A potential founder variant in CARMIL2/RLTPR in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction.

BACKGROUND: Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of human papilloma virus (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected. METHODS AND RESULTS: The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies. No disease-causing variants were identified in known primary immunodeficiency genes or in other disease-related OMIM genes. However, the same homozygous missense variant in CARMIL2 (also known as RLTPR) was identified in all four patients. In each family, the variant was located within a narrow region of homozygosity, representing a potential region of autozygosity. CARMIL2 is a protein of undetermined function. A role in T-cell activation has been suggested and the mouse protein homolog (Rltpr) is essential for costimulation of T-cell activation via CD28, and for the development of regulatory T cells. Immunophenotyping demonstrated reduced regulatory, CD4+ memory, and CD4+ follicular T cells in all four patients. In addition, they all seem to have a deficiency in IFN γ -synthesis in CD4+ T cells and NK cells. CONCLUSIONS: We report a novel primary immunodeficiency, and a differential molecular diagnosis to CXCR4-,DOCK8-,GATA2-,MAGT1-,MCM4-,STK4-,RHOH-,TMC6-, and TMC8-related diseases. The specific variant may represent a Norwegian founder variant segregating on a population-specific haplotype.

PGM3 mutations cause a congenital disorder of glycosylation with severe immunodeficiency and skeletal dysplasia.

Human phosphoglucomutase 3 (PGM3) catalyzes the conversion of N-acetyl-glucosamine (GlcNAc)-6-phosphate into GlcNAc-1-phosphate during the synthesis of uridine diphosphate (UDP)-GlcNAc, a sugar nucleotide critical to multiple glycosylation pathways. We identified three unrelated children with recurrent infections, congenital leukopenia including neutropenia, B and T cell lymphopenia, and progression to bone marrow failure. Whole-exome sequencing demonstrated deleterious mutations in PGM3 in all three subjects, delineating their disease to be due to an unsuspected congenital disorder of glycosylation (CDG). Functional studies of the disease-associated PGM3 variants in E. coli cells demonstrated reduced PGM3 activity for all mutants tested. Two of the three children had skeletal anomalies resembling Desbuquois dysplasia: short stature, brachydactyly, dysmorphic facial features, and intellectual disability. However, these additional features were absent in the third child, showing the clinical variability of the disease. Two children received hematopoietic stem cell transplantation of cord blood and bone marrow from matched related donors; both had successful engraftment and correction of neutropenia and lymphopenia. We define PGM3-CDG as a treatable immunodeficiency, document the power of whole-exome sequencing in gene discoveries for rare disorders, and illustrate the utility of genomic analyses in studying combined and variable phenotypes.

Haploinsufficiency of XPO1 and USP34 by a de novo 230 kb deletion in 2p15, in a patient with mild intellectual disability and cranio-facial dysmorphisms.

2p15p16.1-deletion syndrome was first described in 2007 based on the clinical presentation of two patients. The syndrome is characterized by intellectual disability, autism spectrum disorders, microcephaly, dysmorphic facial features and a variety of congenital organ defects. The precise genotype-phenotype correlation in 2p15-deletion syndrome is not understood. However, greater insight can be obtained by thorough clinical investigation of patients carrying deletions, especially those of small size. We report a 21-year-old male patient with features overlapping the clinical spectrum of the 2p15p16.1-deletion syndrome, such as intellectual disability, dysmorphic facial features, and congenital defects. He carried a 230 kb de novo deletion (chr2:61500346-61733075 bp, hg19), which affects the genes USP34, SNORA70B and XPO1. While there is a lack of functional data on SNORA70B, the involvement of USP34 and XPO1 in the regulation of fundamental developmental processes is well known. We suggest that haploinsufficiency of one or both of these genes is likely to be responsible for the disease in our patient.

De novo 19p13.2 microdeletion encompassing the insulin receptor and resistin genes in a patient with obesity and learning disability.

Genetic studies have provided novel insights of appetite regulation and pathophysiology of obesity. The adipose tissue is an active endocrine organ secreting several hormones contributing to insulin resistance and the development of the comorbidities of obesity, such as type 2 diabetes and cardiovascular disease. Herein, we report on a patient with severe obesity and mild learning disability with a 750 kb de novo deletion of chromosome 19. The deletion encompasses several genes, including resistin and the first part of the insulin receptor, genes that are relevant for obesity. This novel deletion may therefore represent a region for obesity research. Plasma analyses and gene expression demonstrated that the deletion resulted in haploinsufficiency for resistin and insulin receptor in the patient compared to controls. We then studied the biochemical and adipocytokine profile in these subjects. We observed no differences in glucose and lipid parameters between the patient and the controls. Thus, haploinsufficiency of insulin receptor and resistin does not appear to influence glucose and lipid metabolism. However, the patient had considerably higher values of adiponectin and TNFα than controls. In conclusion, we identified a 19p13.2 microdeletion encompassing the insulin receptor and resistin genes resulting in haploinsufficiency in an obese, but otherwise healthy patient. No firm conclusions could be drawn regarding the potential effect of the microdeletion on adipokine profile.

Copy number variation findings among 50 children and adolescents with autism spectrum disorder.

OBJECTIVES: Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopment disorders with a complex genetic aetiology. The aim of this study was to identify copy number variations (CNVs) with a clinical significance for ASD. MATERIALS AND METHODS: Array-based comparative genomic hybridization was applied to detect CNVs in a clinically well-characterized population of 50 children and adolescents with ASD. RESULTS: Nine CNVs with predicted clinical significance were identified among eight individuals (detection rate 16%). Three of the CNVs are recurrently associated with ASDs (15q11.2q13.1) or have been identified in ASD populations [3p14.2 and t(8;12)(p23.1;p13.31)]. The remaining regions (15q11.2, 10q21.1, Xp22.2, 16p13.3 and 22q13.1) have not been reported previously as candidate genes for ASD. CONCLUSION: This study identified five novel CNVs among the individuals. The causal relationship between identified CNVs and the ASD phenotype is not fully established. However, the genes involved are associated with ASD and/or other neuropsychiatric disorders, or implicated in synaptic and neuronal activity, thus suggesting clinical significance. Further identification of ASD-associated CNVs is required, together with a broad clinical characterization of affected individuals to identify genotype-phenotype correlations.

A de novo 163 kb interstitial 1q44 microdeletion in a boy with thin corpus callosum, psychomotor delay and seizures.

The 1q44 deletion syndrome has shown to be a recognizable phenotype with developmental delay, short stature and corpus callosum abnormalities as relatively consistent features. However, the disorder is still clinically heterogeneous and a genotype-phenotype correlation has been challenging to establish. In particular, a delineation of a critical region for the corpus callosum development has turned out to be difficult, and many candidate genes have been proposed. We present here a patient boy with a clinical picture of the 1q44 deletion syndrome, including a thin corpus callosum, and a small de novo 1q44 deletion. The deletion spans a maximum of 163 kb, a region which only contains the two genes FAM36A and HNRNPU. This finding supports the previously suggested hypothesis that the HNRNPU is an essential gene to the development of corpus callosum. However, as patients with deletions outside this interval also have been reported to have corpus callosum abnormalities, other mechanisms are probably also involved. We also identified two conserved non-coding regions in the deleted region of the patient, and speculate that also other elements interfere with the complex interplay and spatiotemporal gene expression during embryonic development.

Exon trapping analysis of c.301-19G > A in intron 1 of the SHH gene in a patient with a microform of holoprosencephaly.

It can be difficult to assess the clinical significance of novel genomic sequence variants which may potentially alter mRNA splicing. Segregation analysis is not helpful in isolated cases or small families. Bioinformatic tools can provide additional information, but direct analysis of mRNA from an appropriate tissue remains the preferred approach for analyzing the effect of a sequence variant on splicing. However, hundreds of disease-associated and developmental genes, including the Sonic Hedgehog homolog (SHH) gene, are not expressed in blood or fibroblasts postnatally. We identified a de novo nucleotide change, c.301-19G > A, in intron 1 of SHH in a four year old boy with a microform of holoprosencephaly. In silico analyses predicted unaltered splicing. We used a minigene approach to study the variant more closely. The genomic region of interest was inserted into an exon trapping vector to create an artificial pre-mRNA in transfected cells. We found virtually complete inactivation of the splice acceptor site in intron 1 in two different transfected cell lines. In light of the clinical context, the de novo nature of the substitution and the results of the exon trapping analyses, we conclude that the detected variant is pathogenic and that the recurrence risk for sibs is low. This case demonstrates that in the absence of a readily available mRNA source, exon trapping can be a robust and practical aid in clinical practice for assessing the effect of genomic variants on pre-mRNA splicing.

Two brothers with a microduplication including the MECP2 gene: rapid head growth in infancy and resolution of susceptibility to infection.

Microduplications in chromosome Xq28, which include the methyl-CPG binding protein (MECP2) gene, cause severe X-linked mental retardation. Serious recurrent infections are a feature of this condition. Affected males are micro or normocephalic. We report two normocephalic brothers with an approximately 0.5 Mb duplication which includes MECP2 who had rapid head growth in infancy. The younger boy had chronic constipation until the age of 3 years. For both boys, the susceptibility to infection subsided in the second year of life. Whether or not rapid head growth in infancy and/or constipation are frequent features of the phenotype remains to be seen as more patients are described. Susceptibility to infection can remit after early childhood and could theoretically be related to overexpression of the interleukin 1 receptor-associated kinase IRAK1 gene.

ABCB4 sequence variations in young adults with cholesterol gallstone disease.

BACKGROUND AND AIMS: Mutations in the gene encoding the ABCB4 [adenosine triphosphate (ATP)-binding cassette, sub-family B (MDR/TAP), member 4] transporter lower phosphatidylcholine output into bile and contribute to cholesterol gallstone formation by decreasing the solubility of cholesterol in bile. Mutations in ABCB4 have been identified in patients with low phospholipid-associated cholelithiasis. The aim of the present study was to determine the types and frequencies of ABCB4 mutations in cholecystectomized patients aged <40 years. PATIENTS AND METHODS: Hundred and four patients (mean age 30.6 years, range 12-39) were included in the study and the ABCB4 gene was sequenced. The frequency of missense mutations found in the patient material was measured in 95 healthy controls. The potential functional implications of the ABCB4 missense variations were assessed by computerized analysis (BLOSUM62 and Grantham substitution matrices, polymorphism phenotyping and sorting intolerant from tolerant). RESULTS: One patient was heterozygous for a frameshift mutation (c.1399_1400ins10/p.Y467F fsX25). Another patient was heterozygous for a nonsense mutation (c.3136C>T/p.R1046X). These two mutations are considered detrimental to ABCB4 protein function. In addition, six missense mutations were found in the ABCB4 gene, and three of these were only present in patients. CONCLUSION: In our study, <2% of young gallstone patients were found to be heterozygous for detrimental ABCB4 mutations. The functional implication of several missense mutations remains to be clarified. Thus, mutations in the ABCB4 gene are a rare cause of gallstone disease.

1.4Mb recurrent 22q11.2 distal deletion syndrome, two new cases expand the phenotype.

We report two new patients with the 1.4Mb recurrent 22q11.2 distal deletion syndrome. Features common to both children, as well as to several of the previously reported cases, include normal palate, smooth philtrum, hypoplastic alae nasi and delayed development. Both children are small but not growth retarded, and are microcephalic. Their developmental delay is global and most pronounced for language acquisition. One child has unilateral sensorineural hearing loss and encopresis, and the other child has treatment-responsive nocturnal epileptogenic activity. These two new cases confirm the recurrent nature of the deletion and help to further delineate the phenotype.

Differential gene expression before and after ionizing radiation of subcutaneous fibroblasts identifies breast cancer patients resistant to radiation-induced fibrosis.

BACKGROUND AND PURPOSE: Differentially gene expression between patients with either very low or very high risk of radiation-induced fibrosis (RIF) in patient-derived fibroblasts after irradiation has previously been reported. In the present study, we are investigating the robustness of radiation-induced changes in gene expression in fibroblasts, whether differential expression is more pronounced when looking at the fold induction levels, taking into account the differences in background expression levels between patients, and whether there is a linear correlation between individual risk of RIF and changes in radiation-induced gene expression in fibroblasts. MATERIAL AND METHODS: Gene expression was analysed by quantitative real-time PCR before and after a fractionated scheme with 3x3.5Gy/3 days in fibroblasts derived from 26 patients with breast cancer treated with post-mastectomy radiotherapy. RESULTS: Robust radiation-induced changes in gene expression were observed, with differential gene expression between low and high risk patients being most pronounced for the fold induction level ('after' value divided by 'before' value for each patient). When including patients with intermediate risk, there was no linear correlation between individual risk of RIF and differential expression of the genes investigated. Rather, differential gene expression could divide patients into two clearly separated groups, a larger, sensitive group and a smaller resistant group. CONCLUSIONS: Differential gene expression in irradiated fibroblasts might be an important tool in the identification of differences in the genetic background between patients with variable risk of RIF, and in the identification of new targets for prevention and intervention of the fibrotic process.