Dominant Splice Site Mutations in PIK3R1 Cause Hyper IgM Syndrome, Lymphadenopathy and Short Stature

Abstract

The purpose of this research was to use next generation sequencing to identify mutations in patients with primary immunodeficiency diseases whose pathogenic gene mutations had not been identified. Remarkably, four unrelated patients were found by next generation sequencing to have the same heterozygous mutation in an essential donor splice site of PIK3R1 (NM_181523.2:c.1425 + 1G > A) found in three prior reports. All four had the Hyper IgM syndrome, lymphadenopathy and short stature, and one also had SHORT syndrome. They were investigated with in vitro immune studies, RT-PCR, and immunoblotting studies of the mutation's effect on mTOR pathway signaling. All patients had very low percentages of memory B cells and class-switched memory B cells and reduced numbers of naïve CD4+ and CD8+ T cells. RT-PCR confirmed the presence of both an abnormal 273 base-pair (bp) size and a normal 399 bp size band in the patient and only the normal band was present in the parents. Following anti-CD40 stimulation, patient's EBV-B cells displayed higher levels of S6 phosphorylation (mTOR complex 1 dependent event), Akt phosphorylation at serine 473 (mTOR complex 2 dependent event), and Akt phosphorylation at threonine 308 (PI3K/PDK1 dependent event) than controls, suggesting elevated mTOR signaling downstream of CD40. These observations suggest that amino acids 435–474 in PIK3R1 are important for its stability and also its ability to restrain PI3K activity. Deletion of Exon 11 leads to constitutive activation of PI3K signaling. This is the first report of this mutation and immunologic abnormalities in SHORT syndrome.

Defining how oncogenic and developmental mutations ofPIK3R1alter the regulation of class IA phosphoinositide 3-kinases

“…These previous mutations all lead to upregulated PI3K activity, however, mutations and truncations in both the iSH2 and cSH2 have been discovered that downregulate PI3K activity through decreased sensitivity to insulin signalling. These mutations cause SHORT syndrome (Short stature, hyper-extensibility, hernia, ocular depression, Rieger anomaly, and teething delay) (Chudasama et al, 2013;Dyment et al, 2013;Huang-Doran et al, 2016;Petrovski et al, 2016;Schroeder et al, 2014;Thauvin-Robinet et al, 2013), with the most common mutation disrupting the phosphotyrosine binding site in the cSH2 domain (R649W). We have characterised the molecular mechanism of activation of a C-terminal truncation of p85α (Q572*) and a point mutant in the cSH2 (R649W) that disrupts phosphorylated tyrosine binding leading to impaired insulin signalling.…”

PI3Kδ and primary immunodeficiencies

“…Subsequently, a number of additional studies have identified APDS patients with mutations in PIK3CD 5, 7, 64–69 or PIK3R1 6, 70–73. Patients with GOF mutations in either of these genes appear to largely phenocopy each other, despite the fact that p85α is ubiquitously expressed and can pair with p110α and p110β in addition to p110δ.…”

“…Growth retardation is common in patients with APDS2 6, 73, 74 but does not seem to be a feature of APDS1 and may relate to the association of heterozygous mutations in PIK3R1 with SHORT syndrome (short stature, hyperextensibility of joints, hernia, ocular depression, Rieger anomaly and teething delay)88–91.…”

“…It is unclear why the ΔEx11 mutations that cause APDS2 manifest primarily as PID; however, it is of interest to note at least one case where this mutation was suggested to relate to SHORT syndrome 73. This indicates that PIK3R1 ΔEx11 may have distinct effects on different p110 isoforms in different tissues.…”

Clinical, Immunological, and Functional Characterization of Six Patients with Very High IgM Levels

“…Whole exome sequencing (WES) was performed in 5 cases (P6 died before). Since mutations in PIK3CD or PIK3R1 genes have been recently reported as responsible for novel PIDs characterized by elevated IgM, normal/low IgG levels, lymphopenia, respiratory infections, lymph node enlargement, and elevated risk of lymphomas [26][27][28][29][30], these genes were analyzed by direct sequencing. Variants in causative or potential candidate genes identified through WES were confirmed through Sanger sequencing.…”