Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum: Identification of Novel Candidate Modifier Genes and Disease Pathways Through Mixture of Effects Analysis

Identification of modifier gene variants overrepresented in familial hypomagnesemia with hypercalciuria and nephrocalcinosis patients with a more aggressive renal phenotype

Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is an ultra-rare autosomal recessive renal tubular disease with an incidence of <1/1.000.000 individuals, caused by loss-of-function mutations in CLDN16 and CLDN19. Our study includes a unique cohort representing all known FHHNC patients in Spain, with 90% harbouring mutations in CLDN19. Of these, 70% carry the p.G20D mutation in homozygosis. Despite this high genetic homogeneity, our FHHNC cohort display a high phenotypic variability, even among siblings harbouring identical mutations. Patients were stratified at the extremes of the renal phenotype according to their estimated glomerular filtration rate annual decline and subjected to whole exome sequencing (WES) aiming to find candidate phenotype-modifier genes. Initial statistical analysis by SKAT-O identified numerous variants, which were then filtered based on P-value <0.01 and kidney expression. A thorough prioritization strategy was then applied by an exhaustive disease knowledge-driven exploitation of data from public databases (Human Protein Atlas, GWAS catalog, GTEx) to further refine candidate genes. Odds ratios were also calculated to identify potential risk variants. This analysis pipeline suggested several gene variants associated with a higher risk of developing a more aggressive renal phenotype. While these findings hint at the existence of genetic modifiers in FHHNC, further research is needed to confirm their role and potential clinical significance. Clinical decisions should not be based on these preliminary findings, and additional cohorts should be studied to validate and expand upon our results. This exploratory study provides a foundation for future investigations into the genetic factors influencing FHHNC progression and may contribute to our understanding of the disease's variable expressivity potentially enabling the implementation of more tailored therapeutic strategies.

Matrix Metalloproteinases Contribute to the Calcification Phenotype in Pseudoxanthoma Elasticum

Ectopic calcification and dysregulated extracellular matrix remodeling are prominent hallmarks of the complex heterogenous pathobiochemistry of pseudoxanthoma elasticum (PXE). The disease arises from mutations in ABCC6, an ATP-binding cassette transporter expressed predominantly in the liver. Neither its substrate nor the mechanisms by which it contributes to PXE are completely understood. The fibroblasts isolated from PXE patients and Abcc6-/- mice were subjected to RNA sequencing. A group of matrix metalloproteinases (MMPs) clustering on human chromosome 11q21-23, respectively, murine chromosome 9, was found to be overexpressed. A real-time quantitative polymerase chain reaction, enzyme-linked immunosorbent assay and immunofluorescent staining confirmed these findings. The induction of calcification by CaCl2 resulted in the elevated expression of selected MMPs. On this basis, the influence of the MMP inhibitor Marimastat (BB-2516) on calcification was assessed. PXE fibroblasts (PXEFs) exhibited a pro-calcification phenotype basally. PXEF and normal human dermal fibroblasts responded with calcium deposit accumulation and the induced expression of osteopontin to the addition of Marimastat to the calcifying medium. The raised MMP expression in PXEFs and during cultivation with calcium indicates a correlation of ECM remodeling and ectopic calcification in PXE pathobiochemistry. We assume that MMPs make elastic fibers accessible to controlled, potentially osteopontin-dependent calcium deposition under calcifying conditions.

Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients

Neurological phenotypes such as intellectual disability occur in almost half of patients with neurofibromatosis 1 (NF1). Current genotype-phenotype studies have failed to reveal the mechanism underlying this clinical variability. Despite the presence of pathogenic variants of NF1, modifier genes likely determine the occurrence and severity of neurological phenotypes. Exome sequencing data were used to identify genetic variants in 13 NF1 patients and 457 healthy controls, and this information was used to identify candidate modifier genes underlying neurological phenotypes based on an optimal sequence kernel association test. Thirty-six genes were identified as significant modifying factors in patients with neurological phenotypes and all are highly expressed in the nervous system. A review of the literature confirmed that 19 genes including CUL7, DPH1, and BCO1 are clearly associated with the alteration of neurological functioning and development. Our study revealed the enrichment of rare variants of 19 genes closely related to neurological development and functioning in NF1 patients with neurological phenotypes, indicating possible modifier genes and variants affecting neurodevelopment. Further studies on rare genetic variants of candidate modifier genes may help explain the clinical heterogeneity of NF1.

The Impact of Inflammatory Stimuli on Xylosyltransferase-I Regulation in Primary Human Dermal Fibroblasts

Inflammation plays a vital role in regulating fibrotic processes. Beside their classical role in extracellular matrix synthesis and remodeling, fibroblasts act as immune sentinel cells participating in regulating immune responses. The human xylosyltransferase-I (XT-I) catalyzes the initial step in proteoglycan biosynthesis and was shown to be upregulated in normal human dermal fibroblasts (NHDF) under fibrotic conditions. Regarding inflammation, the regulation of XT-I remains elusive. This study aims to investigate the effect of lipopolysaccharide (LPS), a prototypical pathogen-associated molecular pattern, and the damage-associated molecular pattern adenosine triphosphate (ATP) on the expression of XYLT1 and XT-I activity of NHDF. We used an in vitro cell culture model and mimicked the inflammatory tissue environment by exogenous LPS and ATP supplementation. Combining gene expression analyses, enzyme activity assays, and targeted gene silencing, we found a hitherto unknown mechanism involving the inflammasome pathway components cathepsin B (CTSB) and caspase-1 in XT-I regulation. The suppressive role of CTSB on the expression of XYLT1 was further validated by the quantification of CTSB expression in fibroblasts from patients with the inflammation-associated disease Pseudoxanthoma elasticum. Altogether, this study further improves the mechanistic understanding of inflammatory XT-I regulation and provides evidence for fibroblast-targeted therapies in inflammatory diseases.

ENPP1 variants in patients with GACI and PXE expand the clinical and genetic heterogeneity of heritable disorders of ectopic calcification

Pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI) are clinically distinct genetic entities of ectopic calcification associated with differentially reduced circulating levels of inorganic pyrophosphate (PPi), a potent endogenous inhibitor of calcification. Variants in ENPP1, the gene mutated in GACI, have not been associated with classic PXE. Here we report the clinical, laboratory, and molecular evaluations of ten GACI and two PXE patients from five and two unrelated families registered in GACI Global and PXE International databases, respectively. All patients were found to carry biallelic variants in ENPP1. Among ten ENPP1 variants, one homozygous variant demonstrated uniparental disomy inheritance. Functional assessment of five previously unreported ENPP1 variants suggested pathogenicity. The two PXE patients, currently 57 and 27 years of age, had diagnostic features of PXE and had not manifested the GACI phenotype. The similarly reduced PPi plasma concentrations in the PXE and GACI patients in our study correlate poorly with their disease severity. This study demonstrates that in addition to GACI, ENPP1 variants can cause classic PXE, expanding the clinical and genetic heterogeneity of heritable ectopic calcification disorders. Furthermore, the results challenge the current prevailing concept that plasma PPi is the only factor governing the severity of ectopic calcification.

Biallelic inactivating mutations in the ENPP1 gene cause generalized arterial calcification of infancy (GACI), a frequently fatal disease characterized by infantile onset of widespread arterial calcification and/or narrowing of large and medium-sized vessels often resulting in the early demise of affected individuals. Significantly reduced, almost zero plasma levels of a potent and endogenous calcification inhibitor, inorganic pyrophosphate (PPi), is thought to be the underlying cause of vascular calcification in GACI. Mutations in ENPP1 have not been found in patients with pseudoxanthoma elasticum (PXE), another genetic multisystem ectopic calcification disorder caused by mutations in the ABCC6 gene. This study reports that ENPP1 mutations can also cause PXE with more favorable clinical outcomes. In addition, it was previously thought that plasma PPi levels correlate with vascular calcification severity. However, we here show that vascular calcification severity does not correlate with plasma PPi levels. The results suggest that in addition to PPi, the long-believed determinant of ectopic calcification, additional mechanisms may be at play in regulating ectopic calcification.