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Alontaga AY, Cano P, Ozakinci H, Puskas JA, Stewart PA, Welsh EA, Yoder SJ, Hicks JK, Saltos AN, Bossler AD, Haura EB, Koomen JM, Boyle TA. Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care. J Mol Diagn 2024:S1525-1578(24)00101-6. [PMID: 38777037 DOI: 10.1016/j.jmoldx.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next-generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant formalin-fixed, paraffin-embedded-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility, with excellent correlation (r > 0.97, P < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement of 69.4% and negative percentage agreement of 93.8%. Moderate correlation was observed between platforms (r = 0.53, P < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene, and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.
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Affiliation(s)
- Aileen Y Alontaga
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Pedro Cano
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Hilal Ozakinci
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John A Puskas
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric A Welsh
- Department of Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Sean J Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - J Kevin Hicks
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Andreas N Saltos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aaron D Bossler
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John M Koomen
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Theresa A Boyle
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
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2
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Stögbauer F, Otto R, Jöhrens K, Tinhofer I, Keilholz U, Poremba C, Keller U, Leser U, Weichert W, Boxberg M, Klinghammer K. Molecular subtyping of head and neck cancer - Clinical applicability and correlations with morphological characteristics. Oral Oncol 2024; 149:106678. [PMID: 38219707 DOI: 10.1016/j.oraloncology.2023.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/27/2023] [Accepted: 12/23/2023] [Indexed: 01/16/2024]
Abstract
AIM We aimed to evaluate the applicability of a customized NanoString panel for molecular subtyping of recurrent or metastatic head and neck squamous cell carcinoma (R/M-HNSCC). Additionally, histological analyses were conducted, correlated with the molecular subtypes and tested for their prognostic value. MATERIAL AND METHODS We conducted molecular subtyping of R/M-HNSCC according to the molecular subtypes defined by Keck et al. For molecular analyses a 231 gene customized NanoString panel (the most accurately subtype defining genes, based on previous analyses) was applied to tumor samples from R/M-HNSCC patients that were treated in the CeFCiD trial (AIO/IAG-KHT trial 1108). A total of 130 samples from 95 patients were available for sequencing, of which 80 samples from 67 patients passed quality controls and were included in histological analyses. H&E stained slides were evaluated regarding distinct morphological patterns (e.g. tumor budding, nuclear size, stroma content). RESULTS Determination of molecular subtypes led to classification of tumor samples as basal (n = 46, 45 %), inflamed/mesenchymal (n = 31, 30 %) and classical (n = 26, 25 %). Expression levels of Amphiregulin (AREG) were significantly higher for the basal and classical subtypes compared to the mesenchymal subtype. While molecular subtypes did not have an impact on survival, high levels of tumor budding were associated with poor outcomes. No correlation was found between molecular subtypes and histological characteristics. CONCLUSIONS Utilizing the 231-gene NanoString panel we were able to determine the molecular subtype of R/M-HNSCC samples by the use of FFPE material. The value to stratify for different treatment options remains to be explored in the future. The prognostic value of tumor budding was underscored in this clinically well annotated cohort.
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Affiliation(s)
- Fabian Stögbauer
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany
| | - Raik Otto
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstr. 74, 01307 Dresden, TU, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Department of Radiooncology and Radiotherapy, Charité-Universitätsmedizin Berlin, Germany
| | - Ulrich Keilholz
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Berlin Institute of Health, Berlin, Germany; Charité Comprehensive Cancer Center, Berlin, Germany
| | | | - Ulrich Keller
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; German Center for Translational Cancer Research (DKTK), DKFZ, Heidelberg, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Wilko Weichert
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Melanie Boxberg
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany; Charité Comprehensive Cancer Center, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Konrad Klinghammer
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Charité Comprehensive Cancer Center, Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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3
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Li H, Zhang Y, Xu Y, Huang Z, Cheng G, Xie M, Zhou Z, Yu Y, Xi W, Fan Y. Tumor immune microenvironment and immunotherapy efficacy in BRAF mutation non-small-cell lung cancer. Cell Death Dis 2022; 13:1064. [PMID: 36543792 PMCID: PMC9772302 DOI: 10.1038/s41419-022-05510-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Previous small-size studies reported BRAF-mutated NSCLC patients have comparable sensitivity to immune checkpoint inhibitors (ICIs). However, how BRAF mutation affects the tumor immune microenvironment (TIME) is unknown. We performed Nanostring-panel RNA sequencing to evaluate TIME in 57 BRAF mutated and wild-type (WT) NSCLC specimens (cohort A). The efficacy of ICI monotherapy or combined therapies was determined in 417 patients with WT and BRAF mutated NSCLC (cohort B). We found that BRAF-mutant tumors had similar ratios of CD8+ T cells to Tregs, the balance of cytotoxicity gene expression signatures and immune suppressive features, and similar ICI-response-related biomarkers to WT NSCLC. A similar TIME pattern was observed between the BRAF V600E and Non-V600E subgroups of NSCLC. The further retrospective study confirmed that treatment with ICI monotherapy or combined therapies resulted in similar overall survival (OS) (HR: 0.85; 95% CI, 0.56 to 1.30; p = 0.47) and progress-free survival (PFS) (HR: 1.02; 95% CI, 0.72 to 1.44; p = 0.91) of patients with WT (n = 358) and BRAF mutant (n = 59) NSCLC. Similarly, both patients with BRAF V600E or Non-V600E NSCLC had similar responses to immunotherapy. Our findings support that BRAF mutation did not modulate TIME in NSCLC and therapeutic responses to ICIs. Patients with NSCLC harboring BRAF mutation should not be denied treatment with ICIs.
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Affiliation(s)
- Hui Li
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Yongchang Zhang
- grid.216417.70000 0001 0379 7164Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410022 China
| | - Yanjun Xu
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Zhiyu Huang
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Guoping Cheng
- grid.9227.e0000000119573309Department of Pathology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Mingyin Xie
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Zichao Zhou
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
| | - Yangyang Yu
- grid.495450.90000 0004 0632 5172The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu 210042 China
| | - Wenjing Xi
- grid.495450.90000 0004 0632 5172The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu 210042 China
| | - Yun Fan
- grid.9227.e0000000119573309Department of Medical Oncology, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China
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4
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Zheng CM, Piao XM, Byun YJ, Song SJ, Kim SK, Moon SK, Choi YH, Kang HW, Kim WT, Kim YJ, Lee SC, Kim WJ, Yun SJ. Study on the use of Nanostring nCounter to analyze RNA extracted from formalin-fixed-paraffin-embedded and fresh frozen bladder cancer tissues. Cancer Genet 2022; 268-269:137-143. [PMID: 36368127 DOI: 10.1016/j.cancergen.2022.10.143] [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: 05/18/2022] [Revised: 09/28/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is the most common source of archived material for genomic medicine. However, FFPE tissue is suboptimal for high-throughput analyses, such as RNA sequencing, because the quality of nucleic acids in FFPE tissues is low. We compared RNA-seq with the nCounter system to evaluate use of FFPE tissue for genomic medicine. Twelve fresh frozen bladder cancer samples were analyzed by both RNA sequencing and nCounter, and matched FFPE samples, by nCounter. Gene-expression values obtained by these two platforms were compared by calculating Pearson correlation coefficients for each sample (across the set of matched genes) and for each matched gene (across the set of samples). For each sample, gene-expression levels measured by RNA sequencing highly correlated with those measured by nCounter (all Pearson's R > 0.8, P < 0.0001), as seen by hierarchical clustering. RNA sequencing results for fresh frozen tissues positively correlated with nCounter results for FFPE tissues (R ranged from 0.675 to 0.873, all P < 0.0001). Correlation and hierarchical-clustering analyses of nCounter data from the two specimens demonstrated a strong positive correlation between each group (R ranged from 0.779 to 0.977, all P < 0.0001). Our findings suggest that the nCounter system is useful for assaying archived-FFPE samples and that the gene-expression signatures obtained from FFPE samples represent those from fresh frozen tissues.
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Affiliation(s)
- Chuang-Ming Zheng
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Xuan-Mei Piao
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Young Joon Byun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Sun Jin Song
- Department of emergency, Chungbuk National University Hospital, Cheongju, Korea
| | - Seon-Kyu Kim
- Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung-Kwon Moon
- Department of Food Science and Technology, Chung-Ang University, Ansung, Korea
| | - Yung-Hyun Choi
- Department of Biochemistry, Dongeui University College of Oriental Medicine, Busan, Korea
| | - Ho Won Kang
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Won Tae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Yong-June Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Sang-Cheol Lee
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | | | - Seok Joong Yun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, Korea.
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5
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Miyawaki K, Sugio T. Lymphoma Microenvironment in DLBCL and PTCL-NOS: the key to uncovering heterogeneity and the potential for stratification. J Clin Exp Hematop 2022; 62:127-135. [PMID: 36171096 DOI: 10.3960/jslrt.22027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) and peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) are the most common subtypes of mature B cell neoplasm and T/NK cell lymphoma, respectively. They share a commonality in that they are, by definition, highly heterogeneous populations. Recent studies are revealing more about the heterogeneity of these diseases, and at the same time, there is an active debate on how to stratify these heterogeneous diseases and make them useful in clinical practice. The various immune cells and non-cellular components surrounding lymphoma cells, i.e., the lymphoma microenvironment, have been the subject of intense research since the late 2000s, and much knowledge has been accumulated over the past decade. As a result, it has become clear that the lymphoma microenvironment, despite its paucity in tissues, significantly impacts the lymphoma pathogenesis and clinical behavior, such as its prognosis and response to therapy. In this article, we review the role of the lymphoma microenvironment in DLBCL and PTCL-NOS, with particular attention given to its impact on the prognosis and stratification.
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Affiliation(s)
- Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takeshi Sugio
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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6
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Banerjee P, Elliott E, Rifai OM, O'Shaughnessy J, McDade K, Abrahams S, Chandran S, Smith C, Gregory JM. NLRP3 inflammasome as a key molecular target underlying cognitive resilience in amyotrophic lateral sclerosis. J Pathol 2022; 256:262-268. [PMID: 34883532 DOI: 10.1002/path.5846] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022]
Abstract
Up to 50% of amyotrophic lateral sclerosis patients present with cognitive deficits in addition to motor dysfunction, but the molecular mechanisms underlying diverse clinical and pathological presentations remain poorly understood. There is therefore an unmet need to identify molecular drivers of cognitive dysfunction to enable better therapeutic targeting and prognostication. To address this, we employed a non-biased approach to identify molecular targets using a deeply phenotyped, clinically stratified cohort of cognitively affected and unaffected brain regions from three brain regions of 13 amyotrophic lateral sclerosis patients with the same cognitive screening test performed during life. Using NanoString molecular barcoding as a sensitive mRNA sequencing technique on post-mortem tissue, we profiled a data-driven panel of 770 genes using the Neuropathology Panel, followed by region and cell type-specific validation using BaseScope in situ hybridisation and immunohistochemistry. We identified 50 significantly dysregulated genes that are distinct between cognitively affected and unaffected brain regions. Using BaseScope in situ hybridisation, we also demonstrate that macromolecular complex regulation, notably NLRP3 inflammasome modulation, is a potential, therapeutically targetable, pathological correlate of cognitive resilience in ALS. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Poulomi Banerjee
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
| | - Elizabeth Elliott
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
| | - Olivia M Rifai
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
| | - Judi O'Shaughnessy
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Karina McDade
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Sharon Abrahams
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
- School of Philosophy, Psychology and Language Science, University of Edinburgh, Edinburgh, UK
- The Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
- The Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
| | - Jenna M Gregory
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
- The Euan MacDonald Centre, University of Edinburgh, Edinburgh, UK
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7
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Budczies J, Kirchner M, Kluck K, Kazdal D, Glade J, Allgäuer M, Kriegsmann M, Heußel CP, Herth FJ, Winter H, Meister M, Muley T, Goldmann T, Fröhling S, Wermke M, Waller CF, Tufman A, Reck M, Peters S, Schirmacher P, Thomas M, Christopoulos P, Stenzinger A. Deciphering the immunosuppressive tumor microenvironment in ALK- and EGFR-positive lung adenocarcinoma. Cancer Immunol Immunother 2021; 71:251-265. [PMID: 34125345 PMCID: PMC8783861 DOI: 10.1007/s00262-021-02981-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 06/04/2021] [Indexed: 01/05/2023]
Abstract
Introduction The advent of immune checkpoint blockade (ICB) has led to significantly improved disease outcome in lung adenocarcinoma (ADC), but response of ALK/EGFR-positive tumors to immune therapy is limited. The underlying immune biology is incompletely understood. Methods We performed comparative mRNA expression profiling of 31 ALK-positive, 40 EGFR-positive and 43 ALK/EGFR-negative lung ADC focused on immune gene expression. The presence and levels of tumor infiltration lymphocytes (TILs) as well as fourteen specific immune cell populations were estimated from the gene expression profiles. Results While total TILs were not lower in ALK-positive and EGFR-positive tumors compared to ALK/EGFR-negative tumors, specific immunosuppressive characteristics were detected in both subgroups: In ALK-positive tumors, regulatory T cells were significantly higher compared to EGFR-positive (fold change: FC = 1.9, p = 0.0013) and ALK/EGFR-negative tumors (FC = 2.1, p = 0.00047). In EGFR-positive tumors, cytotoxic cells were significantly lower compared to ALK-positive (FC = − 1.7, p = 0.016) and to ALK/EGFR-negative tumors (FC = − 2.1, p = 2.0E-05). A total number of 289 genes, 40 part of cytokine–cytokine receptor signaling, were differentially expressed between the three subgroups. Among the latter, five genes were differently expressed in both ALK-positive and EGFR-positive tumors, while twelve genes showed differential expression solely in ALK-positive tumors and eleven genes solely in EGFR-positive tumors. Conclusion Targeted gene expression profiling is a promising tool to read out tumor microenvironment characteristics from routine diagnostic lung cancer biopsies. Significant immune reactivity including specific immunosuppressive characteristics in ALK- and EGFR-positive lung ADC, but not a total absence of immune infiltration supports further clinical evaluation of immune-modulators as partners of ICB in such tumors. Supplementary Information The online version contains supplementary material available at 10.1007/s00262-021-02981-w.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Julia Glade
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Claus-Peter Heußel
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology With Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,Department of Diagnostic and Interventional Radiology, University Hospital, Heidelberg, Germany
| | - Felix J Herth
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Pneumology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Torsten Goldmann
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), Member of German Center of Lung Research (DZL), Giessen, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Martin Wermke
- Department of Thoracic Oncology, Dresden University Hospital, Dresden, Germany
| | - Cornelius F Waller
- Department of Haematology, Oncology and Stem Cell Transplantation, University Medical Centre Freiburg, Freiburg, Germany
| | - Amanda Tufman
- Division of Respiratory Medicine and Thoracic Oncology, Department of Internal Medicine V and Thoracic Oncology Centre Munich, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), University of Munich (LMU), Munich, Germany
| | - Martin Reck
- Airway Research Center North (ARCN), Member of German Center of Lung Research (DZL), Giessen, Germany.,Department of Thoracic Oncology, Lung Clinic Grosshansdorf, Grosshansdorf, Germany
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne University, Lausanne, Switzerland
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik At Heidelberg University Hospital, Heidelberg, Germany
| | - Petros Christopoulos
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik At Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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Wullweber A, Strick R, Lange F, Sikic D, Taubert H, Wach S, Wullich B, Bertz S, Weyerer V, Stoehr R, Breyer J, Burger M, Hartmann A, Strissel PL, Eckstein M. Bladder Tumor Subtype Commitment Occurs in Carcinoma In Situ Driven by Key Signaling Pathways Including ECM Remodeling. Cancer Res 2021; 81:1552-1566. [PMID: 33472889 DOI: 10.1158/0008-5472.can-20-2336] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/24/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
Basal and luminal subtypes of invasive bladder tumors have significant prognostic and predictive impacts for patients. However, it remains unclear whether tumor subtype commitment occurs in noninvasive urothelial lesions or in carcinoma in situ (CIS) and which gene pathways are important for bladder tumor progression. To understand the timing of this commitment, we used gene expression and protein analysis to create a global overview of 36 separate tissues excised from a whole bladder encompassing urothelium, noninvasive urothelial lesions, CIS, and invasive carcinomas. Additionally investigated were matched CIS, noninvasive urothelial lesions, and muscle-invasive bladder cancers (MIBC) from 22 patients. The final stage of subtype commitment to either a luminal or basal MIBC occurred at the CIS transition. For all tissues combined, hierarchical clustering of subtype gene expression revealed three subtypes: "luminal," "basal," and a "luminal p53-/extracellular matrix (ECM)-like" phenotype of ECM-related genes enriched in tumor-associated urothelium, noninvasive urothelial lesions, and CIS, but rarely invasive, carcinomas. A separate cohort of normal urothelium from noncancer patients showed significantly lower expression of ECM-related genes compared with tumor-associated urothelium, noninvasive urothelial lesions, and CIS. A PanCancer Progression Panel of 681 genes unveiled pathways specific for the luminal p53-/ECM-like cluster, for example, ECM remodeling, angiogenesis, epithelial-to-mesenchymal transition, cellular discohesion, cell motility involved in tumor progression, and cell proliferation and oncogenic ERBB2/ERBB3 signaling for invasive carcinomas. In conclusion, this study provides insights into bladder cancer subtype commitment and associated signaling pathways, which could help predict therapy response and enhance our understanding of therapy resistance. SIGNIFICANCE: This study demonstrates that CIS is the stage of commitment for determining MIBC tumor subtype, which is relevant for patient prognosis and therapy response.
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Affiliation(s)
- Adrian Wullweber
- Department of Internal Medicine, Evangelisches Krankenhaus Düsseldorf, Düsseldorf, Germany.,Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Reiner Strick
- Translational Research Centre (TRC), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Fabienne Lange
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Danijel Sikic
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Helge Taubert
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sven Wach
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Bernd Wullich
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Simone Bertz
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Veronika Weyerer
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Johannes Breyer
- Department of Urology, Caritas Hospital St. Josef, University of Regensburg, Regensburg, Germany
| | - Maximilian Burger
- Department of Urology, Caritas Hospital St. Josef, University of Regensburg, Regensburg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Pamela L Strissel
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Translational Research Centre (TRC), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Budczies J, Kirchner M, Kluck K, Kazdal D, Glade J, Allgäuer M, Kriegsmann M, Heußel CP, Herth FJ, Winter H, Meister M, Muley T, Fröhling S, Peters S, Seliger B, Schirmacher P, Thomas M, Christopoulos P, Stenzinger A. A gene expression signature associated with B cells predicts benefit from immune checkpoint blockade in lung adenocarcinoma. Oncoimmunology 2021; 10:1860586. [PMID: 33520406 PMCID: PMC7808386 DOI: 10.1080/2162402x.2020.1860586] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 01/19/2023] Open
Abstract
Immune checkpoint blockade (ICB) expands the therapeutic options for metastatic lung cancer nowadays representing a standard frontline strategy as monotherapy or combination therapy, as well as an option in oncogene-addicted NSCLC after exhaustion of targeted therapies. Predictive markers are urgently needed, since only a minority of patients benefits from ICB, while serious adverse effects of immunotoxicity may occur. The study cohort included 43 ICB-treated metastatic lung adenocarcinoma showing long-term response (n = 16), rapid progression (n = 21) or intermediate patterns of response (n = 6). Lung biopsies acquired before initiation of ICB were analyzed by targeted mRNA expression profiling of 770 genes. Level and proportions of 14 immune cell types were estimated using characteristic gene expression signatures. Abundance of B cells (HR = 0.66, p = .00074), CD45+ cells (HR = 0.61, p = .01) and total TILs (HR = 0.62, p = .025) was associated with prolonged progression-free survival after ICB treatment. In a ROC analysis, B cells (AUC = 0.77, p = .0055) and CD45+ cells (AUC = 0.73, p = .019) predicted benefit of ICB, which was not the case for PD-L1 mRNA (AUC = 0.54, p = .72) and PD-L1 protein expression (AUC = 0.68, p = .082). Clustering of 79 candidate predictive markers identified among 770 investigated genes revealed two distinct predictive clusters which included cytotoxic cell or macrophage markers, respectively. In summary, targeted gene expression profiling was feasible using routine diagnostics biopsies. This study proposes B cells and total TILs as complementary predictors of ICB benefit in NSCLC. While further preferably prospective validation is required, gene expression profiling could be integrated in the routine diagnostic work-up complementing existing NGS protocols.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Julia Glade
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Claus-Peter Heußel
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix J. Herth
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pneumology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne University, Lausanne, Switzerland
| | - Barbara Seliger
- Institute for Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Thomas
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor Diseases at Heidelberg University Hospital, Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor Diseases at Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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