China.
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45
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Ma X, Wei X, Yang G, Li S, Liu R. A Novel Natural Killer Cell-related Gene Signature for Improving the Prediction of Prognosis and Immunotherapy Response in Bladder Cancer. Comb Chem High Throughput Screen 2024; 27:1205-1221. [PMID: 37653625 DOI: 10.2174/1386207326666230831164358] [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: 05/03/2023] [Revised: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Bladder cancer (BLCA) is a commonly diagnosed cancer worldwide that exhibits high rates of recurrence and metastasis. Immunotherapy is increasingly being recognised in the clinical management of bladder cancer. In addition, the prospect of developing Natural Killer (NK) cell-related immunotherapy is promising in BLCA. METHODS We established and verified a prognostic signature based on NK cell-related gene expression. We then calculated the NKscore of BLCA samples and correlated it with the clinical outcomes, molecular subtypes of BLCA, tumour microenvironment (TME), and predicted efficacy of immune checkpoint inhibitors (ICI) and chemotherapy drugs to thoroughly explore the implications of the NKscore. Finally, the role of the NK signature gene HECTD1 in BLCA was verified by Quantitative Real-time PCR, Cell Counting Kit-8 Assay (CCK-8), Transwell Assay and Colony Formation Experiment. RESULTS We analysed NK cell-associated genes and identified six genes with significant prognostic relevance. A high NK score significantly represents a worse prognosis. NKscore was significantly correlated with seven types of classical molecular subtype classifications of BLCA. In addition, NKscore positively correlates with NK-related immune checkpoints, suggesting that emerging NK cell immune checkpoint inhibitors, such as monalizumab, may have potential therapeutic promise for patients with high NKscore. The results of the T cell inflamed score (TIS) and tumour immune dysfunction exclusion (TIDE) score confirmed the suitability of immunotherapy for patients with a high NK score. Likewise, patients with a high NK score may be more suitable for several significant chemotherapeutic drugs. Functional experiments showed that the knockdown of HECTD1 significantly attenuated the proliferation, migration, and invasion ability of tumour cells. CONCLUSION To sum up, the capability of our signature to predict prognosis and immunotherapy response was robust. Hopefully, these results will provide new insights for BLCA research and patient immunotherapy.
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Affiliation(s)
- Xudong Ma
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, Baotou Central Hospital, Inner Mongolia Medical University, Baotou, China
| | - Xifeng Wei
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Guanghua Yang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Third Hospital of Shanxi Medical University, Taiyuan, 030032, People's Republic of China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Shuai Li
- Department of Urology, Baotou Central Hospital, Inner Mongolia Medical University, Baotou, China
| | - Ranlu Liu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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Warrick JI, Al-Ahmadie H, Berman DM, Black PC, Flaig TW, Höglund M, Bubendorf L, van der Kwast TH, Cheng L. International Society of Urological Pathology Consensus Conference on Current Issues in Bladder Cancer. Working Group 4: Molecular Subtypes of Bladder Cancer-Principles of Classification and Emerging Clinical Utility. Am J Surg Pathol 2024; 48:e32-e42. [PMID: 37199442 DOI: 10.1097/pas.0000000000002053] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Molecular subtyping has been a major focus of bladder cancer research over the past decade. Despite many promising associations with clinical outcomes and treatment response, its clinical impact has yet to be defined. As part of the 2022 International Society of Urological Pathology Conference on Bladder Cancer, we reviewed the current state of the science for bladder cancer molecular subtyping. Our review included several different subtyping systems. We derived the following 7 principles, which summarize progress and challenges of molecular subtyping: (1) bladder cancer has 3 major molecular subtypes: luminal, basal-squamous, and neuroendocrine; (2) signatures of the tumor microenvironment differ greatly among bladder cancers, particularly among luminal tumors; (3) luminal bladder cancers are biologically diverse, and much of this diversity results from differences in features unrelated to the tumor microenvironment, such as FGFR3 signaling and RB1 inactivation; (4) molecular subtype of bladder cancer associates with tumor stage and histomorphology; (5) many subtyping systems include idiosyncrasies, such as subtypes recognized by no other system; (6) there are broad fuzzy borders between molecular subtypes, and cases that fall on these fuzzy borders are often classified differently by different subtyping systems; and (7) when there are histomorphologically distinct regions within a single tumor, the molecular subtypes of these regions are often discordant. We reviewed several use cases for molecular subtyping, highlighting their promise as clinical biomarkers. Finally, we conclude that data are currently insufficient to support the routine use of molecular subtyping to guide bladder cancer management, an opinion shared with the majority of conference attendees. We also conclude that molecular subtype should not be considered an "intrinsic" property of a tumor but should instead be considered the result of a specific laboratory test, performed using a specific testing platform and classification algorithm, validated for a specific clinical application.
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Affiliation(s)
- Joshua I Warrick
- Penn State College of Medicine, Departments of Pathology and Urology, Hershey, PA
| | - Hikmat Al-Ahmadie
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, NY
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston
| | - Peter C Black
- Department of Urologic Sciences, Univeristy of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas W Flaig
- Department of Medicine-Medical Oncology, University of Colorado School of Medicine, Aurora, CO
| | - Mattias Höglund
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School; Lifespan Academic Medical Center, and the Legorreta Cancer Center at Brown University, Providence, RI
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Conci N, Tassinari E, Tateo V, Rosellini M, Marchetti A, Ricci C, Chessa F, Santoni M, Grande E, Mollica V, Massari F. How Do Molecular Classifications Affect the Neoadjuvant Treatment of Muscle-Invasive Urothelial Carcinoma? Mol Diagn Ther 2024; 28:37-51. [PMID: 37874465 DOI: 10.1007/s40291-023-00679-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/25/2023]
Abstract
Despite the significant improvements in the field of oncological treatments in recent decades, and the advent of targeted therapies and immunotherapy, urothelial carcinoma of the bladder remains a highly heterogeneous and difficult-to-treat neoplasm with a poor prognosis. In this context, owing to the new methods of genomic sequencing, numerous studies have analyzed the genetic features of muscle-invasive bladder cancer, providing a consensus set of molecular classes, to identify malignancies that may respond better to specific treatments (standard chemotherapy, immunotherapy, target therapy, local-regional treatment, or combinations) and improve the survival. The aim of the current review is to provide an overview of the current status of the molecular landscape of muscle-invasive bladder cancer, focusing our attention on therapeutic and prognostic implications in order to select the most effective and tailored therapeutic regimen for the individual patient.
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Affiliation(s)
- Nicole Conci
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Elisa Tassinari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Valentina Tateo
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Matteo Rosellini
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Andrea Marchetti
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Costantino Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
| | - Francesco Chessa
- Division of Urology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Enrique Grande
- Department of Medical Oncology, MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Veronica Mollica
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, Bologna, Italy.
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
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48
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Lee SY, Lee YH, Kim TM, Ha US. Longitudinal Transcription Profiling of Bladder Cancers Dictate the Response to BCG Treatment and Disease Progression. Int J Mol Sci 2023; 25:144. [PMID: 38203315 PMCID: PMC10778820 DOI: 10.3390/ijms25010144] [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: 11/27/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Although the intravesical instillation of Bacillus Calmette-Guerin (BCG) is widely used as adjuvant treatment for nonmuscle-invasive bladder cancers, the clinical benefit is variable across patients, and the molecular mechanisms underlying the sensitivity to BCG administration and disease progression are poorly understood. To establish the molecular signatures that predict the responsiveness and disease progression of bladder cancers treated with BCG, we performed transcriptome sequencing (RNA-seq) for 13 treatment-naïve and 22 post-treatment specimens obtained from 14 bladder cancer patients. To overcome disease heterogeneity, we used non-negative matrix factorization to identify the latent molecular features associated with drug responsiveness and disease progression. At least 12 molecular features were present, among which the immune-related feature was associated with drug responsiveness, indicating that pre-treatment anti-cancer immunity might dictate BCG responsiveness. We also identified disease progression-associated molecular features indicative of elevated cellular proliferation in post-treatment specimens. The progression-associated molecular features were validated in an extended cohort of BCG-treated bladder cancers. Our study advances understanding of the molecular mechanisms of BCG activity in bladder cancers and provides clinically relevant gene markers for evaluating and monitoring patients.
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Affiliation(s)
- Seo-Young Lee
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea;
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea
| | - Yun-Hee Lee
- Department of Urology, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea;
| | - Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea;
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 03083, Republic of Korea
| | - U-Syn Ha
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea
- Department of Urology, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea;
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49
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Kamran SC, Zhou Y, Otani K, Drumm M, Otani Y, Wu S, Wu CL, Feldman AS, Wszolek M, Lee RJ, Saylor PJ, Lennerz J, Van Allen E, Willers H, Hong TS, Liu Y, Davicioni E, Gibb EA, Shipley WU, Mouw KW, Efstathiou JA, Miyamoto DT. Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. Clin Cancer Res 2023; 29:5116-5127. [PMID: 37870965 PMCID: PMC10722135 DOI: 10.1158/1078-0432.ccr-23-0792] [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: 03/15/2023] [Revised: 05/20/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
PURPOSE There is an urgent need for biomarkers of radiation response in organ-sparing therapies. Bladder preservation with trimodality therapy (TMT), consisting of transurethral tumor resection followed by chemoradiation, is an alternative to radical cystectomy for muscle-invasive bladder cancer (MIBC), but molecular determinants of response are poorly understood. EXPERIMENTAL DESIGN We characterized genomic and transcriptomic features correlated with long-term response in a single institution cohort of patients with MIBC homogeneously treated with TMT. Pretreatment tumors from 76 patients with MIBC underwent whole-exome sequencing; 67 underwent matched transcriptomic profiling. Molecular features were correlated with clinical outcomes including modified bladder-intact event-free survival (mBI-EFS), a composite endpoint that reflects long-term cancer control with bladder preservation. RESULTS With a median follow-up of 74.6 months in alive patients, 37 patients had favorable long-term response to TMT while 39 had unfavorable long-term response. Tumor mutational burden was not associated with outcomes after TMT. DNA damage response gene alterations were associated with improved locoregional control and mBI-EFS. Of these alterations, somatic ERCC2 mutations stood out as significantly associated with favorable long-term outcomes; patients with ERCC2 mutations had significantly improved mBI-EFS [HR, 0.15; 95% confidence interval (CI), 0.06-0.37; P = 0.030] and improved BI-EFS, an endpoint that includes all-cause mortality (HR, 0.33; 95% CI, 0.15-0.68; P = 0.044). ERCC2 mutant bladder cancer cell lines were significantly more sensitive to concurrent cisplatin and radiation treatment in vitro than isogenic ERCC2 wild-type cells. CONCLUSIONS Our data identify ERCC2 mutation as a candidate biomarker associated with sensitivity and long-term response to chemoradiation in MIBC. These findings warrant validation in independent cohorts.
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Affiliation(s)
- Sophia C. Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keisuke Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Drumm
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Yukako Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Chin-Lee Wu
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Adam S. Feldman
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Wszolek
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Richard J. Lee
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Philip J. Saylor
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen Lennerz
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Eliezer Van Allen
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Theodore S. Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yang Liu
- Veracyte, San Francisco, California
| | | | | | - William U. Shipley
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kent W. Mouw
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason A. Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - David T. Miyamoto
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts
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50
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Radvanyi F, Real FX, McConkey D. What is a Bladder Cancer Molecular Subtype? - Counterpoint. Bladder Cancer 2023; 9:299-304. [PMID: 38994248 PMCID: PMC11165934 DOI: 10.3233/blc-230059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/09/2023] [Indexed: 07/13/2024]
Abstract
In an accompanying paper, Mattias Höglund discusses on what is a bladder cancer molecular subtype. He emphasizes the need to consider the aim of tumor classification, which is obviously critical to the approach. He also focuses on considering primarily the identity features of the neoplastic cells. Here, we provide a counterpoint. While largely agreeing with his views, we underline that other parameters that may vary in a spatial or temporal scale, and the tumor microenvironment, can also provide relevant information to render tumor classifications clinically useful. Furthermore, tumor heterogeneity and evolution during the disease course - natural or under therapeutic pressure - should be considered.
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Affiliation(s)
- François Radvanyi
- Equipe Oncologie Moléculaire, Equipe Labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Francisco X. Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
- Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - David McConkey
- Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Greenberg Bladder Cancer Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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