Genetic basis of incomplete penetrance of RPSA haploinsufficiency for congenital asplenia

PROJECT SUMMARY
Isolated congenital asplenia (ICA) is characterized by the absence of a spleen at birth without any detectable
associated developmental abnormalities (OMIM #271400). ICA is the only known human developmental defect
affecting only a lymphoid organ. Patients with ICA are prone to life-threatening bacterial disease. We discovered
germline heterozygous variants in the exons of RPSA, encoding ribosomal protein SA, as the first genetic
etiology of ICA, in about half of the kindreds studied in our unique international cohort. The observation that
variants of a ribosomal protein caused ICA was surprising, as deleterious variants in 20 other ribosomal proteins
underlie Diamond-Blackfan anemia (DBA), a complex malformation syndrome with normal development of the
spleen. Autosomal dominance at the RPSA locus operates by haploinsufficiency (HI). For unknown reasons,
most RPSA variants display incomplete penetrance for ICA. In this context, we hypothesize that (1) incomplete
penetrance may be mediated by the genetically determined levels of expression of the WT RPSA allele, (2) ICA
in other kindreds may be explained by mutations in other genes, including genes whose translation is impaired
in cells with RPSA HI, and that (3) RPSA HI may impair the translation of genes, some of which differ from those
impaired in DBA cells. We will test these three related hypotheses. First, we will identify candidate cis-eQTLs
governing WT RPSA expression using pre-existing statistical methodologies and databases. We will assign
genotypes at these eQTL positions on the WT RPSA alleles of ICA and non-ICA cohort members heterozygous
for an ICA-causing RPSA mutant allele, and assess the segregation between WT RPSA eQTL genotype and
phenotype (with or without a spleen). Second, we will search for new genetic etiologies of ICA by genome-wide
approaches. Third, we will test the hypothesis that RPSA HI leads to ICA by impacting the translation of a subset
of mRNAs. We will use genetic and biochemical approaches to identify candidate genes whose mRNA is
selectively sensitive to RPSA HI. Our preliminary data are exciting. First, we have already sequenced the whole
genome of 63 RPSA heterozygotes from 31 families, including 38 and 25 individuals with and without a spleen,
respectively. We have delineated 3 groups of eQTLs that independently modulate RPSA expression. Using these
three groups, we have segregated the WT RPSA alleles of 31 families into groups that tightly correlate with the
presence or absence of a spleen. Second, we have found 4 kindreds with bi-allelic mutations in C6orf25. Third,
we have performed Ribo-seq and started analyzing the data. An understanding of how RPSA HI underlies ICA
with incomplete penetrance will provide proof-of-principle that the levels of expression of the WT allele can drive
the penetrance of a human dominant trait. Identification of a new genetic etiology of ICA will provide a long-
awaited explanation for the unexplained cases. Finally, investigating the translational impact of RPSA HI will
provide insights into the mechanisms by which RPSA HI leads to a distinct, limited phenotype, when compared
with DBA, thereby laying the groundwork for fundamental studies on the function of human ribosomal proteins.

Grant Number: 1R21AI186048-01A1
NIH Institute/Center: NIH
Principal Investigator: Bertrand Boisson