Mapping Data

Experiment

• Experiment
  TEXT-QTL
• Chromosome
  5
• Reference
  J:252459 Hai Q, et al., Quantitative Trait Locus Mapping of Macrophage Cholesterol Metabolism and CRISPR/Cas9 Editing Implicate an ACAT1 Truncation as a Causal Modifier Variant. Arterioscler Thromb Vasc Biol. 2018 Jan;38(1):83-91
• ID
  MGI:6140017

Genes

Gene	Assay Type
Mcmm4	visible phenotype
Mepe
Spp1
Pkd2

Notes

• Experiment
  Quantitative trait loci mapping was used to identify candidate genes that regulate cholesterol metabolism in bone marrow-derived macrophages (BMDMs) derived from 122 (AKR/J x DBA/2J)F4 mice (70 males, 52 females). AKR/J and DBA/2J mice differ substantially in their susceptibility to atherosclerosis, where DBA/2J-Apoe^tm1Bres mice develop ~ 10 times larger aortic root lesions than AKR/J-Apoe^tm1Bres mice. Cultured BMDMs from DBA/2J (DBA/2) versus AKR/J (AKR) mice accumulate much more cholesterol ester (CE) after cholesterol loading than with acetylated LDL (acLDL). The aim was to discover genes that play causal roles in macrophage cholesterol metabolism.
  
  The BMDMs of the 122 (AKR x DBA/2)F4 mice were acLDL loaded and their free cholesterol (FC) and CE levels normalized to cell protein were measured as well as their CE/FC ratio. After genotyping using a high-density SNP microarray using 16975 informative SNPs, QTL mapping was performed of the BMDM cholesterol phenotypes using R/qtl software. Ten distinct macrophage cholesterol metabolism QTL were identified, Table 1 (mapped locations relative to NCBI B37):
  
  QTL Mcmm1 (macrophage cholesterol metabolism modifier 1) mapped to Chromosome 1 with the highest LOD score for FC levels (p<0.0001) of 10.64 at peak position 155.51 Mb ; LOD=10.76 at 156.34 Mb for CE (p<0.0001) and LOD=12.46 at 156.35 for the CE/FC ratio (p<0.0001). There was strong dosage effect of Mcmm1 with the DBA/2 allele associated with lower FC and higher CE and CE/FC ratio. Mcmm1 was associated with 30% of variance in FC, 33% of the variance in CE and 31% of variance in CE/FC. Thirty four genes mapped within the Mcmm1 interval. Soat1, encoding ACAT1, was the top causal candidate gene, which was confirmed using CRISPR/Cas9 gene editing in DBA/2 ES cells. AKR mice are known to harbor a 33 amino acid N-terminal truncation in ACAT1 because of a 6.8 kb genomic deletion in Soat1.
  
  Because Mcmm1 had the highest LOD scores for the measured BMDM cholesterol phenotypes, CE levels for QTL Mcmm2 to Mcmm10 were determined after correcting for Mcmm1 genotype as an additive covariate.
  
  QTL Mcmm2 (macrophage cholesterol metabolism modifier 2) mapped to Chromosome 1 with a LOD score for CE levels (p<0.01 of 5.6 and a LOD score of 6.1 for CE/FC (p<0.01) at peak position 184.65 Mb. Mcmm2 is a very small locus at the distal end of chromosome 1 with a Bayesian credible interval of 184.65-184.89 Mb. This locus harbors only three genes; Tlr5, Susd4, and Ccdc185.
  
  QTL Mcmm3 (macrophage cholesterol metabolism modifier 3) mapped to Chromosome 2 with a LOD score of 4.7 for CE levels (p<0.05) at peak position 118.97 Mb and a LOD score of 3.5 for CE/FC levels (p<0.02) at peak position 126.97 Mb.
  
  QTL Mcmm4 (macrophage cholesterol metabolism modifier 4) mapped to Chromosome 5 with a LOD score of 5.7 for CE levels (p<0.01) and a LOD score of 4.6 for CE/FC levels (p<0.05) at peak position 105.44 Mb. Mcmm4 is located in the middle of chromosome 5 with a Bayesian credible interval of 68.02-107.43 Mb and harbors 428 genes. The top candidates for this locus are Mepe, Spp1, and Pkd2.
  
  QTL Mcmm5 (macrophage cholesterol metabolism modifier 5) mapped to Chromosome 6 with a LOD score of 5.3 for CE levels (p<0.01) and a LOD score 2.4 for CE/FC levels (p>0.63) at peak position 120.13 Mb. Mcmm5 is located at the distal end of chromosome 6 with a Bayesian credible interval of 118.95-122.59 Mb and harbors 64 genes. Bid and Atp6v1e1 stood out as top candidates because of their relatively strong BMDM cis-eQTL scores in prior studies.
  
  QTL Mcmm6 (macrophage cholesterol metabolism modifier 6) mapped to Chromosome 9 with a LOD score of 5.3 for CE levels (p<0.01) at peak position 31.70 Mb and a LOD score of 3.6 for CE/FC levels (p=.15) at peak position 31.19 Mb. Mcmm6 is located at the proximal end of chromosome 9 with a Bayesian credible interval of 3.58-34.82 Mb and harbors 318 genes. Casp1 was a top candidate for this locus, Fli1 was also a candiate.
  
  QTL Mcmm7 (macrophage cholesterol metabolism modifier 7) mapped to Chromosome 10 with a LOD score of 4.6 for CE levels (p<0.05) at peak position 127.52 Mb and a LOD score of 3.9 for CE/FC levels (p<0.10) at peak position 17.54 Mb. Os9 was a plausible cadidate for this locas, as it had a strong BMDM cis-eQTL in prior studies and was shown to be associated with lipid storage in adipocytes.
  
  QTL Mcmm8 (macrophage cholesterol metabolism modifier 8) mapped to Chromosome 11 with a LOD score of 6.0 for CE levels (p<0.01) at peak position 7.27 Mb and a LOD score of 3.8 for CE/FC levels (p<0.10) at peak position 4.03 Mb. Mcmm8 is located at the proximal end of chromosome 11 with a Bayesian credible interval of 4.03-36.44 Mb and harbors 468 genes. Camk2b was the strongest candidate gene for this locus.
  
  QTL Mcmm9 (macrophage cholesterol metabolism modifier 9) mapped to Chromosome 12 with a LOD score of 5.7 for CE levels (p<0.01) at peak position 95.60 Mb and a LOD score of 4.8 for CE/FC levels (p<0.05) at peak position 80.45 Mb. Mcmm9 is located at the distal end of chromosome 12 with a Bayesian credible interval of 79.09-95.60. There was no clear candidate gene.
  
  QTL Mcmm10 (macrophage cholesterol metabolism modifier 10) mapped to Chromosome 17 with a LOD score of 5.3 for CE levels (p<0.01) at peak position 88.56 Mb and a LOD score of 3.8 for CE/FC levels (p<0.15) at peak position 77.30 Mb. Mcmm10 is located at the distal end of chromosome 17 with a Bayesian credible interval of 68.68-89.29 Mb and harbors 191 genes. The strongest candidate was Dync2li1.