Post on 24-Dec-2021
Using Genetically Diverse Collaborative Cross Mouse Strains
to Model Alzheimer’s Disease
Asli Uyar for the MODEL-AD Consortium
AD/PD 2021– 03.13.2021
Mouse Models of AD on the C57BL/6J (B6J) Genetic Background
• Mouse models of Alzheimer’s disease (AD), carrying well-known early onset AD mutations, such as APP and PS1 (APP/PS1), or LOAD risk factors, such as APOE4, have usually been created on the C57BL/6J (B6J) genetic background.
• While these strains often exhibit amyloid accumulation and neuroinflammation, many additional molecular alterations present in human AD are absent in the mouse models.
• Previous work by our labs, and others, reveal the benefits of incorporating diverse mouse strains to model human AD.
• Mouse models of AD on genetically distinct wild-derived mouse strains demonstrated robust differences in immune response to amyloid and neurodegeneration, better recapitulating the heterogeneity in human AD than previous models.
Background and Motivation
Collaborative Cross (CC) lines
Saul et al 2019
• To broaden the phenotypes of mouse models further, we introduced genetic diversity by incorporating Collaborative Cross (CC) lines.
Objective
• CC lines is a recombinant inbred mouse panel created from eight highly diverse founder strains.
• Together, these founder strains recapitulate about 90% of the genetic variation observed in Mus musculus and represent genotypic variation comparable to human populations.
• CC strains are considered genetically homogenous once it reached a minimum level of inbreeding, typically once at least 90% of the genome is fixed after ~20 generations of inbreeding.
CC lines
Expression levels of AD risk genes varies across CC strains
AJB6129NODNZOCASTPWKWSB
2.5
3.0
3.5
4.0
4.5
log2(TP
M)
Trem2
F M F M F M F M F MCC002 CC006 CC013 CC037 CC041
Trem2 p = 1.91e-08
4.0
4.5
5.0
5.5
log2(TP
M)
Tyrobp
F M F M F M F M F MCC002 CC006 CC013 CC037 CC041
Tyrobp p = 0.0007
1.5
2.0
2.5
3.0
log2(TP
M)
Cd33
F M F M F M F M F MCC002 CC006 CC013 CC037 CC041
Cd33 p = 0.008
Five CC mouse strains were selected for maximal genetic and gene expression
variation at twelve late-onset GWAS loci, including TREM2, TYROBP, and CD33.
Genomic heterogeneity across CC strainsCC
002
CC01
3
CC04
1
CC00
6
CC03
7
Transcriptomic similarity
AJB6129NODNZOCASTPWKWSB
Model generation• Transgenic APP and PS1 alleles with a humanized APOE4 allele on a B6J background were
crossed with each CC line.
CC013CC006CC002B6.APOE4<HOM>.APPPS1<HEMI>
APOE4-KIAPP/PS1-Tg
CC037 CC041
B6 AD Model WT CC strains
F1
lethal
B6.CCn(F1).APOE4<HET>.APPPS1<HEMI> B6.CCn(F1).APOE4<HET>.APPPS1<WT>
• PC1 separates CC002 and CC013 from other strains; PC2 is Sex
Brain transcriptomes are separated by strain and sex
−5
0
5
0 10PC1: 39% variance
PC2:
12%
var
ianc
efactor(pcaData$Sex)
F
M
factor(pcaData$Strain)B6
CC002
CC006
CC013
CC037
CC041
• RNA-seq transcriptomes of brain hemisphere were assessed at 8-months for male and female mice.
• Six biological replicates per group.
Sex
Strain
Differential expression - Genotype effectB6.CCn(F1).APOE4<HET>.APPPS1<HEMI> vs. B6.CCn(F1).APOE4<HET>.APPPS1<WT>
269
73 6544
33 25 208 5 5 4 4 3 3 1
0
100
200
300
Inte
rsec
tion
Size
CC002 CC037 CC006 CC041
0100200300400Set Size
App Trem2 Gfap Tyrobp Itgb2 C1qa Ctsd Ctsz Ctss
Cd52 Ccl3 Prnp Mpeg1 Lpl Fcrls Cd68 Ccl6 Vsir
Ly86 Hexb Csf1r Gusb Slc111a1 Ptprc Olfml3 Laptm5 Cd9
Itgax St14 Arpp21 Grn Dhcr24 C1qc C1qb C3ar1 Rims1
Tent5c Fcgr3 Cts7 Lyz2 Cd300c2 C4b Clec7a Lamr1-ps1
Common DE genes across CC strains
• Number of DE genes in response to APP/PS1 transgenes on APOE4 background varies:• highest in CC002 (383) and lowest in
CC041 (104)
• Genes that are differentially expressed in all four strains are associated with microglia.
padj < 0.1
Sex specific differential expression
padj < 0.1
Itgb2
Cd52
Man2b1
Ctsd
Cybb
Cd48
Ccl6
Vsir
Plek
GfapLy86
Cd180
Hexb
Plau
Srebf2
Itgb5
App
Trem2
Myo1f
Csf1r Slc15a3
Gusb
Slc11a1
Usp50
Olfml3
Tnfsf8
Csf3r
Fgr
Gpnmb
Tbxas1
St14
Arpp21
Tlr13
Grn
C1qa
C1qc
C1qb
CtssC3ar1
Irf8
Rims1
Tent5c
Lncpint
Selplg
Ch25h
Cx3cr1
Capg
Fcer1g
Fcgr3
B2m
Hvcn1
Lyz1
Lyz2
C4b
Il4i1
Prnp
Bcl2a1b
Gm170870
5
10
15
−2 −1 0 1 2log2FoldChange
−log10(padj) diffexpressed
aaa
DOWN
NO
UP
Itgb2
Ccl3
Ctsd
Lnx2
Cd68
Ccl6
Gfap
Ly86
App
Tmem176a
Trem2
Tcf7l2
Hexa Laptm5
Tyrobp
Arpp21
Grn
Lysmd3
C1qc
Islr2
Fcgr3
Lyz2
C4b
Prnp
Gm5936Gm4767
0.0
2.5
5.0
7.5
10.0
−2 −1 0 1 2log2FoldChange
−log10(padj_scaled)
diffexpressedaaa
DOWN
NO
UP
B6.CC2(F1).APOE4<HET>.APPPS1<HEMI> vs. B6.CC2(F1).APOE4<HET>.APPPS1<WT>
#down=160
Female
#up=253 #down=7
Male
#up=63
KEGG pathways - CC lines and wild strains
Th17 cell differentiationViral myocarditis
AsthmaCircadian rhythm
Steroid biosynthesisSystemic lupus erythematosus
Glycosaminoglycan degradationRheumatoid arthritis
Viral protein interaction with cytokine and cytokine receptorB cell receptor signaling pathway
Cell adhesion moleculesAntigen processing and presentation
Chemokine signaling pathwayFc gamma R−mediated phagocytosis
Chagas diseaseStaphylococcus aureus infection
PertussisHematopoietic cell lineage
TuberculosisComplement and coagulation cascades
Proteoglycans in cancerLeishmaniasis
PhagosomeCoronavirus disease − COVID−19
Osteoclast differentiationLysosome
Acute myeloid leukemia
CC002_F(191)
CC006_F(37)
CC037_F(99)
CC041_F(63)
B6_F(40)
CAST_F(90)
PWK_F(278)
WSB_F(55)
GeneRatio0.05
0.10
0.15
0.20
0.04
0.03
0.02
0.01
p.adjust
B6 and wild strain data: Onos et al, 2020
Female
KEGG pathways - CC lines and wild strains
Thyroid hormone synthesisGlutamatergic synapse
Phospholipase D signaling pathwayCholinergic synapse
Gastric acid secretionSynaptic vesicle cycle
Neuroactive ligand−receptor interactionCalcium signaling pathway
AsthmaAntigen processing and presentation
Rheumatoid arthritisVarious types of N−glycan biosynthesis
Terpenoid backbone biosynthesisViral protein interaction with cytokine and cytokine receptor
Hematopoietic cell lineageProteoglycans in cancer
LeishmaniasisGlycosphingolipid biosynthesis − globo and isoglobo series
Glycosphingolipid biosynthesis − ganglio seriesPhagosome
Chagas diseaseOsteoclast differentiation
TuberculosisGlycosaminoglycan degradation
Steroid biosynthesisOther glycan degradation
PertussisComplement and coagulation cascades
Staphylococcus aureus infectionLysosome
CC002_M(40)
CC006_M(58)
CC037_M(55)
CC041_M(22)
CAST_M(72)
PWK_M(118)
WSB_M(244)
GeneRatio0.1
0.2
0.04
0.03
0.02
0.01
p.adjust
B6 and wild strain data: Onos et al, 2020
Male
B6_FCAST_FPWK_FWSB_F
CC002_FCC006_FCC037_FCC041_FCC002_MCC006_MCC037_MCC041_M
AMP-AD module mapping
B6_MCAST_MPWK_MWSB_M
CC lines
B6 and wild strains
• Mouse models of AD on diverse CC line background demonstrate • significant strain and sex-specific differences in transcriptomic signatures in presence of APP/PS1
mutant transgenes and APOE4 allele• higher variation than common B6 background
• Using diverse genetic backgrounds introduce further variation to AD related pathologies at molecular level.
• Each mouse model strain recapitulates a different transcriptomic pattern in human data.
• These novel strains has the potential to enhance the translatability of AD mouse models.
Summary
National Institute on AgingU54 AG054345, U54 AG054349
Contactwww.model-ad.orgmodelad@iupui.edu@Model_ad_alz
Indiana University Bruce Lamb, Program Director
Paul Territo, PTC HeadAndrew Saykin, BDMC Co-HeadAdrian Oblak, Project Manager
Kwangsik NhoTatiana Foroud
Dino GhettiAndi Masters
Carla Biesdorf De AlmeidaSara Quinney
Deborah DeBusk, Administrator
The Jackson Laboratory Gareth Howell, DMP HeadGreg Carter, BDMC Head
Mike Sasner, DMP Co-HeadHarriet WilliamsDylan GarceauKevin Kotredes
Christoph PreussAsli Uyar
Yi LiRavi PandeyNikhil MilindKristen Onos
Martha Abbott, AdministratorSage Bionetworks
Lara Mangravite, BDMC Co-HeadLarsson Omberg
Ben LogsdonMette Peters
Solveig SiebertsYooree Chae
Anna GreenwoodKara Woo
Zoe Leanza
The MODEL-AD ConsortiumUC Irvine
Frank LaFerla, Program DirectorAndrea Tenner, Program Director
Grant MacGregor, DMP HeadAli Mortazavi, BDMC HeadKim Green, DMP Co-Head
Marcelo Wood, DMP Co-HeadStefania Forner, Project Manager
David Baglietto-Vargas Shan Jiang
Shimako KawauchiSherrilyn Collins
Jonathan NeumannEniko KramarEdna HingcoDina MatheosMaria Fonseca
Andrea Wasserman, Administrator
University of PittsburghStacey Rizzo, PTC Co-Head
Zackary CopeGabi Little
Sean Williams