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Zhou K, Zhang M, Zhai D, Wang Z, Liu T, Xie Y, Shi Y, Shi H, Chen Q, Li X, Xu J, Cai Z, Zhang Y, Shao N, Lin Y. Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers. Breast Cancer Res Treat 2024; 208:441-459. [PMID: 39030466 DOI: 10.1007/s10549-024-07437-0] [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: 02/23/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
PURPOSE Inflammatory breast cancer (IBC), a rare and highly aggressive form of breast cancer, accounts for 10% of breast cancer-related deaths. Previous omics studies of IBC have focused solely on one of genomics or transcriptomics and did not discover common differences that could distinguish IBC from non-IBC. METHODS Seventeen IBC patients and five non-IBC patients as well as additional thirty-three Asian breast cancer samples from TCGA-BRCA were included for the study. We performed whole-exon sequencing (WES) to investigate different somatic genomic alterations, copy number variants, and large structural variants between IBC and non-IBC. Bulk RNA sequencing (RNA-seq) was performed to examine the differentially expressed genes, pathway enrichment, and gene fusions. WES and RNA-seq data were further investigated in combination to discover genes that were dysregulated in both genomics and transcriptomics. RESULTS Copy number variation analysis identified 10 cytobands that showed higher frequency in IBC. Structural variation analysis showed more frequent deletions in IBC. Pathway enrichment and immune infiltration analysis indicated increased immune activation in IBC samples. Gene fusions including CTSC-RAB38 were found to be more common in IBC. We demonstrated more commonly dysregulated RAS pathway in IBC according to both WES and RNA-seq. Inhibitors targeting RAS signaling and its downstream pathways were predicted to possess promising effects in IBC treatment. CONCLUSION We discovered differences unique in Asian women that could potentially explain IBC etiology and presented RAS signaling pathway as a potential therapeutic target in IBC treatment.
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Affiliation(s)
- Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, Guangdong, China
| | - Yunjian Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
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Al-Hawary SIS, Alsalamy A, Gupta R, Alsaab HO, Hjazi A, Edilboyev U, Ramadan MF, Hussien BM, Ahmed M, Hosseini-Fard SR. VAV3 in human cancers: Mechanism and clinical implication. Pathol Res Pract 2023; 248:154681. [PMID: 37467637 DOI: 10.1016/j.prp.2023.154681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Guanine nucleotide exchange factors (GEFs) are primarily involved in signal transmission between cell membrane receptors and intracellular mediators. Upon replacing GDP with GTP, GEFs can alter their conformation, resulting in their binding to downstream effectors, such as GTPases like Ras homologous (Rho). VAV GEF family are versatile proteins working as an adaptor mediator and GEF for Rho GTPase. They act as a phosphorylation-dependent molecular switcher, fluctuating between active (tyrosine phosphorylated) and inactive (non-phosphorylated) conformation in cell signaling. Accumulating data showed that VAV3 is implicated in cancer progression. The higher levels of VAV3 in human cancers proposed that it may have an oncogenic role in cancer progression. Available studies demonstrated that VAV3 promoted cell proliferation, epithelial-mesenchymal transition (EMT), colony formation, cell cycle, survival, migration and invasion, and suppressed cell apoptosis. In addition, other studies indicated that VAV3 may have a prognostic value in cancer as well as it may act as a mediator in cancer chemoresistance. Here, we aimed to investigate the underlying molecular mechanism of VAV3 in cancer progression as well as to review its value as a prognostic biomarker and chemoresistance mediator in human cancers.
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Affiliation(s)
| | - Ali Alsalamy
- College of Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Reena Gupta
- Institute of Pharmaceutical Research, GLA University, District-Mathura, U.P., 281406, India
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif 21944, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Unarbek Edilboyev
- Department of Engineering Graphics and Design Theory, Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, National Research University, Tashkent, Uzbekistan
| | | | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Muhja Ahmed
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Seyed Reza Hosseini-Fard
- Biochemistry Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Røyrvik EC, Husebye ES. The genetics of autoimmune Addison disease: past, present and future. Nat Rev Endocrinol 2022; 18:399-412. [PMID: 35411072 DOI: 10.1038/s41574-022-00653-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/23/2022]
Abstract
Autoimmune Addison disease is an endocrinopathy that is fatal if not diagnosed and treated in a timely manner. Its rarity has hampered unbiased studies of the predisposing genetic factors. A 2021 genome-wide association study, explaining up to 40% of the genetic susceptibility, has revealed new disease loci and reproduced some of the previously reported associations, while failing to reproduce others. Credible risk loci from both candidate gene and genome-wide studies indicate that, like one of its most common comorbidities, type 1 diabetes mellitus, Addison disease is primarily caused by aberrant T cell behaviour. Here, we review the current understanding of the genetics of autoimmune Addison disease and its position in the wider field of autoimmune disorders. The mechanisms that could underlie the effects on the adrenal cortex are also discussed.
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Affiliation(s)
- Ellen C Røyrvik
- Department of Clinical Science, University of Bergen, Bergen, Norway.
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway.
| | - Eystein S Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Park I, Son M, Ahn E, Kim YW, Kong YY, Yun Y. The Transmembrane Adaptor Protein LIME Is Essential for Chemokine-Mediated Migration of Effector T Cells to Inflammatiory Sites. Mol Cells 2020; 43:921-934. [PMID: 33243936 PMCID: PMC7700840 DOI: 10.14348/molcells.2020.0124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 11/27/2022] Open
Abstract
Lck-interacting transmembrane adaptor 1 (LIME) has been previously identified as a raft-associated transmembrane protein expressed predominantly in T and B lymphocytes. Although LIME is shown to transduce the immunoreceptor signaling and immunological synapse formation via its tyrosine phosphorylation by Lck, a Src-family kinase, the in vivo function of LIME has remained elusive in the previous studies. Here we report that LIME is preferentially expressed in effector T cells and mediates chemokine-mediated T cell migration. Interestingly, in LIME-/- mice, while T cell receptor stimulation-dependent proliferation, differentiation to effector T cells, cytotoxic T lymphocyte (CTL) function and regulatory T lymphocyte (Treg) function were normal, only T cell-mediated inflammatory response was significantly defective. The reduced inflammation was accompanied by the impaired infiltration of leukocytes and T cells to the inflammatory sites of LIME-/- mice. More specifically, the absence of LIME in effector T cells resulted in the reduced migration and defective morphological polarization in response to inflammatory chemokines such as CCL5 and CXCL10. Consistently, LIME-/- effector T cells were found to be defective in chemokine-mediated activation of Rac1 and Rap1, and dysregulated phosphorylation of Pyk2 and Cas. Taken together, the present findings show that LIME is a critical regulator of inflammatory chemokine-mediated signaling and the subsequent migration of effector T cells to inflammatory sites.
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Affiliation(s)
- Inyoung Park
- Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Myongsun Son
- Department of Life Science, Ewha Womans University, Seoul 03760, Korea
| | - Eunseon Ahn
- Department of Life Science, Ewha Womans University, Seoul 03760, Korea
| | - Young-Woong Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Young-Yun Kong
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yungdae Yun
- Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
- Department of Life Science, Ewha Womans University, Seoul 03760, Korea
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Ban M, Liao W, Baker A, Compston A, Thorpe J, Molyneux P, Fraser M, Khadake J, Jones J, Coles A, Sawcer S. Transcript specific regulation of expression influences susceptibility to multiple sclerosis. Eur J Hum Genet 2020; 28:826-834. [PMID: 31932686 DOI: 10.1038/s41431-019-0569-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 11/03/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified over 100 loci containing single nucleotide variants (SNVs) that influence the risk of developing multiple sclerosis (MS). Most of these loci lie in non-coding regulatory regions of the genome that are active in immune cells and are therefore thought to modify risk by altering the expression of key immune genes. To explore this hypothesis we screened genes flanking MS-associated variants for evidence of allele specific expression (ASE) by quantifying the transcription of coding variants in linkage disequilibrium with MS-associated SNVs. In total, we were able to identify and successfully analyse 200 such coding variants (from 112 genes) in both CD4+ and CD8+ T cells from 106 MS patients and 105 controls. Fifty-six of these coding variants (from 43 genes) showed statistically significant evidence of ASE in one or both cell types. In the Lck interacting transmembrane adaptor 1 gene (LIME1), for example, we were able to show that in both cell types, the MS-associated variant rs2256814 increased the expression of some transcripts while simultaneously reducing the expression of other transcripts. In CD4+ cells from an additional independent set of 96 cases and 93 controls we were able to replicate the effect of this SNV on the balance of alternate LIME1 transcripts using qPCR (p = 5 × 10-24). Our data thus indicate that some of the MS-associated SNVs identified by GWAS likely exert their effects on risk by distorting the balance of alternate transcripts rather than by changing the overall level of gene expression.
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Affiliation(s)
- Maria Ban
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Wenjia Liao
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Amie Baker
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Alastair Compston
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - John Thorpe
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Paul Molyneux
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Mary Fraser
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Jyoti Khadake
- NIHR BioResource for Translational Research, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Box 299, Cambridge, CB2 0QQ, UK
| | - Joanne Jones
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Alasdair Coles
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
| | - Stephen Sawcer
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Box 165, Hills Road, Cambridge, CB2 0QQ, UK
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Rodríguez-Fdez S, Bustelo XR. The Vav GEF Family: An Evolutionary and Functional Perspective. Cells 2019; 8:E465. [PMID: 31100928 PMCID: PMC6562523 DOI: 10.3390/cells8050465] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Vav proteins play roles as guanosine nucleotide exchange factors for Rho GTPases and signaling adaptors downstream of protein tyrosine kinases. The recent sequencing of the genomes of many species has revealed that this protein family originated in choanozoans, a group of unicellular organisms from which animal metazoans are believed to have originated from. Since then, the Vav family underwent expansions and reductions in its members during the evolutionary transitions that originated the agnates, chondrichthyes, some teleost fish, and some neoaves. Exotic members of the family harboring atypical structural domains can be also found in some invertebrate species. In this review, we will provide a phylogenetic perspective of the evolution of the Vav family. We will also pay attention to the structure, signaling properties, regulatory layers, and functions of Vav proteins in both invertebrate and vertebrate species.
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Affiliation(s)
- Sonia Rodríguez-Fdez
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
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Abstract
The Vav family is a group of tyrosine phosphorylation-regulated signal transduction molecules hierarchically located downstream of protein tyrosine kinases. The main function of these proteins is to work as guanosine nucleotide exchange factors (GEFs) for members of the Rho GTPase family. In addition, they can exhibit a variety of catalysis-independent roles in specific signaling contexts. Vav proteins play essential signaling roles for both the development and/or effector functions of a large variety of cell lineages, including those belonging to the immune, nervous, and cardiovascular systems. They also contribute to pathological states such as cancer, immune-related dysfunctions, and atherosclerosis. Here, I will provide an integrated view about the evolution, regulation, and effector properties of these signaling molecules. In addition, I will discuss the pros and cons for their potential consideration as therapeutic targets.
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Key Words
- Ac, acidic
- Ahr, aryl hydrocarbon receptor
- CH, calponin homology
- CSH3, most C-terminal SH3 domain of Vav proteins
- DAG, diacylglycerol
- DH, Dbl-homology domain
- Dbl-homology
- GDP/GTP exchange factors
- GEF, guanosine nucleotide exchange factor
- HIV, human immunodeficiency virus
- IP3, inositoltriphosphate
- NFAT, nuclear factor of activated T-cells
- NSH3, most N-terminal SH3 domain of Vav proteins
- PH, plekstrin-homology domain
- PI3K, phosphatidylinositol-3 kinase
- PIP3, phosphatidylinositol (3,4,5)-triphosphate
- PKC, protein kinase C
- PKD, protein kinase D
- PLC-g, phospholipase C-g
- PRR, proline-rich region
- PTK, protein tyrosine kinase
- Phox, phagocyte oxidase
- Rho GTPases
- SH2, Src homology 2
- SH3, Src homology 3
- SNP, single nucleotide polymorphism
- TCR, T-cell receptor
- Vav
- ZF, zinc finger region
- cGMP, cyclic guanosine monophosphate
- cancer
- cardiovascular biology
- disease
- immunology
- nervous system
- signaling
- therapies
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Affiliation(s)
- Xosé R Bustelo
- a Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer ; Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca ; Campus Unamuno; Salamanca , Spain
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Palmitoylated transmembrane adaptor proteins in leukocyte signaling. Cell Signal 2014; 26:895-902. [PMID: 24440308 DOI: 10.1016/j.cellsig.2014.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 12/14/2022]
Abstract
Transmembrane adaptor proteins (TRAPs) are structurally related proteins that have no enzymatic function, but enable inducible recruitment of effector molecules to the plasma membrane, usually in a phosphorylation dependent manner. Numerous surface receptors employ TRAPs for either propagation or negative regulation of the signal transduction. Several TRAPs (LAT, NTAL, PAG, LIME, PRR7, SCIMP, LST1/A, and putatively GAPT) are known to be palmitoylated that could facilitate their localization in lipid rafts or tetraspanin enriched microdomains. This review summarizes expression patterns, binding partners, signaling pathways, and biological functions of particular palmitoylated TRAPs with an emphasis on the three most recently discovered members, PRR7, SCIMP, and LST1/A. Moreover, we discuss in silico methodology used for discovery of new family members, nature of their binding partners, and microdomain localization.
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