title: Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice.
abstract: OBJECTIVE
  In a previous study, several quantitative trait loci (QTL) that influence age-related degeneration (ageRD) were identified in a cross between the albino strains B6(Cg)-Tyr(c-2J)/J (B6a) and BALB/cByJ (C). The Chromosome (Chr) 6 and Chr 10 QTL were the strongest and most highly significant loci and both involved B6a protective alleles. The QTL were responsible for 21% and 9% of the variance in phenotypes, respectively. We focused on these two QTL to identify candidate genes.
  
  
  METHODS
  DNA microarrays were used for the two mouse strains at four and eight months of age to identify genes that are differentially regulated and map to either QTL. Gene Ontology (GO) analysis of the differentially expressed genes was performed to identify possible processes and pathways associated with ageRD. To identify additional candidates, database analyses (Positional Medline or PosMed) were used. Based on differential expression, PosMed, and the presence of reported polymorphisms, five genes per QTL were selected for further study by sequencing analysis and qRT-PCR. Tumor necrosis factor, alpha- induced protein 3 (Tnfaip3; on a C57BL/6J (B6) background) was phenotypically tested. Single nucleotide polymorphisms (SNPs) flanking this gene were correlated with outer nuclear layer thickness (ONL), and eight-month-old Tnfaip3(+/-) mice were tested for ageRD.
  
  
  RESULTS
  Polymorphisms were found in the coding regions of eight genes. Changes in gene expression were identified by qRT-PCR for Hexokinase 2 (Hk2) and Docking protein 1 (Dok1) at four months and for Dok1 and Tnfaip3 at eight months. Tnfaip3 was selected for phenotypic testing due to differential expression and the presence of two nonsynonymous mutations. However, when ONL thickness was compared in eight-month-old congenic Tnfaip3(+/-) and Tnfaip3(+/+) mice, no differences were found, suggesting that Tnfaip3 is not the quantitative trait gene (QTG) for the Chr 10 QTL. The GO analysis revealed that GO terms associated with stress and cell remodeling are overrepresented in the ageRD-sensitive C strain compared with the B6a strain with age (eight months). In the ageRD-resistant B6a strain, compared with the C strain, GO terms associated with antioxidant response and the regulation of blood vessel size are overrepresented with age.
  
  
  CONCLUSIONS
  The analyses of differentially expressed genes and the PosMed database yielded candidate genes for the Chr 6 and Chr 10 QTL. HtrA serine peptidase 2 (Htra2), Dok1, and Tnfaip3 were deemed most promising because of their known roles in apoptosis and our finding of nonsynonymous substitutions between B6a and C strains. While Tnfaip3 was excluded as the QTG for the Chr 10 QTL, Dok1 and Htra2 remain good candidates for the Chr 6 QTL. Finally, the GO term analysis further supports the general hypothesis that oxidative stress is involved in ageRD.
authors.affiliation: Department of Biology, Loyola Marymount University, Los Angeles, CA 90045-2659, USA. dieogando@gmail.com
authors.forename: Diego G
authors.initials: DG
authors.lastname: Ogando
authors.forename: Kam D
authors.initials: KD
authors.lastname: Dahlquist
authors.forename: Mitra
authors.initials: M
authors.lastname: Alizadeh
authors.forename: Kannan
authors.initials: K
authors.lastname: Kunchithapautham
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Nicole
authors.initials: N
authors.lastname: Yu
authors.forename: Matthew M
authors.initials: MM
authors.lastname: LaVail
authors.forename: Bärbel
authors.initials: B
authors.lastname: Rohrer
authors.forename: Douglas
authors.initials: D
authors.lastname: Vollrath
authors.forename: Michael
authors.initials: M
authors.lastname: Danciger
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D003546:Cysteine Endopeptidases / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D056726:Genetic Association Studies; D000074923:High-Temperature Requirement A Serine Peptidase 2; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D051379:Mice; D008815:Mice, Inbred Strains; D018345:Mice, Knockout; D046228:Microarray Analysis; D024101:Mitochondrial Proteins / Q000235:genetics; D018384:Oxidative Stress; D010641:Phenotype; D010750:Phosphoproteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D016601:RNA-Binding Proteins / Q000235:genetics; D012162:Retinal Degeneration / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012697:Serine Endopeptidases / Q000235:genetics; D000072598:Tumor Necrosis Factor alpha-Induced Protein 3
chemical_list: D004268:DNA-Binding Proteins; C489561:Dok1 protein, mouse; D047908:Intracellular Signaling Peptides and Proteins; D024101:Mitochondrial Proteins; D010750:Phosphoproteins; D016601:RNA-Binding Proteins; D000072598:Tumor Necrosis Factor alpha-Induced Protein 3; D012697:Serine Endopeptidases; D000074923:High-Temperature Requirement A Serine Peptidase 2; C000615915:Htra2 protein, mouse; D003546:Cysteine Endopeptidases; C513261:Tnfaip3 protein, mouse