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Witt J, Haupt S, Ahadova A, Bohaumilitzky L, Fuchs V, Ballhausen A, Przybilla MJ, Jendrusch M, Seppälä TT, Fürst D, Walle T, Busch E, Haag GM, Hüneburg R, Nattermann J, von Knebel Doeberitz M, Heuveline V, Kloor M. A simple approach for detecting HLA-A*02 alleles in archival formalin-fixed paraffin-embedded tissue samples and an application example for studying cancer immunoediting. HLA 2023; 101:24-33. [PMID: 36251018 DOI: 10.1111/tan.14846] [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: 05/26/2022] [Revised: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 12/13/2022]
Abstract
The HLA system represents a central component of the antigen presentation machinery. As every patient possesses a defined set of HLA molecules, only certain antigens can be presented on the cell surface. Thus, studying HLA type-dependent antigen presentation can improve the understanding of variation in susceptibility to various diseases, including infectious diseases and cancer. In archival formalin-fixed paraffin-embedded (FFPE) tissue, the HLA type is difficult to analyze because of fragmentation of DNA, hindering the application of commonly used assays that rely on long DNA stretches. Addressing these difficulties, we present a refined approach for characterizing presence or absence of HLA-A*02, the most common HLA-A allele in the Caucasian population, in archival samples. We validated our genotyping strategy in a cohort of 90 samples with HLA status obtained by an NGS-based method. 90% (n = 81) of the samples could be analyzed with the approach. For all of them, the presence or absence of HLA-A*02 alleles was correctly determined with the method, demonstrating 100% sensitivity and specificity (95% CI: 91.40%-100% and 91.19%-100%). Furthermore, we provide an example of application in an independent cohort of 73 FFPE microsatellite-unstable (MSI) colorectal cancer samples. As MSI cancer cells encompass a high number of mutations in coding microsatellites, leading to the generation of highly immunogenic frameshift peptide antigens, they are ideally suited for studying relations between the mutational landscape of tumor cells and interindividual differences in the immune system, including the HLA genotype. Overall, our method can help to promote studying HLA type-dependency during the pathogenesis of a wide range of diseases, making archival and historic tissue samples accessible for identifying HLA-A*02 alleles.
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Affiliation(s)
- Johannes Witt
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saskia Haupt
- Engineering Mathematics and Computing Lab, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Bohaumilitzky
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vera Fuchs
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexej Ballhausen
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité -Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Jakob Przybilla
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Jendrusch
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Toni T Seppälä
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland.,Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland.,Department of Gastrointestinal Surgery, Helsinki University Central Hospital, Helsinki, Finland.,Applied Tumor Genomics Research Program, University of Helsinki, Helsinki, Finland
| | - Daniel Fürst
- Department of Transplantation Immunology, Institute of clinical Transfusion Medicine and Immune Genetics, Ulm, Germany
| | - Thomas Walle
- Department of Medical Oncology, National Centre for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Elena Busch
- Department of Medical Oncology, National Centre for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Georg Martin Haag
- Department of Medical Oncology, National Centre for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Hüneburg
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Robinson MH, Vasquez J, Kaushal A, MacDonald TJ, Velázquez Vega JE, Schniederjan M, Dhodapkar K. Subtype and grade-dependent spatial heterogeneity of T-cell infiltration in pediatric glioma. J Immunother Cancer 2020; 8:e001066. [PMID: 32788236 PMCID: PMC7422651 DOI: 10.1136/jitc-2020-001066] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related mortality in children and have distinct genomic and molecular features compared with adult glioma. However, the properties of immune cells in these tumors has been vastly understudied compared with their adult counterparts. We combined multiplex immunofluorescence immunohistochemistry coupled with machine learning and single-cell mass cytometry to evaluate T-cells infiltrating pediatric glial tumors. We show that low-grade tumors are characterized by greater T-cell density compared with high-grade glioma (HGG). However, even among low-grade tumors, T-cell infiltration can be highly variable and subtype-dependent, with greater T-cell density in pleomorphic xanthoastrocytoma and ganglioglioma. CD3+ T-cell infiltration correlates inversely with the expression of SOX2, an embryonal stem cell marker commonly expressed by glial tumors. T-cells within both HGG and low-grade glioma (LGG) exhibit phenotypic heterogeneity and tissue-resident memory T-cells consist of distinct subsets of CD103+ and TCF1+ cells that exhibit distinct spatial localization patterns. TCF1+ T-cells are located closer to the vessels while CD103+ resident T-cells reside within the tumor further away from the vasculature. Recurrent tumors are characterized by a decline in CD103+ tumor-infiltrating T-cells. BRAFV600E mutation is immunogenic in children with LGG and may serve as a target for immune therapy. These data provide several novel insights into the subtype-dependent and grade-dependent changes in immune architecture in pediatric gliomas and suggest that harnessing tumor-resident T-cells may be essential to improve immune control in glioma.
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Affiliation(s)
- M Hope Robinson
- Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Juan Vasquez
- Pediatric Oncology, Yale University, New Haven, Connecticut, USA
| | - Akhilesh Kaushal
- Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Tobey J MacDonald
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | | | | | - Kavita Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
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