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J Allergy Clin Immunol Glob. 2024 Feb 2;3(2):100224. doi: 10.1016/j.jacig.2024.100224. eCollection 2024 May.

ABSTRACT

BACKGROUND: There are now approximately 450 discrete inborn errors of immunity (IEI) described; however, diagnostic rates remain suboptimal. Use of structured health record data has proven useful for patient detection but may be augmented by natural language processing (NLP). Here we present a machine learning model that can distinguish patients from controls significantly in advance of ultimate diagnosis date.

OBJECTIVE: We sought to create an NLP machine learning algorithm that could identify IEI patients early during the disease course and shorten the diagnostic odyssey.

METHODS: Our approach involved extracting a large corpus of IEI patient clinical-note text from a major referral center’s electronic health record (EHR) system and a matched control corpus for comparison. We built text classifiers with simple machine learning methods and trained them on progressively longer time epochs before date of diagnosis.

RESULTS: The top performing NLP algorithm effectively distinguished cases from controls robustly 36 months before ultimate clinical diagnosis (area under precision recall curve > 0.95). Corpus analysis demonstrated that statistically enriched, IEI-relevant terms were evident 24+ months before diagnosis, validating that clinical notes can provide a signal for early prediction of IEI.

CONCLUSION: Mining EHR notes with NLP holds promise for improving early IEI patient detection.

PMID:38439946 | PMC:PMC10910118 | DOI:10.1016/j.jacig.2024.100224

Ther Adv Med Oncol. 2024 Feb 28;16:17588359241229433. doi: 10.1177/17588359241229433. eCollection 2024.

ABSTRACT

BACKGROUND: Currently, there is no recommended standard third-line chemotherapy for metastatic gastric cancer.

OBJECTIVES: In this study, we aimed to evaluate irinotecan’s efficacy and safety in treating metastatic gastric cancer after the failure of first- and second-line chemotherapy.

DESIGN: Prospective single-arm, two-center, phase II trial.

METHODS: Patients were aged 18-70 years, with histologically confirmed gastric adenocarcinoma and an Eastern Cooperative Oncology Group performance status of 0-1, progressed during or within 3 months following the last administration of second-line chemotherapy and had no other severe hematologic, cardiac, pulmonary, hepatic, or renal functional abnormalities or immunodeficiency diseases. Eligible patients received 28-day cycles of irinotecan (180 mg/m² intravenously, days 1 and 15) and were assessed according to the RECIST 1.1 criteria every two cycles. Patients who discontinued treatment for any reason were followed up every 2 months until death. The primary endpoint was overall survival (OS), and the secondary endpoints were progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and toxicity.

RESULTS: A total of 98 eligible patients were enrolled in this study. In the intention-to-treat population, the median OS was 7.17 months, the median PFS was 3.47 months, and the ORR and DCR were 4.08% and 47.96%, respectively. In the per-protocol population, the median OS was 7.77 months, the median PFS was 3.47 months, and the ORR and DCR were 4.82% and 50.60%, respectively. The incidence of grade 3 or 4 hematological and non-hematological toxicities was 19.4%, and none of the patients died owing to adverse events. Cox regression analysis revealed neutropenia and baseline thrombocyte levels were independently correlated with PFS and OS.

CONCLUSION: Irinotecan monotherapy is an efficient, well-tolerated, and economical third-line treatment for patients with metastatic gastric cancer as a third-line treatment.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT02662959.

PMID:38425987 | PMC:PMC10903192 | DOI:10.1177/17588359241229433

Clin Immunol. 2024 Feb 27:110165. doi: 10.1016/j.clim.2024.110165. Online ahead of print.

ABSTRACT

Mutations in NFkB pathway genes can cause inborn errors of immunity (IEI), with NFKB1 haploinsufficiency being a significant etiology for common variable immunodeficiency (CVID). Indeed, mutations in NFKB1 are found in 4 to 5% of in European and United States CVID cohorts, respectively; CVID representing almost ¼ of IEI patients in European countries registries. This case study presents a 49-year-old patient with respiratory infections, chronic diarrhea, immune thrombocytopenia, hypogammaglobulinemia, and secondary lymphoma. Comprehensive genetic analysis, including high-throughput sequencing of 300 IEI-related genes and copy number variation analysis, identified a critical 2.7-kb deletion spanning the first untranslated exon and its upstream region. The region’s importance was confirmed through genetic markers indicative of enhancers and promoters. The deletion was also found in the patient’s brother, who displayed similar but milder symptoms. Functional analysis supported haploinsufficiency with reduced mRNA and protein expression in both patients. This case underscores the significance of copy number variation (CNV) analysis and targeting noncoding exons within custom gene panels, emphasizing the broader genomic approaches needed in medical genetics.

PMID:38423196 | DOI:10.1016/j.clim.2024.110165

Mol Ther Methods Clin Dev. 2024 Feb 6;32(1):101208. doi: 10.1016/j.omtm.2024.101208. eCollection 2024 Mar 14.

ABSTRACT

Wiskott-Aldrich syndrome (WAS) is a severe X-linked primary immunodeficiency resulting from a diversity of mutations distributed across all 12 exons of the WAS gene. WAS encodes a hematopoietic-specific and developmentally regulated cytoplasmic protein (WASp). The objective of this study was to develop a gene correction strategy potentially applicable to most WAS patients by employing nuclease-mediated, site-specific integration of a corrective WAS gene sequence into the endogenous WAS chromosomal locus. In this study, we demonstrate the ability to target the integration of WAS_2-12-containing constructs into intron 1 of the endogenous WAS gene of primary CD34⁺ hematopoietic stem and progenitor cells (HSPCs), as well as WASp-deficient B cell lines and WASp-deficient primary T cells. This intron 1 targeted integration (TI) approach proved to be quite efficient and restored WASp expression in treated cells. Furthermore, TI restored WASp-dependent function to WAS patient T cells. Edited CD34⁺ HSPCs exhibited the capacity for multipotent differentiation to various hematopoietic lineages in vitro and in transplanted immunodeficient mice. This methodology offers a potential editing approach for treatment of WAS using patient’s CD34⁺ cells.

PMID:38414825 | PMC:PMC10897892 | DOI:10.1016/j.omtm.2024.101208

J Clin Immunol. 2024 Feb 27;44(3):71. doi: 10.1007/s10875-024-01671-3.

ABSTRACT

PURPOSE: Primary immunodeficiency disorder (PID) is a heterogeneous group of diseases characterized by immune dysregulation and increased susceptibility to infections, with various cognitive, emotional, behavioral, and social effects on patients. This study aimed to evaluate loneliness, social adaptation, anxiety, and depression and to identify associated factors in adults with immunodeficiency.

METHODS: A cross-sectional study in Turkey (Feb-Aug 2022) obtained sociodemographic data from patient records. The Social Adaptation Self-Evaluation Scale (SASS), UCLA-Loneliness Scale (UCLA-LS), and Hospital Anxiety and Depression Scale (HADS) were administered in individual patient interviews. HADS-Anxiety (HADS-A) and HADS-Depression (HADS-D) scores were assessed using cut-offs of 10 and 7, respectively; SASS cut-offs for social imbalance and normalcy were < 25 and > 35, respectively.

RESULTS: A total of 104 patients (60 women, 44 men) with a median age of 34 years (range: 18-89) were included in the study. Mean scores were SASS: 34.46 ± 8.11, UCLA-LS: 44.89 ± 12.66, HADS-A: 9.87 ± 4.77, and HADS-D: 9.12 ± 4.80. SASS score was negatively correlated with HADS-A, HADS-D, and UCLA-LS scores. There were positive correlations between UCLA-LS and HADS-A (r = -0.355, p < 0.01) and HADS-D (r = -0.614, p < 0.01) and between HADS-A and HADS-D (r = -0.454, p < 0.01). Low-income level was associated with higher HADS-A, HADS-D, and UCLA-LS scores and lower SASS score (p = 0.012, p = 0.041, p = 0.008, and p = 0.001, respectively).

CONCLUSION: Adults with PID are at risk for depression and experience high levels of loneliness. Social maladjustment and loneliness contribute to anxiety and depression, and loneliness is correlated with impaired social functioning. These findings emphasize the importance of biopsychosocial evaluation of individuals diagnosed with PID.

PMID:38411715 | DOI:10.1007/s10875-024-01671-3

Biomolecules. 2024 Feb 2;14(2):180. doi: 10.3390/biom14020180.

ABSTRACT

Severe combined immunodeficient (SCID) mice serve as a critical model for human xenotransplantation studies, yet they often suffer from low engraftment rates and susceptibility to graft-versus-host disease (GVHD). Moreover, certain SCID strains demonstrate ‘immune leakage’, underscoring the need for novel model development. Here, we introduce an SCID mouse model with a targeted disruption of the dclre1c gene, encoding Artemis, which is essential for V(D)J recombination and DNA repair during T cell receptor (TCR) and B cell receptor (BCR) assembly. Artemis deficiency precipitates a profound immunodeficiency syndrome, marked by radiosensitivity and compromised T and B lymphocyte functionality. Utilizing CRISPR/Cas9-mediated gene editing, we generated dclre1c-deficient mice with an NOD genetic background. These mice exhibited a radiosensitive SCID phenotype, with pronounced DNA damage and defective thymic, splenic and lymph node development, culminating in reduced T and B lymphocyte populations. Notably, both cell lines and patient-derived tumor xenografts were successfully engrafted into these mice. Furthermore, the human immune system was effectively rebuilt following peripheral blood mononuclear cells (PBMCs) transplantation. The dclre1c-knockout NOD mice described herein represent a promising addition to the armamentarium of models for xenotransplantation, offering a valuable platform for advancing human immunobiological research.

PMID:38397417 | PMC:PMC10887050 | DOI:10.3390/biom14020180

Intractable Rare Dis Res. 2024 Feb;13(1):69-72. doi: 10.5582/irdr.2023.01102.

ABSTRACT

Wiskott-Aldrich syndrome (WAS) is a rare X-linked recessive primary immunodeficiency disorder. Mutations in the WAS gene are considered to be the primary cause of WAS. In this work, we report a boy who presented with intracranial hemorrhage (ICH) as an initial symptom and detects a novel pathogenic synonymous mutation in his WAS gene. His mother was a carrier of the mutant gene. The mutation, located at position c.273 (c.273 G>A) in exon 2, is a synonym mutation and predicted to affect protein expression by disrupting gene splicing. This study summarizes the diagnosis and treatment process of the patient and expands the genetic spectrum of WAS.

PMID:38404734 | PMC:PMC10883844 | DOI:10.5582/irdr.2023.01102

Diagnostics (Basel). 2024 Feb 14;14(4):420. doi: 10.3390/diagnostics14040420.

ABSTRACT

Flow cytometry is a vital diagnostic tool for hematologic and immunologic disorders, but manual analysis is prone to variation and time-consuming. Over the last decade, artificial intelligence (AI) has advanced significantly. In this study, we developed and validated an AI-assisted flow cytometry workflow using 379 clinical cases from 2021, employing a 3-tube, 10-color flow panel with 21 antibodies for primary immunodeficiency diseases and related immunological disorders. The AI software (DeepFlow™, version 2.1.1) is fully automated, reducing analysis time to under 5 min per case. It interacts with hematopatholoists for manual gating adjustments when necessary. Using proprietary multidimensional density-phenotype coupling algorithm, the AI model accurately classifies and enumerates T, B, and NK cells, along with important immune cell subsets, including CD4+ helper T cells, CD8+ cytotoxic T cells, CD3+/CD4-/CD8- double-negative T cells, and class-switched or non-switched B cells. Compared to manual analysis with hematopathologist-determined lymphocyte subset percentages as the gold standard, the AI model exhibited a strong correlation (r > 0.9) across lymphocyte subsets. This study highlights the accuracy and efficiency of AI-assisted flow cytometry in diagnosing immunological disorders in a clinical setting, providing a transformative approach within a concise timeframe.

PMID:38396459 | DOI:10.3390/diagnostics14040420

Pathogens. 2024 Feb 1;13(2):136. doi: 10.3390/pathogens13020136.

ABSTRACT

Common variable immunodeficiency (CVID) is the most frequent form of primary hypogammaglobulinemia in adults. In addition to recurrent infections and respiratory manifestations, CVID patients may present several non-infection complications such as autoimmune diseases. The mechanisms that lead to immune dysregulation in CVID are not completely understood. Given the role of IgD on naïve B cells in the maintenance of tolerance and secreted IgD in the respiratory mucosa, we evaluated the frequency of IgD⁺ naïve and IgD⁺ memory B cells in CVID patients. Here, no differences were observed in the percentages and proliferative responses of anergic IgD⁺IgM^–CD27^– B cells between CVID patients, with or without autoimmune disease, and the control group. Interestingly, in the compartment of memory B cells, the percentage of IgD⁺IgM^– cells was higher only in CVID patients with allergic rhinitis/allergic asthma. Our results may indicate that anergic IgD⁺IgM^–CD27^– B cells may not be compromised in our CVID cohort. However, IgD⁺IgM^– memory B cells may play a role in the immunopathogenesis of allergic rhinitis/allergic asthma in CVID patients. Further studies are needed to better understand the participation of IgD⁺IgM^– memory B cells in the immunopathogenesis of allergic rhinitis/allergic asthma in CVID patients.

PMID:38392874 | DOI:10.3390/pathogens13020136

Eur J Med Genet. 2024 Feb 19:104927. doi: 10.1016/j.ejmg.2024.104927. Online ahead of print.

ABSTRACT

BACKGROUND: Alpha mannosidosis is an autosomal recessive lysosomal storage disorder caused by biallelic pathogenic variants in the MAN2B1 gene. It manifests with clinical features, including intellectual disability, hearing impairment, coarse facial appearance, skeletal anomalies, immunodeficiency, central nervous system involvement, psychiatric comorbidities, corneal opacity, and hepatosplenomegaly. This multicenter study assesses the long-term outcomes of individuals diagnosed with alpha-mannosidosis, examining demographic, clinical, laboratory, and molecular characteristics.

METHOD: Sixteen patients diagnosed with alpha-mannosidosis who presented to four pediatric metabolic units were included in the study. The patients’ medical records were analyzed and data on demographics, clinical presentation and laboratory findings were recorded.

RESULTS: Of the 16 patients (6 females, 10 males) with alpha mannosidosis included in the study, the mean age at the time of diagnosis was 79.4 ± 56.1 (16-208) months, and the mean diagnosis delay time was 57.9 ± 51.9 (4-181) months. Hearing loss was the primary manifestation found in seven out of 16 patients (43.8%), followed by speech delay in 37.8%. On clinical follow-up, 87.5% of patients experienced recurrent infections, mainly in the upper respiratory tract, with 12 requiring the use of a hearing aid. Hepatomegaly was found in six out of 13 patients who received abdominal ultrasonography; two out of 12 patients who underwent echocardiography were found to have mitral valve prolapse (16.6%). Upon neurological evaluation, five patients displayed no neurological manifestation. Delayed language development was observed in nine (56.3%) patients, intellectual disability in eight (50%) patients, and hypertonicity was identified in one (6.3%) patient with the severe form of the disease. Homozygous c.2477C>A (p.Ser826Ter) and homozygous c.967G>A (p.Glu323Lys) novel variants were detected in four patients and one patient, respectively. The most common variant observed in the study was c.2477C>A (p.Ser826Ter).

CONCLUSION: The present study identified two novel MAN2B1 variants. An evaluation of the long-term outcome of alpha-mannosidosis, in which the early initiation of enzyme replacement therapy (ERT) may lead to a better clinical outcome, can permit a better analysis of the effect of ERT on the natural progression of the disease.

PMID:38382588 | DOI:10.1016/j.ejmg.2024.104927