Characterization of the cellular and molecular bases of inborn errors of immunity

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications, trials & patents

Abstract

In FY2022, we have contributed to the genetic characterization of 1000 patients with complex immune phenotypes. We have also helped identify a novel form of IEI due to OTULIN deficiency. We have also expanded knowledge on the clinical phenotype associated with previously described forms of IEI. By participating at multi-center studies, we have helped define clinical outcome following hematopoietic cell transplantation (HCT) for adenosine deaminase (ADA) deficiency. Use of patient-derived induced pluripotent stem cells (iPSCs) has allowed us to gain insights into the pathophysiology of ADA and purine nucleoside phosphorylase (PNP) deficiencies. We have also demonstrated that high throughput sequencing of the T cell receptor (TCR) repertoire is a powerful way to assess the robustness of immune reconstitution after HCT for SCID. Finally, we have participated at studies exploring the efficacy of stablished as well as novel therapeutic modalities for various forms of IEI. In particular, the main results of the studies performed have been the following: 1) Whole-exome sequencing (WES) of 1,000 patients with a complex clinical phenotype enrolled in the Centralized Sequencing Initiative at NIAID enabled molecular diagnoses in 361 of them (publication #10). Re-analysis of the data added 22 molecular diagnoses. These findings included also the identification of novel disease-causing genes as reported last year for SASH3 deficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into more than one management option. Overall, these results demonstrate that comprehensive analysis of WES data has diagnostic and clinical utility for patients with suspected IEI 2) By performing longitudinal analysis of the TCR beta (TRB) repertoire in patients who had received HCT for severe combined immune deficiency (SCID), we have demonstrated that SCID genotype and type of conditioning used have a significant impact on the diversity of TRB repertoire and on the quality of immune reconstitution overall (publication #5). Our data support the notion that TRB repertoire analysis after HCT provides a quantitative and qualitative measure of diversity and robustness of immune reconstitution. 3) Using iPSCs as a model to investigate myeloid development, we have demonstrated that ADA deficiency leads to a significant reduction in the number of early multipotent hematopoietic progenitor cells and severely impairs generation of neutrophils in vitro. Supplementing iPSCs with exogenous ADA reversed these abnormalities (publication #13). These data have helped clarify the mechanisms underlying the neutropenia that is associated with ADA deficiency in vivo. 4) Similarly, we have used iPSCs derived from patients with PNP deficiency to investigate the basis of neurological impairment associated with this condition. Upon differentiation of iPSCs into neurons, we observed that PNP-deficient cells had reduced soma and nuclear volume, and displayed enhanced apoptosis via the intrinsic (mitochondrial) pathway. Similar features were observed when control-derived neurons were treated in vitro with drugs inhibiting ribonucleotide reductase, whose activity is affected by PNP deficiency (publication #12). These findings establish a potential mechanism for the neurological defects observed in PNP deficiency. 5) We have helped describe a novel form of IEI due to OTULIN haploinsufficiency (publication #11). This condition is characterized by increased risk of life-threatening infection sustained by Staphylococcus aureus. Experimental work has shown that OTULIN haploinsufficiency causes accumulation of linear ubiquitin in patients fibroblasts, facilitating the damage inflicted by staphylococcal alpha-toxin. This defect of cell-intrinsic immunity to Staphylococcus aureus may explain interindividual clinical variability upon S. aureus infection. 6) We have contributed to studies investigating outcome of HCT in two diferent forms of IEI. In particular, review of the experience of HCT at the NIH in patients with GATA2 deficiency showed that use of post-transplantation cyclophosphamide (PT/Cy) influences clinical outcome, with reduced risk of acute and chronic graft-versus-host disease (publication #8). In a collaborative study with centers of the primary Immune Deficiency Treatment Consortium (PIDTC), we have demonstrated that 5-year overall survival was superior in patients treated by gene therapy compared to those who received enzyme replacement therapy or HCT as first definitive treatments. However, when considering patients treated after year 2000 (when newborn screening became broadly available), no difference in OS or in event-free survival was observed between patients treated by gene therapy or HCT (publication #3). These results indicate that early identification and treatment of ADA deficiency may allow optimal outcome. 7) We have expanded the clinical phenotype associated with certain IEI by documenting the association of visceral leishmaniasis and mycobacterium avium infection in a child with autosomal recessive IFNGR1 deficiency (publication #6) and by reviewing clinical presentation outcome of patients with chronic granulomatous disease who have received granulocyte transfusions (publication #1) and of those manifesting inflammatory bowel disease (publication #7). Finally, we have discussed the potential significance of the identification of the vaccine strain of rubella virus in granulomatous lesions of patients with combined immune deficiency as well as of apparently immunocompetent individuals (publication #9). 8) We have collaborated with the Malech group at the investigation of the safety profile of lentivirus-mediated gene transfer in patients with X-linked SCID. Longitudinal analysis of the integration profile revealed increased frequency of hematopoietic stem and progenitor cells expressing truncated HMGA2 as a result of a cryptic splicing event within the lentiviral vector (publication #4). These data indicate the importance of functional analysis of lentiviral vectors for preclinical safety assessment. 9) Finally, we have published a review on congenital and acquired errors of immunity (publication #2)