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Chen H, Cai Z, Dong X, Chen W, Cao C, Zheng S, Wu J, Zhong D, Cheng S, Gao Y, Shou J. Cigarette smoking-related OLC1 overexpression associated with poor prognosis in bladder urothelial carcinoma. Life Sci 2024; 351:122821. [PMID: 38880167 DOI: 10.1016/j.lfs.2024.122821] [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: 02/26/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
AIMS To explore the clinical significance of OLC1 and cigarette smoking in bladder urothelial carcinoma (UBC). MATERIALS AND METHODS OLC1 mRNA expression was detected in 106 UBC samples by mRNA array or reverse real-time PCR. OLC1 protein expression in 114 UBC samples was detected by immunohistochemical staining. Wild-type C57BL/6J mice were injected with cigarette smoke condensate (n = 12) or exposed to cigarette smoke (n = 6) to investigate the correlations between cigarette smoking and OLC1 expression using mRNA array. KEY FINDINGS The mRNA and protein expression of OLC1 were higher in tumor samples (p < 0.01) and significantly correlated with tumor stage (p < 0.05). OLC1 protein expression and smoking history were correlated with disease-free survival (p < 0.05). OLC1 expression was significantly elevated in smoking patients with higher smoking intensity on both mRNA and protein levels (p < 0.05). Cigarette smoke exposure experiments revealed that OLC1 mRNA overexpressed in bladder uroepithelium of mice. SIGNIFICANCE OLC1 could serve as a potential prognosis biomarker of UBC, especially for smoking patients.
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Affiliation(s)
- Huang Chen
- Department of Pathology, China-Japan Friendship Hospital, 2# Yinghuadongjie, Chaoyang District, Beijing 100029, China
| | - Zhao Cai
- Department of Ultrasound, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Xin Dong
- State Key Laboratory of Molecular Oncology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Wenting Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Chuanzhen Cao
- Department of Urology, China-Japan Friendship Hospital, 2# Yinghuadongjie, Chaoyang District, Beijing, 100029, China
| | - Shan Zheng
- Department of Pathology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Jie Wu
- Department of Urology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, 2# Yinghuadongjie, Chaoyang District, Beijing 100029, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Yanning Gao
- State Key Laboratory of Molecular Oncology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.
| | - Jianzhong Shou
- Department of Urology, National Cancer Center, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.
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2
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Linscott JA, Miyagi H, Murthy PB, Yao S, Grass GD, Vosoughi A, Xu H, Wang X, Yu X, Yu A, Zemp L, Gilbert SM, Poch MA, Sexton WJ, Spiess PE, Li R. From Detection to Cure - Emerging Roles for Urinary Tumor DNA (utDNA) in Bladder Cancer. Curr Oncol Rep 2024:10.1007/s11912-024-01555-0. [PMID: 38837106 DOI: 10.1007/s11912-024-01555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
PURPOSE OF REVIEW This review sought to define the emerging roles of urinary tumor DNA (utDNA) for diagnosis, monitoring, and treatment of bladder cancer. Building from early landmark studies the focus is on recent studies, highlighting how utDNA could aid personalized care. RECENT FINDINGS Recent research underscores the potential for utDNA to be the premiere biomarker in bladder cancer due to the constant interface between urine and tumor. Many studies find utDNA to be more informative than other biomarkers in bladder cancer, especially in early stages of disease. Points of emphasis include superior sensitivity over traditional urine cytology, broad genomic and epigenetic insights, and the potential for non-invasive, real-time analysis of tumor biology. utDNA shows promise for improving all phases of bladder cancer care, paving the way for personalized treatment strategies. Building from current research, future comprehensive clinical trials will validate utDNA's clinical utility, potentially revolutionizing bladder cancer management.
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Affiliation(s)
- Joshua A Linscott
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Hiroko Miyagi
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Prithvi B Murthy
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sijie Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - G Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Aram Vosoughi
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Hongzhi Xu
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alice Yu
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Logan Zemp
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Scott M Gilbert
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael A Poch
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wade J Sexton
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Roger Li
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Okholm TLH, Kamstrup AB, Nielsen MM, Hollensen AK, Graversgaard ML, Sørensen MH, Kristensen LS, Vang S, Park SS, Yeo GW, Dyrskjøt L, Kjems J, Pedersen JS, Damgaard CK. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557527. [PMID: 37745562 PMCID: PMC10515936 DOI: 10.1101/2023.09.14.557527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Specifically, we use temporal depletion of circHIPK3 or specific RNA binding proteins (RBPs) and identify several perturbed genes by RNA sequencing analyses. Using expression-coupled motif analyses of mRNA expression data from various knockdown experiments, we identify an 11-mer motif within circHIPK3, which is also enriched in genes that become downregulated upon circHIPK3 depletion. By mining eCLIP datasets, we find that the 11-mer motif constitutes a strong binding site for IGF2BP2 and validate this circHIPK3-IGF2BP2 interaction experimentally using RNA-immunoprecipitation and competition assays in bladder cancer cell lines. Our results suggest that circHIPK3 and IGF2BP2 mRNA targets compete for binding. Since the identified 11-mer motif found in circHIPK3 is enriched in upregulated genes following IGF2BP2 knockdown, and since IGF2BP2 depletion conversely globally antagonizes the effect of circHIPK3 knockdown on target genes, our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2- STAT3 mRNA binding and thereby STAT3 mRNA levels. However, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Finally, we show that circHIPK3 expression correlates with overall survival of patients with bladder cancer. Our results are consistent with a model where relatively few cellular circHIPK3 molecules function as inducers of IGF2BP2 condensation thereby regulating STAT3 and other key factors for cell proliferation and potentially cancer progression.
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4
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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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5
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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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6
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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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7
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Bilski K, Żeber-Lubecka N, Kulecka M, Dąbrowska M, Bałabas A, Ostrowski J, Dobruch A, Dobruch J. Microbiome Sex-Related Diversity in Non-Muscle-Invasive Urothelial Bladder Cancer. Curr Issues Mol Biol 2024; 46:3595-3609. [PMID: 38666955 PMCID: PMC11048804 DOI: 10.3390/cimb46040225] [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: 03/11/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Sex-specific discrepancies in bladder cancer (BCa) are reported, and new studies imply that microbiome may partially explain the diversity. We aim to provide characterization of the bladder microbiome in both sexes diagnosed with non-muscle-invasive BCa with specific insight into cancer grade. In our study, 16S rRNA next-generation sequencing was performed on midstream urine, bladder tumor sample, and healthy-appearing bladder mucosa. Bacterial DNA was isolated using QIAamp Viral RNA Mini Kit. Metagenomic analysis was performed using hypervariable fragments of the 16S rRNA gene on Ion Torrent Personal Genome Machine platform. Of 41 sample triplets, 2153 taxa were discovered: 1739 in tumor samples, 1801 in healthy-appearing bladder mucosa and 1370 in midstream urine. Women were found to have smaller taxa richness in Chao1 index than men (p = 0.03). In comparison to low-grade tumors, patients with high-grade lesions had lower bacterial diversity and richness in urine. Significant differences between sexes in relative abundance of communities at family level were only observed in high-grade tumors.
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Affiliation(s)
- Konrad Bilski
- Department of Urology, Centre of Postgraduate Medical Education, Independent Public Hospital of Prof. W. Orlowski, 00-416 Warsaw, Poland;
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, 02-781 Warsaw, Poland; (N.Ż.-L.); (M.K.); (J.O.)
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (M.D.); (A.B.)
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, 02-781 Warsaw, Poland; (N.Ż.-L.); (M.K.); (J.O.)
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (M.D.); (A.B.)
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (M.D.); (A.B.)
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (M.D.); (A.B.)
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, 02-781 Warsaw, Poland; (N.Ż.-L.); (M.K.); (J.O.)
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (M.D.); (A.B.)
| | | | - Jakub Dobruch
- Department of Urology, Centre of Postgraduate Medical Education, Independent Public Hospital of Prof. W. Orlowski, 00-416 Warsaw, Poland;
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8
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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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9
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Linscott JA, Meeks JJ, Dyrskjøt L, Li R. The Elusive Horizon: Biomarkers in Urothelial Carcinoma. Eur Urol 2024; 85:317-319. [PMID: 38278663 DOI: 10.1016/j.eururo.2024.01.004] [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: 11/15/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
Urinary tests for circulating tumor DNA have potential for accurate discrimination of bladder cancer from other common inflammatory processes. Efforts are still needed to determine whether these tests can differentiate between cancer and field cancerization and to demonstrate clinical benefit in prospective trials.
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Affiliation(s)
- Joshua A Linscott
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Joshua J Meeks
- Departments of Urology and Biochemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Jesse Brown VAMC, Chicago, IL, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA; Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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10
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Kim SK, Byun YJ, Park SH, Piao XM, Zheng CM, Moon S, Kim K, Song SJ, Kang HW, Kim WT, Lee OJ, Choi YH, Moon SK, Kim WJ, Choi YD, Kim SY, Yun SJ. A 23-Gene Prognostic Index Predicts Progression and Bacillus Calmette-Guérin Response in Non-muscle-invasive Bladder Cancer. Eur Urol 2024; 85:400-402. [PMID: 38216401 DOI: 10.1016/j.eururo.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/11/2023] [Accepted: 01/01/2024] [Indexed: 01/14/2024]
Affiliation(s)
- Seon-Kyu Kim
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bioscience, University of Science and Technology, Daejeon, Republic of Korea; Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Young Joon Byun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Seong-Hwan Park
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Xuan-Mei Piao
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Chuang-Ming Zheng
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Seongmin Moon
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Integrated Medical Science, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Kyeong Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Sun Jin Song
- Department of Integrated Medical Science, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea; Department of Emergency, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Ho Won Kang
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Won Tae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Ok-Jun Lee
- Department of Pathology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Yung Hyun Choi
- Department of Biochemistry, Dong-eui University College of Korean Medicine, Busan, Republic of Korea
| | - Sung-Kwon Moon
- Department of Food and Nutrition, Chung-Ang University, Ansung, Republic of Korea
| | - Wun-Jae Kim
- Institute of Urotech, Cheongju, Republic of Korea
| | - Young Deuk Choi
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seok Joong Yun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Republic of Korea.
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11
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Fan J, Chen B, Luo Q, Li J, Huang Y, Zhu M, Chen Z, Li J, Wang J, Liu L, Wei Q, Cao D. Potential molecular biomarkers for the diagnosis and prognosis of bladder cancer. Biomed Pharmacother 2024; 173:116312. [PMID: 38417288 DOI: 10.1016/j.biopha.2024.116312] [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: 12/18/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/01/2024] Open
Abstract
Bladder cancer (BC) is a common malignant tumor of urinary system, which can be divided into muscle-invasive BC (MIBC) and nonmuscle-invasive BC (NMIBC). The number of BC patients has been gradually increasing currently. At present, bladder tumours are diagnosed and followed-up using a combination of cystoscopic examination, cytology and histology. However, the detection of early grade tumors, which is much easier to treat effectively than advanced stage disease, is still insufficient. It frequently recurs and can progress when not expeditiously diagnosed and monitored following initial therapy for NMIBC. Treatment strategies are totally different for different stage diseases. Therefore, it is of great practical significance to study new biomarkers for diagnosis and prognosis. In this review, we summarize the current state of biomarker development in BC diagnosis and prognosis prediction. We retrospectively analyse eight diagnostic biomarkers and eight prognostic biomarkers, in which CK, P53, PPARγ, PTEN and ncRNA are emphasized for discussion. Eight molecular subtype systems are also identified. Clinical translation of biomarkers for diagnosis, prognosis, monitoring and treatment will hopefully improve outcomes for patients. These potential biomarkers provide an opportunity to diagnose tumors earlier and with greater accuracy, and help identify those patients most at risk of disease recurrence.
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Affiliation(s)
- Junping Fan
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Bo Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Qiuping Luo
- Out-patient Department, West China Hospital, Sichuan University, Chengdu, China
| | - Jinze Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Yin Huang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Mengli Zhu
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, China
| | - Zeyu Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Jin Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China; West China School of Medicine, Sichuan University, Chengdu, China
| | - Jia Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Liangren Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
| | - Dehong Cao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.
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12
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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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13
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Ikuma S, Akatsuka J, Takeda H, Endo Y, Kiriyama T, Hamasaki T, Kimura G, Kondo Y. Determining the clinicopathological significance of the VI-RADS ≧4 group: a retrospective study. BMC Urol 2024; 24:63. [PMID: 38509503 PMCID: PMC10953073 DOI: 10.1186/s12894-024-01452-5] [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: 03/29/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The Vesical Imaging Reporting and Data System (VI-RADS) is widely used for predicting muscle-invasive bladder cancer (MIBC). This study aimed to determine the clinicopathological significance of the VI-RADS ≧4 (VI≧4) group. METHODS Patients who underwent transurethral resections of bladder tumors during the study period and preoperative magnetic resonance imaging were considered. The patients were pathologically diagnosed with urothelial carcinoma (UC). We first compared the results of patients with VI-RADS scores of 3 and 4 to determine the cut-off score for MIBC; thereafter, the patients were divided into the VI≧4 and VI-RADS ≦3 (VI≦3) groups using VI-RADS. The clinicopathological significance of the VI≧4 group was examined retrospectively by comparing the characteristics of each group. RESULTS In total, 121 cases were examined, of which 28 were pathologically diagnosed with MIBC. Of the 28 MIBC cases, three (10.7%) had a VI-RADS score of ≦3, and 25 (89.3%) had a VI-RADS score of ≧4. Of the 93 NMIBC cases, 86 (92.5%) had a VI-RADS score of ≦3, and seven (7.5%) had a VI-RADS score of ≧4. The diagnostic performance of the VI-RADS with a cut-off score of 4 was 89.3% for sensitivity, 92.5% for specificity, and an area under the curve (AUC) of 0.91. Contrastingly, for a cut-off score of 3, the sensitivity was 89.3%, specificity was 62.0%, and AUC was 0.72. A VI-RADS score of ≥ 4 could predict MIBC. In the VI≧4 group, 30 of 32 (93.8%) patients had high-grade tumors. The VI≧4 group had significantly more high-grade bladder cancers than the VI≦3 group (p < 0.001 OR = 31.77 95%CI:8.47-1119.07). In addition, the VI≧4 group had more tumor necrosis (VI≧4 vs VI≦3, p < 0.001 OR = 7.46 95%CI:2.61-21.34) and more UC variant cases (VI≧4 vs VI≦3, p = 0.034 OR = 3.28 95%CI:1.05-10.25) than the VI≦3 group. CONCLUSIONS This study suggests that VI-RADS has a high diagnostic performance in predicting MIBC and that VI-RADS could diagnose high-grade tumors, necrosis, and UC variants.
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Affiliation(s)
- Shunsuke Ikuma
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Jun Akatsuka
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Hayato Takeda
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Yuki Endo
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Tomonari Kiriyama
- Department of Radiology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Tsutomu Hamasaki
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Go Kimura
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan
| | - Yukihiro Kondo
- Department of Urology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan.
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14
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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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15
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Anurag M, Strandgaard T, Kim SH, Dou Y, Comperat E, Al-Ahmadie H, Inman BA, Taber A, Nordentoft I, Jensen JB, Dyrskjøt L, Lerner SP. Multiomics profiling of urothelial carcinoma in situ reveals CIS-specific gene signature and immune characteristics. iScience 2024; 27:109179. [PMID: 38439961 PMCID: PMC10910238 DOI: 10.1016/j.isci.2024.109179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/20/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors, and normal urothelium showed lower immune marker expression in CIS compared to papillary tumors. We identified a 46-gene expression signature in CIS samples including selectively upregulated known druggable targets MTOR, TYK2, AXIN1, CPT1B, GAK, and PIEZO1 and selectively downregulated BRD2 and NDUFB2. High expression of selected genes was significantly associated with CIS in an independent dataset. Mutation analysis of matched CIS and papillary tumors revealed shared mutations between samples across time points and mutational heterogeneity. CCDC138 was the most frequently mutated gene in CIS. The immunological landscape showed higher levels of PD-1-positive cells in CIS lesions compared to papillary tumors. We identified CIS lesions to have distinct characteristics compared to papillary tumors potentially contributing to the aggressive phenotype.
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Affiliation(s)
- Meenakshi Anurag
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center and Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Trine Strandgaard
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Sung Han Kim
- Scott Department of Urology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Urology, Urological Cancer Center, National Cancer Center, Goayng, Gyeonggi, Rep. Korea
| | - Yongchao Dou
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center and Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Eva Comperat
- Department of Pathology, Medical University Vienna, Vienna General Hospital, 1090 Wien, Austria
| | - Hikmat Al-Ahmadie
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brant A. Inman
- Department of Urologic Oncology, Western University, London, ON, USA
| | - Ann Taber
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Seth P. Lerner
- Scott Department of Urology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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Toren P, Wilkins A, Patel K, Burley A, Gris T, Kockelbergh R, Lodhi T, Choudhury A, Bryan RT. The sex gap in bladder cancer survival - a missing link in bladder cancer care? Nat Rev Urol 2024; 21:181-192. [PMID: 37604983 DOI: 10.1038/s41585-023-00806-2] [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: 07/17/2023] [Indexed: 08/23/2023]
Abstract
The differences in bladder cancer outcomes between the sexes has again been highlighted. Uncommon among cancers, bladder cancer outcomes are notably worse for women than for men. Furthermore, bladder cancer is three to four times more common among men than among women. Factors that might explain these sex differences include understanding the importance of haematuria as a symptom of bladder cancer by both clinicians and patients, the resultant delays in diagnosis and referral of women with haematuria, and health-care access. Notably, these factors seem to have geographical variation and are not consistent across all health-care systems. Likewise, data relating to sex-specific treatment responses for patients with non-muscle-invasive or muscle-invasive bladder cancer are inconsistent. The influence of differences in the microbiome, bladder wall thickness and urine dwell times remain to be elucidated. The interplay of hormone signalling, gene expression, immunology and the tumour microenvironment remains complex but probably underpins the sexual dimorphism in disease incidence and stage and histology at presentation. The contribution of these biological phenomena to sex-specific outcome differences is probable, albeit potentially treatment-specific, and further understanding is required. Notwithstanding these aspects, we identify opportunities to harness biological differences to improve treatment outcomes, as well as areas of fundamental and translational research to pursue. At the level of policy and health-care delivery, improvements can be made across the domains of patient awareness, clinician education, referral pathways and guideline-based care. Together, we aim to highlight opportunities to close the sex gap in bladder cancer outcomes.
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Affiliation(s)
- Paul Toren
- CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Anna Wilkins
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospitals NHS Trust, London, UK
| | - Keval Patel
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Amy Burley
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Typhaine Gris
- CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Roger Kockelbergh
- University Hospitals of Leicester NHS Trust, Leicester, UK
- Action Bladder Cancer UK, Tetbury, UK
| | - Taha Lodhi
- Division of Cancer Sciences, University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Richard T Bryan
- Action Bladder Cancer UK, Tetbury, UK.
- Bladder Cancer Research Centre, Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK.
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17
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Haas M, Engelmann SU, Mayr R, Gossler C, Pickl C, Kälble S, Yang Y, Otto W, Hartmann V, Burger M, Hartmann A, Breyer J, Eckstein M. A novel grading approach predicts worse outcomes in stage pT1 non-muscle-invasive bladder cancer. BJU Int 2024. [PMID: 38409965 DOI: 10.1111/bju.16298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
OBJECTIVE To develop a prognostically relevant scoring system for stage pT1 non-muscle-invasive bladder cancer (NMIBC) incorporating tumour budding, growth pattern and invasion pattern because the World Health Organisation grading system shows limited prognostic value in such patients. PATIENTS AND METHODS The tissue specimens and clinical data of 113 patients with stage pT1 NMIBC who underwent transurethral resection of bladder tumour were retrospectively investigated. Tumour budding, and growth and invasion patterns were evaluated and categorised into two grade groups (GGs). GGs and other clinical and histopathological variables were investigated regarding recurrence-free survival (RFS), progression-free survival (PFS), cancer-specific survival (CSS) and overall survival (OS) using univariable and multivariable Cox regression analyses. RESULTS The integration of two tumour budding groups, two growth patterns, and two invasion patterns yielded an unfavourable GG (n = 28; 24.7%) that had a high impact on oncological outcomes. The unfavourable GG was identified as an independent RFS and OS predictor (P = 0.004 and P = 0.046, respectively) and linked to worse PFS (P = 0.001) and CSS (P = 0.001), irrespective of the European Association of Urology risk group. The unfavourable GG was associated with higher rates of BCG-unresponsive tumours (P = 0.006). Study limitations include the retrospective, single-centre design, diverse therapies and small cohort. CONCLUSIONS We present a morphology-based grading system for stage pT1 NMIBC that correlates with disease aggressiveness and oncological patient outcomes. It therefore identifies a highest risk group of stage pT1 NMIBC patients, who should be followed up more intensively or receive immediate radical cystectomy. The grading incorporates objective variables assessable on haematoxylin and eosin slides and immunohistochemistry, enabling an easy-to-use low-cost approach that is applicable in daily routine. Further studies are needed to validate and confirm these results.
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Affiliation(s)
- Maximilian Haas
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Simon U Engelmann
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Roman Mayr
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Christopher Gossler
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Christoph Pickl
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Sebastian Kälble
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Yushan Yang
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Wolfgang Otto
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Valerie Hartmann
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Maximilian Burger
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Johannes Breyer
- Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Markus Eckstein
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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18
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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 2024:10.1038/s41585-023-00847-7. [PMID: 38321289 DOI: 10.1038/s41585-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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19
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Kim SW, Yu H, Kim Y, Nam KH, Chae HK, Nam W, Eom DW, Park JY, Kim SJ. HER2 overexpression predicts pathological T2 stage and improved survival in de novo muscle-invasive bladder cancer after immediate radical cystectomy: a retrospective cohort study. Int J Surg 2024; 110:847-858. [PMID: 37916931 PMCID: PMC10871625 DOI: 10.1097/js9.0000000000000859] [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: 07/27/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
INTRODUCTION Human epidermal growth factor receptor type 2 (HER2) overexpression is a prognostic factor and a therapeutic target for breast cancer; however, anti-HER2 therapies are ineffective in patients with bladder cancer. The authors investigated the effect of HER2 overexpression (HER2 + ) on the prognosis of muscle-invasive bladder cancer (MIBC). MATERIALS AND METHODS This retrospective cohort study included patients who underwent initial transurethral resection of bladder tumors between 2005 and 2013 and were registered in the Korea National Health Insurance Database, which provides data on overall survival (OS). Sixty-one patients with clinically nonmetastatic de novo MIBC were included in this study. As a subgroup, 33 patients who underwent immediate radical cystectomy (RC) were analyzed. Univariate and multivariate Cox proportional hazards models were used to identify prognostic factors for survival. A multivariable binary logistic regression model was used to identify the favorable T stage. RESULTS Among the 61 patients with d-MIBC, 14 were HER2 + and 47 HER2 - . Age less than 70 years [hazard ratio (HR): 0.312, CI: 0.16-0.59, P <0.001] and HER2 + status (HR: 0.40, CI: 0.19-0.85, P =0.02) were favorable prognostic factors for OS after adjusting for clinical variables. In the RC subgroup, HER2 + status was a significant predictive factor for the pT2 stage (HR): 36.8, CI: 4.83-797.41, P <0.01). Age less than 70 years (HR: 0.15, CI: 0.05-0.42, P <0.001) and HER2 + status (HR: 0.11, CI: 0.02-0.54, P =0.01) were favorable prognostic factors for OS after adjusting for RC pathological variables. CONCLUSIONS HER2 + status could be a marker for an indolent subset of MIBC and could predict favorable survival regardless of RC status. Moreover, HER2 + status not only consistently predicted a favorable T stage after RC, but also predicted better survival than pathological outcomes.
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Affiliation(s)
- So Won Kim
- Department of Pharmacology
- Bio-Medical Institute of Technology, University of Ulsan, Seoul
| | - Hoon Yu
- Bio-Medical Institute of Technology, University of Ulsan, Seoul
- Department of Nephrology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Younjuong Kim
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine
| | - Kyeng Hyun Nam
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine
| | | | | | | | | | - Sung Jin Kim
- Bio-Medical Institute of Technology, University of Ulsan, Seoul
- Department of Urology
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20
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Viergever BJ, Raats DAE, Geurts V, Mullenders J, Jonges TN, van der Heijden MS, van Es JH, Kranenburg O, Meijer RP. Urine-derived bladder cancer organoids (urinoids) as a tool for cancer longitudinal response monitoring and therapy adaptation. Br J Cancer 2024; 130:369-379. [PMID: 38102228 PMCID: PMC10844626 DOI: 10.1038/s41416-023-02494-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Bladder cancer is one of the most common cancer types worldwide. Generally, research relies on invasive sampling strategies. METHODS Here, we generate bladder cancer organoids directly from urine (urinoids). In this project, we establish 12 urinoid lines from 22 patients with non-muscle and muscle-invasive bladder tumours, with an efficiency of 55%. RESULTS The histopathological features of the urinoids accurately resemble those of the original bladder tumours. Genetically, there is a high concordance of single nucleotide polymorphisms (92.56%) and insertions & deletions (91.54%) between urinoids and original tumours from patient 4. Furthermore, these urinoids show sensitivity to bladder cancer drugs, similar to their tissue-derived organoid counterparts. Genetic analysis of longitudinally generated tumoroids and urinoids from one patient receiving systemic immunotherapy, identify alterations that may guide the choice for second-line therapy. Successful treatment adaptation was subsequently demonstrated in the urinoid setting. CONCLUSION Therefore, urinoids can advance precision medicine in bladder cancer as a non-invasive platform for tumour pathogenesis, longitudinal drug-response monitoring, and therapy adaptation.
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Affiliation(s)
- Bastiaan J Viergever
- Laboratory Translational Oncology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Department of Oncological Urology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
| | - Daniëlle A E Raats
- Laboratory Translational Oncology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Utrecht Platform for Organoid Technology, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Veerle Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Jasper Mullenders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Trudy N Jonges
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | | | - Johan H van Es
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Onno Kranenburg
- Laboratory Translational Oncology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Utrecht Platform for Organoid Technology, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Richard P Meijer
- Laboratory Translational Oncology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands.
- Department of Oncological Urology, Division of Imaging and Oncology, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands.
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21
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Lobo N, Duan Z, Sood A, Tan WS, Grajales V, Contieri R, Lindskrog SV, Dyrskjøt L, Zhao H, Giordano SH, Williams SB, Bree KK, Kamat AM. Association of Age with Non-muscle-invasive Bladder Cancer: Unearthing a Biological Basis for Epidemiological Disparities? Eur Urol Oncol 2024:S2588-9311(24)00036-1. [PMID: 38302322 DOI: 10.1016/j.euo.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/04/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Age disparity in patients with non-muscle-invasive bladder cancer (NMIBC) exists. Whether this is due to differences in adequate cancer care or tumour biology is unclear. OBJECTIVE To investigate age disparities in NMIBC using the Surveillance, Epidemiology, and End Results (SEER)-Medicare and UROMOL datasets. DESIGN, SETTING, AND PARTICIPANTS The SEER-Medicare data were used to identify patients with clinical stage Ta, Tis, and T1 NMIBC between 2005 and 2017 (n = 32 225). Using the UROMOL cohort (n = 834), age disparities across transcriptomic, genomic, and spatial proteomic domains were assessed. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS For the SEER-Medicare data, multivariable competing-risk regression was used to examine the association between age and recurrence, progression, and bladder cancer-specific mortality (BCSM). For the UROMOL cohort, multivariable general linear model and multinomial logistic regression were performed to evaluate the association between age and tumour biology. RESULTS AND LIMITATIONS An analysis of the SEER-Medicare cohort revealed 5-yr recurrence rates of 55.2%, 57.4%, and 58.9%; 5-yr progression rates of 25.6%, 29.2%, and 36.9%; and 5-yr BCSM rates of 3.9%, 5.8%, and 11.8% in patients aged 66-70, 71-80, and ≥81 yr, respectively. After multivariable adjustment, age ≥81 yr was associated with a higher risk of recurrence (hazard ratio [HR] 1.07, 95% confidence interval [CI] 1.03-1.12; p = 0.001), progression (HR 1.32, p < 0.001), and BCSM (HR 2.58, p < 0.001). UROMOL2021 transcriptomic class 2a was most frequently observed in patients with advanced age (34.0% in ≥76 yr vs 21.6% in ≤65 yr; p = 0.004), a finding confirmed on multivariable analysis (risk ratio [RR] 3.86, p = 0.002). UROMOL2021 genomic class 3 was observed more frequently in patients aged ≥76 yr (4.9% vs 24.2%; p = 0.001). Limitations include the definitions used for recurrence and progression, which may lead to under- or overestimation of true rates. CONCLUSIONS Among SEER-Medicare patients with NMIBC, advanced age is associated with inferior oncological outcomes. These results reflect age-related molecular biological differences observed across transcriptomic and genomic domains, providing further evidence that innate tumour biology contributes to observed disparities in NMIBC outcomes. PATIENT SUMMARY Older patients with non-muscle-invasive bladder cancer have worse oncological outcomes than younger patients. Some of this age disparity may be due to differences in tumour biology.
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Affiliation(s)
- Niyati Lobo
- Department of Urology, Royal Free London NHS Trust, London, UK; Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhigang Duan
- Department of Health Services Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akshay Sood
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Shen Tan
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Valentina Grajales
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roberto Contieri
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sia V Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Hui Zhao
- Department of Health Services Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon H Giordano
- Department of Health Services Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen B Williams
- Department of Urology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kelly K Bree
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish M Kamat
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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22
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Kvikstad V, Lillesand M, Gudlaugsson E, Mangrud OM, Rewcastle E, Skaland I, Baak JPA, Janssen EAM. Proliferation and immunohistochemistry for p53, CD25 and CK20 in predicting prognosis of non-muscle invasive papillary urothelial carcinomas. PLoS One 2024; 19:e0297141. [PMID: 38277354 PMCID: PMC10817121 DOI: 10.1371/journal.pone.0297141] [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: 05/12/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024] Open
Abstract
Non-muscle invasive papillary urothelial carcinoma is a prevalent disease with a high recurrence tendency. Good prognostic and reproducible biomarkers for tumor recurrence and disease progression are lacking. Currently, WHO grade and tumor stage are essential in risk stratification and treatment decision-making. Here we present the prognostic value of proliferation markers (Ki67, mitotic activity index (MAI) and PPH3) together with p53, CD25 and CK20 immunohistochemistry (IHC). In this population-based retrospective study, 349 primary non-muscle invasive bladder cancers (NMIBC) were available. MAI and PPH3 were calculated manually according to highly standardized previously described methods, Ki-67 by the semi-automated QPRODIT quantification system, p53 and CD25 by the fully automated digital image analysis program Visipharm® and CK20 with the help of the semi-quantitative immunoreactive score (IRS). Survival analyses with log rank test, as well as univariate and multivariate Cox regression analyses were performed for all investigated variables. Age and multifocality were the only significant variables for tumor recurrence. All investigated variables, except gender, were significantly associated with stage progression. In multivariate analysis, MAI was the only prognostic variable for stage progression (p<0.001).
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Affiliation(s)
- Vebjørn Kvikstad
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Melinda Lillesand
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Einar Gudlaugsson
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | | | - Emma Rewcastle
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Ivar Skaland
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | - Jan P. A. Baak
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Dr. Med. Jan Baak AS, Tananger, Norway
| | - Emiel A. M. Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
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23
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Kim K, Byun YJ, Zheng CM, Moon S, Jo SJ, Kang HW, Kim WT, Choi YH, Moon SK, Kim WJ, Piao XM, Yun SJ. COL6A1 expression as a potential prognostic biomarker for risk stratification of T1 high grade bladder cancer: Unveiling the aggressive nature of a distinct non-muscle invasive subtype. Investig Clin Urol 2024; 65:94-103. [PMID: 38197756 PMCID: PMC10789541 DOI: 10.4111/icu.20230227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 01/11/2024] Open
Abstract
PURPOSE T1 high grade (T1HG) bladder cancer (BC) is a type of non-muscle invasive BC (NMIBC) that is recognized as an aggressive subtype with a heightened propensity for progression. Current risk stratification methods for NMIBC rely on clinicopathological indicators; however, these approaches do not adequately capture the aggressive nature of T1HG BC. Thus, new, more accurate biomarkers for T1HG risk stratification are needed. Here, we enrolled three different patient cohorts and investigated expression of collagen type VI alpha 1 (COL6A1), a key component of the extracellular matrix, at different stages and grades of BC, with a specific focus on T1HG BC. MATERIALS AND METHODS Samples from 298 BC patients were subjected to RNA sequencing and real-time polymerase chain reaction. RESULTS We found that T1HG BC and muscle invasive BC (MIBC) exhibited comparable expression of COL6A1, which was significantly higher than that by other NMIBC subtypes. In particular, T1HG patients who later progressed to MIBC had considerably higher expression of COL6A1 than Ta, T1 low grade patients, and patients that did not progress, highlighting the aggressive nature and higher risk of progression associated with T1HG BC. Moreover, Cox and Kaplan-Meier survival analyses revealed a significant association between elevated expression of COL6A1 and poor progression-free survival of T1HG BC patients (multivariate Cox hazard ratio, 16.812; 95% confidence interval, 3.283-86.095; p=0.001 and p=0.0002 [log-rank test]). CONCLUSIONS These findings suggest that COL6A1 may be a promising biomarker for risk stratification of T1HG BC, offering valuable insight into disease prognosis and guidance of personalized treatment decisions.
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Affiliation(s)
- Kyeong Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Young Joon Byun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Chuang-Ming Zheng
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Sungmin Moon
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
- Department of Convergence of Medical Science, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Soo Jeong Jo
- Department of Convergence of Medical Science, Chungbuk National University College of Medicine, Cheongju, Korea
- Department of Rehabilitation Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Ho Won Kang
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Won Tae Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dong-Eui University, Busan, Korea
| | - Sung-Kwon Moon
- Department of Food Science and Technology, Chung-Ang University, Ansung, Korea
| | | | - Xuan-Mei Piao
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea.
| | - Seok Joong Yun
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea.
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24
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Ramal M, Corral S, Kalisz M, Lapi E, Real FX. The urothelial gene regulatory network: understanding biology to improve bladder cancer management. Oncogene 2024; 43:1-21. [PMID: 37996699 DOI: 10.1038/s41388-023-02876-3] [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: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
The urothelium is a stratified epithelium composed of basal cells, one or more layers of intermediate cells, and an upper layer of differentiated umbrella cells. Most bladder cancers (BLCA) are urothelial carcinomas. Loss of urothelial lineage fidelity results in altered differentiation, highlighted by the taxonomic classification into basal and luminal tumors. There is a need to better understand the urothelial transcriptional networks. To systematically identify transcription factors (TFs) relevant for urothelial identity, we defined highly expressed TFs in normal human bladder using RNA-Seq data and inferred their genomic binding using ATAC-Seq data. To focus on epithelial TFs, we analyzed RNA-Seq data from patient-derived organoids recapitulating features of basal/luminal tumors. We classified TFs as "luminal-enriched", "basal-enriched" or "common" according to expression in organoids. We validated our classification by differential gene expression analysis in Luminal Papillary vs. Basal/Squamous tumors. Genomic analyses revealed well-known TFs associated with luminal (e.g., PPARG, GATA3, FOXA1) and basal (e.g., TP63, TFAP2) phenotypes and novel candidates to play a role in urothelial differentiation or BLCA (e.g., MECOM, TBX3). We also identified TF families (e.g., KLFs, AP1, circadian clock, sex hormone receptors) for which there is suggestive evidence of their involvement in urothelial differentiation and/or BLCA. Genomic alterations in these TFs are associated with BLCA. We uncover a TF network involved in urothelial cell identity and BLCA. We identify novel candidate TFs involved in differentiation and cancer that provide opportunities for a better understanding of the underlying biology and therapeutic intervention.
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Affiliation(s)
- Maria Ramal
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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25
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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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26
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Nam W, Chae HK, Jung Y, Kang H, Park M, Choi A, Park JY, Eom DW, Kim SJ. HER2 positivity predicts BCG unresponsiveness and adaptive immune cell exhaustion in EORTC risk-stratified cohort of bladder cancer. Front Immunol 2023; 14:1301510. [PMID: 38143745 PMCID: PMC10748406 DOI: 10.3389/fimmu.2023.1301510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Predicting the response to Bacillus Calmette-Guérin (BCG) therapy in high-risk patients with non-muscle invasive bladder cancer (NMIBC) is crucial, as failure may necessitate interventions, such as radical cystectomy or salvage therapy. With the recent classification of genetic class 2a (which has HER2 protein abundance as its signature mutation of ERBB2), evaluating its prognostic role and relationship with BCG response could yield important results. Methods This retrospective study included 160 patients with NMIBC who underwent transurethral resection of bladder tumors at Gangneung Asan Hospital between 2000 and 2013 and were stratified based on the European Organization for Research and Treatment of Cancer (EORTC) risk criteria. In addition, we analyzed a subset of 67 patients who had received BCG induction therapy to identify factors predictive of BCG treatment response. Univariate and multivariate analyses were used to assess the impact of clinicopathological factors, HER2 positivity, and EORTC risk on recurrence, progression, survival, and BCG response. Each variable's prognostic significance was determined using the Kaplan-Meier analysis. The tumor microenvironments (TMEs) were evaluated in relation to HER2 and EORTC risk. Results Patients with HER2+ had a higher median age, a greater prevalence of high-grade tumors, and more frequent recurrences. The univariate analysis demonstrated that the HER2+, intermediate (vs. low-risk) high (vs. low-risk), and EORTC recurrence risk groups were significantly associated with recurrence. In patients treated with BCG, only the HER2+ status predicted recurrence. In the univariate analysis for progression, age, high EORTC progression risk (vs. low-to-intermediate), HER2+, and programmed death-ligand 1 positive (PD-L1+) were significant factors. In multivariate analyses for progression, age, high EORTC progression risk, and PD-L1+ were significant factors for progression. HER2 expression was associated with the TME, influencing the proportion of PD-L1+ cells, as well as other markers of PD-1, CD8, and Ki67. Conclusion The HER2+ status may be related to genetic characteristics that appear more frequently in older age, which suggests a potential for predicting the recurrence and response to BCG treatment. Additionally, analyzing TME trends of aggressive adaptive immune response characterized by HER2 expression provides insight into recurrence and BCG response mechanisms.
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Affiliation(s)
- Wook Nam
- Department of Urology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Han Kyu Chae
- Department of Urology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Yeonuk Jung
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Homin Kang
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Myungchan Park
- Department of Urology, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Ahnryul Choi
- Department of Biomedical Engineering, College of Medical Convergence, Catholic Kwandong University, Gangneung, Republic of Korea
| | - Jong Yeon Park
- Department of Urology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Dae-Woon Eom
- Department of Pathology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Sung Jin Kim
- Department of Urology, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
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Shi X, Peng X, Chen Y, Shi Z, Yue C, Zuo L, Zhang L, Gao S. Overexpression of MTHFD2 represents an inflamed tumor microenvironment and precisely predicts the molecular subtype and immunotherapy response of bladder cancer. Front Immunol 2023; 14:1326509. [PMID: 38130721 PMCID: PMC10733511 DOI: 10.3389/fimmu.2023.1326509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), whose aberrant expression is common in cancers, has recently been identified as a potential regulator of immune response. However, its immune-related role in bladder cancer (BLCA) and its association with immunotherapy efficacy remain unclear. Methods RNA sequencing data from The Cancer Genome Atlas (TCGA) was applied to analyze the immunological roles and prognostic value of MTHFD2 in pan-cancers. The association of MTHFD2 with several immunological features of tumor microenvironment (TME), including cancer-immunity cycle, immune cells infiltration, immune checkpoints expression, and T cell inflamed score was analyzed in TCGA-BLCA cohort. The predictors of cancer treatments effectiveness, including the expression and mutation of certain genes, molecular subtypes, and several signatures were evaluated as well. These results were validated by another independent cohort (GSE48075). Finally, the predictive value of MTHFD2 for TME and immunotherapy efficacy were validated using immunohistochemistry assay and RNA sequencing data from IMvigor210 cohort, respectively. Results MTHFD2 was found to be positively associated with several immunological features of an inflamed tumor microenvironment (TME) in various cancers and could predict BLCA patients' prognosis. In BLCA, high expression of MTHFD2 was observed to be positively related with the cancer-immunity cycle, the infiltration of several immune cells, and the expression of immunoregulators and T-cell inflamed scores, indicating a positive correlation with the inflamed TME. Moreover, patients with high MTHFD2 expression were more likely to be basal-like subtypes and respond to BLCA treatments, including immunotherapy, chemotherapy, and target therapy. The clinical data of the IMvigor210 cohort confirmed the higher response rates and better survival benefits of immunotherapy in high-MTHFD2-expression patients. Conclusion Collectively, high MTHFD2 predicts an inflamed TME, a basal-like subtype, and a better response to various therapeutic strategies, especially the ICB therapy, in bladder cancer.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Zebin 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
| | - Chuang Yue
- 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
| | - Lifeng 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
| | - 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
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Liu G, Zhang T, Gui D, Liu Q. Clinical significance and immune landscape of angiogenesis-related genes in bladder cancer. Aging (Albany NY) 2023; 15:13118-13133. [PMID: 37988196 DOI: 10.18632/aging.205222] [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: 05/06/2023] [Accepted: 10/17/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Angiogenesis is a major promotor of tumor progression and metastasis. Nevertheless, it is undetermined how angiogenesis-related genes (ARGs) influence bladder cancer. METHODS The profiles of bladder cancer gene expression were collected from the TCGA-BLCA cohort. The LASSO regression analysis was used to build an angiogenesis-related signature (ARG_score) with the prognostic ARGs. Verification analyses were conducted across the GSE48075 dataset to demonstrate the robustness of the signature. Differences between the two risk groups based on clinical outcomes, immune landscape, mutation status, chemotherapeutic effectiveness for anticancer drugs, and immunotherapy efficacy were analyzed. A nomogram was developed to improve the clinical efficacy of this predictive tool. The expression levels of model genes in normal bladder epithelial cell lines (SV-HUC-1) and bladder cancer cell lines (T24 and 5637) were detected by qRT-PCR assay. RESULTS Four angiogenesis-associated gene signature was constructed based on the LASSO regression algorithm. The signature showed independent risk factors of overall survival for bladder cancer, validated using two external survival datasets. Additionally, we built a prognostic nomogram to improve the practicality of the ARG_score. High-risk individuals showed stronger immunocyte infiltration, immune-related functions, elevated expression of immune checkpoints, reduced TIDE score, and higher combined IPS-PD-1 and IPS-CTLA4 scores, suggesting a heightened responsiveness to immune checkpoint inhibitors. Furthermore, patients with low and high risk showed distinct responsiveness to anticancer drugs. The expression levels of 5 model genes (COL5A2, JAG1, MSX1, OLR1, and STC) were significantly increased in bladder cancer cell lines (T24 and 5637) compared with the normal bladder epithelial cell line SV-HUC-1. CONCLUSIONS The model constructed based on ARGs may have wide application in predicting outcomes and therapeutic responses.
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Affiliation(s)
- Gang Liu
- Department of Urology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Tingting Zhang
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Dingwen Gui
- Department of Urology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
| | - Qin Liu
- Department of Breast Surgery, Thyroid Surgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People’s Republic of China
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Dyrskjøt L, Hansel DE, Efstathiou JA, Knowles MA, Galsky MD, Teoh J, Theodorescu D. Bladder cancer. Nat Rev Dis Primers 2023; 9:58. [PMID: 37884563 DOI: 10.1038/s41572-023-00468-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Bladder cancer is a global health issue with sex differences in incidence and prognosis. Bladder cancer has distinct molecular subtypes with multiple pathogenic pathways depending on whether the disease is non-muscle invasive or muscle invasive. The mutational burden is higher in muscle-invasive than in non-muscle-invasive disease. Commonly mutated genes include TERT, FGFR3, TP53, PIK3CA, STAG2 and genes involved in chromatin modification. Subtyping of both forms of bladder cancer is likely to change considerably with the advent of single-cell analysis methods. Early detection signifies a better disease prognosis; thus, minimally invasive diagnostic options are needed to improve patient outcomes. Urine-based tests are available for disease diagnosis and surveillance, and analysis of blood-based cell-free DNA is a promising tool for the detection of minimal residual disease and metastatic relapse. Transurethral resection is the cornerstone treatment for non-muscle-invasive bladder cancer and intravesical therapy can further improve oncological outcomes. For muscle-invasive bladder cancer, radical cystectomy with neoadjuvant chemotherapy is the standard of care with evidence supporting trimodality therapy. Immune-checkpoint inhibitors have demonstrated benefit in non-muscle-invasive, muscle-invasive and metastatic bladder cancer. Effective management requires a multidisciplinary approach that considers patient characteristics and molecular disease characteristics.
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Affiliation(s)
- Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Donna E Hansel
- Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremy Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Yu SH, Kim SS, Lee H, Kim S, Kang TW. Somatic Mutation of the Non-Muscle-Invasive Bladder Cancer Associated with Early Recurrence. Diagnostics (Basel) 2023; 13:3201. [PMID: 37892022 PMCID: PMC10606398 DOI: 10.3390/diagnostics13203201] [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: 08/23/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Next-generation sequencing (NGS) is widely used in muscle-invasive bladder cancer but has limited use in non-muscle-invasive bladder cancer (NMIBC) due to significant heterogeneity and high cancer-specific survival. Therefore, we evaluated the genomic information of NMIBC and identified molecular alterations associated with tumour recurrence. A total of 43 patients with NMIBC who underwent transurethral resection of the bladder were enrolled. We performed NGS using an Oncomine panel of tumour specimens and blood samples corresponding to each specimen. The somatic mutation results were analysed by pairwise comparison and logistic regression according to the recurrence of bladder tumours within 1 year. The median incidence of genetic variations in 43 tumour samples was 56 variations per sample, and a high tumour mutation burden (TMB) was associated with tumour recurrence (median variation 33 vs. 64, p = 0.023). The most mutated gene was adipose tissue macrophages (ATM) (79%), followed by neurofibromatosis-1 (NF1) (79%), and neurogenic locus notch homolog protein 1 (NOTCH1) (79%). In multivariable analysis, mutation of epidermal growth factor receptor (EGFR) (odds ratio [OR], 9.95; 95% confidence interval [CI], 1.40-70.96; p = 0.022) and telomerase reverse transcriptase (TERT) (OR, 7.92; 95% CI, 1.22-51.51; p = 0.030) were significant factors associated with the recurrence of bladder tumour within 1 year. Our results revealed that high TMB, EGFR mutation, and TERT mutation had a significant association with tumour recurrence in NMIBC. In addition, somatic mutations in EGFR and TERT could be useful prognostic biomarkers in NMIBC.
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Affiliation(s)
- Seong Hyeon Yu
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Sung Sun Kim
- Department of Pathology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Hyungki Lee
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (H.L.); (S.K.)
| | - Shinseung Kim
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (H.L.); (S.K.)
| | - Taek Won Kang
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
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Rani B, Ignatz-Hoover JJ, Rana PS, Driscoll JJ. Current and Emerging Strategies to Treat Urothelial Carcinoma. Cancers (Basel) 2023; 15:4886. [PMID: 37835580 PMCID: PMC10571746 DOI: 10.3390/cancers15194886] [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: 07/29/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Urothelial cell carcinoma (UCC, bladder cancer, BC) remains a difficult-to-treat malignancy with a rising incidence worldwide. In the U.S., UCC is the sixth most incident neoplasm and ~90% of diagnoses are made in those >55 years of age; it is ~four times more commonly observed in men than women. The most important risk factor for developing BC is tobacco smoking, which accounts for ~50% of cases, followed by occupational exposure to aromatic amines and ionizing radiation. The standard of care for advanced UCC includes platinum-based chemotherapy and programmed cell death (PD-1) or programmed cell death ligand 1 (PD-L1) inhibitors, administered as frontline, second-line, or maintenance therapy. UCC remains generally incurable and is associated with intrinsic and acquired drug and immune resistance. UCC is lethal in the metastatic state and characterized by genomic instability, high PD-L1 expression, DNA damage-response mutations, and a high tumor mutational burden. Although immune checkpoint inhibitors (ICIs) achieve long-term durable responses in other cancers, their ability to achieve similar results with metastatic UCC (mUCC) is not as well-defined. Here, we discuss therapies to improve UCC management and how comprehensive tumor profiling can identify actionable biomarkers and eventually fulfill the promise of precision medicine for UCC patients.
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Affiliation(s)
- Berkha Rani
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.R.); (J.J.I.-H.); (P.S.R.)
| | - James J. Ignatz-Hoover
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.R.); (J.J.I.-H.); (P.S.R.)
- Division of Hematology & Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Adult Hematologic Malignancies & Stem Cell Transplant Section, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Priyanka S. Rana
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.R.); (J.J.I.-H.); (P.S.R.)
- Division of Hematology & Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Adult Hematologic Malignancies & Stem Cell Transplant Section, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - James J. Driscoll
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.R.); (J.J.I.-H.); (P.S.R.)
- Division of Hematology & Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Adult Hematologic Malignancies & Stem Cell Transplant Section, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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32
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Rao N, Starrett GJ, Piaskowski ML, Butler KE, Golubeva Y, Yan W, Lawrence SM, Dean M, Garcia-Closas M, Baris D, Johnson A, Schwenn M, Malats N, Real FX, Kogevinas M, Rothman N, Silverman DT, Dyrskjøt L, Buck CB, Koutros S, Prokunina-Olsson L. Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection. Cancer Prev Res (Phila) 2023; 16:561-570. [PMID: 37477495 PMCID: PMC10592262 DOI: 10.1158/1940-6207.capr-23-0112] [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: 03/30/2023] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
FGFR3 and PIK3CA are among the most frequently mutated genes in bladder tumors. We hypothesized that recurrent mutations in these genes might be caused by common carcinogenic exposures such as smoking and other factors. We analyzed 2,816 bladder tumors with available data on FGFR3 and/or PIK3CA mutations, focusing on the most recurrent mutations detected in ≥10% of tumors. Compared to tumors with other FGFR3/PIK3CA mutations, FGFR3-Y375C was more common in tumors from smokers than never-smokers (P = 0.009), while several APOBEC-type driver mutations were enriched in never-smokers: FGFR3-S249C (P = 0.013) and PIK3CA-E542K/PIK3CA-E545K (P = 0.009). To explore possible causes of these APOBEC-type mutations, we analyzed RNA sequencing (RNA-seq) data from 798 bladder tumors and detected several viruses, with BK polyomavirus (BKPyV) being the most common. We then performed IHC staining for polyomavirus (PyV) Large T-antigen (LTAg) in an independent set of 211 bladder tumors. Overall, by RNA-seq or IHC-LTAg, we detected PyV in 26 out of 1,010 bladder tumors with significantly higher detection (P = 4.4 × 10-5), 25 of 554 (4.5%) in non-muscle-invasive bladder cancers (NMIBC) versus 1 of 456 (0.2%) of muscle-invasive bladder cancers (MIBC). In the NMIBC subset, the FGFR3/PIK3CA APOBEC-type driver mutations were detected in 94.7% (18/19) of PyV-positive versus 68.3% (259/379) of PyV-negative tumors (P = 0.011). BKPyV tumor positivity in the NMIBC subset with FGFR3- or PIK3CA-mutated tumors was also associated with a higher risk of progression to MIBC (P = 0.019). In conclusion, our results support smoking and BKPyV infection as risk factors contributing to bladder tumorigenesis in the general patient population through distinct molecular mechanisms. PREVENTION RELEVANCE Tobacco smoking likely causes one of the most common mutations in bladder tumors (FGFR3-Y375C), while viral infections might contribute to three others (FGFR3-S249C, PIK3CA-E542K, and PIK3CA-E545K). Understanding the causes of these mutations may lead to new prevention and treatment strategies, such as viral screening and vaccination.
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Affiliation(s)
- Nina Rao
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mary L Piaskowski
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kelly E Butler
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yelena Golubeva
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Scott M Lawrence
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Francisco X Real
- CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
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Qin Y, Zu X, Li Y, Han Y, Tan J, Cai C, Shen E, Liu P, Deng G, Feng Z, Wu W, Peng Y, Liu Y, Ma J, Zeng S, Chen Y, Shen H. A cancer-associated fibroblast subtypes-based signature enables the evaluation of immunotherapy response and prognosis in bladder cancer. iScience 2023; 26:107722. [PMID: 37694141 PMCID: PMC10485638 DOI: 10.1016/j.isci.2023.107722] [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: 11/28/2022] [Revised: 01/28/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Bladder cancer (BLCA) is one of the most prevalent and heterogeneous urinary malignant tumors. Previous researches have reported a significant association between cancer-associated fibroblasts (CAFs) and poor prognosis of tumor patients. However, uncertainty surrounds the role of CAFs in the BLCA tumor microenvironment, necessitating further investigation into the CAFs-related gene signatures in BLCA. In this study, we identified three CAF subtypes in BLCA according to single-cell RNA-seq data and constructed CAFs-related risk score (CRRS) by screening 102,714 signatures. The survival analysis, ROC curves, and nomogram suggested that CRRS was a valuable predictor in 2,042 patients from 9 available public datasets and Xiangya real-world cohort. We further revealed the significant correlation between CRRS and clinicopathological characteristics, genome alterations, and epithelial-mesenchymal transition (EMT). A high CRRS indicated a non-inflamed phenotype and a lower remission rate of immunotherapy in BLCA. In conclusion, the CRRS had the potential to predict the prognosis and immunotherapy response of BLCA patients.
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Affiliation(s)
- Yiming Qin
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiongbing Zu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Edward Shen
- Department of Life Science, McMaster University, Hamilton L8S 4L8, ON, Canada
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ganlu Deng
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530022, Guangxi, China
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yongting Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jiayao Ma
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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Heishima K, Sugito N, Abe C, Hirata A, Sakai H, Akao Y. Targeting microRNA-145-mediated progressive phenotypes of early bladder cancer in a molecularly defined in vivo model. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:960-982. [PMID: 37727442 PMCID: PMC10505924 DOI: 10.1016/j.omtn.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/09/2023] [Indexed: 09/21/2023]
Abstract
A progressive subclass of early-stage non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progress into invasive carcinoma, thus decreasing the overall survival rate of NMIBC. However, therapeutic development for progressive NMIBC has been challenging due to the lack of molecularly validated in vivo models and agents targeting its genetic vulnerability. We herein molecularly characterized an interventional model of progressive NMIBC and revealed the principal functions and therapeutic potential of microRNA-145 (miR-145) in early bladder tumorigenesis. N-butyl-N-(4-hydroxybutyl)nitrosamine-induced premalignant lesions (BiPLs) in rats exhibited downregulated expression of miR-145 as well as highly similar mutation/expression profiles to those of the human progressive NMIBC subclass with the worst prognosis. The expression patterns of miR-145 inversely correlated with those of BC-related oncogenes in BiPLs. We also demonstrated that miR-145 dominantly regulated interferon pathways and c-Myc expression, which play a crucial role in the pathogenesis of progressive NMIBC. Furthermore, we demonstrated that miR-145 replacement with a novel miR-145-based intravesical agent (miR-145S1) significantly inhibited the progression of BiPLs in vivo. These results provide insights into the essential role of miR-145 as the earliest-acting oncogenic driver of bladder tumorigenesis as well as a validated interventional model and novel miR-145-based nucleic acid therapeutic agent for progressive NMIBC.
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Affiliation(s)
- Kazuki Heishima
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
- Institute for Advanced Study (GUiAS), Gifu University, Gifu, Gifu, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
| | - Nobuhiko Sugito
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
| | - Chikara Abe
- Department of Physiology, Gifu University Graduate School of Medicine, Gifu, Gifu, Japan
| | - Akihiro Hirata
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Hiroki Sakai
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Yukihiro Akao
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
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Schwarzova L, Varchulova Novakova Z, Danisovic L, Ziaran S. Molecular classification of urothelial bladder carcinoma. Mol Biol Rep 2023; 50:7867-7877. [PMID: 37525073 PMCID: PMC10460735 DOI: 10.1007/s11033-023-08689-7] [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: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Urothelial bladder carcinoma (UC) ranks among the top ten most commonly diagnosed cancers worldwide on an annual basis. The standardized classification system for urothelial bladder tumors is the Tumor, Node, Metastasis classification, which reflects differences between non-muscle-invasive bladder carcinoma (NMIBC) and muscle-invasive bladder carcinoma (MIBC) and it depends on the extent to which tumor has infiltrated the bladder wall and other tissues and organs. NMIBC and MIBC exhibit great intrinsic heterogeneity regarding different prognoses, survival, progression, and treatment outcomes. In recent years, studies based on mRNA expression profiling revealed the existence of biologically relevant molecular subtypes of UC, which show variant molecular features that can provide more precise stratification of UC patients. Here, we present a complex classification of UC based on mRNA expression studies and molecular subtypes of NMIBC and MIBC in detail with regard to different mRNA expression profiles, mutational signatures, and infiltration by non-tumor cells. The possible impact of molecular subtyping on treatment decisions and patients' outcomes is outlined, too.
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Affiliation(s)
- Lucia Schwarzova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Zuzana Varchulova Novakova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
| | - Stanislav Ziaran
- Department of Urology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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Rasmussen A, Okholm T, Knudsen M, Vang S, Dyrskjøt L, Hansen T, Pedersen J. Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR Cancer 2023; 5:zcad041. [PMID: 37554968 PMCID: PMC10405568 DOI: 10.1093/narcan/zcad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.
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Affiliation(s)
- Asta M Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
| | - Trine Line H Okholm
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Michael Knudsen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Søren Vang
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus 8000, Denmark
| | - Jakob S Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
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Albarakati N, Al-Ghamdi H, Al-Sowayan B, Alshareeda A. Homologous recombination mRNAs (RAD21, RAD50 and BARD1) have a potentially poor prognostic role in ERBB2-low bladder cancer patients. Sci Rep 2023; 13:11738. [PMID: 37474724 PMCID: PMC10359419 DOI: 10.1038/s41598-023-38923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2/ERBB2) factor is known to be implicated in many malignancies and the potential of it as a prognostic biomarker was reported years ago. Molecular subtypes of HER2/ERBB2 negative and positive with distinct clinical outcomes have been identified in recent years; however, it is still under investigation for bladder cancer. This study evaluates the biological and prognostic significance of RAD21, RAD50 and BARD1 (homologous recombination biomarkers) mRNA levels with ERBB2 low and high expression to explore their impact on bladder cancer patient survival and cancer aggressiveness. The expression of ERBB2, RAD21, RAD50 and BARD1 mRNA levels was assessed in The Cancer Genome Atlas (TCGA) bladder cancer dataset along with four validation cohorts. Outcome analysis was evaluated using disease-free survival (DFS) and overall survival (OS). Univariate and multivariate analysis were used to evaluate the relationship between RAD21, RAD50, BARD1 and ERBB2 expression and clinicopathological variables. A significant increase in mRNA expression levels of RAD21, RAD50 and BARD1 was noticed in ERBB2-low patients compared to ERBB2-high patients. This overexpression of the homologous recombination repair transcripts was associated with poor outcome in ERBB2-low tumors, not in ERBB2-high tumors. Furthermore, the combined expression of high RAD21/RAD50, high RAD21/BARD1 or high RAD50/BARD1 were significantly associated with worse DFS and a better outcome for those with low co-expression in the ERBB2-low cohort. High expression of either RAD21/RAD50 or RAD21/BARD1 in ERBB2-low cohort associated with higher chance of metastasis. In addition, gene expression of BARD1 alone or in combination with RAD50 acted as an independent prognostic factor for worst survival. The data presented in this study reveal a connection between RAD21, RAD50, BARD1 and ERBB2 and patient survival. Importantly, it provided novel findings and potential prognostic markers, particularly in ERBB2-low bladder cancer.
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Affiliation(s)
- Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia.
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia.
| | - Hanin Al-Ghamdi
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Batla Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
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Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 2023; 619:624-631. [PMID: 37344596 PMCID: PMC10975863 DOI: 10.1038/s41586-023-06234-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10-40% of bladder cancers1-6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR-Cas9. Y-positive (Y+) and Y-negative (Y-) tumours grew similarly in vitro, whereas Y- tumours were more aggressive than Y+ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y- tumours promote striking dysfunction or exhaustion of CD8+ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y+ tumours, Y- tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.
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Affiliation(s)
- Hany A Abdel-Hafiz
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johanna M Schafer
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
- Roche Diagnostics Solutions, Oro Valley, AZ, USA
| | - Xingyu Chen
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cedars-Sinai Cancer Center, Los Angeles, CA, USA.
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Zhang M, Zhu J, Zhang P, Li L, Min M, Li T, He W. Development and validation of cancer-associated fibroblasts-related gene landscape in prognosis and immune microenvironment of bladder cancer. Front Oncol 2023; 13:1174252. [PMID: 37397364 PMCID: PMC10309557 DOI: 10.3389/fonc.2023.1174252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Backgrounds Bladder cancer (BLCA) is one of the most prevalent cancers of the genitourinary system, the clinical outcomes of patients with BLCA are bad, and the morbidity rate is high. One of the key components of the tumor microenvironment (TME) is cancer-associated fibroblasts (CAFs) which are critically involved in BLCA tumorigenesis. Previous studies have shown the involvement of CAFs in tumor growth, cancer progression, immune evasion, angiogenesis, and chemoresistance in several cancers such as breast, colon, pancreatic, ovarian, and prostate cancers. However, only a few studies have shown the role of CAFs in the occurrence and development of BLCA. Methods We have retrieved and merged the data on RNA-sequencing of patients with BLCA from databases including "the Cancer Genome Atlas" and "Gene Expression Omnibus." Next, we compared the differences in CAFs-related genes (CRGs) expression between normal and BLCA tissues. Based on CRGs expression, we randomly divided patients into two groups. Next, we determined the correlation between CAFs subtypes and differentially expressed CRGs (DECRGs) between the two subtypes. Furthermore, the "Gene Ontology" and "Kyoto Encyclopedia of Genes and Genomes pathway" enrichment analyses were conducted to determine the functional characteristics between the DECRGs and clinicopathology. Results We identified five genes (POF1B, ARMCX1, ALDOC, C19orf33, and KRT13) using multivariate COX regression and "Least Absolute Shrinkage and Selection Operator (LASSO) COX regression analysis" for developing a prognostic model and calculating the CRGs-risk score. The TME, mutation, CSC index, and drug sensitivity were also analyzed. Conclusion We constructed a novel five- CRGs prognostic model, which sheds light on the roles of CAFs in BLCA.
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Affiliation(s)
- Meng Zhang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Urology, The Third Hospital of Mianyang, Sichuan Mental Health Center, Mianyang, China
| | - Junlong Zhu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pan Zhang
- Department of Urology, The Third Hospital of Mianyang, Sichuan Mental Health Center, Mianyang, China
| | - Lingxun Li
- Department of Urology, The Third Hospital of Mianyang, Sichuan Mental Health Center, Mianyang, China
| | - Min Min
- Department of Urology, The Third Hospital of Mianyang, Sichuan Mental Health Center, Mianyang, China
| | - Tinghao Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyang He
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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40
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Seiler R, Egger M, De Menna M, Wehrli S, Minoli M, Radić M, Lyatoshinsky P, Hösli R, Blarer J, Abt D, Kruithof-de Julio M. Guidance of adjuvant instillation in intermediate-risk non-muscle invasive bladder cancer by drug screens in patient derived organoids: a single center, open-label, phase II trial. BMC Urol 2023; 23:89. [PMID: 37170307 PMCID: PMC10176900 DOI: 10.1186/s12894-023-01262-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND In intermediate-risk non-muscle invasive bladder cancer (NMIBC) clinical guidelines suggest an adjuvant instillation with a chemotherapeutic agent. However, the agent and regimen are not clearly defined. Worldwide, less than 15% of patients receive this adjuvant chemotherapeutic instillation. We recently developed a pipeline for the generation of patient derived organoids (PDO) in NMIBC. In this phase II trial, we aim to use our in vitro pipeline to select the most effective drug for chemotherapeutic instillation in NMIBC patients. METHODS Patients with first diagnosis of intermediate-risk NMIBC that are directed to transurethral resection of bladder tumor (TURBT) are enrolled. During TURBT, tumor is sampled, and specimens are directed to generate PDO. Once the PDO are formed, drug screens on them for Epirubicin, Mitomycin C, Gemcitabine and Docetaxel are performed. The drug with the highest antitumor activity in vitro will then be selected for 6 adjuvant intravesical instillations once weekly. Thereafter, patients are followed according to clinical guidelines by cystoscopy. DISCUSSION The aim of this trial is to use drug screens in PDO to precise treatment selection for adjuvant instillation therapies in patients with intermediate-risk NMIBC. The ultimate goal of this trial is to reduce the risk of cancer recurrence. In the future, we aim to conduct clinical multicenter trials with an increased sample size, a broader panel of compounds and a focus on the reduction of cancer recurrence by precision delivery of care. Trial registration NCT05024734.
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Affiliation(s)
- Roland Seiler
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland.
- Department for BioMedical Research, Translational Organoid Resource Core, University of Bern, Bern, Switzerland.
| | - Martin Egger
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland
| | - Marta De Menna
- Department for BioMedical Research, Translational Organoid Resource Core, University of Bern, Bern, Switzerland
| | - Saskia Wehrli
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland
| | - Martina Minoli
- Department for BioMedical Research, Translational Organoid Resource Core, University of Bern, Bern, Switzerland
| | - Martina Radić
- Department for BioMedical Research, Translational Organoid Resource Core, University of Bern, Bern, Switzerland
| | - Pavel Lyatoshinsky
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland
- Department of Urology, St. Gallen Cantonal Hospital, St. Gallen, Switzerland
| | - Raphael Hösli
- Department of Pharmacy, Hospital Center Biel, Biel, Switzerland
| | - Jennifer Blarer
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland
| | - Dominik Abt
- Department of Urology, Hospital Center Biel, Spitalzentrum Biel, Vogelsang 84, 2501, Biel, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, Translational Organoid Resource Core, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
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41
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Yuan H, Xiu Y, Liu T, Fan Y, Xu D. The cuproptosis-associated 11 gene signature as a predictor for outcomes and response to Bacillus Calmette-Guerin and immune checkpoint inhibitor therapies in bladder carcinoma. Front Immunol 2023; 14:1126247. [PMID: 37207200 PMCID: PMC10189141 DOI: 10.3389/fimmu.2023.1126247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
Bladder cancer (BC) or carcinoma (BLCA) is predominantly derived from urothelium and includes non-muscle invasive BC (NMIBC) and muscle invasive BC (MIBC). Bacillus Calmette-Guerin (BCG) has long been applied for NMIBC to effectively reduce disease recurrence or progression, whereas immune checkpoint inhibitors (ICIs) were recently introduced to treat advanced BLCA with good efficacy. For BCG and ICI applications, reliable biomarkers are required to stratify potential responders for better personalized interventions, and ideally, they can replace or reduce invasive examinations such as cystoscopy in monitoring treatment efficacy. Here we developed the cuproptosis-associated 11 gene signature (CuAGS-11) model to accurately predict survival and response to BCG and ICI regimens in BLCA patients. In both discovery and validation cohorts where BLCA patients were divided into high- and low-risk groups based on a median CuAGS-11 score as the cutoff, the high-risk group was associated with significantly shortened overall survival (OS) and progression-free survival (PFS) independently. The survival predictive accuracy was comparable between CuAGS-11 and stage, and their combination-based nomograms showed high consistence between predicted and observed OS/PFS. The analysis of 3 BLCA cohorts treated with BCG unveiled lower response rates and higher frequencies of recurrence or progression coupled with shorter survival in CuAGS-11 high-risk groups. In contrast, almost none of patients underwent progression in low-risk groups. In IMvigor210 cohort of 298 BLCA patients treated with ICI Atezolizumab, complete/partial remissions were 3-fold higher accompanied by significantly longer OS in the CuAGS-11 low- than high-risk groups (P = 7.018E-06). Very similar results were obtained from the validation cohort (P = 8.65E-05). Further analyses of Tumor Immune Dysfunction and Exclusion (TIDE) scores revealed that CuAGS-11 high-risk groups displayed robustly higher T cell exclusion scores in both discovery (P = 1.96E-05) and validation (P = 0.008) cohorts. Collectively, the CuAGS-11 score model is a useful predictor for OS/PFS and BCG/ICI efficacy in BLCA patients. For BCG-treated patients, reduced invasive examinations are suggested for monitoring the CuAGS-11 low-risk patients. The present findings thus provide a framework to improve BLCA patient stratification for personalized interventions and to reduce invasive monitoring inspections.
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Affiliation(s)
- Huiyang Yuan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Yuchen Xiu
- Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Tiantian Liu
- Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden
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Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. [PMID: 37024582 PMCID: PMC10181943 DOI: 10.1038/s41588-023-01355-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.
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Affiliation(s)
- Arvind Ravi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Monica B Arniella
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Mark Holton
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme for Research in South Africa, Durban, South Africa
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aaron T Griffin
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie I Vokes
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Mustafa Sakhi
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Vashine Kamesan
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Patrick M Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Don L Gibbons
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Vamsidhar Velcheti
- Department of Hematology and Oncology, NYU Langone Health, New York, NY, USA
| | - Subba R Digumarthy
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, New York, NY, USA
| | - John V Heymach
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Roy S Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Julie R Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt A Schalper
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Victor E Velculescu
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian S Henick
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrew Chow
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marta Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice T Shaw
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA.
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Castaneda PR, Theodorescu D, Rosser CJ, Ahdoot M. Identifying novel biomarkers associated with bladder cancer treatment outcomes. Front Oncol 2023; 13:1114203. [PMID: 37064102 PMCID: PMC10090444 DOI: 10.3389/fonc.2023.1114203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
Bladder cancer is a complex disease with variable prognosis. Recent investigations into the molecular landscape of bladder cancer have revealed frequent genetic alterations and molecular subtypes with therapeutic implications. Consequently, a shift toward personalized treatment of bladder cancer is underway. To this end, several biomarkers have been developed and tested in their ability to predict response to treatment in patients with bladder cancer and potentially help direct therapy. We performed a search of recently published PubMed articles using terms "biomarker," "bladder cancer," and the respective treatment discussed (i.e., "neoadjuvant" or "BCG"). In this review, we summarize the latest studies on novel biomarkers in bladder cancer with a focus on those intended to improve risk stratification and treatment selection.
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Affiliation(s)
- Peris R. Castaneda
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, United States
| | - Charles J. Rosser
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, United States
| | - Michael Ahdoot
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [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: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
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Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Zhu J, Xu X, Jiang M, Yang F, Mei Y, Zhang X. Comprehensive characterization of ferroptosis in hepatocellular carcinoma revealing the association with prognosis and tumor immune microenvironment. Front Oncol 2023; 13:1145380. [PMID: 37051544 PMCID: PMC10083400 DOI: 10.3389/fonc.2023.1145380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BackgroundFerroptosis is a type of regulatory cell death (RCD) mode that depends on iron-mediated oxidative damage. It has the potential to improve the efficacy of tumor immunotherapy by modulating the tumor microenvironment (TME). Currently, immunotherapy has significantly improved the overall treatment strategy for advanced hepatocellular carcinoma (HCC), but the distinct immune microenvironment and high tolerance to the immune make massive differences in the immunotherapy effect of HCC patients. As a result, it is imperative to classify HCC patients who may benefit from immune checkpoint therapy. Simultaneously, the predictive value of ferroptosis in HCC and its potential role in TME immune cell infiltration also need to be further clarified.MethodsThree ferroptosis molecular models were built on the basis of mRNA expression profiles of ferroptosis-related genes (FRGs), with notable variations in immunocyte infiltration, biological function, and survival prediction. In order to further investigate the predictive impact of immunotherapy response in HCC patients, the ferroptosis score was constructed using the principal component analysis (PCA) algorithm to quantify the ferroptosis molecular models of individual tumors.ResultsIn HCC, there were three totally different ferroptosis molecular models. The ferroptosis score can be used to assess genetic variation, immunotherapy response, TME characteristics, and prognosis. Notably, tumors with low ferroptosis scores have extensive tumor mutations and immune exhaustion, which are associated with a poor prognosis and enhanced immunotherapy response.ConclusionsOur study indicates that ferroptosis plays an indispensable role in the regulation of the tumor immune microenvironment. For HCC, the ferroptosis score is an independent prognostic indicator. Assessing the molecular model of ferroptosis in individual tumors will assist us in better understanding the characteristics of TME, predicting the effect of immunotherapy in HCC patients, and thus guiding a more reasonable immunotherapy program.
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Affiliation(s)
- Jingjuan Zhu
- Cancer Precision Medical Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiao Xu
- Cancer Precision Medical Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Man Jiang
- Cancer Precision Medical Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fangfang Yang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yingying Mei
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiaochun Zhang
- Cancer Precision Medical Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- *Correspondence: Xiaochun Zhang,
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Jiang L, Sun G, Zou L, Guan Y, Hang Y, Liu Y, Zhou Z, Zhang X, Huang X, Pan H, Rong S, Ma H. Noncoding RNAs as a potential biomarker for the prognosis of bladder cancer: a systematic review and meta-analysis. Expert Rev Mol Diagn 2023; 23:325-334. [PMID: 36970945 DOI: 10.1080/14737159.2023.2195554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
OBJECTIVE The relationship between noncoding RNAs and the prognosis of bladder cancer (BC) is still controversial. The purpose of this study is to evaluate the relationship between noncoding RNAs and prognosis by meta-analysis. METHODS Comprehensive retrieval of PubMed, Embase, the Cochrane Library, the Web of Science, CNKI, and WanFang databases is related to the correlation between noncoding RNAs and the prognosis of BC. Data were extracted, and the literature quality was evaluated. STATA16.0 served for the meta-analysis. RESULTS 1. CircRNAs: High circ-ZFR expression led to poor overall survival (OS) of BC. 2. LncRNAs: Low lnc-GAS5 expression predicted poor OS of BC, high lnc-TUG1 expression predicted poor OS of BC. 3. MiRNAs: High miR-21 expression predicted poor OS of BC, high miR-222 expression led to poor OS of BC, high miR-155 expression predicted poor progression-free survival (PFS) of BC, high miR-143 expression caused poor PFS of BC, low miR-214 expression could result in poor recurrence-free survival (RFS) of BC. CONCLUSIONS High circ-ZFR, lnc-TUG1, miR-222, and miR-21 expressions were correlated with poor OS of BC; high miR-155 and miR-143 expression predicted poor PFS of BC; low lnc-GAS5 expression predicted poor OS of BC; low miR-214 expression predicted poor RFS of BC.
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Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F. Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks. Oncogene 2023; 42:1524-1542. [PMID: 36944729 PMCID: PMC10162941 DOI: 10.1038/s41388-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2, respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.
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Affiliation(s)
- Hélène Neyret-Kahn
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France.
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France.
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France.
| | - Jacqueline Fontugne
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Xiang Yu Meng
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- College of Basic Medical Sciences, Medical School, Hubei Minzu University, Enshi, 445000, China
| | - Clarice S Groeneveld
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Université de Paris, Centre de Recherche des Cordeliers, Paris, France
| | - Luc Cabel
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg,1 rue Laurent Fries, 67404, Illkirch, France
| | - Elodie Guyon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Clémentine Krucker
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Florent Dufour
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Elodie Chapeaublanc
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Audrey Rapinat
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Laura Tanguy
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Victoria Dixon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Yann Neuzillet
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - Thierry Lebret
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - David Gentien
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genétique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, 67404, Illkirch Cedex, France
| | - Yves Allory
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Isabelle Bernard-Pierrot
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - François Radvanyi
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
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Omar M, Dinalankara W, Mulder L, Coady T, Zanettini C, Imada EL, Younes L, Geman D, Marchionni L. Using biological constraints to improve prediction in precision oncology. iScience 2023; 26:106108. [PMID: 36852282 PMCID: PMC9958363 DOI: 10.1016/j.isci.2023.106108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 12/20/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Many gene signatures have been developed by applying machine learning (ML) on omics profiles, however, their clinical utility is often hindered by limited interpretability and unstable performance. Here, we show the importance of embedding prior biological knowledge in the decision rules yielded by ML approaches to build robust classifiers. We tested this by applying different ML algorithms on gene expression data to predict three difficult cancer phenotypes: bladder cancer progression to muscle-invasive disease, response to neoadjuvant chemotherapy in triple-negative breast cancer, and prostate cancer metastatic progression. We developed two sets of classifiers: mechanistic, by restricting the training to features capturing specific biological mechanisms; and agnostic, in which the training did not use any a priori biological information. Mechanistic models had a similar or better testing performance than their agnostic counterparts, with enhanced interpretability. Our findings support the use of biological constraints to develop robust gene signatures with high translational potential.
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Affiliation(s)
- Mohamed Omar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wikum Dinalankara
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lotte Mulder
- Technical University Delft, 2628 CD Delft, the Netherlands
| | - Tendai Coady
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Eddie Luidy Imada
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Laurent Younes
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Donald Geman
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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Wang X, Bai Y, Zhang F, Li D, Chen K, Wu R, Tang Y, Wei X, Han P. Prognostic value of COL10A1 and its correlation with tumor-infiltrating immune cells in urothelial bladder cancer: A comprehensive study based on bioinformatics and clinical analysis validation. Front Immunol 2023; 14:955949. [PMID: 37006317 PMCID: PMC10063846 DOI: 10.3389/fimmu.2023.955949] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/22/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionBladder cancer (BLCA) is one of the most lethal diseases. COL10A1 is secreted small-chain collagen in the extracellular matrix associated with various tumors, including gastric, colon, breast, and lung cancer. However, the role of COL10A1 in BLCA remains unclear. This is the first research focusing on the prognostic value of COL10A1 in BLCA. In this research, we aimed to uncover the association between COL10A1 and the prognosis, as well as other clinicopathological parameters in BLCA.MethodsWe obtained gene expression profiles of BLCA and normal tissues from the TCGA, GEO, and ArrayExpress databases. Immunohistochemistry staining was performed to investigate the protein expression and prognostic value of COL10A1 in BLCA patients. GO and KEGG enrichment along with GSEA analyses were performed to reveal the biological functions and potential regulatory mechanisms of COL10A1 based on the gene co-expression network. We used the “maftools” R package to display the mutation profiles between the high and low COL10A1 groups. GIPIA2, TIMER, and CIBERSORT algorithms were utilized to explore the effect of COL10A1 on the tumor immune microenvironment.ResultsWe found that COL10A1 was upregulated in the BLCA samples, and increased COL10A1 expression was related to poor overall survival. Functional annotation of 200 co-expressed genes positively correlated with COL10A1 expression, including GO, KEGG, and GSEA enrichment analyses, indicated that COL10A1 was basically involved in the extracellular matrix, protein modification, molecular binding, ECM-receptor interaction, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling pathway. The most commonly mutated genes of BLCA were different between high and low COL10A1 groups. Tumor immune infiltrating analyses showed that COL10A1 might have an essential role in recruiting infiltrating immune cells and regulating immunity in BLCA, thus affecting prognosis. Finally, external datasets and biospecimens were used, and the results further validated the aberrant expression of COL10A1 in BLCA samples.ConclusionsIn conclusion, our study demonstrates that COL10A1 is an underlying prognostic and predictive biomarker in BLCA.
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Semeniuk-Wojtaś A, Poddębniak-Strama K, Modzelewska M, Baryła M, Dziąg-Dudek E, Syryło T, Górnicka B, Jakieła A, Stec R. Tumour microenvironment as a predictive factor for immunotherapy in non-muscle-invasive bladder cancer. Cancer Immunol Immunother 2023:10.1007/s00262-023-03376-9. [PMID: 36928373 DOI: 10.1007/s00262-023-03376-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/09/2023] [Indexed: 03/18/2023]
Abstract
Bladder cancer (BC) can be divided into two subgroups depending on invasion of the muscular layer: non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC). Its aggressiveness is associated, inter alia, with genetic aberrations like losses of 1p, 6q, 9p, 9q and 13q; gain of 5p; or alterations in the p53 and p16 pathways. Moreover, there are reported metabolic disturbances connected with poor diagnosis-for example, enhanced aerobic glycolysis, gluconeogenesis or haem catabolism.Currently, the primary way of treatment method is transurethral resection of the bladder tumour (TURBT) with adjuvant Bacillus Calmette-Guérin (BCG) therapy for NMIBC or radical cystectomy for MIBC combined with chemotherapy or immunotherapy. However, intravesical BCG immunotherapy and immune checkpoint inhibitors are not efficient in every case, so appropriate biomarkers are needed in order to select the proper treatment options. It seems that the success of immunotherapy depends mainly on the tumour microenvironment (TME), which reflects the molecular disturbances in the tumour. TME consists of specific conditions like hypoxia or local acidosis and different populations of immune cells including tumour-infiltrating lymphocytes, natural killer cells, neutrophils and B lymphocytes, which are responsible for shaping the response against tumour neoantigens and crucial pathways like the PD-L1/PD-1 axis.In this review, we summarise holistically the impact of the immune system, genetic alterations and metabolic changes that are key factors in immunotherapy success. These findings should enable better understanding of the TME complexity in case of NMIBC and causes of failures of current therapies.
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Affiliation(s)
| | | | | | | | | | - Tomasz Syryło
- Department of General, Active and Oncological Urology, Military Institute of Medicine, Warsaw, Poland
| | - Barbara Górnicka
- Pathomorphology Department, Medical University of Warsaw, Warsaw, Poland
| | - Anna Jakieła
- Oncology Department, 4 Military Clinical Hospital with a Polyclinic, Wroclaw, Poland
| | - Rafał Stec
- Oncology Department, Medical University of Warsaw, Warsaw, Poland
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