Current genetic diagnostics in inborn errors of immunity

Conflicts of Interests: EYW receives consulting and speaker fees from Pharming Healthcare, Inc. regarding their work on the medication leniolisib approved for activated PI3 kinase delta syndrome (APDS). The remaining authors AHS and MK declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.The number of inborn errors of immunity (IEI) is growing rapidly (1). They can be challenging to diagnose given the expanding and variable clinical phenotypes (2,3). Specifically, there is an increasing recognition that immune dysregulation can be an initial or predominant manifestation of a substantive portion of IEIs (4,5). Immune dysregulation can also have a large impact on disease treatment, monitoring, and outcomes. Significant progress has been made in the elucidation of molecular and cellular mechanisms underlying the immune dysregulation of IEIs. Tremendous improvement has also been made in the management of IEIs with availability of therapies expanding to include biologics and small molecular inhibitors. Despite progress, more understanding is needed to tailor the use of immunomodulatory therapy in IEIs. This Research Topic "Immune Dysregulation in Inborn Errors of Immunity" highlights recent advances in the understanding of the prevalence, mechanisms, spectrum of manifestations, and management of immune dysregulation in IEIs. Gagne et al. provide a concise review of how Mendelian type I interferonopathies can masquerade as non-Mendelian autoimmune disorders like systemic lupus erythematosus (SLE) and dermatomyositis, which are also associated with increased type I interferon (IFN) expression. Similarly, Hetrick et al. described how autoinflammatory bone disorders characterized by sterile osteomyelitis can be seen with both monogenic forms including Majeed syndrome and deficiency of the interleukin-1 antagonist (DIRA) and the more common sporadic form chronic nonbacterial osteomyelitis (CNO) or chronic recurrent multifocal osteomyelitis (CRMO). Other autoimmune manifestations of IEIs include, but are not limited to, autoimmune cytopenia, endocrinopathies, inflammatory bowel disease, neutrophilic dermatoses, arthritis, and vasculitis as illustrated by the case of activated phosphoinositide 3-kinase delta (PI3Kd) syndrome (APDS) from Sood et al.The highly variable clinical manifestations of IEIs can contribute to diagnostic delays, which in turn, can lead to poorer outcomes. Autoimmunity and autoinflammation can negatively impact morbidity and mortality and are an independent prognostic factor for death among individuals with IEIs (5). Immune dysregulation may also contribute to the increased risk of malignancy observed in IEIs as with the APDS case presented by Sood et al.Improving awareness and early recognition of IEIs is also critical because making a diagnosis can impact treatment and surveillance. There may be disease-specific treatments available like leniolisib, an oral selective PI3Kd inhibitor, for APDS as discussed by Sood et al. Because type 1 IFN work through the janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, Gagne et al. also consider the increasing use of JAK inhibition in autoinflammatory IFN-mediated monogenic diseases. The study by Berrueco et al. showed mycophenolate mofetil may be an effective and safe treatment for pediatric patients with autoimmune cytopenia and IEI, even cases of autoimmune cytopenia refractory to first-line therapies like corticosteroids and intravenous immunoglobulin (IVIG).These articles also nicely illustrate the need for a multidisciplinary approach to the immune dysregulatory manifestations in IEIs as there are contributions from Rheumatology (inteferonopathies and pediatric autoinflammatory bone disorders), Hematology (autoimmune cytopenias), and Allergy/Immunology (APDS). The conditions covered in this topic represent only a fraction of disordered immune conditions in IEIs and should be considered in more detail in the future.The recognition of immune dysregulation in IEIs continues to increase as the number of patients impacted expands. There is a clear need for ongoing investigation into the epidemiology and pathophysiology for clinical manifestations and the risk factors for developing immune dysregulation as well as a collaborative multidisciplinary approach to improve diagnosis and management of this population. Our hope is that this topic has piqued the interest of researchers and clinicians in this area to provide better understanding, care, and outcomes to these patients.Lastly, we would like to thank the reviewers for their time and valuable assessments. This important collection of articles would not be possible without their contributions.

Inborn errors of immunity (IEIs) are a heterogeneous group of disorders, genetically diverse but phenotypically overlapping. Over 500 IEI-related genes have been identified. Next generation sequencing (NGS) enables the simultaneous evaluation of a large number of genes in multiple patients in parallel. Since 2017, in our setting, custom IEI panels have been useful mainly for patients displaying clinical phenotypes of immune dysregulation and autoinflammatory disorders. Our aim is to evaluate the performance of targeted NGS panels based on International Union of Immunological Societies (IUIS) gene categories by examining how many patients achieved a conclusive diagnosis. A retrospective analysis was performed on 361 index cases submitted to four chronologically successive targeted NGS custom panels. The first panel included 124 IUIS genes, most of them related to autoimmune and immune dysregulation disease categories. The second panel contained 143 IUIS genes, including defects of innate immunity. The third and fourth, large panels covering 314 and 325 IUIS genes, respectively, included/comprised the majority of IUIS disease categories, with focus on autoinflammatory, immune dysregulation, and intrinsic immunity disease categories. From a total of 361 samples studied, 264 were referred due to clinical suspicion of immune dysregulation, autoinflammatory disease, or defects in innate immunity. Twenty-three percent of them (61/264) achieved a confirmed or highly probable genetic etiology. According to the main IEI IUIS disease categories included in targeted panels, immune dysregulation represented 26% (32/123) of these diagnoses, autoinflammatory disorders 21% (18/85), and defects in innate immunity 19% (11/56). In the remaining patients studied, 42% (41/97) of them achieved a conclusive diagnosis in others IEI IUIS disease categories. The NGS approach demonstrated the expected IEI diagnostic rate. The strategy of designing panels oriented toward IEI disease categories that present the greatest variability in clinical presentations with overlapping phenotypes proved to be effective regarding achievement of conclusive diagnoses in our cohort.

Background: Due to the absence of curative treatments for inborn errors of immunity (IEI), children born with IEI require long-term follow-up for disease manifestations and related complications that occur over the lifespan. Effective transition from pediatric to adult services is known to significantly improve adherence to treatment and long-term outcomes. It is currently not known what transition services are available for young people with IEI in Europe. Objective: To understand the prevalence and practice of transition services in Europe for young people with IEI, encompassing both primary immunodeficiencies (PID) and systemic autoinflammatory disorders (AID). Methods: A survey was generated by the European Reference Network on immunodeficiency, autoinflammatory, and autoimmune diseases Transition Working Group and electronically circulated, through professional networks, to pediatric centers across Europe looking after children with IEI. Results: Seventy-six responses were received from 52 centers, in 45 cities across 17 different countries. All services transitioned patients to adult services, mainly to specialist PID or AID centers, typically transferring up to ten patients to adult care each year. The transition process started at a median age of 16–18 years with transfer to the adult center occurring at a median age of 18–20 years. 75% of PID and 68% of AID centers held at least one joint appointment with pediatric and adult services prior to the transfer of care. Approximately 75% of PID and AID services reported having a defined transition process, but few centers reported national disease-specific transition guidelines to refer to. Conclusions: Transition services for children with IEI in Europe are available in many countries but lack standardized guidelines to promote best practice.

Newborn screening by T cell receptor excision circle (TREC) measurement has transformed the care of severe combined immunodeficiency disease (SCID) by identifying babies and intervening prior to symptoms and/or infection. Many other inborn errors of immunity (IEI) could be managed similarly but cannot be identified by the TREC screen. The Genomic Uniform-screening Against Rare Disease In All Newborns (GUARDIAN) study was initiated with the aim of expanded genome-based newborn screening for actionable diseases across disciplines—including an expanded and evolving list of IEI—within a diverse population of newborns. Out of the first ∼10,000 asymptomatic newborns screened, four possible IEI were identified, none of whom had abnormalities on the standard TREC screen. These included 1) a male with hemizygous IL2RG c.664 C>A p.R222S—previously reported in 2 patients with atypical X-SCID. He had a CD3 count of 1319 (polyclonal, 63% naïve), B cell count of 704, and NK cell count of 2792 cells/µL with normal proliferation to phytohemagglutinin, but markedly decreased IL-2– and IL-7–induced pSTAT5 activation. He underwent successful haploidentical stem cell transplantation; 2) a male with compound heterozygous variants in ADA (c.454C>A p.L152M—reported in SCID, and c.548C>A p.A183D—a variant of uncertain significance [VUS]). Despite normal percentages and numbers of naïve and memory CD4 and CD8 T cells, recent thymic emigrants, B cells, and NK cells, his RBC ADA activity level was 0 with a modest elevation in dAXP—consistent with ADA-deficient combined immunodeficiency associated with a delayed onset presentation. Therapeutic intervention is under consideration; 3) a female with compound heterozygous C9 variants (- c.346 C>T p.R116* - pathogenic and c.1511 A>T p. E504V - VUS). Complement studies showed low normal C9 function and low normal CH50 indicating minimal risk for terminal complement deficiency-associated infection; and 4) a female with heterozygous STAT1 c. 181del p. L61Cfs*23 that is being evaluated now. These cases illustrate the potential for expanded genome-based newborn screening to identify newborns with medically actionable IEI at frequencies likely much higher than standard TREC screening. They also highlight the importance of efficient laboratory immunophenotying, VUS assessment, genetic counseling, and, when indicated, prompt management.

Inborn errors of immunity (IEI) or primary immune deficiencies (PIDD) are caused by variants in genes encoding for molecules that are relevant to the innate or adaptive immune response. To date, defects in more than 450 different genes have been identified as causes of IEI, causing a constellation of heterogeneous clinical manifestations ranging from increased susceptibility to infection, to autoimmunity or autoinflammation. IEI that are mainly characterized by autoinflammation are broadly classified according to the inflammatory pathway that they predominantly perturb. Among autoinflammatory IEI are those characterized by the transcriptional upregulation of type I interferon genes and are referred to as interferonopathies. Within the spectrum of interferonopathies, genetic defects that affect the proteasome have been described to cause autoinflammatory disease and represent a growing area of investigation. This review is focused on describing the clinical, genetic, and molecular aspects of IEI associated with mutations that affect the proteasome and how the study of these diseases has contributed to delineate therapeutic interventions.

Whole Exome Sequencing and Extended Thrombophilia Testing in Patients with Venous Thromboembolism

Diagnosis, treatment and management of rare diseases (RD) pose unique challenges due to their complex nature, significantly impacting the daily experiences of researchers and healthcare professionals working in this field. Despite increasing awareness and progress in the field of RD worldwide in recent years, a significant gap remains in our understanding of the specific barriers that these professionals face in their work with RD. This study provides a detailed survey analysis that sheds light on the challenges that researchers and healthcare professionals face in diagnosing, treating, managing and conducting research on RD. We developed a national online survey with three RD stakeholder groups (Researchers, Healthcare professionals and researcher-healthcare professionals) to identify the main challenges and needs in Türkiye for the diagnosis, treatment and follow-up processes of rare and undiagnosed diseases. The survey was completed by 363 participants, revealing that participants face key challenges such as the need to refer patients to specialized centers, financial burdens, limited access to necessary tests, inadequate support for rare disease research and a lack of interdisciplinary collaboration. Participants also noted that RD are inherently difficult to conduct research on with small cohorts. Survey results also suggest a number of policy improvements to accelerate research on RD: increased funding, establishment of robust surveillance systems, and development of comprehensive national action plans and guidelines on RD. To the best of our knowledge, this is the first study to be conducted in Türkiye. This study contributes to the understanding of the needs of professionals in rare disease research and highlights the urgent need for system improvements to support them.

SummaryInborn errors of immunity (IEI), comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.

ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

BackgroundCurrent standard-of-care (SOC) methods for genetic testing are capable of resolving deletions and sequence variants, but they mostly fail to provide information on the breakpoints of duplications and balanced structural...

The prevalence of inborn errors of immunity (IEI)-related gene germline variants and its prognostic impact in Chinese pediatric patients with lymphoma

Inborn Errors of Immunity (IEIs) are rare genetic disorders that cause immunodeficiency. Diagnosis and classification of these disorders are challenging due to the heterogeneous clinical manifestations and genetic mutations. This is the first study to fully describe the spectrum of gene mutations and genetic diversity of IEIs in Vietnamese pediatric patients. A cross-sectional study was conducted on pediatric patients diagnosed with IEIs at Children’s Hospital 1, Vietnam, from 2014 to 2024. Ninety-two patients with identified mutations were enrolled. Genetic testing was performed using Sanger, fluorescence in situ hybridization, and whole exome sequencing to identify pathogenic variants. Clinical and epidemiological data were collected from medical records and mutations were classified according to the IUIS 2024 classification. The study identified 99 mutations in 33 different genes, with X-linked inheritance being predominant (53.2%). The antibody deficiency and immune dysregulation groups were the most common (22.8% for each mutation). Nineteen novel mutations were identified, all of which were predictively classified as pathogenic or likely pathogenic. The majority of mutations caused protein truncations, leading to loss of function, especially in the immunodeficiencies affecting cellular and humoral immunity and the phagocyte disorder groups. Clinical manifestations differed markedly between the different gene groups, highlighting the complexity of diagnosing IEIs. The number of cases with mutations causing X-linked inheritance was dominant, which was similar to studies from Asian countries, though different from studies from Africa due to the rates of consanguineous marriage. In addition, the variability between clinical phenotype and genotype in IEIs noted from our study has been a significant obstacle to the classification of diseases and their efficient treatment. This is the largest single center cohort to date in Vietnam to describe gene mutations in children with IEIs. The results of the study emphasize the importance of genetic testing in the diagnosis and treatment of IEIs, and open possible directions for further research for novel mutations.

Inborn errors of immunity (IEIs) are a frequently underdiagnosed group of disorders, with infectious complications posing significant clinical challenges. Recognizing atypical presentations of common infections and the presence of rare opportunistic pathogens can be critical in suspecting an underlying IEI. Among the infectious complications, chronic viral infections are particularly difficult to manage due to limited evidence-based guidelines. Intra-host viral evolution in these patients can lead to treatment resistance and the emergence of novel viral strains, raising concerns about their potential role as reservoirs for mutant viruses. Novel pathogens such as Aichivirus have been identified as significant causes of infection in individuals with IEIs. Furthermore, infections such as talaromycosis, tuberculosis, BCG-related disease, leishmaniasis, and melioidosis may be underrecognized in certain groups of patients with IEIs, largely due to differences in geographic exposure and environmental risk factors. The effects of emerging infections, such as mpox and Middle East respiratory syndrome coronavirus, on individuals with IEIs remain largely unknown. Management strategies for infections in this population include vaccinations, immunoglobulin replacement, and antimicrobial prophylaxis. However, newer higher valency conjugate pneumococcal vaccines may limit the utility of traditional pneumococcal polysaccharide vaccines in assessing immune function. While immunoglobulin replacement is cost-effective, it can interfere with serological diagnostics. Additionally, antimicrobial resistance is a growing issue, emphasizing the need for improved empiric antibiotic strategies and research into optimal treatment durations. This review highlights the key challenges faced by infectious disease clinicians in the care of patients with IEIs.

Severe infectious diseases remain the leading cause of death in children and young adults worldwide. Monogenic inborn errors of immunity (IEIs) are traditionally defined as a heterogeneous group of rare inborn genetic diseases affecting the functioning of the immune system. Greater awareness has led to the clinical definition of 485 monogenic IEIs and whole exome sequencing (WES) is becoming increasingly relevant for IEI genetic diagnosis. The current protocol for IEI genetic studies includes manual filtering of the list of genes obtained as a WES read-out providing a shortlist of candidate genes. This procedure is time-consuming andcan produce mistakes due to human error in manual filtering. IEIVariantFilter is a new web-based bioinformatics tool to speed up and refine the genetic diagnosis of IEI patients oriented for users in the biomedical field without needing bioinformatics expertise. IEIVariantFilter prioritizes genetic variants based on ranges of zygosity, the quality of reads, the predicted variant effect, and genes related to immunity, considering a consanguineous hypothesis whenever necessary. IEIVariantFilter facilitates gene and variant list prioritization, speeding up the identification of candidate disease-causing variants for validation by experimental studies. The software improves the genetic diagnosis of patients, thereby facilitating precision medicine and fast and proper treatment.

Genetic counseling in direct-to-consumer exome sequencing: a case report.