A Novel Multigenic Immunodeficiency Affecting Interferon Mediated Immunity

Primary immunodeficiencies are classically considered monogenic disorders characterized by host susceptibility to specific infectious pathogens. Patients with genetic defects in the IL-12/interferon gamma (IFN-γ) axis have susceptibility to weakly virulent mycobacteria, Mycobacteria tuberculosis, and Salmonella, but are resistant to the majority of other infectious pathogens. Host susceptibility to disseminated cytomegalovirus (CMV) infections typically results from genetic defects in T cell development or function. We studied a patient with disseminated M. tuberculosis and cytomegalovirus viremia. Whole exome sequencing identified two novel homozygous mutations affecting two distinct IFN pathways: the signal transducing chain of the IFN-γ receptor (IFNGR2) and the signaling chain of the IFN-α receptor (IFNAR1). The frameshift deletion in IFNGR2 resulted in a truncated protein with significantly decreased protein expression and absent downstream signaling, as demonstrated by a lack of STAT1 phosphorylation and HLA-DR upregulation in response to IFN-γ stimulation. Human defects in IFNAR1 have not been previously described. The patient’s IFNAR1 mutation replaced the protein’s native stop codon with 46 novel C-terminal amino acids (IFNAR1*557Gluext*46). The IFNAR1*557Gluext*46 mutant was expressed in patient fibroblasts at a level comparable to that of wild-type IFNAR1 in control fibroblasts. However, the IFNAR1*557Gluext*46 mutant led to impaired STAT1/STAT2 phosphorylation and decreased nuclear translocation of STAT1 in response to IFN-α stimulation. Furthermore, the patient had impaired expression of the IFN-α stimulated genes, IFIT1, IFIT2, and IRF7, which are critical for host immunity to CMV. Patient and control fibroblasts were equally susceptible to CMV entry; however, cells expressing IFNAR1*557Gluext*46 presented impaired expression of the ISG IFIT2, IFN-β and IFI16 after infection with CMV. Moreover, pretreatment with IFN-α did not prevent CMV replication in patient fibroblasts compared to cells expressing the wild type IFNAR1. The patient’s susceptibility to multiple types of infectious pathogens thus resulted from dual defects in Type I and Type II IFN signaling. These findings highlight the utility of whole exome sequencing in the discovery of multigenic primary immunodeficiencies

Uses of Next-Generation Sequencing Technologies for the Diagnosis of Primary Immunodeficiencies

Primary immunodeficiencies (PIDs) are genetic disorders impairing host immunity, leading to life-threatening infections, autoimmunity, and/or malignancies. Genomic technologies have been critical for expediting the discovery of novel genetic defects underlying PIDs, expanding our knowledge of the complex clinical phenotypes associated with PIDs, and in shifting paradigms of PID pathogenesis. Once considered Mendelian, monogenic, and completely penetrant disorders, genomic studies have redefined PIDs as a heterogeneous group of diseases found in the global population that may arise through multigenic defects, non-germline transmission, and with variable penetrance. This review examines the uses of next-generation DNA sequencing (NGS) in the diagnosis of PIDs. While whole genome sequencing identifies variants throughout the genome, whole exome sequencing sequences only the protein-coding regions within a genome, and targeted gene panels sequence only a specific cohort of genes. The advantages and limitations of each sequencing approach are compared. The complexities of variant interpretation and variant validation remain the major challenge in wide-spread implementation of these technologies. Lastly, the roles of NGS in newborn screening and precision therapeutics for individuals with PID are also addressed

Combined immunodeficiency with EBV positive B cell lymphoma and epidermodysplasia verruciformis due to a novel homozygous mutation in RASGRP1

RASGRP1 is a guanine-nucleotide-exchange factor essential for MAP-kinase mediated signaling in lymphocytes. We report the second case of RASGRP1 deficiency in a patient with a homozygous nonsense mutation in the catalytic domain of the protein. The patient had epidermodysplasia verruciformis, suggesting a clinically important intrinsic T cell function defect. Like the previously described patient, our proband also presented with CD4+ T cell lymphopenia, impaired T cell proliferation to mitogens and antigens, reduced NK cell function, and EBV-associated lymphoma. The severity of the disease and the development of EBV lymphoma in both patients suggest that hematopoietic stem cell transplantation should be performed rapidly in patients with RASGRP1 deficiency

Solar radiation is inversely associated with inflammatory bowel disease admissions

<p><b>Objective:</b> To explore the associations between latitude and solar radiation with inflammatory bowel disease admission rates in Chile, the country with the largest variation in solar radiation in the world.</p> <p><b>Patients and methods:</b> This is an ecological study, which included data on all hospital-admitted population for inflammatory bowel disease between 2001 and 2012, according to different latitudes and solar radiation exposures in Chile. The data were acquired from the national hospital discharge database from the Department of Health Statistics and Information of the Chilean Ministry of Health.</p> <p><b>Results:</b> Between 2001 and 2012 there were 12,869 admissions due to inflammatory bowel disease (69% ulcerative colitis, 31% Crohn’s disease). Median age was 36 years (IQR: 25–51); 57% were female. The national inflammatory bowel disease admission rate was 6.52 (95% CI: 6.40–6.63) per 100,000 inhabitants with increasing rates over the 12-year period. In terms of latitude, the highest admission rates for pediatric ulcerative colitis and Crohn’s disease, as well as adult ulcerative colitis, were observed in the southernmost region with lowest annual solar radiation. Linear regression analysis showed that regional solar radiation was inversely associated with inflammatory bowel disease admissions in Chile (<i>β</i>: −.44, <i>p</i> = .03).</p> <p><b>Conclusions:</b> Regional solar radiation was inversely associated with inflammatory bowel disease admission rates in Chile; inflammatory bowel disease admissions were highest in the southernmost region with lowest solar radiation. Our results support the potential role of vitamin D deficiency on inflammatory bowel disease flares.</p

Early origins of allergy and asthma (ARIES): study protocol for a prospective prenatal birth cohort in Chile

Background Growing evidence shows that atopic dermatitis (AD), food allergy (FA), allergic rhinitis, and asthma are largely determined during the first 1000 days (time elapsed from conception to the 2nd birthday). The ARIES birth cohort aims to determine prenatal and perinatal conditions, as well as genetic and epigenetic factors, that participate in the early setting of immune responses, and the role of these in the later determination of the risk of allergic diseases and asthma in the offspring. Methods We have designed a birth cohort of 250 families with prenatal recruitment (similar to 14 weeks). We will genotype relevant allergy/asthma-associated variants in trios and will perform immunophenotyping and evaluation of allergy biomarkers in cord blood. At 1 and 2 years of age we will assess if infants have developed allergic sensitization, AD, FA, as well as biomarkers of asthma including the asthma predictive index. We will also evaluate how maternal conditions modify immune programming through epigenetic modifications and will then depict newborn epigenetic cues of allergy/asthma risk. Next, we will assess composition/diversity of maternal gut, placenta, breastmilk and infant gut microbiome and their association with immunophenotype and biomarkers at birth, and clinical outcomes at age 1 and 2. Finally, we plan to assess how environmental exposures (perinatal outdoor and indoor pollution, allergens and endotoxin) affect the incidence of allergic sensitization, AD, FA, and risk of asthma. Discussion The in-depth study of the ARIES birth cohort shall provide crucial information to understand the rising incidence of allergies and asthma in developing countries, and hopefully provide cues on how to prevent and treat these diseases.Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT PIA/ANILLOS ACT172097 CONICYT-PIA ANILLO committe