DataSheet1_Reduced B cell frequencies in cord blood of HIV-exposed uninfected infants: an immunological and transcriptomic analysis.pdf

IntroductionIn the course of immune development, HIV-exposed uninfected (HEU) infants exhibit abnormal immune function and increased infectious morbidity compared to HIV-unexposed uninfected (HUU) infants. Yet the specific functional phenotypes and regulatory mechanisms associated with in-utero HIV and/or ART exposure remain largely obscure.
MethodsWe utilized flow cytometry and RNA-seq technologies to conduct the immunological and transcriptomic profiling in cord blood from 9 HEU mother-infant pairs and 24 HUU pairs. On top of that, we compared the cord blood dataset with the maternal venous blood dataset to characterize unique effects induced by in-utero HIV and/or ART exposure.
ResultsFlow cytometry immunophenotyping revealed that the level of B lymphocyte subsets was significantly decreased in HEU cord blood as compared to HUU (P < 0.001). Expression profiling-based cell abundance assessment, includes CIBERSORT and ssGSEA algorithm, showed a significantly reduced abundance of naive B cells in HEU cord blood (both P < 0.05), supporting the altered composition of B lymphocyte subsets in HEU. Functional enrichment analysis demonstrated suppressed innate immune responses and impaired immune regulatory function of B cells in HEU cord blood. Furthermore, through differential expression analysis, co-expression network analysis using WGCNA, and feature selection analysis using LASSO, we identified a 4-gene signature associated with HEU status. This signature effectively assesses B cell levels in cord blood, enabling discrimination between HEU and HUU infants.
DiscussionOur study provides the first comprehensive immunological and transcriptomic characterization of HEU cord blood. Additionally, we establish a 4-gene-based classifier that holds potential for predict immunological abnormalities in HEU infants.

引言：在免疫发育过程中，与HIV未暴露且未感染（HIV-unexposed uninfected, HUU）婴儿相比，HIV暴露但未感染（HIV-exposed uninfected, HEU）婴儿表现出免疫功能异常与感染性疾病发病率升高的特征。然而，与宫内HIV暴露及/或抗反转录病毒治疗（Antiretroviral Therapy, ART）暴露相关的特定功能表型与调控机制仍不甚明晰。
方法：本研究借助流式细胞术（flow cytometry）与RNA测序（RNA-seq）技术，对9对HEU母婴队列及24对HUU母婴队列的脐带血样本开展免疫学与转录组学谱分析。此外，本研究将脐带血数据集与母体静脉血数据集进行对比，以阐明宫内HIV及/或ART暴露所诱导的独特生物学效应。
结果：流式细胞术免疫表型分析结果显示，与HUU队列相比，HEU队列脐带血中的B淋巴细胞亚群水平显著降低（P < 0.001）。基于表达谱的细胞丰度评估（包括CIBERSORT与ssGSEA算法）结果显示，HEU队列脐带血中的初始B细胞丰度显著降低（两组均P < 0.05），这一结果佐证了HEU队列中B淋巴细胞亚群组成的改变。功能富集分析表明，HEU队列脐带血中的天然免疫应答受到抑制，且B细胞的免疫调控功能受损。此外，本研究通过差异表达分析、加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA）以及最小绝对收缩和选择算子（Least Absolute Shrinkage and Selection Operator, LASSO）特征选择分析，筛选出了与HEU状态相关的4基因特征标记。该特征标记可有效评估脐带血中的B细胞水平，实现HEU与HUU婴儿的区分鉴别。
讨论：本研究首次对HEU婴儿的脐带血开展了全面的免疫学与转录组学特征解析。此外，本研究构建了基于4基因的分类器，其有望用于预测HEU婴儿的免疫功能异常。