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 |