Abstract
Background.
Visceral leishmaniasis (VL) is caused by
Leishmania donovani
and
Leishmania
infantum chagasi
. Genome-wide linkage studies from Sudan and Brazil identified a putative susceptibility locus on chromosome 6q27.
Methods.
Twenty-two single-nucleotide polymorphisms (SNPs) at genes
PHF10
, C6orf70
, DLL1
, FAM120B
, PSMB1
,
and
TBP
were genotyped in 193 VL cases from 85 Sudanese families, and 8 SNPs at genes
PHF10
, C6orf70
, DLL1
, PSMB1
,
and
TBP
were genotyped in 194 VL cases from 80 Brazilian families. Family-based association, haplotype, and linkage disequilibrium analyses were performed. Multispecies comparative sequence analysis was used to identify conserved noncoding sequences carrying putative regulatory elements. Quantitative reverse-transcription polymerase chain reaction measured expression of candidate genes in splenic aspirates from Indian patients with VL compared with that in the control spleen sample.
Results.
Positive associations were observed at
PHF10, C6orf70, DLL1, PSMB1,
and
TBP
in Sudan, but only at
DLL1
in Brazil (combined
P
= 3 × 10
−4
at
DLL1
across Sudan and Brazil). No functional coding region variants were observed in resequencing of 22 Sudanese VL cases.
DLL1
expression was significantly (
P
= 2 × 10
−7
) reduced (mean fold change, 3.5 [SEM, 0.7]) in splenic aspirates from patients with VL, whereas other 6q27 genes showed higher levels (1.27 × 10
−6
<
P
< .01) than did the control spleen sample. A cluster of conserved noncoding sequences with putative regulatory variants was identified in the distal promoter of
DLL1
.
Conclusions.
DLL1,
which encodes Delta-like 1, the ligand for Notch3, is strongly implicated as the chromosome 6q27 VL susceptibility gene.