Functional evaluation of PDGFB-variants in idiopathic basal ganglia calcification, using patient-derived iPS cells

Abstract

Causative genes in patients with idiopathic basal ganglia calcification (IBGC) (also called primary familial brain calcification (PFBC)) have been reported in the past several years. In this study, we surveyed the clinical and neuroimaging data of 70 sporadic patients and 16 families (86 unrelated probands in total) in Japan, and studied variants of PDGFB gene in the patients. Variant analyses of PDGFB showed four novel pathogenic variants, namely, two splice site variants (c.160 + 2T > A and c.457−1G > T), one deletion variant (c.33_34delCT), and one insertion variant (c.342_343insG). Moreover, we developed iPS cells (iPSCs) from three patients with PDGFB variants (c.160 + 2T > A, c.457−1G > T, and c.33_34 delCT) and induced endothelial cells. Enzyme-linked immunoassay analysis showed that the levels of PDGF-BB, a homodimer of PDGF-B, in the blood sera of patients with PDGFB variants were significantly decreased to 34.0% of that of the control levels. Those in the culture media of the endothelial cells derived from iPSCs of patients also significantly decreased to 58.6% of the control levels. As the endothelial cells developed from iPSCs of the patients showed a phenotype of the disease, further studies using IBGC-specific iPSCs will give us more information on the pathophysiology and the therapy of IBGC in the future.

Partial reduced Pi transport function of PiT-2 might not be sufficient to induce brain calcification of idiopathic basal ganglia calcification

“…IBGC is characterized by abnormal mineral deposits, mostly calcium, in brain regions, including the basal ganglia, thalamus, cerebellum, and others. We have investigated the patients in Japan 4,5 . We have 231 patients with 33 familial case now in Japan.…”

“…Most recently, MYORG is identified as a new causative gene of IBGC and is associated with recessive IBGC 10 . Among these, IBGC1 is the most frequent and accounts for about 30%–50% of familial cases 2,4,5 . Currently, no effective therapy is available for patients with IBGC 2 .…”

Case Report: Two Novel Frameshift Mutations in SLC20A2 and One Novel Splice Donor Mutation in PDGFB Associated With Primary Familial Brain Calcification

“…As of the end of January 2021, according to the Human Gene Mutation Database (HGMD, www.hgmd.cf.ac.uk/ac/index.php), 142 mutations in SLC20A2 have been identified, including 75 missense and non-sense mutations, 15 splice-site mutations, 32 small deletions, 5 small insertions and duplications, and 15 gross mutations; 24 mutations were identified in PDGFB, including 19 missense and non-sense mutations, three splice-site mutations, and two gross deletions. We summarized and compiled the other four pathogenic mutations in PDGFB from the literature (Sekine et al, 2019). In the present study, we identified two novel frameshift mutations in SLC20A2 (c.806delC and c.1154delG) and one splice donor site mutation in PDGFB (c.456+1G>C), which have broadened and enriched the SLC20A2 and PDGFB mutation spectrum (Supplementary Figure 2).…”

“…However, both patients in the nuclear family had a severe migraine, a history of depression, and calcification in the basal ganglia, thalamus (only mother affected), cerebral cortex (only proband affected), and subcortical white matter (Ramos et al, 2018). Another splice acceptor site mutation in the same intron (c.457-1G>T) may lead to exon 5 (NM_002608.4) skipping and frameshift protein in carriers, leading to chronic headache and intellectual disability (Sekine et al, 2019). These results suggest that different substitutions on the same splicing unit (GT-AG in DNA code) could result in distinct molecular events and disease phenotypes.…”

“…These results suggest that different substitutions on the same splicing unit (GT-AG in DNA code) could result in distinct molecular events and disease phenotypes. Of note, another three splice site mutations in PDGFB (c.64-3C>G, c.160+2T>A, and c.602-1G>T) also resulted in aberrant splicing processes and frameshift outcomes (Nicolas et al, 2015;Koyama et al, 2017;Sekine et al, 2019). In our study, the c.456+1G>C variant was functionally deleterious, as revealed by the comprehensive bioinformatic analyses (Table 2), and could activate the upstream cryptic splice donor site residing in exon 4 and create a novel mature transcript with an in-frame 21 bp deletion (NM_002608.4, r.436_456del).…”