Epigenetics Cardiovascular Lab, Department of Genetic Medicine, Weill Cornell Medicine - Qatar, PO box 24144, Doha, Qatar.
Bioinformatics Core, Weill Cornell Medicine - Qatar, Doha, Qatar.
Cardiovasc Diabetol. 2024 Jun 7;23(1):196. doi: 10.1186/s12933-024-02292-1.
Monocytes play a central role in the pathophysiology of cardiovascular complications in type 2 diabetes (T2D) patients through different mechanisms. We investigated diabetes-induced changes in lncRNA genes from T2D patients with cardiovascular disease (CVD), long-duration diabetes, and poor glycemic control.
We performed paired-end RNA sequencing of monocytes from 37 non-diabetes controls and 120 patients with T2D, of whom 86 had either macro or microvascular disease or both. Monocytes were sorted from peripheral blood using flow cytometry; their RNA was purified and sequenced. Alignments and gene counts were obtained with STAR to reference GRCh38 using Gencode (v41) annotations followed by batch correction with CombatSeq. Differential expression analysis was performed with EdgeR and pathway analysis with IPA software focusing on differentially expressed genes (DEGs) with a p-value < 0.05. Additionally, differential co-expression analysis was done with csdR to identify lncRNAs highly associated with diabetes-related expression networks with network centrality scores computed with Igraph and network visualization with Cytoscape.
Comparing T2D vs. non-T2D, we found two significantly upregulated lncRNAs (ENSG00000287255, FDR = 0.017 and ENSG00000289424, FDR = 0.048) and one significantly downregulated lncRNA (ENSG00000276603, FDR = 0.017). Pathway analysis on DEGs revealed networks affecting cellular movement, growth, and development. Co-expression analysis revealed ENSG00000225822 (UBXN7-AS1) as the highest-scoring diabetes network-associated lncRNA. Analysis within T2D patients and CVD revealed one lncRNA upregulated in monocytes from patients with microvascular disease without clinically documented macrovascular disease. (ENSG00000261654, FDR = 0.046). Pathway analysis revealed DEGs involved in networks affecting metabolic and cardiovascular pathologies. Co-expression analysis identified lncRNAs strongly associated with diabetes networks, including ENSG0000028654, ENSG00000261326 (LINC01355), ENSG00000260135 (MMP2-AS1), ENSG00000262097, and ENSG00000241560 (ZBTB20-AS1) when we combined the results from all patients with CVD. Similarly, we identified from co-expression analysis of diabetes patients with a duration ≥ 10 years vs. <10 years two lncRNAs: ENSG00000269019 (HOMER3-AS10) and ENSG00000212719 (LINC02693). The comparison of patients with good vs. poor glycemic control also identified two lncRNAs: ENSG00000245164 (LINC00861) and ENSG00000286313.
We identified dysregulated diabetes-related genes and pathways in monocytes of diabetes patients with cardiovascular complications, including lncRNA genes of unknown function strongly associated with networks of known diabetes genes.
单核细胞通过不同的机制在 2 型糖尿病（T2D）患者的心血管并发症的病理生理学中发挥核心作用。我们研究了伴有心血管疾病（CVD）、长病程糖尿病和血糖控制不佳的 T2D 患者单核细胞中长链非编码 RNA 基因的糖尿病诱导变化。
我们对 37 名非糖尿病对照者和 120 名 T2D 患者的单核细胞进行了配对末端 RNA 测序，其中 86 名患者有或无大血管或微血管疾病或两者兼有。使用流式细胞术从外周血中分离单核细胞；纯化并测序其 RNA。使用 STAR 以 Gencode（v41）注释为参照，在进行批次校正（CombatSeq）后，对 STAR 进行比对和基因计数。采用 EdgeR 进行差异表达分析，采用 IPA 软件进行通路分析，重点关注具有 p 值<0.05 的差异表达基因（DEGs）。此外，还使用 csdR 进行差异共表达分析，以确定与糖尿病相关表达网络高度相关的 lncRNA，使用 Igraph 计算网络中心性评分，并使用 Cytoscape 进行网络可视化。
与非 T2D 相比，我们发现两个显著上调的 lncRNA（ENSG00000287255， FDR=0.017 和 ENSG00000289424， FDR=0.048）和一个显著下调的 lncRNA（ENSG00000276603， FDR=0.017）。DEGs 的通路分析显示，影响细胞运动、生长和发育的网络。共表达分析显示，ENSG00000225822（UBXN7-AS1）是糖尿病网络相关 lncRNA 中得分最高的。在 T2D 患者和 CVD 内的分析中，我们发现一种 lncRNA 在无临床记录的大血管疾病的微血管疾病患者的单核细胞中上调（ENSG00000261654， FDR=0.046）。通路分析显示，涉及影响代谢和心血管病理的网络的 DEGs。共表达分析确定了与糖尿病网络密切相关的 lncRNA，包括 ENSG0000028654、ENSG00000261326（LINC01355）、ENSG00000260135（MMP2-AS1）、ENSG00000262097 和 ENSG00000241560（ZBTB20-AS1），当我们将所有 CVD 患者的结果结合起来时。同样，我们从糖尿病患者（病程≥10 年与<10 年）的共表达分析中鉴定出两个 lncRNA：ENSG00000269019（HOMER3-AS10）和 ENSG00000212719（LINC02693）。对血糖控制良好与较差的患者的比较也鉴定出两个 lncRNA：ENSG00000245164（LINC00861）和 ENSG00000286313。
我们鉴定了伴有心血管并发症的 T2D 患者单核细胞中失调的糖尿病相关基因和通路，包括与已知糖尿病基因网络密切相关的功能未知的 lncRNA 基因。
