Juvenile polyposis syndrome (JPS) is a rare autosomal dominant disorder 
predisposing to gastrointestinal hamartomatous polyps and cancer with a 
pathogenic SMAD4 or BMPR1A germline mutation (1st-hit) being identified in about 
40-50% of patients. Little is known, however, about the occurrence and nature of 
somatic alterations (2nd-hit) in SMAD4-/BMPR1A-related juvenile polyps. In this 
study, we screened 25 polyps from three patients carrying either a pathogenic 
SMAD4 (c.1244-1247delACAG) or BMPR1A (c.583C>T; p.Gln195*) germline mutation for 
somatic alterations. The SMAD4-related polyps were also analyzed for SMAD4 
protein expression by immunohistochemistry. Despite comprehensive screening for 
loss of heterozygosity (LOH), mutations in the coding sequence, chromosomal 
rearrangements, and promoter methylation, no somatic alterations could be 
identified in 14 SMAD4-related polyps. SMAD4 protein expression, however, was 
lost in 8 (57%) of 14 juvenile polyps with 6 showing concomitant loss in both, 
the epithelial and stromal, compartments. In the BMPR1A-related polyps, five out 
of nine (56%) displayed LOH. Further analysis of selected polyps revealed that 
LOH was gene copy number neutral and had occurred in the epithelial compartment. 
The heterogeneity of genetic mutations and protein expression levels indicates 
that different modes of gene inactivation can be operational in SMAD4- and 
BMPR1A-related polyp formation. Our observation, that about half of 
BMPR1A-related polyps displayed LOH, predominantly in the epithelial 
compartment, is compatible with BMPR1A acting as a tumour suppressor gene. 
Still, it remains to be determined whether juvenile polyp development generally 
requires loss of BMPR1A expression or, as observed in some SMAD4-related polyps, 
can occur despite normal protein expression.