Littérature scientifique sur le sujet « Common variable immunodeficiency, immunodeficiency, genetics, whole-exome sequencing »

Common variable immunodeficiency (CVID) belongs to the primary immunodeficiency disorders (PIDs), presenting a profound heterogeneity in phenotype and genotype, with monogenic or complex causes. Recurrent respiratory infections are the most common clinical manifestations. CVID patients can also develop various autoimmune and lymphoproliferative complications. Genetic testing such as whole exome sequencing (WES) can be utilized to investigate likely genetic defects, helping for better clinical management. We described the clinical phenotypes of three sporadic cases of CVID, who developed recurrent respiratory infections with different autoimmune and lymphoproliferative complications. WES was applied to screen disease-causing or disease-associated mutations. Two patients were identified to have monogenic disorders, with compound heterozygous mutations in LRBA for one patient and a frameshift insertion in NFKB1 for another. The third patient was identified to be a complex form of CVID. Two novel mutations were identified, respectively, in LRBA and NFKB1. A combination of clinical and genetic diagnosis can be more extensively utilized in the clinical practice due to the complexity and heterogeneity of CVID.

Abstract Common Variable Immunodeficiency (CVID) is a heterogenous disorder characterized by hypogammaglobulinemia, failure to mount vaccine responses, recurrent sinopulmonary infections. Furthermore, a subset of CVID patients develop various autoimmune and lymphoproliferative complications, highlighting the dysregulated immune mechanisms underlying the disorder. One such autoimmune complication is granulomatous lymphocytic interstitial lung disease (GLILD) which is a major cause of mortality in CVID. The clinical heterogeneity of CVID indicate that it is a collection of disorders with monogenic and polygenic defects. Due to the genetic and phenotypic complexity of CVID, our understanding of the immunopathogenesis of CVID and the development of its complications is limited. Our goal is to elucidate relationships between genetic variants and their downstream phenotypic and signaling defects in CVID patients with GLILD. We hypothesize that specific genetic variants will result in unique immune cellular (and signaling) signatures in CVID with GLILD. To identify these cellular and molecular signatures, we integrate whole exome sequencing and mass cytometry data. We examined cellular subsets affected by perturbed T and B cell receptor signaling pathways via mass cytometry, and then correlate these signatures with specific genetic variants identified through whole exome sequencing. These results will reveal mechanisms of immune dysregulation in CVID with GLILD. In CVID patients with GLILD, we find expansion of CD57+ CD8+ T cells, which may represent a class of senescent cells. We also find enrichment of CD21-low B cells within CVID patients, regardless of GLILD status.

Abstract Using whole-exome sequencing to examine the genetic causes of immune deficiency in 235 common variable immunodeficiency (CVID) patients seen in the United States (Mount Sinai, New York), 128 patients from Sweden, and 208 from Iran revealed 68 known disease-causing genes underlying this heterogeneous immune defect. The patients at the time of study ranged from 4 to 90 years of age. Overall, 31%, 36%, and 54% of the patients in the US, Swedish, or Iranian cohorts had mutations. The multiplicity of genes identified in the 571 subjects reflects the complex requirements of B-cell antigen signaling, activation, survival, migration, maturation, and maintenance of antibody-secreting memory B-cell populations to the plasma cell stage. For the US and Swedish cohorts, CVID subjects with noninfectious complications, lymphoid infiltrations, inflamatory conditions, or autoimmunity were somewhat more likely to have an identifiable gene, but in both cohorts, numerous subjects with these medical conditions had no potential gene that could be assigned. Specific clinical patterns of illnesses were also not linked to any given gene defect as there was considerable overlap in clinical presentations. These observations led to a new perspective on the complexity of the immunologic phenotype found in CVID syndrome.

To identify host genetic determinants involved in humoral immunity and associated with the risk of developing severe COVID-19, we analyzed 500 SARS-CoV-2 positive subjects from Southern Italy. We examined the coding sequences of 10 common variable immunodeficiency-associated genes obtained by the whole-exome sequencing of 121 hospitalized patients. These 10 genes showed significant enrichment in predicted pathogenic point mutations in severe patients compared with the non-severe ones. Moreover, in the TNFRSF13C gene, the minor allele of the p.His159Tyr variant, which is known to increase NF-kB activation and B-cell production, was significantly more frequent in the 38 severe cases compared to both the 83 non-severe patients and the 375 asymptomatic subjects further genotyped. This finding identified a potential genetic risk factor of severe COVID-19 that not only may serve to unravel the mechanisms underlying the disease severity but, also, may contribute to build the rationale for individualized management based on B-cell therapy.

Abstract Context Deficient anterior pituitary with variable immune deficiency (DAVID) syndrome is a recently described, rare disorder characterized by anterior pituitary hormone deficiencies and common variable immunodeficiency associated with NFKB2 mutations. Posterior pituitary hormone deficiencies have not been reported in patients with DAVID syndrome. Case Description We report a pediatric patient who initially presented with hypogammaglobulinemia and alopecia totalis, who was identified to have a de novo NFKB2 mutation at one year of age. He developed central diabetes insipidus and central adrenal insufficiency at three and four years of age, respectively. At seven years of age, he had not developed GH or TSH deficiencies. Whole exome sequencing ruled out known genetic causes of central diabetes insipidus, adrenal insufficiency, and hypopituitarism. Conclusion This is a report of central diabetes insipidus in a patient with DAVID syndrome caused by an NFKB2 mutation. This case report expands the evolving endocrine phenotype associated with NFKB2 mutations beyond anterior pituitary deficiencies.

Background: Common variable immunodeficiency (CVID) is a term used to define a heterogeneous group of patients who commonly have hypogammaglobulinemia and variable degrees of modest T cell dysfunction. Recent advances made in next generation sequencing technologies have accelerated the identification of CVID disease-causing genes, including NFKB1, a component of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. Objective: We sought to identify the genetic defect in a 3-generation family of patients with CVID who presented with cytopenias, eczema, and recurrent sinopulmonary infections. Methods: Whole exome sequencing and Sanger confirmation was performed, and a combination of molecular and cellular techniques used to assess the variant impact on B and T cell function. Results: A novel heterozygous frameshift mutation in NFKB1, encoding the transcriptional regulator protein p50/p105, was identified. This resulted in c.1584dupG (p.M528fs). We demonstrate that c.1584dupG is a loss-of-function variant, responsible for reduced p105/p50 protein expression in affected individuals as well as variable increased CD21low B cell numbers. Conclusion: This novel mutation affecting NFKB1 causes a CVID phenotype with variable clinical manifestations. Given the wide spectrum of age in this kindred, this may reflect diversity of phenotype expression, or more probably, age-related expression of typical features. Statement of novelty: We report here a novel loss-of-function frameshift mutation in NFKB1.

Introduction: Dyskeratosis Congenita (DKC) is caused by mutations in genes related to telomere maintenance resulting in prematurely shortened telomeres. Clinically, classical DKC is characterized by mucocutaneous abnormalities, bone marrow failure and other variable features such as lung or liver fibrosis. In adults, mono- or oligosymptomatic DKC is typically presenting with a clinically more heterogeneous and often cryptic picture without classical symptoms of DKC. Data on immunodeficiency as a predominant symptom in DKC patients is limited. The common variable immunodeficiency (CVID) represents a heterogenous group of disease with no universally accepted definition. Typically, patients show hypogammaglobulinaemia and impaired vaccine response. In most cases the genetic basis of CVID remains unknown and to date, the disease is primarily via exclusion of other reasons for hypogammaglobulinaemia. In this study, we aimed to retrospectively analyze the frequency and characteristics of adult patients with altered telomere maintenance (manifesting themselves as "cryptic DKC") within a well-defined cohort of patients with clinical findings of CVID. Materials and Methods: 200 patients of the Freiburg registry of adult CVID patients underwent whole-exome sequencing (WES). Diagnosis of CVID was established based on the recommendations of the European Society of Immune Deficiencies. Retrospectively, all patients were screened for mutations/variants in the following DKC causing genes: TERT, RTEL1, DKC1, NHP2, TERC, NOP10, TCAB1, TIN2 and CTC1. Screening identified 23 patients (age: 45 +/- 13 years; mean +/- S.D.) with mutations/polymorphisms in these genes. All identified variants were heterozygous. One patient showed polymorphisms in three different genes. To analyze the functional consequences on telomere maintenance, telomere length (TL) of peripheral blood mononuclear cells (PBMCs) were analyzed via MM-Q-PCR in all 23 patients. Furthermore, Flow-FISH analysis of lymphocytes as well as granulocytes was carried out in 22 and 14 patients, respectively. Results: TL analysis measured with MM-Q-PCR showed in most of the 23 patients shortened TL compared to an age-matched control group. We measured premature TL shortening below the 1% percentile in 44% (10/23) and below the 10% percentile in 52% (12/23). TL determined via flow-FISH showed TL in lymphocytes below the 10% percentile in 64% (14/22) and below 1% in 27% (6/22). WES revealed 24 polymorphisms/mutations in RTEL1 (n=5), TERT (n=3), NHP2 (n=6), DKC1 (n=8) and CTC1 (n=2). Based on bioinformatic prediction, 78 % (19/24) of all polymorphisms were classified as likely benign variants. Two patients with pathogenic mutations were identified: One 30 year old patient with previously described pathogenic TERT mutation (c.1234C>T, p.His412Tyr) was identified showing lymphocyte and granulocyte TL with flow-FISH between the 1% and 10% percentile and below the 1% percentile using MM-Q-PCR. One 23 year old patient with a bioinformatic predicted pathogenic mutation in RTEL1 (c.2313_2315delAGA, p.Glu771del) showed TL in flow-FISH and MM-Q-PCR below the 1% percentile. Of note, this patient developed few years after initial CVID diagnosis severe interstitial lung disease. Three patients were identified with possible DKC showing variants of unknown significance in the RTEL1 (41 years: c.380G>A, p.Arg127Gln) and TERT (65 years: c.3257G>A, p.Arg1086His and 42 years: c.1843G>A, p.Ala615Thr) gene having both TL in lymphocytes/granulocytes (flow-FISH) and leukocytes (MM-Q-PCR) below the 5% percentile. Conclusions: Clinical signs of immunodeficiency can be a rare first manifestation of cryptic/late-onset DKC in adult patients. We found out that at least 1% of all patients with CVID syndrome is caused by mutations typically found in DKC. Our data adds a further important clinical manifestation to the broad clinical spectrum of cryptic DKC. In return, awareness of CVID as a possible first manifestation of cryptic DKC can improve patient management. TL analysis in addition to genetic work-up provides a valuable tool to identify DKC as underlying disease of CVID and other disorders characterized by impaired replicative potential. Disclosures Brümmendorf: Ariad: Consultancy; Merck: Consultancy; University Hospital of the RWTH Aachen: Employment; Pfizer: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Janssen: Consultancy. Beier:Novartis: Honoraria; Repeat Dx: Other: Partner.

Common variable immunodeficiency (CVID) is one form of the primary immunodeficiencies (PIDs). CVID is characterized by variable clinical manifestations. Genetic alteration is a cause of the disease in many cases. In the current paper we described Patient N of 45 years old, who have been suffering from frequent various infections and therefore attended an immunologist and clinical geneticist. Immunoglobulins (Ig) A, M, and G deficiency was found in the patient. As a result of medical genetic counselling primary immunodeficiency has been suggested as a diagnosis. Further molecular genetic testing using clinical exome sequencing (Next Generation Sequencing method) revealed a likely-pathogenic variant c.204dupA (p.Leu69ThrfsX12, rs72553875) of TNFRSF13B gene in the patient. The gene variant was found in homozygous state. According to the international medical literature and genomic databases TNFRSF13B gene mutations lead to the CVID development and in some patients are characterized by isolated IgA deficiency and in the other group of patients can lead to decrease of IgA, IgM, and IgG. The patient had a family history of cancer and autoimmune inflammatory bowel disease (erosive-ulcerative enterocolitis). Moreover, one sibling of the patient died at the age of 3 weeks from complications of toxoplasmosis infection. The other sibling of 51 years old have been also suffering from recurrent infectious diseases. Thus, the genetic cause of the disease was identified in the proband. It has been shown that homozygosity for variant c.204dupA of TNFRSF13B gene is characterized by the deficiency of all three classes of Ig. Medical genetic counselling and modern molecular genetic methods application is an important step in management of people with signs of immunodeficiency. Such approach helps to make a diagnosis to the patient, to find an exact molecular reason of the condition, to use effective treatment, and to perform preventive measures in patient`s family.

Objectives: A pair of female Malay monozygotic twins who presented with recurrent upper respiratory tract infections, hepatosplenomegaly, bronchiectasis and bicytopenia were recruited in this study. Both patients were suspected with primary immunodeficiency diseases. However, the definite diagnosis was not clear due to complex disease phenotypes. The objective of this study was to identify the causative gene mutation in these patients. Methods: Lymphocyte subset enumeration test and whole exome sequencing were performed. Results: We identified a compound heterozygous CR2 mutation (c.1916G>A and c.2012G>A) in both patients. These variants were then confirmed using Sanger sequencing. Conclusion: Whole exome sequencing analysis of the monozygotic twins revealed compound heterozygous missense mutations in CR2.

Au-delà du bénéfice clinique du diagnostic, l'étude des patients atteints de déficits immunitaires héréditaires a aussi largement contribué à la compréhension des mécanismes moléculaires complexes impliqués dans la réponse adaptative humaine contre les pathogènes. Cependant, un grand nombre d’immunodéficiences primaires n’a pas encore été génétiquement défini, en particulier le déficit immunitaire commun variable (ou CVID en anglais). Au cours de ma thèse, j'ai cherché à identifier et caractériser de nouvelles causes moléculaires aux immunodéficiences primaires en me basant sur des mutants naturels humains comme modèle de recherche. Par séquençage entier de l'ADN de patients présentant une forme pédiatrique ou familiale de lupus érythémateux disséminé (ou SLE en anglais) et CVID, nous avons identifié trois variations hétérozygotes distinctes prédites comme délétères chez un patient atteint de CVID (RELAWT/Y306X), un patient pédiatrique SLE (RELAWT/R329X) et les patients atteints de SLE (RELAWT/H86N). Afin de comprendre comment les mutations identifiées peuvent affecter le rôle de RELA dans la voie NF-kB, nous avons confirmé que les deux mutations non-sens de RELA entraînent l'expression de formes tronquées de la protéine, tandis que la mutation faux-sens menait à l'expression de formes mutées de la protéine. Par immunoblot des protéines nucléaires et par immunofluorescence cellulaire, nous avons démontré que les deux formes tronquées de RELA peuvent entrer dans le noyau. Ensuite, en utilisant un oligonucléotide consensus NF-κB marqué, nous avons démontré que les deux formes tronquées de RELA étaient capables de se lier à l'ADN. Les trois protéines RELA mutées, lorsqu'elles étaient exprimées de manière ectopique, présentaient une altération de l'activité transcriptionnelle. Enfin, nous avons montré par co-immunoprécipitation que les trois protéines RELA mutées exprimées de manière ectopique sont capables d'interagir avec ses partenaires protéiques et de former des homodimères. En conclusion, nos résultats indiquent que des mutations affectant le facteur de transcription RELA peuvent être associées à des CVID ou des SLE. Étant donnés les cas précédents décrivant des haploinsuffisances de RELA liées à un syndrome lymphoprolifératif avec auto-immunité associé à une cytopénie auto-immune ainsi qu’aux ulcérations cutanéo-muqueuses TNF-dépendantes associées à des inflammations intestinales, notre travail élargit le spectre des maladies et des phénotypes cliniques liés à un dysfonctionnement de la protéine RELA et suggère que différentes mutations du gène RELA entraînent diverses conséquences fonctionnelles
Beyond the clinical benefit for diagnosis, the study of patients with primary immunodeficiency (PID) has also largely contributed to the deciphering of the complex molecular mechanisms involved in the human adaptive response against pathogens. Still, a large number of PIDs, especially common variable immunodeficiency (CVID), are genetically not defined. During my thesis, I aimed to identify and characterize novel molecular causes of PIDs based on human natural mutants as a research model (1). By whole-exome sequencing of DNA from patients presenting either with pediatric or familial form of CVID and Systemic Lupus Erythematosus (SLE), we identified three distinct heterozygous single nucleotide variations predicted deleterious in a CVID patient (RELAY306X), a pediatric SLE patient (RELAR329X) and familial SLE patients (RELAH86N). To better understand how the identified mutations may impact the role of RELA in the NF-kB pathway, we confirmed that the two nonsense RELA mutations led to the expression of truncated forms of the protein, while the missense mutation led to the expression of mutated forms of the protein. By immunoblotting of nuclear protein extracts and cellular immunofluorescence, we demonstrated that the two truncated forms of RELA can translocate into the nucleus. Then, using a labeled NF-κB consensus oligonucleotide, we demonstrated that the two truncated forms of RELA were able to bind to DNA. All three mutated RELA proteins, when expressed ectopically, had an impaired transcriptional activity. Finally, we showed by immunoprecipitation that all three ectopically expressed mutated RELA proteins are able to interact with protein partners and form homodimers. As a whole, our results indicate that mutations affecting the transcription factor RELA can be associated with CVID or SLE. Given the previous cases associating RELA haploinsufficiency to autoimmune lymphoproliferative syndrome with autoimmune cytopenia and to TNF-dependent mucocutaneous ulceration and inflammatory intestinal disease, our work widens the spectrum of disease and clinical phenotypes associated with RELA dysfunction and suggests that different RELA mutations lead to different functional consequences

Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency (PID) in adulthood. CVID is clinically and genetically heterogeneous. Patients have an increased susceptibility to infections, as well as autoimmunity, autoinflammation, lymphoproliferation, atopy, and cancer. In the last decades, Next Generation Sequencing (NGS) revolutionized the field of genetics. In the current 2018 IUIS classification, the number of molecularly defined immunodeficiency syndromes exceeded 450. Whole exome sequencing (WES) is widely considered an efficient and cost-effective approach to patients with PIDs. This study aimed to recruit a cohort of CVID patients and characterize them clinically, immunologically, and genetically. Using WES, we identified candidate variants in 50% of patients, including common disease-associated variants in TACI and BAFF-R genes, and novel variants in CTLA-4, CARD11, NFKB1, NFKB2, CD40LG, PIK3CD, PTEN, and TCF3. An unbiased approach like WES allows for unexpected discoveries. A pathogenic variant of CD40LG was found in a patient diagnosed with CVID. We also showed that in silico Copy Number Variants (CNV) prediction from NGS data can improve the diagnostic yield of WES. In a patient we found a deletion encompassing CD28, CTLA-4, and ICOS, leading to CTLA-4 haploinsufficiency. The discovery of the genetic defects of PID diseases contributed to our understanding of the immune system. Moreover, dissecting the underlying molecular mechanisms of CVID can improve clinical management. A genetic diagnosis can give relevant prognostic information, help tailor targeted therapies and it can inform about the heritability of the disease.