Bone marrow transplantation for primary immunodeficiency diseases

Low frequency of treatable pediatric disease alleles in gnomAD: An opportunity for future genomic screening of newborns

Hematopoietic stem cell transplant (HSCT) can prevent progression of several genetic disorders. Although a subset of these disorders are identified on newborn screening panels, others are not identified until irreversible symptoms develop. Genetic testing is an efficient methodology to ascertain pre-symptomatic children, but the penetrance of risk-associated variants in the general population is not well understood. We developed a list of 127 genes associated with disorders treatable with HSCT. We identified likely pathogenic or pathogenic (LP/P) and loss-of-function (LoF) variants in these genes in the Genome Aggregation Database (gnomAD), a dataset containing exome and genome sequencing data from 141,456 healthy adults. Within gnomAD, we identified 59 individuals with a LP/P or LoF variant in 15 genes. Genes were associated with bone marrow failure syndromes, bleeding disorders, primary immunodeficiencies, osteopetrosis, metabolic disorders, and epidermolysis bullosa. In conclusion, few ostensibly healthy adults had genotypes associated with pediatric disorders treatable with HSCTs. Given that most of these disorders do not have biomarkers that could be cheaply and universally assessed on a standard newborn screen, our data suggest that genetic testing may be a complementary approach to traditional newborn screening methodology that has the potential to improve mortality and is not expected to lead to a high burden of false-positive results.

Trends in Pediatric Primary Immunodeficiency: Incidence, Utilization, Transplantation, and Mortality

BACKGROUND

Primary immunodeficiency disorders (PIDDs) describe a myriad of diseases caused by inherited defects within the immune system. As the number of identified genetic defects associated with PIDDs increases, understanding the incidence and outcomes of PIDD patients becomes imperative.

OBJECTIVE

To characterize the frequency of new diagnoses, patterns of health care utilization, rates of hematopoietic stem cell transplantation (HSCT), and mortality in pediatric patients with PIDDs.

METHODS

A retrospective cohort analysis of the Pediatric Health Information System database from 2004 to 2018 for pediatric inpatients with an International Classification of Diseases, Ninth and 10th Revisions (ICD-9/ICD-10). code associated with PIDD.

RESULTS

A total of 17,234 patients with a PIDD were hospitalized from 2004 to 2018. There were 2.8 new PIDD diagnoses and 6.3 PIDD hospitalizations per 1,000 discharges; these metrics were unchanged during the study period. The number of new diagnoses for B-cell and antibody defects significantly increased over time. The number of new PIDD diagnoses significantly increased in adolescents or adults and decreased in infants. T-cell disorders had the highest number of intensive care unit admissions. There were 747 PIDD patients who underwent HSCT; complications of HSCT significantly decreased over time. Mortality rates significantly decreased in all PIDD patients and in patients receiving HSCT.

CONCLUSIONS

The total hospitalizations and incidence of PIDDs within the hospitalized pediatric population were unchanged. There were significant changes in the class of PIDD diagnosed, the age at diagnosis, and health care utilization metrics. Mortality significantly decreased over time within the PIDD cohort.

Reduced-intensity single-unit unrelated cord blood transplant with optional immune boost for nonmalignant disorders

Children with many inherited nonmalignant disorders can be cured or their condition alleviated by hematopoietic stem cell transplantation (HSCT). Umbilical cord blood (UCB) units are a rapidly available stem cell source and offer great flexibility in HLA matching, allowing nearly uniform access to HSCT. Although reduced-intensity conditioning (RIC) regimens promise decreased treatment-related morbidity and mortality, graft failure and infections have limited their use in chemotherapy-naive patients. We prospectively evaluated a novel RIC regimen of alemtuzumab, hydroxyurea, fludarabine, melphalan, and thiotepa with a single-unit UCB graft in 44 consecutive patients with inborn errors of metabolism, immunity, or hematopoiesis. In addition, 5% of the UCB graft was re-cryopreserved and reserved for cord donor leukocyte infusion (cDLI) posttransplant. All patients engrafted at a median of 15 days posttransplant, and chimerism was >90% donor in the majority of patients at 1-year posttransplant with only 1 secondary graft failure. The incidence of grade II to IV graft-versus-host disease (GVHD) was 27% (95% confidence interval [CI], 17-43) with no extensive chronic GVHD. Overall survival was 95% (95% CI, 83-99) and 85% (95% CI, 64-93) at 1 and 5 years posttransplant, respectively. No significant end-organ toxicities were observed. The use of cDLI did not affect GVHD and showed signals of efficacy for infection control or donor chimerism. This RIC transplant regimen using single-unit UCB graft resulted in outstanding survival and remarkably low rates of graft failure. Implementation of the protocol not requiring pharmacokinetic monitoring would be feasible and applicable worldwide for children with inherited disorders of metabolism, immunity, or hematopoiesis. This trial was registered at www.clinicaltrials.gov as #NCT01962415.

Hematopoietic Stem Cell Transplantation for Children With Inborn Errors of Immunity

This is a retrospective analysis of clinical characteristics of children with inborn errors of immunity who underwent hematopoietic stem cell transplant (HSCT). Although the mean age at diagnosis was 24.4 months, it was 51.9 months at HSCT. There is an urgent need to improve awareness, expand donor registries and initiate newborn screening for inborn errors or immunity.

Immune reconstitution after HSCT in SCID-a cohort of conditioned and unconditioned patients

Allogeneic hematopoietic stem cell transplantation (HSCT) is the effective mean of immune restoration in severe combined immunodefiency (SCID). Usually, HSCT without cytoreductive conditioning is attempted. Nevertheless, conditioning procedures are still preferred in a subset of patients. Herein, we describe the immunological outcome in a cohort of conditioned and unconditioned patients, from diagnosis, through transplantation, to follow-up. This retrospective study was conducted on 17 patients with SCID (10 conditioned, 7 unconditioned) who later underwent HSCT. Immune reconstitution was assessed in the post-transplant year by quantification of T cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs), among additional laboratory and clinical evaluations. Unconditioned patients were diagnosed and transplanted earlier. TREC and KREC quantification showed a gradual increase in both groups, with higher levels in the conditioned group. Engraftment percentages differed drastically between groups, favoring the conditioned group. Unconditioned patients were significantly more dependent on intravenous immunoglobulins (IVIGs). One patient from each group succumbed to disease complications. Conditioning demonstrated superior laboratorial outcomes. Patients with unique characteristics (i.e., consanguinity, Bacillus Calmette-Guérin vaccination, impaired access to IVIG) may require personalized considerations. The effort to implement secondary prevention of SCID with newborn screening should continue.

Use of TCR α+β+/CD19+-Depleted Haploidentical Hematopoietic Stem Cell Transplant Is a Viable Option in Patients With Primary Immune Deficiency Without Matched Sibling Donor

Allogeneic hematopoietic stem cell transplantation (HSCT) is curative for many patients with primary immune deficiency (PID). Haploidentical donors have historically been associated with higher rates of graft-versus-host disease (GvHD) and graft failure. Use of T cell receptor (TCR) α⁺β⁺/CD19⁺-depleted grafts has resulted in improved haploidentical HSCT outcomes. We sought to evaluate outcomes of TCR α⁺β⁺/CD19⁺-depleted haploidentical HSCT in pediatric patients with PID at a single center in Australia. Specifically, we evaluated immune reconstitution, looking at time to T cell and B cell reconstitution, and B cell function post-HSCT. Eleven patients with a mean age of 7.92 years (range 0.33-17.17 years) were included. The median time to B cell recovery was 93 days (range 41-205 days), and the median time to cessation of immunoglobulin replacement was 281.5 days (range 41-205 days). All patients who had ceased immunoglobulin replacement had an adequate response to pneumococcal conjugate (Prevenar 13) vaccine. The median time to CD4⁺ recovery was 132 days (range 30-296 days), and naive T cells were present in all surviving patients by 4 months post-HSCT. Eight of 11 patients are surviving, with six patients having whole blood chimerism greater than 95%, one patient with whole blood chimerism of 82.8%, and another with 76.0%. All of these patients clinically had no evidence of underlying immunodeficiency. Likelihood of overall survival at 2 years post-HSCT was 81.8%. Cumulative incidence of acute GvHD was 27.3%. Cumulative incidence of CMV viremia was 63.6%. All patients previously exposed to CMV had reactivation post-HSCT, but were controlled with pre-emptive CMV treatment. Assuming most children with PID have a haploidentical donor available, use of this technique is likely to result in good outcomes for patients who do not have a suitable matched sibling or matched unrelated donor.

Function and Safety of Lentivirus-Mediated Gene Transfer for CSF2RA-Deficiency

Hereditary pulmonary alveolar proteinosis (hPAP) is a rare disorder of pulmonary surfactant accumulation and hypoxemic respiratory failure caused by mutations in CSF2RA (encoding the granulocyte/macrophage colony-stimulating factor [GM-CSF] receptor α-chain [CD116]), which results in reduced GM-CSF-dependent pulmonary surfactant clearance by alveolar macrophages. While no pharmacologic therapy currently exists for hPAP, it was recently demonstrated that endotracheal instillation of wild-type or gene-corrected mononuclear phagocytes (pulmonary macrophage transplantation [PMT]) results in a significant and durable therapeutic efficacy in a validated murine model of hPAP. To facilitate the translation of PMT therapy to human hPAP patients, a self-inactivating (SIN) lentiviral vector was generated expressing a codon-optimized human CSF2RA-cDNA driven from an EF1α short promoter (Lv.EFS.CSF2RA^coop), and a series of nonclinical efficacy and safety studies were performed in cultured macrophage cell lines and primary human cells. Studies in cytokine-dependent Ba/F3 cells demonstrated efficient transduction, vector-derived CD116 expression proportional to vector copy number, and GM-CSF-dependent cell survival and proliferation. Using a novel cell line constructed to express a normal GM-CSF receptor β subunit and a dysfunctional α subunit (due to a function-altering CSF2RA^G196R mutation) that reflects the macrophage disease phenotype of hPAP patients, it was demonstrated that Lv.EFS.CSF2RA^coop transduction restored GM-CSF receptor function. Further, Lv.EFS.CSF2RA^coop transduction of healthy primary CD34⁺ cells did not adversely affect cell proliferation or affect the cell differentiation program. Results demonstrate Lv.EFS.CSF2RA^coop reconstituted GM-CSF receptor α expression, restoring GM-CSF signaling in hPAP macrophages, and had no adverse effects in the intended target cells, thus supporting testing of PMT therapy of hPAP in humans.

History and current status of newborn screening for severe combined immunodeficiency

The development of a T-cell receptor excision circle (TREC) assay utilizing dried blood spots in universal newborn screening has allowed the early detection of T-cell lymphopenia in newborns. Diagnosis of severe combined immunodeficiency (SCID) in affected infants in the neonatal period, while asymptomatic, permits early treatment and restoration of a functional immune system. SCID was the first immunodeficiency disease to be added to the Recommended Uniform Screening Panel of Core Conditions in the United States in 2010, and it is now implemented in 26 states in the U.S. This review covers the development of newborn screening for SCID, the biology of the TREC test, its current implementation in the U.S., new findings for SCID in the newborn screening era, and future directions.

Primary immunodeficiencies in the Netherlands: national patient data demonstrate the increased risk of malignancy

PURPOSE

To analyze the data of the national registry of all Dutch primary immune deficiency (PID) patients, according to the European Society for Immunodeficiencies (ESID) definitions.

RESULTS

In the Netherlands, 745 patients had been registered between 2009 and 2012. An overall prevalence of 4.0 per 100,000 inhabitants was calculated. The most prevalent PID was 'predominantly antibody disorder (PAD)' (60.4%). In total, 118 transplantations were reported, mostly hematopoietic stem cell transplantations (HSCT). Almost 10% of the PID patients suffered from a malignancy, in particular 'lymphoma' and 'skin cancer'. Compared to the general Dutch population, the relative risk of developing any malignancy was 2.3-fold increased, with a >10-fold increase for some solid tumors (thymus, endocrine organs) and hematological disease (lymphoma, leukemia), varying per disease category.

CONCLUSIONS

The incidence rate and characteristics of PID in the Netherlands are similar to those in other European countries. Compared to the general population, PID patients carry an increased risk to develop a malignancy.

A novel reduced-intensity conditioning regimen for unrelated umbilical cord blood transplantation in children with nonmalignant diseases

Reduced-intensity conditioning (RIC) regimens have the potential to decrease transplantation-related morbidity and mortality. However, engraftment failure has been prohibitively high after RIC unrelated umbilical cord blood transplantation (UCBT) in chemotherapy-naïve children with nonmalignant diseases (NMD). Twenty-two children with a median age of 2.8 years, many with severe comorbidities and prior viral infections, were enrolled in a novel RIC protocol consisting of hydroxyurea, alemtuzumab, fludarabine, melphalan, and thiotepa followed by single UCBT. Patients underwent transplantation for inherited metabolic disorders (n = 8), primary immunodeficiencies (n = 9), hemoglobinopathies (n = 4) and Diamond Blackfan anemia (n = 1). Most umbilical cord blood (UCB) units were HLA-mismatched with median infused total nucleated cell dose of 7.9 × 10(7)/kg. No serious organ toxicities were attributable to the regimen. The cumulative incidence of neutrophil engraftment was 86.4% (95% confidence interval [CI], 65% to 100%) in a median of 20 days, with the majority sustaining > 95% donor chimerism at 1 year. Cumulative incidence of acute graft-versus-host disease (GVHD) grades II to IV and III to IV by day 180 was 27.3% (95% CI, 8.7% to 45.9%) and 13.6% (95 CI, 0% to 27.6%), respectively. Cumulative incidence of extensive chronic GVHD was 9.1% (95% CI, 0% to 20.8%). The primary causes of death were viral infections (n = 3), acute GVHD (n = 1) and transfusion reaction (n = 1). One-year overall and event-free survivals were 77.3% (95% CI, 53.7% to 89.8%) and 68.2% (95% CI, 44.6% to 83.4%) with 31 months median follow-up. This is the first RIC protocol demonstrating durable UCB engraftment in children with NMD. Future risk-based modifications of this regimen could decrease the incidence of viral infections. (www.clinicaltrials.gov/NCT00744692).

Bone marrow transplantation in Schimke immuno-osseous dysplasia

Schimke immuno-osseous dysplasia (SIOD, OMIM 242900) is a rare autosomal recessive multisystem childhood disorder characterized by short stature, renal failure, T-cell immunodeficiency, and hypersensitivity to genotoxic agents. SIOD is associated with biallelic mutations in SMARCAL1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin, subfamily a-like 1), which encodes a DNA stress response enzyme with annealing helicase activity. Two features of SIOD causing much morbidity and mortality are bone marrow failure and T-cell deficiency with the consequent opportunistic infections. To address the safety and efficacy of bone marrow transplantation (BMT) in SIOD, we reviewed the outcomes of the only five SIOD patients known to us in whom bone marrow or hematopoietic stem cell transplantation has been attempted. We find that only one patient survived the transplantation procedure and that the existing indicators of a good prognosis for bone marrow transplantation were not predictive in this small cohort. Given these observations, we also discuss some considerations for the poor outcomes.

Reviewing the follow-up care of pediatric patients' status post-hematopoietic stem cell transplantation for the primary care pediatrician

BACKGROUND

Hematopoietic stem cell transplantation (HSCT) is a treatment modality for many oncologic as well as non-oncologic disorders. Although the side effects of different chemotherapy regimens have been well studied by several oncology consortiums, limited data is available regarding the late adverse effects of HSCT. Furthermore, pediatric-focused post-HSCT follow-up guidelines for primary care pediatricians do not exist.

OBJECTIVE

To provide a summary of the most common late adverse effects of HSCT and give the primary care pediatrician guidance and evidence-based information for the screening and management of this patient population.

DESIGN

The literature was searched using PubMed using keywords, including pediatric bone marrow transplant, hematopoietic stem cell transplant guidelines, pediatric bone marrow transplant guidelines, and pediatric bone marrow transplant immunizations. The most relevant articles out of the hundreds of results were reviewed.

RESULTS

Based on 9 review articles from the Pediatric Clinics of North America and 3 articles from the Biology of Blood and Marrow Transplant Journal as well as their original references, a summary of the most common late adverse effects after HSCT was constructed. Pediatric HSCT patients have a high incidence of late adverse effects, with 93% of survivors having at least 1 late adverse effect after 7 years of follow-up.

CONCLUSION

Late adverse effects after pediatric HSCT are common and require close screening and monitoring, which can be done by the primary care provider along with the oncologist.

Current translational and clinical practices in hematopoietic cell and gene therapy

Clinical trials over the last 15 years have demonstrated that cell and gene therapies for cancer, monogenic and infectious disease are feasible and can lead to long-term benefit for patients. However, these trials have been limited to proof-of-principle and were conducted on modest numbers of patients or over long periods of time. In order for these studies to move towards standard practice and commercialization, scalable technologies for the isolation, ex vivo manipulation and delivery of these cells to patients must be developed. Additionally, regulatory strategies and clinical protocols for the collection, creation and delivery of cell products must be generated. In this article we review recent progress in hematopoietic cell and gene therapy, describe some of the current issues facing the field and discuss clinical, technical and regulatory approaches used to navigate the road to product development.

A single-center study of hematopoietic stem cell transplantation for primary immune deficiencies (PIDD)

PIDD are rare inherited disorders that can result in life-threatening infections. Allogeneic HSCT is the only cure for many primary immune deficiencies; however, the specific diseases and optimal type(s) of transplants are not clear. This study compares transplant outcomes in a large cohort with a relatively uniform pre- and post-transplant management strategies. We conducted a retrospective analysis of 39 pediatric patients who underwent HSCT for SCID (n = 25) or other immune deficiencies (n = 14) from 1986 to 2010. A structured case report form was used to collect clinical information. The outcomes of survival, immune reconstitution, engraftment, incidence of GvHD and IVIG dependency were tabulated. Overall survival rates were 88% for SCID and 86% for other primary immune deficiencies, which are high compared to other historical series. No single variable was associated with mortality. Immunoglobulin dependence occurred only in patients who had X-linked SCID and a parental donor haploidentical transplant. Because of improved supportive care and use of alternative donors and conditioning regimens, HSCT has become an acceptable option for an increasing number of PIDD subtypes not previously transplanted with high frequency. This study encourages greater use of transplantation.

Ex vivo gene transfer and correction for cell-based therapies

Cell-based therapies are fast-growing forms of personalized medicine that make use of the steady advances in stem cell manipulation and gene transfer technologies. In this Review, I highlight the latest developments and the crucial challenges for this field, with an emphasis on haematopoietic stem cell gene therapy, which is taken as a representative example given its advanced clinical translation. New technologies for gene correction and targeted integration promise to overcome some of the main hurdles that have long prevented progress in this field. As these approaches marry with our growing capacity for genetic reprogramming of mammalian cells, they may fulfil the promise of safe and effective therapies for currently untreatable diseases.

HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes

MOTIVATION

Genetic variation at classical HLA alleles influences many phenotypes, including susceptibility to autoimmune disease, resistance to pathogens and the risk of adverse drug reactions. However, classical HLA typing methods are often prohibitively expensive for large-scale studies. We previously described a method for imputing classical alleles from linked SNP genotype data. Here, we present a modification of the original algorithm implemented in a freely available software suite that combines local data preparation and QC with probabilistic imputation through a remote server.

RESULTS

We introduce two modifications to the original algorithm. First, we present a novel SNP selection function that leads to pronounced increases (up by 40% in some scenarios) in call rate. Second, we develop a parallelized model building algorithm that allows us to process a reference set of over 2500 individuals. In a validation experiment, we show that our framework produces highly accurate HLA type imputations at class I and class II loci for independent datasets: at call rates of 95-99%, imputation accuracy is between 92% and 98% at the four-digit level and over 97% at the two-digit level. We demonstrate utility of the method through analysis of a genome-wide association study for psoriasis where there is a known classical HLA risk allele (HLA-C*06:02). We show that the imputed allele shows stronger association with disease than any single SNP within the region. The imputation framework, HLA*IMP, provides a powerful tool for dissecting the architecture of genetic risk within the HLA.

AVAILABILITY

HLA*IMP, implemented in C++ and Perl, is available from http://oxfordhla.well.ox.ac.uk and is free for academic use.

Otitis media in children with congenital immunodeficiencies

Otitis media represents one of the most common infections in childhood. Within the first 3 years of life, up to 80% of children experience at least one episode of otitis media. It is often resolved with supportive therapies and consequently not considered a worrisome problem. However, it may be an early manifestation of a severe underlying disease. Primary immunodeficiencies are rare congenital defects of the immune system that often remain unrecognized, or diagnosis can be delayed, sometimes resulting in fatal consequences for the child. Patients suffer from recurrent, prolonged, and/or unusual infections leading to local sequelae, failure to thrive, developmental delays, and systemic infections with severe courses. This review provides a brief insight into primary immunodeficiencies and an overview of leading findings that should result in further evaluation of the immune system in cases of otitis media. A stepwise diagnostic approach is proposed to facilitate early and accurate diagnosis and, consequently, effective and timely therapy to improve the patient's outcome and quality of life.