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Gong B, Qu T, Zhang J, Jia Y, Song Z, Chen C, Yang J, Wang C, Liu Y, Jin Y, Cao W, Zhao Q. Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway. Comput Struct Biotechnol J 2024; 23:1547-1561. [PMID: 38645433 PMCID: PMC11031727 DOI: 10.1016/j.csbj.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 04/23/2024] Open
Abstract
Neuroblastoma (NB) is the most prevalent extracranial solid tumor in pediatric patients, and its treatment failure often associated with metastasis. In this study, LASSO, SVM-RFE, and random forest tree algorithms, was used to identify the pivotal gene involved in NB metastasis. NB cell lines (SK-N-AS and SK-N-BE2), in conjunction with NB tissue were used for further study. ABLIM3 was identified as the hub gene and can be an independent prognostic factor for patients with NB. The immunohistochemical analysis revealed that ABLIM3 is negatively correlated with the metastasis of NB. Patients with low expression of ABLIM3 had a poor prognosis. High ABLIM3 expression correlated with APC co-stimulation and Type1 IFN response, and TIDE analysis indicated that patients with low ABLIM3 expression exhibited enhanced responses to immunotherapy. Downregulation of ABLIM3 by shRNA transfection increased the migration and invasion ability of NB cells. Gene Set Enrichment Analysis (GSEA) revealed that genes associated with ABLIM3 were primarily enriched in the cell adhesion molecules (CAMs) pathway. RT-qPCR and western blot analyses demonstrated that downregulation of ABLIM3 led to decreased expression of ITGA3, ITGA8, and KRT19, the key components of CAMs. This study indicated that ABLIM3 can be an independent prognostic factor for NB patients, and CAMs may mediate the effect of ABLIM3 on the metastasis of NB, suggesting that ABLIM3 is a potential therapeutic target for NB metastasis, which provides a novel strategy for future research and treatment strategies for NB patients.
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Affiliation(s)
- Baocheng Gong
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Tongyuan Qu
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jiaojiao Zhang
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yubin Jia
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Zian Song
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chong Chen
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiaxing Yang
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chaoyu Wang
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yun Liu
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yan Jin
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Wenfeng Cao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Qiang Zhao
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
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2
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Chatterjee D, Rahman MM, Saha AK, Siam MKS, Sharif Shohan MU. Transcriptomic analysis of esophageal cancer reveals hub genes and networks involved in cancer progression. Comput Biol Med 2023; 159:106944. [PMID: 37075603 DOI: 10.1016/j.compbiomed.2023.106944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023]
Abstract
Esophageal carcinoma (ESCA) has a 5-year survival rate of fewer than 20%. The study aimed to identify new predictive biomarkers for ESCA through transcriptomics meta-analysis to address the problems of ineffective cancer therapy, lack of efficient diagnostic tools, and costly screening and contribute to developing more efficient cancer screening and treatments by identifying new marker genes. Nine GEO datasets of three kinds of esophageal carcinoma were analyzed, and 20 differentially expressed genes were detected in carcinogenic pathways. Network analysis revealed four hub genes, namely RAR Related Orphan Receptor A (RORA), lysine acetyltransferase 2B (KAT2B), Cell Division Cycle 25B (CDC25B), and Epithelial Cell Transforming 2 (ECT2). Overexpression of RORA, KAT2B, and ECT2 was identified with a bad prognosis. These hub genes modulate immune cell infiltration. These hub genes modulate immune cell infiltration. Although this research needs lab confirmation, we found interesting biomarkers in ESCA that may aid in diagnosis and treatment.
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Affiliation(s)
- Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Mostafijur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Bangladesh
| | - Anik Kumar Saha
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
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3
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Wang T, Dang N, Tang G, Li Z, Li X, Shi B, Xu Z, Li L, Yang X, Xu C, Ye K. Integrating bulk and single-cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma. Mol Oncol 2022; 16:2195-2213. [PMID: 35124891 PMCID: PMC9168757 DOI: 10.1002/1878-0261.13190] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/07/2021] [Accepted: 02/04/2022] [Indexed: 11/09/2022] Open
Abstract
Efficacy of immunotherapy in hepatocellular carcinoma (HCC) is blocked by its high degree of inter- and intra-tumor heterogeneity and immunosuppressive tumor microenvironment. However, the correlation between tumor heterogeneity and immunosuppressive microenvironment in HCC has not been well addressed. Here, we endeavored to dissect inter- and intra-tumor heterogeneity in HCC and uncover how they contribute to the immunosuppressive microenvironment. We performed consensus molecular subtyping with non-negative matrix factorization (NMF) clustering to stratify the inter-heterogeneity profile of HCC tumors. We grouped HCC tumors from the Cancer Genome Atlas (TCGA) patients into three subtypes (S1, S2 and S3), where S1 was characterized as a 'hot tumor' profile with high expression level of T cell genes and rate of immune scores. S2 was characterized as a 'cold tumor' profile with the highest tumor purity score, and S3 as an 'immunosuppressed tumor' profile with the poorest prognosis and a high expression level of immunosuppressive genes such as cytotoxic T-lymphocyte-associated protein-4, TIGIT, and PDCD1. Moreover, we combined weighted gene co-expression network analysis and single-cell regulatory network inference and clustering (SCENIC) in the single-cell dataset of the S3-like subtype (CS3) and identified a transcription factor, BATF, which could upregulate immunosuppressive genes. Finally, we identified a cell interaction network in which a myeloid-derived suppressor cell-like macrophage subtype could promote the formation of immunosuppressive T-cells.
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Affiliation(s)
- Tingjie Wang
- School of Automation Science and EngineeringFaculty of Electronic and Information EngineeringXi’an Jiaotong UniversityChina
| | - Ningxin Dang
- Genome InstituteThe First Affiliated Hospital of Xi’an Jiaotong UniversityChina
| | - Guangbo Tang
- School of Life Science and TechnologyXi’an Jiaotong UniversityXi’an, ShaanxiChina
| | - Zihang Li
- School of Life Science and TechnologyXi’an Jiaotong UniversityXi’an, ShaanxiChina
| | - Xiujuan Li
- School of Automation Science and EngineeringFaculty of Electronic and Information EngineeringXi’an Jiaotong UniversityChina
| | - Bingyin Shi
- Department of EndocrinologyThe First Affiliated Hospital of Xi’an Jiaotong UniversityChina
| | - Zhong Xu
- Guizhou Provincial People's HospitalGuiyangChina
| | - Lei Li
- School of PharmacyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaofei Yang
- Genome InstituteThe First Affiliated Hospital of Xi’an Jiaotong UniversityChina
- School of Computer Science and TechnologyFaculty of Electronic and Information EngineeringXi’an Jiaotong UniversityChina
| | - Chuanrui Xu
- School of PharmacyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Kai Ye
- School of Automation Science and EngineeringFaculty of Electronic and Information EngineeringXi’an Jiaotong UniversityChina
- Genome InstituteThe First Affiliated Hospital of Xi’an Jiaotong UniversityChina
- School of Life Science and TechnologyXi’an Jiaotong UniversityXi’an, ShaanxiChina
- Faculty of ScienceLeiden UniversityThe Netherlands
- MOE Key Lab for Intelligent Networks & Networks SecurityFaculty of Electronic and Information EngineeringXi’an Jiaotong UniversityChina
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4
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Pineau F, Shumyatsky G, Owuor N, Nalamala N, Kotnala S, Bolla S, Marchetti N, Kelsen S, Criner GJ, Sajjan US. Microarray analysis identifies defects in regenerative and immune response pathways in COPD airway basal cells. ERJ Open Res 2020; 6:00656-2020. [PMID: 33313308 PMCID: PMC7720690 DOI: 10.1183/23120541.00656-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 01/07/2023] Open
Abstract
Background Airway basal cells are specialised stem cells and regenerate airway epithelium. Airway basal cells isolated from patients with COPD regenerate airway epithelium with an abnormal phenotype. We performed gene expression analysis to gain insights into the defective regenerative programme in COPD basal cells. Methods We conducted microarray analysis and compared COPD versus normal basal cells to identify differentially regulated genes (DEGs) and the enriched biological pathways. We determined the correlation of DEGs with cell polarisation and markers of ciliated and goblet cells. HOXB2 was knocked down in 16HBE14o− cells and monitored for polarisation of cells. HOXB2 expression in the lung sections was determined by immunofluorescence. Results Comparison of normal and COPD basal cell transcriptomic profiles highlighted downregulation of genes associated with tissue development, epithelial cell differentiation and antimicrobial humoral response. Expression of one of the tissue development genes, HOXB2 showed strong correlation with transepithelial resistance and this gene was downregulated in COPD basal cells. Knockdown of HOXB2, abrogated polarisation of epithelial cells in normal cells. Finally, HOXB2 expression was substantially reduced in the bronchial epithelium of COPD patients. Conclusions Defect in gene signatures involved in tissue development and epithelial differentiation were implicated in COPD basal cells. One of the tissue developmental genes, HOXB2, is substantially reduced in bronchial epithelium of COPD patients. Since HOXB2 contributes to airway epithelial cell polarisation, we speculate that reduced expression of HOXB2 in COPD may contribute to abnormal airway epithelial regeneration in COPD. COPD airway basal cells show downregulation of gene sets that are involved in intercellular junctions, epithelial differentiation and immune responses, highlighting the possible mechanisms of defective airway epithelial repair in COPDhttps://bit.ly/3kneloj
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Affiliation(s)
- Fanny Pineau
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | | | - Nicole Owuor
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Nisha Nalamala
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Sudhir Kotnala
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Sudhir Bolla
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Nathaniel Marchetti
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Steven Kelsen
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard J Criner
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Uma S Sajjan
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA.,Dept of Physiology, Lewis Katz Medical School, Temple University, Philadelphia, PA, USA
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5
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Fearnley GW, Young KA, Edgar JR, Antrobus R, Hay IM, Liang WC, Martinez-Martin N, Lin W, Deane JE, Sharpe HJ. The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell-cell adhesion. eLife 2019; 8:44597. [PMID: 30924770 PMCID: PMC6440744 DOI: 10.7554/elife.44597] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
Cell-cell communication in multicellular organisms depends on the dynamic and reversible phosphorylation of protein tyrosine residues. The receptor-linked protein tyrosine phosphatases (RPTPs) receive cues from the extracellular environment and are well placed to influence cell signaling. However, the direct events downstream of these receptors have been challenging to resolve. We report here that the homophilic receptor PTPRK is stabilized at cell-cell contacts in epithelial cells. By combining interaction studies, quantitative tyrosine phosphoproteomics, proximity labeling and dephosphorylation assays we identify high confidence PTPRK substrates. PTPRK directly and selectively dephosphorylates at least five substrates, including Afadin, PARD3 and δ-catenin family members, which are all important cell-cell adhesion regulators. In line with this, loss of PTPRK phosphatase activity leads to disrupted cell junctions and increased invasive characteristics. Thus, identifying PTPRK substrates provides insight into its downstream signaling and a potential molecular explanation for its proposed tumor suppressor function.
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Affiliation(s)
- Gareth W Fearnley
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Katherine A Young
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Iain M Hay
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Wei-Ching Liang
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Nadia Martinez-Martin
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, United States
| | - WeiYu Lin
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Hayley J Sharpe
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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6
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Jin SH, Kim H, Gu DR, Park KH, Lee YR, Choi Y, Lee SH. Actin-binding LIM protein 1 regulates receptor activator of NF-κB ligand-mediated osteoclast differentiation and motility. BMB Rep 2018; 51:356-361. [PMID: 29921413 PMCID: PMC6089868 DOI: 10.5483/bmbrep.2018.51.7.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 01/15/2023] Open
Abstract
Actin-binding LIM protein 1 (ABLIM1), a member of the LIM-domain protein family, mediates interactions between actin filaments and cytoplasmic targets. However, the role of ABLIM1 in osteoclast and bone metabolism has not been reported. In the present study, we investigated the role of ABLIM1 in the receptor activator of NF-κB ligand (RANKL)-mediated osteoclastogenesis. ABLIM1 expression was induced by RANKL treatment and knockdown of ABLIM1 by retrovirus infection containing Ablim1-specific short hairpin RNA (shAblim1) decreased mature osteoclast formation and bone resorption activity in a RANKL-dose dependent manner. Coincident with the downregulated expression of osteoclast differentiation marker genes, the expression levels of c-Fos and the nuclear factor of activated T-cells cytoplasmic 1 (NFATc1), critical transcription factors of osteoclastogenesis, were also decreased in shAblim1-infected osteoclasts during RANKL-mediated osteoclast differentiation. In addition, the motility of preosteoclast was reduced by ABLIM1 knockdown via modulation of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/Akt/Rac1 signaling pathway, suggesting another regulatory mechanism of ABLIM1 in osteoclast formation. These data demonstrated that ABLIM1 is a positive regulator of RANKL-mediated osteoclast formation via the modulation of the differentiation and PI3K/Akt/Rac1-dependent motility.
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Affiliation(s)
- Su Hyun Jin
- Center for Metabolic Function Regulation (CMFR), Wonkwang University School of Medicine, Iksan 54538, Korea
| | - Hyunsoo Kim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dong Ryun Gu
- Center for Metabolic Function Regulation (CMFR), Wonkwang University School of Medicine, Iksan 54538, Korea; Department of Oral Microbiology and Immunology, Wonkwang University, Iksan 54538, Korea
| | - Keun Ha Park
- Center for Metabolic Function Regulation (CMFR), Wonkwang University School of Medicine, Iksan 54538, Korea; Department of Oral Microbiology and Immunology, Wonkwang University, Iksan 54538, Korea
| | - Young Rae Lee
- Center for Metabolic Function Regulation (CMFR), Wonkwang University School of Medicine, Iksan 54538, Korea; Department of Oral Biochemistry, and Institute of BiomaterialsㆍImplant, College of Dentistry, Wonkwang University, Iksan 54538, Korea
| | - Yongwon Choi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Seoung Hoon Lee
- Center for Metabolic Function Regulation (CMFR), Wonkwang University School of Medicine, Iksan 54538, Korea; Department of Oral Microbiology and Immunology, Wonkwang University, Iksan 54538, Korea; Institute of BiomaterialsㆍImplant, College of Dentistry, Wonkwang University, Iksan 54538, Korea
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7
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Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. MUNC, an Enhancer RNA Upstream from the MYOD Gene, Induces a Subgroup of Myogenic Transcripts in trans Independently of MyoD. Mol Cell Biol 2018; 38:e00655-17. [PMID: 30037979 DOI: 10.1128/MCB.00655-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 07/13/2018] [Indexed: 11/20/2022] Open
Abstract
MyoD upstream noncoding RNA (MUNC) initiates in the distal regulatory region (DRR) enhancer of MYOD and is formally classified as an enhancer RNA (DRReRNA). MUNC is required for optimal myogenic differentiation, induces specific myogenic transcripts in trans (MYOD, MYOGENIN, and MYH3), and has a functional human homolog. The vast majority of eRNAs are believed to act in cis primarily on their neighboring genes (1, 2), making it likely that MUNC action is dependent on the induction of MYOD RNA. Surprisingly, MUNC overexpression in MYOD -/- C2C12 cells induces many myogenic transcripts in the complete absence of MyoD protein. Genomewide analysis showed that, while many genes are regulated by MUNC in a MyoD-dependent manner, there is a set of genes that are regulated by MUNC, both upward and downward, independently of MyoD. MUNC and MyoD even appear to act antagonistically on certain transcripts. Deletion mutagenesis showed that there are at least two independent functional sites on the MUNC long noncoding RNA (lncRNA), with exon 1 more active than exon 2 and with very little activity from the intron. Thus, although MUNC is an eRNA of MYOD, it is also a trans-acting lncRNA whose sequence, structure, and cooperating factors, which include but are not limited to MyoD, determine the regulation of many myogenic genes.
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8
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Liu CF, Angelozzi M, Haseeb A, Lefebvre V. SOX9 is dispensable for the initiation of epigenetic remodeling and the activation of marker genes at the onset of chondrogenesis. Development 2018; 145:dev164459. [PMID: 30021842 PMCID: PMC6078338 DOI: 10.1242/dev.164459] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
SOX9 controls cell lineage fate and differentiation in major biological processes. It is known as a potent transcriptional activator of differentiation-specific genes, but its earliest targets and its contribution to priming chromatin for gene activation remain unknown. Here, we address this knowledge gap using chondrogenesis as a model system. By profiling the whole transcriptome and the whole epigenome of wild-type and Sox9-deficient mouse embryo limb buds, we uncover multiple structural and regulatory genes, including Fam101a, Myh14, Sema3c and Sema3d, as specific markers of precartilaginous condensation, and we provide evidence of their direct transactivation by SOX9. Intriguingly, we find that SOX9 helps remove epigenetic signatures of transcriptional repression and establish active-promoter and active-enhancer marks at precartilage- and cartilage-specific loci, but is not absolutely required to initiate these changes and activate transcription. Altogether, these findings widen our current knowledge of SOX9 targets in early chondrogenesis and call for new studies to identify the pioneer and transactivating factors that act upstream of or along with SOX9 to prompt chromatin remodeling and specific gene activation at the onset of chondrogenesis and other processes.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Marco Angelozzi
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Abdul Haseeb
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Véronique Lefebvre
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
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Guo N, Soden ME, Herber C, Kim MT, Besnard A, Lin P, Ma X, Cepko CL, Zweifel LS, Sahay A. Dentate granule cell recruitment of feedforward inhibition governs engram maintenance and remote memory generalization. Nat Med 2018. [PMID: 29529016 PMCID: PMC5893385 DOI: 10.1038/nm.4491] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Memories become less precise and generalize over time as memory traces re-organize in hippocampal-cortical networks. Increased time-dependent loss of memory precision characterizes overgeneralization of fear in post-traumatic stress disorder (PTSD) and age-related cognitive impairments. In the hippocampal dentate gyrus (DG), memories are thought to be encoded by so-called “engram-bearing” dentate granule cells (eDGCs). Here we show using rodents that contextual fear conditioning increases connectivity between eDGCs and inhibitory interneurons in the downstream hippocampal CA3 region. We identify actin-binding LIM protein 3 (abLIM3) as a mossy fiber terminal localized cytoskeletal factor, whose levels decrease upon learning. Downregulation of abLIM3 in DGCs was sufficient to increase connectivity with CA3 stratum lucidum interneurons (SLINs), promote parvalbumin (PV) SLIN activation, enhance feed-forward inhibition onto CA3, and maintain a fear memory engram in the dentate gyrus (DG) over time. Furthermore, abLIM3 downregulation in DGCs conferred conditioned context-specific reactivation of memory traces in hippocampal-cortical and amygdalar networks and decreased fear memory generalization at remote time points. Consistent with age-related hyperactivity of CA3, learning failed to increase DGC-SLIN connectivity in 17 month-old mice, whereas abLIM3 downregulation was sufficient to restore DGC-SLIN connectivity, increase PV-SLIN activation and improve remote memory precision. These studies exemplify a connectivity-based strategy targeting a molecular brake of feedforward inhibition in DG-CA3 that may be harnessed to decrease time-dependent memory generalization in PTSD and improve memory precision in aging.
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Affiliation(s)
- Nannan Guo
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marta E Soden
- Department of Pharmacology, University of Washington, Seattle, Washington, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Charlotte Herber
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Michael TaeWoo Kim
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Antoine Besnard
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Paoyan Lin
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiang Ma
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Constance L Cepko
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Larry S Zweifel
- Department of Pharmacology, University of Washington, Seattle, Washington, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Amar Sahay
- Center for Regenerative Medicine, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,BROAD Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
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10
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Marçola M, Lopes-Ramos CM, Pereira EP, Cecon E, Fernandes PA, Tamura EK, Camargo AA, Parmigiani RB, Markus RP. Light/Dark Environmental Cycle Imposes a Daily Profile in the Expression of microRNAs in Rat CD133+Cells. J Cell Physiol 2016; 231:1953-63. [DOI: 10.1002/jcp.25300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/04/2016] [Indexed: 02/07/2023]
Affiliation(s)
- Marina Marçola
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
| | - Camila M. Lopes-Ramos
- Centro de Oncologia Molecular; Hospital Sírio-Libanês; São Paulo City São Paulo Brazil
| | - Eliana P. Pereira
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
| | - Erika Cecon
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
| | - Pedro A. Fernandes
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
| | - Eduardo K. Tamura
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
| | - Anamaria A. Camargo
- Centro de Oncologia Molecular; Hospital Sírio-Libanês; São Paulo City São Paulo Brazil
| | - Raphael B. Parmigiani
- Centro de Oncologia Molecular; Hospital Sírio-Libanês; São Paulo City São Paulo Brazil
| | - Regina P. Markus
- Department of Physiology; Laboratory of Chronopharmacology; Institute of Bioscience; University of São Paulo; São Paulo City São Paulo Brazil
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Järvinen PM, Laiho M. LIM-domain proteins in transforming growth factor β-induced epithelial-to-mesenchymal transition and myofibroblast differentiation. Cell Signal 2012; 24:819-25. [DOI: 10.1016/j.cellsig.2011.12.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 11/15/2011] [Accepted: 12/04/2011] [Indexed: 12/16/2022]
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Koch BJ, Ryan JF, Baxevanis AD. The diversification of the LIM superclass at the base of the metazoa increased subcellular complexity and promoted multicellular specialization. PLoS One 2012; 7:e33261. [PMID: 22438907 DOI: 10.1371/journal.pone.0033261] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 02/07/2012] [Indexed: 01/15/2023] Open
Abstract
Background Throughout evolution, the LIM domain has been deployed in many different domain configurations, which has led to the formation of a large and distinct group of proteins. LIM proteins are involved in relaying stimuli received at the cell surface to the nucleus in order to regulate cell structure, motility, and division. Despite their fundamental roles in cellular processes and human disease, little is known about the evolution of the LIM superclass. Results We have identified and characterized all known LIM domain-containing proteins in six metazoans and three non-metazoans. In addition, we performed a phylogenetic analysis on all LIM domains and, in the process, have identified a number of novel non-LIM domains and motifs in each of these proteins. Based on these results, we have formalized a classification system for LIM proteins, provided reasonable timing for class and family origin events; and identified lineage-specific loss events. Our analysis is the first detailed description of the full set of LIM proteins from the non-bilaterian species examined in this study. Conclusion Six of the 14 LIM classes originated in the stem lineage of the Metazoa. The expansion of the LIM superclass at the base of the Metazoa undoubtedly contributed to the increase in subcellular complexity required for the transition from a unicellular to multicellular lifestyle and, as such, was a critically important event in the history of animal multicellularity.
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Christie JD, Wurfel MM, Feng R, O'Keefe GE, Bradfield J, Ware LB, Christiani DC, Calfee CS, Cohen MJ, Matthay M, Meyer NJ, Kim C, Li M, Akey J, Barnes KC, Sevransky J, Lanken PN, May AK, Aplenc R, Maloney JP, Hakonarson H. Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma. PLoS One 2012; 7:e28268. [PMID: 22295056 PMCID: PMC3266233 DOI: 10.1371/journal.pone.0028268] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 11/04/2011] [Indexed: 12/29/2022] Open
Abstract
Acute Lung Injury (ALI) is a syndrome with high associated mortality characterized by severe hypoxemia and pulmonary infiltrates in patients with critical illness. We conducted the first investigation to use the genome wide association (GWA) approach to identify putative risk variants for ALI. Genome wide genotyping was performed using the Illumina Human Quad 610 BeadChip. We performed a two-stage GWA study followed by a third stage of functional characterization. In the discovery phase (Phase 1), we compared 600 European American trauma-associated ALI cases with 2266 European American population-based controls. We carried forward the top 1% of single nucleotide polymorphisms (SNPs) at p<0.01 to a replication phase (Phase 2) comprised of a nested case-control design sample of 212 trauma-associated ALI cases and 283 at-risk trauma non-ALI controls from ongoing cohort studies. SNPs that replicated at the 0.05 level in Phase 2 were subject to functional validation (Phase 3) using expression quantitative trait loci (eQTL) analyses in stimulated B-lymphoblastoid cell lines (B-LCL) in family trios. 159 SNPs from the discovery phase replicated in Phase 2, including loci with prior evidence for a role in ALI pathogenesis. Functional evaluation of these replicated SNPs revealed rs471931 on 11q13.3 to exert a cis-regulatory effect on mRNA expression in the PPFIA1 gene (p = 0.0021). PPFIA1 encodes liprin alpha, a protein involved in cell adhesion, integrin expression, and cell-matrix interactions. This study supports the feasibility of future multi-center GWA investigations of ALI risk, and identifies PPFIA1 as a potential functional candidate ALI risk gene for future research.
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Affiliation(s)
- Jason D. Christie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Mark M. Wurfel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Rui Feng
- Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Grant E. O'Keefe
- Department of Surgery, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Jonathan Bradfield
- Division of Human Genetics, Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health and Pulmonary and Critical Care Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Carolyn S. Calfee
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California San Francisco, San Francisco, California, United States of America
| | - Mitchell J. Cohen
- Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Michael Matthay
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California San Francisco, San Francisco, California, United States of America
| | - Nuala J. Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Cecilia Kim
- Division of Human Genetics, Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joshua Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kathleen C. Barnes
- Division of Pulmonary, Allergy, and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jonathan Sevransky
- Division of Pulmonary, Allergy, and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Paul N. Lanken
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Addison K. May
- Department of Surgical Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Richard Aplenc
- Division of Oncology, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - James P. Maloney
- Division of Pulmonary and Critical Care Medicine, University of Colorado Health Sciences Center, Denver, Colorado, United States of America
| | - Hakon Hakonarson
- Division of Human Genetics, Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Voutsadakis IA, Cairoli A. A critical review of the molecular pathophysiology of lenalidomide sensitivity in 5q − myelodysplastic syndromes. Leuk Lymphoma 2011; 53:779-88. [DOI: 10.3109/10428194.2011.623255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Yang Q, Orman MA, Berthiaume F, Ierapetritou MG, Androulakis IP. Dynamics of short-term gene expression profiling in liver following thermal injury. J Surg Res 2011; 176:549-58. [PMID: 22099593 DOI: 10.1016/j.jss.2011.09.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/23/2011] [Accepted: 09/27/2011] [Indexed: 02/01/2023]
Abstract
BACKGROUND Severe trauma, including burns, triggers a systemic response that significantly impacts on the liver, which plays a key role in the metabolic and immune responses aimed at restoring homeostasis. While many of these changes are likely regulated at the gene expression level, there is a need to better understand the dynamics and expression patterns of burn injury-induced genes in order to identify potential regulatory targets in the liver. Herein we characterized the response within the first 24 h in a standard animal model of burn injury using a time series of microarray gene expression data. METHODS Rats were subjected to a full thickness dorsal scald burn injury covering 20% of their total body surface area while under general anesthesia. Animals were saline resuscitated and sacrificed at defined time points (0, 2, 4, 8, 16, and 24 h). Liver tissues were explanted and analyzed for their gene expression profiles using microarray technology. Sham controls consisted of animals handled similarly but not burned. After identifying differentially expressed probe sets between sham and burn conditions over time, the concatenated data sets corresponding to these differentially expressed probe sets in burn and sham groups were combined and analyzed using a "consensus clustering" approach. RESULTS The clustering method of expression data identified 621 burn-responsive probe sets in four different co-expressed clusters. Functional characterization revealed that these four clusters are mainly associated with pro-inflammatory response, anti-inflammatory response, lipid biosynthesis, and insulin-regulated metabolism. Cluster 1 pro-inflammatory response is rapidly up-regulated (within the first 2 h) following burn injury, while Cluster 2 anti-inflammatory response is activated later on (around 8 h post-burn). Cluster 3 lipid biosynthesis is down-regulated rapidly following burn, possibly indicating a shift in the utilization of energy sources to produce acute phase proteins, which serve the anti-inflammatory response. Cluster 4 insulin-regulated metabolism was down-regulated late in the observation window (around 16 h post-burn), which suggests a potential mechanism to explain the onset of hypermetabolism, a delayed but well-known response that is characteristic of severe burns and trauma with potential adverse outcome. CONCLUSIONS Simultaneous analysis and comparison of gene expression profiles for both burn and sham control groups provided a more accurate estimation of the activation time, expression patterns, and characteristics of a certain burn-induced response based on which the cause-effect relationships among responses were revealed.
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Affiliation(s)
- Qian Yang
- Chemical and Biochemical Engineering Department, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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Andl CD. The Misregulation of Cell Adhesion Components during Tumorigenesis: Overview and Commentary. J Oncol 2010; 2010:174715. [PMID: 20953359 DOI: 10.1155/2010/174715] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/23/2010] [Accepted: 09/10/2010] [Indexed: 12/18/2022]
Abstract
Cell adhesion complexes facilitate attachment between cells or the binding of cells to the extracellular matrix. The regulation of cell adhesion is an important step in embryonic development and contributes to tissue homeostasis allowing processes such as differentiation and cell migration. Many mechanisms of cancer progression are reminiscent of embryonic development, for example, epithelial-mesenchymal transition, and involve the disruption of cell adhesion and expression changes in components of cell adhesion structures. Tight junctions, adherens junctions, desmosomes, and focal adhesion besides their roles in cell-cell or cell-matrix interaction also possess cell signaling function. Perturbations of such signaling pathways can lead to cancer. This article gives an overview of the common structures of cell adhesion and summarizes the impact of their loss on cancer development and progression with articles highlighted from the present issue.
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