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del Pino-Molina L, Bravo Gallego LY, Soto Serrano Y, Reche Yebra K, Marty Lobo J, González Martínez B, Bravo García-Morato M, Rodríguez Pena R, van der Burg M, López Granados E. Research-based flow cytometry assays for pathogenic assessment in the human B-cell biology of gene variants revealed in the diagnosis of inborn errors of immunity: a Bruton's tyrosine kinase case-study. Front Immunol 2023; 14:1095123. [PMID: 37197664 PMCID: PMC10183671 DOI: 10.3389/fimmu.2023.1095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
Introduction Inborn errors of immunity (IEI) are an expanding group of rare diseases whose field has been boosted by next-generation sequencing (NGS), revealing several new entities, accelerating routine diagnoses, expanding the number of atypical presentations and generating uncertainties regarding the pathogenic relevance of several novel variants. Methods Research laboratories that diagnose and provide support for IEI require accurate, reproducible and sustainable phenotypic, cellular and molecular functional assays to explore the pathogenic consequences of human leukocyte gene variants and contribute to their assessment. We have implemented a set of advanced flow cytometry-based assays to better dissect human B-cell biology in a translational research laboratory. We illustrate the utility of these techniques for the in-depth characterization of a novel (c.1685G>A, p.R562Q) de novo gene variant predicted as probably pathogenic but with no previous insights into the protein and cellular effects, located in the tyrosine kinase domain of the Bruton's tyrosine kinase (BTK) gene, in an apparently healthy 14-year-old male patient referred to our clinic for an incidental finding of low immunoglobulin (Ig) M levels with no history of recurrent infections. Results and discussion A phenotypic analysis of bone marrow (BM) revealed a slightly high percentage of pre-B-I subset in BM, with no blockage at this stage, as typically observed in classical X-linked agammaglobulinemia (XLA) patients. The phenotypic analysis in peripheral blood also revealed reduced absolute numbers of B cells, all pre-germinal center maturation stages, together with reduced but detectable numbers of different memory and plasma cell isotypes. The R562Q variant allows Btk expression and normal activation of anti-IgM-induced phosphorylation of Y551 but diminished autophosphorylation at Y223 after anti IgM and CXCL12 stimulation. Lastly, we explored the potential impact of the variant protein for downstream Btk signaling in B cells. Within the canonical nuclear factor kappa B (NF-κB) activation pathway, normal IκBα degradation occurs after CD40L stimulation in patient and control cells. In contrast, disturbed IκBα degradation and reduced calcium ion (Ca2+) influx occurs on anti-IgM stimulation in the patient's B cells, suggesting an enzymatic impairment of the mutated tyrosine kinase domain.
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Affiliation(s)
- L. del Pino-Molina
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III (ISCII)I (CIBERER), Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- *Correspondence: L. del Pino-Molina, ; E. López Granados,
| | - L. Y. Bravo Gallego
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III (ISCII)I (CIBERER), Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Y. Soto Serrano
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - K. Reche Yebra
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - J. Marty Lobo
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - B. González Martínez
- Pediatric Hemato-Oncology Unit, La Paz University Hospital Madrid, Madrid, Spain
| | - M. Bravo García-Morato
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III (ISCII)I (CIBERER), Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Clinical Immunology Department, La Paz University Hospital Madrid, Madrid, Spain
| | - R. Rodríguez Pena
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III (ISCII)I (CIBERER), Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Clinical Immunology Department, La Paz University Hospital Madrid, Madrid, Spain
| | - M. van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children’s Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - E. López Granados
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III (ISCII)I (CIBERER), Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
- Clinical Immunology Department, La Paz University Hospital Madrid, Madrid, Spain
- *Correspondence: L. del Pino-Molina, ; E. López Granados,
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Abstract
BACKGROUND Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DNA, RNA and protein levels. RESULTS VariO use and terms for DNA variations are described in depth. VariO provides systematic names for variation types and detailed descriptions for changes in DNA function, structure and properties. The principles of VariO are presented along with examples from published articles or databases, most often in relation to human diseases. VariO terms describe local DNA changes, chromosome number and structure variants, chromatin alterations, as well as genomic changes, whether of genetic or non-genetic origin. CONCLUSIONS DNA variation systematics facilitates unambiguous descriptions of variations and their effects and further reuse and integration of data from different sources by both human and computers.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184, Lund, Sweden.
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