The recombination-activating genes (RAG) 1 and 2 are indispensable for diversifying the primary B cell receptor repertoire and pruning self-reactive clones via receptor editing in the bone marrow; however, the impact of RAG1/RAG2 on peripheral tolerance is unknown. Partial RAG deficiency (pRD) manifesting with late-onset immune dysregulation represents an 'experiment of nature' to explore this conundrum. By studying B cell development and subset-specific repertoires in pRD, we demonstrate that reduced RAG activity impinges on peripheral tolerance through the generation of a restricted primary B cell repertoire, persistent antigenic stimulation and an inflammatory milieu with elevated B cell-activating factor. This unique environment gradually provokes profound B cell dysregulation with widespread activation, remarkable extrafollicular maturation and persistence, expansion and somatic diversification of self-reactive clones. Through the model of pRD, we reveal a RAG-dependent 'domino effect' that impacts stringency of tolerance and B cell fate in the periphery.

• MeSH
• B-Lymphocytes * MeSH
• Cell Differentiation MeSH
• DNA-Binding Proteins * deficiency   genetics   MeSH
• Homeodomain Proteins * genetics   MeSH
• Immune Tolerance MeSH
• Nuclear Proteins * deficiency   MeSH
• Humans MeSH
• Lymphocyte Count MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, N.I.H., Intramural MeSH

SCID (Severe combined immunodeficiency) neboli těžký kombinovaný imunodeficit je klinicky i geneticky heterogenní skupina nejzávažnějších vrozených poruch imunity. Toto vzácné onemocnění vede především k selhávání obrany proti infekcím na základě abnormálního vývoje lymfocytů a jejich funkcí. Jako život ohrožující stav vyžaduje co nejčasnější diagnostiku k zajištění adekvátního managementu směřujícímu k časné transplantaci kmenových buněk krvetvorby. Kromě klasických forem SCID, manifestujících se v časném kojeneckém věku, existují také formy, jež se mohou projevit později a/nebo mohou mít mírnější klinické příznaky. V tomto článku prezentujeme kazuistiku 5měsíčního kojence s autosomálně recesivním RAG2 SCID s atypickým fenotypem, který je jediným diagnostikovaným pacientem se SCID v České republice v letech 2018 a 2019.

Severe combined immunodeficiency (SCID) is clinically and genetically heterogeneous group of the most severe inborn errors of immunity. The disease typically presents as a failure of antimicrobial defences due to various defects of lymphocyte development and functions. Being a life-threatening condition, SCID requires a prompt diagnosis in order to implement an appropriate management aimed towards early hematopoietic stem cell transplantation. Besides the classic forms of SCID, atypical or leaky phenotypes exist, that may manifest later in life or/and with milder symptoms. In this report, we describe a 5-months-old infant with autosomal recessive atypical RAG2 SCID, who is the only patient diagnosed with SCID in the Czech Republic in the years 2018 and 2019.

• Keywords
• SCID screening, SCID,
• MeSH
• Infant MeSH
• Humans MeSH
• Lymphopenia diagnosis   etiology   MeSH
• Severe Combined Immunodeficiency * diagnosis   therapy   MeSH
• Bone Marrow Transplantation methods   MeSH
• Treatment Outcome MeSH
• Check Tag
• Infant MeSH
• Humans MeSH
• Male MeSH
• Publication type
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH

Background: Variants in recombination-activating genes (RAG) are common genetic causes of autosomal recessive forms of combined immunodeficiencies (CID) ranging from severe combined immunodeficiency (SCID), Omenn syndrome (OS), leaky SCID, and CID with granulomas and/or autoimmunity (CID-G/AI), and even milder presentation with antibody deficiency. Objective: We aim to estimate the incidence, clinical presentation, genetic variability, and treatment outcome with geographic distribution of patients with the RAG defects in populations inhabiting South, West, and East Slavic countries. Methods: Demographic, clinical, and laboratory data were collected from RAG-deficient patients of Slavic origin via chart review, retrospectively. Recombinase activity was determined in vitro by flow cytometry-based assay. Results: Based on the clinical and immunologic phenotype, our cohort of 82 patients from 68 families represented a wide spectrum of RAG deficiencies, including SCID (n = 20), OS (n = 37), and LS/CID (n = 25) phenotypes. Sixty-seven (81.7%) patients carried RAG1 and 15 patients (18.3%) carried RAG2 biallelic variants. We estimate that the minimal annual incidence of RAG deficiency in Slavic countries varies between 1 in 180,000 and 1 in 300,000 live births, and it may vary secondary to health care disparities in these regions. In our cohort, 70% (n = 47) of patients with RAG1 variants carried p.K86Vfs*33 (c.256_257delAA) allele, either in homozygous (n = 18, 27%) or in compound heterozygous (n = 29, 43%) form. The majority (77%) of patients with homozygous RAG1 p.K86Vfs*33 variant originated from Vistula watershed area in Central and Eastern Poland, and compound heterozygote cases were distributed among all Slavic countries except Bulgaria. Clinical and immunological presentation of homozygous RAG1 p.K86Vfs*33 cases was highly diverse (SCID, OS, and AS/CID) suggestive of strong influence of additional genetic and/or epigenetic factors in shaping the final phenotype. Conclusion: We propose that RAG1 p.K86Vfs*33 is a founder variant originating from the Vistula watershed region in Poland, which may explain a high proportion of homozygous cases from Central and Eastern Poland and the presence of the variant in all Slavs. Our studies in this cohort of RAG1 founder variants confirm that clinical and immunological phenotypes only partially depend on the underlying genetic defect. As access to HSCT is improving among RAG-deficient patients in Eastern Europe, we anticipate improvements in survival.

• MeSH
• White People * MeSH
• Child MeSH
• DNA-Binding Proteins genetics   MeSH
• Phenotype MeSH
• Gene Frequency MeSH
• Genotype * MeSH
• Homeodomain Proteins genetics   MeSH
• Incidence MeSH
• Nuclear Proteins genetics   MeSH
• Infant MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Infant, Newborn MeSH
• Polymorphism, Genetic MeSH
• Child, Preschool MeSH
• Retrospective Studies MeSH
• Sequence Deletion genetics   MeSH
• Immunologic Deficiency Syndromes genetics   MeSH
• Treatment Outcome MeSH
• Check Tag
• Child MeSH
• Infant MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Male MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, N.I.H., Intramural MeSH

The EuroFlow PID consortium developed a set of flow cytometry tests for evaluation of patients with suspicion of primary immunodeficiency (PID). In this technical report we evaluate the performance of the SCID-RTE tube that explores the presence of recent thymic emigrants (RTE) together with T-cell activation status and maturation stages and discuss its applicability in the context of the broader EuroFlow PID flow cytometry testing algorithm for diagnostic orientation of PID of the lymphoid system. We have analyzed peripheral blood cells of 26 patients diagnosed between birth and 2 years of age with a genetically defined primary immunodeficiency disorder: 15 severe combined immunodeficiency (SCID) patients had disease-causing mutations in RAG1 or RAG2 (n = 4, two of them presented with Omenn syndrome), IL2RG (n = 4, one of them with confirmed maternal engraftment), NHEJ1 (n = 1), CD3E (n = 1), ADA (n = 1), JAK3 (n = 3, two of them with maternal engraftment) and DCLRE1C (n = 1) and 11 other PID patients had diverse molecular defects [ZAP70 (n = 1), WAS (n = 2), PNP (n = 1), FOXP3 (n = 1), del22q11.2 (DiGeorge n = 4), CDC42 (n = 1) and FAS (n = 1)]. In addition, 44 healthy controls in the same age group were analyzed using the SCID-RTE tube in four EuroFlow laboratories using a standardized 8-color approach. RTE were defined as CD62L+CD45RO-HLA-DR-CD31+ and the activation status was assessed by the expression of HLA-DR+. Naïve CD8+ T-lymphocytes and naïve CD4+ T-lymphocytes were defined as CD62L+CD45RO-HLA-DR-. With the SCID-RTE tube, we identified patients with PID by low levels or absence of RTE in comparison to controls as well as low levels of naïve CD4+ and naïve CD8+ lymphocytes. These parameters yielded 100% sensitivity for SCID. All SCID patients had absence of RTE, including the patients with confirmed maternal engraftment or oligoclonally expanded T-cells characteristic for Omenn syndrome. Another dominant finding was the increased numbers of activated CD4+HLA-DR+ and CD8+HLA-DR+ lymphocytes. Therefore, the EuroFlow SCID-RTE tube together with the previously published PIDOT tube form a sensitive and complete cytometric diagnostic test suitable for patients suspected of severe PID (SCID or CID) as well as for children identified via newborn screening programs for SCID with low or absent T-cell receptor excision circles (TRECs).

• MeSH
• HLA-DR Antigens analysis   MeSH
• Immunophenotyping methods   MeSH
• Infant MeSH
• Humans MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Primary Immunodeficiency Diseases diagnosis   immunology   MeSH
• Flow Cytometry methods   MeSH
• T-Lymphocytes immunology   MeSH
• Severe Combined Immunodeficiency immunology   MeSH
• Thymus Gland immunology   MeSH
• Check Tag
• Infant MeSH
• Humans MeSH
• Male MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

We find that cardiac group 2 innate lymphoid cells (ILC2s) are essential for the development of IL-33-induced eosinophilic pericarditis. We show a pathogenic role for ILC2s in cardiac inflammation, in which ILC2s activated by IL-33 drive the development of eosinophilic pericarditis in collaboration with cardiac fibroblasts. ILCs, not T and B cells, are required for the development of pericarditis. ILC2s transferred to the heart of Rag2-/-Il2rg-/- mice restore their susceptibility to eosinophil infiltration. Moreover, ILC2s direct cardiac fibroblasts to produce eotaxin-1. We also find that eosinophils reside in the mediastinal cavity and that eosinophils transferred to the mediastinal cavity of eosinophil-deficient ΔdblGATA1 mice following IL-33 treatment migrate to the heart. Thus, the serous cavities may serve as a reservoir of cardiac-infiltrating eosinophils. In humans, patients with pericarditis show higher amounts of ILCs in pericardial fluid than do healthy controls and patients with other cardiac diseases. We demonstrate that ILCs play a critical role in pericarditis.

• MeSH
• Chemokine CCL11 genetics   metabolism   MeSH
• Eosinophils drug effects   pathology   MeSH
• Fibroblasts drug effects   metabolism   MeSH
• Heart Function Tests drug effects   MeSH
• Interleukin-33 pharmacology   MeSH
• Interleukin-1 Receptor-Like 1 Protein deficiency   metabolism   MeSH
• Interleukin-5 metabolism   MeSH
• Humans MeSH
• Lymphocytes drug effects   immunology   MeSH
• Mediastinum pathology   MeSH
• Mice, Inbred BALB C MeSH
• Disease Susceptibility MeSH
• Pericarditis genetics   immunology   physiopathology   MeSH
• Cell Movement drug effects   MeSH
• Immunity, Innate * drug effects   MeSH
• Gene Expression Regulation drug effects   MeSH
• Signal Transduction drug effects   MeSH
• Heart drug effects   physiopathology   MeSH
• Up-Regulation drug effects   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

Cryptic genetic diversity and erroneous morphological species determination represent frequent problems in biodiversity research. Here, examination of 138 specimens of Synodontis (Mochokidae, Siluriformes) from the Nile River and Lake Turkana revealed the presence of both S. schall-like and S. frontosus-like morphotypes, with a phenotypic gradient between them. We concluded phylogenetic and population genetic analyses based on two mitochondrial and one nuclear marker including 131 coxI (565 bp), 96 cytb (973 bp) and 19 RAG2 (896 bp) sequences from the Nile-Turkana population, plus additional GenBank data of Synodontis spp. Whilst nuclear data were inconclusive, mitochondrial sequences suggested that both morphotypes and intermediate forms are conspecific. The results imply probable synonymy of S. frontosus with S. schall. Conversely, a strong biogeographical signal was revealed among widely distributed and supposedly conspecific S. schall-like catfish of the Nilo-Sudanian ichthyological province. Synodontis schall sensu stricto (=Eastern clade), as defined by type locality in the Nile, is apparently restricted to the eastern part of the Nilo-Sudanian ichthyological province (e.g. Nile, Turkana, Chad). Synodontis schall Western clade (Senegambia, Niger, Chad) most probably represents a cryptic taxon, unrecognized thus far due to the absence of distinctive morphological differences.

• MeSH
• Bayes Theorem MeSH
• Biodiversity * MeSH
• Cytochromes b classification   genetics   MeSH
• Phylogeny MeSH
• Haplotypes MeSH
• Genetics, Population MeSH
• Electron Transport Complex IV classification   genetics   MeSH
• Catfishes classification   genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Diet is a major factor determining gut microbiota composition and perturbances in this complex ecosystem are associated with the inflammatory bowel disease (IBD). Here, we used gnotobiotic approach to analyze, how interaction between diet rich in proteins and gut microbiota influences the sensitivity to intestinal inflammation in murine model of ulcerative colitis. We found that diet rich in animal protein (aHPD) exacerbates acute dextran sulfate sodium (DSS)-induced colitis while diet rich in plant protein (pHPD) does not. The deleterious effect of aHPD was also apparent in chronic DSS colitis and was associated with distinct changes in gut bacteria and fungi. Therefore, we induced acute DSS-colitis in germ-free mice and transferred gut microbiota from aCD or aHPD fed mice to find that this effect requires presence of microbes and aHPD at the same time. The aHPD did not change the number of regulatory T cells or Th17 cells and still worsened the colitis in immuno-deficient RAG2 knock-out mice suggesting that this effect was not dependent on adaptive immunity. The pro-inflammatory effect of aHPD was, however, abrogated when splenic macrophages were depleted with clodronate liposomes. This treatment prevented aHPD induced increase in colonic Ly-6Chigh pro-inflammatory monocytes, but the ratio of resident Ly-6C-/low macrophages was not changed. These data show that the interactions between dietary protein of animal origin and gut microbiota increase sensitivity to intestinal inflammation by promoting pro-inflammatory response of monocytes.

• MeSH
• Adaptive Immunity immunology   MeSH
• Th17 Cells immunology   metabolism   MeSH
• Diet adverse effects   MeSH
• Dietary Proteins administration & dosage   adverse effects   MeSH
• DNA-Binding Proteins metabolism   MeSH
• Colitis immunology   metabolism   pathology   MeSH
• Colon immunology   metabolism   pathology   MeSH
• Macrophages immunology   metabolism   pathology   MeSH
• Disease Models, Animal MeSH
• Monocytes immunology   metabolism   pathology   MeSH
• Mice, Inbred BALB C MeSH
• Mice, Knockout MeSH
• Mice MeSH
• T-Lymphocytes, Regulatory immunology   metabolism   MeSH
• Intestines immunology   pathology   MeSH
• Gastrointestinal Microbiome immunology   physiology   MeSH
• Inflammation immunology   metabolism   pathology   MeSH
• Animals MeSH
• Check Tag
• Mice MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The understanding of the diversity of species in the Palearctic and the processes that have generated it is still weak for large parts of the arid areas of North Africa and Arabia. Reptiles are among their most remarkable representatives, with numerous groups well adapted to the diverse environments. The Ptyodactylus geckos are a strictly rock-dwelling genus with homogeneous morphology distributed across mountain formations and rocky plateaus from the western African ranges in Mauritania and the Maghreb to the eastern tip of the Arabian Peninsula, with an isolated species in southern Pakistan. Here, we use a broad sampling of 378 specimens, two mitochondrial (12S and cytb) and four nuclear (c-mos, MC1R, ACM4, RAG2) markers in order to obtain the first time-calibrated molecular phylogeny of the genus and place its diversification in a temporal framework. The results reveal high levels of intraspecific variability, indicative of undescribed diversity, and they do not support the monophyly of one species (P. ragazzii). Ptyodactylus species are allopatric across most of their range, which may relate to their high preference for the same type of structural habitat. The onset of their diversification is estimated to have occurred in the Late Oligocene, while that of several deep clades in the phylogeny took place during the Late Miocene, a period when an increase in aridification in North Africa and Arabia initiated.

• MeSH
• Bayes Theorem MeSH
• Phylogeny * MeSH
• Phylogeography MeSH
• Lizards classification   genetics   MeSH
• DNA, Mitochondrial genetics   MeSH
• Likelihood Functions MeSH
• Sequence Analysis, DNA MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Africa, Northern MeSH
• Middle East MeSH

A molecular phylogeny of the sphaerodactylid geckos of the genus Pristurus is inferred based on an alignment of 1845 base pairs (bp) of concatenated mitochondrial (12S) and nuclear (acm4, cmos, rag1 and rag2) genes for 80 individuals, representing 18 of the 23-26 species, and the three subspecies of P. rupestris. The results indicate that P. rupestris is polyphyletic and includes two highly divergent clades: the eastern clade, found in coastal Iran and throughout the Hajar Mountain range in northern Oman and eastern UAE; and the western clade, distributed from central coastal Oman, through Yemen, Saudi Arabia and north to southern Jordan. Inferred haplotype networks for the four nuclear genes show that the eastern and western clades of "P. rupestris" are highly differentiated and do not share any alleles. Moreover, although the two clades are differentiated by a morphological multivariate analysis, no one character or set of characters was found to be diagnostic. Based on the molecular analysis of specimens from the type locality of P. rupestris rupestris, the name P. rupestris is applied to the eastern clade. The name that should apply to the western clade cannot be clarified until morphological and genetic data for "P. rupestris" is available from the vicinity of Bosaso, Somalia, and therefore we refer to it as Pristurus sp. 1. The phylogenetic tree of Pristurus supports the hypothesis that P. celerrimus is sister to all the other species in the analyses and that the Socotra Archipelago was independently colonized a minimum of two times.

• MeSH
• Phylogeny * MeSH
• Lizards classification   genetics   MeSH
• DNA, Mitochondrial genetics   MeSH
• Animal Distribution MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Somalia MeSH
• Middle East MeSH

BACKGROUND: V(D)J recombination takes place during lymphocyte development to generate a large repertoire of T- and B-cell receptors. Mutations in recombination-activating gene 1 (RAG1) and RAG2 result in loss or reduction of V(D)J recombination. It is known that different mutations in RAG genes vary in residual recombinase activity and give rise to a broad spectrum of clinical phenotypes. OBJECTIVE: We sought to study the immunologic mechanisms causing the clinical spectrum of RAG deficiency. METHODS: We included 22 patients with similar RAG1 mutations (c.519delT or c.368_369delAA) resulting in N-terminal truncated RAG1 protein with residual recombination activity but presenting with different clinical phenotypes. We studied precursor B-cell development, immunoglobulin and T-cell receptor repertoire formation, receptor editing, and B- and T-cell numbers. RESULTS: Clinically, patients were divided into 3 main categories: T(-)B(-) severe combined immunodeficiency, Omenn syndrome, and combined immunodeficiency. All patients showed a block in the precursor B-cell development, low B- and T-cell numbers, normal immunoglobulin gene use, limited B- and T-cell repertoires, and slightly impaired receptor editing. CONCLUSION: This study demonstrates that similar RAG mutations can result in similar immunobiological effects but different clinical phenotypes, indicating that the level of residual recombinase activity is not the only determinant for clinical outcome. We postulate a model in which the type and moment of antigenic pressure affect the clinical phenotypes of these patients.

• MeSH
• B-Lymphocytes immunology   metabolism   MeSH
• Gene Expression MeSH
• Phenotype * MeSH
• Genetic Association Studies * MeSH
• Genotype MeSH
• Homeodomain Proteins genetics   metabolism   MeSH
• Complementarity Determining Regions genetics   MeSH
• Infant MeSH
• Humans MeSH
• Mutation * MeSH
• Infant, Newborn MeSH
• Lymphocyte Count MeSH
• Child, Preschool MeSH
• T-Lymphocytes immunology   metabolism   MeSH
• Severe Combined Immunodeficiency diagnosis   genetics   immunology   metabolism   MeSH
• Immunoglobulin Heavy Chains genetics   MeSH
• V(D)J Recombination MeSH
• Check Tag
• Infant MeSH
• Humans MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH