Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France.
INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France.
Genome Biol. 2024 Aug 6;25(1):210. doi: 10.1186/s13059-024-03340-5.
Microsatellite instability (MSI) due to mismatch repair deficiency (dMMR) is common in colorectal cancer (CRC). These cancers are associated with somatic coding events, but the noncoding pathophysiological impact of this genomic instability is yet poorly understood. Here, we perform an analysis of coding and noncoding MSI events at the different steps of colorectal tumorigenesis using whole exome sequencing and search for associated splicing events via RNA sequencing at the bulk-tumor and single-cell levels.
Our results demonstrate that MSI leads to hundreds of noncoding DNA mutations, notably at polypyrimidine U2AF RNA-binding sites which are endowed with cis-activity in splicing, while higher frequency of exon skipping events are observed in the mRNAs of MSI compared to non-MSI CRC. At the DNA level, these noncoding MSI mutations occur very early prior to cell transformation in the dMMR colonic crypt, accounting for only a fraction of the exon skipping in MSI CRC. At the RNA level, the aberrant exon skipping signature is likely to impair colonic cell differentiation in MSI CRC affecting the expression of alternative exons encoding protein isoforms governing cell fate, while also targeting constitutive exons, making dMMR cells immunogenic in early stage before the onset of coding mutations. This signature is characterized by its similarity to the oncogenic U2AF1-S34F splicing mutation observed in several other non-MSI cancer.
Overall, these findings provide evidence that a very early RNA splicing signature partly driven by MSI impairs cell differentiation and promotes MSI CRC initiation, far before coding mutations which accumulate later during MSI tumorigenesis.
由于错配修复缺陷（dMMR）导致的微卫星不稳定（MSI）在结直肠癌（CRC）中很常见。这些癌症与体细胞编码事件有关，但这种基因组不稳定性的非编码病理生理影响还知之甚少。在这里，我们使用全外显子组测序分析结直肠肿瘤发生过程中不同步骤的编码和非编码 MSI 事件，并在肿瘤和单细胞水平的 RNA 测序中搜索相关的剪接事件。
我们的结果表明，MSI 导致数百个非编码 DNA 突变，特别是在多嘧啶 U2AF RNA 结合位点，这些突变在剪接中具有顺式活性，而在 MSI 与非 MSI CRC 的 mRNA 中观察到更高频率的外显子跳跃事件。在 DNA 水平上，这些非编码 MSI 突变在 dMMR 结肠隐窝的细胞转化之前很早就发生了，仅占 MSI CRC 中外显子跳跃的一部分。在 RNA 水平上，异常的外显子跳跃特征可能会损害 MSI CRC 中的结肠细胞分化，影响编码细胞命运的蛋白异构体的替代外显子的表达，同时也针对组成性外显子，使 dMMR 细胞在编码突变发生之前的早期阶段具有免疫原性。该特征的特点是与在几种其他非 MSI 癌症中观察到的致癌 U2AF1-S34F 剪接突变相似。
总的来说，这些发现提供了证据表明，一个非常早期的 RNA 剪接特征部分由 MSI 驱动，会损害细胞分化并促进 MSI CRC 的启动，远远早于在 MSI 肿瘤发生过程中积累的编码突变。
