1
|
Sousa RT, Silva S, Pesquita C. Explaining protein-protein interactions with knowledge graph-based semantic similarity. Comput Biol Med 2024; 170:108076. [PMID: 38308873 DOI: 10.1016/j.compbiomed.2024.108076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/11/2023] [Accepted: 01/27/2024] [Indexed: 02/05/2024]
Abstract
The application of artificial intelligence and machine learning methods for several biomedical applications, such as protein-protein interaction prediction, has gained significant traction in recent decades. However, explainability is a key aspect of using machine learning as a tool for scientific discovery. Explainable artificial intelligence approaches help clarify algorithmic mechanisms and identify potential bias in the data. Given the complexity of the biomedical domain, explanations should be grounded in domain knowledge which can be achieved by using ontologies and knowledge graphs. These knowledge graphs express knowledge about a domain by capturing different perspectives of the representation of real-world entities. However, the most popular way to explore knowledge graphs with machine learning is through using embeddings, which are not explainable. As an alternative, knowledge graph-based semantic similarity offers the advantage of being explainable. Additionally, similarity can be computed to capture different semantic aspects within the knowledge graph and increasing the explainability of predictive approaches. We propose a novel method to generate explainable vector representations, KGsim2vec, that uses aspect-oriented semantic similarity features to represent pairs of entities in a knowledge graph. Our approach employs a set of machine learning models, including decision trees, genetic programming, random forest and eXtreme gradient boosting, to predict relations between entities. The experiments reveal that considering multiple semantic aspects when representing the similarity between two entities improves explainability and predictive performance. KGsim2vec performs better than black-box methods based on knowledge graph embeddings or graph neural networks. Moreover, KGsim2vec produces global models that can capture biological phenomena and elucidate data biases.
Collapse
Affiliation(s)
- Rita T Sousa
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
| | - Sara Silva
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Catia Pesquita
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
2
|
Song XQ, Li Q, Zhang J. A double-edged sword: DLG5 in diseases. Biomed Pharmacother 2023; 162:114611. [PMID: 37001186 DOI: 10.1016/j.biopha.2023.114611] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Discs large homolog 5 (DLG5), a key member of the membrane-associated guanylate kinase (MAGUKs) family, is a scaffold molecule for signal transduction complexes and is responsible for assembling receptors and adapters. This scaffold protein stabilizes adhesion and tight bonding complexes in many organs and tissues, and is involved of maintaining epithelial polarity. Although DLG5 plays a role in normal development in mice, it has also been linked to the onset and development of several diseases, particularly Crohn's disease and various malignancies. DLG5 has been shown to impact the progression of cancer through direct or indirect interactions with H-catenin, E-cadherin, Vimentin, p53, P21, Cyclin D1, TGF-β1, AKT, Hippo, and classic G protein signaling pathways. DLG5 and DLG5 variants has been found to have a dual role in human diseases. Although it is overexpressed in pancreatic adenocarcinoma, its expression is reduced in lung, liver, breast, prostate, and bladder cancers. However, two independent studies on glioblastoma (GBM) have shown the opposite effects of DLG5. Our study evaluates the existing literature on the role of DLG5 and DLG5 variants in disease processes, and summarizes the available data on the role of DLG5 in disease based on cell experiments, clinical samples, and animal models, while highlighting its future potential in disease treatment.
Collapse
|
3
|
A genotype-first analysis in a cohort of Mullerian anomaly. J Hum Genet 2022; 67:347-352. [PMID: 35022528 DOI: 10.1038/s10038-021-00996-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/08/2022]
Abstract
Müllerian anomaly (M.A.) is a group of congenital anatomic abnormalities caused by aberrations of the development process of the Müllerian duct. M.A. can either be isolated or be involved in Mendelian syndromes, such as Dandy-Walker syndrome, Holt-Oram syndrome and Bardet-Biedl syndrome, which are often associated with both uterus and kidney malformations. In this study, we applied a genotype-first approach to analyze the whole-exome sequencing data of 492 patients with M.A. Six potential pathogenic variants were found in five genes previously related to female urogenital deformities (PKD1, SON, SALL1, BMPR1B, ITGA8), which are partially overlapping with our patients' phenotypes. We further identified eight incidental findings in seven genes related to Mendelian syndromes without known association with reproductive anomalies (TEK, COL11A1, ANKRD11, LEMD3, DLG5, SPTB, BMP2), which represent potential phenotype expansions of these genes.
Collapse
|
4
|
Marquez J, Mann N, Arana K, Deniz E, Ji W, Konstantino M, Mis EK, Deshpande C, Jeffries L, McGlynn J, Hugo H, Widmeier E, Konrad M, Tasic V, Morotti R, Baptista J, Ellard S, Lakhani SA, Hildebrandt F, Khokha MK. DLG5 variants are associated with multiple congenital anomalies including ciliopathy phenotypes. J Med Genet 2021; 58:453-464. [PMID: 32631816 PMCID: PMC7785698 DOI: 10.1136/jmedgenet-2019-106805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/01/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cilia are dynamic cellular extensions that generate and sense signals to orchestrate proper development and tissue homeostasis. They rely on the underlying polarisation of cells to participate in signalling. Cilia dysfunction is a well-known cause of several diseases that affect multiple organ systems including the kidneys, brain, heart, respiratory tract, skeleton and retina. METHODS Among individuals from four unrelated families, we identified variants in discs large 5 (DLG5) that manifested in a variety of pathologies. In our proband, we also examined patient tissues. We depleted dlg5 in Xenopus tropicalis frog embryos to generate a loss-of-function model. Finally, we tested the pathogenicity of DLG5 patient variants through rescue experiments in the frog model. RESULTS Patients with variants of DLG5 were found to have a variety of phenotypes including cystic kidneys, nephrotic syndrome, hydrocephalus, limb abnormalities, congenital heart disease and craniofacial malformations. We also observed a loss of cilia in cystic kidney tissue of our proband. Knockdown of dlg5 in Xenopus embryos recapitulated many of these phenotypes and resulted in a loss of cilia in multiple tissues. Unlike introduction of wildtype DLG5 in frog embryos depleted of dlg5, introduction of DLG5 patient variants was largely ineffective in restoring proper ciliation and tissue morphology in the kidney and brain suggesting that the variants were indeed detrimental to function. CONCLUSION These findings in both patient tissues and Xenopus shed light on how mutations in DLG5 may lead to tissue-specific manifestations of disease. DLG5 is essential for cilia and many of the patient phenotypes are in the ciliopathy spectrum.
Collapse
Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nina Mann
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kathya Arana
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julie McGlynn
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hannah Hugo
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Martin Konrad
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Skopje, North Macedonia
| | - Raffaella Morotti
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, Exeter, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, Exeter, UK
| | - Saquib Ali Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
5
|
Che J, Wang J, Li H, Zhen H, Shang K, Yang Y, Cao B. Decreased expression of Dlg5 is associated with a poor prognosis and epithelial-mesenchymal transition in squamous cell lung cancer. J Thorac Dis 2021; 13:3115-3125. [PMID: 34164202 PMCID: PMC8182517 DOI: 10.21037/jtd-21-752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Discs large homolog 5 (Dlg5) is a newly discovered member of the membrane-associated guanylate kinase superfamily (MAGUK) that is involved in several important processes, including the maintenance of epithelial cell polarity, cell proliferation control, and cell migration and invasion. Decreased expression of Dlg5 has been reported in malignancies arising from different organs. In the present study, we analyzed Dlg5 expression and its prognostic value in squamous cell lung cancer (SqCLC). Methods Tumor tissue and adjacent normal tissue sections were collected from 98 patients with SqCLC. The expression levels of Dlg5 and epithelial-mesenchymal transition (EMT) biomarkers in the tissue sections were examined by immunohistochemistry and western blot. Results There were 80 males and 18 females in the study cohort. Patients at pathological stages I and IIIA accounted for 64.3% and 35.7% of the cohort, respectively. Western blot showed that Dlg5 expression differed between SqCLC and healthy tissues. Western blot also revealed low Dlg5 expression to be associated with low E-cadherin expression and high vimentin expression, which was consistent with the findings of immunohistochemical staining. Dlg5 expression was significantly correlated with lymph node (LN) metastasis (P=0.001) and disease recurrence (P<0.001), as well as with E-cadherin and vimentin expression (P=0.025 and P=0.001, respectively). Univariate analysis showed that overall survival was significantly correlated with the tumor-node-metastasis (P<0.001) and T (P=0.001) stages, LN metastasis (P<0.001), Dig5 expression (P<0.001), β-catenin expression (P=0.004), and vimentin expression (P=0.002). Patients with overexpression of Dlg5 and β-catenin had a more favorable prognosis than those without. Multivariate analysis revealed that tumor-node-metastasis stage [hazard ratio (HR) =2.124; 95% confidence interval (CI), 1.195–3.777; P=0.010], Dlg5 expression (HR =0.548; 95% CI, 0.313–0.959; P=0.035), β-catenin expression (HR =0.545; 95% CI, 0.312–0.953; P=0.033), and vimentin expression (HR =1.850; 95% CI, 1.050–3.258; P=0.033) could all independently predict the overall survival of patients with SqCLC. Conclusions Dlg5 is an important player in EMT which may have potential predictive value for SqCLC prognosis after surgery.
Collapse
Affiliation(s)
- Juanjuan Che
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jing Wang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Huihui Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hongchao Zhen
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Kun Shang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yan Yang
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Bangwei Cao
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
6
|
Bhattacharya S, Mereness JA, Baran AM, Misra RS, Peterson DR, Ryan RM, Reynolds AM, Pryhuber GS, Mariani TJ. Lymphocyte-Specific Biomarkers Associated With Preterm Birth and Bronchopulmonary Dysplasia. Front Immunol 2021; 11:563473. [PMID: 33552042 PMCID: PMC7859626 DOI: 10.3389/fimmu.2020.563473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
Many premature babies who are born with neonatal respiratory distress syndrome (RDS) go on to develop Bronchopulmonary Dysplasia (BPD) and later Post-Prematurity Respiratory Disease (PRD) at one year corrected age, characterized by persistent or recurrent lower respiratory tract symptoms frequently related to inflammation and viral infection. Transcriptomic profiles were generated from sorted peripheral blood CD8+ T cells of preterm and full-term infants enrolled with consent in the NHLBI Prematurity and Respiratory Outcomes Program (PROP) at the University of Rochester and the University at Buffalo. We identified outcome-related gene expression patterns following standard methods to identify markers for oxygen utilization and BPD as outcomes in extremely premature infants. We further identified predictor gene sets for BPD based on transcriptomic data adjusted for gestational age at birth (GAB). RNA-Seq analysis was completed for CD8+ T cells from 145 subjects. Among the subjects with highest risk for BPD (born at <29 weeks gestational age (GA); n=72), 501 genes were associated with oxygen utilization. In the same set of subjects, 571 genes were differentially expressed in subjects with a diagnosis of BPD and 105 genes were different in BPD subjects as defined by physiologic challenge. A set of 92 genes could predict BPD with a moderately high degree of accuracy. We consistently observed dysregulation of TGFB, NRF2, HIPPO, and CD40-associated pathways in BPD. Using gene expression data from both premature and full-term subjects (n=116), we identified a 28 gene set that predicted the PRD status with a moderately high level of accuracy, which also were involved in TGFB signaling. Transcriptomic data from sort-purified peripheral blood CD8+ T cells from 145 preterm and full-term infants identified sets of molecular markers of inflammation associated with independent development of BPD in extremely premature infants at high risk for the disease and of PRD among the preterm and full-term subjects.
Collapse
Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Jared A Mereness
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Ravi S Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Rita M Ryan
- Department of Pediatrics, University at Buffalo, Buffalo, NY, United States.,Department of Pediatrics, Case Western Reserve University, Cleveland, OH, United States
| | | | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| |
Collapse
|
7
|
Luo J, Zhou P, Guo X, Wang D, Chen J. The polarity protein Dlg5 regulates collective cell migration during Drosophila oogenesis. PLoS One 2019; 14:e0226061. [PMID: 31856229 PMCID: PMC6922378 DOI: 10.1371/journal.pone.0226061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/19/2019] [Indexed: 01/17/2023] Open
Abstract
Collective migration plays critical roles in animal development, physiological events, and cancer metastasis. However, the molecular mechanisms of collective cell migration are not well understood. Drosophila border cells represent an excellent in vivo genetic model to study collective cell migration and identify novel regulatory genes for cell migration. Using the Mosaic Analysis with a Repressible Cell Marker (MARCM) system, we screened 240 P-element insertion lines to identify essential genes for border cell migration. Two genes were uncovered, including dlg5 (discs large 5) and CG31689. Further analysis showed that Dlg5 regulates the apical-basal polarity and cluster integrity in border cell clusters. Dlg5 is enriched in lateral surfaces between border cells and central polar cells but also shows punctate localization between border cells. We found that the distribution of Dlg5 in border cell clusters is regulated by Armadillo. Structure-function analysis revealed that the N-terminal Coiled-coil domain and the C-terminal PDZ3-PDZ4-SH3-GUK domains but not the PDZ1-PDZ2 domains of Dlg5 are required for BC migration. The Coiled-coil domain and the PDZ4-SH3-GUK domains are critical for Dlg5’s cell surface localization in border cell clusters.
Collapse
Affiliation(s)
- Jun Luo
- College of Life Science, Shangrao Normal University, Shangrao, China
- * E-mail: (JL); (JC)
| | - Ping Zhou
- College of Life Science, Shangrao Normal University, Shangrao, China
| | - Xuan Guo
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Dou Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiong Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- * E-mail: (JL); (JC)
| |
Collapse
|
8
|
Zhang X, Xie H, Chang P, Zhao H, Xia Y, Zhang L, Guo X, Huang C, Yan F, Hu L, Lin C, Li Y, Xiong Z, Wang X, Li G, Deng L, Wang S, Tao L. Glycoprotein M6B Interacts with TβRI to Activate TGF-β-Smad2/3 Signaling and Promote Smooth Muscle Cell Differentiation. Stem Cells 2018; 37:190-201. [PMID: 30372567 PMCID: PMC7379588 DOI: 10.1002/stem.2938] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 01/01/2023]
Abstract
Smooth muscle cells (SMCs), which form the walls of blood vessels, play an important role in vascular development and the pathogenic process of vascular remodeling. However, the molecular mechanisms governing SMC differentiation remain poorly understood. Glycoprotein M6B (GPM6B) is a four-transmembrane protein that belongs to the proteolipid protein family and is widely expressed in neurons, oligodendrocytes, and astrocytes. Previous studies have revealed that GPM6B plays a role in neuronal differentiation, myelination, and osteoblast differentiation. In the present study, we found that the GPM6B gene and protein expression levels were significantly upregulated during transforming growth factor-β1 (TGF-β1)-induced SMC differentiation. The knockdown of GPM6B resulted in the downregulation of SMC-specific marker expression and repressed the activation of Smad2/3 signaling. Moreover, GPM6B regulates SMC Differentiation by Controlling TGF-β-Smad2/3 Signaling. Furthermore, we demonstrated that similar to p-Smad2/3, GPM6B was profoundly expressed and coexpressed with SMC differentiation markers in embryonic SMCs. Moreover, GPM6B can regulate the tightness between TβRI, TβRII, or Smad2/3 by directly binding to TβRI to activate Smad2/3 signaling during SMC differentiation, and activation of TGF-β-Smad2/3 signaling also facilitate the expression of GPM6B. Taken together, these findings demonstrate that GPM6B plays a crucial role in SMC differentiation and regulates SMC differentiation through the activation of TGF-β-Smad2/3 signaling via direct interactions with TβRI. This finding indicates that GPM6B is a potential target for deriving SMCs from stem cells in cardiovascular regenerative medicine. Stem Cells 2018 Stem Cells 2019;37:190-201.
Collapse
Affiliation(s)
- Xiaomeng Zhang
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Huaning Xie
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Pan Chang
- Central Laboratory, Second Affiliated Hospital, Xi'an Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Huishou Zhao
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Yunlong Xia
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Ling Zhang
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Xiong Guo
- Department of Cardiology, Hospital of People's Liberation Army, Golmud, Qinghai, People's Republic of China
| | - Chong Huang
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Feng Yan
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Lang Hu
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Chen Lin
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Yueyang Li
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Zhenyu Xiong
- Department of Cardiology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Xiong Wang
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Guohua Li
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Longxiang Deng
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Shan Wang
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Ling Tao
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| |
Collapse
|
9
|
Ke Y, Bao T, Zhou Q, Wang Y, Ge J, Fu B, Wu X, Tang H, Shi Z, Lei X, Zhang C, Tan Y, Chen H, Guo Z, Wang L. Discs large homolog 5 decreases formation and function of invadopodia in human hepatocellular carcinoma via Girdin and Tks5. Int J Cancer 2017; 141:364-376. [PMID: 28390157 DOI: 10.1002/ijc.30730] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/23/2017] [Accepted: 03/22/2017] [Indexed: 12/21/2022]
Abstract
Invadopodium formation is a crucial early event of invasion and metastasis of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying regulation of invadopodia remain elusive. This study aimed to investigate the potential role of discs large homolog 5 (Dlg5) in invadopodium formation and function in HCC. We found that Dlg5 expression was significantly lower in human HCC tissues and cell lines than adjacent nontumor tissues and liver cells. Lower Dlg5 expression was associated with advanced stages of HCC, and poor overall and disease-free survival of HCC patients. Dlg5-silencing promoted epithelial-mesenchymal transition, invadopodium formation, gelatin degradation function, and invadopodium-associated invasion of HepG2 cells. In contrast, Dlg5 overexpression inhibited epithelial-mesenchymal transition, functional invadopodium formation, and invasion of SK-Hep1 cells. Both Girdin and Tks5, but not the Tks5 nonphosphorylatable mutant, were responsible for the enhanced invadopodium formation and invasion of Dlg5-silenced HepG2 cells. Furthermore, Dlg5 interacted with Girdin and interfered with the interaction of Girdin and Tks5. Dlg5 silencing promoted Girdin and Tks5 phosphorylation, which was abrogated by Girdin silencing and rescued by inducing shRNA-resistant Girdin expression. Moreover, Dlg5 overexpression significantly inhibited HCC intrahepatic and lung metastasis in vivo. Taken together, our data indicate that Dlg5 acts as a novel regulator of invadopodium-associated invasion via Girdin and by interfering with the interaction between Girdin and Tks5, which might be important for Tks5 phosphorylation in HCC cells. Conceivably, Dlg5 may act as a new biomarker for prognosis of HCC patients.
Collapse
Affiliation(s)
- Yang Ke
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tianhao Bao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.,The Mental Health Center of Kunming Medical University, Kunming, China
| | - Qixin Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yan Wang
- Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiayun Ge
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Bimang Fu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuesong Wu
- Department of Gastroenterological Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haoran Tang
- Department of Gastroenterological Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhitian Shi
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuefen Lei
- Deparment of Medical Oncology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Cheng Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuqi Tan
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haotian Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhitang Guo
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lin Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| |
Collapse
|
10
|
Olferiev M, Jacek E, Kirou KA, Crow MK. Novel molecular signatures in mononuclear cell populations from patients with systemic lupus erythematosus. Clin Immunol 2016; 172:34-43. [PMID: 27576056 DOI: 10.1016/j.clim.2016.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 12/12/2022]
Abstract
To gain novel insights into the immunopathogenesis of systemic lupus erythematosus we have analyzed gene expression data from isolated CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD56+ NK-cell enriched peripheral blood cell fractions from patients and healthy donors. As predicted, type I interferon-inducible gene transcripts are overexpressed in all populations. Transcripts preferentially expressed in SLE CD4+ and CD8+ T cells include those associated with Tregulatory and Th17 effector cell programs, respectively, but in each case additional transcripts predicted to limit differentiation of those effector cells are detected. Evidence for involvement of the Wnt/β-catenin pathway was observed in both B and T cell fractions, and novel transcripts were identified in each cell population. These data point to disrupted T effector cell differentiation and the Wnt/β-catenin pathway as contributors to immune dysfunction in SLE while further supporting a central role for the type I interferon pathway in lupus.
Collapse
Affiliation(s)
- Mikhail Olferiev
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA
| | - Elzbieta Jacek
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA
| | - Kyriakos A Kirou
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA
| | - Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA.
| |
Collapse
|
11
|
Dlg5 maintains apical polarity by promoting membrane localization of Crumbs during Drosophila oogenesis. Sci Rep 2016; 6:26553. [PMID: 27211898 PMCID: PMC4876392 DOI: 10.1038/srep26553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/03/2016] [Indexed: 12/25/2022] Open
Abstract
Apical-basal polarity plays critical roles in the functions of epithelial tissues. However, the mechanisms of epithelial polarity establishment and maintenance remain to be fully elucidated. Here we show that the membrane-associated guanylate kinase (MAGUK) family protein Dlg5 is required for the maintenance of apical polarity of follicle epithelium during Drosophila oogenesis. Dlg5 localizes at the apical membrane and adherens junction (AJ) of follicle epithelium in early stage egg chambers. Specifically, we demonstrate that the major function of Dlg5 is to promote apical membrane localization of Crumbs, since overexpression of Crumbs but not other major apical or AJ components could rescue epithelial polarity defects resulted from loss of Dlg5. Furthermore, we performed a structure-function analysis of Dlg5 and found that the C-terminal PDZ3 and PDZ4 domains are required for all Dlg5’s functions as well as its ability to localize to apical membrane. The N-terminal coiled-coil motif could be individually targeted to the apical membrane, while the central linker region could be targeted to AJ. Lastly, the MAGUK core domains of PDZ4-SH3-GUK could be individually targeted to apical, AJ and basolateral membranes.
Collapse
|
12
|
Lin WH, Asmann YW, Anastasiadis PZ. Expression of polarity genes in human cancer. Cancer Inform 2015; 14:15-28. [PMID: 25991909 PMCID: PMC4390136 DOI: 10.4137/cin.s18964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 01/01/2023] Open
Abstract
Polarity protein complexes are crucial for epithelial apical–basal polarity and directed cell migration. Since alterations of these processes are common in cancer, polarity proteins have been proposed to function as tumor suppressors or oncogenic promoters. Here, we review the current understanding of polarity protein functions in epithelial homeostasis, as well as tumor formation and progression. As most previous studies focused on the function of single polarity proteins in simplified model systems, we used a genomics approach to systematically examine and identify the expression profiles of polarity genes in human cancer. The expression profiles of polarity genes were distinct in different human tissues and classified cancer types. Additionally, polarity expression profiles correlated with disease progression and aggressiveness, as well as with identified cancer types, where specific polarity genes were commonly altered. In the case of Scribble, gene expression analysis indicated its common amplification and upregulation in human cancer, suggesting a tumor promoting function.
Collapse
Affiliation(s)
- Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | |
Collapse
|
13
|
Andersen V, Vogel U. Systematic review: interactions between aspirin, and other nonsteroidal anti-inflammatory drugs, and polymorphisms in relation to colorectal cancer. Aliment Pharmacol Ther 2014; 40:147-59. [PMID: 24889212 PMCID: PMC4225470 DOI: 10.1111/apt.12807] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/29/2014] [Accepted: 05/03/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Nonsteroidal anti-inflammatory drugs (NSAIDs) include aspirin (acetylsalicylic acid, ASA). Long-term use of NSAIDs has been associated with lowered risk of colorectal cancer (CRC), but the use is hampered by adverse effects. Also, the anti-carcinogenic effects of NSAIDs are incompletely understood. Understanding biological effects of NSAIDs may help developing new preventive medical strategies. AIM To identify gene-environment interactions between genetic variation and NSAID use in relation to risk of CRC. METHODS We performed a PubMed literature search and all studies reporting original data on interactions between NSAIDs and polymorphisms in relation to CRC were evaluated. RESULTS We found indications that aspirin interacted with rs6983267 close to MYC (encoding a transcription factor involved in cell cycle progression, apoptosis and cellular transformation) and NSAIDs interacted with rs3024505 and rs1800872 in or close to IL10 (encoding IL-10) in preventing CRC. Homozygous carriers of the variant allele of rs6983267 (ca. 25% of the population) halved their risk for CRC by aspirin use compared to homozygous wildtype carriers who did not benefit from aspirin intake. No interaction between use of NSAIDs and PTGS-2 (encoding COX-2) in relation to CRC risk was detected. Other findings of interactions between genes in inflammatory and oncogenic pathways and NSAIDs were considered suggestive. CONCLUSIONS Knowledge of underlying biological effects of NSAIDs in relation to CRC is scarce and the basis for stratifying the patients for preventive treatment is not yet available. Further studies assessing interactions between long-term NSAID exposure and genetic variation in relation to CRC are warranted in large well-characterised prospective cohorts.
Collapse
Affiliation(s)
- V Andersen
- Organ Center, Hospital of Southern JutlandAabenraa, Denmark,Institute of Regional Health Research, University of Southern DenmarkOdense, Denmark,Medical Department, Regional Hospital ViborgViborg, Denmark
| | - U Vogel
- National Research Centre for the Working EnvironmentCopenhagen, Denmark
| |
Collapse
|
14
|
Anguria P, Kitinya J, Ntuli S, Carmichael T. The role of heredity in pterygium development. Int J Ophthalmol 2014; 7:563-73. [PMID: 24967209 DOI: 10.3980/j.issn.2222-3959.2014.03.31] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 03/01/2014] [Indexed: 11/02/2022] Open
Abstract
Several risk factors, which include heredity, ultra-violet (UV) light and chronic inflammation, contribute to pterygium development. However, there is no report integrating these factors in the pathogenesis of pterygium. The aim of this review is to describe the connection between heredity, UV, and inflammation in pterygium development. Existing reports indicate that sunlight exposure is the main factor in pterygium occurrence by inducing growth factor production or chronic inflammation or DNA damage. Heredity may be a factor. Our studies on factors in pterygium occurrence and recurrence identify that heredity is crucial for pterygium to develop, and that sunlight is only a trigger, and that chronic inflammation promotes pterygium enlargement. We propose that genetic factors may interfere with the control of fibrovascular proliferation while UV light or (sunlight) most likely only triggers pterygium development by inducing growth factors which promote vibrant fibrovascular proliferation in predisposed individuals. It also just triggers inflammation and collagenolysis, which may be promoters of the enlargement of the fibrovascular mass. Pterygium probably occurs in the presence of exuberant collagen production and profuse neovascularisation.
Collapse
Affiliation(s)
- Peter Anguria
- Department of Neurosciences, Division of Ophthalmology, University of the Witwatersrand Johannesburg, 7 York Road, Park Town 2193, South Africa
| | - James Kitinya
- Department of Anatomic Pathology, University of Limpopo Polokwane Campus, Private Bag X9316 Polokwane 0700, South Africa
| | - Sam Ntuli
- Department of Public Health Medicine, University of Limpopo Polokwane Campus, Private Bag X9316 Polokwane 0700, South Africa
| | - Trevor Carmichael
- Department of Neurosciences, Division of Ophthalmology, University of the Witwatersrand Johannesburg, 7 York Road, Park Town 2193, South Africa
| |
Collapse
|
15
|
Liu J, Li J, Ren Y, Liu P. DLG5 in cell polarity maintenance and cancer development. Int J Biol Sci 2014; 10:543-9. [PMID: 24910533 PMCID: PMC4046881 DOI: 10.7150/ijbs.8888] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/17/2014] [Indexed: 01/11/2023] Open
Abstract
Failure in establishment and maintenance of epithelial cell polarity contributes to tumorigenesis. Loss of expression and function of cell polarity proteins is directly related to epithelial cell polarity maintenance. The polarity protein discs large homolog 5 (DLG5) belongs to a family of molecular scaffolding proteins called Membrane Associated Guanylate Kinases (MAGUKs). As the other family members, DLG5 contains the multi-PDZ, SH3 and GUK domains. DLG5 has evolved in the same manner as DLG1 and ZO1, two well-studied MAGUKs proteins. Just like DLG1 and ZO1, DLG5 plays a role in cell migration, cell adhesion, precursor cell division, cell proliferation, epithelial cell polarity maintenance, and transmission of extracellular signals to the membrane and cytoskeleton. Since the roles of DLG5 in inflammatory bowel disease (IBD) and Crohn's disease (CD) have been reviewed, here, our review focuses on the roles of DLG5 in epithelial cell polarity maintenance and cancer development.
Collapse
Affiliation(s)
- Jie Liu
- 1. Center for Translational Medicine, the First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Juan Li
- 1. Center for Translational Medicine, the First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Yu Ren
- 2. Department of Surgical Oncology, the First Affiliated Hospital of Xian Jiaotong University College of Medicine
| | - Peijun Liu
- 1. Center for Translational Medicine, the First Affiliated Hospital of Xian Jiaotong University College of Medicine
| |
Collapse
|
16
|
Loss of Dlg5 expression promotes the migration and invasion of prostate cancer cells via Girdin phosphorylation. Oncogene 2014; 34:1141-9. [DOI: 10.1038/onc.2014.31] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 12/11/2013] [Accepted: 12/24/2013] [Indexed: 01/18/2023]
|
17
|
Ameliorating replicative senescence of human bone marrow stromal cells by PSMB5 overexpression. Biochem Biophys Res Commun 2014; 443:1182-8. [PMID: 24393841 DOI: 10.1016/j.bbrc.2013.12.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 12/20/2013] [Indexed: 02/08/2023]
Abstract
Multipotent human bone marrow stromal cells (hBMSCs) potentially serve as a source for cell-based therapy in regenerative medicine. However, in vitro expansion was inescapably accompanied with cell senescence, characterized by inhibited proliferation and compromised pluripotency. We have previously demonstrated that this aging process is closely associated with reduced 20S proteasomal activity, with down-regulation of rate-limiting catalytic β-subunits particularly evident. In the present study, we confirmed that proteasomal activity directly contributes to senescence of hBMSCs, which could be reversed by overexpression of the β5-subunit (PSMB5). Knocking down PSMB5 led to decreased proteasomal activity concurrent with reduced cell proliferation in early-stage hBMSCs, which is similar to the senescent phenotype observed in late-stage cells. In contrast, overexpressing PSMB5 in late-stage cells efficiently restored the normal activity of 20S proteasomes and promoted cell growth, possibly via upregulating the Cyclin D1/CDK4 complex. Additionally, PSMB5 could enhance cell resistance to oxidative stress, as evidenced by the increased cell survival upon exposing senescent hBMSCs to hydrogen peroxide. Furthermore, PSMB5 overexpression retained the pluripotency of late-stage hBMSCs by facilitating their neural differentiation both in vitro and in vivo. Collectively, our work reveals a critical role of PSMB5 in 20S proteasome-mediated protection against replicative senescence, pointing to a possible strategy for maintaining the integrity of culture-expanded hBMSCs by manipulating the expression of PSMB5.
Collapse
|