Study Overview
In their 2021 study published in Leukemia, Hübschmann et al. conducted a comprehensive analysis of 181 germinal center-derived B-cell lymphomas (gcBCLs) using whole-genome and transcriptome sequencing. The research aimed to elucidate the mutational mechanisms influencing both coding and noncoding regions of the genome in these lymphomas.
Key Findings
Mutational Signatures
- The study identified distinct mutational signatures associated with somatic hypermutation (SHM) and class-switch recombination (CSR).
- Both SHM and CSR were found to contribute to off-target mutations in non-immunoglobulin (non-IG) genes, suggesting a broader impact on genomic integrity.
Noncoding Regions
- Mutations were prevalent in noncoding regions, including promoters and enhancers, indicating potential regulatory disruptions.
- These noncoding mutations may influence gene expression and contribute to lymphomagenesis.
Pathway Alterations
- Recurrent mutations were observed in pathways related to B-cell development and function, such as the NF-κB and JAK-STAT signaling pathways.
- These alterations underscore the role of specific signaling cascades in the pathogenesis of gcBCLs.
Clinical Implications
- The findings highlight the significance of both coding and noncoding mutations in the development of gcBCLs.
- Understanding these mutational mechanisms may inform targeted therapeutic strategies and improve diagnostic precision.
Conclusion
Hübschmann et al.’s study provides valuable insights into the mutational processes shaping the genomes of germinal center-derived B-cell lymphomas. By revealing the contributions of SHM and CSR to off-target mutations and emphasizing the importance of noncoding regions, this research advances our understanding of lymphoma biology and potential avenues for treatment.
Summary of novel genes
| Entity | Tier 1 genes | Tier 2 genes | Tier 3 genes |
|---|---|---|---|
| FL | 2 | 16 | 0 |
| DLBCL | 4 | 20 | 3 |
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This study, New Tier 1, 4
New Tier 1, DLBCL Tier 1, 4
This study, New Tier 2, 20
New Tier 2, DLBCL Tier 2, 20
This study, New Tier 3, 3
New Tier 3, DLBCL Tier 3, 3
All other DLBCL studies, DLBCL Tier 1, 121
All other DLBCL studies, DLBCL Tier 2, 190
All other DLBCL studies, DLBCL Tier 3, 384
Novel genes reported in this study
Tier 1
| New gene | FL tier | DLBCL tier | Average variant quality | QC outcome |
|---|---|---|---|---|
| ACTG1 | 2 | 1 | ||
| EEF1A1 | 1 | 1 | ||
| HLA-DMB | 1 | |||
| MEF2C | 2 | 1 | ||
| VMA21 | 1 |
Tier 2
| New gene | FL tier | DLBCL tier | Average variant quality | QC outcome |
|---|---|---|---|---|
| ADAMTS1 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| ANKRD12 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| ATP6V1A | 2 | |||
| CADPS2 | 2 | ★ ★ ★ ★ ☆ | PASS | |
| CDC42BPB | 2 | |||
| CNOT2 | 2 | ★ ★ ★ ★ ☆ | PASS | |
| CPNE8 | 2 | |||
| DHX15 | 2 | |||
| DHX16 | 2 | ★ ★ ★ ★ ☆ | PASS | |
| DNM2 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| FZR1 | 2 | |||
| IKBKE | 2 | ★ ★ ★ ★ ☆ | PASS | |
| IRF1 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| JUP | 2 | |||
| LAPTM5 | 2 | 2 | ★ ★ ★ ★ ☆ | PASS |
| LRP12 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| MGEA5 | 2 | |||
| MYCBP2 | 2 | |||
| PDS5B | 2 | 2 | ★ ★ ★ ★ ☆ | PASS |
| PNPO | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| PPP4C | 2 | |||
| PRKDC | 2 | 2 | ||
| RAC2 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| RBM6 | 2 | |||
| SIAH2 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| SLC34A2 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| TPP1 | 2 | |||
| TRAF6 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| UNC5B | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| WNK1 | 2 | ★ ★ ★ ☆ ☆ | PASS | |
| ZNF217 | 2 | ★ ★ ★ ☆ ☆ | PASS |
Tier 3
| New gene | FL tier | DLBCL tier | Average variant quality | QC outcome |
|---|---|---|---|---|
| GAK | 3 | ★ ★ ☆ ☆ ☆ | FAIL | |
| HLA-DQA1 | 3 | ★ ★ ☆ ☆ ☆ | FAIL | |
| NR2F2 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
Details
Hübschmann, Daniel, Kortine Kleinheinz, Rabea Wagener, Stephan H.
Bernhart, Cristina López, Umut H. Toprak, Stephanie Sungalee, et al.
2021. “Mutational Mechanisms Shaping the Coding and Noncoding
Genome of Germinal Center Derived B-cell
Lymphomas.” Leukemia 35 (7): 2002–16. https://doi.org/10.1038/s41375-021-01251-z.


