1
|
Peng L, He W, Ye F, Song Y, Shi X, Zhang J, Li Q, Fang Q, Xiao W, Han Y. Identification of tumor-infiltrating lymphocyte subpopulations correlated with patient prognosis in esophageal squamous cell carcinoma. J Int Med Res 2021; 49:3000605211016206. [PMID: 34044599 PMCID: PMC8168053 DOI: 10.1177/03000605211016206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objective To identify biomarkers related to esophageal squamous cell carcinoma (ESCC) prognosis by analyzing genetic variations and the infiltration levels of tumor-infiltrating lymphocytes (TILs) in patients. Methods The clinical features of 61 patients with ESCC were collected. DNA panel sequencing was performed to screen differentially expressed genes (DEGs). Transcriptome sequencing was performed to identify gene expression profiles, and subsequent enrichment analysis of DEGs was conducted using Metascape. Results We identified 488 DEGs between patients with ESCC with distinct prognoses that were mainly enriched in the human immune response, fibrinogen complex, and protein activation cascade pathways. Among patients with ESCC treated with postoperative chemotherapy, those with a high infiltration level of myeloid-derived suppressor cells (MDSCs) had longer overall survival (OS), and OS was positively correlated with the infiltration level of T helper type 2 (Th2) cells among patients treated without chemotherapy after surgery. Additionally, in the case of MDSCs >0.7059 or Th2 cells <0.6290, patients receiving postoperative chemotherapy had a longer OS than those treated without chemotherapy following surgery. Conclusion The level of MDSCs or Th2 cells can be used as a biomarker for assessing the prognosis of patients with ESCC treated with or without postoperative chemotherapy, respectively.
Collapse
Affiliation(s)
- Lin Peng
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenwu He
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng Ye
- Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Yane Song
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Xinying Shi
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Jiao Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Qingyun Li
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Qiang Fang
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenguang Xiao
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yongtao Han
- Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
2
|
Stichel D, Schrimpf D, Sievers P, Reinhardt A, Suwala AK, Sill M, Reuss DE, Korshunov A, Casalini BM, Sommerkamp AC, Ecker J, Selt F, Sturm D, Gnekow A, Koch A, Simon M, Hernáiz Driever P, Schüller U, Capper D, van Tilburg CM, Witt O, Milde T, Pfister SM, Jones DTW, von Deimling A, Sahm F, Wefers AK. Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data. Neuropathol Appl Neurobiol 2021; 47:406-414. [PMID: 33336421 DOI: 10.1111/nan.12683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/14/2020] [Accepted: 12/13/2020] [Indexed: 12/20/2022]
Abstract
AIMS KIAA1549-BRAF fusions occur in certain brain tumours and provide druggable targets due to a constitutive activation of the MAP-kinase pathway. We introduce workflows for calling the KIAA1549-BRAF fusion from DNA methylation array-derived copy number as well as DNA panel sequencing data. METHODS Copy number profiles were analysed by automated screening and visual verification of a tandem duplication on chromosome 7q34, indicative of the KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC cohort with known fusion status were used for validation. KIAA1549-BRAF fusions were called from DNA panel sequencing data using the fusion callers Manta, Arriba with modified filtering criteria and deFuse. We screened DNA methylation and panel sequencing data of 7790 specimens from brain tumour and sarcoma entities. RESULTS We identified the fusion in 337 brain tumours with both DNA methylation and panel sequencing data. Among these, we detected the fusion from copy number data in 84% and from DNA panel sequencing data in more than 90% using Arriba with modified filters. While in 74% the KIAA1549-BRAF fusion was detected from both methylation array-derived copy number and panel sequencing data, in 9% it was detected from copy number data only and in 16% from panel data only. The fusion was almost exclusively found in pilocytic astrocytomas, diffuse leptomeningeal glioneuronal tumours and high-grade astrocytomas with piloid features. CONCLUSIONS The KIAA1549-BRAF fusion can be reliably detected from either DNA methylation array or DNA panel data. The use of both methods is recommended for the most sensitive detection of this diagnostically and therapeutically important marker.
Collapse
Affiliation(s)
- Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Belén M Casalini
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander C Sommerkamp
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Astrid Gnekow
- Swabian Children's Cancer Center, University Hospital Augsburg, Augsburg, Germany
| | - Arend Koch
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK, Partner Site Berlin, German Cancer Research Center (DKFZ, Heidelberg, Germany
| | - Michèle Simon
- Department of Pediatric Oncology/Hematology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology/Hematology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK, Partner Site Berlin, German Cancer Research Center (DKFZ, Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| |
Collapse
|