Abstract
Linker for activation of T cells (LAT) is a transmembrane adaptor protein playing a key role in the development, activation and maintenance of peripheral homeostasis of T cells. In this study we identified a functional isoform of LAT. It originates from an intron 6 retention event generating an in-frame splice variant of LAT mRNA denoted as LATi6. Comparison of LATi6 expression in peripheral blood leukocytes of human and several other mammalian species revealed that it varied from being virtually absent in the mouse to being predominant in the cow. Analysis of LAT isoform frequency expressed from minigene splicing reporters carrying loss- or gain-of-function point mutations within intronic polyguanine sequences showed that these elements are critical for controlling the intron 6 removal. The protein product of LATi6 isoform (LATi6) ectopically expressed in LAT-deficient JCam 2.5 cell line localized correctly to subcellular compartments and supported T-cell receptor signaling but differed from the canonical LAT protein by displaying a shorter half-life and mediating an increased interleukin-2 secretion upon prolonged CD3/CD28 crosslinking. Altogether, our data suggest that the appearance of LATi6 isoform is an evolutionary innovation that may contribute to a more efficient proofreading control of effector T-cell response.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 6 digital issues and online access to articles
$119.00 per year
only $19.83 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ . Detection and evaluation of intron retention events in the human transcriptome. RNA 2004; 10: 757–765.
Sakabe NJ, de Souza SJ . Sequence features responsible for intron retention in human. BMC Genomics 2007; 8: 59.
Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T et al. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. PLoS ONE 2013; 8: e76194.
Lareau LF, Green RE, Bhatnagar RS, Brenner SE . The evolving roles of alternative splicing. Curr Opin Struct Biol 2004; 14: 273–282.
Wong JJ, Ritchie W, Ebner OA, Selbach M, Wong JW, Huang Y et al. Orchestrated intron retention regulates normal granulocyte differentiation. Cell 2013; 154: 583–595.
Popp MW, Maquat LE . Organizing principles of Mammalian nonsense-mediated mRNA decay. Annu Rev Genet 2013; 47: 139–165.
Tan S, Guo J, Huang Q, Chen X, Li-Ling J, Li Q et al. Retained introns increase putative microRNA targets within 3' UTRs of human mRNA. FEBS Lett 2007; 581: 1081–1086.
Fujimura A, Michiue H, Nishiki T, Ohmori I, Wei FY, Matsui H et al. Expression of a constitutively active calcineurin encoded by an intron-retaining mRNA in follicular keratinocytes. PLoS ONE 2011; 6: e17685.
Li Y, Bor YC, Misawa Y, Xue Y, Rekosh D, Hammarskjold ML . An intron with a constitutive transport element is retained in a Tap messenger RNA. Nature 2006; 443: 234–237.
Yoshimura K, Chu CS, Crystal RG . Alternative splicing of intron 23 of the human cystic fibrosis transmembrane conductance regulator gene resulting in a novel exon and transcript coding for a shortened intracytoplasmic C terminus. J Biol Chem 1993; 268: 686–690.
Gao B, Williams A, Sewell A, Elliott T . Generation of a functional, soluble tapasin protein from an alternatively spliced mRNA. Genes Immun 2004; 5: 101–108.
Walsh NC, Alexander KA, Manning CA, Karmakar S, Wang JF, Weyand CM et al. Activated human T cells express alternative mRNA transcripts encoding a secreted form of RANKL. Genes Immun 2013; 14: 336–345.
Kralovicova J, Vorechovsky I . Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs. J Immunol 2006; 176: 2381–2388.
Ghosh A, Kuppusamy H, Pilarski LM . Aberrant splice variants of HAS1 (Hyaluronan Synthase 1) multimerize with and modulate normally spliced HAS1 protein: a potential mechanism promoting human cancer. J Biol Chem 2009; 284: 18840–18850.
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 2012; 338: 1587–1593.
Carlo T, Sterner DA, Berget SM . An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 1996; 2: 342–353.
McCullough AJ, Berget SM . G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol Cell Biol 1997; 17: 4562–4571.
Modafferi EF, Black DL . A complex intronic splicing enhancer from the c-src pre-mRNA activates inclusion of a heterologous exon. Mol Cell Biol 1997; 17: 6537–6545.
Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB . Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat Struct Mol Biol 2009; 16: 1094–1100.
Facchetti F, Chan JK, Zhang W, Tironi A, Chilosi M, Parolini S et al. Linker for activation of T cells (LAT), a novel immunohistochemical marker for T cells, NK cells, mast cells, and megakaryocytes: evaluation in normal and pathological conditions. Am J Patholo 1999; 154: 1037–1046.
Malissen B, Aguado E, Malissen M . Role of the LAT adaptor in T-cell development and Th2 differentiation. Adv Immunol 2005; 87: 1–25.
Malbec O, Malissen M, Isnardi I, Lesourne R, Mura AM, Fridman WH et al. Linker for activation of T cells integrates positive and negative signaling in mast cells. J Immunol 2004; 173: 5086–5094.
Moraes LA, Barrett NE, Jones CI, Holbrook LM, Spyridon M, Sage T et al. Platelet endothelial cell adhesion molecule-1 regulates collagen-stimulated platelet function by modulating the association of phosphatidylinositol 3-kinase with Grb-2-associated binding protein-1 and linker for activation of T cells. J Thromb Haemost 2010; 8: 2530–2541.
Mingueneau M, Roncagalli R, Gregoire C, Kissenpfennig A, Miazek A, Archambaud C et al. Loss of the LAT adaptor converts antigen-responsive T cells into pathogenic effectors that function independently of the T cell receptor. Immunity 2009; 31: 197–208.
Sommers CL, Menon RK, Grinberg A, Zhang W, Samelson LE, Love PE . Knock-in mutation of the distal four tyrosines of linker for activation of T cells blocks murine T cell development. J Exp Med 2001; 194: 135–142.
Zhang W, Sommers CL, Burshtyn DN, Stebbins CC, DeJarnette JB, Trible RP et al. Essential role of LAT in T cell development. Immunity 1999; 10: 323–332.
Zhang W, Trible RP, Zhu M, Liu SK, McGlade CJ, Samelson LE . Association of Grb2, Gads, and phospholipase C-gamma 1 with phosphorylated LAT tyrosine residues. Effect of LAT tyrosine mutations on T cell angigen receptor-mediated signaling. J Biol Chem 2000; 275: 23355–23361.
Martinez-Florensa M, Garcia-Blesa A, Yelamos J, Munoz-Suano A, Dominguez-Villar M, Valdor R et al. Serine residues in the LAT adaptor are essential for TCR-dependent signal transduction. J Leukoc Biol 2011; 89: 63–73.
Zhang W, Trible RP, Samelson LE . LAT palmitoylation: its essential role in membrane microdomain targeting and tyrosine phosphorylation during T cell activation. Immunity 1998; 9: 239–246.
Balagopalan L, Ashwell BA, Bernot KM, Akpan IO, Quasba N, Barr VA et al. Enhanced T-cell signaling in cells bearing linker for activation of T-cell (LAT) molecules resistant to ubiquitylation. Proc Natl Acad Sci USA 2011; 108: 2885–2890.
Garcia-Blesa A, Klossowicz M, Lopez-Osuna C, Martinez-Florensa M, Malissen B, Garcia-Cozar FJ et al. The membrane adaptor LAT is proteolytically cleaved following Fas engagement in a tyrosine phosphorylation-dependent fashion. Biochem J 2013; 450: 511–521.
Klossowicz M, Scirka B, Suchanek J, Marek-Bukowiec K, Kisielow P, Aguado E et al. Assessment of caspase mediated degradation of linker for activation of T cells (LAT) at a single cell level. J Immunol Methods 2013; 389: 9–17.
Windpassinger C, Kroisel PM, Wagner K, Petek E . Chromosomal localization and genomic organization of the human Linker for Activation of T cells (LAT) gene. Cytogenet Genome Res 2002; 97: 155–157.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S et al. Ensembl 2013. Nucleic Acids Res 2013; 41 (Database issue): D48–D55.
Takahashi T, D'Amico D, Chiba I, Buchhagen DL, Minna JD . Identification of intronic point mutations as an alternative mechanism for p53 inactivation in lung cancer. J Clin Invest 1990; 86: 363–369.
Schwartz S, Hall E, Ast G . SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res 2009; 37 (Web Server issue): W189–W192.
Black DL . Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003; 72: 291–336.
Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE . The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol 2007; 623: 190–211.
McKeithan TW . Kinetic proofreading in T-cell receptor signal transduction. Proc Natl Acad Sci USA 1995; 92: 5042–5046.
Peters D, Tsuchida M, Manthei ER, Alam T, Cho CS, Knechtle SJ et al. Potentiation of CD3-induced expression of the linker for activation of T cells (LAT) by the calcineurin inhibitors cyclosporin A and FK506. Blood 2000; 95: 2733–2741.
Zsori KS, Muszbek L, Csiki Z, Shemirani AH . Validation of reference genes for the determination of platelet transcript level in healthy individuals and in patients with the history of myocardial infarction. Int J Mol Sci 2013; 14: 3456–3466.
Adam RM, Yang W, Di Vizio D, Mukhopadhyay NK, Steen H . Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis. BMC Cell Biol 2008; 9: 30.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947–2948.
Acknowledgements
This work has been supported by the Polish National Science Centre (NCN) project number 2012/05/B/NZ5/01339 and co-financed by the European Union as part of the European Social Fund. This research was in part supported by the Consejeria de Salud, Junta de Andalucia (Spain), Grant Number PI-0365-2013. We are grateful to Dr Jacek Bania, Aleksandra Orłowska and Marta Lisowska for discussions and expert technical assistance. We thank Dr Pawel Kisielow for critical reading of this manuscript
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Author contributions
All the authors performed experiments and analyzed results, AM and EA designed the study and AM wrote the manuscript.
Supplementary Information accompanies this paper on Genes and Immunity website
Rights and permissions
About this article
Cite this article
Kłossowicz, M., Marek-Bukowiec, K., Arbulo-Echevarria, M. et al. Identification of functional, short-lived isoform of linker for activation of T cells (LAT). Genes Immun 15, 449–456 (2014). https://doi.org/10.1038/gene.2014.35
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/gene.2014.35