Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers

Objective

Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands.

Study Design

We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications.

Results

For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients.

Conclusion

In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance.

Treatment Strategies for GLILD in Common Variable Immunodeficiency: A Systematic Review

Introduction

Besides recurrent infections, a proportion of patients with Common Variable Immunodeficiency Disorders (CVID) may suffer from immune dysregulation such as granulomatous-lymphocytic interstitial lung disease (GLILD). The optimal treatment of this complication is currently unknown. Experienced-based expert opinions have been produced, but a systematic review of published treatment studies is lacking.

Goals

To summarize and synthesize the published literature on the efficacy of treatments for GLILD in CVID.

Methods

We performed a systematic review using the PRISMA guidelines. Papers describing treatment and outcomes in CVID patients with radiographic and/or histologic evidence of GLILD were included. Treatment regimens and outcomes of treatment were summarized.

Results

6124 papers were identified and 42, reporting information about 233 patients in total, were included for review. These papers described case series or small, uncontrolled studies of monotherapy with glucocorticoids or other immunosuppressants, rituximab monotherapy or rituximab plus azathioprine, abatacept, or hematopoietic stem cell transplantation (HSCT). Treatment response rates varied widely. Cross-study comparisons were complicated because different treatment regimens, follow-up periods, and outcome measures were used. There was a trend towards more frequent GLILD relapses in patients treated with corticosteroid monotherapy when compared to rituximab-containing treatment regimens based on qualitative endpoints. HSCT is a promising alternative to pharmacological treatment of GLILD, because it has the potential to not only contain symptoms, but also to resolve the underlying pathology. However, mortality, especially among immunocompromised patients, is high.

Conclusions

We could not draw definitive conclusions regarding optimal pharmacological treatment for GLILD in CVID from the current literature since quantitative, well-controlled evidence was lacking. While HSCT might be considered a treatment option for GLILD in CVID, the risks related to the procedure are high. Our findings highlight the need for further research with uniform, objective and quantifiable endpoints. This should include international registries with standardized data collection including regular pulmonary function tests (with carbon monoxide-diffusion), uniform high-resolution chest CT radiographic scoring, and uniform treatment regimens, to facilitate comparison of treatment outcomes and ultimately randomized clinical trials.

Managing Granulomatous-Lymphocytic Interstitial Lung Disease in Common Variable Immunodeficiency Disorders: e-GLILDnet International Clinicians Survey

Background

Granulomatous-lymphocytic interstitial lung disease (GLILD) is a rare, potentially severe pulmonary complication of common variable immunodeficiency disorders (CVID). Informative clinical trials and consensus on management are lacking.

Aims

The European GLILD network (e-GLILDnet) aims to describe how GLILD is currently managed in clinical practice and to determine the main uncertainties and unmet needs regarding diagnosis, treatment and follow-up.

Methods

The e-GLILDnet collaborators developed and conducted an online survey facilitated by the European Society for Immunodeficiencies (ESID) and the European Respiratory Society (ERS) between February-April 2020. Results were analyzed using SPSS.

Results

One hundred and sixty-one responses from adult and pediatric pulmonologists and immunologists from 47 countries were analyzed. Respondents treated a median of 27 (interquartile range, IQR 82-maximum 500) CVID patients, of which a median of 5 (IQR 8-max 200) had GLILD. Most respondents experienced difficulties in establishing the diagnosis of GLILD and only 31 (19%) had access to a standardized protocol. There was little uniformity in diagnostic or therapeutic interventions. Fewer than 40% of respondents saw a definite need for biopsy in all cases or performed bronchoalveolar lavage for diagnostics. Sixty-six percent used glucocorticosteroids for remission-induction and 47% for maintenance therapy; azathioprine, rituximab and mycophenolate mofetil were the most frequently prescribed steroid-sparing agents. Pulmonary function tests were the preferred modality for monitoring patients during follow-up.

Conclusions

These data demonstrate an urgent need for clinical studies to provide more evidence for an international consensus regarding management of GLILD. These studies will need to address optimal procedures for definite diagnosis and a better understanding of the pathogenesis of GLILD in order to provide individualized treatment options. Non-availability of well-established standardized protocols risks endangering patients.

Modified protocol of omalizumab treatment to prevent carboplatin-induced drug hypersensitivity reactions: a case study

Carboplatin administration can usually be safely continued via a so-called desensitisation protocol when hypersensitivity reactions arise. Severe break-through reactions that occur early during desensitisation are likely to be IgE-mediated; in that case, addition of omalizumab premedication should be strongly considered.

The role of prolonged viral gastrointestinal infections in the development of immunodeficiency-related enteropathy

Patients with primary immunodeficiencies are prone to develop enteropathy of unknown pathogenesis. We hypothesize that ineffective clearance of gastrointestinal pathogens, particularly viruses, in combination with defective immune regulation may cause inflammatory enteropathy in certain immunodeficient hosts. We reviewed publications related to prolonged enteric viral infection, immunodeficiency, and the subsequent development of inflammatory enteropathy. Prolonged infection with especially enteroviral infections was reported more often in immunocompromised hosts than in healthy individuals. Protracted enteric viral shedding was not always associated with the presence or duration of gastrointestinal symptoms. The development of immunodeficiency-associated enteropathy after prolonged viral infections was described in sporadic cases. Clinical consequences of viral gut infections in immunocompromised hosts comprise isolation issues and supportive care. Prospective studies in cohorts of immunodeficient patients are required to study the impact of prolonged enteric viral replication with respect to the pathogenesis of non-infectious enteropathy.

Defective calcium signaling and disrupted CD20-B-cell receptor dissociation in patients with common variable immunodeficiency disorders

BACKGROUND

B cells of patients with common variable immunodeficiency (CVID) disorders display impairment in production of immunoglobulin class-switched antibodies, which is possibly contributed to by defects in early B-cell activation. On resting B cells, B-cell receptors (BCRs) are organized in oligomers that are signaling inactive. Their triggering by cognate antigen causes the lateral reorganization of BCRs and associated proteins into signalosomes, resulting in BCR-activated calcium entry. In resting cells the B-cell surface antigen CD20 is associated with the BCR but dissociates on signalosome formation.

OBJECTIVE

We sought to determine whether CD20 dissociation from the BCR during early B-cell activation might contribute to the development of CVID disorders.

METHODS

We evaluated BCR signalosome formation, internalization, and signaling in primary B cells of pediatric patients with CVID disorders and healthy control subjects.

RESULTS

In many pediatric patients with CVID disorders, B cells exhibit significant deficits in BCR triggering-mediated calcium entry in the cytosol, which correlates with impaired plasmablast differentiation in vitro. These alterations did not originate from upregulation of CD22 or defects in calcium channels and did not involve gene mutations in phospholipase Cγ2 or Bruton tyrosine kinase. Instead, B cells from patients with CVID disorders exhibited reduced BCR dissociation from CD20. BCR or CD20 cross-linking induced less BCR internalization, and antibody-mediated CD20 triggering elicited less BCR downstream signaling, as measured based on secondary fluxes.

CONCLUSIONS

We propose that CD20 dissociation from the BCR signalosome is pivotal to BCR-mediated calcium mobilization in the cytosol. Defects in CD20/BCR signalosome conformation might predispose to the spectrum of CVID disorders.

Pleconaril-resistant chronic parechovirus-associated enteropathy in agammaglobulinaemia

A 14 year old common variable immunodeficiency patient developed severe protein-losing enteropathy. A chronic enteral infection with human parechovirus type 1 and norovirus was diagnosed. Treatment strategies aimed at virus eradication and providing supportive care were ineffective. The antipicornavirus agent pleconaril did not have any effect on viral replication. Symptoms improved on immunosuppressive therapy, suggesting infection-related immune dysregulation in an immunocompromised host.

A CT scan score for the assessment of lung disease in children with common variable immunodeficiency disorders

BACKGROUND

The prevalence and severity of structural lung disease in children with common variable immunodeficiency (CVID) disorders is not well known, and a dedicated CT scanning protocol and CT scan scoring system have not been described in this category.

METHODS

This was a cohort study of 54 children (34 CVID, 20 CVID-like disorder) in a stable condition who underwent volumetric inspiratory and end-expiratory CT scans. Scans were scored for airway abnormalities, interstitial and parenchymal lung disease, and lymphadenopathy using a newly developed CT scan scoring system. Scores were normalized to a 0% to 100% scale. Observer agreement was assessed using an intraclass correlation coefficient (Ri). Prevalence and severity of CT scan abnormalities were calculated.

RESULTS

Structural lung disease was common (85%-93%), but usually mild as reflected in the relatively low scores (bronchiectasis score 2.8% +/- 6.4%). Moderate-to-severe bronchiectasis was found in three (5%) patients. Expiratory air trapping was the most common finding, found in 71% to 80%, but often in a mild form; application of a cut off level of > 10% reduced its prevalence to 33% to 38%. In 9% to 15% of all patients, air trapping was the only abnormality. Multiple lung nodules were seen in 24% to 25% and could disappear after corticosteroid treatment. Observer agreement was moderate (Ri 0.6-0.79) to good (Ri > 0.8) for all items and the composite scores, except airway wall thickening.

CONCLUSION

In children with CVID disorders, mild structural lung disease is common. Expiratory CT scans show the most frequent abnormality, air trapping. The occurrence of (silent) lung disease progression and the clinical impact of CT scans require further investigations.

Lymphocyte characteristics in children with common variable immunodeficiency

The diagnosis of common variable immunodeficiency (CVID) is reserved for patients who suffer from undefined B cell dysfunction. Division of the CVID population into subgroups enables research for underlying disease causes. We studied clinical features and lymphocyte characteristics in 38 children with CVID and compared them to 30 children with less severe antibody deficiencies (e.g. specific antibody deficiency combined with IgG subclass deficiency) and with 65 pediatric controls. Most pediatric immune phenotypes were comparable to adult CVID phenotypes, including a selective increase in newly formed B cells and a decrease in memory B cells and CD4(+) T cells. Eighteen percent of pediatric patients had a mutation in the TNFRSF13B gene, which requires further investigation. Finally, pediatric patients with decreased class-switched memory B cells had significantly more complications. A pediatric classification for CVID may enable prediction and early diagnosis of disease related complications and provide a framework for further etiologic research.