TY - JOUR
T1 - Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma
AU - Gomez, Felicia
AU - Fisk, Bryan
AU - McMichael, Joshua F.
AU - Mosior, Matthew
AU - Foltz, Jennifer A.
AU - Skidmore, Zachary L.
AU - Duncavage, Eric J.
AU - Miller, Christopher A.
AU - Abel, Haley
AU - Li, Yi Shan
AU - Russler-Germain, David A.
AU - Krysiak, Kilannin
AU - Watkins, Marcus P.
AU - Ramirez, Cody A.
AU - Schmidt, Alina
AU - Rodrigues, Fernanda Martins
AU - Trani, Lee
AU - Khanna, Ajay
AU - Wagner, Julia A.
AU - Fulton, Robert S.
AU - Fronick, Catrina C.
AU - O'Laughlin, Michelle D.
AU - Schappe, Timothy
AU - Cashen, Amanda F.
AU - Mehta-Shah, Neha
AU - Kahl, Brad S.
AU - Walker, Jason
AU - Bartlett, Nancy L.
AU - Griffith, Malachi
AU - Fehniger, Todd A.
AU - Griffith, Obi L.
N1 - Publisher Copyright:
© 2023 The Authors.
PY - 2023/11
Y1 - 2023/11
N2 - 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 gainmutations 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 amalignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrentmutations inHRScells 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.
AB - 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 gainmutations 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 amalignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrentmutations inHRScells 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.
UR - http://www.scopus.com/inward/record.url?scp=85182950470&partnerID=8YFLogxK
U2 - 10.1158/2767-9764.CRC-23-0140
DO - 10.1158/2767-9764.CRC-23-0140
M3 - Article
C2 - 37910143
AN - SCOPUS:85182950470
SN - 2767-9764
VL - 3
SP - 2312
EP - 2330
JO - Cancer research communications
JF - Cancer research communications
IS - 11
ER -