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Rathbun LA, Magliocco AM, Bamezai AK. Human LY6 gene family: potential tumor-associated antigens and biomarkers of prognosis in uterine corpus endometrial carcinoma. Oncotarget 2023; 14:426-437. [PMID: 37141412 PMCID: PMC10159366 DOI: 10.18632/oncotarget.28409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The human Lymphocyte antigen-6 (LY6) gene family has recently gained interest for its possible role in tumor progression. We have carried out in silico analyses of all known LY6 gene expression and amplification in different cancers using TNMplot and cBioportal. We also have analyzed patient survival by Kaplan-Meier plotter after mining the TCGA database. We report that upregulated expression of many LY6 genes is associated with poor survival in uterine corpus endometrial carcinoma (UCEC) cancer patients. Importantly, the expression of several LY6 genes is elevated in UCEC when compared to the expression in normal uterine tissue. For example, LY6K expression is 8.25× higher in UCEC compared to normal uterine tissue, and this high expression is associated with poor survival with a hazard ratio of 2.42 (p-value = 0.0032). Therefore, some LY6 gene products may serve as tumor-associated antigens in UCEC, biomarkers for UCEC detection, and possibly targets for directing UCEC patient therapy. Further analysis of tumor-specific expression of LY6 gene family members and LY6-triggered signaling pathways is needed to uncover the function of LY6 proteins and their ability to endow tumor survival and poor prognosis in UCEC patients.
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Affiliation(s)
- Luke A Rathbun
- Department of Biology, Villanova University, Villanova, PA 19085, USA
| | | | - Anil K Bamezai
- Department of Biology, Villanova University, Villanova, PA 19085, USA
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Premanand A, Rajkumari BR. In silico analysis of gene expression data from bald frontal and haired occipital scalp to identify candidate genes in male androgenetic alopecia. Arch Dermatol Res 2019; 311:815-824. [DOI: 10.1007/s00403-019-01973-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 07/06/2019] [Accepted: 08/30/2019] [Indexed: 12/28/2022]
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Additional Biomarkers beyond RAS That Impact the Efficacy of Cetuximab plus Chemotherapy in mCRC: A Retrospective Biomarker Analysis. JOURNAL OF ONCOLOGY 2018; 2018:5072987. [PMID: 30305811 PMCID: PMC6165607 DOI: 10.1155/2018/5072987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 06/17/2018] [Accepted: 06/27/2018] [Indexed: 12/22/2022]
Abstract
Purpose We aimed to identify new predictive biomarkers for cetuximab in first-line treatment for patients with RAS wild-type metastatic colorectal cancer (mCRC). Methods The study included patients with KRAS wild-type unresectable liver-limited mCRC treated with chemotherapy with or without cetuximab. Next-generation sequencing was done for single nucleotide polymorphism according to custom panel. Potential predictive biomarkers were identified and integrated into a predictive model within a training cohort. The model was validated in a validation cohort. Results Thirty-one of 247(12.6%) patients harbored RAS mutations. In training cohort (N=93), six potential predictive genes, namely, ATP6V1B1, CUL9, ERBB2, LY6G6D, PTCH1, and RBMXL3, were identified. According to predictive model, patients were divided into responsive group (n=66) or refractory group (n=27). In responsive group, efficacy outcomes were significantly improved by addition of cetuximab to chemotherapy. In refractory group, no benefit was observed. Interaction test was significant across all endpoints. In validation cohort (N=123), similar results were also observed. Conclusions In the first-line treatment of mCRC, the predictive model integrating six new predictive mutations divided patients well, indicating a promising approach to further refine patient selection for cetuximab on the basis of RAS mutations.
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Chen IH, Aguilar HA, Paez Paez JS, Wu X, Pan L, Wendt MK, Iliuk AB, Zhang Y, Tao WA. Analytical Pipeline for Discovery and Verification of Glycoproteins from Plasma-Derived Extracellular Vesicles as Breast Cancer Biomarkers. Anal Chem 2018; 90:6307-6313. [PMID: 29629753 DOI: 10.1021/acs.analchem.8b01090] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- I-Hsuan Chen
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - J. Sebastian Paez Paez
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Pan
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael K. Wendt
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Anton B. Iliuk
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Ying Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - W. Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Organization, evolution and functions of the human and mouse Ly6/uPAR family genes. Hum Genomics 2016; 10:10. [PMID: 27098205 PMCID: PMC4839075 DOI: 10.1186/s40246-016-0074-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/14/2016] [Indexed: 01/08/2023] Open
Abstract
Members of the lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) superfamily of proteins are cysteine-rich proteins characterized by a distinct disulfide bridge pattern that creates the three-finger Ly6/uPAR (LU) domain. Although the Ly6/uPAR family proteins share a common structure, their expression patterns and functions vary. To date, 35 human and 61 mouse Ly6/uPAR family members have been identified. Based on their subcellular localization, these proteins are further classified as GPI-anchored on the cell membrane, or secreted. The genes encoding Ly6/uPAR family proteins are conserved across different species and are clustered in syntenic regions on human chromosomes 8, 19, 6 and 11, and mouse Chromosomes 15, 7, 17, and 9, respectively. Here, we review the human and mouse Ly6/uPAR family gene and protein structure and genomic organization, expression, functions, and evolution, and introduce new names for novel family members.
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Milanesi E, Bonvicini C, Alberici A, Pilotto A, Cattane N, Premi E, Gazzina S, Archetti S, Gasparotti R, Cancelli V, Gennarelli M, Padovani A, Borroni B. Molecular signature of disease onset in granulin mutation carriers: a gene expression analysis study. Neurobiol Aging 2013; 34:1837-45. [PMID: 23419701 DOI: 10.1016/j.neurobiolaging.2012.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 11/09/2012] [Accepted: 11/22/2012] [Indexed: 11/17/2022]
Abstract
Mutations within Granulin (GRN) gene are causative of autosomal dominant frontotemporal lobar degeneration (FTLD). Though GRN mutations are inherited at birth, the disease onset usually occurs in the sixth decade of life. The objective of this study was to identify new genetic pathways linked to inherited GRN disease and involved in the shift from asymptomatic to symptomatic stages. Microarray gene expression analysis on leukocytes was carried out on 15 patients carrying GRN T272SfsX10 mutation, and their asymptomatic siblings with (n = 14) or without (n = 11) GRN mutation. The results were then validated by real-time polymerase chain reaction, and compared with those obtained in a cohort of FTLD without GRN mutation (n = 16). The association between candidate genes and damage of specific brain areas was investigated by voxel-based morphometry on magnetic resonance imaging scans (family-wise error-corrected). Leukocytes mRNA levels of TMEM40 and LY6G6F and other genes mainly involved in inflammation were significantly higher in patients carrying GRN mutations compared with asymptomatic carriers and other FTLD. The higher the levels of TMEM40 the greater is the damage of parietal lobule; the higher the LY6G6F gene expression the greater is the atrophy in superior frontal gyrus. Enhanced inflammation associated with the onset of GRN disease might be either related to disease pathogenetic mechanism leading to neurodegeneration or to a compensatory pathway that counteracts disease progression. The identification of specific molecular targets of GRN-FTLD disease is essential when considering future disease-modifying therapies.
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Affiliation(s)
- Elena Milanesi
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
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Ohashi K, Takizawa F, Tokumaru N, Nakayasu C, Toda H, Fischer U, Moritomo T, Hashimoto K, Nakanishi T, Dijkstra JM. A molecule in teleost fish, related with human MHC-encoded G6F, has a cytoplasmic tail with ITAM and marks the surface of thrombocytes and in some fishes also of erythrocytes. Immunogenetics 2010; 62:543-59. [PMID: 20614118 DOI: 10.1007/s00251-010-0460-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 06/17/2010] [Indexed: 12/15/2022]
Abstract
In teleost fish, a novel gene G6F-like was identified, encoding a type I transmembrane molecule with four extracellular Ig-like domains and a cytoplasmic tail with putative tyrosine phosphorylation motifs including YxN and an immunoreceptor tyrosine-based activation motif (ITAM). G6F-like maps to a teleost genomic region where stretches corresponding to human chromosomes 6p (with the MHC), 12p (with CD4 and LAG-3), and 19q are tightly linked. This genomic organization resembles the ancestral "Ur-MHC" proposed for the jawed vertebrate ancestor. The deduced G6F-like molecule shows sequence similarity with members of the CD4/LAG-3 family and with the human major histocompatibility complex-encoded thrombocyte marker G6F. Despite some differences in molecular organization, teleost G6F-like and tetrapod G6F seem orthologous as they map to similar genomic location, share typical motifs in transmembrane and cytoplasmic regions, and are both expressed by thrombocytes/platelets. In the crucian carps goldfish (Carassius auratus auratus) and ginbuna (Carassius auratus langsdorfii), G6F-like was found expressed not only by thrombocytes but also by erythrocytes, supporting that erythroid and thromboid cells in teleost fish form a hematopoietic lineage like they do in mammals. The ITAM-bearing of G6F-like suggests that the molecule plays an important role in cell activation, and G6F-like expression by erythrocytes suggests that these cells have functional overlap potential with thrombocytes.
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Affiliation(s)
- Ken Ohashi
- Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
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Beliakov IS, Karakasheva TA, Mazurenko NN. Exon-intron structure of the LY6G6D gene. Mol Biol 2009. [DOI: 10.1134/s0026893309040025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chu PY, Huang LY, Hsu CH, Liang CC, Guan JL, Hung TH, Shen TL. Tyrosine phosphorylation of growth factor receptor-bound protein-7 by focal adhesion kinase in the regulation of cell migration, proliferation, and tumorigenesis. J Biol Chem 2009; 284:20215-26. [PMID: 19473962 DOI: 10.1074/jbc.m109.018259] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have previously reported that growth factor receptor-bound protein-7 (Grb7), an Src-homology 2 (SH2)-containing adaptor protein, enables interaction with focal adhesion kinase (FAK) to regulate cell migration in response to integrin activation. To further elucidate the signaling events mediated by FAK*Grb7 complexes in promoting cell migration and other cellular functions, we firstly examined the phosphorylated tyrosine site(s) of Grb7 by FAK using an in vivo mutagenesis. We found that FAK was capable of phosphorylating at least 2 of 12 tyrosine residues within Grb7, Tyr-188 and Tyr-338. Moreover, mutations converting the identified Tyr to Phe inhibited integrin-dependent cell migration as well as impaired cell proliferation but not survival compared with the wild-type control. Interestingly, the above inhibitory effects caused by the tyrosine phosphorylation-deficient mutants are probably attributed to their down-regulation of phospho-Tyr-397 of FAK, thereby implying a mechanism by competing with wild-type Grb7 for binding to FAK. Consequently, these tyrosine phosphorylation-deficient mutants evidently altered the phospho-Tyr-118 of paxillin and phosphorylation of ERK1/2 but less on phospho-Ser-473 of AKT, implying their involvement in the FAK*Grb7-mediated cellular functions. Additionally, we also illustrated that the formation of FAK*Grb7 complexes and Grb7 phosphorylation by FAK in an integrin-dependent manner were essential for cell migration, proliferation and anchorage-independent growth in A431 epidermal carcinoma cells, indicating the importance of FAK*Grb7 complexes in tumorigenesis. Our data provide a better understanding on the signal transduction event for FAK*Grb7-mediated cellular functions as well as to shed light on a potential therapeutic in cancers.
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Affiliation(s)
- Pei-Yu Chu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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Calvanese V, Mallya M, Campbell RD, Aguado B. Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism. BMC Mol Biol 2008; 9:81. [PMID: 18817541 PMCID: PMC2562388 DOI: 10.1186/1471-2199-9-81] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 09/25/2008] [Indexed: 11/24/2022] Open
Abstract
Background Regulation of the expression of particular genes can rely on mechanisms that are different from classical transcriptional and translational control. The LY6G5B and LY6G6D genes encode LY-6 domain proteins, whose expression seems to be regulated in an original fashion, consisting of an intron retention event which generates, through an early premature stop codon, a non-coding transcript, preventing expression in most cell lines and tissues. Results The MHC LY-6 non-coding transcripts have shown to be stable and very abundant in the cell, and not subject to Nonsense Mediated Decay (NMD). This retention event appears not to be solely dependent on intron features, because in the case of LY6G5B, when the intron is inserted in the artificial context of a luciferase expression plasmid, it is fully spliced but strongly stabilises the resulting luciferase transcript. In addition, by quantitative PCR we found that the retained and spliced forms are differentially expressed in tissues indicating an active regulation of the non-coding transcript. EST database analysis revealed that these genes have an alternative expression pathway with the formation of Transcription Induced Chimeras (TIC). This data was confirmed by RT-PCR, revealing the presence of different transcripts that would encode the chimeric proteins CSNKβ-LY6G5B and G6F-LY6G6D, in which the LY-6 domain would join to a kinase domain and an Ig-like domain, respectively. Conclusion In conclusion, the LY6G5B and LY6G6D intron-retained transcripts are not subjected to NMD and are more abundant than the properly spliced forms. In addition, these genes form chimeric transcripts with their neighbouring same orientation 5' genes. Of interest is the fact that the 5' genes (CSNKβ or G6F) undergo differential splicing only in the context of the chimera (CSNKβ-LY6G5B or G6F-LY6G6C) and not on their own.
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Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60:1-18. [PMID: 18193213 PMCID: PMC2206249 DOI: 10.1007/s00251-007-0262-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/29/2007] [Indexed: 02/05/2023]
Abstract
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
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Affiliation(s)
- Roger Horton
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard Gibson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Marcos Miretti
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard J. Allcock
- School of Surgery and Pathology, University of Western Australia, Nedlands, 6009 WA Australia
| | - Jeff Almeida
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Simon Forbes
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - James G. R. Gilbert
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Karen Halls
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Jennifer L. Harrow
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Elizabeth Hart
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Kevin Howe
- CRUK Cambridge Research Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Anne N. Roberts
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - C. Andrew Stewart
- National Cancer Institute, P.O. Box B., 567/206, Frederick, MD 21702 USA
| | - James A. Traherne
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Steve Trevanion
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Laurens Wilming
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609-1673 USA
| | - John F. Elliott
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BD UK
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Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, Burns P, Langford CF, Ellis PD, Dudbridge F, Zwaginga JJ, Watkins NA, van der Schoot CE, Ouwehand WH. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Blood 2006; 109:3260-9. [PMID: 17192395 PMCID: PMC6485507 DOI: 10.1182/blood-2006-07-036269] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.
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Affiliation(s)
- Iain C. Macaulay
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - Marloes R. Tijssen
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
| | - Daphne C. Thijssen-Timmer
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
| | - Arief Gusnanto
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | | | - Philippa Burns
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | | | - Peter D. Ellis
- Microarray Facility, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Frank Dudbridge
- Medical Research Council (MRC) Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | - Jaap-Jan Zwaginga
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Immunohematology–Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Nicholas A. Watkins
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
| | - C. Ellen van der Schoot
- Department of Experimental Immunohaematology, Sanquin Research at Central Laboratory for the Blood Transfusion Service (CLB), Amsterdam, The Netherlands
- Landsteiner Laboratory, Academic Medical Center (AMC), University of Amsterdam, The Netherlands
- Department of Hematology, Amsterdam Medical Centre, University of Amsterdam, The Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, United Kingdom
- National Blood Service, Cambridge, United Kingdom
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García A, Senis YA, Antrobus R, Hughes CE, Dwek RA, Watson SP, Zitzmann N. A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter. Proteomics 2006; 6:5332-43. [PMID: 16941570 PMCID: PMC1869047 DOI: 10.1002/pmic.200600299] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Collagen-related peptide (CRP) stimulates powerful activation of platelets through the glycoprotein VI (GPVI)-FcR gamma-chain complex. We have combined proteomics and traditional biochemistry approaches to study the proteome of CRP-activated platelets, focusing in detail on tyrosine phosphorylation. In two separate approaches, phosphotyrosine immunoprecipitations followed by 1-D-PAGE, and 2-DE, were used for protein separation. Proteins were identified by MS. By following these approaches, 96 proteins were found to undergo PTM in response to CRP in human platelets, including 11 novel platelet proteins such as Dok-1, SPIN90, osteoclast stimulating factor 1, and beta-Pix. Interestingly, the type I transmembrane protein G6f was found to be specifically phosphorylated on Tyr-281 in response to platelet activation by CRP, providing a docking site for the adapter Grb2. G6f tyrosine phoshporylation was also found to take place in response to collagen, although not in response to the G protein-coupled receptor agonists, thrombin and ADP. Further, we also demonstrate for the first time that Grb2 and its homolog Gads are tyrosine-phosphorylated in CRP-stimulated platelets. This study provides new insights into the mechanism of platelet activation through the GPVI collagen receptor, helping to build the basis for the development of new drug targets for thrombotic disease.
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Affiliation(s)
- Angel García
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK.
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Lewandrowski U, Moebius J, Walter U, Sickmann A. Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach. Mol Cell Proteomics 2005; 5:226-33. [PMID: 16263699 DOI: 10.1074/mcp.m500324-mcp200] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among known platelet proteins, a prominent and functionally important group is represented by glycoprotein isoforms. They account e.g. for secretory proteins and plasma membrane receptors including integrins and glycoprotein VI as well as intracellular components of cytosol and organelles including storage proteins (multimerin 1 etc.). Although many of those proteins have been studied for some time with regard to their function, little attention has been paid with respect to their glycosylation sites. Here we report the analysis of N-glycosylation sites of human platelet proteins. For the enrichment of glycopeptides, lectin affinity chromatography as well as chemical trapping of protein bound oligosaccharides was used. Therefore, concanavalin A was used for specific interaction with carbohydrate species along with periodic acid oxidation and hydrazide bead trapping of glycosylated proteins. Derivatization by peptide:N-glycosidase F yielded deglycosylated peptides, which provided the basis for the elucidation of proteins and their sites of modification. Using both methods in combination with nano-LC-ESI-MS/MS analysis 70 different glycosylation sites within 41 different proteins were identified. Comparison with the Swiss-Prot database established that the majority of these 70 sites have not been specifically determined by previous research projects. With this approach including hydrazide bead affinity trapping, the immunoglobulin receptor G6f, which is known to couple to the Ras-mitogen-activated protein kinase pathway in the immune system, was shown here for the first time to be present in human platelets.
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Affiliation(s)
- Urs Lewandrowski
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf Virchow Center for Experimental Biomedicine, Versbacher Strasse 9, 97078 Wuerzburg, Germany
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15
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Abstract
The Grb proteins (growth factor receptor-bound proteins) Grb7, Grb10 and Grb14 constitute a family of structurally related multidomain adapters with diverse cellular functions. Grb10 and Grb14, in particular, have been implicated in the regulation of insulin receptor signalling, whereas Grb7 appears predominantly to be involved in focal adhesion kinase-mediated cell migration. However, at least in vitro, these adapters can bind to a variety of growth factor receptors. The highest identity within the Grb7/10/14 family occurs in the C-terminal SH2 (Src homology 2) domain, which mediates binding to activated receptors. A second well-conserved binding domain, BPS [between the PH (pleckstrin homology) and SH2 domains], can act to enhance binding to the IR (insulin receptor). Consistent with a putative adapter function, some non-receptor-binding partners, including protein kinases, have also been identified. Grb10 and Grb14 are widely, but not uniformly, expressed in mammalian tissues, and there are various isoforms of Grb10. Binding of Grb10 or Grb14 to autophosphorylated IR in vitro inhibits tyrosine kinase activity towards other substrates, but studies on cultured cell lines have been conflicting as to whether Grb10 plays a positive or negative role in insulin signalling. Recent gene knockouts in mice have established that Grb10 and Grb14 act as inhibitors of intracellular signalling pathways regulating growth and metabolism, although the phenotypes of the two knockouts are distinct. Ablation of Grb14 enhances insulin action in liver and skeletal muscle and improves whole-body tolerance, with little effect on embryonic growth. Ablation of Grb10 results in disproportionate overgrowth of the embryo and placenta involving unidentified pathways, and also impacts on hepatic glycogen synthesis, and probably on glucose homoeostasis. This review discusses the extent to which previous studies in vitro can account for the observed phenotype of knockout animals, and considers evidence that aberrant function of Grb10 or Grb14 may contribute to disorders of growth and metabolism in humans.
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Affiliation(s)
- Lowenna J Holt
- University of Cambridge, Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge CB2 2QR, UK.
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16
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de Vet ECJM, Newland SAB, Lyons PA, Aguado B, Campbell RD. The cell surface receptor G6b, a member of the immunoglobulin superfamily, binds heparin. FEBS Lett 2005; 579:2355-8. [PMID: 15848171 DOI: 10.1016/j.febslet.2005.03.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Revised: 03/11/2005] [Accepted: 03/14/2005] [Indexed: 10/25/2022]
Abstract
The G6b gene, located in the human Major Histocompatibility Complex, encodes a receptor of the immunoglobulin (Ig) superfamily. In this study, we show using a variety of techniques that the extracellular domain of the G6b protein, containing a single Ig-like domain, binds to heparin with high affinity. In an ELISA assay, this binding was displaceable with soluble heparin with an IC50 value of approximately 0.5 microg/ml. Other sulfated glycans showed weaker or no competition. The observed interaction between G6b and heparin is strongly salt dependent suggesting a mainly electrostatic interaction. Heparin might modulate the interaction of G6b with its as yet unidentified protein ligand.
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Affiliation(s)
- Edwin C J M de Vet
- MRC Rosalind Franklin Centre for Genomics Research, Hinxton, Cambridge, UK
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17
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Abstract
The MHC, primarily known for its antigen-presenting class I and II molecules, harbours, within a central segment of less than 1 Mb, a dense collection of genes involved in various biological functions. Although MHC I and MHC II are principal players of adaptive immunity, several loci within this central (still called class III) MHC region encode members of the innate immune system. These include the long known factors of the complement system--potentially inhibitory and triggering natural killer receptors as well as stress proteins. Whether this physical proximity is fortuitous or functionally advantageous is an important question for the future of MHC genetics.
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Affiliation(s)
- Georges Hauptmann
- Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, 4 rue Kirschleger, F-67085 Strasbourg Cedex, France.
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