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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 S EMA3D  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 (ΔC T  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.

Aberrant Expressions and Variant Screening of SEMA3D in Indonesian Hirschsprung Patients