IL-12Rβ1 Deficiency in Two of Fifty Children with Severe Tuberculosis from Iran, Morocco, and Turkey

BACKGROUND AND OBJECTIVES: In the last decade, autosomal recessive IL-12Rβ1 deficiency has been diagnosed in four children with severe tuberculosis from three unrelated families from Morocco, Spain, and Turkey, providing proof-of-principle that tuberculosis in otherwise healthy children may result from single-gene inborn errors of immunity. We aimed to estimate the fraction of children developing severe tuberculosis due to IL-12Rβ1 deficiency in areas endemic for tuberculosis and where parental consanguinity is common. METHODS AND PRINCIPAL FINDINGS: We searched for IL12RB1 mutations in a series of 50 children from Iran, Morocco, and Turkey. All children had established severe pulmonary and/or disseminated tuberculosis requiring hospitalization and were otherwise normally resistant to weakly virulent BCG vaccines and environmental mycobacteria. In one child from Iran and another from Morocco, homozygosity for loss-of-function IL12RB1 alleles was documented, resulting in complete IL-12Rβ1 deficiency. Despite the small sample studied, our findings suggest that IL-12Rβ1 deficiency is not a very rare cause of pediatric tuberculosis in these countries, where it should be considered in selected children with severe disease. SIGNIFICANCE: This finding may have important medical implications, as recombinant IFN-γ is an effective treatment for mycobacterial infections in IL-12Rβ1-deficient patients. It also provides additional support for the view that severe tuberculosis in childhood may result from a collection of single-gene inborn errors of immunity

A Mild Form of SLC29A3 Disorder: A Frameshift Deletion Leads to the Paradoxical Translation of an Otherwise Noncoding mRNA Splice Variant

We investigated two siblings with granulomatous histiocytosis prominent in the nasal area, mimicking rhinoscleroma and Rosai-Dorfman syndrome. Genome-wide linkage analysis and whole-exome sequencing identified a homozygous frameshift deletion in SLC29A3, which encodes human equilibrative nucleoside transporter-3 (hENT3). Germline mutations in SLC29A3 have been reported in rare patients with a wide range of overlapping clinical features and inherited disorders including H syndrome, pigmented hypertrichosis with insulin-dependent diabetes, and Faisalabad histiocytosis. With the exception of insulin-dependent diabetes and mild finger and toe contractures in one sibling, the two patients with nasal granulomatous histiocytosis studied here displayed none of the many SLC29A3-associated phenotypes. This mild clinical phenotype probably results from a remarkable genetic mechanism. The SLC29A3 frameshift deletion prevents the expression of the normally coding transcripts. It instead leads to the translation, expression, and function of an otherwise noncoding, out-of-frame mRNA splice variant lacking exon 3 that is eliminated by nonsense-mediated mRNA decay (NMD) in healthy individuals. The mutated isoform differs from the wild-type hENT3 by the modification of 20 residues in exon 2 and the removal of another 28 amino acids in exon 3, which include the second transmembrane domain. As a result, this new isoform displays some functional activity. This mechanism probably accounts for the narrow and mild clinical phenotype of the patients. This study highlights the ‘rescue’ role played by a normally noncoding mRNA splice variant of SLC29A3, uncovering a new mechanism by which frameshift mutations can be hypomorphic

Characterization of greater middle eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia1-3, has resulted in an elevated burden of recessive disease4. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized ‘genetic purging’. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics

La lèpre

Il y a cinquante ans, la première identification d’une contribution génétique non mendélienne au développement d’une maladie infectieuse commune, l’association entre le paludisme et la drépanocytose, fut établie par une approche supervisée dont le principe consiste à tester des gènes candidats par hypothèse. Depuis, les quelques gènes associés de façon convaincante à une prédisposition aux maladies infectieuses humaines ont été identifiés en suivant la même stratégie. L’étude de la lèpre a fortement contribué à modifier ce mode de pensée. En effet, en raison de l’absence de modèle expérimental satisfaisant et de l’impossibilité de cultiver l’agent causal in vitro, l’approche par gène candidat s’est avérée d’un intérêt limité. À l’inverse, le criblage positionnel a permis d’identifier deux gènes majeurs impliqués dans le contrôle de la maladie, établissant pour la première fois le caractère oligogénique de la contribution génétique humaine à une maladie infectieuse. Il est probable que ces résultats décisifs obtenus dans la lèpre et l’explosion récente des outils de la génomique vont imposer les approches de criblage complet du génome (positionnel et/ou fonctionnel) comme la stratégie principale de dissection fine de la prédisposition génétique à de nombreuses maladies infectieuses communes

Evaluation of Approaches to Identify Associated SNPs That Explain the Linkage Evidence in Nuclear Families with Affected Siblings

Linkage analysis is often followed by association mapping to localize disease variants. In this paper, we evaluate approaches to determine how much of the observed linkage evidence, namely the identity-by-descent (IBD) sharing at the linkage peak, is explained by associated SNPs. We study several methods: Homozygote Sharing Tests (HST), Genotype Identity-by-Descent Sharing Test (GIST), and a permutation approach. We also propose a new approach, HSTMLB, combining HST and the Maximum Likelihood Binomial (MLB) linkage statistic. These methods can identify SNPs partially explaining the linkage peak, but only HST and HSTMLB can identify SNPs that do not fully explain the linkage evidence and be applied to multiple-SNPs. We contrast these methods with the association tests implemented in the software LAMP. In our simulations, GIST is more powerful at finding SNPs that partially explain the linkage peak, while HST and HSTMLB are equally powerful at identifying SNPs that do not fully explain the linkage peak. When applied to the North American Rheumatoid Arthritis Consortium data, HST and HSTMLB identify marker pairs that may fully explain the linkage peak on chromosome 6. In conclusion, HST and HSTMLB provide simple and flexible tools to identify SNPs that explain the IBD sharing at the linkage peak

PARK2 mediates interleukin 6 and monocyte chemoattractant protein 1 production by human macrophages.

Leprosy is a persistent infectious disease caused by Mycobacterium leprae that still affects over 200,000 new patients annually. The host genetic background is an important risk factor for leprosy susceptibility and the PARK2 gene is a replicated leprosy susceptibility candidate gene. The protein product of PARK2, Parkin, is an E3 ubiquitin ligase that is involved in the development of various forms of Parkinsonism. The human macrophage is both a natural host cell of M. leprae as well as a primary mediator of natural immune defenses, in part by secreting important pro-inflammatory cytokines and chemokines. Here, we report that down-regulation of Parkin in THP-1 macrophages, human monocyte-derived macrophages and human Schwann cells resulted in a consistent and specific decrease in interleukin-6 (IL-6) and monocyte chemoattractant protein 1 (MCP-1/CCL2) production in response to mycobacteria or LPS. Interestingly, production of IL-6 at 6 hours by THP-1 cells stimulated with live M. leprae and M. bovis BCG was dependent on pretreatment with 1,25-dihydroxyvitamin D(3) (VD). Parkin knockdown in VD-treated cells blocked IL-6 induction by mycobacteria. However, IκB-α phosphorylation and levels of IκB-ξ, a nuclear protein required for IL-6 expression, were not affected by Parkin silencing. Phosphorylation of MAPK ERK1/2 and p38 was unaffected by Parkin silencing while JNK activation was promoted but did not explain the altered cytokine production. In a final set of experiments we found that genetic risk factors of leprosy located in the PARK2 promoter region were significantly correlated with M. leprae sonicate triggered CCL2 and IL6 transcript levels in whole blood assays. These results associated genetically controlled changes in the production of MCP-1/CCL2 and IL-6 with known leprosy susceptibility factors

Whisker plots of <i>CCL2</i> and <i>IL6</i> transcript levels in whole blood cultures in the presence an absence of <i>M. leprae</i> sonicate.

<p>Whole blood from 62 Vietnamese subjects was stimulated with 10 µg/ml <i>M. leprae</i> sonicate and transcript levels of <i>CCL2</i> and <i>IL-6</i> were determined by real time PCR. (<b>A</b>) Transcript levels were normalized with the <i>HPRT</i> house keeping gene and expressed as ΔC_t in the absence (NON-STIM) and presence (STIM) of <i>M. leprae</i> sonicate. The median of the distribution is indicated by a solid line within the box. The resulting subdivision of the box indicates the distribution of the flanking 25% percentile in each direction while the error bars give the distribution of the upper and lower 25% of the ΔC_t values. (<b>B</b>) The increase of <i>CCL2</i> and <i>IL6</i> transcripts resulting from stimulation with <i>M. leprae</i> sonicate expressed as ΔΔC_t. Plots as described in A.</p

Parkin-silenced THP-1 macrophages cytokine screen.

<p>(<b>A</b>) Parkin was detected by indirect immunofluorescence of THP-1 cells following transfection with either scrambled siRNA (upper panel) or siRNA targeting Parkin (lower panel). Insets represent DAPI-stained nuclei. (<b>B</b>) PMA-differentiated THP-1 macrophages were transfected with control or Parkin-silencing siRNA. After 48 hours, cells were treated with H37Ra at an MOI of 10, <i>M. leprae</i> (ML) at an MOI 50, or left untreated (Neg.). After 6 hours, supernatants were collected and analyzed with a Milliplex 42-cytokine assay. Cytokines with detectable values (12 out of 42) are plotted on the graph. Cytokine production is expressed as ratio of cytokine secreted by cells transfected with siRNA for <i>PARK2</i> (Parkin) to cytokine secreted by cells transfected with control siRNA (scrambled). (<b>C</b>) PMA- differentiated THP-1 macrophages were transfected with control or Parkin-silencing siRNA. After 48 hours, cells were treated with LPS (10 ng/ml), <i>M. bovis</i> BCG at an MOI of 10, <i>M. leprae</i> (ML) at an MOI 50, or left untreated (Neg). After 6 hours supernatants were collected and analyzed with a Q-Plex custom cytokine multiplex assay. Values represent the ratio of concentrations produced by Parkin-silenced cells over controls ± SD of at least three independent experiments. (<b>D</b>) As described for <b>C</b> except that supernatants were collected after 24 hrs incubation with stimulants. * <i>p</i><0.05, non-parametric t test of unpaired samples.</p

Human genetics of infectious diseases: between proof of principle and paradigm

The observation that only a fraction of individuals infected by infectious agents develop clinical disease raises fundamental questions about the actual pathogenesis of infectious diseases. Epidemiological and experimental evidence is accumulating to suggest that human genetics plays a major role in this process. As we discuss here, human predisposition to infectious diseases seems to cover a continuous spectrum from monogenic to polygenic inheritance. Although many studies have provided proof of principle that infectious diseases may result from various types of inborn errors of immunity, the genetic determinism of most infectious diseases in most patients remains unclear. However, in the future, studies in human genetics are likely to establish a new paradigm for infectious diseases