PO.BCS01.09 · 生物信息与计算
从单细胞RNA测序中捕获的细胞类型特异性体细胞变异是恶变前血液转录程序的基础
Cell type-specific somatic variants captured from single-cell RNA sequencing underlie transcriptional programs in pre-malignant blood
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：血液中的体细胞变异及其在血液系统恶性肿瘤中的预后潜力，在克隆性造血（CH）的背景下已得到充分确立，但其对全局基因表达和转录程序的功能性影响仍未得到充分研究。我们对频繁出现的体细胞变异（包括已知癌症驱动基因内和基因外的变异）与转录程序之间进行了关联分析，以在分子层面理解血液中遗传嵌合的表型后果。
方法：在安大略健康研究（Ontario Health Study）中的400份样本队列上开展了单细胞RNA测序（scRNAseq）、bulk ATAC测序（ATAC-seq）和RipTide全基因组测序（WGS）。这些样本按年龄（<45岁或>65岁）和Intermountain风险评分（低风险或高风险）进行分层，该评分与全因死亡率强相关。利用scRNAseq在每份样本中按细胞类型鉴定体细胞变异，并过滤掉通过ATAC-seq和RipTide WGS鉴定的种系变异。使用Hotspot提取细胞类型特异性基因表达模块，并对假bulk谱进行每个模块使用度的评分。开展线性回归，在给定体细胞变异携带状态并校正协变量的情况下，预测每种细胞类型的模块评分。
结果：我们在B细胞中鉴定出6个体细胞变异，在初始T细胞中鉴定出10个，这些变异在整个队列中至少出现15次。在B细胞中，AFF3和IL3RA的体细胞变异与模块I的上调相关（AFF3：OR=1.26，adj(p)=0.067；IL3RA：OR=1.26，adj(p)=0.076），该模块在低风险样本中相较高风险样本升高（adj(p)=0.020）。B细胞中AFF3体细胞变异的变异等位基因频率（VAF）与模块C的上调相关（ρ=0.510，p=0.0055），通过基因集富集分析该模块富集了热休克反应相关条目。在初始T细胞中，MIR4426的VAF与模块H的上调相关（ρ=0.694，p=4.8e-4），该模块在年轻样本中相较老年样本升高（adj(p)=4.7e-29）。
结论：我们描述了体细胞变异如何在400名个体中塑造血液细胞类型特异性转录程序的格局。有趣的是，我们鉴定出AFF3的相关信号（其基因融合事件在急性淋巴细胞白血病中已有充分描述）以及IL3RA的相关信号（其表达升高是急性髓系白血病的确立特征）。仍需进一步工作以将转录程序的使用与新发血液系统恶性肿瘤结局相关联。
查看英文原文 English abstract
Background: Somatic variants in blood and their prognostic potential in hematological malignancy are well-established in the context of clonal hematopoiesis (CH), but their functional impacts on global gene expression and transcriptional programs remain understudied. We conducted associations between frequently occurring somatic variants, both within and outside of known cancer driver genes, and transcriptional programs to understand phenotypic consequences of genetic mosaicism in blood at the molecular level.
Methods: Single-cell RNA sequencing (scRNAseq), bulk ATAC-sequencing (ATAC-seq), and RipTide whole-genome sequencing (WGS) were conducted on a cohort of 400 samples within the Ontario Health Study. These samples were stratified according to age (<45 or >65 years) and the Intermountain Risk Score (low-risk or high-risk), which is strongly correlated with all-cause mortality. Somatic variants were identified per cell type in each sample with scRNAseq, filtering out germline variants identified with ATAC-seq and RipTide WGS. Cell type-specific gene expression modules were extracted using Hotspot, and pseudobulk profiles were scored for the usage of each module. Linear regressions were conducted to predict module scores for each cell type given somatic variant carrier status and adjusted for covariates.
Results: We identified 6 somatic variants in B cells and 10 in naive T cells which occurred at least 15 times across the cohort. In B cells, somatic variants in AFF3 and IL3RA associated with an upregulation of Module I (AFF3: OR=1.26, adj(p)=0.067; IL3RA: OR=1.26, adj(p)=0.076), which is increased in low-risk samples compared to high-risk (adj(p)=0.020). The variant allele frequency (VAF) of AFF3 somatic variants in B cells was correlated with an upregulation of Module C (ρ=0.510, p=0.0055), which is enriched for heat shock response terms with gene set enrichment analysis. In Naive T cells, MIR4426 VAF correlated with an upregulation of Module H (ρ=0.694, p=4.8e-4), which is increased in young samples compared to aged samples (adj(p)=4.7e-29).
Conclusions: We described how somatic variants shape the landscape of cell type-specific transcriptional programs in blood across 400 individuals. Interestingly, we identified hits in AFF3, of which gene fusion events are well-described in acute lymphoblastic leukemia, and in IL3RA, whose increased expression is an established feature of acute myeloid leukemia. Further work is needed to correlate transcriptional program usage with incident hematological malignancy outcomes.
利益披露 Disclosure
J. Kang, None..
M. Agbessi, None..
J. Kim, None..
I. Nofech-Mozes, None..
M. Fave, None..
P. Awadalla, None.