hubschmannMutationalMechanismsShaping2021 - morinlab/LLMPP GitHub Wiki
In their 2021 study published in Leukemia, HΓΌbschmann 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.
- 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.
- 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.
- Recurrent mutations were observed in pathways related to B-cell development and function, such as the NF-ΞΊB and JAK-STAT signaling pathways.
- These alterations underscore the role of specific signaling cascades in the pathogenesis of gcBCLs.
- 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.
HΓΌbschmann 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.
| 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
| 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 |
| New gene | FL tier | DLBCL tier | Average variant quality | QC outcome |
|---|---|---|---|---|
| ADAMTS1 | 2 | β β β β β | PASS | |
| ANKRD12 | 2 | β β β β β | PASS | |
| ATP6V1A | 2 | |||
| CADPS2 | 2 | β β β β β | PASS | |
| CDC42BPB | 2 | |||
| CNOT2 | 2 | β β β β β | PASS | |
| CPNE8 | 2 | |||
| DHX15 | 2 | |||
| DHX16 | 2 | β β β β β | PASS | |
| DNM2 | 2 | β β β β β | PASS | |
| FZR1 | 2 | |||
| IKBKE | 2 | β β β β β | PASS | |
| IRF1 | 2 | β β β β β | PASS | |
| JUP | 2 | |||
| LAPTM5 | 2 | 2 | β β β β β | PASS |
| LRP12 | 2 | β β β β β | PASS | |
| MGEA5 | 2 | |||
| MYCBP2 | 2 | |||
| PDS5B | 2 | 2 | β β β β β | PASS |
| PNPO | 2 | β β β β β | PASS | |
| PPP4C | 2 | |||
| PRKDC | 2 | 2 | ||
| RAC2 | 2 | β β β β β | PASS | |
| RBM6 | 2 | |||
| SIAH2 | 2 | β β β β β | PASS | |
| SLC34A2 | 2 | β β β β β | PASS | |
| TPP1 | 2 | |||
| TRAF6 | 2 | β β β β β | PASS | |
| UNC5B | 2 | β β β β β | PASS | |
| WNK1 | 2 | β β β β β | PASS | |
| ZNF217 | 2 | β β β β β | PASS |
| New gene | FL tier | DLBCL tier | Average variant quality | QC outcome |
|---|---|---|---|---|
| GAK | 3 | β β β β β | FAIL | |
| HLA-DQA1 | 3 | β β β β β | FAIL | |
| NR2F2 | 3 | β β β β β | FAIL |
