Microdeletion at ESR1 Intron 6 (DEL_6_75504) Is a Susceptibility Factor for Cryptorchidism and Hypospadias

Context We have previously reported that a specific AGATC haplotype in a >34 kb tight linkage disequilibrium (LD) block within ESR1 is strongly associated with cryptorchidism and hypospadias in Japanese boys.Objective We aimed to determine the true susceptibility factor for cryptorchidism and hypospadias linked to the AGATC haplotype.Methods We performed various molecular studies in hitherto unreported 230 Italian boys (80 with cryptorchidism and 150 with normal genitalia) and previously reported and newly recruited 415 Japanese boys (149 with cryptorchidism, 141 with hypospadias, and 125 with normal genitalia). We also performed ESR1 expression analyses using breast cancer-derived MCF-7 cells.Results Haplotype analysis revealed the LD block and positive association of the AGATC haplotype with cryptorchidism in Italian boys. Whole genome sequencing identified an identical 2249-bp microdeletion (?ESR1) generated by a microhomology-mediated replication error in both Japanese and Italian boys with the specific haplotype. ?ESR1 was found to be strongly associated with cryptorchidism and hypospadias by Cochran-Armitage trend test and was revealed to show nearly absolute LD with the AGATC haplotype. ESR1 expression was upregulated in MCF-7 cells with a homozygous deletion encompassing Delta ESR1 and those with a homozygous deletion involving a CTCF-binding site within Delta ESR1.Conclusion The results reveal that ?ESR1, which has been registered as DEL_6_75504 in gnomAD SVs v2.1, is the true susceptibility factor for cryptorchidism and hypospadias. It appears that ?ESR1 was produced in a single ancestral founder of modern humans and has been maintained within the genome of multiple ethnic groups by selection.

Automated summary

The AGATC haplotype is strongly associated with cryptorchidism in Italian boys. The study identified a 2249-bp microdeletion (?ESR1) in boys with the specific haplotype, which is strongly associated with cryptorchidism and hypospadias. This finding suggests that ?ESR1 is the true susceptibility factor for cryptorchidism and hypospadias.