综合分析基因芯片和单细胞 RNA-seq 数据，全面鉴定活动性肺结核的免疫相关转录特征。

Comprehensive identification of immuno-related transcriptional signature for active pulmonary tuberculosis by integrated analysis of array and single cell RNA-seq.

机构信息

Department of Clinical Laboratory, Shenzhen Baoan Hospital, The Second Affiliated Hospital of Shenzhen University, Shenzhen 518101, China.

Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou/State Key Laboratory of Respiratory Disease, Hengzhigang Road 1066, Guangzhou 510095, China.

出版信息

J Infect. 2022 Nov;85(5):534-544. doi: 10.1016/j.jinf.2022.08.017. Epub 2022 Aug 22.

DOI:10.1016/j.jinf.2022.08.017

PMID:36007657

Abstract

BACKGROUND

Tuberculosis (TB) continues to be a major cause of morbidity and mortality worldwide. However, the molecular mechanism underlying immune response to human infection with Mycobacterium tuberculosis (Mtb) remains unclear. Assessing changes in transcript abundance in blood between health and disease on a genome-wide scale affords a comprehensive view of the impact of Mtb infection on the host defense and a reliable way to identify novel TB biomarkers.

METHODS

We combined expression profiling by array and single cell RNA-sequencing (scRNA-seq) via 10X Genomics platform to better illustrate the immuno-related transcriptional signature of TB and explore potential diagnostic markers for differentiating TB from latent tuberculosis infection (LTBI) and healthy control (HC).

FINDINGS

Pathway analysis based on differential expressed genes (DEGs) revealed that immune transcriptional profiling could effectively differ TB with LTBI and HC. Following WGCNA and PPI network analysis based on DEGs, we screened out three key immuno-related hub genes (ADM, IFIT3 and SERPING1) highly associated with TB. Further validation found only ADM expression significantly increased in TB patients in both adult and children's datasets. By comparing the scRNA-seq datasets from TB, LTBI and HC, we observed a remarkable elevated expression level and proportion of ADM in TB Myeloid cells, further supporting that ADM expression changes could distinguish patients with TB from LTBI and HC. Besides, the hsa-miR-24-3p-NEAT1-ADM-CEBPB regulation pathway might be one of the critical networks regulating the pathogenesis of TB. Although further investigation in a larger cohort is warranted, we provide useful and novel insight to explore the potential candidate genes for TB diagnosis and intervention.

INTERPRETATION

We propose that the expression of ADM in peripheral blood could be used as a novel biomarker for differentiating TB with LTBI and HC.

摘要

背景

结核病（TB）仍然是全球发病率和死亡率的主要原因。然而，人类感染结核分枝杆菌（Mtb）后免疫反应的分子机制仍不清楚。在全基因组范围内评估健康和疾病状态下血液中转录物丰度的变化，可以全面了解 Mtb 感染对宿主防御的影响，并为鉴定新的 TB 生物标志物提供可靠方法。

方法

我们通过 10X Genomics 平台结合芯片表达谱和单细胞 RNA 测序（scRNA-seq），更好地阐明了 TB 的免疫相关转录特征，并探索了潜在的诊断标志物，用于区分 TB 与潜伏性结核感染（LTBI）和健康对照（HC）。

发现

基于差异表达基因（DEGs）的通路分析表明，免疫转录组分析可有效区分 TB 与 LTBI 和 HC。基于 DEGs 的 WGCNA 和 PPI 网络分析后，我们筛选出三个与 TB 高度相关的关键免疫相关枢纽基因（ADM、IFIT3 和 SERPING1）。进一步验证发现，只有 ADM 在 TB 患者中的表达在成人和儿童数据集均显著增加。通过比较来自 TB、LTBI 和 HC 的 scRNA-seq 数据集，我们观察到 TB 髓细胞中 ADM 的表达水平和比例显著升高，进一步表明 ADM 表达变化可将 TB 患者与 LTBI 和 HC 区分开来。此外，hsa-miR-24-3p-NEAT1-ADM-CEBPB 调控通路可能是调节 TB 发病机制的关键网络之一。尽管需要在更大的队列中进行进一步研究，但我们为探索 TB 诊断和干预的潜在候选基因提供了有用和新颖的见解。