Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells

PMID: 36723991 · DOI: 10.1158/2643-3230.BCD-22-0128 · Journal: Blood Cancer Discovery (2023)

TL;DR

Maura and colleagues performed whole-genome sequencing on FACS-purified Hodgkin and Reed Sternberg (HRS) cells from 25 patients with classic Hodgkin lymphoma (cHL), combined with whole-exome sequencing of 36 additional cases, to build the first comprehensive WGS landscape of cHL and reconstruct the temporal order of pathogenic events. They identified new driver genes, APOBEC mutational activity, complex structural variants including chromothripsis, and showed that high ploidy in cHL is frequently reached via multiple independent chromosomal gains including whole-genome duplication. Timing analyses demonstrate that RAG-motif-enriched structural variants, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and AID-driven mutagenesis generally precede large chromosomal gains PMID:36723991.

Cohort & data

• 25 cHL cases profiled by WGS on FACS-isolated HRS cells with matched intratumoral T cells as germline control, plus 36 additional cases profiled by WES, for a combined driver-gene cohort of 61 patients PMID:36723991.
• Cancer type: classic Hodgkin lymphoma (CHL).
• Primary cohort: chl_sccc_2023.
• Two age peaks represented: pediatric/adolescent/young adult (ped/AYA, ages 7–27, n=19 WGS) and older adults (ages 55–85, n=6 WGS). 22/25 samples were from diagnosis, 3/25 from relapse.
• Median HRS DNA input 13.6 ng (range 4.2–226 ng); sequencing libraries required whole-genome amplification (median 10 cycles), and palindromic amplification artifacts were computationally removed.
• Mutational burden was benchmarked against PCAWG (n=2,780) and a multiple myeloma WGS cohort (n=71) (pcawg).
• Assays: whole-genome-seq and whole-exome-seq.

Key findings

• Post-artifact-removal median mutational burden in HRS cells was 5,279 SBS+indels per genome (range 1,880–18,883) with a median indel burden of 342 (range 108–953); this places cHL within the range of other cancers in PCAWG PMID:36723991.
• Ped/AYA cases carried a significantly higher genome-wide SBS+indel burden than older adults (median 6,270 vs 3,723, Wilcoxon P = 0.0033), independent of coverage, histology, and cancer cell fraction.
• 26 mutated driver genes/hotspots were recovered across 61 cHL patients using OncodriveFML, MutSigCV, and dndscv. Most common driver alterations: SOCS1 (62%), TNFAIP3 (36%), B2M (~32–33%), ITPKB (28%), GNA13 (26%), STAT6 (20%), BCL7A (18%), NFKBIE (15%), PTPN1 (8%), TP53 (8%), XPO1 (8%).
• Eight driver genes were newly described in cHL in this study (not previously reported in earlier WES-based cHL studies).
• APOBEC mutagenesis (SBS2 and SBS13) was highly prevalent in HRS cells, comparable to or exceeding that seen in multiple myeloma and significantly higher than in non-Hodgkin lymphoma (P < 0.00001) and CLL (P < 0.00001), suggesting a pathogenic role for APOBEC in cHL. APOBEC contribution was similar in ped/AYA and older adults and slightly enriched at relapse; no significant difference between EBV+ and EBV− cases.
• AID mutational activity (COSMIC SBS84) was detected genome-wide and concentrated on noncoding footprints of several driver genes. BCL7A, SOCS1, TMSB4X, IL4R, and ITPKB showed elevated noncoding-to-coding mutation ratios consistent with AID off-target activity.
• Complex structural variants including chromothripsis were identified, and SV breakpoints were enriched for RAG recombination motifs.
• High ploidy in cHL was typically achieved through multiple independent chromosomal gain events, including whole-genome duplication (WGD), rather than a single catastrophic event.
• Evolutionary timing analysis placed RAG-motif-enriched SVs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID mutagenesis before the large chromosomal gains/WGD, establishing these as early events in cHL pathogenesis.

Genes & alterations

• SOCS1 — mutated in 62% of cases; most common cHL driver; elevated noncoding:coding mutation ratio consistent with AID off-target activity PMID:36723991.
• TNFAIP3 — mutated in 36%; NF-κB pathway driver.
• B2M — mutated in ~32–33%; immune escape driver; timed as an early event preceding chromosomal gains.
• ITPKB — mutated in 28%; tended to carry more than one nonsynonymous mutation per case; elevated noncoding:coding ratio.
• GNA13 — mutated in 26%; enriched in EBV-negative cases; early event by timing analysis.
• STAT6 — mutated in 20%; JAK/STAT pathway.
• BCL7A — mutated in 18%; elevated noncoding:coding mutation ratio; early event by timing analysis.
• NFKBIE — mutated in 15%; NF-κB pathway.
• PTPN1 — mutated in 8%; early event by timing analysis.
• TP53 — mutated in 8%.
• XPO1 — mutated in 8%.
• TMSB4X — elevated noncoding:coding mutation ratio, consistent with AID off-target activity.
• IL4R — elevated noncoding:coding mutation ratio.

Clinical implications

• The identification of new cHL drivers and the high prevalence of APOBEC mutagenesis expand the set of candidate biomarkers and potential therapeutic vulnerabilities beyond the JAK/STAT and NF-κB pathways highlighted by prior WES studies.
• Because WGD and large chromosomal gains occur late in cHL evolution, driver events in B2M, BCL7A, GNA13, and PTPN1 and AID mutagenesis may represent earlier, potentially trackable biomarkers of cHL initiation PMID:36723991.
• The paper does not evaluate specific drug responses, so treatment implications are inferential only.

Limitations & open questions

• Small WGS cohort (n=25), particularly few older-adult (n=6) and relapse (n=3) samples, limits subgroup inferences such as age- and EBV-stratified analyses.
• HRS cells required whole-genome amplification, introducing palindromic SBS artifacts that had to be computationally removed; residual artifact could affect rare-variant and signature calling despite SBS45/SBS49 being modeled.
• Intratumoral T cells were used as germline control; any shared clonal events with HRS cells would be invisible.
• Cross-paper question: how do the temporally early drivers in cHL (B2M, BCL7A, GNA13, PTPN1) relate to the equivalent early events in DLBCL and other B-cell lymphomas that also undergo AID-driven mutagenesis?

Citations from this paper used in the wiki

• “we now report the whole-genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events leading to cHL” — Abstract.
• “We identified alterations in driver genes not previously described in cHL, APOBEC mutational activity, and the presence of complex structural variants including chromothripsis.” — Abstract.
• “high ploidy in cHL is often acquired through multiple, independent chromosomal gains events including whole-genome duplication” — Abstract.
• “structural variants enriched for RAG motifs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID-driven mutagenesis usually preceded large chromosomal gains” — Abstract.
• “WGS from 25 cases of cHL … WES from an additional 36 cases” — Introduction.
• “median SBS and indel burden of 5,279 per genome (range, 1,880–18,883) and 342 (range, 108–953)” — Results.
• “Pediatric, adolescent, and young adult patients had a higher genome-wide SBS and indel burden than older adults (median 6,270 vs. 3,723, P = 0.0033 using Wilcoxon test)” — Results.
• “The most common driver alterations were in SOCS1 (62% of cases), TNFAIP3 (36%), and B2M (32%)” — Results.
• Oncoplot frequencies: SOCS1 62%, TNFAIP3 36%, B2M 33%, ITPKB 28%, GNA13 26%, STAT6 20%, BCL7A 18%, NFKBIE 15%, PTPN1 8%, TP53 8%, XPO1 8% — Figure 1D.
• “BCL7A, SOCS1, TMSB4X, IL4R, and ITPKB showed a higher noncoding:coding mutation ratio compared with other driver [genes]” — Results (AID section).

This page was processed by crosslinker on 2026-04-10.