Manish Butte

J Allergy Clin Immunol. 2023 Jun 8:S0091-6749(23)00749-2. doi: 10.1016/j.jaci.2023.05.022. Online ahead of print.

ABSTRACT

BACKGROUND: Inborn errors of immunity (IEI) are a group of monogenic diseases that confer susceptibility to infection, autoimmunity and cancer. Despite the life-threatening consequences of some IEI, their genetic cause remains unknown in many patients.

OBJECTIVE: We investigated a patient with an IEI of unknown genetic aetiology.

METHODS: Whole-exome sequencing identified a homozygous missense mutation of the gene encoding ezrin (EZR), substituting a threonine for an alanine at position 129.

RESULTS: Ezrin is one of the subunits of the ERM complex, which also contains radixin and moesin. The ERM complex links the plasma membrane to the cytoskeleton and is crucial for the assembly of an efficient immune response. The A129T mutation abolishes basal phosphorylation and decreases calcium signalling, leading to a complete loss of function. Consistent with the pleiotropic function of ezrin in myriad immune cells, multidimensional immunophenotyping by mass and flow cytometry revealed that, in addition to hypogammaglobulinaemia, the patient had low frequencies of switched memory B cells, CD4⁺ and CD8⁺ T cells, MAIT, γδ T and centralnaïve CD4⁺ cells.

CONCLUSIONS: In conclusion, autosomal recessive human ezrin deficiency is a new genetic cause of B cell deficiency affecting cellular and humoral immunity.

PMID:37301410 | DOI:10.1016/j.jaci.2023.05.022

Int Forum Allergy Rhinol. 2023 Jun 10. doi: 10.1002/alr.23206. Online ahead of print.

ABSTRACT

BACKGROUND: There is clear evidence that prevalence of primary antibody deficiency (PAD) is higher in patients with recurrent and chronic rhinosinusitis (CRS) than in the general population. The purpose of this multi-institutional and multidisciplinary evidence-based review with recommendations (EBRR) is to thoroughly review the literature on rhinosinusitis with PAD, summarize the existing evidence, and provide recommendations on the evaluation and management of rhinosinusitis in patients with PAD.

METHODS: The PubMed, EMBASE, and Cochrane databases were systematically reviewed from inception through August 2022. Studies on the evaluation and management of rhinosinusitis in PAD patients were included. An iterative review process was utilized in accordance with EBRR guidelines. Levels of evidence and recommendations on the evaluation and management principles for PAD were generated.

RESULTS: A total of 42 studies were included in this evidence-based review. These studies were evaluated on incidence of PAD in rhinosinusitis patients, incidence of rhinosinusitis in PAD patients, and on the different treatment modalities used and their outcome. The aggregate quality of evidence was varied across reviewed domains.

CONCLUSION: Based on the currently available evidence, PAD can occur in up to 50% of patients with recalcitrant CRS. Despite presence of multiple studies addressing rhinosinusitis and PAD, the level of evidence supporting different treatment options continues to be lacking. Optimal management require multidisciplinary approach through collaboration with clinical immunology. There is need for higher level studies that compare different treatments in patients with PAD and rhinosinusitis. This article is protected by copyright. All rights reserved.

PMID:37300852 | DOI:10.1002/alr.23206

Nat Commun. 2023 Jun 9;14(1):3413. doi: 10.1038/s41467-023-39094-0.

ABSTRACT

Increasing detections of vaccine-derived poliovirus (VDPV) globally, including in countries previously declared polio free, is a public health emergency of international concern. Individuals with primary immunodeficiency (PID) can excrete polioviruses for prolonged periods, which could act as a source of cryptic transmission of viruses with potential to cause neurological disease. Here, we report on the detection of immunodeficiency-associated VDPVs (iVDPV) from two asymptomatic male PID children in the UK in 2019. The first child cleared poliovirus with increased doses of intravenous immunoglobulin, the second child following haematopoetic stem cell transplantation. We perform genetic and phenotypic characterisation of the infecting strains, demonstrating intra-host evolution and a neurovirulent phenotype in transgenic mice. Our findings highlight a pressing need to strengthen polio surveillance. Systematic collection of stool from asymptomatic PID patients who are at high risk for poliovirus excretion could improve the ability to detect and contain iVDPVs.

PMID:37296153 | DOI:10.1038/s41467-023-39094-0

Transplant Cell Ther. 2023 Jun 4:S2666-6367(23)01321-0. doi: 10.1016/j.jtct.2023.05.019. Online ahead of print.

ABSTRACT

BACKGROUND: A minority of children experience significant graft dysfunction after an allogeneic hematopoietic stem cell transplant (HSCT) for inborn errors of immunity (IEI). The optimal approach to salvage HSCT is unclear with respect to conditioning regimen and stem cell source. This single-centre retrospective case series reports the outcomes of salvage CD3+TCRαβ/CD19 depleted mismatched family or unrelated donor stem cell transplantation (TCRαβ-SCT) between 2013 – 2022 for graft dysfunction in 12 children with IEI.

OBJECTIVES: Outcomes of interest were overall survival (OS), event free survival (EFS), graft-versus-host disease (GvHD)-free and event-free survival (GEFS), toxicities, GvHD, viremia and long-term graft function.

STUDY DESIGN: A retrospective audit of patients who underwent second CD3+TCRαβ/CD19 depleted mismatched donor graft using Treosulfan-based reduced toxicity myeloablative conditioning.

RESULTS: Median age at first HSCT was 8.76 months (range, 2.5 months – 6 years) and at second TCRαβ-SCT was 3.6 years (1.2 – 11 years). Median interval between first and second HSCT was 1.7 years (3 months – 9 years). The primary diagnoses were: severe combined immunodeficiency (SCID) (n=5) and non-SCID IEI (n=7). The indications for second HSCT were: primary aplasia (n=1), secondary autologous reconstitution (n=6), refractory aGVHD (n=3) and secondary leukemia (n=1). Donors were either haploidentical parental donors (n=10) or mismatched unrelated donors (n=2). All received TCRαβ/CD19-depleted-PBSC with a median CD34+ cell dose of 9.3 × 10⁶/kg (2.8-32.3 × 10⁶/kg) and a median TCRαβ+ cell dose of 4 × 10⁴/kg (1.3-19.2 × 10⁴/kg). All engrafted with median days to neutrophil and platelet recovery of 15 (12-24) and 12 (9-19). One developed secondary aplasia and one had secondary autologous reconstitution, but both underwent a successful third HSCT. Four (33%) had grade II aGvHD and none had grade III-IV aGvHD. None had cGvHD but one developed extensive cutaneous cGVHD after third HSCT using PBSC and ATG. Nine (75%) were noted to have at least one episode of blood viremia with HHV6 (n=6, 50%), adenovirus (n=6, 50%), EBV (n=3, 25%) or CMV (n=3; 25%). Median duration of follow-up was 2.3 years (range: 0.5 – 10 years) and the 2-year OS, EFS and GEFS were 100% (95% confidence interval, 0-100%), 73% (37-90%) and 73% (37%-90%) respectively.

CONCLUSIONS: TCRαβ-SCT from mismatched family or unrelated donors, using a chemotherapy only regimen, is a safe alternative donor salvage transplant strategy for second HSCT in patients without a suitably matched donor.

PMID:37279857 | DOI:10.1016/j.jtct.2023.05.019

BMC Genomics. 2023 Jun 6;24(1):305. doi: 10.1186/s12864-023-09391-5.

ABSTRACT

Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are not predicted to be pathogenic using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

PMID:37280537 | DOI:10.1186/s12864-023-09391-5

J Allergy Clin Immunol. 2023 Jun 3:S0091-6749(23)00712-1. doi: 10.1016/j.jaci.2023.05.017. Online ahead of print.

ABSTRACT

BACKGROUND: TCF3 is a transcription factor contributing to early lymphocyte differentiation. Germline monoallelic dominant negative (DN) and biallelic loss-of-function (LOF) Null TCF3 mutations cause a fully penetrant severe immunodeficiency. We identified 8 individuals from 7 unrelated families with monoallelic LOF TCF3 variants presenting with immunodeficiency with incomplete clinical penetrance.

OBJECTIVE: To define TCF3 haploinsufficiency biology and its association with immunodeficiency.

METHODS: Patient clinical data and blood samples were analyzed. Flow cytometry, western blotting, plasmablast differentiation, immunoglobulin secretion, and transcriptional activity studies were conducted on individuals carrying TCF3 variants. Mice with a heterozygous Tcf3 deletion were analyzed for lymphocyte development and phenotyping.

RESULTS: Individuals carrying monoallelic LOF TCF3 variants showed B cell defects (e.g., reduced total, class-switched memory and/or plasmablasts), and reduced serum immunoglobulin levels; most but not all presented with recurrent, non-severe infections. These TCF3 LOF variants were either not transcribed or translated, resulting in reduced wildtype TCF3 protein expression, strongly suggesting haploinsufficiency (HI) pathophysiology for the disease. Targeted RNAseq analysis of T cell blasts from TCF3 Null, DN, or HI individuals clustered away from healthy donors, implying that two WT copies of TCF3 are needed to sustain a tightly regulated TCF3 gene-dosage effect. Murine TCF3 HI resulted in a reduction of circulating B cells but overall normal humoral immune responses.

CONCLUSION: Monoallelic LOF TCF3 mutations cause a gene-dosage-dependent reduction in wildtype protein expression, B cell defects and a dysregulated transcriptome, resulting in immunodeficiency. Tcf3^+-/- mice partially recapitulate the human phenotype underscoring differences between TCF3 in humans and mice.

PMID:37277074 | DOI:10.1016/j.jaci.2023.05.017

Allergy Asthma Clin Immunol. 2023 Jun 5;19(1):50. doi: 10.1186/s13223-023-00799-y.

ABSTRACT

BACKGROUND: Common variable Immunodeficiency (CVID) is a primary immunodeficiency disorder and the most common form of severe antibody deficiency. Both children and adults are affected and clinical manifestations vary widely. Often, CVID manifests with infections, autoimmune phenomena or chronic lung disease, but it also frequently affects the liver. The differential diagnoses of hepatopathies in CVID patients are diverse and the characteristics of CVID patients often make it difficult to determine the correct diagnosis.

CASE PRESENTATION: We present the case of a 39-year-old patient with CVID and elevated liver enzymes, nausea and unintended weight loss, who was referred to our clinic with the suspected diagnose of autoimmune hepatitis or immunoglobulin-induced hepatopathy. Prior, the patient had undergone an extensive diagnostic work-up including liver biopsy but viral hepatitides had only been investigated serologically – with negative antibody results. We searched for viral nucleic acid by polymerase chain reaction and detected hepatitis E virus-RNA. Antiviral therapy was started and the patient recovered quickly.

CONCLUSION: Hepatopathies in CVID patients are common with a broad spectrum of possible causes. While treating CVID patients, the distinct diagnostic and therapeutic requirements of the CVID patients should be closely considered and diagnosed by the appropriate measures.

PMID:37277808 | DOI:10.1186/s13223-023-00799-y

IET Syst Biol. 2023 Jun 5. doi: 10.1049/syb2.12066. Online ahead of print.

ABSTRACT

Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment and improving its early detection based on their tumour origin. There exist previous studies focusing on the identification of tumour-based biomarkers for glioblastoma. However, these biomarkers inadequately represent the underlying pathological state and incompletely illustrate the tumour because of non-recursive nature of this approach to monitor the disease. Also, contrary to the tumour biopsies, liquid biopsies are non-invasive and can be performed at any interval during the disease span to surveil the disease. Therefore, in this study, a unique dataset of blood-based liquid biopsies obtained primarily from tumour-educated blood platelets (TEP) is utilised. This RNA-seq data from ArrayExpress is acquired comprising human cohort with 39 glioblastoma subjects and 43 healthy subjects. Canonical and machine learning approaches are applied for identification of the genomic biomarkers for glioblastoma and their crosstalks. In our study, 97 genes appeared enriched in 7 oncogenic pathways (RAF-MAPK, P53, PRC2-EZH2, YAP conserved, MEK-MAPK, ErbB2 and STK33 signalling pathways) using GSEA, out of which 17 have been identified participating actively in crosstalks. Using PCA, 42 genes are found enriched in 7 pathways (cytoplasmic ribosomal proteins, translation factors, electron transport chain, ribosome, Huntington’s disease, primary immunodeficiency pathways, and interferon type I signalling pathway) harbouring tumour when altered, out of which 25 actively participate in crosstalks. All the 14 pathways foster well-known cancer hallmarks and the identified DEGs can serve as genomic biomarkers, not only for the diagnosis and prognosis of Glioblastoma but also in providing a molecular foothold for oncogenic decision making in order to fathom the disease dynamics. Moreover, SNP analysis for the identified DEGs is performed to investigate their roles in disease dynamics in an elaborated manner. These results suggest that TEPs are capable of providing disease insights just like tumour cells with an advantage of being extracted anytime during the course of disease in order to monitor it.

PMID:37277696 | DOI:10.1049/syb2.12066

Front Immunol. 2023 May 19;14:1183273. doi: 10.3389/fimmu.2023.1183273. eCollection 2023.

ABSTRACT

INTRODUCTION: Humans with gain-of-function (GOF) mutations in STAT1 (Signal Transducer and Activator of Transcription 1), a potent immune regulator, experience frequent infections. About one-third, especially those with DNA-binding domain (DBD) mutations such as T385M, also develop autoimmunity, sometimes accompanied by increases in T-helper 1 (Th1) and T-follicular helper (Tfh) CD4 effector T cells, resembling those that differentiate following infection-induced STAT1 signaling. However, environmental and molecular mechanisms contributing to autoimmunity in STAT1 GOF patients are not defined.

METHODS: We generated Stat1T385M/+ mutant mice to model the immune impacts of STAT1 DBD GOF under specific-pathogen free (SPF) conditions.

RESULTS: Stat1T385M/+ lymphocytes had more total Stat1 at baseline and also higher amounts of IFNg-induced pStat1. Young mutants exhibited expansion of Tfh-like cells, while older mutants developed autoimmunity accompanied by increased Tfh-like cells, B cell activation and germinal center (GC) formation. Mutant females exhibited these immune changes sooner and more robustly than males, identifying significant sex effects of Stat1T385M-induced immune dysregulation. Single cell RNA-Seq (scRNA-Seq) analysis revealed that Stat1T385M activated transcription of GC-associated programs in both B and T cells. However, it had the strongest transcriptional impact on T cells, promoting aberrant CD4 T cell activation and imparting both Tfh-like and Th1-like effector programs.

DISCUSSION: Collectively, these data demonstrate that in the absence of overt infection, Stat1T385M disrupted naïve CD4 T cell homeostasis and promoted expansion and differentiation of abnormal Tfh/Th1-like helper and GC-like B cells, eventually leading to sex-biased autoimmunity, suggesting a model for STAT1 GOF-induced immune dysregulation and autoimmune sequelae in humans.

PMID:37275873 | PMC:PMC10235531 | DOI:10.3389/fimmu.2023.1183273

World J Clin Cases. 2023 May 16;11(14):3295-3303. doi: 10.12998/wjcc.v11.i14.3295.

ABSTRACT

BACKGROUND: Pulmonary mucormycosis is a rare but life-threatening invasive fungal infection that mostly affects immunocompromised patients. This disease usually develops acutely and progresses rapidly, often leading to a poor clinical prognosis. Chronic pulmonary mucormycosis is highly unusual in immunocompetent patients.

CASE SUMMARY: A 43-year-old man, who was a house improvement worker with a long history of occupational dust exposure, presented with an irritating cough that had lasted for two months. The patient was previously in good health, without dysglycemia or any known immunodeficiencies. Chest computed tomography revealed a mass in the left lower lobe, measuring approximately 6 cm in diameter, which was suspected to be primary lung carcinoma complicated with obstructive pneumonia. Thoracoscopic-assisted left lower lobectomy was performed, and metagenomic next-generation sequencing detection, along with special pathological staining of surgical specimens, suggested Rhizopus microsporus infection. Postoperatively, the patient’s respiratory symptoms were relieved, and no signs of recurrence were found during the six-month follow-up.

CONCLUSION: This article reports a rare case of chronic pulmonary mucormycosis caused by Rhizopus microsporus in a middle-aged male without dysglycemia or immunodeficiency. The patient’s surgical outcome was excellent, reaffirming that surgery remains the cornerstone of pulmonary mucormycosis treatment.

PMID:37274035 | PMC:PMC10237139 | DOI:10.12998/wjcc.v11.i14.3295