Long terminal repeat insertion in &lt;i&gt;Kit&lt;/i&gt; causes unilateral renal agenesis in rats

Ara, Shiori; Miyazaki, Akira; Trung, Hieu Hoang; Yokoe, Mayuko; Nakagawa, Yuki; Kaneko, Takehito; Kuramoto, Takashi

doi:10.33611/trs.2_30

Cited by 1 publication

(3 citation statements)

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“…Elements of the KIT intron 1 Erv insertion by founder strain are presented. *Erv element composition for F344 strain reported by Ara et al (2020), including 7,098 nts (GenBank accession number AP012487). The theorized incomplete penetrance mechanism present in HS is described, including the Erv insertion composition by founder strain and the selected strain HSRA.…”

Section: Founder Haplotype Mosaic and Exclusive Allelesmentioning

confidence: 99%

“…Human unilateral renal agenesis (URA) is a congenital urinary tract malformation, and affected individuals have only one kidney (Ara et al, 2020). Human URA occurs at around 1 in 500-1,000 births.…”

Section: Introductionmentioning

confidence: 99%

“…An endogenous retrovirus-derived long terminal repeat within the first intron of KIT could be the causative polymorphism for URA (Erv insertion). More recently, Ara et al (2020) used a CRISPR/Cas9 system to remove one of the Ltr sequences of the Erv insertion and reported suppression of URA phenotype in ACI rats.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers theKITgene andAHR,ATF3,GATA3,HNF1B,POU2F2, andTFCP2transcription factors as potential candidates to explain incomplete penetrance

Leal-Gutiérrez,

Munro,

Chen

et al. 2023

Preprint

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Human unilateral renal agenesis is a congenital urinary tract malformation. Affected individuals have only one kidney, which is often an asymptomatic developmental defect. A total of 5,585 male and female HS rats were assessed for unilateral renal agenesis and genotyped for 3,513,321 markers. The R package SAIGEgds was used for the association analysis. The adjusted p-value threshold for the association analysis determined by permutation was equal to 5.6 (-log10). Two additional datasets were used as validation tests. Population two included 1,577 rats genotyped for 7,425,889 markers and a case-control imbalance equal to 1:174; population three included 1,407 rats, genotyped for 254,932 markers and case-control ratio equal to 1:38. The python package GxTheta was used to perform a polygenic epistasis analysis for the analyzed HS rat population. A founder haplotype mosaic determination was performed using the R package QTL2. Associated regions were selected for further analysis, including long-read PacBio sequencing for founder individuals and a founder haplotype prediction test. A similarity analysis at a genomic level and for loci encoding transcription factors predicted to interact with selected sequences inside the associated loci were accomplished. A total of 1,181 polymorphisms were associated with URA. All associated polymorphisms were located on chromosome 14 between 32.9 and 36.6 Mb. The most significant polymorphism was chr14:36,411,266, a G/T transversion. The same associated region was identified in population three. Polygenic epistasis was determined as not predominant for the presentation of URA. Based on the haplotype mosaic probability estimation, cases display a higher probability of inheriting the ACI allele. The long-read sequencing analysis showed the presence of an Erv insertion inside the intron one of the KIT gene located inside the associated region. The Erv insertion comprises one Erv sequence and two Ltr sequences located downstream and upstream of the former. No Erv insertion was identified for the founder strain BN. For ACI and HSRA, only one Ltr sequence was identified. One hundred and seven genes encoding TFs that recognize binding sites on the Erv insertion were analyzed for sequence similarity against the reference HSRA. The TF similarity score analysis for the interaction genotype and phenotype showed significance after FDR correction for 20 TFs, including AHR, HNF1B, JUNB, RARG, and RXRA. A mechanism identifying URA as a threshold phenotype is suggested in HS rats. It implies the existence of a minimum threshold for the final number of nephrons and kidney associated structures required for stalling the apoptotic process of the metanephric rudiments. Animals exhibiting a quantitative cumulative defect would express URA, being this malformation identified as a phenotype with decreased penetrance in the assessed population of HS rats. All these processes are described as mediated by KIT and TFs able to interact with sequences of the Erv insertion.

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Section: Founder Haplotype Mosaic and Exclusive Allelesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%