Dataset Information

Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE116630 | GEO | 2018/07/06

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Fear conditioning (FC) is a behavioral paradigm that measures an animalâs ability to learn fear related information. FC is measured by pairing a mild foot-shock with the surroundings in which the shock was received. Upon being placed back in the context, mice exhibit freezing behavior, which is a species-specific response to fear. We have used selective breeding to produce lines of mice with high or low levels of freezing behavior. We are able to identify alleles that govern the genetic variability for FC by using chromosomal markers in these lines. Using microarrays, we will identify differences in gene expression in two key brain regions: amygdala and hippocampus. Gene expression differences and data regarding chromosomal regions involved in the behavior will be compared to identify particular genes that are both differentially expressed and whose expression is governed by alleles that fall into critical chromosomal regions.,We will compare gene expression in the amygdala and hippocampus (brain regions known to be relevant to fear behavior) from the two lines of mice and use Bayesian statistics in an effort to identify gene expression that affects fear behavior.,We hypothesize that selection has acted in part by changing the frequency of alleles that cause differential expression of key genes in the amygdala and hippocampus of our selected lines. Selective breeding changes the frequency of trait relevant (FC) alleles. A relevant allele is expected to increase in one selected line and decrease in the oppositely selected line. Some trait relevant alleles are expected cause changes in the level of expression at particular genes.,Amygdala and hippocampus will be rapidly dissected out of experimentally naÃ¯ve mice from each line. NaÃ¯ve mice will be used for expression studies since the behavior of the mice in the FC test can be reliably anticipated due to their lineage. We have practiced these procedures, and can accurately and reproducibly remove these regions in less than 5 minutes. Different mice will be used to collect each brain region, since the dissection of hippocampus disrupts the removal of amygdala. We will collect enough samples from each region to accommodate a total of 6 microarrays per brain region, per line, thus we will use a total of 24 microarrays. We anticipate that a single brain region will be sufficient to for a microarray. However, we propose to utilize three samples per microarray, because this will reduce variability due to environmental factors and due to slight variability in our dissection procedures. Once this tissue is removed, we will isolate RNA for shipment to the Microarray consortium. We will also collect spleens from each subject as a source of genomic DNA, in order to permit direct comparison of genotype and expression phenotypes. Once we have the results of the microarray analysis, we use WebQTL.org to identify the chromosomal locations of alleles that are know to influence the expression of genes for which we have found differential expression. We will then superimpose this information on trait relevant chromosomal regions identified from our selected lines. This will allow us to rapidly identify genes which may account for genetic variability in FC due to differential expression. Such genes will then be subjected to further study.

Project description:Fear conditioning (FC) is a behavioral paradigm that measures an animal's ability to learn fear related information. FC is measured by pairing a mild foot-shock with the surroundings in which the shock was recieved. Upon being placed back in the context, mice exhibit freezing behavior, which is a species-specific response to fear. We have previously used selective breeding to produce lines of mice with high or low levels of freezing behavior. This experiment is a replication of a previous experiment that produced lines of mice with high or low levels of freezing behavior. These lines derive from different progenitor mouse strains. We are able to identify alleles that govern the genetic variability for FC by using chromosomal markers in these selected lines. Using microarrays, we will identify differences in gene expression in two key brain regions: amygdala and hippocampus. Gene expression differences and data regarding chromosomal regions involved in the behavior will be compared to identify particular genes that are both differentially expressed and whose expression is governed by alleles that fall into critical chromosomal regions.,We will compare gene expresion in the amygdala and hippocampus (brain regions known to be relevant to fear behavior) from the these two lines of mice and to the those in the previous experiment. Bayesian statistics will be used in an effort to identify gene expression that affects fear behavior.,We hypothesize that selection has acted in part by changing the frequency of alleles that cause differential expression of key genes in the amygdala and hippocampus of our selected lines. Slective breeding changes the frequency of trait relevand (FC) alleles. A relevant allele is expected to increas in one selected line and decrease in the oppositely selected line. Some trait relevant alleles are expected to cause changes in the level of expression at particular genes.,Amygdala and hippocampus will be rapidly dissected out of experimentally naÃ¯ve mice from each line. NaÃ¯ve mice will be used for expression studies since the behavior of the mice in the FC test can be reliably anticipated due to their lineage. We have practiced these procedures, and can accurately and reproducibly remove these regions in less than 5 minutes. Different mice will be used to collect each brain region, since the dissection of hippocampus disrupts the removal of amygdala. We will collect enough samples from each region to accommodate a total of 6 microarrays per brain region, per line, thus we will use a total of 24 microarrays. We anticipate that a single brain region will be sufficient to for a microarray. However, we propose to utilize three samples per microarray, because this will reduce variability due to environmental factors and due to slight variability in our dissection procedures. Once this tissue is removed, we will isolate RNA for shipment to the Microarray consortium. We will also collect spleens from each subject as a source of genomic DNA, in order to permit direct comparison of genotype and expression phenotypes. Once we have the results of the microarray analysis, we use WebQTL.org to identify the chromosomal locations of alleles that are know to influence the expression of genes for which we have found differential expression. We will then superimpose this information on trait relevant chromosomal regions identified from our selected lines. This will allow us to rapidly identify genes which may account for genetic variability in FC due to differential expression. Such genes will then be subjected to further study.

Dataset Information

Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets