Identification of Leukemia-Enriched Signature Through the Development of a Comprehensive Pediatric Single-Cell Atlas

Single-cell transcriptome profiling enables unparalleled characterization of the heterogeneous microenvironment of pediatric leukemias. To facilitate comparative analyses and generate pediatric leukemia signatures, we collect, process, and annotate single-cell data comprising over 540,000 cells from 159 different pediatric acute leukemia (myeloid, lymphoid, mixed phenotype lineages) and healthy bone marrow (BM) samples, profiled in our lab and curated from publicly available studies. The analysis identifies a leukemia-enriched signature of nine genes with over-expression in leukemic blast as compared to healthy BM cells. The signature is also consistently over-expressed in leukemia samples compared to normal BM in bulk RNA-seq data from the TARGET initiative. Outcome-based analysis using measurable residual disease (MRD) status depicts the enrichment of oncogene-induced senescence and g-protein activation pathways in leukemia patients at diagnosis who achieve MRD positivity at the end of induction. MRD positivity across pediatric leukemias is associated with significant depletion of CD8+ and CD4+ naïve T-cells and M1-macrophages at diagnosis. To enable easy access to this uniformly integrated pediatric leukemia single-cell atlas, we develop the Pediatric Single-cell Cancer Atlas (PedSCAtlas, https://bhasinlab.bmi.emory.edu/PediatricSCAtlas/) resource. The atlas allows for quick exploration of single-cell data based on genes, cell types, and clinical outcomes to understand the cellular landscape of pediatric leukemias. Single-cell RNA sequencing performed on two healthy pediatric bone marrow samples, with 10x Genomics 3'V2 kit. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************

单细胞转录组分析（single-cell transcriptome profiling）可实现对儿童白血病异质性微环境的前所未有的精准解析。为助力比较分析并构建儿童白血病特征基因集，我们收集、处理并注释了来自159例不同类型儿童急性白血病（髓系、淋系、混合表型谱系）及健康骨髓（BM）样本的单细胞数据，共计超过54万个细胞；这些数据既来源于本实验室的测序工作，也从已公开的研究中整理获取。本分析鉴定出一组由9个基因构成的白血病富集特征集，与健康骨髓细胞相比，该特征集在白血病原始细胞中呈现显著高表达。该特征集在TARGET计划的批量RNA测序数据中，同样在白血病样本中相较于正常骨髓样本呈现持续高表达。基于可测量残留病（measurable residual disease, MRD）状态的预后分析显示，在诱导治疗结束时出现MRD阳性的初诊白血病患者中，癌基因诱导的细胞衰老及G蛋白激活通路显著富集。在各类儿童白血病中，初诊时出现MRD阳性与CD8+及CD4+初始T细胞、M1型巨噬细胞的显著耗竭存在关联。为方便用户便捷使用这一统一整合的儿童白血病单细胞图谱，我们构建了儿童单细胞癌症图谱（Pediatric Single-cell Cancer Atlas, PedSCAtlas，https://bhasinlab.bmi.emory.edu/PediatricSCAtlas/）数据库资源。该图谱支持基于基因、细胞类型及临床结局的单细胞数据快速探索，以解析儿童白血病的细胞图谱特征。本研究使用10x Genomics 3'V2试剂盒对2例健康儿童骨髓样本开展了单细胞RNA测序。
**************************************************************** 由于担心提交可公开获取的人类/患者样本的可识别个体序列数据存在隐私风险，本研究未将人类/患者样本的原始测序文件上传至GEO数据库。 ****************************************************************