A recurrent ACTA1 amino acid change in mosaic form causes milder asymmetric myopathy.

We describe three patients with asymmetric congenital myopathy without definite nemaline bodies and one patient with severe nemaline myopathy. In all four patients, the phenotype had been caused by pathogenic missense variants in ACTA1 leading to the same amino acid change, p.(Gly247Arg). The three patients with milder myopathy were mosaic for their variants. In contrast, in the severely affected patient, the missense variant was present in a de novo, constitutional form. The grade of mosaicism in the three mosaic patients ranged between 20 % and 40 %. We speculate that the milder clinical and histological manifestations of the same ACTA1 variant in the patients with mosaicism reflect the lower abundance of mutant actin in their muscle tissue. Similarly, the asymmetry of body growth and muscle weakness may be a consequence of the affected cells being unevenly distributed. The partial improvement in muscle strength with age in patients with mosaicism might be due to an increased proportion over time of nuclei carrying and expressing two normal alleles.

A novel partial de novo duplication of JARID2 gene causing a neurodevelopmental phenotype.

BACKGROUND: Deletions covering the entire or partial JARID2 gene as well as pathogenic single nucleotide variants leading to haploinsufficiency of JARID2 have recently been shown to cause a clinically distinct neurodevelopmental syndrome. Here, we present a previously undescribed partial de novo duplication of the JARID2 gene in a patient displaying features similar to those of patients with JARID2 loss-of-function variants. CASE REPORT: The index patient presents with abnormalities in gross motor skills and speech development as well as neuropsychiatric disorders. The patient has markedly dark infraorbital circles and slightly prominent supraorbital ridges.Whole-genome sequencing and array comparative genomic hybridization revealed a novel disease-causing variant type, a partial tandem duplication of JARID2, covering the exons 1-7. Furthermore, RNA sequencing validated the increased expression of these exons. Expression alterations were also detected in target genes of the PRC2 complex, in which JARID2 acts as an essential member. CONCLUSION: Our data add to the variety of different pathogenic variants associated with JARID2 neurodevelopmental syndrome.

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health.

We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activity and sleep. We generated a resource of >20,000 biological samples from this study and a compendium of >53 million primary data points for 558,032 distinct features. Multiomics factor analysis revealed distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet, and hormonal effects. For example, ethinyl estradiol, a common oral contraceptive, produced characteristic molecular and physiological effects, including increased levels of inflammation and impact on thyroid, cortisol levels, and pulse, that were distinct from other sources of variability observed in our study. In total, this work illustrates the value of combining deep molecular and digital monitoring of human health. A record of this paper's transparent peer review process is included in the supplemental information.

Loss-of-function mutation in IKZF2 leads to immunodeficiency with dysregulated germinal center reactions and reduction of MAIT cells.

The Ikaros family transcription factors regulate lymphocyte development. Loss-of-function variants in IKZF1 cause primary immunodeficiency, but Ikaros family members IKZF2 and IKZF3 have not yet been associated with immunodeficiency. Here, we describe a pedigree with a heterozygous truncating variant in IKZF2, encoding the transcriptional activator and repressor Helios, which is highly expressed in regulatory T cells and effector T cells, particularly of the CD8+ T cell lineage. Protein-protein interaction analysis revealed that the variant abolished heterodimerization of Helios with Ikaros and Aiolos and also prevented Helios binding to members of the Mi-2/NuRD chromatin remodeling complex. Patients carrying the IKZF2 variant presented with a combined immunodeficiency phenotype characterized by recurrent upper respiratory infections, thrush and mucosal ulcers, and chronic lymphadenopathy. With extensive immunophenotyping, functional assays, and transcriptional analysis, we show that reduced Helios expression was associated with chronic T cell activation and increased production of proinflammatory cytokines both in effector and regulatory T cells. Lymph node histology from patients indicated dysregulated germinal center reactions. Moreover, affected individuals displayed a profound reduction in circulating MAIT cell numbers. In summary, we show that this previously undescribed loss-of-function variant in Helios leads to an immunodeficiency with signs of immune overactivation.

A nearly fatal primary Epstein-Barr virus infection associated with low NK-cell counts in a patient receiving azathioprine: a case report and review of literature.

BACKGROUND: Symptomatic primary Epstein-Barr virus infection is a usually self-limiting illness in adolescents. We present a case of an adolescent who had been receiving azathioprine for inflammatory bowel disease for four years and developed a life-threatening primary Epstein-Barr virus infection successfully treated with rituximab. CASE PRESENTATION: An 11-year-old girl presented with chronic, bloody diarrhea. Endoscopic biopsies confirmed a diagnosis of chronic ulcerative colitis with features of Crohn's disease. Azathioprine was initiated after one year due to active colitis. She responded well and remission was achieved. At the age of 16 years she developed a life-threatening Epstein-Barr virus infection including severe multiple organ failure and was critically ill for 4 weeks in the intensive care unit. Natural killer cells were virtually absent in the lymphocyte subset analysis. Azathioprine was stopped on admission. She was initially treated with corticosteroids, acyclovir and intravenous immunoglobulin. Approximately 30 days after admission, she developed signs of severe hepatitis and pneumonitis and received weekly rituximab infusions for 8 weeks. Primary immunodeficiency was excluded by whole exome sequencing in two independent laboratories. Persistent viremia stopped when the natural killer cell count started to rise, approximately 90 days after the cessation of azathioprine. CONCLUSIONS: We found 17 comparable cases in the literature. None of the previous cases reported in the literature, who had been treated with azathioprine and developed either a severe or a fatal Epstein-Barr virus infection, underwent full genetic and prospective immunological workup to rule out known primary immunodeficiencies. Recently, azathioprine has been shown to cause rather specific immunosuppression, resulting in natural killer cell depletion. Our case demonstrates that slow recovery from azathioprine-induced natural killer cell depletion, 3 months after the stopping of azathioprine, coincided with the clearance of viremia and clinical recovery. Finally, our choice of treating the patient with rituximab, as previously used for patients with a severe immunosuppression and Epstein-Barr virus viremia, appeared to be successful in this case. We suggest testing for Epstein-Barr virus serology before starting azathioprine and measuring natural killer cell counts during the treatment to identify patients at risk of developing an unusually severe primary Epstein-Barr virus infection.

SNP Analysis of Caries and Initial Caries in Finnish Adolescents.

BACKGROUND: Dental caries is the most common infection in the world and is influenced by genetic and environmental factors. Environmental factors are largely known, but the role of genetic factors is quite unknown. The aim was to investigate the genetic background of caries in Finnish adolescents. MATERIALS AND METHODS: This study was carried out at the Kotka Health Center in Eastern Finland. 94 participants aged 15-17 years gave approval for the saliva and DNA analyses. However, one was excluded in DNA analysis; thus, the overall number of participants in analysis was 93. Caries status was recorded clinically and from bite-wing X-rays to all 94 participants. Genomic DNA was extracted by genomic QIAamp® DNA Blood Mini Kit and genotyped for polymorphisms. The results were analyzed using additive and logistic regression models. RESULTS: No significant associations between caries and the genes studied were found. However, SNPs in DDX39B and MPO showed association tendencies but were not statistically significant after false discovery rate (FDR) analysis. SNPs in VDR, LTA, and MMP3 were not statistically significant with initial caries lesions after FDR analysis. CONCLUSION: The present study could not demonstrate statistically significant associations between caries and the genes studied. Further studies with larger populations are needed.

Who would benefit from exome sequencing?

Next-generation sequencing methods have revolutionized the possibilities for analyzing the human genome. Sequencing the exome, the protein-encoding portion of the genome, is used, in clinical medicine, especially in the diagnosis of rare hereditary diseases, congenital developmental disorders and cancer. Using exome sequencing as a diagnostic test is justified when the results could lead to an accurate diagnosis, significantly influence the treatment and genetic counseling. It is a reliable method for detecting single base mutations as minor deletions and insertions. However, with current methods the reliable analysis of larger changes in the number of copies, the length or repeats and areas present in multiple copies in the genome is challenging. Every human has many mutations in their exome, and distinguishing between insignificant and pathogenic mutations is thus a key challenge when interpreting the results of exome sequencing.

Periodontal Initial Radiological Findings of Genetically Predisposed Finnish Adolescents.

INTRODUCTION: Periodontitis is a multifactorial infectious disease of the supporting tissues of teeth in which bacterial, genetic and lifestyle factors such as smoking have an important role. AIM: The aim was to examine if Bleeding On Probing (BOP ≥ 20%) and ≥ 4 mm deep pockets correlated with any suspicion of initial radiological findings of periodontitis and bone loss. We also investigated whether any pro-inflammatory-related candidate Single Nucleotide Polymorphisms (SNPs) were associated with any suspicion of radiological findings. MATERIALS AND METHODS: Altogether 47 generally healthy adolescent patients of one birth cohort had given their approval for their saliva samples to be used for DNA analysis. One participant was excluded after discrepant gender check. An oral radiologist analysed right and left bitewing radiographs of 47 patients. Clinical parameters such as BOP ≥ 20%, ≥ 4 mm pockets, Visible Plaque Index of all teeth (VPI%), as well as smoking habits were recorded. DNA was extracted and 71 SNPs from candidate genes for initial periodontitis were genotyped. The association between ≥ 4 mm pockets and BOP ≥ 20% with radiological findings and selected SNPs was modelled using logistic regression. RESULTS: Variants in Toll-Like Receptors 4 (TLR4) gene (rs498670) (OR=5.8, {CI95% 1.6-20.7}, p=0.02, FDR q-value=0.13) and TNFSF11 gene (rs2277438, OR=0.3 {CI95% 0.1-0.9}, p=0.002, FDR q-value=0.56) were associated with any suspicious radiological findings; however the significance vanished after False Discovery Rate analysis (FDR). The association between BOP ≥ 20% and any radiographic signs of periodontitis was found to be statistically significant, OR=1.6, CI 95% 1.0-2.4, p=0.04. CONCLUSION: Only TLR4 (rs498670) and TNFSF11 (rs2277438) genes were found to have a positive correlation with radiological findings suggestive of initial periodontitis after adjustment for smoking and visible plaque.

Pilot Study on the Genetic Background of an Active Matrix Metalloproteinase-8 Test in Finnish Adolescents.

BACKGROUND: In periodontitis, genetics and smoking play important roles in host immune system response. The aim of this study is to determine whether the genetic background of initial periodontitis and caries could be detected using an active matrix metalloproteinase (aMMP)-8 chairside test in Finnish adolescents. METHODS: Forty-seven participants gave approval for analysis of both oral fluid collection and DNA. An aMMP-8 chairside test was performed on participants (adolescents aged 15 to 17 years), and full-mouth clinical parameters of oral health were assessed including periodontal, oral mucosal, and caries status in Eastern Finland from 2014 to 2015. DNA was extracted from oral fluid samples and genotyped for 71 polymorphisms in 29 candidate genes for periodontitis. Results were analyzed using a logistic regression model. P values were corrected for multiple testing using false discovery rate (<0.05). RESULTS: aMMP-8 chairside test positivity and three or more ≥4 mm pockets were associated with vitamin D receptor (VDR) (rs2228570, P = 0.002, q = 0.04) and MMP3 (rs520540, rs639752, rs679620, P = 0.0009, 0.003, 0.003, q = 0.04, respectively). None of the other single-nucleotide polymorphisms studied showed a significant association with the aMMP-8 chairside test and at least one caries lesion positivity. CONCLUSION: Genetic polymorphisms of MMP3 and VDR are linked to initial periodontitis in Finnish adolescents, and the aMMP-8 chairside test can eventually detect initial periodontitis in young patients with predisposing genetic background.

Trim37-deficient mice recapitulate several features of the multi-organ disorder Mulibrey nanism.

Mulibrey nanism (MUL) is a rare autosomal recessive multi-organ disorder characterized by severe prenatal-onset growth failure, infertility, cardiopathy, risk for tumors, fatty liver, and type 2 diabetes. MUL is caused by loss-of-function mutations in TRIM37, which encodes an E3 ubiquitin ligase belonging to the tripartite motif (TRIM) protein family and having both peroxisomal and nuclear localization. We describe a congenic Trim37 knock-out mouse (Trim37(-/-)) model for MUL. Trim37(-/-) mice were viable and had normal weight development until approximately 12 months of age, after which they started to manifest increasing problems in wellbeing and weight loss. Assessment of skeletal parameters with computer tomography revealed significantly smaller skull size, but no difference in the lengths of long bones in Trim37(-/-) mice as compared with wild-type. Both male and female Trim37(-/-) mice were infertile, the gonads showing germ cell aplasia, hilus and Leydig cell hyperplasia and accumulation of lipids in and around Leydig cells. Male Trim37(-/-) mice had elevated levels of follicle-stimulating and luteinizing hormones, but maintained normal levels of testosterone. Six-month-old Trim37(-/-) mice had elevated fasting blood glucose and low fasting serum insulin levels. At 1.5 years Trim37(-/-) mice showed non-compaction cardiomyopathy, hepatomegaly, fatty liver and various tumors. The amount and morphology of liver peroxisomes seemed normal in Trim37(-/-) mice. The most consistently seen phenotypes in Trim37(-/-) mice were infertility and the associated hormonal findings, whereas there was more variability in the other phenotypes observed. Trim37(-/-) mice recapitulate several features of the human MUL disease and thus provide a good model to study disease pathogenesis related to TRIM37 deficiency, including infertility, non-alcoholic fatty liver disease, cardiomyopathy and tumorigenesis.

Inflammatory mediator polymorphisms associate with initial periodontitis in adolescents.

Several studies have addressed cytokine gene polymorphisms and their possible associations with periodontitis. We examined the association between salivary anti- and pro-inflammatory mediator polymorphisms and initial periodontitis in Finnish adolescents, taking into account the effect of smoking. Salivary samples of 93 clinically examined adolescents from Eastern Finland were analyzed. Their oral health and smoking habits were recorded. Periodontal probing depth (PPD), and bleeding on probing (BOP) at four sites per tooth, root calculus (RC), and visible plaque index (VPI) were recorded from the index teeth. Salivary MMP-8 median values were assessed. The sites with ≥4 mm PD were categorized as follows: PPD1 = one or more ≥4 mm pocket, PPD2 = two or more ≥4 mm pockets, and PPD3 = three or more ≥4 mm pockets. Genomic DNA was extracted from 300 µl of the saliva samples by genomic QIAamp® DNA Blood Mini Kit and genotyped for polymorphisms. Genetic variants for genotyping were selected from the following genes of interest: S100A8, FCGR2A, FCGR2B, IL10, MMP8, MMP3, MMP13, VDR, TLR4, MMP2, MPO, ELANE, IL1A, IL1B, IL1RN, CD28, MMP9, DDX39B, NFKBIL1, LTA, TNF, SOD2, IL6, TLR4, TIMP1, and SYN1. After false discovery rate control (FDR), polymorphisms in MMP3 (rs679620, rs520540, rs639752), CD28 (rs3116496), and VDR (rs2228570) associated (FDR q < 0.05) with deepened periodontal pockets. Smoking did not affect the results. Genetic polymorphisms of pro-inflammatory mediators MMP3, CD28, and VDR seem to link to initial periodontitis.

Prevalence of PI*Z and PI*S alleles of alpha-1-antitrypsin deficiency in Finland.

The prevalence of PI*Z and PI*S alleles of SERPINA1 gene related to alpha-1-antitrypsin deficiency has previously been estimated to be lower in Finland than in the other countries of Northern Europe. The prevalence of PI*M (Malton) has not been studied in Finland before. We determined alpha-1-antitrypsin PI*Z and PI*S and PI*M (Malton) genotypes from a representative population sample. The number of subjects was 6,354 in the PI*S and PI*M (Malton) genotyping. PI*Z genotyping was performed in a subsample of 2,482 subjects. The allele frequencies were PI*Z 19.7/1,000 and PI*S 10.2/1,000. No PI*M (Malton) was found. The number of carriers of PI*Z and PI*S is significantly higher than previously estimated. The prevalences are in line with the findings in the neighboring countries.