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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] [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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Carrillo-Tapia E, Espinosa-Padilla SE, Perez-Perez D, Gonzalez-Serrano ME, Berron-Ruiz L, Espinosa-Rosales FJ, Rodriguez-Alba JC, Mújica-Guzman F, Yokoyama-Rebollar E, García-Flores JR, Herrera-González NE, Scheffler-Mendoza S, Yamazaki-Nakashimada MA, Staines-Boone AT, Lopez-Herrera G. Improved HUMARA for the Detection of X-Linked Agammaglobulinemia Carriers. Genet Test Mol Biomarkers 2022; 26:220-227. [PMID: 35394812 DOI: 10.1089/gtmb.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Fragment analysis of exon 1 of the human androgen receptor, known as HUMARA, is a polymerase chain reaction (PCR)-based method for detecting X-linked agammaglobulinemia (XLA) carriers. This method takes advantage of X-chromosome inactivation (XCI) in female cells. XLA is caused by mutations in the Bruton tyrosine kinase (BTK) gene, located in Xq22.1. In this study, XCI is nonrandom or skewed in B cells. B cells with an active X-chromosome carrying a BTK mutation do not mature. Peripheral B cells in XLA carriers inactivate the mutated X-chromosome. Methods: HUMARA was performed using DNA from purified B cells and total leukocytes. DNA was digested using methylation-sensitive HhaI. The PCR of the HUMARA polymorphic marker was performed with the HhaI digested samples. The lengths of the PCR product were determined. If a suspected carrier showed skewed XCI in B cells, the marker length that corresponded with the length determined in the index patient indicated their carrier status. Results: HUMARA was conducted on purified B cells; this allowed easier identification of the mutated or inactive allele, as the active allele was enzymatically digested. Analysis of 30 possible carriers using modified HUMARA corroborated that the carrier status in all samples that were heterozygous for the marker using XCI calculation for leukocytes showed a Gaussian distribution, while the carrier B cell DNA showed a skewed XCI. Conclusion: Carrier status was successfully determined for most of the analyzed samples. B cell enrichment resulted in precise carrier determination data, reduced the sample size, and facilitated inactive and active allele identification.
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Affiliation(s)
| | - Sara E Espinosa-Padilla
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Daniela Perez-Perez
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Ciudad de México, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Laura Berron-Ruiz
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Ciudad de México, México
| | | | | | - Fabiola Mújica-Guzman
- Laboratorio de Hematología, Instituto Nacional de Pediatría, Ciudad de México, México
| | | | - Jose R García-Flores
- Posgrado en Ciencias de la Salud, Escuela Superior de Medicina, Ciudad de México, México
| | | | | | | | | | - Gabriela Lopez-Herrera
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Ciudad de México, México
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Zhou Q, Teng Y, Pan J, Shi Q, Liu Y, Liang D, Li Z, Wu L. Identification of four novel mutations in BTK from six Chinese families with X-linked agammaglobulinemia. Clin Chim Acta 2022; 531:48-55. [PMID: 35245483 DOI: 10.1016/j.cca.2022.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND The defect of Bruton's tyrosine kinase (BTK) gene resulted in X-linked agammaglobulinemia (XLA), which is characterized by recurrent bacterial infections, immunodeficiency with low B-cell numbers and immunoglobulin. Diagnosis of XLA depends on clinical phenotype and genetic testing. METHODS Six unrelated Chinese families with high suspicion of XLA were enrolled in this study. Potential pathogenic variants were detected and validated by Whole Exome Sequencing (WES) and Sanger Sequencing. Western blot, Quantitative PCR (qPCR) analysis and immunofluorescence analysis were used to evaluate the preliminary function of candidate BTK variants. RESULTS A total of six variants were identified, four of which were not reported before. The novel missense mutation(c.1900T>G) and deletion(c.897delG) were found that the mutant protein and mRNA expression levels have fallen by Western Blot and qPCR identification. We also constructed minigene expression vector to determine the deletion (c.1751-6_1755delttctagGGGTT) resulting a 35bp skipping in exon 18. Meanwhile, the break point of gross deletion (Exon2-5) discovered based on WES was confirmed to be located at site ChX:101367539_101376531 through qPCR and Gap-PCR. CONCLUSION This study makes definitive diagnosis for 6 families with suspected XLA and further expands the spectrum of BTK mutations, providing new information for the diagnosis of the disease.
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Affiliation(s)
- Qimin Zhou
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Yanling Teng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Jianyan Pan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Qingxin Shi
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Yingdi Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China; Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China; Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.
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Qiu S, Liu Y, Li Q. A mechanism for localized dynamics-driven activation in Bruton's tyrosine kinase. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210066. [PMID: 34457331 PMCID: PMC8371364 DOI: 10.1098/rsos.210066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/19/2021] [Indexed: 05/28/2023]
Abstract
Bruton's tyrosine kinase (BTK) plays a vital role in mature B-cell proliferation, development and function. Its inhibitors have gradually been applied for the treatment of many B-cell malignancies. However, because of treatment-associated drug resistance or low efficacy, it is urgent to develop new inhibitors and/or improve the efficacy of current inhibitors, where finding the intrinsic activation mechanism becomes the key to solve this problem. Here, we used BTK T474M mutation as a resistance model for inhibitors to study the mechanism of BTK activation and drug resistance by free molecular dynamics simulations. The results showed that the increase of kinase activity of T474M mutation is coming from the conformation change of the activation ring and ATP binding sites located in BTK N-terminus region. Specifically, the Thr474 mutation changed the structure of A-loop and stabilized the binding site of ATP, thus promoting the catalytic ability in the kinase domain. This localized dynamics-driven activation mechanism and resistance mechanism of BTK may provide new ideas for drug development in B-cell malignancies.
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Affiliation(s)
- Simei Qiu
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou People's Republic of China
| | - Yunfeng Liu
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
| | - Quhuan Li
- Institute of Biomechanics/School of Bioscience and Bioengineering, South China University of Technology, Guangzhou People's Republic of China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou People's Republic of China
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5
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Vihinen M. Functional effects of protein variants. Biochimie 2020; 180:104-120. [PMID: 33164889 DOI: 10.1016/j.biochi.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Genetic and other variations frequently affect protein functions. Scientific articles can contain confusing descriptions about which function or property is affected, and in many cases the statements are pure speculation without any experimental evidence. To clarify functional effects of protein variations of genetic or non-genetic origin, a systematic conceptualisation and framework are introduced. This framework describes protein functional effects on abundance, activity, specificity and affinity, along with countermeasures, which allow cells, tissues and organisms to tolerate, avoid, repair, attenuate or resist (TARAR) the effects. Effects on abundance discussed include gene dosage, restricted expression, mis-localisation and degradation. Enzymopathies, effects on kinetics, allostery and regulation of protein activity are subtopics for the effects of variants on activity. Variation outcomes on specificity and affinity comprise promiscuity, specificity, affinity and moonlighting. TARAR mechanisms redress variations with active and passive processes including chaperones, redundancy, robustness, canalisation and metabolic and signalling rewiring. A framework for pragmatic protein function analysis and presentation is introduced. All of the mechanisms and effects are described along with representative examples, most often in relation to diseases. In addition, protein function is discussed from evolutionary point of view. Application of the presented framework facilitates unambiguous, detailed and specific description of functional effects and their systematic study.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184, Lund, Sweden.
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Abstract
Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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7
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Impact of amino acid substitution in the kinase domain of Bruton tyrosine kinase and its association with X-linked agammaglobulinemia. Int J Biol Macromol 2020; 164:2399-2408. [PMID: 32784026 DOI: 10.1016/j.ijbiomac.2020.08.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
X-linked agammaglobulinemia (XLA) is a rare disease that affects the immune system, characterized by a serial development of bacterial infection from the onset of infantile age. Bruton tyrosine kinase (BTK) is a non-receptor cytoplasmic kinase that plays a crucial role in the B-lymphocyte maturation. The altered expression, mutation and/or structural variations of BTK are responsible for causing XLA. Here, we have performed extensive sequence and structure analyses of BTK to find deleterious variations and their pathogenic association with XLA. First, we screened the pathogenic variations in the BTK from a pool of publicly available resources, and their pathogenicity/tolerance and stability predictions were carried out. Finally, two pathogenic variations (E589G and M630K) were studied in detail and subjected to all-atom molecular dynamics simulation for 200 ns. Intramolecular hydrogen bonds (H-bonds), secondary structure, and principal component analysis revealed significant conformational changes in variants that support the structural basis of BTK dysfunction in XLA. The free energy landscape analysis revealed the presence of multiple energy minima, suggests that E589G brings a large destabilization and consequently unfolding behavior compared to M630K. Overall, our study suggests that amino acid substitutions, E589G, and M630K, significantly alter the structural conformation and stability of BTK.
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Rafi SK, Fernández-Jaén A, Álvarez S, Nadeau OW, Butler MG. High Functioning Autism with Missense Mutations in Synaptotagmin-Like Protein 4 (SYTL4) and Transmembrane Protein 187 (TMEM187) Genes: SYTL4- Protein Modeling, Protein-Protein Interaction, Expression Profiling and MicroRNA Studies. Int J Mol Sci 2019; 20:ijms20133358. [PMID: 31323913 PMCID: PMC6651166 DOI: 10.3390/ijms20133358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
We describe a 7-year-old male with high functioning autism spectrum disorder (ASD) and maternally-inherited rare missense variant of Synaptotagmin-like protein 4 (SYTL4) gene (Xq22.1; c.835C>T; p.Arg279Cys) and an unknown missense variant of Transmembrane protein 187 (TMEM187) gene (Xq28; c.708G>T; p. Gln236His). Multiple in-silico predictions described in our study indicate a potentially damaging status for both X-linked genes. Analysis of predicted atomic threading models of the mutant and the native SYTL4 proteins suggest a potential structural change induced by the R279C variant which eliminates the stabilizing Arg279-Asp60 salt bridge in the N-terminal half of the SYTL4, affecting the functionality of the protein’s critical RAB-Binding Domain. In the European (Non-Finnish) population, the allele frequency for this variant is 0.00042. The SYTL4 gene is known to directly interact with several members of the RAB family of genes, such as, RAB27A, RAB27B, RAB8A, and RAB3A which are known autism spectrum disorder genes. The SYTL4 gene also directly interacts with three known autism genes: STX1A, SNAP25 and STXBP1. Through a literature-based analytical approach, we identified three of five (60%) autism-associated serum microRNAs (miRs) with high predictive power among the total of 298 mouse Sytl4 associated/predicted microRNA interactions. Five of 13 (38%) miRs were differentially expressed in serum from ASD individuals which were predicted to interact with the mouse equivalent Sytl4 gene. TMEM187 gene, like SYTL4, is a protein-coding gene that belongs to a group of genes which host microRNA genes in their introns or exons. The novel Q236H amino acid variant in the TMEM187 in our patient is near the terminal end region of the protein which is represented by multiple sequence alignments and hidden Markov models, preventing comparative structural analysis of the variant harboring region. Like SYTL4, the TMEM187 gene is expressed in the brain and interacts with four known ASD genes, namely, HCFC1; TMLHE; MECP2; and GPHN. TMM187 is in linkage with MECP2, which is a well-known determinant of brain structure and size and is a well-known autism gene. Other members of the TMEM gene family, TMEM132E and TMEM132D genes are associated with bipolar and panic disorders, respectively, while TMEM231 is a known syndromic autism gene. Together, TMEM187 and SYTL4 genes directly interact with recognized important ASD genes, and their mRNAs are found in extracellular vesicles in the nervous system and stimulate target cells to translate into active protein. Our evidence shows that both these genes should be considered as candidate genes for autism. Additional biological testing is warranted to further determine the pathogenicity of these gene variants in the causation of autism.
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Affiliation(s)
- Syed K Rafi
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | | | - Sara Álvarez
- Genomics and Medicine, NIM Genetics, 28108 Madrid, Spain
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Niroula A, Vihinen M. PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat 2017; 38:1085-1091. [PMID: 28224672 DOI: 10.1002/humu.23199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/25/2017] [Accepted: 02/17/2017] [Indexed: 01/14/2023]
Abstract
Computational tools are widely used for ranking and prioritizing variants for characterizing their disease relevance. Since numerous tools have been developed, they have to be properly assessed before being applied. Critical Assessment of Genome Interpretation (CAGI) experiments have significantly contributed toward the assessment of prediction methods for various tasks. Within and outside the CAGI, we have addressed several questions that facilitate development and assessment of variation interpretation tools. These areas include collection and distribution of benchmark datasets, their use for systematic large-scale method assessment, and the development of guidelines for reporting methods and their performance. For us, CAGI has provided a chance to experiment with new ideas, test the application areas of our methods, and network with other prediction method developers. In this article, we discuss our experiences and lessons learned from the various CAGI challenges. We describe our approaches, their performance, and impact of CAGI on our research. Finally, we discuss some of the possibilities that CAGI experiments have opened up and make some suggestions for future experiments.
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Affiliation(s)
- Abhishek Niroula
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mauno Vihinen
- Protein Structure and Bioinformatics Group, Department of Experimental Medical Science, Lund University, Lund, Sweden
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Chen XF, Wang WF, Zhang YD, Zhao W, Wu J, Chen TX. Clinical characteristics and genetic profiles of 174 patients with X-linked agammaglobulinemia: Report from Shanghai, China (2000-2015). Medicine (Baltimore) 2016; 95:e4544. [PMID: 27512878 PMCID: PMC4985333 DOI: 10.1097/md.0000000000004544] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
X-linked agammaglobulinemia (XLA) is a humoral primary immunodeficiency. XLA patients typically present with very low numbers of peripheral B cells and a profound deficiency of all immunoglobulin isotypes. Most XLA patients carry mutations in Bruton tyrosine kinase (BTK) gene.The genetic background and clinical features of 174 Chinese patients with XLA were investigated. The relationship between specific BTK gene mutations and severity of clinical manifestations was also examined. Mutations were graded from mild to severe based on structural and functional prediction through bioinformatics analysis.One hundred twenty-seven mutations were identified in 142 patients from 124 families, including 45 novel mutations and 82 recurrent mutations that were distributed over the entire BTK gene sequence. Variation in phenotypes was observed, and there was a tendency of association between genotype and age of disease onset.This report constitutes the largest group of patients with BTK mutations in China. A genotype-phenotype correlation was observed in this study. Early diagnosis of congenital agammaglobulinemia should be based on clinical symptoms, family history, and molecular analysis of the BTK gene.
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Affiliation(s)
- Xia-Fang Chen
- Department of Allergy and Immunology, Shanghai Children's Medical Center
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai
| | - Wei-Fan Wang
- Department of Allergy and Immunology, Shanghai Children's Medical Center
| | - Yi-Dan Zhang
- Department of Internal Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Wei Zhao
- Division of Allergy and Immunology, Department of Pediatrics, Virginia Commonwealth University, Richmond, VA
| | - Jing Wu
- Department of Allergy and Immunology, Shanghai Children's Medical Center
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai
| | - Tong-Xin Chen
- Department of Allergy and Immunology, Shanghai Children's Medical Center
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai
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Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant. Leukemia 2016; 31:177-185. [PMID: 27282255 PMCID: PMC5220130 DOI: 10.1038/leu.2016.153] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 01/01/2023]
Abstract
Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce, because two nucleotide changes are needed. (3) As BTK variants replaced with other residues are catalytically inactive, they presumably need compensatory mutations, therefore being very scarce. Glycine and tryptophan variants were not yet reported but likely also provide resistance.
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12
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Clinical and mutational features of X-linked agammaglobulinemia in Mexico. Clin Immunol 2016; 165:38-44. [PMID: 26960951 DOI: 10.1016/j.clim.2016.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/14/2015] [Accepted: 02/29/2016] [Indexed: 11/20/2022]
Abstract
X-linked agammaglobulinemia (XLA) is caused by BTK mutations, patients typically show <2% of peripheral B cells and reduced levels of all immunoglobulins; they suffer from recurrent infections of bacterial origin; however, viral infections, autoimmune-like diseases, and an increased risk of developing gastric cancer are also reported. In this work, we report the BTK mutations and clinical features of 12 patients diagnosed with XLA. Furthermore, a clinical revision is also presented for an additional cohort of previously reported patients with XLA. Four novel mutations were identified, one of these located in the previously reported mutation refractory SH3 domain. Clinical data support previous reports accounting for frequent respiratory, gastrointestinal tract infections and other symptoms such as the occurrence of reactive arthritis in 19.2% of the patients. An equal proportion of patients developed septic arthritis; missense mutations and mutations in SH1, SH2 and PH domains predominated in patients who developed arthritis.
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Teocchi MA, Domingues Ramalho V, Abramczuk BM, D'Souza-Li L, Santos Vilela MM. BTK mutations selectively regulate BTK expression and upregulate monocyte XBP1 mRNA in XLA patients. Immun Inflamm Dis 2015; 3:171-81. [PMID: 26417435 PMCID: PMC4578518 DOI: 10.1002/iid3.57] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 12/14/2022] Open
Abstract
Mutations in the Bruton agammaglobulinemia tyrosine kinase (BTK) gene are responsible for X-linked agammaglobulinemia (XLA). Unfolded or misfolded proteins can trigger stress pathways in the endoplasmic reticulum (ER), known as unfolded protein response (UPR). The aim was to clarify the involvement of UPR in XLA pathophysiology. By reverse transcription-quantitative PCR, we evaluated the expression of BTK and 12 UPR-related genes in eight patients. Moreover, we assessed the BTK protein expression and pattern in the patients' monocytes by flow cytometry and fluorescence immunocytochemistry. We found a reduced BTK expression in patients with stop codon mutations (P < 0.02). However, missense mutations did not affect BTK expression. Flow cytometry showed a reduction of BTK in patients which was corroborated by an absent or nonfunctional protein synthesis revealed by immunocytochemistry. In contrast with the other UPR-related genes, X-box binding protein 1 (XBP1) was markedly upregulated in the patients (P < 0.01), suggesting Toll-like receptor (TLR) activation since BTK directly interacts with TLRs as a negative regulator and XBP1 can be activated in direct response to TLR ligation. Different BTK mutations can be identified by the BTK expression. Inasmuch as UPR-related genes were downregulated or unaltered in patients, we speculate the involvement of the TLRs-XBP1 axis in the XLA pathophysiology. Such data could be the basis for further studies of this novel pathomechanism concerning XLA.
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Affiliation(s)
- Marcelo A Teocchi
- Center for Investigation in Pediatrics, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil
| | - Vanessa Domingues Ramalho
- Center for Investigation in Pediatrics, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil
| | - Beatriz M Abramczuk
- Center for Investigation in Pediatrics, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil
| | - Lília D'Souza-Li
- Center for Investigation in Pediatrics, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil ; Department of Pediatrics, Faculty of Medical Sciences, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil
| | - Maria Marluce Santos Vilela
- Center for Investigation in Pediatrics, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil ; Department of Pediatrics, Faculty of Medical Sciences, University of Campinas (UNICAMP) Campinas, São Paulo, Brazil
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Vihinen M. Types and effects of protein variations. Hum Genet 2015; 134:405-21. [DOI: 10.1007/s00439-015-1529-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/09/2015] [Indexed: 12/12/2022]
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Marron TU, Martinez-Gallo M, Yu JE, Cunningham-Rundles C. Toll-like receptor 4-, 7-, and 8-activated myeloid cells from patients with X-linked agammaglobulinemia produce enhanced inflammatory cytokines. J Allergy Clin Immunol 2011; 129:184-90.e1-4. [PMID: 22088613 DOI: 10.1016/j.jaci.2011.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 10/05/2011] [Accepted: 10/10/2011] [Indexed: 12/15/2022]
Abstract
BACKGROUND Bruton tyrosine kinase (BTK) is a component of signaling pathways downstream from Toll-like receptors (TLRs) 2, 4, 7, 8, and 9. Previous work in BTK-deficient mice, cell lines, and cultured cells from patients with X-linked agammaglobulinemia (XLA) suggested defective TLR-driven cytokine production. OBJECTIVE We sought to compare TLR-4-, TLR-7-, and TLR-8-induced cytokine production of primary cells from patients with XLA with that seen in control cells. METHODS PBMCs from patients with XLA, freshly isolated plasmacytoid dendritic cells, monocytes, and monocytoid dendritic cells were activated with TLR-4, TLR-7, and TLR-8 agonists. Signaling intermediates and intracellular and secreted cytokine levels were compared with those seen in control cells. RESULTS Although TLR-4, TLR-7, and TLR-8 activation of nuclear factor κB and mitogen-activated protein kinase pathways in cells from patients with XLA and control cells were comparable, TLR-activated freshly isolated monocytes and monocytoid dendritic cells from patients with XLA produced significantly more TNF-α, IL-6, and IL-10 than control cells. TLR-7/8-activated plasmacytoid dendritic cells produced normal amounts of IFN-α. In murine models BTK regulates the degradation of Toll-IL-1 receptor domain-containing adaptor protein, terminating TLR-4-induced cytokine production. Although this might explain the heightened TLR-4-driven cytokine production we observed, Toll-IL-1 receptor domain-containing adaptor protein degradation is intact in cells from patients with XLA, excluding this explanation. CONCLUSION In contrast to previous studies with BTK-deficient mice, cell lines, and cultured cells from patients with XLA suggesting impaired TLR-driven cytokine production, these data suggest that BTK inhibits TLR-induced cytokine production in primary human cells.
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Affiliation(s)
- Thomas U Marron
- Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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Ramalho VD, Oliveira Júnior EB, Tani SM, Roxo Júnior P, Vilela MMS. Mutations of Bruton's tyrosine kinase gene in Brazilian patients with X-linked agammaglobulinemia. Braz J Med Biol Res 2010; 43:910-3. [PMID: 20721470 DOI: 10.1590/s0100-879x2010007500079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 07/28/2010] [Indexed: 11/21/2022] Open
Abstract
Mutations in Bruton's tyrosine kinase (BTK) gene are responsible for X-linked agammaglobulinemia (XLA), which is characterized by recurrent bacterial infections, profound hypogammaglobulinemia, and decreased numbers of mature B cells in peripheral blood. We evaluated 5 male Brazilian patients, ranging from 3 to 10 years of age, from unrelated families, whose diagnosis was based on recurrent infections, markedly reduced levels of IgM, IgG and IgA, and circulating B cell numbers <2%. BTK gene analysis was carried out using PCR-SSCP followed by sequencing. We detected three novel (Ala347fsX55, I355T, and Thr324fsX24) and two previously reported mutations (Q196X and E441X). Flow cytometry revealed a reduced expression of BTK protein in patients and a mosaic pattern of BTK expression was obtained from mothers, indicating that they were XLA carriers.
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Affiliation(s)
- V D Ramalho
- Centro de Investigação em Pediatria, Departamento de Pediatria, Universidade Estadual de Campinas, SP, Brasil
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Mikels A, Minami Y, Nusse R. Ror2 receptor requires tyrosine kinase activity to mediate Wnt5A signaling. J Biol Chem 2009; 284:30167-76. [PMID: 19720827 PMCID: PMC2781572 DOI: 10.1074/jbc.m109.041715] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Wnts include a large family of secreted proteins that serve as important signals during embryonic development and adult homeostasis. In the most well understood Wnt signaling pathway, Wnt binding to Frizzled and low density lipoprotein receptor-related protein induces β-catenin protein stabilization and entry into the nucleus, resulting in changes in target gene transcription. Emerging evidence suggests that Wnt5a can inhibit Wnt/β-catenin signaling through interaction with the receptor Ror2. The Ror2 protein belongs to the receptor tyrosine kinase superfamily and contains several recognizable structural motifs. However, limited information is available regarding which specific domains are required for the inhibitory signaling activity of Wnt5a. Through mutation and deletion analysis, we have analyzed which specific domains and residues, including those necessary for tyrosine kinase activity, mediate the Wnt5a signal. To determine whether Ror2 can inhibit canonical Wnt signaling in vivo, we examined the effect of Ror2 loss on the expression of the Wnt reporter Axin2LacZ, finding increased reporter activity in Ror2 null mice, demonstrating that Ror2 can also inhibit Wnt/β-catenin signaling in the context of intact tissues.
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Affiliation(s)
- Amanda Mikels
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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Thusberg J, Vihinen M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 2009; 30:703-14. [PMID: 19267389 DOI: 10.1002/humu.20938] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many gene defects are relatively easy to identify experimentally, but obtaining information about the effects of sequence variations and elucidation of the detailed molecular mechanisms of genetic diseases will be among the next major efforts in mutation research. Amino acid substitutions may have diverse effects on protein structure and function; thus, a detailed analysis of the mutations is essential. Experimental study of the molecular effects of mutations is laborious, whereas useful and reliable information about the effects of amino acid substitutions can readily be obtained by theoretical methods. Experimentally defined structures and molecular modeling can be used as a basis for interpretation of the mutations. The effects of missense mutations can be analyzed even when the 3D structure of the protein has not been determined, although structure-based analyses are more reliable. Structural analyses include studies of the contacts between residues, their implication for the stability of the protein, and the effects of the introduced residues. Investigations of steric and stereochemical consequences of substitutions provide insights on the molecular fit of the introduced residue. Mutations that change the electrostatic surface potential of a protein have wide-ranging effects. Analyses of the effects of mutations on interactions with ligands and partners have been performed for elucidation of functional mutations. We have employed numerous methods for predicting the effects of amino acid substitutions. We discuss the applicability of these methods in the analysis of genes, proteins, and diseases to reveal protein structure-function relationships, which is essential to gain insights into disease genotype-phenotype correlations.
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Affiliation(s)
- Janita Thusberg
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
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Mohamed AJ, Yu L, Bäckesjö CM, Vargas L, Faryal R, Aints A, Christensson B, Berglöf A, Vihinen M, Nore BF, Smith CIE. Bruton's tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain. Immunol Rev 2009; 228:58-73. [PMID: 19290921 DOI: 10.1111/j.1600-065x.2008.00741.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bruton's agammaglobulinemia tyrosine kinase (Btk) is a cytoplasmic tyrosine kinase important in B-lymphocyte development, differentiation, and signaling. Btk is a member of the Tec family of kinases. Mutations in the Btk gene lead to X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency (Xid) in mice. Activation of Btk triggers a cascade of signaling events that culminates in the generation of calcium mobilization and fluxes, cytoskeletal rearrangements, and transcriptional regulation involving nuclear factor-kappaB (NF-kappaB) and nuclear factor of activated T cells (NFAT). In B cells, NF-kappaB was shown to bind to the Btk promoter and induce transcription, whereas the B-cell receptor-dependent NF-kappaB signaling pathway requires functional Btk. Moreover, Btk activation is tightly regulated by a plethora of other signaling proteins including protein kinase C (PKC), Sab/SH3BP5, and caveolin-1. For example, the prolyl isomerase Pin1 negatively regulates Btk by decreasing tyrosine phosphorylation and steady state levels of Btk. It is intriguing that PKC and Pin1, both of which are negative regulators, bind to the pleckstrin homology domain of Btk. To this end, we describe here novel mutations in the pleckstrin homology domain investigated for their transforming capacity. In particular, we show that the mutant D43R behaves similar to E41K, already known to possess such activity.
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Affiliation(s)
- Abdalla J Mohamed
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Huddinge University Hospital, Huddinge, Sweden
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Phylogeny of Tec Family Kinases: Identification of a Premetazoan Origin of Btk, Bmx, Itk, Tec, Txk, and the Btk Regulator SH3BP5. ADVANCES IN GENETICS 2008; 64:51-80. [DOI: 10.1016/s0065-2660(08)00803-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Khan S, Vihinen M. Spectrum of disease-causing mutations in protein secondary structures. BMC STRUCTURAL BIOLOGY 2007; 7:56. [PMID: 17727703 PMCID: PMC1995201 DOI: 10.1186/1472-6807-7-56] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Accepted: 08/29/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND Most genetic disorders are linked to missense mutations as even minor changes in the size or properties of an amino acid can alter or prevent the function of the protein. Further, the effect of a mutation is also dependent on the sequence and structure context of the alteration. RESULTS We investigated the spectrum of disease-causing missense mutations in secondary structure elements in proteins with numerous known mutations and for which an experimentally defined three-dimensional structure is available. We obtained a comprehensive map of the differences in mutation frequencies, location and contact energies, and the changes in residue volume and charge - both in the mutated (original) amino acids and in the mutant amino acids in the different secondary structure types. We collected information for 44 different proteins involved in a large number of diseases. The studied proteins contained a total of 2413 mutations of which 1935 (80%) appeared in secondary structures. Differences in mutation patterns between secondary structures and whole proteins were generally not statistically significant whereas within the secondary structural elements numerous highly significant features were observed. CONCLUSION Numerous trends in mutated and mutant amino acids are apparent. Among the original residues, arginine clearly has the highest relative mutability. The overall relative mutability among mutant residues is highest for cysteine and tryptophan. The mutability values are higher for mutated residues than for mutant residues. Arginine and glycine are among the most mutated residues in all secondary structures whereas the other amino acids have large variations in mutability between structure types. Statistical analysis was used to reveal trends in different secondary structural elements, residue types as well as for the charge and volume changes.
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Affiliation(s)
- Sofia Khan
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
| | - Mauno Vihinen
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
- Research Unit, Tampere University Hospital, FI-33520 Tampere, Finland
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23
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Thusberg J, Vihinen M. The structural basis of hyper IgM deficiency – CD40L mutations. Protein Eng Des Sel 2007; 20:133-41. [PMID: 17307885 DOI: 10.1093/protein/gzm004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
X-linked hyper-IgM syndrome (XHIGM) is a primary immunodeficiency characterised by an inability to produce immunoglobulins of the IgG, IgA and IgE isotypes. It is caused by mutations of CD40 ligand (CD40L, CD154), expressed on T-lymphocytes. The interaction of CD40L on T-cells and its receptor CD40 on B-cells is essential for lymphocyte signalling leading to immunoglobulin class switching and B-cell maturation. To understand the structural basis for XHIGM, we utilised bioinformatics methods to analyse all the known CD40L missense mutations at both the sequence and structural level. Our results demonstrate that the 35 different missense mutations have diverse effects on CD40L structure and function, affecting structural disorder and aggregation tendencies, stability maintaining contacts and electrostatic properties. Several mutations also affect residues essential in receptor binding and trimerisation. Experimental study of effects of mutations is laborious and time-consuming and at the structural level often almost impossible. By contrast, precise and useful information about effects of mutations on protein structure and function can readily be obtained by theoretical methods. In this study, all the XHIGM causing missense mutations could be explained in terms of CD40L structure and function. Thus, the molecular basis of the syndrome could be elucidated.
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Affiliation(s)
- J Thusberg
- Institute of Medical Technology, FI-33014, University of Tampere, Finland
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24
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Thusberg J, Vihinen M. Bioinformatic analysis of protein structure-function relationships: case study of leukocyte elastase (ELA2) missense mutations. Hum Mutat 2006; 27:1230-43. [PMID: 16986121 DOI: 10.1002/humu.20407] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyclic and congenital neutropenia are caused by mutations in the human neutrophil elastase (HNE) gene (ELA2), leading to an immunodeficiency characterized by decreased or oscillating levels of neutrophils in the blood. The HNE mutations presumably cause loss of enzyme activity, consequently leading to compromised immune system function. To understand the structural basis for the disease, we implemented methods from bioinformatics to analyze all the known HNE missense mutations at both the sequence and structural level. Our results demonstrate that the 32 different mutations have diverse effects on HNE structure and function, affecting structural disorder and aggregation tendencies, stability maintaining contacts, and electrostatic properties. A large proportion of the mutations are located at conserved amino acids, which are usually essential in determining protein structure and function. The majority of the disease-causing HNE missense mutations lead to major structural changes and loss of stability in the protein. A few mutations also affect functional residues, leading into decreased catalytic activity or altered ligand binding. Our analysis reveals the putative effects of all known missense mutations in HNE, thus allowing the structural basis of cyclic and congenital neutropenia to be elucidated. We have employed and analyzed a set of some 30 different methods for predicting the effects of amino acid substitutions. We present results and experience from the analysis of the applicability of these methods in the analysis of numerous genes, proteins, and diseases to reveal protein structure-function relationships and disease genotype-phenotype correlations.
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Affiliation(s)
- Janita Thusberg
- Institute of Medical Technology, University of Tampere, Finland
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Abstract
Primary immunodeficiencies (IDs) are a heterogenic group of inherited disorders of the immune system. Immunodeficiency patients have increased susceptibility to recurrent and persistent, even life-threatening infections. Mutations in a large number of genes can cause defects in different cellular functions and lead to impaired immune response. To date, approximately 150 IDs and more than 100 affected genes have been identified. ID-related genes are distributed throughout the genome, and diseases can be inherited in an X-linked, an autosomal recessive, or an autosomal dominant way. We have collected ID mutation data into locus-specific patient-related mutation databases, IDbases (http://bioinf.uta.fi/IDbases). Mutations are described at DNA, mRNA, and protein levels with links to reference sequences and reference articles. The mutation data has been collated into entries along with some clinical information. IDbases offer an easy way, e.g., to find recently identified mutations, to reveal genotype-phenotype correlations, and to discover a specific mutation or to examine the most common mutations in a single immunodeficiency related gene. At the moment we have databases for 107 ID genes with 4,140 public patient entries. An exhaustive statistical analysis of mutation data from the IDbases was made. Missense and nonsense mutations are the most common mutation types, and the most common single substitution is a nonsense mutation from tryptophan to a stop codon. Arginine is the most mutated as well as the most abundant mutant amino acid.
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Affiliation(s)
- Hilkka Piirilä
- Institute of Medical Technology, University of Tampere, Finland
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26
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Abstract
The restoration of catalytic activity to mutant enzymes by small molecules is well established for in vitro systems. Here, we show that the protein tyrosine kinase Src arginine-388-->alanine (R388A) mutant can be rescued in live cells with the use of the small molecule imidazole. Cellular rescue of a viral Src homolog was rapid and reversible and conferred predicted oncogenic properties. Using chemical rescue in combination with mass spectrometry, we confirmed six known Src kinase substrates and identified several new protein targets. Chemical rescue data suggest that cellular Src is active under basal conditions. Rescue of R388A cellular Src provided insights into the mitogen-activated protein kinase pathway. This chemical rescue approach will likely have many applications in cell signaling.
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Affiliation(s)
- Yingfeng Qiao
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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27
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Väliaho J, Smith CIE, Vihinen M. BTKbase: the mutation database for X-linked agammaglobulinemia. Hum Mutat 2006; 27:1209-17. [PMID: 16969761 DOI: 10.1002/humu.20410] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency caused by mutations in the gene encoding Bruton tyrosine kinase (BTK). XLA patients have a decreased number of mature B cells and a lack of all immunoglobulin isotypes, resulting in susceptibility to severe bacterial infections. XLA-causing mutations are collected in a mutation database (BTKbase), which is available at http://bioinf.uta.fi/BTKbase. For each patient the following information is given (when available): the identification of the entry, a plain English description of the mutation followed by a reference, formal characterization of the mutation, and the various parameters from the patient. BTKbase is implemented with the MUTbase program suite, which provides an easy, interactive, and quality controlled submission of information to mutation databases. BTKbase version 8 lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. The distribution of the mutations in the five structural domains is approximately proportional to the length of the domains, except for the Tec homology (TH) domain. The most frequently affected sites are CpG dinucleotides. The majority of the missense mutations are structural-disturbing Bruton tyrosine kinase (Btk) folding or decreasing stability. Many of the mutations affect functionally significant, conserved residues. The structural consequences of the mutations in all the domains have been studied based on crystallographic and nuclear magnetic resonance (NMR) structures as well as computer-aided molecular modeling.
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Affiliation(s)
- Jouni Väliaho
- Institute of Medical Technology, University of Tampere, Finland
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Afzal AR, Jeffery S. One gene, two phenotypes: ROR2 mutations in autosomal recessive Robinow syndrome and autosomal dominant brachydactyly type B. Hum Mutat 2003; 22:1-11. [PMID: 12815588 DOI: 10.1002/humu.10233] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autosomal recessive Robinow syndrome (RRS) is a severe skeletal dysplasia with short stature, generalized limb shortening, segmental defects of the spine, brachydactyly, and a dysmorphic facial appearance. The gene encoding receptor orphan receptor tyrosine kinase 2 (ROR2) is located on chromosome 9q22 and homozygous loss-of-function mutations in this gene are responsible for RRS. Moreover, knocking out the mouse Ror2 gene causes mesomelic dwarfism in the homozygous state, with almost identical features to recessive Robinow syndrome. The protein product of this gene is a cell membrane receptor, containing distinct motifs including an immunoglobulin-like (Ig) domain, a Frizzled-like cysteine-rich domain (FRZ or CRD), and a kringle domain (KD) in the extracellular region; and an intracellular region with tyrosine kinase (TK), serine/threonine-rich, and proline-rich structures. The extracellular motifs of the ROR2 protein are known to be involved in protein-protein interactions. The tyrosine kinase domain is involved in an as yet uncharacterized signaling pathway. Interestingly, heterozygous mutations in ROR2 have recently been shown to give rise to autosomal dominant brachydactyly type B1 (BDB1). This condition is characterized by terminal deficiency of fingers and toes. A variety of mutations have been reported in ROR2. Here, these genetic defects are compiled and possible genotype-phenotype correlations are discussed.
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Affiliation(s)
- Ali R Afzal
- Medical Genetics Unit, St George's Hospital Medical School, London, UK.
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Noordzij JG, de Bruin-Versteeg S, Hartwig NG, Weemaes CMR, Gerritsen EJA, Bernatowska E, van Lierde S, de Groot R, van Dongen JJM. XLA patients with BTK splice-site mutations produce low levels of wild-type BTK transcripts. J Clin Immunol 2002; 22:306-18. [PMID: 12405164 DOI: 10.1023/a:1019982206951] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
X-linked agammaglobulinemia is caused by mutations in the BTK gene, which result in a precursor B-cell differentiation arrest in the bone marrow and the absence of or strongly reduced B lymphocytes in blood. We identified a patient with a mild clinical phenotype, low numbers of B lymphocytes, and a splice-site mutation in the BTK gene. The precursor B-cell compartment in the bone marrow of this patient was almost identical to that in healthy children. Using real-time quantitative polymerase chain reaction, we were able to detect low levels of wild-type BTK transcripts in his granulocytes. Therefore, we speculated that wild-type BTK transcripts might be responsible for a milder clinical and immunological phenotype, as has been shown in several other diseases. Consequently, we quantified the expression of wild-type BTK transcripts in granulocytes of eight additional patients with splice-site mutations and compared their phenotypes with 17 patients with other types of BTK mutations. In these eight patients, the presence of low levels of wild-type BTK transcripts did not show a clear correlation with the percentage, absolute number, or immunophenotype of B lymphocytes nor with age or serum immunoglobulin levels at diagnosis. Nevertheless, we postulate that the presence of wild-type BTK transcripts can be one of the many factors that influence the clinical and immunological phenotype in X-linked agammaglobulinemia.
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Affiliation(s)
- Jeroen G Noordzij
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
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Noordzij JG, de Bruin-Versteeg S, Comans-Bitter WM, Hartwig NG, Hendriks RW, de Groot R, van Dongen JJM. Composition of precursor B-cell compartment in bone marrow from patients with X-linked agammaglobulinemia compared with healthy children. Pediatr Res 2002; 51:159-68. [PMID: 11809909 DOI: 10.1203/00006450-200202000-00007] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
X-linked agammaglobulinemia (XLA) is characterized by a severe B-cell deficiency, resulting from a differentiation arrest in the bone marrow (BM). Because XLA is clinically and immunologically heterogeneous, we investigated whether the B-cell differentiation arrest in BM of XLA patients is heterogeneous as well. First, we analyzed BM samples from 19 healthy children by flow cytometry. This resulted in a normal B-cell differentiation model with eight consecutive stages. Subsequently, we analyzed BM samples from nine XLA patients. Eight patients had amino acid substitutions in the Bruton's tyrosine kinase (BTK) domain or premature stop codons, resulting in the absence of functional BTK proteins. In seven of these eight patients a major differentiation arrest was observed at the transition between cytoplasmic Ig(mu-) pre-B-I cells and cytoplasmic Ig(mu+) pre-B-II cells, consistent with a role for BTK in pre-B-cell receptor signaling. However, one patient exhibited a very early arrest at the transition between pro-B cells and pre-B-I cells, which could not be explained by a different nature of the BTK mutation. We conclude that the absence of functional BTK proteins generally leads to an almost complete arrest of B-cell development at the pre-B-I to pre-B-II transition. The ninth XLA patient had a splice site mutation associated with the presence of low levels of wild-type BTK mRNA. His BM showed an almost normal composition of the precursor B-cell compartment, suggesting that low levels of BTK can rescue the pre-B-cell receptor signaling defect, but do not lead to sufficient numbers of mature B lymphocytes in the peripheral blood.
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Affiliation(s)
- Jeroen G Noordzij
- Department of Immunology, Erasmus University Rotterdam/University Hospital Rotterdam-Dijkzigt, 3000 DR, Rotterdam, The Netherlands
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31
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Abstract
X-linked, or Bruton's, agammaglobulinemia (XLA) was described in 1952 as the congenital inability to form antibodies. Patients were typically infants or young children with recurrent, severe bacterial infections. Other, milder cases of hypogammaglobulinemia were considered "acquired," and often presented later in life. Since the discovery of the defective gene in XLA in 1993, it has been shown that a significant number of male patients with sporadic or acquired hypogammaglobulinemia actually have XLA. We present here a case of atypical XLA and discuss similar cases in the literature. We conclude that any male with hypogammaglobulinemia, regardless of age of presentation, might have XLA. Males with low B-cell numbers are particularly likely to have XLA and should have Bruton's tyrosine kinase levels assessed.
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Affiliation(s)
- D M Stewart
- Metabolism Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, MSC 1374, Bethesda, MD 20892-1374, USA.
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32
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Speletas M, Kanariou M, Kanakoudi-Tsakalidou F, Papadopoulou-Alataki E, Arvanitidis K, Pardali E, Constantopoulos A, Kartalis G, Vihinen M, Sideras P, Ritis K. Analysis of Btk mutations in patients with X-linked agammaglobulinaemia (XLA) and determination of carrier status in normal female relatives: a nationwide study of Btk deficiency in Greece. Scand J Immunol 2001; 54:321-7. [PMID: 11555397 DOI: 10.1046/j.1365-3083.2001.00967.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bruton's tyrosine kinase (Btk) is a nonreceptor tyrosine kinase, critical for B-cell development and function. Mutations that inactivate this kinase were found in families with X-linked agammaglobulinaemia (XLA). In this study the Btk gene was analyzed in 13 registered Greek patients with XLA phenotype originated from 12 unrelated families, in order to provide a definite diagnosis of the XLA. The structure of Btk was analyzed at the cDNA level using the recently developed method, NIRCA (Non-Isotopic-Rnase-Cleavage-Assay). Alterations were detected in all patients and sequencing analysis confirmed the results and defined six novel XLA-associated Btk mutations (three missense mutations: C337G, L346R, L452P; one nonsense mutation: Y392X, and two frameshift alterations: c1211-1212delA, c1306-1307insA). Having defined the genetic alteration in the affected males of these families, the information was used to design polymerase chain reaction (PCR) primers and the Btk segments containing the mutated sequences were amplified from peripheral blood derived genomic DNA of potential female carriers. The PCR products were directly sequenced and carrier status was determined in 12 out of 16 phenotypically normal females analyzed. This protocol can be used once the nature of the Btk mutation has been defined in one of the affected males and provides a convenient, simple and reliable way to determine the carrier status of other female family members. Molecular genetic analysis constitutes a determinative tool for the definitive diagnosis of XLA and may allow accurate carrier and prenatal diagnosis for genetic counselling.
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Affiliation(s)
- M Speletas
- First Division of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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33
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Abstract
X-linked agammaglobulinemia (XLA), caused by mutations in Bruton's tyrosine kinase (BTK), typically presents in early childhood. We report here the case of a male diagnosed at age 23 years with hypogammaglobulinemia, originally classified as common variable immunodeficiency (CVID). On further analysis at age 40, flow cytometric analysis of lymphocytes showed only 0.1% B cells and Western blot analysis showed a deficiency of BTK protein in peripheral blood mononuclear cells, indicating the patient has XLA. BTK cDNA and genomic DNA analysis revealed a splice site mutation at the 3' end of intron 13. Multiple abnormally spliced mRNA species were identified, one of which was predicted to produce a protein with a 24-amino-acid insertion between the SH2 and kinase domains. In vitro kinase assay of this product showed weak kinase activity, perhaps resulting in milder than usual disease. XLA can present in adult males, and sporadic cases may be misdiagnosed as CVID.
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Affiliation(s)
- D M Stewart
- Metabolism Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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34
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Afzal AR, Rajab A, Fenske CD, Oldridge M, Elanko N, Ternes-Pereira E, Tüysüz B, Murday VA, Patton MA, Wilkie AO, Jeffery S. Recessive Robinow syndrome, allelic to dominant brachydactyly type B, is caused by mutation of ROR2. Nat Genet 2000; 25:419-22. [PMID: 10932186 DOI: 10.1038/78107] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The autosomal recessive form of Robinow syndrome (RRS; MIM 268310) is a severe skeletal dysplasia with generalized limb bone shortening, segmental defects of the spine, brachydactyly and a dysmorphic facial appearance. We previously mapped the gene mutated in RRS to chromosome 9q22 (ref. 4), a region that overlaps the locus for autosomal dominant brachydactyly type B (refs 5,6). The recent identification of ROR2, encoding an orphan receptor tyrosine kinase, as the gene mutated in brachydactyly type B (BDB1; ref. 7) and the mesomelic dwarfing in mice homozygous for a lacZ and/or a neo insertion into Ror2 (refs 8,9) made this gene a candidate for RRS. Here we report homozygous missense mutations in both intracellular and extracellular domains of ROR2 in affected individuals from 3 unrelated consanguineous families, and a nonsense mutation that removes the tyrosine kinase domain and all subsequent 3' regions of the gene in 14 patients from 7 families from Oman. The nature of these mutations suggests that RRS is caused by loss of ROR2 activity. The identification of mutations in three distinct domains (containing Frizzled-like, kringle and tyrosine kinase motifs) indicates that these are all essential for ROR2 function.
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Affiliation(s)
- A R Afzal
- Medical Genetics Unit, St George's Hospital Medical School, London, UK
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35
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Vihinen M, Villa A, Mella P, Schumacher RF, Savoldi G, O'Shea JJ, Candotti F, Notarangelo LD. Molecular modeling of the Jak3 kinase domains and structural basis for severe combined immunodeficiency. Clin Immunol 2000; 96:108-18. [PMID: 10900158 DOI: 10.1006/clim.2000.4880] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hereditary severe combined immunodeficiency (SCID) includes a heterogeneous group of diseases that profoundly affect both cellular and humoral immune responses and require treatment by bone marrow transplantation. Characterization of the cellular and molecular bases of SCID is essential to provide accurate genetic counseling and prenatal diagnosis, and it may offer the grounds for alternative forms of treatment. The Jak3 gene is mutated in most cases of autosomal recessive T(-)B(+) SCID in humans. Jak3 belongs to the family of intracellular Janus tyrosine kinases. It is physically and functionally coupled to the common gamma chain, gammac, shared by several cytokine receptors. We have established the JAK3base registry for disease and mutation information. In order to study the structural consequences of the Jak3 mutations, the structure of the human Jak3 kinase and pseudokinase domains was modeled. Residues involved in ATP and Mg(2+) binding were highly conserved in the kinase domain whereas the substrate binding region is somewhat different compared to other kinases. We have identified the first naturally occurring mutations disrupting the function of the human Jak3 kinase domain. The structural basis of all of the known Jak3 mutations reported so far is discussed based on the modeled structure. The model of the Jak3 protein also permits us to study Jak3 phosphorylation at the structural level and may thus serve in the design of novel immune suppressive drugs.
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Affiliation(s)
- M Vihinen
- Institute of Medical Technology, University of Tampere, FIN-33014, Finland
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36
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Vihinen M, Kwan SP, Lester T, Ochs HD, Resnick I, Väliaho J, Conley ME, Smith CI. Mutations of the human BTK gene coding for bruton tyrosine kinase in X-linked agammaglobulinemia. Hum Mutat 2000; 13:280-5. [PMID: 10220140 DOI: 10.1002/(sici)1098-1004(1999)13:4<280::aid-humu3>3.0.co;2-l] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations lists 544 mutation entries from 471 unrelated families showing 341 unique molecular events. In addition to mutations, a number of variants or polymorphisms have been found. Mutations in all the five domains of BTK cause the disease, the single most common event being missense mutations. Most mutations lead to truncation of the enzyme. The mutations appear almost uniformly throughout the molecule. About one-third of point mutations affect CpG sites, which usually code for arginine residues. The putative structural implications of all the missense mutations are provided in the database. BTKbase is available at http://www.uta.fi/imt/bioinfo.
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Affiliation(s)
- M Vihinen
- Institute of Medical Technology, University of Tampere, Finland.
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37
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Vorechovský I, Luo L, Hertz JM, Frøland SS, Klemola T, Fiorini M, Quinti I, Paganelli R, Ozsahin H, Hammarström L, Webster AD, Smith CI. Mutation pattern in the Bruton's tyrosine kinase gene in 26 unrelated patients with X-linked agammaglobulinemia. Hum Mutat 2000; 9:418-25. [PMID: 9143921 DOI: 10.1002/(sici)1098-1004(1997)9:5<418::aid-humu7>3.0.co;2-#] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mutation pattern was characterized in the Bruton's tyrosine kinase gene (BTK) in 26 patients with X-linked agammaglobulinemia, the first described immunoglobulin deficiency, and was related to BTK expression. A total of 24 different mutations were identified. Most BTK mutations were found to result in premature termination of the translation product. Mutations were detected in most BTK exons with a predominance of frameshift and nonsense mutations in the 5' end of the gene and missense mutations in its 3' part, corresponding to the catalytic domain of the enzyme. Nonsense and frameshift mutations were associated with diminished levels of BTK mRNA expression, except for a frameshift mutation in exon 17 and two nonsense mutations in exon 2, indicating that these cases are not confined to penultimate exons. One amino acid substitution (R28H) was found in the pleckstrin homology domain's residue, which is mutated in mice bearing the X-linked immunodeficiency phenotype; another substitution (R307G) was identified in the src homology domain 2. All remaining amino acid substitutions were found in the catalytic domain of Btk.
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Affiliation(s)
- I Vorechovský
- Karolinska Institute, Department of Biosciences, NOVUM, Huddinge, Sweden
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38
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Gaspar HB, Ferrando M, Caragol I, Hernandez M, Bertran JM, De Gracia X, Lester T, Kinnon C, Ashton E, Espanol T. Kinase mutant Btk results in atypical X-linked agammaglobulinaemia phenotype. Clin Exp Immunol 2000; 120:346-50. [PMID: 10792386 PMCID: PMC1905636 DOI: 10.1046/j.1365-2249.2000.01230.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
X-linked agammaglobulinaemia (XLA) is a B cell humoral abnormality arising from mutations in the gene encoding Bruton's tyrosine kinase (Btk). The phenotype of XLA can be variable, with some individuals having a less severe immunophenotype, although in most cases this cannot be correlated with the Btk mutation or expression of Btk protein. In this study we describe clinical and immunological heterogeneity within the same pedigree. Analysis of the genetic defect identified a missense mutation in the kinase domain of Btk which, unusually, preserved Btk protein expression but at reduced levels, and also considerably diminished autophosphorylation activity. Structural analysis of the effect of this mutation on the kinase domain suggests that this mutation is not an integral part of the ATP or substrate binding domains but may affect the interaction of the kinase domain with its own kinase domain and other substrates. Together, these data may provide an explanation for the variable XLA phenotype.
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Affiliation(s)
- H B Gaspar
- Molecular Immunology Unit, Institute of Child Health, University College London, London, UK.
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39
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Curtis SK, Hebert MD, Saha BK. Twin carriers of X-linked agammaglobulinemia (XLA) due to germline mutation in the Btk gene. AMERICAN JOURNAL OF MEDICAL GENETICS 2000; 90:229-32. [PMID: 10678660 DOI: 10.1002/(sici)1096-8628(20000131)90:3<229::aid-ajmg8>3.0.co;2-q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on an X-linked agammaglobulinemia (XLA) family in which mothers of two affected cousins were monozygotic twins. We analyzed the Btk gene of several members in three generations of the family by SSCP analysis, DNA sequencing, and RFLP analysis following polymerase chain reaction-amplification of the individual exons. We identified a missense point mutation, G1817C (R562P), in exon 17 of the Btk gene in the affected cousins. The same mutation was also present in both mothers (twin sisters) of the cousins identifying them as carriers. However, the mutation was absent in all other relatives including the grandmother of the cousins (mother of the twin sisters). This strongly suggests that the mutation in the Btk gene had originated in one of the germ lines or in the zygote. This may be the first demonstration of a germ line (or zygotic) mutation in XLA.
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Affiliation(s)
- S K Curtis
- Department of Pathology, Emory University School of Medicine, Altanta, Georgia, USA
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40
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Stenberg KA, Riikonen PT, Vihinen M. KinMutBase, a database of human disease-causing protein kinase mutations. Nucleic Acids Res 2000; 28:369-71. [PMID: 10592276 PMCID: PMC102425 DOI: 10.1093/nar/28.1.369] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
KinMutBase (http://www.uta.fi/imt/bioinfo/KinMutBase/) is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders. The first release of KinMutBase contained information for protein tyrosine kinases. The current release includes also serine/threonine protein kinases, as well as an update of the tyrosine kinases. There are 251 entries altogether, representing 337 families and 621 patients. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns.
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Affiliation(s)
- K A Stenberg
- Department of Biosciences, Division of Biochemistry, FIN-00014 University of Helsinki, Finland
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41
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Abstract
The high affinity receptor for immunoglobulin E (designated Fc epsilon RI) is the member of the antigen (Ag) receptor superfamily responsible for linking pathogen-or allergen-specific IgEs with cellular immunologic effector functions. This review provides background information on Fc epsilon RI function combined with more detailed summaries of recent progress in understanding specific aspects of Fc epsilon RI biology and biochemistry. Topics covered include the coordination and function of the large multiprotein signaling complexes that are assembled when Fc epsilon RI and other Ag receptors are engaged, new information on human receptor structures and tissue distribution, and the role of the FcR beta chain in signaling and its potential contribution to atopic phenotypes.
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Affiliation(s)
- J P Kinet
- Harvard Medical School, Boston, Massachusetts, USA.
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42
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Till JH, Chan PM, Miller WT. Engineering the substrate specificity of the Abl tyrosine kinase. J Biol Chem 1999; 274:4995-5003. [PMID: 9988744 DOI: 10.1074/jbc.274.8.4995] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
c-Abl is a non-receptor tyrosine kinase that is involved in a variety of signaling pathways. Activated forms of c-Abl are associated with some forms of human leukemia. Presently, no high resolution structure of the tyrosine kinase domain of Abl is available. We have developed a structural homology model of the catalytic domain of Abl based on the crystal structure of the insulin receptor tyrosine kinase. Using this model as a guide, we selected residues near the active site predicted to play a role in peptide/protein substrate recognition. We expressed and purified 15 mutant forms of Abl with single amino acid substitutions at these positions and tested their peptide substrate specificity. We report here the identification of seven residues involved in recognition of the P-1, P+1, and P+3 positions of bound peptide substrate. Mutations in these residues cause distinct changes in substrate specificity. The results suggest features of Abl substrate recognition that may be relevant to related tyrosine kinases.
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Affiliation(s)
- J H Till
- Department of Physiology and Biophysics, School of Medicine, State University of New York, Stony Brook, New York 11794-8661, USA
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43
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Stenberg KA, Riikonen PT, Vihinen M. KinMutBase, a database of human disease-causing protein kinase mutations. Nucleic Acids Res 1999; 27:362-4. [PMID: 9847229 PMCID: PMC148184 DOI: 10.1093/nar/27.1.362] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
KinMutBase (http://www.uta.fi/laitokset/imt/KinMut Base.html) is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signalling molecules, in which mutations can lead into diseases including, e.g., immunodeficiencies, cancers and endocrine disorders. The first release of KinMutBase contains information for nine protein tyrosine kinases. There are altogether 170 entries representing 273 families and 403 patients. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations, restriction enzyme patterns and online submission.
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Affiliation(s)
- K A Stenberg
- Department of Biosciences, Division of Biochemistry, PO Box 56, FIN-00014, University of Helsinki, Helsinki, Finland
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44
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Smith CI, Bäckesjö CM, Berglöf A, Brandén LJ, Islam T, Mattsson PT, Mohamed AJ, Müller S, Nore B, Vihinen M. X-linked agammaglobulinemia: lack of mature B lineage cells caused by mutations in the Btk kinase. SPRINGER SEMINARS IN IMMUNOPATHOLOGY 1998; 19:369-81. [PMID: 9618763 DOI: 10.1007/bf00792597] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C I Smith
- Department of Biosciences at Novum, Karolinska Institute, Huddinge, Sweden
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45
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Knapp S, Mattson PT, Christova P, Berndt KD, Karshikoff A, Vihinen M, Smith CI, Ladenstein R. Thermal unfolding of small proteins with SH3 domain folding pattern. Proteins 1998; 31:309-19. [PMID: 9593201 DOI: 10.1002/(sici)1097-0134(19980515)31:3<309::aid-prot7>3.0.co;2-d] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy. The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 < pH < 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec). At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12-16 kJ/mol but show quite high melting temperatures. Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities.
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Affiliation(s)
- S Knapp
- Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
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46
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Holinski-Feder E, Weiss M, Brandau O, Jedele KB, Nore B, Bäckesjö CM, Vihinen M, Hubbard SR, Belohradsky BH, Smith CI, Meindl A. Mutation screening of the BTK gene in 56 families with X-linked agammaglobulinemia (XLA): 47 unique mutations without correlation to clinical course. Pediatrics 1998; 101:276-84. [PMID: 9445504 DOI: 10.1542/peds.101.2.276] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES To determine the utility of single-stranded conformation polymorphism (SSCP) analysis for mutation screening in the BTK (Bruton's tyrosine kinase) gene, we investigated 56 X-linked agammaglobulinemia (XLA) families. To obtain genotype/ phenotype correlations, predicted protein aberrations were correlated with the clinical course of the disease. PATIENTS This study included 56 patients with XLA, with or without a positive family history, who were diagnosed on the basis of their clinical features, low peripheral B-cell count, and low immunoglobulin levels. Ten patients with isolated hypogammaglobulinemia and 50 healthy males served as controls. METHODS SSCP analysis was performed for the entire BTK gene, including the exon-intron boundaries and the promoter region. Structural implications of the missense mutations were investigated by molecular modeling, and the functional consequences of some mutations also were evaluated by in vitro kinase assays and Western blot analysis. RESULTS We report the largest series of patients with XLA to date. All but 5 of the 56 index patients with XLA screened with SSCP analysis showed BTK gene abnormalities, and in 2 of the 5 SSCP-negative patients, no BTK protein was found by Western blot analysis. There were 51 mutations, including 37 novel ones, distributed across the entire gene. This report contains the first promoter mutation as well as 14 novel missense mutations with the first ones described for the Tec homology domain and the glycine-rich motif in the SH1 domain. Each index patient had a different mutation, except for four mutations, each in two unrelated individuals. This result supports the strong tendency for private mutations in this disease. No mutations were found in the controls. CONCLUSIONS Our results demonstrate that molecular genetic testing by SSCP analysis provides an accurate tool for the definitive diagnosis of XLA and the discrimination of borderline cases, such as certain hypogammaglobulinemia or common variable immunodeficiency patients with overlapping clinical features. Genotype/ phenotype correlations are not currently possible, making prediction of the clinical course based on molecular genetic data infeasible.
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Affiliation(s)
- E Holinski-Feder
- Abteilung Medizinische Genetik, Klinikum Innenstadt, Universität München, Germany
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47
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Vihinen M, Brandau O, Brandén LJ, Kwan SP, Lappalainen I, Lester T, Noordzij JG, Ochs HD, Ollila J, Pienaar SM, Riikonen P, Saha BK, Smith CI. BTKbase, mutation database for X-linked agammaglobulinemia (XLA). Nucleic Acids Res 1998; 26:242-7. [PMID: 9399844 PMCID: PMC147244 DOI: 10.1093/nar/26.1.242] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites that code for arginine residues. The putative structural implications of all the missense mutations are given in the database. The improved version of the registry having a number of new features is available at http://www. helsinki.fi/science/signal/btkbase.html
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Affiliation(s)
- M Vihinen
- Department of Biosciences, Division of Biochemistry, PO Box 56, FIN-00014 University of Helsinki, Finland.
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48
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Affiliation(s)
- C I Smith
- Department of Clinical Immunology, Karolinska Institute, Huddinge, Sweden
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49
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Saha BK, Curtis SK, Vogler LB, Vihinen M. Molecular and structural characterization of five novel mutations in the Bruton's tyrosine kinase gene from patients with X-linked agammaglobulinemia. Mol Med 1997; 3:477-85. [PMID: 9260159 PMCID: PMC2230218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The Btk (Bruton's tyrosine kinase) gene has been shown to be mutated in the human immunodeficiency disease, XLA (X-linked agammaglobulinemia). Btk is a member of the Tec family of cytosolic protein tyrosine kinases with distinct functional domains PH, TH, SH3, SH2, and kinase. Mutations have been observed in each of the Btk subdomains in XLA. We have analyzed the Btk gene in six XLA patients from five unrelated families. MATERIALS AND METHODS DNA was prepared from the patients peripheral blood. The Btk exons including the junctional sequences were analyzed by single-strand conformation polymorphism (SSCP) followed by direct nucleotide sequencing after PCR-amplification. For structural analysis, the missense mutations were introduced into three-dimensional models of the PH and kinase domains of Btk and the outcome was predicted based on the knowledge of the protein function. RESULTS Five novel mutations and two novel polymorphisms, all of which resulted from single-base alterations, were identified. Three of the five mutations were in the PH domain and two were in the kinase domain of Btk. Three of these mutations were of the missense type, two of which altered the same codon in the PH domain; the third one was located in the kinase domain. The fourth mutation was a point deletion in the PH domain causing a frameshift followed by premature termination. The fifth mutation was a splice donor-site mutation within the kinase domain which could result in an exon skipping. In four of the five instances, mothers of the patients were shown to be obligate carriers. In one instance, a sibling sister was identified as a heterozygote establishing her as a carrier. CONCLUSIONS Functional consequences of the mutations causing frameshifts and altered splicing can be inferred directly. Functional consequences of the missense mutations were interpreted by 3-dimensional structural modeling of Btk domains. It is proposed that the two PH domain mutations will interfere with membrane localization while the kinase domain mutation will interfere with the enzymatic function of Btk. This study provides further insight into the role of Btk in XLA.
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Affiliation(s)
- B K Saha
- Department of Pathology, Emory University, Atlanta, Georgia, USA.
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