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Lanz AL, Erdem S, Ozcan A, Ceylaner G, Cansever M, Ceylaner S, Conca R, Magg T, Acuto O, Latour S, Klein C, Patiroglu T, Unal E, Eken A, Hauck F. A Novel Biallelic LCK Variant Resulting in Profound T-Cell Immune Deficiency and Review of the Literature. J Clin Immunol 2023; 44:1. [PMID: 38100037 PMCID: PMC10724324 DOI: 10.1007/s10875-023-01602-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023]
Abstract
Lymphocyte-specific protein tyrosine kinase (LCK) is an SRC-family kinase critical for initiation and propagation of T-cell antigen receptor (TCR) signaling through phosphorylation of TCR-associated CD3 chains and recruited downstream molecules. Until now, only one case of profound T-cell immune deficiency with complete LCK deficiency [1] caused by a biallelic missense mutation (c.1022T>C, p.L341P) and three cases of incomplete LCK deficiency [2] caused by a biallelic splice site mutation (c.188-2A>G) have been described. Additionally, deregulated LCK expression has been associated with genetically undefined immune deficiencies and hematological malignancies. Here, we describe the second case of complete LCK deficiency in a 6-month-old girl born to consanguineous parents presenting with profound T-cell immune deficiency. Whole exome sequencing (WES) revealed a novel pathogenic biallelic missense mutation in LCK (c.1393T>C, p.C465R), which led to the absence of LCK protein expression and phosphorylation, and a consecutive decrease in proximal TCR signaling. Loss of conventional CD4+ and CD8+ αβT-cells and homeostatic T-cell expansion was accompanied by increased γδT-cell and Treg percentages. Surface CD4 and CD8 co-receptor expression was reduced in the patient T-cells, while the heterozygous mother had impaired CD4 and CD8 surface expression to a lesser extent. We conclude that complete LCK deficiency is characterized by profound T-cell immune deficiency, reduced CD4 and CD8 surface expression, and a characteristic TCR signaling disorder. CD4 and CD8 surface expression may be of value for early detection of mono- and/or biallelic LCK deficiency.
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Affiliation(s)
- Anna-Lisa Lanz
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Serife Erdem
- Department of Medical Biology, Faculty of Medicine, Erciyes University, 38030, Kayseri, Turkey
- Molecular Biology and Genetics Department, Gevher Nesibe Genome and Stem Cell Institute, Betul-Ziya Eren Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Alper Ozcan
- Molecular Biology and Genetics Department, Gevher Nesibe Genome and Stem Cell Institute, Betul-Ziya Eren Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | | | - Murat Cansever
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | | | - Raffaele Conca
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Thomas Magg
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Oreste Acuto
- T Cell Signalling Laboratory, Sir William Dunn School of Pathology, Oxford University, Oxford, OX2 3RE, UK
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Paris, France
| | - Christoph Klein
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, 80337, Munich, Germany
| | - Turkan Patiroglu
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Ekrem Unal
- Molecular Biology and Genetics Department, Gevher Nesibe Genome and Stem Cell Institute, Betul-Ziya Eren Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Intergen, Ankara, Turkey
- Hasan Kalyoncu University, Faculty of Health Sciences, Medical Point Hospital, Gaziantep, Türkiye
| | - Ahmet Eken
- Department of Medical Biology, Faculty of Medicine, Erciyes University, 38030, Kayseri, Turkey.
- Molecular Biology and Genetics Department, Gevher Nesibe Genome and Stem Cell Institute, Betul-Ziya Eren Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey.
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, 80337, Munich, Germany.
- Munich Centre for Rare Diseases (M-ZSELMU), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
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2
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Banerjee S, Galarza-Muñoz G, Garcia-Blanco MA. Role of RNA Alternative Splicing in T Cell Function and Disease. Genes (Basel) 2023; 14:1896. [PMID: 37895245 PMCID: PMC10606310 DOI: 10.3390/genes14101896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative RNA splicing, a ubiquitous mechanism of gene regulation in eukaryotes, expands genome coding capacity and proteomic diversity. It has essential roles in all aspects of human physiology, including immunity. This review highlights the importance of RNA alternative splicing in regulating immune T cell function. We discuss how mutations that affect the alternative splicing of T cell factors can contribute to abnormal T cell function and ultimately lead to autoimmune diseases. We also explore the potential applications of strategies that target the alternative splicing changes of T cell factors. These strategies could help design therapeutic approaches to treat autoimmune disorders and improve immunotherapy.
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Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | - Mariano A. Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
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Li R, Wu K, Li Y, Liang X, Lai KP, Chen J. Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses. Brief Bioinform 2021; 22:1161-1174. [PMID: 32662814 PMCID: PMC7462346 DOI: 10.1093/bib/bbaa141] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Coronavirus disease 2019 (COVID-19) is a fatal and fast-spreading viral infection. To date, the number of COVID-19 patients worldwide has crossed over six million with over three hundred and seventy thousand deaths (according to the data from World Health Organization; updated on 2 June 2020). Although COVID-19 can be rapidly diagnosed, efficient clinical treatment of COVID-19 remains unavailable, resulting in high fatality. Some clinical trials have identified vitamin C (VC) as a potent compound pneumonia management. In addition, glycyrrhizic acid (GA) is clinically as an anti-inflammatory medicine against pneumonia-induced inflammatory stress. We hypothesized that the combination of VC and GA is a potential option for treating COVID-19. METHODS The aim of this study was to determine pharmacological targets and molecular mechanisms of VC + GA treatment for COVID-19, using bioinformational network pharmacology. RESULTS We uncovered optimal targets, biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of VC + GA against COVID-19. Our findings suggested that combinatorial VC and GA treatment for COVID-19 was associated with elevation of immunity and suppression of inflammatory stress, including activation of the T cell receptor signaling pathway, regulation of Fc gamma R-mediated phagocytosis, ErbB signaling pathway and vascular endothelial growth factor signaling pathway. We also identified 17 core targets of VC + GA, which suggest as antimicrobial function. CONCLUSIONS For the first time, our study uncovered the pharmacological mechanism underlying combined VC and GA treatment for COVID-19. These results should benefit efforts to address the most pressing problem currently facing the world.
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Affiliation(s)
| | - Ka Wu
- Guilin Medical University
| | - Yu Li
- Guilin Medical University
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Rouer E. [Neuronal isoforms of Src, Fyn and Lck tyrosine kinases: A specific role for p56lckN in neuron protection]. C R Biol 2010; 333:1-10. [PMID: 20176329 DOI: 10.1016/j.crvi.2009.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/14/2009] [Accepted: 10/15/2009] [Indexed: 12/06/2022]
Abstract
The two main tyrosine kinases (TK) in the brain are p60Src and p59Fyn, expressed as specific isoforms (p60SrcNI, p60SrcNI+NII and p59fynB). They play a pivotal role in some major processes such as neuronal growth and myelinisation. Another member of this TK family was then reported in brain, the p56lck. Its name Lck (lymphocyte cell kinase) indicates its cellular specificity observed initially, so its presence in the brain was intriguing. But no further studies were performed to understand its role in brain until recent clinical studies on Alzheimer patients' brains. One study reveals a decreased p56lck level in the brains of these patients while another study shows an association between one peculiar SNP (single nucleotide polymorphism) of the lck gene and some cases of the disease. These new data prompt us to reinvestigate the original biochemical data and to confront them with the present knowledge. This analysis suggests some hypothesis concerning both the Lck protein expressed in the brain (rather an isoform than the lymphocyte protein itself) and its role (to maintain the neuronal survival presumably by protecting them from inflammation, the main pathway that leads to neuron degeneracy).
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Affiliation(s)
- Evelyne Rouer
- Inserm U-839, institut du Fer-à-Moulin, 37, rue du Fer-à-Moulin, 75005 Paris, France.
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Corsi JM, Rouer E, Girault JA, Enslen H. Organization and post-transcriptional processing of focal adhesion kinase gene. BMC Genomics 2006; 7:198. [PMID: 16889663 PMCID: PMC1570463 DOI: 10.1186/1471-2164-7-198] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 08/04/2006] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase critical for processes ranging from embryo development to cancer progression. Although isoforms with specific molecular and functional properties have been characterized in rodents and chicken, the organization of FAK gene throughout phylogeny and its potential to generate multiple isoforms are not well understood. Here, we study the phylogeny of FAK, the organization of its gene, and its post-transcriptional processing in rodents and human. RESULTS A single orthologue of FAK and the related PYK2 was found in non-vertebrate species. Gene duplication probably occurred in deuterostomes after the echinoderma embranchment, leading to the evolution of PYK2 with distinct properties. The amino acid sequence of FAK and PYK2 is conserved in their functional domains but not in their linker regions, with the absence of autophosphorylation site in C. elegans. Comparison of mouse and human FAK genes revealed the existence of multiple combinations of conserved and non-conserved 5'-untranslated exons in FAK transcripts suggesting a complex regulation of their expression. Four alternatively spliced coding exons (13, 14, 16, and 31), previously described in rodents, are highly conserved in vertebrates. Cis-regulatory elements known to regulate alternative splicing were found in conserved alternative exons of FAK or in the flanking introns. In contrast, other reported human variant exons were restricted to Homo sapiens, and, in some cases, other primates. Several of these non-conserved exons may correspond to transposable elements. The inclusion of conserved alternative exons was examined by RT-PCR in mouse and human brain during development. Inclusion of exons 14 and 16 peaked at the end of embryonic life, whereas inclusion of exon 13 increased steadily until adulthood. Study of various tissues showed that inclusion of these exons also occurred, independently from each other, in a tissue-specific fashion. CONCLUSION The alternative coding exons 13, 14, 16, and 31 are highly conserved in vertebrates and their inclusion in mRNA is tightly but independently regulated. These exons may therefore be crucial for FAK function in specific tissues or during development. Conversely pathological disturbance of the expression of FAK and of its isoforms could lead to abnormal cellular regulation.
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Affiliation(s)
- Jean-Marc Corsi
- Unité Mixte de Recherche-Santé (UMR-S) 536, Institut National de la Santé et de la Recherche Médicale (INSERM) F-75005, Paris, France; Université Pierre et Marie Curie-Paris 6, F-75005, Paris, France; Institut du Fer-à-Moulin, F-75005, Paris, France
| | - Evelyne Rouer
- Unité Mixte de Recherche-Santé (UMR-S) 536, Institut National de la Santé et de la Recherche Médicale (INSERM) F-75005, Paris, France; Université Pierre et Marie Curie-Paris 6, F-75005, Paris, France; Institut du Fer-à-Moulin, F-75005, Paris, France
| | - Jean-Antoine Girault
- Unité Mixte de Recherche-Santé (UMR-S) 536, Institut National de la Santé et de la Recherche Médicale (INSERM) F-75005, Paris, France; Université Pierre et Marie Curie-Paris 6, F-75005, Paris, France; Institut du Fer-à-Moulin, F-75005, Paris, France
| | - Hervé Enslen
- Unité Mixte de Recherche-Santé (UMR-S) 536, Institut National de la Santé et de la Recherche Médicale (INSERM) F-75005, Paris, France; Université Pierre et Marie Curie-Paris 6, F-75005, Paris, France; Institut du Fer-à-Moulin, F-75005, Paris, France
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Nervi S, Guinamard R, Delaval B, Lécine P, Vialettes B, Naquet P, Imbert J. A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene with intron B retention and exon 7 skipping encodes a putative protein with altered SH3-dependent molecular interactions. Gene 2005; 359:18-25. [PMID: 16107303 DOI: 10.1016/j.gene.2005.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 06/06/2005] [Accepted: 06/16/2005] [Indexed: 10/25/2022]
Abstract
A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene that retains intron B and excludes exon 7 (B+7-) due to alternative splicing of the canonical LCK transcripts was identified and characterized. LCK B+7- mRNA is detected in all tested peripheral blood T lymphocytes total RNA samples but is apparently sequestered in the nucleus. The presence of intron B sequence does not disrupt the reading frame and results in the insertion of 58 aminoacids, containing a proline-rich region just upstream of p56lck SH3 domain. This putative isoform encodes an unstable 516 aminoacids protein (LckB+7-) which can be expressed in transfected COS-7 cells. Furthermore in Jurkat T cell extracts, a recombinant intron B plus SH3 p56lck domain fails to interact with some TCR-induced tyrosine phosphorylated polypeptides and known p56lck partners such as Sam68 and c-Cbl. The biological function of this rare messenger remains to be elucidated.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Western
- COS Cells
- Cells, Cultured
- Chlorocebus aethiops
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Humans
- Introns/genetics
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Jurkat Cells
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism
- Molecular Sequence Data
- Mutagenesis, Insertional
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- T-Lymphocytes/cytology
- T-Lymphocytes/enzymology
- T-Lymphocytes/metabolism
- Transcription, Genetic/genetics
- src Homology Domains/genetics
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Affiliation(s)
- Solange Nervi
- Institut de Cancérologie de Marseille, UMR599 INSERM-Institut Paoli-Calmettes-Université de la Méditerranée, 27 boulevard Leï Roure, 13009 Marseille, France
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Abstract
Alternative splicing is widely recognized to be a ubiquitous and crucial mechanism for generating protein diversity and regulating protein expression. Numerous immunologically relevant genes have been found to undergo alternative splicing; however, there has been little effort to develop a coherent picture of how alternative splicing might be used as a general mechanism to regulate the function of the immune system. In this review, I summarize the mechanisms by which splicing is controlled in T cells, and discuss the role of alternative splicing and alternative isoform expression in the regulation of T-cell activation and function.
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Affiliation(s)
- Kristen W Lynch
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines boulevard, Dallas, Texas 75390-9038, USA.
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