Aberrant Expressions and Variant Screening of SEMA3D in Indonesian Hirschsprung Patients

Background: The semaphorin 3D (SEMA3D) gene has been implicated in the
pathogenesis of Hirschsprung disease (HSCR), a complex genetic disorder characterized
by the loss of ganglion cells in varying lengths of gastrointestinal tract. We wished to
investigate the role of SEMA3D variants, both rare and common variants, as well as its
mRNA expression in Indonesian HSCR patients.
Methods: Sanger sequencing was performed in 54 HSCR patients to find a pathogenic
variant in SEMA3D. Next, we determined SEMA3D expression in 18 HSCR patients and
13 anorectal malformation colons as controls by quantitative real-time polymerase chain
reaction (qPCR).
Results: No rare variant was found in the SEMA3D gene, except one common
variant in exon 17, p.Lys701Gln (rs7800072). The risk allele (C) frequency at rs7800072
among HSCR patients (23%) was similar to those reported for the 1,000 Genomes
(27%) and ExAC (28%) East Asian ancestry controls (p = 0.49 and 0.41, respectively).
A significant difference in SEMA3D expression was observed between groups (p =
0.04). Furthermore, qPCR revealed that SEMA3D expression was strongly up-regulated
(5.5-fold) in the ganglionic colon of HSCR patients compared to control colon (1CT 10.8
± 2.1 vs. 13.3 ± 3.9; p = 0.025).
Conclusions: We report the first study of aberrant SEMA3D expressions in HSCR
patients and suggest further understanding into the contribution of aberrant SEMA3D
expression in the development of HSCR. In addition, this study is the first comprehensive
analysis of SEMA3D variants in the Asian ancestry.