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Levillayer L, Brighelli C, Demeret C, Sakuntabhai A, Bureau JF. Role of two modules controlling the interaction between SKAP1 and SRC kinases comparison with SKAP2 architecture and consequences for evolution. PLoS One 2024; 19:e0296230. [PMID: 38483858 PMCID: PMC10939263 DOI: 10.1371/journal.pone.0296230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
SRC kinase associated phosphoprotein 1 (SKAP1), an adaptor for protein assembly, plays an important role in the immune system such as stabilizing immune synapses. Understanding how these functions are controlled at the level of the protein-protein interactions is necessary to describe these processes and to develop therapeutics. Here, we dissected the SKAP1 modular organization to recognize SRC kinases and compared it to that of its paralog SRC kinase associated phosphoprotein 2 (SKAP2). Different conserved motifs common to either both proteins or specific to SKAP2 were found using this comparison. Two modules harboring different binding properties between SKAP1 and SKAP2 were identified: one composed of two conserved motifs located in the second interdomain interacting at least with the SH2 domain of SRC kinases and a second one composed of the DIM domain modulated by the SH3 domain and the activation of SRC kinases. This work suggests a convergent evolution of the binding properties of some SRC kinases interacting specifically with either SKAP1 or SKAP2.
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Affiliation(s)
- Laurine Levillayer
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Camille Brighelli
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Caroline Demeret
- Institut Pasteur, Université de Paris-Cité, Laboratoire Interactomique, ARN et Immunité ‐ Interactomics, RNA and Immunity, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Jean-François Bureau
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
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2
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [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: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Zhang T, Zhang M, Xu T, Chen S, Xu A. Transcriptome analysis of larval immune defence in the lamprey Lethenteron japonicum. FISH & SHELLFISH IMMUNOLOGY 2019; 94:327-335. [PMID: 31491528 DOI: 10.1016/j.fsi.2019.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/18/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
The lamprey is a primitive jawless vertebrate that occupies a critical phylogenetic position, and its larval stage represents the major portion of its life cycle [1]. Lamprey larvae have been proven to be an important model organism for studying numerous biological problems, such as the immune system, due to their unique biological features [2]. In addition, early-stage larvae have never been obtained from the wild [3]; therefore, it is necessary to establish artificial breeding of lampreys in the laboratory. However, during early development, the larvae exhibit susceptibility to saprolegniasis, and the immune responses of lamprey larvae to this infection remain poorly understood. Here, we established a model of fungal infection in lamprey larvae and then used RNA sequencing to investigate the transcript profiles of lamprey larvae and their immune responses to Saprolegnia ferax. Among the profiled molecules, genes involved in pathogen recognition, inflammation, phagocytosis, lysosomal degradation, soluble humoral effectors, and lymphocyte development were significantly upregulated. The results were validated by analysis of several genes by quantitative real-time PCR and whole-mount in situ hybridization. Finally, we performed a Western blot for VLRs in infected and uninfected lampreys. This work not only provides an animal model for studying fungal infection but also suggests a molecular basis for developing defensive strategies to manage Saprolegnia ferax infection.
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Affiliation(s)
- Taotao Zhang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Mimi Zhang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Ting Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China; School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Sinha M, Lowell CA. Immune Defense Protein Expression in Highly Purified Mouse Lung Epithelial Cells. Am J Respir Cell Mol Biol 2017; 54:802-13. [PMID: 26574781 DOI: 10.1165/rcmb.2015-0171oc] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lung epithelial cells play critical roles in initiating and modulating immune responses during pulmonary infection or injury. To better understand the spectrum of immune response-related proteins present in lung epithelial cells, we developed an improved method of isolating highly pure primary murine alveolar type (AT) II cells and murine tracheal epithelial cells (mTECs) using negative selection for a variety of lineage markers and positive selection for epithelial cell adhesion molecule (EpCAM), a pan-epithelial cell marker. This method yielded 2-3 × 10(6) ATII cells/mouse lung and 1-2 × 10(4) mTECs/trachea that were highly pure (>98%) and viable (>98%). Using these preparations, we found that both ATII cells and mTECs expressed the Lyn tyrosine kinase, which is best studied as an inhibitory kinase in hematopoietic cells. However, we found little or no expression of Syk in either ATII cells or mTECs, which is in contrast to earlier published reports. Both cell types expressed C-type lectin receptors, anaphylatoxin receptors, and various Toll-like receptors (TLRs). In addition, stimulation of ATII cells with TLR ligands led to secretion of various cytokines and chemokines. Interestingly, lyn(-/-) ATII cells were hyperresponsive to TLR3 stimulation, suggesting that, as in hematopoietic cells, Lyn might be playing an inhibitory role in ATII cells. In conclusion, the improved isolation method reported here, along with expression profiles of various immune defense proteins, will help refocus investigations of immune-related signaling events in pulmonary epithelium.
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Affiliation(s)
- Meenal Sinha
- Department of Laboratory Medicine and the Program in Immunology, University of California, San Francisco, San Francisco, California
| | - Clifford A Lowell
- Department of Laboratory Medicine and the Program in Immunology, University of California, San Francisco, San Francisco, California
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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Targeted therapies of the LKB1/AMPK pathway for the treatment of insulin resistance. Future Med Chem 2011; 2:1785-96. [PMID: 21428801 DOI: 10.4155/fmc.10.264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Type II diabetes is characterized by elevated serum glucose levels and altered lipid metabolism due to peripheral insulin resistance and defects of insulin secretion in the pancreatic β-cells. While some cases of obesity and Type II diabetes result from genetic dysfunction, the increased worldwide incidence of these two disorders strongly suggest that the contribution of environmental factors such as sedentary lifestyles and high-calorie intake may disrupt energy balance. AMP-activated protein kinase and its upstream kinase liver kinase B1 are conserved serine/threonine kinases regulating anabolic and catabolic metabolic processes, therefore representing attractive therapeutic targets for the treatment of obesity and Type II diabetes. In this review, we will discuss the advantages of targeting the liver kinase B1/AMP-activated protein kinase pathway for the treatment of metabolic diseases.
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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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Alternative splicing modulates autoinhibition and SH3 accessibility in the Src kinase Fyn. Mol Cell Biol 2009; 29:6438-48. [PMID: 19805512 DOI: 10.1128/mcb.00398-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Src family kinases are central regulators of a large number of signaling pathways. To adapt to the idiosyncrasies of different cell types, these kinases may need a fine-tuning of their intrinsic molecular control mechanisms. Here, we describe on a molecular level how the Fyn kinase uses alternative splicing to adapt to different cellular environments. Using structural analysis, site-directed mutagenesis, and functional analysis, we show how the inclusion of either exon 7A or 7B affects the autoinhibition of Fyn and how this changes the SH3-dependent interaction and tyrosine phosphorylation of Sam68, with functional consequences for the Sam68-regulated survival of epithelial cells. Our results illustrate a novel mechanism of evolution that may contribute to the complexity of Src kinase regulation.
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Vatish M, Yamada E, Pessin JE, Bastie CC. Fyn kinase function in lipid utilization: a new upstream regulator of AMPK activity? Arch Physiol Biochem 2009; 115:191-8. [PMID: 19728795 PMCID: PMC4324608 DOI: 10.1080/13813450903164348] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The balance of cellular energy levels in response to changes of nutrient availability, stress stimuli or exercise is a critical step in maintaining tissue and whole body homeostasis. Disruption of this balance is associated with various pathologies, including the metabolic syndrome. Recently, accumulating evidence has demonstrated that the AMP-activated protein kinase (AMPK) plays a central role in sensing changes in energy levels. The regulation of AMPK activity is currently the subject of significant investigation since this enzyme is a potential therapeutic target in both metabolic disorders and tumorigenesis. In this review, we present novel evidence of crosstalk between Fyn, one member of the Src kinase family, and AMPK.
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Affiliation(s)
- Manu Vatish
- Albert Einstein College of Medicine, Diabetes Research and Training Center, Department of Medicine, Bronx, NY USA
- Clinical Sciences Research Institute, Warwick Medical School, University of Warwick, Coventry, UK
| | - Eijiro Yamada
- Albert Einstein College of Medicine, Diabetes Research and Training Center, Department of Medicine, Bronx, NY USA
| | - Jeffrey E. Pessin
- Albert Einstein College of Medicine, Diabetes Research and Training Center, Department of Medicine, Bronx, NY USA
| | - Claire C. Bastie
- Albert Einstein College of Medicine, Diabetes Research and Training Center, Department of Medicine, Bronx, NY USA
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Daoud G, Rassart E, Masse A, Lafond J. Src family kinases play multiple roles in differentiation of trophoblasts from human term placenta. J Physiol 2006; 571:537-53. [PMID: 16410281 PMCID: PMC1805791 DOI: 10.1113/jphysiol.2005.102285] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tyrosine phosphorylation plays a major role in controlling many biological processes in different cell types. Src family kinases (SFKs) are one of the most studied groups of tyrosine kinases and can mediate a variety of signalling pathways. However, little is known about the expression of SFKs in human term placenta and their implication in trophoblast differentiation. Therefore, we examined the expression profile of SFK members over time in culture and their implication in differentiation. In vitro, freshly isolated cytotrophoblast cells, cultured in 10% fetal bovine serum (FBS), spontaneously aggregate and fuse to form multinucleated cells that resemble phenotypically mature syncytiotrophoblasts, that concomitantly produce human chorionic gonadotropin (hCG) and human placental lactogen (hPL). In this study, we showed that trophoblasts expressed all SFK members and some of them are expressed as different splice variants. Moreover, using real-time PCR, this study showed two different expression profiles of SFKs in human trophoblasts during culture. In addition, the protein level and phosphorylation status of Src were evaluated using specific antibodies. Src was rapidly phosphorylated at Tyr-416 and dephosphorylated at Tyr-527 after FBS addition. Surprisingly, inhibition of SFKs by 4-amino-5-(4-chlorophenyl)-7-(t-butyl) pyrazolo[3,4-d] pyrimidine (PP2) or herbimycin A had different effects on trophoblast differentiation. While herbimycin A inhibited morphological and hormonal differentiation, PP2 stimulated hormonal differentiation and inhibited cell adhesion and spreading with no effect on cell fusion. In summary, this study showed that SFKs play different roles in trophoblast differentiation, probably depending on SFK members activated. Thus, this study increases our knowledge and understanding of pathology related to impaired trophoblast differentiation such as pre-eclampsia and trophoblast neoplasm.
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Affiliation(s)
- Georges Daoud
- Laboratoire de Physiologie materno-foetale, Département des Sciences Biologiques, Université du Québec à Montréal, C.P. 8888, Succursale Centre-ville, Montréal, Canada, H3C 3P8
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Picard C, Gabert J, Olive D, Collette Y. Altered splicing in hematological malignancies reveals a tissue-specific translational block of the Src-family tyrosine kinase fyn brain isoform expression. Leukemia 2004; 18:1737-9. [PMID: 15356643 DOI: 10.1038/sj.leu.2403499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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