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Rijnders M, Nakauma-González JA, Robbrecht DGJ, Gil-Jimenez A, Balcioglu HE, Oostvogels AAM, Aarts MJB, Boormans JL, Hamberg P, van der Heijden MS, Szabados BE, van Leenders GJLH, Mehra N, Voortman J, Westgeest HM, de Wit R, van der Veldt AAM, Debets R, Lolkema MP. Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer. Nat Commun 2024; 15:1349. [PMID: 38355607 PMCID: PMC10866910 DOI: 10.1038/s41467-024-45714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) improve overall survival in patients with metastatic urothelial cancer (mUC), but therapeutic success at the individual patient level varies significantly. Here we identify predictive markers of response, based on whole-genome DNA (n = 70) and RNA-sequencing (n = 41) of fresh metastatic biopsy samples, collected prior to treatment with pembrolizumab. We find that PD-L1 combined positivity score does not, whereas tumor mutational burden and APOBEC mutagenesis modestly predict response. In contrast, T cell-to-stroma enrichment (TSE) score, computed from gene expression signature data to capture the relative abundance of T cells and stromal cells, predicts response to immunotherapy with high accuracy. Patients with a positive and negative TSE score show progression free survival rates at 6 months of 67 and 0%, respectively. The abundance of T cells and stromal cells, as reflected by the TSE score is confirmed by immunofluorescence in tumor tissue, and its good performance in two independent ICI-treated cohorts of patients with mUC (IMvigor210) and muscle-invasive UC (ABACUS) validate the predictive power of the TSE score. In conclusion, the TSE score represents a clinically applicable metric that potentially supports the prospective selection of patients with mUC for ICI treatment.
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Affiliation(s)
- Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Alberto Nakauma-González
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Debbie G J Robbrecht
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M Oostvogels
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Maureen J B Aarts
- Department of Medical Oncology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paul Hamberg
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland Hospital, Rotterdam/Schiedam, The Netherlands
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Geert J L H van Leenders
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jens Voortman
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Hans M Westgeest
- Department of Internal Medicine, Amphia Hospital Breda, Breda, The Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Amgen Inc., Breda, The Netherlands
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Mahajan S, Balcioglu HE, Oostvogels A, Dik WA, Chan KCA, Lo KW, Hui EP, Tsang A, Tong J, Lam WKJ, Wong K, Chan ATC, Ma BBY, Debets R. Frequency of Peripheral CD8+ T Cells Expressing Chemo-Attractant Receptors CCR1, 4 and 5 Increases in NPC Patients with EBV Clearance upon Radiotherapy. Cancers (Basel) 2023; 15:cancers15061887. [PMID: 36980772 PMCID: PMC10047204 DOI: 10.3390/cancers15061887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Radiotherapy (RT) is the standard-of-care for Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC), where the post-RT clearance of plasma EBV DNA is prognostic. Currently, it is not known whether the post-RT clearance of plasma EBV DNA is related to the presence of circulating T-cell subsets. Blood samples from NPC patients were used to assess the frequency of T-cell subsets relating to differentiation, co-signaling and chemotaxis. Patients with undetectable versus detectable plasma EBV DNA levels post-RT were categorized as clearers vs. non-clearers. Clearers had a lower frequency of PD1+CD8+ T cells as well as CXCR3+CD8+ T cells during RT compared to non-clearers. Clearers exclusively showed a temporal increase in chemo-attractant receptors CCR1, 4 and/or 5, expressing CD8+ T cells upon RT. The increase in CCR-expressing CD8+ T cells was accompanied by a drop in naïve CD8+ T cells and an increase in OX40+CD8+ T cells. Upon stratifying these patients based on clinical outcome, the dynamics of CCR-expressing CD8+ T cells were in concordance with the non-recurrence of NPC. In a second cohort, non-recurrence associated with higher quantities of circulating CCL14 and CCL15. Collectively, our findings relate plasma EBV DNA clearance post-RT to T-cell chemotaxis, which requires validation in larger cohorts.
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Affiliation(s)
- Shweta Mahajan
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
| | - Hayri E Balcioglu
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
| | - Astrid Oostvogels
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
| | - Willem A Dik
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - K C Allen Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Edwin P Hui
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anna Tsang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Joanna Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai Kei Jacky Lam
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Wong
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anthony T C Chan
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Brigette B Y Ma
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Reno Debets
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
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van Hijfte L, Geurts M, Vallentgoed WR, Eilers PH, Sillevis Smitt PA, Debets R, French PJ. Alternative normalization and analysis pipeline to address systematic bias in NanoString GeoMx Digital Spatial Profiling data. iScience 2023; 26:105760. [PMID: 36590163 PMCID: PMC9800292 DOI: 10.1016/j.isci.2022.105760] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/26/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Spatial transcriptomics is a novel technique that provides RNA-expression data with tissue-contextual annotations. Quality assessments of such techniques using end-user generated data are often lacking. Here, we evaluated data from the NanoString GeoMx Digital Spatial Profiling (DSP) platform and standard processing pipelines. We queried 72 ROIs from 12 glioma samples, performed replicate experiments of eight samples for validation, and evaluated five external datasets. The data consistently showed vastly different signal intensities between samples and experimental conditions that resulted in biased analysis. We evaluated the performance of alternative normalization strategies and show that quantile normalization can adequately address the technical issues related to the differences in data distributions. Compared to bulk RNA sequencing, NanoString DSP data show a limited dynamic range which underestimates differences between conditions. Weighted gene co-expression network analysis allowed extraction of gene signatures associated with tissue phenotypes from ROI annotations. Nanostring GeoMx DSP data therefore require alternative normalization methods and analysis pipelines.
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Affiliation(s)
- Levi van Hijfte
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, the Netherlands
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Marjolein Geurts
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, the Netherlands
| | - Wies R. Vallentgoed
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, the Netherlands
| | - Paul H.C. Eilers
- Department of Biostatistics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Peter A.E. Sillevis Smitt
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, the Netherlands
| | - Reno Debets
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Pim J. French
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, the Netherlands
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