Identification of differentially expressed genes and pathways in kidney of ANCA-associated vasculitis by integrated bioinformatics analysis

The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a systematic of relatively rare autoimmune diseases with unknown cause. Kidney involvement is one of the most common clinical manifestations, and the degree of renal damage is closely associated with the development and prognosis of AAV. In this study, we utilized the Robust Rank Aggreg (RRA) method in R to integrate {"type":"entrez-geo","attrs":{"text":"GSE104948","term_id":"104948"}}GSE104948, {"type":"entrez-geo","attrs":{"text":"GSE104954","term_id":"104954"}}GSE104954, {"type":"entrez-geo","attrs":{"text":"GSE108109","term_id":"108109"}}GSE108109, {"type":"entrez-geo","attrs":{"text":"GSE108112","term_id":"108112"}}GSE108112, and {"type":"entrez-geo","attrs":{"text":"GSE108113","term_id":"108113"}}GSE108113 profile datasets loaded from Gene Expression Omnibus (GEO) database and identified a set of differentially expressed genes (DEGs) in kidney between AAV patients and living donors. Then, the results of gene ontology (GO) functional annotation showed that immunity and metabolism involved process of AAV both in glomerulus and tubulointerstitial. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that following pathways, such as complement and coagulation cascades pathway; Staphylococcus aureus infection; disease-COVID-19; and systemic lupus erythematosus (SLE) pathway play a crucial role in AAV. Next, the results analyzed by protein–protein interaction (PPI) network and Cytoscape software exhibited the hub genes ALB, TYROBP, and CYBB existed in both glomerular and tubulointerstitial compartments datasets. Finally, KEGG analysis using genes of two most important modules also further validated complement and coagulation cascades pathway and S. aureus infection existed both in glomerulus and tubulointerstitial compartments datasets. In conclusion, this study identified key genes and pathways involved in kidney of AAV, which was benefit to further uncover the mechanisms underlying the development and progress of AAV, biomarkers, and potential therapeutic targets as well.     

酒精性肝炎自噬关键基因的筛选及生物信息学分析

目的 筛选酒精性肝炎（AH）的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。 方法  采用基因表达综合数据库（GEO）中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析（WGCNA）获取关键基因。对筛选的关键基因进行基因本体（GO）、京都基因和基因组百科全书（KEGG）功能富集分析,蛋白质相互作用（PPI）分析,免疫浸润分析,构建信使RNA（mRNA）-微小RNA（miRNA）网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应（RT-qPCR）在AH患者和小鼠肝脏组织中验证。 结果  本研究筛选得到了11个与AH自噬相关的基因（EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF）,均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。 结论  SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。     

基于加权基因共表达网络鉴定肾移植术后排斥反应中巨噬细胞M1亚型相关基因

目的  鉴定肾移植术后排斥反应中巨噬细胞M1亚型表达的相关基因并构建风险模型预测移植肾存活。方法  在基因表达综合(GEO)数据库下载肾移植术后的GSE36059及GSE21374数据集。GSE36059包括发生排斥反应和稳定移植物的样本,使用该数据集进行加权基因共表达网络分析(WGCNA)和差异分析筛选差异表达的巨噬细胞M1亚型相关差异表达基因(M1-DEG)。随后将GSE21374数据集(包含了移植物丢失的随访数据)按照7∶3拆分为训练集以及验证集,在训练集中使用最小绝对收缩和选择算法(LASSO)筛选变量构建多因素Cox模型,并评估模型预测移植物存活的能力。使用CIBERSORT分析高、低风险组浸润的免疫细胞的差异,并分析两组间人类白细胞抗原(HLA)相关基因的分布,基因集富集分析(GSEA)用于进一步明确高风险组中富集的生物学过程以及通路。最后使用数据库预测与预后基因互作的微小核糖核酸(miRNA)。结果  在GSE36059数据集中,筛选得到14个M1-DEG。在GSE21374数据集中,使用LASSO-Cox回归筛选出Toll样受体8(TLR8)、Fc γ受体1B(FCGR1B)、BCL2相关蛋白A1(BCL2A1)、组织蛋白酶S(CTSS)、鸟苷酸结合蛋白2(GBP2)及半胱氨酸天冬氨酸蛋白酶招募域家族成员16(CARD16),基于这6个M1-DEG构建多因素Cox模型。风险模型在训练集中预测1年及3年移植物存活的受试者工作特征曲线下面积(AUC)分别为0.918和0.877,在验证集中预测1年及3年移植物存活的AUC分别为0.765及0.736。免疫浸润分析表明,高风险组静息及活化的CD4⁺记忆T细胞、γδT细胞、巨噬细胞M1亚型浸润增多(均为P < 0.05)。高风险组HLA Ⅰ类基因表达上调。GSEA分析表明,高风险组免疫反应及移植物排斥反应富集。CTSS与8个miRNA相互作用、BCL2A1和GBP2与3个miRNA相互作用、FCGR1B与1个miRNA相互作用。结论  本研究基于6个M1-DEG构建的预后风险模型对于预测移植肾存活具有良好的表现,可为早期对高风险受者干预提供依据。     

RNA干扰树突细胞主要组织相容性复合物1表达后诱导抑制性T细胞对小肠移植耐受的影响

目的探讨RNA干扰树突细胞（Dc）组织相容性复合物1（MHC-1）表达后获得的CD8＋CD28-抑制性T细胞（Ts）对小肠移植免疫耐受的的影响。方法通过siRNA干扰DC MHC—I表达后,诱导获得CD8^＋CD28^-Ts。建立由Wistar大鼠移植到SD大鼠的小肠移植模型36例,随机分为A组（转染实验组）、B组（未转染组,注射普通T细胞）和C组（移植对照组,注射生理盐水）。术后14d,每组各随机挑选6例,取移植大鼠小肠和血液标本行移植小肠组织病理学检查．并检测移植大鼠血清TGF-β、IFN-γ水平及回肠黏膜Na^＋-K^＋-ATP酶活性,观察移植大鼠的存活时间。结果术后第14天,A组移植大鼠血清中TGF—β和IFN-γ表达水平高于B、C组（P〈0．05）。A组大鼠肠黏膜Na^＋-K^＋-ATP酶活性为（6．3±1．0）kU／g,明显高于B组的（3．6±0．9）kU／g和C组的（2．9±1．3）kU／g（P〈0．05）。A组移植小肠病理Parks评分分级明显低于B组和C组（P〈0．05）。A、B和C组移植后大鼠中位生存时间分别为32．0、17．5和21．0d,A组存活时间明显优于B组和C组（P〈0．05）。结论将RNA干扰DCMHC—I表达所获得的CD8^＋CD28^-Ts过继小肠移植大鼠．可以减轻移植大鼠的损伤程度．抑制免疫排斥反应．     

Cytomegalovirus (CMV) infection and risk of mortality in allogeneic hematopoietic stem cell transplantation (Allo‐HSCT): A systematic review,meta‐analysis,and meta‐regression analysis

Controversy surrounds the potential association between cytomegalovirus (CMV) infection and increased risk of mortality after allogeneic hematopoietic stem cell transplantation (Allo‐HSCT). A systematic literature search was conducted using the PubMed, EMBASE, and Web of Science databases, assessing the association between CMV infection, as documented by the pp65 antigenemia assay or by polymerase chain reaction (PCR) using blood specimens, and overall mortality (OM) and nonrelapse mortality (NRM) in the allo‐HSCT setting. Pooled effects were estimated using the generic inverse variance random effects model. Heterogeneity was evaluated by Cochrane's Q test and I² statistics. The source of heterogeneity was investigated by meta‐regression and subgroup analyses. Twenty‐six of 1367 studies fulfilled eligibility criteria. CMV infection identified by PCR monitoring was significantly associated with an increased risk of OM and NRM (hazard ratio 1.47, 95% confidence interval [1.20‐1.81], P ≤ .001; hazard ratio 1.68, 95% confidence interval [1.14‐2.49], P = .05, respectively). In this setting, the use of preemptive antiviral therapy (PET) resulted in a twofold increased risk of OM and NRM. The estimated effect sizes were associated with allo‐HSCT modalities. Although our analyses point to an association between CMV infection and an increased risk of OM and NRM in allo‐HSCT recipients, the high heterogeneity across studies prevented drawing of robust conclusions on this matter.