GSE116630
Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood
Purpose: Identification the biological response to fear and stress in both brain and blood is vital for investigators performing peripheral studies of psychiatric traits.   The goal of this study was to determine genes responsive to fear conditioning (FC), a well-characterized rodent model of threat-exposure, in the presence or absence of prior stress history, providing insight into the physiological processes underlying traumatic memory formation and trauma-related disorders such as PTSD. Methods: RNA sequencing was performed in blood and amygdala from mice that underwent fear conditioning (FC) with and without prior immobilization stress history (Immo+FC), or untreated animals (home cage HC). Libraries were prepared using the Illumina TruSeq™ RNA kit as per manufacturer's instructions.  Libraries were normalized and 8 samples were multiplexed in each lane of the flowcell. PhiX was used as an internal control on each lane to monitor the error statistics. Cluster generation was performed on the V3 flowcell on the Illumina cBot. The clustered flowcell was then sequenced on the Illumina HiSeq1000 system employing a single-end 101 cycles run. Alignment to the mm10 UCSC Mouse Assembly was performed using STAR version 2.3 (Dobin et al, 2013); parameters were set using the annotation as a splice junction reference.  Sample reads were assembled into transcript models using cufflinks (v2.1.1) which were then merged and processed with cuffdiff v2.1.1, (Trapnell et al, 2012) to produce per sample FPKM expression levels and estimate differential expression between the sample groups. Results: In the amygdala, 607 genes associated with FC vs. HC (FDR<.05). In the same tissue, 516 genes showed different expression in response of immobilization (Immo+FC) compared to the FC group (FDR<.05). In the blood of the same animals, 468 genes had distinct changes in expression (Immo+FC vs FC; FDR<.05) and were enriched for biological processes such as inflammation and cytokine signaling.   Conclusions: This study identified genes and pathways that respond to threat in the amygdala and blood of animals with and without a prior stress history. Future studies will be needed to examine the necessity, function and relevance of these regulated genes in human clinical stress and trauma-related disorders including. Overall design: Each group (FC; IMMO+FC; HC) consisted of 12 mice (C57BL/6J) pooled into 6 samples for sequencing  with Illumina TruSeq™ RNA. The final dataset contained the following number of samples: for blood 5 Immo+FC, 5 FC, and 4HC; for amygdala 4 Immo+FC, 6 FC, and 6 HC.