2'O-ribose methylation of ribosomal RNA (rRNA 2'Ome) in primary human T cells from septic shock and COVID-19 patients

Abstract T cell exhaustion plays a central role in sepsis-induced immunosuppression. Deciphering the precise mechanism of this cellular dysfunction could lead to new therapies. In several pathophysiological contexts, the 2’O-ribose methylation of ribosomal RNA (rRNA 2’Ome) has emerged as a level of epitranscriptomic regulation. Here, we report for the first time site-specific alterations of rRNA 2’Ome epitranscriptomic marks in T cells after sepsis, associated with impaired functionality. Using primary human T cells from septic shock and COVID-19 patients, we identified a subset of sites with high inter-individual variability, the levels of which correlated with lymphocyte effector functions. This was recapitulated in an ex vivo model of stimulated T lymphocytes from healthy donors. Finally, 2’Ome signature discriminated samples from septic patients from those of healthy donors. We describe rRNA 2’Ome regulation as a new molecular mechanism that controls T lymphocyte effector function in sepsis with high potential as biomarker and therapeutic target. --------------------------------------------------- Description of the data and file structure Each folder contains the read-end counts in the sub-directory RiboMethSeq_ReadEnd_Counts and the metadata file. The metadata file describe each file contained in this sub-directory. The read-end count file structure: The name of the RNA on which the read end counting was performed. The number of the position on the RNA. The value of the read end counts at the position. Code/Software Using ribomethseq-nf pipeline, fastq were used to align reads on the human rRNA sequence (NR_046235), compute 5’/3’-end read counts. These files can be the input of rRMSAnalyzer package to adjust batch effect (ComBat-seq method) and calculate C-score corresponding to the end read count at the genomic position of interest normalized to the median of end read counts of the local environment (6 upstream and 6 downstream nucleotides).摘要 T细胞耗竭在脓毒症诱导的免疫抑制中发挥核心作用。阐明该细胞功能异常的确切机制有望催生新型治疗策略。在多种病理生理情境中，核糖体RNA的2'-O-核糖甲基化（rRNA 2'Ome）已被证实是表观转录组调控的重要层面。本研究首次报道了脓毒症后T细胞中rRNA 2'Ome表观转录组标记的位点特异性改变，且该改变与细胞功能受损相关。研究团队利用脓毒症休克及COVID-19患者的原代人T细胞，鉴定出一组具有高个体间差异的位点，其水平与淋巴细胞效应功能呈显著相关。该结果在健康供者刺激T淋巴细胞的体外模型中得到了验证。最终，rRNA 2'Ome特征谱可有效区分脓毒症患者与健康供者的样本。本研究揭示rRNA 2'Ome调控是控制脓毒症中T淋巴细胞效应功能的新型分子机制，具备开发为生物标志物与治疗靶点的巨大潜力。 --------------------------------------------------- 数据及文件结构描述 每个文件夹的子目录RiboMethSeq_ReadEnd_Counts中存储读端计数数据，同时附带元数据文件。元数据文件用于描述该子目录下的各文件。 读端计数文件的命名规则如下： 1. 完成读端计数的RNA分子名称； 2. 该RNA上的位点序号； 3. 该位点的读端计数值。 代码与软件 本研究使用ribomethseq-nf流程，将fastq格式的测序读段比对至人rRNA序列（NR_046235），并计算5’/3’端读端计数。 上述文件可作为rRMSAnalyzer软件包的输入数据，用于校正批次效应（采用ComBat-seq方法），并计算C值：即目标基因组位点的读端计数经其局部环境（上下游各6个核苷酸）的读端计数中位数归一化后得到的数值。