genetic effects of stress in vervet monkey olivera grujic dr. eleazar eskin’s lab, ucla dr. nelson...

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