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Grausenburger R, Herek P, Shariat SF, Englinger B. Recent contributions of single-cell and spatial profiling to the understanding of bladder cancer. Curr Opin Urol 2024; 34:236-243. [PMID: 38650456 PMCID: PMC11155276 DOI: 10.1097/mou.0000000000001183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
PURPOSE OF REVIEW Current risk stratification and treatment decision-making for bladder cancer informed by histopathology as well as molecular diagnostics face limitations. This review summarizes recent advancements in single-cell and spatial omics methodologies for understanding bladder cancer biology and their potential impact on development of novel therapeutic strategies. RECENT FINDINGS Single-cell RNA sequencing and spatial omics techniques offer unprecedented insights into various aspects of tumor microenvironment (TME), bladder cancer heterogeneity, cancer stemness, and cellular plasticity. Studies have identified multiple malignant cell subpopulations within tumors, revealing diverse transcriptional states and clonal evolution. Additionally, intratumor heterogeneity has been linked to tumor progression and therapeutic response. Immune cell composition analysis has revealed immunosuppressive features in the TME, impacting treatment response. Furthermore, studies have elucidated the role of cancer-associated fibroblasts and endothelial cells in shaping the tumor immune landscape and response to therapy. SUMMARY Single-cell and spatial omics technologies have revolutionized our understanding of bladder cancer biology, uncovering previously unseen complexities. These methodologies provide valuable insights into tumor heterogeneity and microenvironmental interactions, with implications for therapeutic development. However, challenges remain in translating research findings into clinical practice and implementing personalized treatment strategies. Continued interdisciplinary collaboration and innovation are essential for overcoming these challenges and leveraging the full potential of single-cell and spatial omics in improving bladder cancer diagnosis and treatment.
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Affiliation(s)
- Reinhard Grausenburger
- Department of Urology and Comprehensive Cancer Center
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Paula Herek
- Department of Urology and Comprehensive Cancer Center
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Shahrokh F. Shariat
- Department of Urology and Comprehensive Cancer Center
- Department of Urology, Weill Cornell Medical College, New York, New York
- Department of Urology, University of Texas Southwestern, Dallas, Texas, USA
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan
- Research Center for Evidence Medicine, Urology Department, Tabriz University of Medical Sciences, Tabriz, Iran
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
| | - Bernhard Englinger
- Department of Urology and Comprehensive Cancer Center
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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Zhang Y, Wu Q, Warrick JI, DeGraff DJ, Raman JD, Truong H, Chen G. Clinicopathological risk factors associated with tumor relapse of upper tract urothelial carcinoma after radical nephroureterectomy: A single institution 20-year experience. Ann Diagn Pathol 2024; 73:152357. [PMID: 38941945 DOI: 10.1016/j.anndiagpath.2024.152357] [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: 05/02/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Upper tract urothelial carcinoma (UTUC) is a relatively rare yet aggressive malignancy. While radical nephroureterectomy (RNU) remains the cornerstone treatment, UTUC has high local and metastatic relapse rates, leading to a dismal prognosis. To identify the clinicopathological factors associated with an increased risk of local and metastatic relapse in UTUC, we conducted a retrospective analysis of 133 consecutive UTUC patients who underwent RNU from 1998 to 2018. Patients lost to follow-up or with a history of bladder cancer were excluded from the study. The remaining 87 patients were categorized into two subgroups: those with tumor recurrence/relapse (40 cases) and those without recurrence/relapse (47 cases). Clinical and pathological characteristics were compared across the two groups. Multiple factors are associated with UTUC recurrence/relapse including larger tumor size, histology divergent differentiations/subtypes, high tumor grade, advanced pathologic T stage, positive margin, lymphovascular invasion (LVI), positive lymph node status, and preoperative hydronephrosis. Multivariate Cox regression analysis revealed that squamous differentiation predicted recurrence/relapse (p = 0.012), independent of tumor stage. Moreover, compared to the conventional histology type, UTUC with squamous differentiation had a significantly higher relapse rate (p = 0.0001) and poorer survival (p = 0.0039). This observation was further validated in invasive high-grade UTUC cases. Our findings suggest that many pathological factors contribute to UTUC recurrence/relapse, particularly, squamous differentiation may serve as an independent risk predictor for relapse and a potent prognosticator for adverse cancer-specific survival in UTUC patients. Recognizing and thoroughly assessing the pathological factors is essential for better oncologic management of UTUC.
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Affiliation(s)
- Yong Zhang
- Department of Pathology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - Qingqing Wu
- Department of Pathology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - Joshua I Warrick
- Department of Pathology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America; Department of Urology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - David J DeGraff
- Department of Pathology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America; Department of Urology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America; Department of Biochemistry and Molecular Biology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - Jay D Raman
- Department of Urology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - Hong Truong
- Department of Urology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America
| | - Guoli Chen
- Department of Pathology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States of America.
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Warrick J. Molecular Subtypes of Bladder Cancer: Component Signatures and Potential Value in Clinical Decision-making. Adv Anat Pathol 2024; 31:178-187. [PMID: 38231156 DOI: 10.1097/pap.0000000000000430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Bladder cancer may be classified into "molecular subtypes" based on gene expression. These are associated with treatment response and patient outcomes. The gene expression signatures that define these subtypes are diverse, including signatures of epithelial differentiation, stromal involvement, cell cycle activity, and immune cell infiltration. Multiple different systems are described. While earlier studies considered molecular subtypes to be intrinsic properties of cancer, recent data have shown molecular subtypes change as tumors progress and evolve, and often differ between histologically distinct regions of a tumor. The data also indicate that some signatures that define molecular subtypes may be treated as independent continuous variables, rather than categorical subtypes, and these individual signatures may be more clinically informative. This review describes molecular subtypes of urothelial carcinoma, including histologic subtypes and tumors with divergent differentiation, and explores potential future uses in patient management.
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Affiliation(s)
- Joshua Warrick
- Departments of Pathology and Urology, Penn State College of Medicine, Hershey, PA
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Chen DP, Wang JC, Liu ZY, Li PL, Chan KW, Wu XN, Yao WDX, Yao T, Kuang DM, Wei Y. miRNome targeting NF-κB signaling orchestrates macrophage-triggered cancer metastasis and recurrence. Mol Ther 2024; 32:1110-1124. [PMID: 38341612 PMCID: PMC11163221 DOI: 10.1016/j.ymthe.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/14/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
Whether and how tumor intrinsic signature determines macrophage-elicited metastasis remain elusive. Here, we show, in detailed studies of data regarding 7,477 patients of 20 types of human cancers, that only 13.8% ± 2.6%/27.9% ± 3.03% of patients with high macrophage infiltration index exhibit early recurrence/vascular invasion. In parallel, although macrophages enhance the motility of various hepatoma cells, their enhancement intensity is significantly heterogeneous. We identify that the expression of malignant Dicer, a ribonuclease that cleaves miRNA precursors into mature miRNAs, determines macrophage-elicited metastasis. Mechanistically, the downregulation of Dicer in cancer cells leads to defects in miRNome targeting NF-κB signaling, which in turn enhances the ability of cancer cells to respond to macrophage-related inflammatory signals and ultimately promotes metastasis. Importantly, transporting miR-26b-5p, the most potential miRNA targeting NF-κB signaling in hepatocellular carcinoma, can effectively reverse macrophage-elicited metastasis of hepatoma in vivo. Our results provide insights into the crosstalk between Dicer-elicited miRNome and cancer immune microenvironments and suggest that strategies to remodel malignant cell miRNome may overcome pro-tumorigenic activities of inflammatory cells.
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Affiliation(s)
- Dong-Ping Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jun-Cheng Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zheng-Yu Liu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pei-Lin Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ka-Wo Chan
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiang-Ning Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wu-De-Xin Yao
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tingting Yao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Dong-Ming Kuang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Yuan Wei
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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YADOLLAHVANDMIANDOAB REZA, JALALIZADEH MEHRSA, DIONATO FRANCIELEAPARECIDAVECHIA, BUOSI KEINI, LEME PATRÍCIAAF, COL LUCIANASBDAL, GIACOMELLI CRISTIANEF, ASSIS ALEXDIAS, BASHIRICHELKASARI NASIM, REIS LEONARDOOLIVEIRA. Clinical implications of single cell sequencing for bladder cancer. Oncol Res 2024; 32:597-605. [PMID: 38560564 PMCID: PMC10972735 DOI: 10.32604/or.2024.045442] [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: 08/27/2023] [Accepted: 01/08/2024] [Indexed: 04/04/2024] Open
Abstract
Bladder cancer (BC) is the 10th most common cancer worldwide, with about 0.5 million reported new cases and about 0.2 million deaths per year. In this scoping review, we summarize the current evidence regarding the clinical implications of single-cell sequencing for bladder cancer based on PRISMA guidelines. We searched PubMed, CENTRAL, Embase, and supplemented with manual searches through the Scopus, and Web of Science for published studies until February 2023. We included original studies that used at least one single-cell technology to study bladder cancer. Forty-one publications were included in the review. Twenty-nine studies showed that this technology can identify cell subtypes in the tumor microenvironment that may predict prognosis or response to immune checkpoint inhibition therapy. Two studies were able to diagnose BC by identifying neoplastic cells through single-cell sequencing urine samples. The remaining studies were mainly a preclinical exploration of tumor microenvironment at single cell level. Single-cell sequencing technology can discriminate heterogeneity in bladder tumor cells and determine the key molecular properties that can lead to the discovery of novel perspectives on cancer management. This nascent tool can advance the early diagnosis, prognosis judgment, and targeted therapy of bladder cancer.
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Affiliation(s)
- REZA YADOLLAHVANDMIANDOAB
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - MEHRSA JALALIZADEH
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | | | - KEINI BUOSI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - PATRÍCIA A. F. LEME
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - LUCIANA S. B. DAL COL
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - CRISTIANE F. GIACOMELLI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - ALEX DIAS ASSIS
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - NASIM BASHIRICHELKASARI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - LEONARDO OLIVEIRA REIS
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
- ImmunOncology, Pontifical Catholic University of Campinas, PUC-Campinas, Campinas, Sao Paulo, 13087-571, Brazil
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6
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Beckabir W, Wobker SE, Damrauer JS, Midkiff B, De la Cruz G, Makarov V, Flick L, Woodcock MG, Grivas P, Bjurlin MA, Harrison MR, Vincent BG, Rose TL, Gupta S, Kim WY, Milowsky MI. Spatial Relationships in the Tumor Microenvironment Demonstrate Association with Pathologic Response to Neoadjuvant Chemoimmunotherapy in Muscle-invasive Bladder Cancer. Eur Urol 2024; 85:242-253. [PMID: 38092611 PMCID: PMC11022933 DOI: 10.1016/j.eururo.2023.11.008] [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: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/09/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Platinum-based neoadjuvant chemotherapy (NAC) is standard for patients with muscle-invasive bladder cancer (MIBC). Pathologic response (complete: ypT0N0 and partial: OBJECTIVE Using the NanoString GeoMx platform, we performed proteomic digital spatial profiling (DSP) on transurethral resections of bladder tumors from 18 responders ( DESIGN, SETTING, AND PARTICIPANTS Pretreatment tumor samples were stained by hematoxylin and eosin and immunofluorescence (panCK and CD45) to select four regions of interest (ROIs): tumor enriched (TE), immune enriched (IE), tumor/immune interface (tumor interface = TX and immune interface = IX). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS DSP was performed with 52 protein markers from immune cell profiling, immunotherapy drug target, immune activation status, immune cell typing, and pan-tumor panels. RESULTS AND LIMITATIONS Protein marker expression patterns were analyzed to determine their association with pathologic response, incorporating or agnostic of their ROI designation (TE/IE/TX/IX). Overall, DSP-based marker expression showed high intratumoral heterogeneity; however, response was associated with markers including PD-L1 (ROI agnostic), Ki-67 (ROI agnostic, TE, IE, and TX), HLA-DR (TX), and HER2 (TE). An elastic net model of response with ROI-inclusive markers demonstrated better validation set performance (area under the curve [AUC] = 0.827) than an ROI-agnostic model (AUC = 0.432). A model including DSP, tumor mutational burden, and clinical data performed no better (AUC = 0.821) than the DSP-only model. CONCLUSIONS Despite high intratumoral heterogeneity of DSP-based marker expression, we observed associations between pathologic response and specific DSP-based markers in a spatially dependent context. Further exploration of tumor region-specific biomarkers may help predict response to neoadjuvant chemoimmunotherapy in MIBC. PATIENT SUMMARY In this study, we used the GeoMx platform to perform proteomic digital spatial profiling on transurethral resections of bladder tumors from 18 responders and 18 nonresponders from two studies of neoadjuvant chemotherapy (gemcitabine and cisplatin) plus immune checkpoint inhibitor therapy (LCCC1520 [pembrolizumab] and BLASST-1 [nivolumab]). We found that assessing protein marker expression in the context of tumor architecture improved response prediction.
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Affiliation(s)
- Wolfgang Beckabir
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey S Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bentley Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vladmir Makarov
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Leah Flick
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Petros Grivas
- Department of Medicine, Division of Medical Oncology, University of Washington, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marc A Bjurlin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Harrison
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA; Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA; Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Tracy L Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shilpa Gupta
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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7
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Wang Y, Wang Y, He H, Xiong Y. Absence of GATA3/FOXA1 co-expression predicts poor prognosis in upper tract urothelial carcinoma. Front Oncol 2024; 14:1302864. [PMID: 38425344 PMCID: PMC10902436 DOI: 10.3389/fonc.2024.1302864] [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: 09/27/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Objective GATA binding protein 3 (GATA3) and forkhead box A1 (FOXA1) have been individually implicated in the progression of upper tract urothelial carcinoma (UTUC). This study aims to evaluate the prognostic value of GATA3/FOXA1 co-expression in UTUC patients. Methods We collected 108 UTUC pathological tissue samples with complete follow-up data and 24 normal control urothelial tissues. We created a 132-site microarray and performed immunohistochemistry (IHC) to measure GATA3 and FOXA1 expression levels. Kaplan-Meier survival and Cox regression analyses were conducted to assess UTUC prognosis. Results GATA3 expression was positively correlated with FOXA1 (P=0.031). Absence of GATA3/FOXA1 co-expression (GATA3-/FOXA1-) was associated with tumor extensive necrosis (P=0.001) after Bonferroni correction for multiple comparisons. GATA3-/FOXA1- was associated with shorter Disease-Free Survival (DFS) (P=0.001) and Cancer-Specific Survival (CSS) (P<0.001) than other combination groups. Multivariate analyses identified extensive necrosis as an independent prognostic factor for CSS (P=0.030). Conclusions Our study revealed a positive correlation between GATA3 and FOXA1 expression in UTUC. GATA3-/FOXA1- is linked to tumor extensive necrosis and poor prognosis in UTUC and may serve as a potential biomarker for UTUC patients.
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Affiliation(s)
- Yue Wang
- Department of Pathology, Peking University First Hospital, Beijing, China
| | - Yunfan Wang
- Department of Pathology, Peking University Shougang Hospital, Beijing, China
| | - Huiying He
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, China
| | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing, China
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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9
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Warrick JI, Al-Ahmadie H, Berman DM, Black PC, Flaig TW, Höglund M, Bubendorf L, van der Kwast TH, Cheng L. International Society of Urological Pathology Consensus Conference on Current Issues in Bladder Cancer. Working Group 4: Molecular Subtypes of Bladder Cancer-Principles of Classification and Emerging Clinical Utility. Am J Surg Pathol 2024; 48:e32-e42. [PMID: 37199442 DOI: 10.1097/pas.0000000000002053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Molecular subtyping has been a major focus of bladder cancer research over the past decade. Despite many promising associations with clinical outcomes and treatment response, its clinical impact has yet to be defined. As part of the 2022 International Society of Urological Pathology Conference on Bladder Cancer, we reviewed the current state of the science for bladder cancer molecular subtyping. Our review included several different subtyping systems. We derived the following 7 principles, which summarize progress and challenges of molecular subtyping: (1) bladder cancer has 3 major molecular subtypes: luminal, basal-squamous, and neuroendocrine; (2) signatures of the tumor microenvironment differ greatly among bladder cancers, particularly among luminal tumors; (3) luminal bladder cancers are biologically diverse, and much of this diversity results from differences in features unrelated to the tumor microenvironment, such as FGFR3 signaling and RB1 inactivation; (4) molecular subtype of bladder cancer associates with tumor stage and histomorphology; (5) many subtyping systems include idiosyncrasies, such as subtypes recognized by no other system; (6) there are broad fuzzy borders between molecular subtypes, and cases that fall on these fuzzy borders are often classified differently by different subtyping systems; and (7) when there are histomorphologically distinct regions within a single tumor, the molecular subtypes of these regions are often discordant. We reviewed several use cases for molecular subtyping, highlighting their promise as clinical biomarkers. Finally, we conclude that data are currently insufficient to support the routine use of molecular subtyping to guide bladder cancer management, an opinion shared with the majority of conference attendees. We also conclude that molecular subtype should not be considered an "intrinsic" property of a tumor but should instead be considered the result of a specific laboratory test, performed using a specific testing platform and classification algorithm, validated for a specific clinical application.
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Affiliation(s)
- Joshua I Warrick
- Penn State College of Medicine, Departments of Pathology and Urology, Hershey, PA
| | - Hikmat Al-Ahmadie
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, NY
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston
| | - Peter C Black
- Department of Urologic Sciences, Univeristy of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas W Flaig
- Department of Medicine-Medical Oncology, University of Colorado School of Medicine, Aurora, CO
| | - Mattias Höglund
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School; Lifespan Academic Medical Center, and the Legorreta Cancer Center at Brown University, Providence, RI
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Ferraz RS, Cavalcante JVF, Magalhães L, Ribeiro‐dos‐Santos Â, Dalmolin RJS. Revealing metastatic castration-resistant prostate cancer master regulator through lncRNAs-centered regulatory network. Cancer Med 2023; 12:19279-19290. [PMID: 37644825 PMCID: PMC10557827 DOI: 10.1002/cam4.6481] [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: 06/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Metastatic castration-resistant prostate cancer (mCRPC) is an aggressive form of cancer unresponsive to androgen deprivation therapy (ADT) that spreads quickly to other organs. Despite reduced androgen levels after ADT, mCRPC development and lethality continues to be conducted by the androgen receptor (AR) axis. The maintenance of AR signaling in mCRPC is a result of AR alterations, androgen intratumoral production, and the action of regulatory elements, such as noncoding RNAs (ncRNAs). ncRNAs are key elements in cancer signaling, acting in tumor growth, metabolic reprogramming, and tumor progression. In prostate cancer (PCa), the ncRNAs have been reported to be associated with AR expression, PCa proliferation, and castration resistance. In this study, we aimed to reconstruct the lncRNA-centered regulatory network of mCRPC and identify the lncRNAs which act as master regulators (MRs). METHODS We used publicly available RNA-sequencing to infer the regulatory network of lncRNAs in mCRPC. Five gene signatures were employed to conduct the master regulator analysis. Inferred MRs were then subjected to functional enrichment and symbolic regression modeling. The latter approach was applied to identify the lncRNAs with greater predictive capacity and potential as a biomarker in mCRPC. RESULTS We identified 31 lncRNAs involved in cellular proliferation, tumor metabolism, and invasion-metastasis cascade. SNHG18 and HELLPAR were the highlights of our results. SNHG18 was downregulated in mCRPC and enriched to metastasis signatures. It accurately distinguished both mCRPC and primary CRPC from normal tissue and was associated with epithelial-mesenchymal transition (EMT) and cell-matrix adhesion pathways. HELLPAR consistently distinguished mCRPC from primary CRPC and normal tissue using only its expression. CONCLUSION Our results contribute to understanding the regulatory behavior of lncRNAs in mCRPC and indicate SNHG18 and HELLPAR as master regulators and potential new diagnostic targets in this tumor.
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Affiliation(s)
- Rafaella Sousa Ferraz
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesFederal University of ParaBelemBrazil
| | | | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesFederal University of ParaBelemBrazil
| | - Ândrea Ribeiro‐dos‐Santos
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesFederal University of ParaBelemBrazil
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Venkadakrishnan VB, Yamada Y, Weng K, Idahor O, Beltran H. Significance of RB Loss in Unlocking Phenotypic Plasticity in Advanced Cancers. Mol Cancer Res 2023; 21:497-510. [PMID: 37052520 PMCID: PMC10239360 DOI: 10.1158/1541-7786.mcr-23-0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 04/14/2023]
Abstract
Cancer cells can undergo plasticity in response to environmental stimuli or under selective therapeutic pressures that result in changes in phenotype. This complex phenomenon of phenotypic plasticity is now recognized as a hallmark of cancer. Lineage plasticity is often associated with loss of dependence on the original oncogenic driver and is facilitated, in part, by underlying genomic and epigenetic alterations. Understanding the molecular drivers of cancer plasticity is critical for the development of novel therapeutic strategies. The retinoblastoma gene RB1 (encoding RB) is the first tumor suppressor gene to be discovered and has a well-described role in cell-cycle regulation. RB is also involved in diverse cellular functions beyond cell cycle including differentiation. Here, we describe the emerging role of RB loss in unlocking cancer phenotypic plasticity and driving therapy resistance across cancer types. We highlight parallels in cancer with the noncanonical role of RB that is critical for normal development and lineage specification, and the downstream consequences of RB loss including epigenetic reprogramming and chromatin reorganization that can lead to changes in lineage program. Finally, we discuss potential therapeutic approaches geared toward RB loss cancers undergoing lineage reprogramming.
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Affiliation(s)
| | - Yasutaka Yamada
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenny Weng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Boston College, Chestnut Hill, Massachusetts, USA
| | - Osasenaga Idahor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard University, Cambridge, Massachusetts, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Mehus AA, Jones M, Trahan M, Kinnunen K, Berwald K, Lindner B, Al-Marsoummi S, Zhou XD, Garrett SH, Sens DA, Sens MA, Somji S. Pevonedistat Inhibits SOX2 Expression and Sphere Formation but Also Drives the Induction of Terminal Differentiation Markers and Apoptosis within Arsenite-Transformed Urothelial Cells. Int J Mol Sci 2023; 24:9149. [PMID: 37298099 PMCID: PMC10252886 DOI: 10.3390/ijms24119149] [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: 05/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Urothelial cancer (UC) is a common malignancy and its development is associated with arsenic exposure. Around 25% of diagnosed UC cases are muscle invasive (MIUC) and are frequently associated with squamous differentiation. These patients commonly develop cisplatin (CIS) resistance and have poor prognosis. SOX2 expression is correlated to reduced overall and disease-free survival in UC. SOX2 drives malignant stemness and proliferation in UC cells and is associated with development of CIS resistance. Using quantitative proteomics, we identified that SOX2 was overexpressed in three arsenite (As3+)-transformed UROtsa cell lines. We hypothesized that inhibition of SOX2 would reduce stemness and increase sensitivity to CIS in the As3+-transformed cells. Pevonedistat (PVD) is a neddylation inhibitor and is a potent inhibitor of SOX2. We treated non-transformed parent and As3+-transformed cells with PVD, CIS, or in combination and monitored cell growth, sphere forming abilities, apoptosis, and gene/protein expression. PVD treatment alone caused morphological changes, reduced cell growth, attenuated sphere formation, induced apoptosis, and elevated the expression of terminal differentiation markers. However, the combined treatment of PVD with CIS significantly elevated the expression of terminal differentiation markers and eventually led to more cell death than either solo treatment. Aside from a reduced proliferation rate, these effects were not seen in the parent. Further research is needed to explore the potential use of PVD with CIS as a differentiation therapy or alternative treatment for MIUC tumors that may have become resistant to CIS.
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Affiliation(s)
- Aaron A. Mehus
- Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (M.J.); (M.T.); (K.K.); (K.B.); (B.L.); (S.A.-M.); (X.D.Z.); (S.H.G.); (D.A.S.); (M.A.S.); (S.S.)
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13
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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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Uppaluri KR, Kambalachenu HR, Challa HJ, Raghuram Y S, Gadicherla R, Ketavath S, Palasamudram K, Sri Manjari K. Mutations in a High-Grade Micropapillary Urothelial Carcinoma of the Renal Pelvis: A Case Report. Case Rep Oncol 2023; 16:972-979. [PMID: 37900819 PMCID: PMC10601746 DOI: 10.1159/000530710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/06/2023] [Indexed: 10/31/2023] Open
Abstract
Micropapillary urothelial carcinoma (MPUC) of the renal pelvis is an upper tract urothelial carcinoma originating in the renal pelvis region. Few genetic studies are available, and the mechanism of pathogenesis of genetically driven models is unclear. We report a case of genomic alterations in MPUC of the renal pelvis and compare the results with existing literature. DNA was extracted, followed by the next-generation sequencing of 351 oncogenes and tumor suppressor genes. Targeted gene sequencing analysis revealed somatic variants in ERBB2, KMT2C, FOXA1, and germline variants in CDKN1B, ELF3, TP53, and RB1 genes. The present case study sheds light on recognizing genetic variants in high-grade MPUC of the renal pelvis. Understanding molecular mechanisms helps with better prognostication and development of more effective therapeutics and treatment.
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