Prevalence and clinical challenges among adults with primary immunodeficiency and recombination-activating gene deficiency
Authors: Dylan Lawless, Christoph B. Geier, Jocelyn R. Farmer, Hana Lango Allen, Daniel Thwaites, Faranaz Atschekzei, Matthew Brown, David Buchbinder, Siobhan O. Burns, Manish J. Butte, Krisztian Csomos, Sri V.V. Deevi, William Egner, Stephan Ehl, Martha M. Eibl, Olajumoke Fadugba, Zsofia Foldvari, Deanna M. Green, Sarah E. Henrickson, Steven M. Holland, Tami John, Christian Klemann, Taco W. Kuijpers, Fernando Moreira, Alexander Piller, Paula Rayner-Matthews, Neil D. Romberg, Ravishankar Sargur, Reinhold E. Schmidt, Claudia Schröder, Catharina Schuetz, Svetlana O. Sharapova, Ken G.C. Smith, Georgios Sogkas, Carsten Speckmann, Kathleen Stirrups, Adrian J. Thrasher, Hermann M. Wolf, Luigi D. Notarangelo, Rashida Anwar, Joan Boyes, Boglarka Ujhazi, James Thaventhiran, Jolan E. Walter, Sinisa Savic
Journal: Journal of Allergy and Clinical Immunology (2018)

Recombination-activating gene (RAG) deficiency has an estimated disease incidence of 1:181,000, including severe combined immunodeficiency (SCID) at a rate of 1:330,000.1Kumanovics A. Lee Y.N. Close D.W. Coonrod E.M. Ujhazi B. Chen K. et al.Estimated disease incidence of RAG1/2 mutations: a case report and querying the Exome Aggregation Consortium.J Allergy Clin Immunol. 2017; 139: 690-692.e3Google Scholar, 2Kwan A. Abraham R.S. Currier R. Brower A. Andruszewski K. Abbott J.K. et al.Newborn screening for severe combined immunodeficiency in 11 screening programs in the United States.JAMA. 2014; 312: 729-738Google Scholar Complete or hypomorphic variants of SCID secondary to low recombinase activity (<5%) present early with severe infections and/or clinical signs of systemic inflammation, such as severe dermatitis, colitis, or both.3Schwarz K. Gauss G.H. Ludwig L. Pannicke U. Li Z. Lindner D. et al.RAG mutations in human B cell-negative SCID.Science. 1996; 274: 97-99Google Scholar, 4Felgentreff K. Perez-Becker R. Speckmann C. Schwarz K. Kalwak K. Markelj G. et al.Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency.Clin Immunol. 2011; 141: 73-82Google Scholar Hypomorphic RAG1/2 mutations with more preserved residual V(D)J recombination activity (5% to 30%) result in a distinct phenotype of combined immunodeficiency with granuloma, autoimmunity, or both.1Kumanovics A. Lee Y.N. Close D.W. Coonrod E.M. Ujhazi B. Chen K. et al.Estimated disease incidence of RAG1/2 mutations: a case report and querying the Exome Aggregation Consortium.J Allergy Clin Immunol. 2017; 139: 690-692.e3Google Scholar, 2Kwan A. Abraham R.S. Currier R. Brower A. Andruszewski K. Abbott J.K. et al.Newborn screening for severe combined immunodeficiency in 11 screening programs in the United States.JAMA. 2014; 312: 729-738Google Scholar, 5Walter J.E. Rosen L.B. Csomos K. Rosenberg J.M. Mathew D. Keszei M. et al.Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency.J Clin Invest. 2015; 125: 4135-4148Google Scholar Beyond combined immunodeficiency, RAG deficiency has been found in patients with predominantly primary antibody deficiencies6Buchbinder D. Baker R. Lee Y.N. Ravell J. Zhang Y. McElwee J. et al.Identification of patients with RAG mutations previously diagnosed with common variable immunodeficiency disorders.J Clin Immunol. 2015; 35: 119-124Google Scholar, 7Geier C.B. Piller A. Linder A. Sauerwein K.M. Eibl M.M. Wolf H.M. Leaky RAG deficiency in adult patients with impaired antibody production against bacterial polysaccharide antigens.PLoS One. 2015; 10: e0133220Google Scholar and naive CD4+ T-cell lymphopenia in most cases. Currently, there is no published systematic evaluation for the presence of an underlying RAG deficiency in patients with primary antibody deficiencies. There is great variability among diagnostic modalities for evaluation and treatment for inflammatory lung disease in case reports of RAG deficiency with no standardized guidelines. Clinical features and lung disease for patients with late presentation of RAG deficiency have not been studied extensively. In addition, no studies have examined the prevalence of RAG deficiency in cohorts of adults with primary immunodeficiency (PID). Here we describe a cohort of 15 patients with late presentation of RAG deficiency. We also estimate the prevalence of RAG deficiency in adults with PID after genetic analysis in 2 separate large cohorts of patients with PID. We have analyzed the canonical regions of RAG1 and RAG2 in a total of 692 patients with PID from 2 separate cohorts, one from the United Kingdom (UK) and one from Austria (Vienna). The UK cohort is part of the National Institute for Health Research BioResource–Rare Diseases PID study, as previously described (Tuijnenburg et al8Tuijnenburg P. Lango Allen H. Burns S.O. Greene D. Jansen M.H. Staples E. et al.Loss of function NFKB1 variants are the most common monogenic cause of CVID in Europeans.J Allergy Clin Immunol. 2018 Feb 22; ([Epub ahead of print])https://doi.org/10.1016/j.jaci.2018.01.039Google Scholar). In the National Institute for Health Research BioResource–Rare Diseases PID cohort of 558 patients (299 adults) and the Vienna cohort of 134 patients (106 adults), we report a total of 5 newly identified cases of RAG deficiency. For details, see the Methods section and Tables E1 to E3 in this article's Online Repository at www.jacionline.org. Based on these findings, we estimate that the prevalence of RAG deficiency in adults with PID ranges from 1% to 1.9%. For all adult patients with PID currently registered with the UK Primary Immunodeficiency Network database (3294 patients older than age 18 years), we expect to find an additional 32.9 to 62.6 cases of RAG deficiency. Gene variants are shown in Fig 1, A. Cohort demographics are discussed in the Methods section in this article's Online Repository. Functional characterization of novel RAG variants is discussed in the Methods section in this article's Online Repository. The activity of mutant RAG1 and RAG2 proteins normally required for catalyzing V(D)J recombination events are shown in Table E2. In addition to the method previously described,9Lee Y.N. Frugoni F. Dobbs K. Walter J.E. Giliani S. Gennery A.R. et al.A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.J Allergy Clin Immunol. 2014; 133: 1099-1108Google Scholar we also used a system to measure recombination activity in compound heterozygous cases by means of in vitro expression of murine RAG1 and RAG2. Both systems simulate the efficiency of protein expressed in patients in their ability to produce a diverse repertoire of T-cell receptor and B-cell receptor coding for immunoglobulins. More than half of the mutant proteins tested show almost complete loss of activity. All patients tested had an overall low combined RAG activity (6.4% to 28%). Immune phenotypes and clinical diagnoses are shown in Fig 1, B. Persistently low IgG and/or low IgA and IgM levels are seen in approximately 50% of cases (see Table E3). Dominant laboratory features were naive CD4+ T-cell lymphopenia with low absolute numbers and fraction of naive CD4+ cells (CD4+CD45RA+), and B-cell counts were variably low (see Table E3). ELISA was used to test for anti-cytokine antibodies (targeting IFN-α, IFN-ω, and IL-12) on plasma from 7 patients (data not shown). Four patients had positive results, which is comparable with our previously reported cohort (56%).5Walter J.E. Rosen L.B. Csomos K. Rosenberg J.M. Mathew D. Keszei M. et al.Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency.J Clin Invest. 2015; 125: 4135-4148Google Scholar Most adult RAG-deficient patients had inflammatory autoimmune complications (87%; see the Methods section and Fig E1, A, in this article's Online Repository at www.jacionline.org). Organ-specific manifestations were most common (73%) and similar to previously described reports of 48% to 77%.5Walter J.E. Rosen L.B. Csomos K. Rosenberg J.M. Mathew D. Keszei M. et al.Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency.J Clin Invest. 2015; 125: 4135-4148Google Scholar, 10Speckmann C. Doerken S. Aiuti A. Albert M.H. Al-Herz W. Allende L.M. et al.A prospective study on the natural history of patients with profound combined immunodeficiency: an interim analysis.J Allergy Clin Immunol. 2017; 139: 1302-1310.e4Google Scholar Granulomatous disease was seen in 40% of patients, with 5 of 6 patients showing granuloma localization within interstitial lung tissue. Other complications were also seen (see Fig E1, E). Similar to recent reports (21% to 77%),5Walter J.E. Rosen L.B. Csomos K. Rosenberg J.M. Mathew D. Keszei M. et al.Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency.J Clin Invest. 2015; 125: 4135-4148Google Scholar, 10Speckmann C. Doerken S. Aiuti A. Albert M.H. Al-Herz W. Allende L.M. et al.A prospective study on the natural history of patients with profound combined immunodeficiency: an interim analysis.J Allergy Clin Immunol. 2017; 139: 1302-1310.e4Google Scholar cytopenias occurred in 40% of patients: autoimmune hemolytic anemia (27%), immune thrombocytopenic purpura (20%), and autoimmune neutropenia in 1 patient. Progressive pulmonary diseases were the leading causes of morbidity and mortality (93%; see Fig E1, D), with pneumonia being the most common, followed by bronchiectasis, chronic bronchitis, granuloma, fibrosis, chronic obstructive pulmonary disease, and bronchiolitis (Fig 1, C). We observed a transition from acute infectious complications (pneumonia; mean onset, 14 years) to chronic inflammatory complications (mean age, 23 years; Fig 2, A). Progressive pulmonary diseases were also the leading concern for successful hematopoietic stem cell transplantation (HSCT). High-resolution computed tomographic imaging of the lung revealed bronchiectasis and granuloma. Histology of lung biopsy specimens (patients 1 and 3) revealed atypical lymphoid hyperplasia with granulomatous features and giant cell formation (Fig 2, B). Germinal center formations in patient 3 were comprised of CD3+ T cells and CD20+ B cells. Patient 1 had peribronchial fibrosis (Fig 2, B). Pulmonary lung function data revealed a median forced vital capacity of 79.55%, diffusing capacity of the lungs for carbon monoxide of 75%, and FEV1/forced vital capacity ratio of 78%. We performed a retrospective analysis of pulmonary function tests over 2 or more years to assess the decrease in respiratory function. Two of 4 patients had a significant decrease, indicating a variable degree of lung function in adult patients with RAG deficiency (see the Methods section and Fig E1, G, in this article's Online Repository). Thirteen (93%) of 14 patients received first-line immunoglobulin replacement therapy (see Fig E1, B, and Table E2). Fifty-seven percent received antibiotic prophylaxis, 21% received antiviral drugs, and 14% received disease-modifying antirheumatic drugs. Five (36%) patients were considered for HSCT. Comparisons of therapeutic approaches revealed no statistically significant difference in survival. Three of 8 patients who received only immunoglobulin replacement therapy were deceased. Among patients undergoing transplantation, the major mortality cause was infection after HSCT (see Fig E1, C). RAG1/2 are the most common defective genes associated with atypical SCID.10Speckmann C. Doerken S. Aiuti A. Albert M.H. Al-Herz W. Allende L.M. et al.A prospective study on the natural history of patients with profound combined immunodeficiency: an interim analysis.J Allergy Clin Immunol. 2017; 139: 1302-1310.e4Google Scholar Patients can survive into adulthood, and our findings suggest that the prevalence of such cases varies between 1% and 1.9% in adult PID cohorts. Total and naive CD4+ T-cell lymphopenia,4Felgentreff K. Perez-Becker R. Speckmann C. Schwarz K. Kalwak K. Markelj G. et al.Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency.Clin Immunol. 2011; 141: 73-82Google Scholar, 10Speckmann C. Doerken S. Aiuti A. Albert M.H. Al-Herz W. Allende L.M. et al.A prospective study on the natural history of patients with profound combined immunodeficiency: an interim analysis.J Allergy Clin Immunol. 2017; 139: 1302-1310.e4Google Scholar autoimmunity, and progressive inflammatory lung disease should all prompt further investigations for RAG deficiency in adults with PIDs. The relative absence of RAG deficiency in the pediatric cohort of 216 patients suggests that milder forms of RAG deficiency might not be diagnosed as readily as a PID in childhood. In the era of whole-exome sequencing, the spectrum of RAG deficiency broadens further to include adults with autoimmune and inflammatory manifestations that can result in progressive decrease. Systemic analysis of PID-related genes9Lee Y.N. Frugoni F. Dobbs K. Walter J.E. Giliani S. Gennery A.R. et al.A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.J Allergy Clin Immunol. 2014; 133: 1099-1108Google Scholar and functional in vitro assays that confirm decreased recombination activity are essential. Laboratory features of naive CD4+ T-cell lymphopenia and the presence of anti-cytokine antibodies can further support the diagnosis of partial RAG deficiency. Where RAG deficiency is confirmed, therapy can be adjusted based on the mechanistic understanding and might ultimately provide a targeted strategy for early intervention. This study was conducted in accordance with the Declaration of Helsinki. Patients provided written informed consent so that anonymized data could be included in a scientific publication. All results presented in this study were obtained as part of the routine medical care received by the patient. This study makes use of data generated by the NIHR BioResource–Rare Disease Consortium. A full list of the consortium members who contributed to the generation of the data is available in this article's Online Repository at www.jacionline.org. We thank Professor Christian J. Müller for providing pathology specimens and Dr Karl Waibel for providing pulmonary function testing. Download .docx (.22 MB) Help with docx files Online Repository text Download .pdf (1.28 MB) Help with pdf files Fig E1 Download .xlsx (.03 MB) Help with xlsx files Table E1 Download .xlsx (.03 MB) Help with xlsx files Table E2 Download .xlsx (.04 MB) Help with xlsx files Table E3 Download .docx (.1 MB) Help with docx files Appendix E1