the hybrid mouse diversity panel - national institute of ... hybrid mouse diversity panel (hmdp) ......

The Hybrid Mouse Diversity Panel: A Resource for Systems Genetics

Brian W. Parks University of California, Los Angeles

The Hybrid Mouse Diversity Panel (HMDP)

Over 100 fully genotyped genetically unique inbred mice

Large diversity in clinically-relevant parameters

Ability to perform systems genetics analysis across multiple scales of biology

Understand biological parameters as they work under natural genetic variation

Microbiome

Clinical Traits

Transcriptome Metabalome

Lipidome

Proteome

Genome

Linkage

Resolution: 20-80mb

Genes: 1000s

Association

Resolution: 0.5-5mb

Genes: 1-60

High-Resolution Association Mapping

AA BB 0 1 2 3 4 5 6 7 8

AA BB 0 1 2 3 4 5 6 7 8

SNP-2

Genome-Wide Association Studies

SNP-1

-log 10

(p)

Bennett, B. et al. Genome Res. 2010

HMDP GWAS: HDL Cholesterol

Using Systems Genetics to Identify Genes and Determine Pathways

Civelek M and Lusis AJ, Nat Rev Genetics. 2014

Identify cis and trans expression QTL (eQTL)

Cis- (Local) acting variant

Trans- acting variant

Leptin

Systems Genetics: Integration of Genome-wide Gene Expression Data

Correlation

No LPS + LPS

m Mouse strains Mouse strains

Ifi20

5

Npl

Orozco et. al. Cell 2012

Genetics of Gene Expression: Gene X Environment Interactions

Sorbitol dehydrogenase is part of the polyol pathway that plays an important role in diabetic complications

cis-acting eQTL mediating gene-by-diet interaction

Genetics of Gene Expression:

Gene X Diet Interactions

HMDP: Gene Identification and Validation

Bone Mineral Density (Asxl2) Farber et.al. Plos Genetics. 2011 Obesity (Cbr1) Parks et.al. Cell Metabolism. 2013 Insulin Resistance (Agpat5) Parks et.al. Cell Metabolism. 2015 Cardiac Fibrosis (Abcc6) Rau et.al. Circ Cardiovasc Genet. 2015 Inflammatory Gene Expression (2310061C15Rik) Orozco et.al. Cell 2012 DNA methylation (Mttr) Orozco et.al. Cell Metabolism (Accepted) Network Integration Osteoblast Lineage (Maged1 and Pard6g) Farber et.al. Plos Genetics 2012

Trait distribution

Association mapping

Farber et.al. Plos Genetics. 2011

GWAS: Bone Mineral Density (BMD)

GWAS: Bone Mineral Density (BMD)

Farber et.al. Plos Genetics. 2011

Validation: Asxl2 Deletion Decreases Bone Mineral Density

Farber et.al. Plos Genetics. 2011

Environment

Genetics

Disease

Food Consumption

Body Composition (NMR)

End Study

0 10 8 12 14 16 Weeks:

High Fat/High Sucrose Diet

HMDP Obesity and Metabolic Syndrome Project: Study Design

Large Variation in Response to Diet

Parks BW, et. al. Cell Metabolism. 2013 Jan 8;17(1):141-52

Fries

Npc1

17 19

GWAS For Response To Diet -lo

g 10(

p)

Parks BW, et. al. Cell Metabolism. 2013

Amy1

Nature Genetics 41, 157 - 159 (2009)

NPC1 and AMY1: Identified In Human Studies

Nature Genetics. 2014 May;46(5):492-7

Male

Female

Ntng1

Ntng1

17 19

16 18

The First GWAS for Food Intake? -lo

g 10

(p)

-log 1

0 (p

)

Molecular Psychiatry 16, 949-959 (2011)

NTNG1 Identified in Human GWAS for Anorexia

Relevance to Humans?

Farber et.al. Plos Genetics. 2011

Parks et.al. Cell Metabolism. 2013

HMDP

Gene Identification

Biological Pathway

Systems Genetics: Pathway Discovery

Chromosome 16 Locus For Body Fat Response To Diet

-log 1

0 (p

)

Parks BW, et. al. Cell Metabolism. 2013

Cbr1 cis eQTL

Systems Genetics: Integration of Gene Expression

Adipose Tissue From High-Fat/High-Sucrose Fed Male Mice

Parks BW, et. al. Cell Metabolism. 2013

Carbonyl Reductase 1

NADPH-dependent reductase with broad substrate specificity.

Catalyzes the reduction of a wide variety of carbonyl compounds including quinones, prostaglandins, plus various xenobiotics.

What is Cbr1?

Never before studied in obesity and metabolism

020406080

100120140160180

Cbr1 +/+ Cbr1 +/-

Body

fat p

erce

ntag

e ch

ange

(8

wee

ks h

igh-

fat/h

igh-

sucr

ose

diet

)

Validation of Cbr1

How is Cbr1 controlling dietary responses?

0 2 4 6 8 10

Lymph nodeSpleen

Subcutaneous adiposeVisceral adipose

Brown adiposeLiverHeart

MuscleHypothalamus

Striatum/cerebellumLung

DuodenumJejunum

IleumColon

KidneyAdrenal Gland

Gall Bladder

Cbr1 Expressed in Multiple Relevant Tissues

Cbr1 expression in liver correlates with hypo-taurine (conjugated to Bile Acids)

Cbr1 is a direct FXR target gene

Cbr1

GW4064 GSK2324

− + − − + − − − + − − +

mR

NA

(Fol

d ch

ange

)

FXR WT FXR KO

Cbr1

FXRE FXR ChIP-Seq

Environment

Genetics

Disease Microbiome

Chow Diet High-Fat/High-Sucrose Diet

Actinobacteria Bacteroidetes Firmicutes Other Proteobacteria Tenericutes Verrucomicrobia

Parks BW, et. al. Cell Metabolism. 2013

Dramatic Shift in Gut Microbiota

Actinobacteria Bacteroidetes Firmicutes Other Proteobacteria Tenericutes Verrucomicrobia

Strain-Specific Shift in Gut Microbiota

Parks BW, et. al. Cell Metabolism. 2013

SWR AXB19

SWR -> AXB19

AXB19 -> SWR SWR

AXB19

Cross-fostering pups

Microbial composition

Cross fostered pups 4 wks after weaning Parents

diet

Cross-fostering Microbial Communities

Elin Org (Unpublished)

Akkermansia Relationship to Obesity

Parks BW, et. al. Cell Metabolism. 2013

Body Fat Percentage Growth – 0 to 8 wks

400 0 100 200 300

Akk

erm

ansi

a

(rela

tive

abun

danc

e)

0.0

0.1

0.2

0.3

0.4

Epigenetics: DNA Methylation

Chr

1 po

sitio

n (M

b)

HMDP Strains

Methylation fraction

DNA Methylation on Chromosome 1 in Liver

Orozco et.al. Cell Metabolism (Accepted)

CpG

posit

ion

in g

enom

e

SNP position in genome

Genetic Control of DNA Methylation

Orozco et.al. Cell Metabolism (Accepted)

Trans Regulation of Methylation in Liver

Orozco et.al. Cell Metabolism (Accepted)

Padmanabhan et al. Cell. 2013

Methionine Synthase Reductase (Mtrr) and Generation of Methyl Groups

Methylation Levels

Mtrr KO Mice Have Altered Methylation at Hotspot Sites

Orozco et.al. Cell Metabolism (Accepted)

Plasma HDL EWAS (CpG methylation association)

Apoa2 gene

Epigenome-wide Association Study (EWAS) Identifies HDL locus on Chromosome 1

Orozco et.al. Cell Metabolism (Accepted)

Hybrid Mouse Diversity Panel (HMDP) Gene Identification/validation: Asxl2 (Bone Mineral Density), Cbr1 (Gene X Diet), Agpat5 (Insulin Resistance), Dusp7 (Insulin Resistance) Pathway Discovery: Cbr1 (Gene X Diet) Bile Acids Integration: Transcriptomics, Microbiome, Epigenetics EWAS: Using variation in epigenetics for association mapping

Poster by Marcus Seldin: “Systems genetics approach uncovers Dusp7 as a novel phosphatase

regulating skeletal muscle insulin signaling. “

Overview

Diabetic complications (Jake Lusis, Rich Davis, NIH grant) Heart failure (Yibin Wang, Jake Lusis, NIH grant) Atherosclerosis (Jake Lusis, Eleazer Eskin, NIH grant) DNA methylation (Matteo Pelligrini, NIH grant) Asthma (Hooman Allayee, USC, NIH grant) Gene-by-diet interactions in obesity (Jake Lusis, Eskin, NIH grant) Osteoporosis (Charles Farber, U. Virginia, NIH grant) Deafness (Rick Friedman, House Ear Inst., NIH grant) Gum disease (Flavia Pirih, Sotirios Tetradis, grant submitted) Hepatotoxicity (Simon Beaven, grant in preparation) Addictive behavior (David Jentsch, NIH grant) Vascular injury (Renee LeBoeuf, U. Wash., NIH grant) Conditioned frea (Des Smith, NIH grant) Gut flora (Tom Drake, grant in preparation) Arrhythmia (Jim Weiss, grant submitted) Mineral metabolism (Chris Vulpe, UC Berkeley, NIH grant) Jaw shape (Sotirios Tetradis, grant in preparation)

Hybrid Mouse Diversity Panel: Ongoing Projects

Jake Lusis, UCLA: diet-metabolic disorders Frank Gilliland, USC: air pollution – asthma Chris Vulpe, UC Berkeley: metals-metabolic traits David Jentsch, UCLA: drugs-addictive behavior Rick Friedman, USC: noise-deafness Yibin Wang, UCLA: adrenergic stimulation-heart failure Karen Reue, UCLA: statins-myopathy

HMDP: Gene X Environment Projects

HMDP: Advantages and Disadvantages

Advantages Mice freeily available (JAX) High Quality Genotypes (Mouse Diversity Array) Inbred mice Repeated Measures Lots of variation in all traits measured Results can be integrated across studies Building database of results Disadvantages Low Power Only 100-150 strains Commitment Long term project Cost Genetic Drift

UCLA Computer Science Eleazar Eskin

Jackson Laboratories Gary Churchill

Bristol Myers Squibb

Isis Pharmaceuticals

Microbiome Elin Org

Rob Knight (Colorado)

Aldons ‘Jake’ Lusis

HMDP Brian Bennett (UNC) Charles Farber (UVA) Luz Orozco (UCLA)

Lab Elizabeth Nam

Margarete Mehrabian Simon Hui

Frode Norheim Hannah Qi

Zhiqiang Zhou Elin Org

Marcus Seldin Mete Civelek Calvin Pan

Acknowledgements

K99/R00 Pathway to Independence

Award

Funding

A toolbox for dissecting complex traits

systems.genetics.ucla.edu