Solano-Aguilar Gloria, Molokin Aleksey, Botelho Christine, Fiorino Anne-Maria, Vinyard Bryan, Li Robert, Chen Celine, Urban Joseph, Dawson Harry, Andreyeva Irina, Haverkamp Miriam, Hibberd Patricia L
Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
Division of Global Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
PLoS One. 2016 Feb 9;11(2):e0147426. doi: 10.1371/journal.pone.0147426. eCollection 2016.
We examined gene expression of whole blood cells (WBC) from 11 healthy elderly volunteers participating on a Phase I open label study before and after oral treatment with Lactobacillus rhamnosus GG-ATCC 53103 (LGG)) using RNA-sequencing (RNA-Seq). Elderly patients (65-80 yrs) completed a clinical assessment for health status and had blood drawn for cellular RNA extraction at study admission (Baseline), after 28 days of daily LGG treatment (Day 28) and at the end of the study (Day 56) after LGG treatment had been suspended for 28 days. Treatment compliance was verified by measuring LGG-DNA copy levels detected in host fecal samples. Normalized gene expression levels in WBC RNA were analyzed using a paired design built within three analysis platforms (edgeR, DESeq2 and TSPM) commonly used for gene count data analysis. From the 25,990 transcripts detected, 95 differentially expressed genes (DEGs) were detected in common by all analysis platforms with a nominal significant difference in gene expression at Day 28 following LGG treatment (FDR<0.1; 77 decreased and 18 increased). With a more stringent significance threshold (FDR<0.05), only two genes (FCER2 and LY86), were down-regulated more than 1.5 fold and met the criteria for differential expression across two analysis platforms. The remaining 93 genes were only detected at this threshold level with DESeq2 platform. Data analysis for biological interpretation of DEGs with an absolute fold change of 1.5 revealed down-regulation of overlapping genes involved with Cellular movement, Cell to cell signaling interactions, Immune cell trafficking and Inflammatory response. These data provide evidence for LGG-induced transcriptional modulation in healthy elderly volunteers because pre-treatment transcription levels were restored at 28 days after LGG treatment was stopped. To gain insight into the signaling pathways affected in response to LGG treatment, DEG were mapped using biological pathways and genomic data mining packages to indicate significant biological relevance.
ClinicalTrials.gov NCT01274598.
我们使用RNA测序（RNA-Seq）技术，检测了11名参与I期开放标签研究的健康老年志愿者口服鼠李糖乳杆菌GG-ATCC 53103（LGG）前后全血细胞（WBC）的基因表达情况。老年患者（65 - 80岁）完成了健康状况的临床评估，并在研究入组时（基线）、每日LGG治疗28天后（第28天）以及LGG治疗暂停28天后的研究结束时（第56天）采集血液用于细胞RNA提取。通过测量宿主粪便样本中检测到的LGG-DNA拷贝水平来验证治疗依从性。使用常用于基因计数数据分析的三个分析平台（edgeR、DESeq2和TSPM）构建的配对设计，分析WBC RNA中的标准化基因表达水平。在检测到的25,990个转录本中，所有分析平台共同检测到95个差异表达基因（DEG），在LGG治疗后的第28天基因表达存在名义上的显著差异（FDR<0.1；77个基因表达下降，18个基因表达增加）。采用更严格的显著性阈值（FDR<0.05）时，只有两个基因（FCER2和LY86）下调超过1.5倍，并且在两个分析平台上均符合差异表达标准。其余93个基因仅在DESeq2平台上在此阈值水平被检测到。对绝对变化倍数为1.5的DEG进行生物学解释的数据分析显示，与细胞运动、细胞间信号相互作用、免疫细胞转运和炎症反应相关的重叠基因下调。这些数据为LGG在健康老年志愿者中诱导的转录调节提供了证据，因为在LGG治疗停止后28天，预处理转录水平得以恢复。为了深入了解LGG治疗后受影响的信号通路，使用生物途径和基因组数据挖掘软件包对DEG进行映射，以表明其显著的生物学相关性。
ClinicalTrials.gov NCT01274598。
Zotero 插件
