1
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Dithmer S, Blasig IE, Fraser PA, Qin Z, Haseloff RF. The Basic Requirement of Tight Junction Proteins in Blood-Brain Barrier Function and Their Role in Pathologies. Int J Mol Sci 2024; 25:5601. [PMID: 38891789 PMCID: PMC11172262 DOI: 10.3390/ijms25115601] [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: 02/07/2024] [Revised: 03/10/2024] [Accepted: 03/28/2024] [Indexed: 06/21/2024] Open
Abstract
This review addresses the role of tight junction proteins at the blood-brain barrier (BBB). Their expression is described, and their role in physiological and pathological processes at the BBB is discussed. Based on this, new approaches are depicted for paracellular drug delivery and diagnostics in the treatment of cerebral diseases. Recent data provide convincing evidence that, in addition to its impairment in the course of diseases, the BBB could be involved in the aetiology of CNS disorders. Further progress will be expected based on new insights in tight junction protein structure and in their involvement in signalling pathways.
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Affiliation(s)
- Sophie Dithmer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany (I.E.B.)
| | - Ingolf E. Blasig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany (I.E.B.)
| | | | - Zhihai Qin
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100049, China
| | - Reiner F. Haseloff
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany (I.E.B.)
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2
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Su Y, Long Y, Xie K. Cingulin family: Structure, function and clinical significance. Life Sci 2024; 341:122504. [PMID: 38354973 DOI: 10.1016/j.lfs.2024.122504] [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: 11/09/2023] [Revised: 01/21/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Cingulin and its paralog paracingulin are vital components of the apical junctional complex in vertebrate epithelial and endothelial cells. They are both found in tight junctions (TJ), and paracingulin is also detectable in adherens junctions (AJ) as TJ cytoplasmic plaque proteins. Cingulin and paracingulin interact with other proteins to perform functions. They interact with cytoskeletal proteins, modulate the activity of small GTPases, such as RhoA and Rac1, and regulate gene expression. In addition, cingulin and paracingulin regulate barrier function and many pathological processes, including inflammation and tumorigenesis. In this review, we summarize the discovery and structure, expression and subcellular distribution, and molecular interactions of cingulin family proteins and discuss their role in development, physiology, and pathological processes.
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Affiliation(s)
- Yuling Su
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, Guangdong 510006, China
| | - You Long
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, Guangdong 510006, China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, Guangdong 510006, China; The Second Affiliated Hospital and Guangzhou First People's Hospital, South China University of Technology School of Medicine, Guangdong 510006, China; The South China University of Technology Comprehensive Cancer Center, Guangzhou, Guangdong 510006, China.
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3
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Hunter JD, Mesfin JM, Ahmed T, Chen A, Reimold K, Hancko A, Braden RL, Davis ME, Christman KL. Myocardial Matrix Hydrogels Mitigate Negative Remodeling and Improve Function in Right Heart Failure Model. JACC Basic Transl Sci 2024; 9:322-338. [PMID: 38559631 PMCID: PMC10978413 DOI: 10.1016/j.jacbts.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 04/04/2024]
Abstract
This study evaluates the effectiveness of myocardial matrix (MM) hydrogels in mitigating negative right ventricular (RV) remodeling in a rat model of RV heart failure. The goal was to assess whether a hydrogel derived from either the right or left ventricle could promote cardiac repair. Injured rat right ventricles were injected with either RV-or left ventricular-derived MM hydrogels. Both hydrogels improved RV function and morphology and reduced negative remodeling. This study supports the potential of injectable biomaterial therapies for treating RV heart failure.
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Affiliation(s)
- Jervaughn D. Hunter
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Joshua M. Mesfin
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Tanzeel Ahmed
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Alexander Chen
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Kate Reimold
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Arielle Hancko
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Rebecca L. Braden
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
| | - Michael E. Davis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Karen L. Christman
- Shu Chien-Gene Lay Department of Bioengineering and Sanford Consortium for Regenerative Medicine, University of California-San Diego, San Diego, California, USA
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4
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Zhong C, Yang D, Zhong L, Xie W, Sun G, Jin D, Li Y. Single-cell and bulk RNA sequencing reveals Anoikis related genes to guide prognosis and immunotherapy in osteosarcoma. Sci Rep 2023; 13:20203. [PMID: 37980450 PMCID: PMC10657454 DOI: 10.1038/s41598-023-47367-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 11/20/2023] Open
Abstract
Anoikis resistance, a notable factor in osteosarcoma, plays a significant role in tumor invasion and metastasis. This study seeks to identify a distinct gene signature that is specifically associated with the anoikis subcluster in osteosarcoma. Clinical, single-cell, and transcriptional data from TARGET and GEO datasets were used to develop a gene signature for osteosarcoma based on the anoikis subcluster. Univariate Cox and LASSO regression analyses were employed. The signature's predictive value was evaluated using time-dependent ROC and Kaplan-Meier analyses. Functional enrichment analyses and drug sensitivity analyses were conducted. Validation of three modular genes was performed using RT-qPCR and Western blotting. Signature (ZNF583, CGNL1, CXCL13) was developed to predict overall survival in osteosarcoma patients, targeting the anoikis subcluster. The signature demonstrated good performance in external validation. Stratification based on the signature revealed significantly different prognoses. The signature was an independent prognostic factor. The low-risk group showed enhanced immune cell infiltration and improved immune function. Drug sensitivity analysis indicated efficacy of chemotherapy agents. Prognostic nomograms incorporating the signature provided greater predictive accuracy and clinical utility. Signatures related to the anoikis subcluster play a significant role in osteosarcoma progression. Incorporating these findings into clinical decision-making can improve osteosarcoma treatment and patient outcomes.
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Affiliation(s)
- Cheng Zhong
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China
- Department of Orthopedics, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China
| | - Dongliang Yang
- Department of Orthopedics, Tai Shan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Chinese Medicine, Jiangmen, 529000, China
| | - Liping Zhong
- Department of Cardiothoracic Surgery, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China
| | - Weixing Xie
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China
| | - Guodong Sun
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Daxiang Jin
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China.
| | - Yuming Li
- Department of Orthopedics, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China.
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5
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Liu X, Zeng L, Wang W, Li Z, Zhou S, Wang F, Wang Y, Du J, Ma X. Integrated analysis of high‑throughput sequencing reveals the regulatory potential of hsa_circ_0035431 in HNSCC. Oncol Lett 2023; 26:435. [PMID: 37664656 PMCID: PMC10472046 DOI: 10.3892/ol.2023.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/14/2023] [Indexed: 09/05/2023] Open
Abstract
Circular RNAs (circRNAs) are molecular sponges that are involved in regulation of multiple types of cancer. The present study aimed to screen and explore the key circRNA/microRNA (miRNA or miR)/mRNA interactions in head and neck squamous cell carcinoma (HNSCC) using bioinformatics. A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome-wide transcriptional sequencing was performed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). Moreover, expression levels of DEGs were verified in HNSCC cells and tissues using reverse transcription-quantitative (RT-q)PCR. A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa-miR-940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa-miR-940/cingulin-like 1 (CGNL1). FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. Low FUT6 and CGNL1 expression levels were associated with lower overall survival rate and progression-free intervals in HNSCC. RT-qPCR demonstrated that hsa_circ_0035431, FUT6 and CGNL1 were downregulated in HNSCC cells and tissue and hsa-miR-940 was upregulated. Notably, these results were consistent with those obtained using high-throughput sequencing. In conclusion, hsa_circ_0035431 may participate in regulation of FUT6 and CGNL1 expression by sponging hsa-miR-940, thus, impacting the occurrence, development and prognosis of HNSCC.
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Affiliation(s)
- Xiaoyan Liu
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
- School of Stomatology, Binzhou Medical University, Yantai, Shandong 264000, P.R. China
| | - Lili Zeng
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
- School of Stomatology, Binzhou Medical University, Yantai, Shandong 264000, P.R. China
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
| | - Wenlong Wang
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
| | - Zhipeng Li
- Department of Stomatology, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang 314001, P.R. China
| | - Siyuan Zhou
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
- School of Stomatology, Binzhou Medical University, Yantai, Shandong 264000, P.R. China
| | - Fang Wang
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
| | - Yue Wang
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong 255000, P.R. China
| | - Jing Du
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
| | - Xiangrui Ma
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, Shandong 256600, P.R. China
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6
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Ma S, Guo J, Zhang X, Yang Y, Bao Y, Zhang S, Li T. The exploration of new biomarkers for oral cancer through the ceRNA network and immune microenvironment analysis. Medicine (Baltimore) 2022; 101:e32249. [PMID: 36626444 PMCID: PMC9750585 DOI: 10.1097/md.0000000000032249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The competitive endogenous RNA (ceRNA) and tumor-penetrating immune cells may be related to the prognosis of oral cancer. However, few studies have focused on the correlation between ceRNAs and immune cells. Thus, we developed a method based on a ceRNA network and tumor-infiltrating immune cells to elucidate the molecular pathways that may predict prognosis in patients with oral cancer. Download RNAseq expression data of oral cancer and control samples from the Cancer Genome Atlas (TCGA), obtain differentially expressed genes and establish a ceRNA network. The cox analysis and lasso regression analysis were used to screen key RNAs to establish a prognostic risk assessment model, and draw a 1.3.5-year forecast nomogram. Then the CIBERSORT algorithm was used to screen important tumor immune infiltrating cells associated with oral cancer. Another prognostic predictive model related to immune cells was established. Finally, co-expression analysis was applied to explore the relationship between key genes in the ceRNA network and important immune cells. Multiple external data sets are used to test the expression of key biomarkers. We constructed prognostic risk models of ceRNA and immune cells, which included 9 differentially expressed mRNAs and 2 types of immune cells. It was discovered from the co-expression analysis that a pair of important biomarkers were associated with the prognosis of oral cancer. T cells regulatory and CGNL1 (R = 0.39, P < .001) showed a significant positive correlation. External data set validation also supports this result. In this study, we found that some crucial ceRNAs (GGCT, TRPS1, CGNL1, HENMT1, LCE3A, S100A8, ZNF347, TMEM144, TMEM192) and immune cells (T cells regulatory and Eosinophils) may be related to the prognosis of oral cancer.
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Affiliation(s)
- Sai Ma
- The First Affiliated Hospital of Hebei North University, oral and maxillofacial surgery, Zhangjiakou, Hebei Province, China
| | - Jie Guo
- The Fourth Hospital of Hebei Medical University, Department of Stomatology, Shijiazhuang, Hebei Province, China
| | - Xuan Zhang
- The First Affiliated Hospital of Hebei North University, oral and maxillofacial surgery, Zhangjiakou, Hebei Province, China
| | - Yongchao Yang
- The First Affiliated Hospital of Hebei North University, oral and maxillofacial surgery, Zhangjiakou, Hebei Province, China
| | - Yang Bao
- The Fourth Hospital of Hebei Medical University, Department of Stomatology, Shijiazhuang, Hebei Province, China
| | - Suxin Zhang
- The Fourth Hospital of Hebei Medical University, Department of Stomatology, Shijiazhuang, Hebei Province, China
| | - Tianke Li
- The Fourth Hospital of Hebei Medical University, Department of Stomatology, Shijiazhuang, Hebei Province, China
- * Correspondence: Tianke Li, The Fourth Hospital of Hebei Medical University, Department of Stomatology, 12 Jiankang Road, Chang’an District, Shijiazhuang, Hebei Province 050011, China (e-mail: )
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7
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Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Proekt I, Yu D, Mandel-Brehm C, Wang CY, Miao B, Sowa G, Zorn K, Chan AY, Tagi VM, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kämpe O, Dobbs K, Delmonte OM, Bacchetta R, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq. eLife 2022; 11:e78550. [PMID: 36300623 PMCID: PMC9711525 DOI: 10.7554/elife.78550] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Phage immunoprecipitation sequencing (PhIP-seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-seq for autoantigen discovery, including our previous work (Vazquez et al., 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), and finally, mild and severe forms of COVID-19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as prodynorphin (PDYN) in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in two patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID-19, including the endosomal protein EEA1. Together, scaled PhIP-seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
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Affiliation(s)
- Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Aaron Bodansky
- Department of Pediatric Critical Care Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Zoe Quandt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Elise MN Ferré
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Nils Landegren
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Science for life Laboratory, Department of Medical Sciences, Uppsala UniversityUppsalaSweden
| | - Daniel Eriksson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
- Centre for Molecular Medicine, Department of Medicine, Karolinska InstitutetStockholmSweden
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San FranciscoSan FranciscoUnited States
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Irina Proekt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - David Yu
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chung-Yu Wang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Gavin Sowa
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Alice Y Chan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology, Bone and Marrow Transplantation, Division of Pediatric Rheumatology, University of California, San FranciscoSan FranciscoUnited States
| | - Veronica M Tagi
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Chisato Shimizu
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Adriana Tremoulet
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Kara Lynch
- Department of Laboratory Medicine, University of California, San FranciscoSan FranciscoUnited States
- Zuckerberg San Francisco GeneralSan FranciscoUnited States
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Olle Kämpe
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Department of Clinical Science and KG Jebsen Center for Autoimmune Disorders, University of BergenBergenNorway
- Center of Molecular Medicine, and Department of Endocrinology, Metabolism and Diabetes, Karolinska University HospitalStockholmSweden
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Rosa Bacchetta
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Jane C Burns
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Michail S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Troy R Torgerson
- Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
| | - Mark S Anderson
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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8
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Identification of Candidate mRNA Isoforms for Prostate Cancer-Risk SNPs Utilizing Iso-eQTL and sQTL Methods. Int J Mol Sci 2022; 23:ijms232012406. [PMID: 36293264 PMCID: PMC9604153 DOI: 10.3390/ijms232012406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) impacting the alternative splicing (AS) process (sQTLs) or isoform expression (iso-eQTL) are implicated as important cancer regulatory elements. To find the sQTL and iso-eQTL, we retrieved prostate cancer (PrCa) tissue RNA-seq and genotype data originating from 385 PrCa European patients from The Cancer Genome Atlas. We conducted RNA-seq analysis with isoform-based and splice event-based approaches. The MatrixEQTL was used to identify PrCa-associated sQTLs and iso-eQTLs. The overlap between sQTL and iso-eQTL with GWAS loci and those that are differentially expressed between cancer and normal tissue were identified. The cis-acting associations (FDR < 0.05) for PrCa-risk SNPs identified 42, 123, and 90 PrCa-associated cassette exons, intron retention, and mRNA isoforms belonging to 25, 95, and 83 genes, respectively; while assessment of trans-acting association (FDR < 0.05) yielded 59, 65, and 196 PrCa-associated cassette exons, intron retention and mRNA isoforms belonging to 35, 55, and 181 genes, respectively. The results suggest that functional PrCa-associated SNPs can play a role in PrCa genesis by making an important contribution to the dysregulation of AS and, consequently, impacting the expression of the mRNA isoforms.
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9
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Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Mandel-Brehm C, Miao B, Sowa G, Zorn K, Chan AY, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kampe O, Dobbs K, Delmonte OM, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.23.485509. [PMID: 35350199 PMCID: PMC8963698 DOI: 10.1101/2022.03.23.485509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
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Affiliation(s)
- Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Diabetes Center, University of California, San Francisco, San Francisco, United States
- School of Medicine, University of California, San Francisc, San Francisco, CA, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Aaron Bodansky
- Department of Pediatric Critical Care Medicine, University of California, San Francisco, San Francisco, United State
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Zoe Quandt
- Department of Medicine, University of California, San Francisc, San Francisco, United States
- Diabetes Center, University of California, San Francisco, San Francisco, United States
| | - Elise M N Ferré
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH)
| | - Nils Landegren
- Department of Medicine (Solna), Karolinska University Hospital, Karolinska Institutet, Stockholm 17176, Sweden
- Science for life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala 75237, Sweden
| | - Daniel Eriksson
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- University of Paris, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University of Paris, Imagine Institute, Paris, France, EU
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, San Francisco, United States
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Gavin Sowa
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Alice Y Chan
- Department of Pediatrics, Division of Pediatric allergy, immunology, bone and marrow transplantation, Division of Pediatric Rheumatology, University of California, San Francisco, San Francisco, United States
| | - Chisato Shimizu
- Kawasaki Disease Research Center, Rady Children's Hospital and Department of Pediatrics, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Adriana Tremoulet
- Kawasaki Disease Research Center, Rady Children's Hospital and Department of Pediatrics, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Kara Lynch
- Zuckerberg San Francisco General, San Francisco, CA 94110, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Olle Kampe
- Department of Clinical Science and KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- Center of Molecular Medicine, and Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jane C Burns
- Kawasaki Disease Research Center, Rady Children's Hospital and Department of Pediatrics, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University of Paris, Imagine Institute, Paris, France, EU
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France, EU
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH)
| | - Troy R Torgerson
- Seattle Children's Research Institute, Seattle, United States
- Department of Pediatrics, University of Washington, Seattle, United States
- Current address: Allen Institute for Immunology, Seattle, United States
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Chan Zuckerberg Biohub, San Francisco, United States
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10
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Oshima S, Asai S, Seki N, Minemura C, Kinoshita T, Goto Y, Kikkawa N, Moriya S, Kasamatsu A, Hanazawa T, Uzawa K. Identification of Tumor Suppressive Genes Regulated by miR-31-5p and miR-31-3p in Head and Neck Squamous Cell Carcinoma. Int J Mol Sci 2021; 22:6199. [PMID: 34201353 PMCID: PMC8227492 DOI: 10.3390/ijms22126199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
We identified the microRNA (miRNA) expression signature of head and neck squamous cell carcinoma (HNSCC) tissues by RNA sequencing, in which 168 miRNAs were significantly upregulated, including both strands of the miR-31 duplex (miR-31-5p and miR-31-3p). The aims of this study were to identify networks of tumor suppressor genes regulated by miR-31-5p and miR-31-3p in HNSCC cells. Our functional assays showed that inhibition of miR-31-5p and miR-31-3p attenuated cancer cell malignant phenotypes (cell proliferation, migration, and invasion), suggesting that they had oncogenic potential in HNSCC cells. Our in silico analysis revealed 146 genes regulated by miR-31 in HNSCC cells. Among these targets, the low expression of seven genes (miR-31-5p targets: CACNB2 and IL34; miR-31-3p targets: CGNL1, CNTN3, GAS7, HOPX, and PBX1) was closely associated with poor prognosis in HNSCC. According to multivariate Cox regression analyses, the expression levels of five of those genes (CACNB2: p = 0.0189; IL34: p = 0.0425; CGNL1: p = 0.0014; CNTN3: p = 0.0304; and GAS7: p = 0.0412) were independent prognostic factors in patients with HNSCC. Our miRNA signature and miRNA-based approach will provide new insights into the molecular pathogenesis of HNSCC.
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Affiliation(s)
- Sachi Oshima
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (S.O.); (C.M.); (A.K.); (K.U.)
| | - Shunichi Asai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; (S.A.); (T.K.); (Y.G.); (N.K.)
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan;
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; (S.A.); (T.K.); (Y.G.); (N.K.)
| | - Chikashi Minemura
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (S.O.); (C.M.); (A.K.); (K.U.)
| | - Takashi Kinoshita
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; (S.A.); (T.K.); (Y.G.); (N.K.)
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan;
| | - Yusuke Goto
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; (S.A.); (T.K.); (Y.G.); (N.K.)
| | - Naoko Kikkawa
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; (S.A.); (T.K.); (Y.G.); (N.K.)
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan;
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan;
| | - Atsushi Kasamatsu
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (S.O.); (C.M.); (A.K.); (K.U.)
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan;
| | - Katsuhiro Uzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (S.O.); (C.M.); (A.K.); (K.U.)
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11
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Tangeman JA, Luz-Madrigal A, Sreeskandarajan S, Grajales-Esquivel E, Liu L, Liang C, Tsonis PA, Del Rio-Tsonis K. Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. Genes (Basel) 2021; 12:genes12060840. [PMID: 34072522 PMCID: PMC8226911 DOI: 10.3390/genes12060840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/22/2021] [Indexed: 12/27/2022] Open
Abstract
The plasticity of human retinal pigment epithelium (RPE) has been observed during proliferative vitreoretinopathy, a defective repair process during which injured RPE gives rise to fibrosis. In contrast, following injury, the RPE of the embryonic chicken can be reprogrammed to regenerate neural retina in a fibroblast growth factor 2 (FGF2)-dependent manner. To better explore the mechanisms underlying embryonic RPE reprogramming, we used laser capture microdissection to isolate RNA from (1) intact RPE, (2) transiently reprogrammed RPE (t-rRPE) 6 h post-retinectomy, and (3) reprogrammed RPE (rRPE) 6 h post-retinectomy with FGF2 treatment. Using RNA-seq, we observed the acute repression of genes related to cell cycle progression in the injured t-rRPE, as well as up-regulation of genes associated with injury. In contrast, the rRPE was strongly enriched for mitogen-activated protein kinase (MAPK)-responsive genes and retina development factors, confirming that FGF2 and the downstream MAPK cascade are the main drivers of embryonic RPE reprogramming. Clustering and pathway enrichment analysis was used to create an integrated network of the core processes associated with RPE reprogramming, including key terms pertaining to injury response, migration, actin dynamics, and cell cycle progression. Finally, we employed gene set enrichment analysis to suggest a previously uncovered role for epithelial-mesenchymal transition (EMT) machinery in the initiation of embryonic chick RPE reprogramming. The EMT program is accompanied by extensive, coordinated regulation of extracellular matrix (ECM) associated factors, and these observations together suggest an early role for ECM and EMT-like dynamics during reprogramming. Our study provides for the first time an in-depth transcriptomic analysis of embryonic RPE reprogramming and will prove useful in guiding future efforts to understand proliferative disorders of the RPE and to promote retinal regeneration.
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Affiliation(s)
- Jared A. Tangeman
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Agustín Luz-Madrigal
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sutharzan Sreeskandarajan
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Lin Liu
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
| | - Chun Liang
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA
| | - Panagiotis A. Tsonis
- Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), Dayton, OH 45469, USA;
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences at Miami University, Miami University, Oxford, OH 45056, USA; (J.A.T.); (A.L.-M.); (S.S.); (E.G.-E.); (L.L.); (C.L.)
- Correspondence: ; Tel.: +513-529-3128; Fax: +513-529-6900
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12
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Jin Y, Qin X. Significance of TP53 mutation in treatment and prognosis in head and neck squamous cell carcinoma. Biomark Med 2021; 15:15-28. [PMID: 33427498 DOI: 10.2217/bmm-2020-0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/19/2020] [Indexed: 12/09/2022] Open
Abstract
Background:TP53 is ranked as the most common mutated gene in head and neck squamous cell carcinoma (HNSCC). Results: The status of TP53 mutation was investigated on International Cancer Genome Consortium and The Cancer Genome Atlas database and TP53-related differentially expressed genes were screened out from transcriptome data and mutation information. A TP53-related prognostic gene signature (TIMP4, ONECUT2, CGNL1, DMRTA2 and NKX2.3) was constructed based on Cox regression analysis and LASSO algorithm. Univariate and multivariate analyses were carried out to identify promising prognosticators for HNSCC. Conclusion: Our findings provide a well-rounded landscape of TP53 mutation in HNSCC and pave the groundwork for developing innovative and effective cancer treatment methods for HNSCC.
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Affiliation(s)
- Yu Jin
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
| | - Xing Qin
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
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13
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Rouaud F, Sluysmans S, Flinois A, Shah J, Vasileva E, Citi S. Scaffolding proteins of vertebrate apical junctions: structure, functions and biophysics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183399. [DOI: 10.1016/j.bbamem.2020.183399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022]
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14
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Zhuravleva K, Goertz O, Wölkart G, Guillemot L, Petzelbauer P, Lehnhardt M, Schmidt K, Citi S, Schossleitner K. The tight junction protein cingulin regulates the vascular response to burn injury in a mouse model. Microvasc Res 2020; 132:104067. [PMID: 32877697 DOI: 10.1016/j.mvr.2020.104067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 02/04/2023]
Abstract
Edema formation due to the collapse of physiological barriers and the associated delayed healing process is still a central problem in the treatment of burn injuries. In healthy individuals, tight junctions form a barrier to fluid and small molecules. Cingulin is a cytoplasmic component of tight junctions and is involved in the regulation of the paracellular barrier. Endothelial specific cingulin knock-out mice provide new insight into the influence of tight junction proteins on edema formation and angiogenesis during wound healing. Knock-out mice lacking the head domain of cingulin in endothelial cells (CgnΔEC) were created by breeding Cgnfl/fl mice with Tie1-cre mice. Using a no-touch hot air jet a burn trauma was induced on the ear of the mouse. Over a period of 12 days microcirculatory parameters such as edema formation, angiogenesis and leukocyte-endothelial interactions were visualized using intravital fluorescence microscopy. At baseline, CgnΔEC mice surprisingly showed significantly less tracer extravasation compared to Cgnfl/fl littermates, whereas, after burn injury, edema was consistently higher in CgnΔEC mice. Non-perfused area after wounding was increased, but there was no difference in vessel diameters, contraction or dilation of arteries in CgnΔEC mice. Moreover, cingulin knock-out did not cause a difference in leukocyte adhesion after burn injury. In summary, cingulin limits non-perfused area after burn injury and maintains the paracellular barrier of blood vessels. Since edema formation with serious systemic effects is a central problem of burn wounds, understanding the importance of tight junction proteins might help to find new treatment strategies for burn wounds.
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Affiliation(s)
- Kristina Zhuravleva
- Department of Plastic and Hand Surgery, Burn Center, BG-University Hospital Bergmannsheil, Ruhr University Bochum, Bochum, Germany; Department of Plastic, Reconstructive and Aesthetic Surgery, Hand Surgery, Martin-Luther Hospital, Berlin, Germany
| | - Ole Goertz
- Department of Plastic and Hand Surgery, Burn Center, BG-University Hospital Bergmannsheil, Ruhr University Bochum, Bochum, Germany; Department of Plastic, Reconstructive and Aesthetic Surgery, Hand Surgery, Martin-Luther Hospital, Berlin, Germany
| | - Gerald Wölkart
- Department of Pharmacology and Toxicology, Institute of Pharmaceutical Sciences, Karl-Franzens-Universität Graz, Graz, Austria
| | - Laurent Guillemot
- Department of Cell Biology, Faculty of Sciences, and Institute of Genetics and Genomics of Geneva, University of Geneva, Switzerland
| | - Peter Petzelbauer
- Skin and Endothelium Research Division, Department of Dermatology, Medical University Vienna, Vienna, Austria
| | - Marcus Lehnhardt
- Department of Plastic and Hand Surgery, Burn Center, BG-University Hospital Bergmannsheil, Ruhr University Bochum, Bochum, Germany
| | - Kurt Schmidt
- Department of Pharmacology and Toxicology, Institute of Pharmaceutical Sciences, Karl-Franzens-Universität Graz, Graz, Austria
| | - Sandra Citi
- Department of Cell Biology, Faculty of Sciences, and Institute of Genetics and Genomics of Geneva, University of Geneva, Switzerland
| | - Klaudia Schossleitner
- Skin and Endothelium Research Division, Department of Dermatology, Medical University Vienna, Vienna, Austria.
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15
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González-Mariscal L, Miranda J, Gallego-Gutiérrez H, Cano-Cortina M, Amaya E. Relationship between apical junction proteins, gene expression and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183278. [PMID: 32240623 DOI: 10.1016/j.bbamem.2020.183278] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/09/2020] [Accepted: 03/06/2020] [Indexed: 12/11/2022]
Abstract
The apical junctional complex (AJC) is a cell-cell adhesion system present at the upper portion of the lateral membrane of epithelial cells integrated by the tight junction (TJ) and the adherens junction (AJ). This complex is crucial to initiate and stabilize cell-cell adhesion, to regulate the paracellular transit of ions and molecules and to maintain cell polarity. Moreover, we now consider the AJC as a hub of signal transduction that regulates cell-cell adhesion, gene transcription and cell proliferation and differentiation. The molecular components of the AJC are multiple and diverse and depending on the cellular context some of the proteins in this complex act as tumor suppressors or as promoters of cell transformation, migration and metastasis outgrowth. Here, we describe these new roles played by TJ and AJ proteins and their potential use in cancer diagnostics and as targets for therapeutic intervention.
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Affiliation(s)
- Lorenza González-Mariscal
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico.
| | - Jael Miranda
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Helios Gallego-Gutiérrez
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Misael Cano-Cortina
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Elida Amaya
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
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16
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Song Y, Jin D, Ou N, Luo Z, Chen G, Chen J, Yang Y, Liu X. Gene Expression Profiles Identified Novel Urine Biomarkers for Diagnosis and Prognosis of High-Grade Bladder Urothelial Carcinoma. Front Oncol 2020; 10:394. [PMID: 32292720 PMCID: PMC7118735 DOI: 10.3389/fonc.2020.00394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/05/2020] [Indexed: 01/18/2023] Open
Abstract
Bladder urothelial carcinoma (BC) has been identified as one of the most common malignant neoplasm worldwide. High-grade bladder urothelial carcinoma (HGBC) is aggressive with a high risk of recurrence, progression, metastasis, and poor prognosis. Therefore, HGBC clinical management is still a challenge. We performed the present study to seek new urine biomarkers for HGBC and investigate how they promote HGBC progression and thus affect the prognosis based on large-scale sequencing data. We identified the overlapped differentially expressed genes (DEGs) by combining GSE68020 and The Cancer Genome Atlas (TCGA) datasets. Subsequent receiver operating characteristic (ROC) curves, Kaplan-Meier (KM) curves, and Cox regression were conducted to test the diagnostic and prognostic role of the hub genes. Chi-square test and logistic regression were carried out to analyze the associations between clinicopathologic characteristics and the hub genes. Ultimately, we performed gene set enrichment analysis (GSEA), protein-protein interaction (PPI) networks, and Bayesian networks (BNs) to explore the underlying mechanisms by which ECM1, CRYAB, CGNL1, and GPX3 are involved in tumor progression. Immunohistochemistry based on The Human Protein Atlas and quantitative real-time polymerase chain reaction based on urine samples confirmed the downregulation and diagnostic values of the hub genes in HGBC. In conclusion, our study indicated that CRYAB, CGNL1, ECM1, and GPX3 are potential urine biomarkers of HGBC. These four novel urine biomarkers will have attractive applications to provide new diagnostic methods, prognostic predictors and treatment targets for HGBC, which could improve the prognosis of HGBC patients, if validated by further experiments and larger prospective clinical trials.
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Affiliation(s)
- Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Donghui Jin
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Ningjing Ou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhiwen Luo
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangyuan Chen
- The Second Clinical Medical School, Nanchang University, Nanchang, China
| | - Jingyi Chen
- Department of Gastroenterology and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing, China
| | - Yongjiao Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
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17
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Cerebral Cavernous Malformation Proteins in Barrier Maintenance and Regulation. Int J Mol Sci 2020; 21:ijms21020675. [PMID: 31968585 PMCID: PMC7013531 DOI: 10.3390/ijms21020675] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/18/2022] Open
Abstract
Cerebral cavernous malformation (CCM) is a disease characterized by mulberry shaped clusters of dilated microvessels, primarily in the central nervous system. Such lesions can cause seizures, headaches, and stroke from brain bleeding. Loss-of-function germline and somatic mutations of a group of genes, called CCM genes, have been attributed to disease pathogenesis. In this review, we discuss the impact of CCM gene encoded proteins on cellular signaling, barrier function of endothelium and epithelium, and their contribution to CCM and potentially other diseases.
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18
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Wang M, Gu B, Yao G, Li P, Wang K. Circular RNA Expression Profiles and the Pro-tumorigenic Function of CircRNA_10156 in Hepatitis B Virus-Related Liver Cancer. Int J Med Sci 2020; 17:1351-1365. [PMID: 32624692 PMCID: PMC7330659 DOI: 10.7150/ijms.45637] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022] Open
Abstract
Liver cancer is one of the most common malignant tumors in the world. Circular RNAs (circRNAs) perform important functions in cancer progression and are regarded as prospective biomarkers for cancer diagnosis and therapy. Here, we used the high-throughput RNA sequencing technology in conjunction with bioinformatics tools to profile circRNA expression in patients with HBV-related liver cancer. A total of 13,124 circRNAs were identified in HBV-related liver cancer, approximately 86.25% of which were sense-overlapping circRNAs. Moreover, 2,996 circRNAs exhibited different expression patterns between liver cancer tissues and matched pericancerous tissues. Function annotation indicated that these aberrantly expressed circRNAs were primarily engaged in cellular processes and cancer-associated pathways. Notably, the circRNA-miRNA interaction networks showed that 6,020 circRNAs were predicted to target 1,654 miRNAs. Quantitative RT-PCR (qRT-PCR) assay indicated that ten randomly selected circRNAs displayed consistent expression patterns with the sequencing results. We further predicted that circRNA_10156 might work as a molecular sponge of miR-149-3p, which served an important function in tumor development. Consequently, our results demonstrated that depletion of circRNA_10156 upregulated miR-149-3p, reduced Akt1 expression, and suppressed liver cancer cell proliferation. The present study will facilitate the elucidation of biological functions of circRNAs in the progression of HBV-related liver cancer providing prospective biomarkers and therapeutic targets for this disease. Our findings also reveal that circRNA_10156 might represent a promising therapeutic target for liver cancer management.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Bianli Gu
- Henan Key Laboratory of Cancer Epigenetics, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Guoliang Yao
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471003, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
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19
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Díaz-Coránguez M, Liu X, Antonetti DA. Tight Junctions in Cell Proliferation. Int J Mol Sci 2019; 20:E5972. [PMID: 31783547 PMCID: PMC6928848 DOI: 10.3390/ijms20235972] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022] Open
Abstract
Tight junction (TJ) proteins form a continuous intercellular network creating a barrier with selective regulation of water, ion, and solutes across endothelial, epithelial, and glial tissues. TJ proteins include the claudin family that confers barrier properties, members of the MARVEL family that contribute to barrier regulation, and JAM molecules, which regulate junction organization and diapedesis. In addition, the membrane-associated proteins such as MAGUK family members, i.e., zonula occludens, form the scaffold linking the transmembrane proteins to both cell signaling molecules and the cytoskeleton. Most studies of TJ have focused on the contribution to cell-cell adhesion and tissue barrier properties. However, recent studies reveal that, similar to adherens junction proteins, TJ proteins contribute to the control of cell proliferation. In this review, we will summarize and discuss the specific role of TJ proteins in the control of epithelial and endothelial cell proliferation. In some cases, the TJ proteins act as a reservoir of critical cell cycle modulators, by binding and regulating their nuclear access, while in other cases, junctional proteins are located at cellular organelles, regulating transcription and proliferation. Collectively, these studies reveal that TJ proteins contribute to the control of cell proliferation and differentiation required for forming and maintaining a tissue barrier.
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Affiliation(s)
| | | | - David A. Antonetti
- Department of Ophthalmology and Visual Sciences, University of Michigan, Kellogg Eye Center, Ann Arbor, MI 48105, USA; (M.D.-C.); (X.L.)
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20
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Pei J, Juni R, Harakalova M, Duncker DJ, Asselbergs FW, Koolwijk P, Hinsbergh VV, Verhaar MC, Mokry M, Cheng C. Indoxyl Sulfate Stimulates Angiogenesis by Regulating Reactive Oxygen Species Production via CYP1B1. Toxins (Basel) 2019; 11:E454. [PMID: 31382511 PMCID: PMC6723868 DOI: 10.3390/toxins11080454] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Indoxyl sulfate (IS) is an accumulative protein-bound uremic toxin found in patients with kidney disease. It is reported that IS impairs the vascular endothelium, but a comprehensive overview of all mechanisms active in IS-injury currently remains lacking. Here we performed RNA sequencing in human umbilical vein endothelial cells (HUVECs) after IS or control medium treatment and identified 1293 genes that were affected in a IS-induced response. Gene enrichment analysis highlighted pathways involved in altered vascular formation and cell metabolism. We confirmed these transcriptome profiles at the functional level by demonstrating decreased viability and increased cell senescence in response to IS treatment. In line with the additional pathways highlighted by the transcriptome analysis, we further could demonstrate that IS exposure of HUVECs promoted tubule formation as shown by the increase in total tubule length in a 3D HUVECs/pericytes co-culture assay. Notably, the pro-angiogenic response of IS and increased ROS production were abolished when CYP1B1, one of the main target genes that was highly upregulated by IS, was silenced. This observation indicates IS-induced ROS in endothelial cells is CYP1B1-dependent. Taken together, our findings demonstrate that IS promotes angiogenesis and CYP1B1 is an important factor in IS-activated angiogenic response.
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Affiliation(s)
- Jiayi Pei
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Regenerative Medicine Utrecht, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
| | - Rio Juni
- Department of Physiology, Amsterdam UMC, VUmc location, Amsterdam Cardiovascular Science, 1081 HV Amsterdam, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Pathology, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
| | - Dirk J Duncker
- Department of Cardiology, Erasmus MC, Rotterdam, 3015 GD, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, NW1 2DA, UK
- Health Data Research UK and Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Pieter Koolwijk
- Department of Physiology, Amsterdam UMC, VUmc location, Amsterdam Cardiovascular Science, 1081 HV Amsterdam, The Netherlands
| | - Victor van Hinsbergh
- Department of Physiology, Amsterdam UMC, VUmc location, Amsterdam Cardiovascular Science, 1081 HV Amsterdam, The Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Regenerative Medicine Utrecht, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
| | - Michal Mokry
- Regenerative Medicine Utrecht, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Clinical Chemistry and Heamatology, University of Utrecht, 3584 CX Utrecht, The Netherlands
- Division of Paediatrics, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, UMC Utrecht, University of Utrecht, 3584 CX Utrecht, The Netherlands.
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