View
218
Download
0
Tags:
Embed Size (px)
Citation preview
Genetic Effects of Stress in Vervet Monkey
Olivera Grujic
Dr. Eleazar Eskin’s Lab, UCLA
Dr. Nelson Freimer’s Lab,UCLA
SoCalBSI, 2008
Project Importance
Evaluate biomedical bases of inter-individual differences in response to stressor.
Stress Related Diseases: •Depression
•Post Traumatic Stress Disorder
Response to stress has genetic component!
Challenging of Studying Genetic Factors of Stress Complex trait Experiments in humans
Need:
Model organism that reacts to stress!
Vervet Research Colony
Inbred pedigree 1000 members Small number brought to the Carribean (300-
400 years ago) 57 wild-caught brought from St. Kitts to UCLA
(1975-1989) Colony moved from UCLA to Wake Forest (in
January 2008)
African Vervets
(Chlorocebus aethiops sabaeus)
• Same stressor• Controlled environment• Good quality of tissue• Simultaneous effect in multiple organ systems• Highly informative pedigree• Vervet genetic map suitable for QTL mapping
Advantages of Researching Vervet over Human Population
Freimer NB, et al. A quantitative trait locus for variation in dopamine metabolism mapped in a primate model using reference sequences from related species. Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15811-6. Epub 2007 Sep 20.
Jasinska AJ, et al. A genetic linkage map of vervet monkey. (2007) Mamm Genome 18:347–360.
Goal: Use samples to determine effects of stress in terms of:
Moving can be stressful.
Vervet Colony exposed to a major stressor - all of them were moved under the same conditions, at the same time (in controlled way)!
Data Collection
Before move:– Blood samples from ~380 individuals– Brain tissue from 12 individuals
After move:– Blood samples from ~340 individuals– Brain tissue from 4 individuals
•gene expression profiles
•interindividual differences
Challenges
1. No vervet genome and no vervet microarrays
2. Not much known about gene expression in primate brain
3. Mostly collecting blood data
4. Available expression data only before move
First Task
Assess quality of DNA probes
Identify inter-species sequence differences
* Vervet BAC end sequences submitted to NCBI in batches
Probe Comparison WorkflowIllumina BeadStudio Output File
Extract and Add Headings
Count Frequency
Parse
Convert to
Compare Using BLAST
341,172 Vervet Sequences
22184 Probe Sequences Vervet Database
BLAST Output File
Top Hit for Each Probe
Probes per Nucleotides Matched
ResultsProbe Comparison
Length Freq
17 nucleotides
28%
18 nucleotides
15%
19 nucleotides
8%
16 nucleotides
23%
50 19749 22548 18647 16046 14645 12144 10443 7042 8141 5540 5739 4538 4437 4336 4335 6434 4433 4132 4531 4730 3529 3928 5127 6126 6725 10424 9423 20822 32221 63820 119819 166218 338217 628616 510015 104614 0
15 nucleotides
5%
20 nucleotides
5%
Probe Alignments
Second Task
Characterize regional gene expression in vervet brain Characterize group of genes with low gene expression variability between brain and blood
Approach: Cluster expression data from blood and following brain tissues:
• Head of Caudate• Cereballar Vermis• Hippocampus• Frontal Pole
• Dorsolateral Prefrontal Cortex• Orbital Frontal Cortex• Pulvinar• Occipital Pole
Obtain a list of genes where more than 75% of variability is due to inter-individual differences!
Pulvinar
Head of Caudate
Cerrebalar Vermus
Hippocampus
Frontal Pole
DLPFC
Orbital Frontal
Occipital pole
Blood
Results: Clustering
Individuals
Tissue Type
Samples
Genes
Cluster1
Cluster2
Blood Tissue
GO Analysis on Cluster 1
GO Analysis on Cluster 2
Future Work Third Task: brain to blood mapping Fourth Task: compare pre-move and
post-move expression data
Acknowledgments
SoCalBSIDr. Jamil MomandDr. Sandra SharpDr. Nancy Warter-PerezDr. Wendie JohnstonDr. Beverly KrilowiczDr. Silvia HeubachDr. Jennifer FaustRonnie ChengSoCalBSI 2008 Interns
Funded by:
UCLADr. Eleazar Eskin
Dr. Nelson Freimer
Dr. Ania Jasinska
My Labmates