RNA-seq data of effect of order of infection stresses and Tet2 deletion to drive transformation of myelodysplastic syndrome

RNA-seq data of this project. Aberrant inflammatory signaling in myelodysplastic syndrome (MDS) hematopoietic stem/progenitor cells (HSPCs) due to environmental stresses including infections and normal aging has been implicated as a driver of the development of MDS. Here, we demonstrate that the earlier short-term stimulation of both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (pIpC), mimics of bacterial and viral infections, facilitated the development of MDS subsequently deleted Tet2 gene in the bone marrow in wild-type recipients, compared to na?ve Tet2-deficient cells; however, the reverse order of Tet2 deletion and the same dosage stimulation of LPS/pIpC in Tet2-deficient bone marrow cells in recipient mice did not. Consistently, normal aging in wild-type background enhanced the competitive repopulating capacity of HSPCs and myeloid cell production upon the deletion of Tet2 at two years age in mice, indicating that the earlier infection and aging stresses in wild-type background and the subsequent driver mutation facilitated the development of MDS. The earlier stimulation of LPC/pIpC and the Tet2 deletion augmented expression of genes involved in innate immune responses and Elf1 transcription factor and altered chromatin accessibility in pre-MDS stem cells dependent on Polo-like kinases downstream of the Tlr3/4-Myd88/Trif signaling, resulting in the development of progressive MDS presenting impaired differentiation and enhanced repopulation of HSPCs. Moreover, this LPS/pIpC-induced Elf1-target signature was significantly enriched in non-5q- MDS HSPCs in patients. Thus, the order of the infection stresses and the acquisition of driver mutation influenced the transcriptional and epigenetic landscapes, cellular functions and clonal expansion of MDS.

本项目的RNA测序（RNA-seq）数据相关研究背景与结果如下：环境应激（包括感染与正常衰老）引发的骨髓增生异常综合征（myelodysplastic syndrome, MDS）造血干/祖细胞（hematopoietic stem/progenitor cells, HSPCs）异常炎症信号通路，已被证实为MDS发生发展的驱动因素。
本研究证实，相较于未经刺激的Tet2缺陷细胞，提前给予细菌感染模拟物脂多糖（lipopolysaccharides, LPS）与病毒感染模拟物聚肌胞苷酸（polyinosinic:polycytidylic acid, pIpC）的短期刺激，可促进野生型受体小鼠骨髓中后续发生Tet2基因缺失的细胞的MDS发生进程；但先进行Tet2基因缺失、再以相同剂量给予LPS/pIpC刺激的Tet2缺陷骨髓细胞组，则未出现该效应。
与之相符的是，在野生型小鼠背景中，于2岁龄时敲除Tet2后，正常衰老可增强HSPCs的竞争性重建造血能力与髓系细胞生成能力，提示野生型背景下的早期感染与衰老应激，联合后续获得的驱动突变，可促进MDS的发生发展。
提前给予LPS/pIpC刺激并联合Tet2基因缺失，可上调天然免疫应答相关基因与Elf1转录因子（Elf1 transcription factor）的表达，并依赖于Tlr3/4-Myd88/Trif信号通路（Tlr3/4-Myd88/Trif signaling）下游的Polo样激酶（Polo-like kinases），改变骨髓增生异常前干细胞（pre-MDS stem cells）的染色质可及性，最终诱发以分化受损、HSPCs重植能力增强为特征的进行性MDS。
此外，LPS/pIpC诱导的Elf1靶基因特征，在非5q-骨髓增生异常综合征（non-5q- MDS）患者的HSPCs中显著富集。
综上，感染应激与驱动突变获得的先后顺序，可影响MDS的转录与表观遗传景观、细胞功能以及克隆扩增能力。