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Wijetunga NA, Gessner KH, Kanchi K, Moore JA, Fleischmann Z, Jin DX, Frampton GM, Sturdivant M, Repka M, Sud S, Corcoran DL, Galsky MD, Milowsky MI, Wobker SE, Kim WY, Rose TL, Damrauer JS. Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features. CANCER RESEARCH COMMUNICATIONS 2024; 4:2320-2334. [PMID: 39113632 DOI: 10.1158/2767-9764.crc-24-0352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024]
Abstract
Radiotherapy (RT) for prostate cancer has been associated with an increased risk for the development of bladder cancer. We aimed to integrate clinical and genomic data to better understand the development of RT-associated bladder cancer. A retrospective analysis was performed to identify control patients (CTRL; n = 41) and patients with RT-associated bladder cancer (n = 41). RT- and CTRL-specific features were then identified through integration and analysis of the genomic sequencing data and clinical variables. RT-associated bladder tumors were significantly enriched for alterations in KDM6A and ATM, whereas CTRL tumors were enriched for CDKN2A mutation. Globally, there were an increased number of variants within RT tumors, albeit at a lower variant allele frequency. Mutational signature analysis revealed three predominate motif patterns, with similarity to SBS2/13 (APOBEC3A), SBS5 (ERCC2/smoking), and SBS6/15 (MMR). Poor prognostic factors in the RT cohort include a short tumor latency, smoking status, the presence of the smoking and X-ray therapy mutational signatures, and CDKN2A copy number loss. Based on the clinical and genomic findings, we suggest at least two potential pathways leading to RT-associated bladder cancer: The first occurs in the setting of field cancerization related to smoking or preexisting genetic alterations and leads to the development of more aggressive bladder tumors, and the second involves RT initiating the oncogenic process in otherwise healthy urothelium, leading to a longer latency and less aggressive disease. SIGNIFICANCE Clinicogenomic analysis of radiation-associated bladder cancer uncovered mutational signatures that, in addition to a short tumor latency, smoking, and CDKN2A loss, are associated with a poor outcome. These clinical and genomic features provide a potential method to identify patients with prostate cancer who are at an increased risk for the development of aggressive bladder cancer following prostate RT.
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Affiliation(s)
- N Ari Wijetunga
- Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Kathryn H Gessner
- Department of Urology, University of North Carolina, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Krishna Kanchi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Jay A Moore
- Foundation Medicine, Inc., Boston, Massachusetts
| | | | - Dexter X Jin
- Foundation Medicine, Inc., Boston, Massachusetts
| | | | - Michael Sturdivant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael Repka
- Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Shivani Sud
- Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - David L Corcoran
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Medicine, Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Pathology and Lab Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Genetics, University of North Carolina, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Medicine, Oncology, University of North Carolina, Chapel Hill, North Carolina
- Pathology and Lab Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Tracy L Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Medicine, Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Jeffrey S Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Medicine, Oncology, University of North Carolina, Chapel Hill, North Carolina
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Wang J, Tan Z, Huang Y, Li C, Zhan P, Wang H, Li H. Integrating single-cell RNA-seq to identify fibroblast-based molecular subtypes for predicting prognosis and therapeutic response in bladder cancer. Aging (Albany NY) 2024; 16:11385-11408. [PMID: 39033778 PMCID: PMC11315389 DOI: 10.18632/aging.206021] [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: 01/09/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Bladder cancer (BLCA) is a highly aggressive and heterogeneous disease, posing challenges for diagnosis and treatment. Cancer immunotherapy has recently emerged as a promising option for patients with advanced and drug-resistant cancers. Fibroblasts, a significant component of the tumor microenvironment, play a crucial role in tumor progression, but their precise function in BLCA remains uncertain. METHODS Single-cell RNA sequencing (scRNA-seq) data for BLCA were obtained from the Gene Expression Omnibus database. The R package "Seurat" was used for processing scRNA-seq data, with uniform manifold approximation and projection (UMAP) for downscaling and cluster identification. The FindAllMarkers function identified marker genes for each cluster. Differentially expressed genes influencing overall survival (OS) of BLCA patients were identified using the limma package. Differences in clinicopathological characteristics, immune microenvironment, immune checkpoints, and chemotherapeutic drug sensitivity between high- and low-risk groups were investigated. RT-qPCR and immunohistochemistry validated the expression of prognostic genes. RESULTS Fibroblast marker genes identified three molecular subtypes in the testing set. A prognostic signature comprising ten genes stratified BLCA patients into high- and low-score groups. This signature was validated in one internal and two external validation sets. High-score patients exhibited increased immune cell infiltration, elevated chemokine expression, and enhanced immune checkpoint expression but had poorer OS and a reduced response to immunotherapy. Six sensitive anti-tumor drugs were identified for the high-score group. RT-qPCR and immunohistochemistry showed that CERCAM, TM4SF1, FN1, ANXA1, and LOX were highly expressed, while EMP1, HEYL, FBN1, and SLC2A3 were downregulated in BLCA. CONCLUSION A novel fibroblast marker gene-based signature was established, providing robust predictions of survival and immunotherapeutic response in BLCA patients.
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Affiliation(s)
- Jia Wang
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Endocrinology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhiyong Tan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yinglong Huang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Charles Li
- Core Facility for Protein Research, Chinese Academy of Sciences, Beijing, China
- Zhongke Jianlan Medical Research Institute, Beijing, China
- Zhejiang Institute of Integrated Traditional and Western Medicine, Hangzhou, China
| | - Peiqin Zhan
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haifeng Wang
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haihao Li
- The Second Clinical Medical College, Kunming Medical University, Kunming, China
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Stormoen DR, Rohrberg KS, Mouw KW, Ørum K, Szallasi Z, Rossing M, Bagger FO, Pappot H. Similar genetic profile in early and late stage urothelial tract cancer. J Cancer Res Clin Oncol 2024; 150:339. [PMID: 38976041 PMCID: PMC11230994 DOI: 10.1007/s00432-024-05850-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/14/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Urothelial tract cancer (UTC) ranks as the tenth most prevalent cancer and holds the seventh position in terms of mortality worldwide. Despite its prevalence and mortality ranking, there are still gaps in the knowledge of the mutational landscape in patients with advanced disease who have limited therapeutic options after multiple lines of prior treatment. This study compares the genomic and transcriptomic landscape, and targeted treatment options between metastatic UTC (mUTC) patients treated with multiple lines of therapy compared to newly diagnosed, untreated Muscle Invasive Bladder Cancer (MIBC). METHODS We compared genomic and clinical data from two cohorts: mUTC patients who received multiple lines of therapy and were referred to the Copenhagen Prospective Personalized Oncology (CoPPO) project at Rigshospitalet, University of Copenhagen. Data for MIBC UTC patients were acquired from the Cancer Genome Atlas Bladder Cancer (TCGA BLCA) cohort. Biopsies in CoPPO were performed at the time of enrollment. 523 highly important cancer-related genes (TrueSight Oncology-500 targeted sequencing panel) were used from both cohorts for comparative analysis. Analyses included RNA count data to compare predicted molecular subtypes in each cohort separately. RESULTS Patients from the CoPPO cohort had a lower median age at first-line treatment than the TCGA BLCA cohort, with no significant gender disparity. The predominant histology was urothelial cell carcinoma in both cohorts. Genomic analysis revealed no significant difference between the top mutated genes in the two cohorts, specifically looking into DNA damage repair genes. Molecular subtyping indicated a higher frequency of neuroendocrine differentiation in the CoPPO cohort. 13% of patients in the CoPPO cohort received targeted therapy based on genomic findings, and 16% received non-targeted treatment, totaling 29% receiving CoPPO treatment (9 patients). The remaining 71% received best supportive care. Kaplan-Meier analysis showed a non-significant survival benefit for the intervention group in the CoPPO cohort. CONCLUSION When focusing on 523 highly relevant cancer genes, the mutational profile of mUTC patients who have undergone numerous treatment lines resembles that of newly diagnosed MIBC. These alterations can be targeted, indicating the potential advantage of early genomic testing for personalized treatment within clinical trials.
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Affiliation(s)
- Dag Rune Stormoen
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Kristoffer Staal Rohrberg
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kent William Mouw
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katrine Ørum
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
| | - Zoltan Szallasi
- Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Translational Cancer Genomics Group, Danish Cancer Society, Copenhagen, Denmark
| | - Maria Rossing
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Department for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Helle Pappot
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Chai D, Wang J, Fan C, Lim JM, Wang X, Neeli P, Yu X, Young KH, Li Y. Remodeling of anti-tumor immunity with antibodies targeting a p53 mutant. J Hematol Oncol 2024; 17:45. [PMID: 38886748 PMCID: PMC11184848 DOI: 10.1186/s13045-024-01566-1] [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: 04/16/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND p53, the most frequently mutated gene in cancer, lacks effective targeted drugs. METHODS We developed monoclonal antibodies (mAbs) that target a p53 hotspot mutation E285K without cross-reactivity with wild-type p53. They were delivered using lipid nanoparticles (LNPs) that encapsulate DNA plasmids. Western blot, BLI, flow cytometry, single-cell sequencing (scRNA-seq), and other methods were employed to assess the function of mAbs in vitro and in vivo. RESULTS These LNP-pE285K-mAbs in the IgG1 format exhibited a robust anti-tumor effect, facilitating the infiltration of immune cells, including CD8+ T, B, and NK cells. scRNA-seq revealed that IgG1 reduces immune inhibitory signaling, increases MHC signaling from B cells to CD8+ T cells, and enriches anti-tumor T cell and B cell receptor profiles. The E285K-mAbs were also produced in the dimeric IgA (dIgA) format, whose anti-tumor activity depended on the polymeric immunoglobulin receptor (PIGR), a membrane Ig receptor, whereas that of IgG1 relied on TRIM21, an intracellular IgG receptor. CONCLUSIONS Targeting specific mutant epitopes using DNA-encoded and LNP-delivered mAbs represents a potential precision medicine strategy against p53 mutants in TRIM21- or PIGR-positive cancers.
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Affiliation(s)
- Dafei Chai
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| | - Junhao Wang
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Chunmei Fan
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Jing-Ming Lim
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xu Wang
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Praveen Neeli
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xinfang Yu
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Ken H Young
- Department of Pathology, Division of Hematopathology, Duke University Medical Center, Durham, NC, USA
| | - Yong Li
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
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Beckabir W, Zhou M, Lee JS, Vensko SP, Woodcock MG, Wang HH, Wobker SE, Atassi G, Wilkinson AD, Fowler K, Flick LM, Damrauer JS, Harrison MR, McKinnon KP, Rose TL, Milowsky MI, Serody JS, Kim WY, Vincent BG. Immune features are associated with response to neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer. Nat Commun 2024; 15:4448. [PMID: 38789460 PMCID: PMC11126571 DOI: 10.1038/s41467-024-48480-1] [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: 07/18/2023] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Neoadjuvant cisplatin-based chemotherapy is standard of care for muscle-invasive bladder cancer (MIBC). Immune checkpoint inhibition (ICI) alone, and ICI in combination with chemotherapy, have demonstrated promising pathologic response (
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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
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, 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
| | - Jin Seok Lee
- Lineberger Comprehensive Cancer Center, 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
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Steven P Vensko
- 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
- Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hsing-Hui Wang
- 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 and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gatphan Atassi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alec D Wilkinson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Fowler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leah M Flick
- Lineberger Comprehensive Cancer Center, 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
| | - Michael R Harrison
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Karen P McKinnon
- 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
| | - 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
| | - 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
| | - Jonathan S Serody
- 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 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.
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, 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.
- Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, 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.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, 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.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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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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Yang J, Liu Q, Shyr Y. A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer Res 2024; 84:626-638. [PMID: 38117502 PMCID: PMC10867621 DOI: 10.1158/0008-5472.can-23-2006] [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: 07/08/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Although considerable efforts have been dedicated to identifying predictive signatures for immune checkpoint inhibitor (ICI) treatment response, current biomarkers suffer from poor generalizability and reproducibility across different studies and cancer types. The integration of large-scale multiomics studies holds great promise for discovering robust biomarkers and shedding light on the mechanisms of immune resistance. In this study, we conducted the most extensive meta-analysis involving 3,037 ICI-treated patients with genetic and/or transcriptomics profiles across 14 types of solid tumor. The comprehensive analysis uncovered both known and novel reliable signatures associated with ICI treatment outcomes. The signatures included tumor mutational burden (TMB), IFNG and PDCD1 expression, and notably, interactions between macrophages and T cells driving their activation and recruitment. Independent data from single-cell RNA sequencing and dynamic transcriptomic profiles during the ICI treatment provided further evidence that enhanced cross-talk between macrophages and T cells contributes to ICI response. A multivariable model based on eight nonredundant signatures significantly outperformed existing models in five independent validation datasets representing various cancer types. Collectively, this study discovered biomarkers predicting ICI response that highlight the contribution of immune cell networks to immunotherapy efficacy and could help guide patient treatment. SIGNIFICANCE Identification of robust immunogenomic connections, particularly macrophage T-cell interactions, in a large-scale pan-cancer meta-analysis and development of a predictive model for immunotherapy response that outperformed existing models could facilitate clinical decision-making.
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Affiliation(s)
- Jing Yang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
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8
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Okato A, Utsumi T, Ranieri M, Zheng X, Zhou M, Pereira LD, Chen T, Kita Y, Wu D, Hyun H, Lee H, Gdowski AS, Raupp JD, Clark-Garvey S, Manocha U, Chafitz A, Sherman F, Stephens J, Rose TL, Milowsky MI, Wobker SE, Serody JS, Damrauer JS, Wong KK, Kim WY. FGFR inhibition augments anti-PD-1 efficacy in murine FGFR3-mutant bladder cancer by abrogating immunosuppression. J Clin Invest 2024; 134:e169241. [PMID: 38226620 PMCID: PMC10786699 DOI: 10.1172/jci169241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
The combination of targeted therapy with immune checkpoint inhibition (ICI) is an area of intense interest. We studied the interaction of fibroblast growth factor receptor (FGFR) inhibition with ICI in urothelial carcinoma (UC) of the bladder, in which FGFR3 is altered in 50% of cases. Using an FGFR3-driven, Trp53-mutant genetically engineered murine model (UPFL), we demonstrate that UPFL tumors recapitulate the histology and molecular subtype of their FGFR3-altered human counterparts. Additionally, UPFL1 allografts exhibit hyperprogression to ICI associated with an expansion of T regulatory cells (Tregs). Erdafitinib blocked Treg proliferation in vitro, while in vivo ICI-induced Treg expansion was fully abrogated by FGFR inhibition. Combined erdafitinib and ICI resulted in high therapeutic efficacy. In aggregate, our work establishes that, in mice, co-alteration of FGFR3 and Trp53 results in high-grade, non-muscle-invasive UC and presents a previously underappreciated role for FGFR inhibition in blocking ICI-induced Treg expansion.
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Affiliation(s)
- Atsushi Okato
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Takanobu Utsumi
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michela Ranieri
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Xingnan Zheng
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Luiza D. Pereira
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Ting Chen
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Yuki Kita
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Di Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyesun Hyun
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hyojin Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Andrew S. Gdowski
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - John D. Raupp
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sean Clark-Garvey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alison Chafitz
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Fiona Sherman
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Janaye Stephens
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Tracy L. Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Matthew I. Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Sara E. Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine
| | - Jonathan S. Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Pathology and Laboratory Medicine
- Department of Microbiology and Immunology
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
| | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York University, New York, New York, USA
| | - William Y. Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine
- Department of Genetics, and
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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9
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Koll FJ, Döring C, Herwig L, Hoeh B, Wenzel M, Cano Garcia C, Banek S, Kluth L, Köllermann J, Weigert A, Chun FKH, Wild P, Reis H. Impact of consensus molecular subtypes on survival with and without adjuvant chemotherapy in muscle-invasive urothelial bladder cancer. J Clin Pathol 2023:jcp-2023-208973. [PMID: 37989554 DOI: 10.1136/jcp-2023-208973] [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: 05/19/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
AIMS Adjuvant chemotherapy after radical cystectomy can reduce the risk of recurrence and death in advanced muscle-invasive urothelial bladder cancer (MIBC). Molecular subtypes have been shown to be associated with survival. However, their predictive value to guide treatment decisions is controversial and data to use subtypes as guidance for adjuvant chemotherapy is sparse. We aimed to assess survival rates based on MIBC consensus molecular subtypes with and without adjuvant chemotherapy. METHODS Gene expression profiles of 143 patients with MIBC undergoing radical cystectomy were determined from formalin-fixed, paraffin-embedded specimen to assign consensus molecular subtypes. Expression of programmed cell death ligand-1 (PD-L1) and immune cell infiltration were determined using multiplex immunofluorescence. Matched-pair analysis was performed to evaluate the effect of adjuvant chemotherapy on overall survival (OS) for molecular subtypes applying Kaplan-Meier and Cox regression survival analyses. RESULTS Samples were luminal papillary: 9.1% (n=13), luminal non-specified: 6.3% (n=9), luminal unstable: 4.9% (n=7), stroma-rich: 27.9% (n=40), basal/squamous (Ba/Sq): 48.9% (n=70) and neuroendocrine-like (NE-like): 2.8% (n=4). Ba/Sq tumours had the highest concentration of PD-L1+ tumour and immune cells. Patients with luminal subtypes had better OS than those with NE-like (HR 0.2, 95% CI 0.1 to 0.7, p<0.05) and Ba/Sq (HR 0.5, 95% CI 0.2 to 0.9, p<0.05). No survival benefit with adjuvant chemotherapy was observed for luminal tumours, whereas Ba/Sq had significantly improved survival rates with adjuvant chemotherapy. Retrospective design and sample size are the main limitations. CONCLUSION Consensus molecular subtypes can be used to stratify patients with MIBC. Luminal tumours have the best prognosis and less benefit when receiving adjuvant chemotherapy compared with Ba/Sq tumours.
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Affiliation(s)
- Florestan J Koll
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
- Frankfurt Cancer Institute (FCI), Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
- University Cancer Center (UCT) Frankfurt, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Leon Herwig
- Dr. Senckenberg Institute of Pathology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Benedikt Hoeh
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Mike Wenzel
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Cristina Cano Garcia
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Severine Banek
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Luis Kluth
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Jens Köllermann
- Dr. Senckenberg Institute of Pathology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Felix K-H Chun
- Department of Urology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Peter Wild
- Frankfurt Cancer Institute (FCI), Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
- Dr. Senckenberg Institute of Pathology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main, Hessen, Germany
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Germany
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10
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, Alonso de la Vega A, Proehl J, Holzhauer AM, Seeman ZJ, Liu X, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases. Cell Rep Med 2023; 4:101211. [PMID: 37797615 PMCID: PMC10591044 DOI: 10.1016/j.xcrm.2023.101211] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many cancers. However, despite years of work, a causal relationship has yet to be established in vivo. Here, we report a murine model that expresses tumor-like levels of human APOBEC3B. Animals expressing full-body APOBEC3B appear to develop normally. However, adult males manifest infertility, and older animals of both sexes show accelerated rates of carcinogenesis, visual and molecular tumor heterogeneity, and metastasis. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Enrichment for APOBEC3B-attributable single base substitution mutations also associates with elevated levels of insertion-deletion mutations and structural variations. APOBEC3B catalytic activity is required for all of these phenotypes. Together, these studies provide a cause-and-effect demonstration that human APOBEC3B is capable of driving both tumor initiation and evolution in vivo.
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Lene Alsøe
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hilde Nilsen
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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11
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Ali W, Xiao W, Jacobs D, Kajdacsy-Balla A. Survival and Enrichment Analysis of Epithelial-Mesenchymal Transition Genes in Bladder Urothelial Carcinoma. Genes (Basel) 2023; 14:1899. [PMID: 37895248 PMCID: PMC10606556 DOI: 10.3390/genes14101899] [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: 08/28/2023] [Revised: 09/16/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The escalating prevalence of bladder cancer, particularly urothelial carcinoma, necessitates innovative approaches for prognosis and therapy. This study delves into the significance of genes related to epithelial-mesenchymal transition (EMT), a process inherently linked to carcinogenesis and comparatively better studied in other cancers. We examined 1184 EMT-related gene expression levels in bladder urothelial cancer cases through the TCGA dataset. Genes shown to be differentially expressed in relation to survival underwent further network and enrichment analysis to uncover how they might shape disease outcomes. Our in silico analysis revealed a subset of 32 genes, including those significantly represented in biological pathways such as VEGF signaling and bacterium response. In addition, these genes interact with genes involved in the JAK-STAT signaling pathway. Additionally, some of those 32 genes have been linked to immunomodulators such as chemokines CCL15 and CCL18, as well as to various immune cell infiltrates. Our findings highlight the prognostic utility of various EMT-related genes and identify possible modulators of their effect on survival, allowing for further targeted wet lab research and possible therapeutic intervention.
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Affiliation(s)
- Waleed Ali
- Albert Einstein College of Medicine, New York, NY 10461, USA; (W.X.); (D.J.)
| | - Weirui Xiao
- Albert Einstein College of Medicine, New York, NY 10461, USA; (W.X.); (D.J.)
| | - Daniel Jacobs
- Albert Einstein College of Medicine, New York, NY 10461, USA; (W.X.); (D.J.)
| | - Andre Kajdacsy-Balla
- Professor of Pathology, University of Illinois at Chicago College of Medicine, Chicago, IL 60607, USA;
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12
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Song Y, Peng Y, Qin C, Wang Y, Yang W, Du Y, Xu T. Fibroblast growth factor receptor 3 mutation attenuates response to immune checkpoint blockade in metastatic urothelial carcinoma by driving immunosuppressive microenvironment. J Immunother Cancer 2023; 11:e006643. [PMID: 37777251 PMCID: PMC10546120 DOI: 10.1136/jitc-2022-006643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) therapy holds promise in metastatic urothelial carcinoma (UC). Fibroblast growth factor receptor 3 (FGFR3) mutation drives T-cell-depleted microenvironment in UC, which led to the hypothesis that FGFR3 mutation might attenuate response to ICB in patients with metastatic UC. The study aims to compare prognosis and response between patients with FGFR3-mutated and FGFR3-wildtype metastatic UC after ICB therapy, and decode the potential molecular mechanisms. METHODS Based on the single-arm, multicenter, phase 2 trial, IMvigor210, we conducted a propensity score matched (PSM) analysis. After a 1:1 ratio PSM method, 39 patients with FGFR3-mutated and 39 FGFR3-wildtype metastatic UC treated with atezolizumab were enrolled. A meta-analysis through systematical database retrieval was conducted for validation. In addition, we performed single-cell RNA sequencing on three FGFR3-mutated and three FGFR3-wildtype UC tumors and analyzed 58,069 single cells. RESULTS The PSM analysis indicated FGFR3-mutated patients had worse overall survival (OS) in comparison to FGFR3-wildtype patients (HR=2.11, 95% CI=(1.16 to 3.85), p=0.015) receiving atezolizumab. The median OS was 9.2 months (FGFR3-mutated) versus 21.0 months (FGFR3-wildtype). FGFR3-mutated patients had lower disease control rate than FGFR3-wildtype patients (41.0% vs 66.7%, p=0.023). The meta-analysis involving 938 patients with metastatic UC confirmed FGFR3 mutation was associated with worse OS after ICB (HR=1.28, 95% CI=(1.04 to 1.59), p=0.02). Single-cell RNA transcriptome analysis identified FGFR3-mutated UC carried a stronger immunosuppressive microenvironment compared with FGFR3-wildtype UC. FGFR3-mutated UC exhibited less immune infiltration, and lower T-cell cytotoxicity. Higher TREM2+ macrophage abundance in FGFR3-mutated UC can undermine and suppress the T cells, potentially contributing to the formation of an immunosuppressive microenvironment. Lower inflammatory-cancer-associated fibroblasts in FGFR3-mutated UC recruited less chemokines in antitumor immunity but expressed growth factors to promote FGFR3-mutated malignant cell development. FGFR3-mutated UC carried abundance of malignant cells characterized by high hypoxia/metabolism and low interferon response phenotype. CONCLUSIONS FGFR3 mutation can attenuate prognosis and response to ICB in patients with metastatic UC. FGFR3-mutated UC carries a stronger immunosuppressive microenvironment in comparison with FGFR3-wildtype UC. Inhibition of FGFR3 might activate the immune microenvironment, and the combination of FGFR inhibitor targeted therapy and ICB might be a promising therapeutic regimen in metastatic UC, providing important implications for UC clinical management.
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Affiliation(s)
- Yuxuan Song
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Yun Peng
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Caipeng Qin
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Yulong Wang
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Wenbo Yang
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Yiqing Du
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Tao Xu
- Department of Urology, Peking University People's Hospital, Beijing, China
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13
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Thomas JF, Valencia-Sánchez MI, Tamburri S, Gloor SL, Rustichelli S, Godínez-López V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ. Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1. SCIENCE ADVANCES 2023; 9:eadg9832. [PMID: 37556531 PMCID: PMC10411902 DOI: 10.1126/sciadv.adg9832] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023]
Abstract
Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.
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Affiliation(s)
- Jonathan F. Thomas
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marco Igor Valencia-Sánchez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Simone Tamburri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | | | - Samantha Rustichelli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Victoria Godínez-López
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Pablo De Ioannes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kristjan Gretarsson
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | | | | | | | | | | | | | | | - William J. Rice
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Diego Pasini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
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14
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Kim M, Lee JL, Shin SJ, Bae WK, Lee HJ, Byun JH, Choi YJ, Youk J, Ock CY, Kim S, Song H, Park KH, Keam B. Phase II study of a trastuzumab biosimilar in combination with paclitaxel for HER2-positive recurrent or metastatic urothelial carcinoma: KCSG GU18-18. ESMO Open 2023; 8:101588. [PMID: 37385153 PMCID: PMC10485395 DOI: 10.1016/j.esmoop.2023.101588] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/11/2023] [Accepted: 05/21/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Human epidermal growth factor receptor 2 (HER2) is a widely explored therapeutic target in solid tumors. We evaluated the efficacy and safety of trastuzumab-pkrb, a biosimilar of trastuzumab, in combination with paclitaxel, in HER2-positive recurrent or metastatic urothelial carcinoma (UC). PATIENTS AND METHODS We enrolled 27 patients; they were administered a loading dose of 8 mg/kg trastuzumab-pkrb on day 1, followed by 6 mg/kg and 175 mg/m2 paclitaxel on day 1 every 3 weeks, intravenously. All patients received six cycles of the combination treatment and continued to receive trastuzumab-pkrb maintenance until disease progression, unacceptable toxicity, or for up to 2 years. HER2 positivity (based on immunohistochemistry analysis) was determined according to the 2013 American Society of Clinical Oncology /College of American Pathologists HER2 testing guidelines. The primary endpoint was objective response rate (ORR); the secondary endpoints were overall survival (OS), progression-free survival (PFS), and safety. RESULTS Twenty-six patients were evaluated via primary endpoint analysis. The ORR was 48.1% (1 complete and 12 partial responses) and the duration of response was 6.9 months [95% confidence interval (CI) 4.4-9.3 months]. With a median follow-up of 10.5 months, the median PFS and OS were 8.4 months (95% CI 6.2-8.8 months) and 13.5 months (95% CI 9.8 months-not reached), respectively. The most common treatment-related adverse event (TRAE) of any grade was peripheral neuropathy (88.9%). The most common grade 3/4 TRAEs were neutropenia (25.9%), thrombocytopenia (7.4%), and anemia (7.4%). CONCLUSIONS Trastuzumab-pkrb plus paclitaxel demonstrates promising efficacy with manageable toxicity profiles in patients with HER2-positive recurrent or metastatic UC.
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Affiliation(s)
- M Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul; Cancer Research Institute, Seoul National University College of Medicine, Seoul
| | - J L Lee
- Department of Oncology and Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - S J Shin
- Division of Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul
| | - W K Bae
- Department of Hemato-Oncology, Chonnam National University Medical School & Hwasun Hospital, Hwasun
| | - H J Lee
- Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon
| | - J H Byun
- Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon
| | - Y J Choi
- Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul
| | - J Youk
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul; Cancer Research Institute, Seoul National University College of Medicine, Seoul
| | - C Y Ock
- Lunit, Seoul, Republic of Korea
| | - S Kim
- Lunit, Seoul, Republic of Korea
| | - H Song
- Lunit, Seoul, Republic of Korea
| | - K H Park
- Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul
| | - B Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul; Cancer Research Institute, Seoul National University College of Medicine, Seoul.
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15
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Koll FJ, Döring C, Olah C, Szarvas T, Köllermann J, Hoeh B, Chun FKH, Reis H, Wild PJ. Optimizing identification of consensus molecular subtypes in muscle-invasive bladder cancer: a comparison of two sequencing methods and gene sets using FFPE specimens. BMC Cancer 2023; 23:504. [PMID: 37270477 DOI: 10.1186/s12885-023-11016-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Molecular subtypes predict prognosis in muscle-invasive bladder cancer (MIBC) and are explored as predictive markers. To provide a common base for molecular subtyping and facilitate clinical applications, a consensus classification has been developed. However, methods to determine consensus molecular subtypes require validation, particularly when FFPE specimens are used. Here, we aimed to evaluate two gene expression analysis methods on FFPE samples and to compare reduced gene sets to classify tumors into molecular subtypes. METHODS RNA was isolated from FFPE blocks of 15 MIBC patients. Massive analysis of 3' cDNA ends (MACE) and the HTG transcriptome panel (HTP) were used to retrieve gene expression. We used normalized, log2-transformed data to call consensus and TCGA subtypes with the consensusMIBC package for R using all available genes, a 68-gene panel (ESSEN1), and a 48-gene panel (ESSEN2). RESULTS Fifteen MACE-samples and 14 HTP-samples were available for molecular subtyping. The 14 samples were classified as Ba/Sq in 7 (50%), LumP in 2 (14.3%), LumU in 1 (7.1%), LumNS in 1 (7.1%), stroma-rich in 2 (14.3%) and NE-like in 1 (7.1%) case based on MACE- or HTP-derived transcriptome data. Consensus subtypes were concordant in 71% (10/14) of cases when comparing MACE with HTP data. Four cases with aberrant subtypes had a stroma-rich molecular subtype with either method. The overlap of the molecular consensus subtypes with the reduced ESSEN1 and ESSEN2 panels were 86% and 100%, respectively, with HTP data and 86% with MACE data. CONCLUSION Determination of consensus molecular subtypes of MIBC from FFPE samples is feasible using various RNA sequencing methods. Inconsistent classification mainly involves the stroma-rich molecular subtype, which may be the consequence of sample heterogeneity with (stroma)-cell sampling bias and highlights the limitations of bulk RNA-based subclassification. Classification is still reliable when analysis is reduced to selected genes.
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Affiliation(s)
- Florestan J Koll
- Department of Urology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany.
- Frankfurt Cancer Institute (FCI), University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany.
- University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany.
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt Am Main, Germany
| | - Csilla Olah
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Tibor Szarvas
- Department of Urology, University of Duisburg-Essen, Essen, Germany
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Jens Köllermann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt Am Main, Germany
| | - Benedikt Hoeh
- Department of Urology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
| | - Felix K-H Chun
- Department of Urology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt Am Main, Germany
| | - Peter J Wild
- Frankfurt Cancer Institute (FCI), University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt Am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt Am Main, Germany
- Frankfurt Institute for Advanced Studies (FIAS), 60438, Frankfurt Am Main, Germany
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16
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, de la Vega AA, Proehl J, Holzhauer AM, Seeman ZJ, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529970. [PMID: 36865194 PMCID: PMC9980288 DOI: 10.1101/2023.02.24.529970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many different cancers. Despite over 10 years of work, a causal relationship has yet to be established between APOBEC3B and any stage of carcinogenesis. Here we report a murine model that expresses tumor-like levels of human APOBEC3B after Cre-mediated recombination. Animals appear to develop normally with full-body expression of APOBEC3B. However, adult males manifest infertility and older animals of both sexes show accelerated rates of tumorigenesis (mostly lymphomas or hepatocellular carcinomas). Interestingly, primary tumors also show overt heterogeneity, and a subset spreads to secondary sites. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Elevated levels of structural variation and insertion-deletion mutations also accumulate in these tumors. Together, these studies provide the first cause-and-effect demonstration that human APOBEC3B is an oncoprotein capable of causing a wide range of genetic changes and driving tumor formation in vivo .
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, Ohio, USA, 43210
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
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