دورية أكاديمية
أعرض في EDS

Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma.

التفاصيل البيبلوغرافية
العنوان: Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma.
المؤلفون: Gomez F; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri.; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri., Fisk B; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., McMichael JF; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Mosior M; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Foltz JA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Skidmore ZL; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Duncavage EJ; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri., Miller CA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Abel H; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Li YS; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri., Russler-Germain DA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Krysiak K; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri.; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri.; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri., Watkins MP; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Ramirez CA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Schmidt A; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Martins Rodrigues F; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Trani L; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Khanna A; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Wagner JA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Fulton RS; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Fronick CC; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., O'Laughlin MD; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Schappe T; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Cashen AF; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Mehta-Shah N; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Kahl BS; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Walker J; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri., Bartlett NL; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri., Griffith M; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri.; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri.; Department of Genetics, Washington University School of Medicine, St Louis, Missouri., Fehniger TA; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri., Griffith OL; Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri.; McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri.; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri.; Department of Genetics, Washington University School of Medicine, St Louis, Missouri.
المصدر: Cancer research communications [Cancer Res Commun] 2023 Nov 15; Vol. 3 (11), pp. 2312-2330.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural
اللغة: English
بيانات الدورية: Publisher: American Association for Cancer Research Country of Publication: United States NLM ID: 9918281580506676 Publication Model: Print Cited Medium: Internet ISSN: 2767-9764 (Electronic) Linking ISSN: 27679764 NLM ISO Abbreviation: Cancer Res Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [Philadelphia, Pennsylvania] : American Association for Cancer Research, [2021]-
مواضيع طبية MeSH: Hodgkin Disease*/genetics, Humans ; Reed-Sternberg Cells/metabolism ; Mutation/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Small Nuclear/metabolism
مستخلص: The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL.
Significance: Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
(© 2023 The Authors; Published by the American Association for Cancer Research.)
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معلومات مُعتمدة: K22 CA266743 United States CA NCI NIH HHS; K22 CA188163 United States CA NCI NIH HHS; U01 CA248235 United States CA NCI NIH HHS; K99 HG007940 United States HG NHGRI NIH HHS; K12 CA167540 United States CA NCI NIH HHS; U01 CA209936 United States CA NCI NIH HHS; P30 CA091842 United States CA NCI NIH HHS; U24 CA237719 United States CA NCI NIH HHS; UL1 TR002345 United States TR NCATS NIH HHS
المشرفين على المادة: 0 (RNA, Small Nuclear)
تواريخ الأحداث: Date Created: 20231101 Date Completed: 20231116 Latest Revision: 20240715
رمز التحديث: 20240715
مُعرف محوري في PubMed: PMC10648575
DOI: 10.1158/2767-9764.CRC-23-0140
PMID: 37910143
قاعدة البيانات: MEDLINE
الوصف
تدمد:2767-9764
DOI:10.1158/2767-9764.CRC-23-0140