DOCSLIB.ORG

Integrative Omics Analysis Reveals Soluble Cadherin-3 As a Survival

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Integrative Omics Analysis Reveals Soluble Cadherin-3 As a Survival Published OnlineFirst March 10, 2020; DOI: 10.1158/1078-0432.CCR-19-3972 CLINICAL CANCER RESEARCH | PRECISION MEDICINE AND IMAGING Integrative Omics Analysis Reveals Soluble Cadherin-3 as a Survival Predictor and an Early Monitoring Marker of EGFR Tyrosine Kinase Inhibitor Therapy in Lung Cancer Ting-Feng Hsiao1, Chih-Liang Wang2,3, Yi-Cheng Wu4, Hsiang-Pu Feng1, Yen-Chuan Chiu1, Hao-Yu Lin1, Ko-Jiunn Liu5,6, Gee-Chen Chang7,8, Kun-Yi Chien1,9,10, Jau-Song Yu9,10,11,12, and Chia-Jung Yu1,3,9,10 ABSTRACT ◥ Purpose: EGFR tyrosine kinase inhibitors (EGFR-TKI) (OS) were assessed to evaluate the prognostic values of the benefit patients with advanced lung adenocarcinoma (ADC) potential biomarkers. harboring activating EGFR mutations. We aimed to iden- Results: Fifteen proteins were identified as potential biomarkers tify biomarkers to monitor and predict the progression of of EGFR-TKI resistance. Cadherin-3 (CDH3) was overexpressed in patients receiving EGFR-TKIs via a comprehensive omic ADC tissues compared with normal tissues. CDH3 knockdown analysis. enhanced EGFR-TKI sensitivity in ADC cells. The PE level of Experimental Design: We applied quantitative proteomics soluble CDH3 (sCDH3) was increased in patients with resistance. to generate the TKI resistance–associated pleural effusion (PE) The altered sCDH3 serum level reflected the efficacy of EGFR-TKI proteome from patients with ADC with or without EGFR-TKI after 1 month of treatment (n ¼ 43). Baseline sCDH3 was signif- resistance. Candidates were selected from integrated genomic icantly associated with PFS and OS in patients with ADC after and proteomic datasets. The PE (n ¼ 33) and serum (n ¼ 329) EGFR-TKI therapy (n ¼ 76). Moreover, sCDH3 was positively levels of potential biomarkers were validated with ELISAs. associated with tumor stage in non–small cell lung cancer (n ¼ 272). Western blotting was applied to detect protein expression in Conclusions: We provide useful marker candidates for drug tissues, PEs, and a cell line. Gene knockdown, TKI treatment, resistance studies. sCDH3 is a survival predictor and real-time and proliferation assays were used to determine EGFR-TKI indicator of treatment efficacy in patients with ADC treated with sensitivity. Progression-free survival (PFS) and overall survival EGFR-TKIs. Introduction lung cancers, and adenocarcinoma (ADC) is the most common subtype of NSCLC (2). EGFR mutations specifically target patients Lung cancer is the leading cause of cancer-related death world- with lung ADC (60%) in East Asian countries, including Tai- wide (1). Non–small cell lung cancer (NSCLC) represents 80% of all wan (3, 4). EGFR-tyrosine kinase inhibitors (EGFR-TKI), such as the first-generation TKIs erlotinib and gefitinib and the second-generation TKI afatinib, have been determined to benefit patients with ADC with 1Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung EGFR-activating mutations (5). These response evaluations of targeted University, Taoyuan, Taiwan. 2School of Medicine, College of Medicine, Chang therapy are based on the RECIST guidelines (6), and an EGFR Gung University, Taoyuan, Taiwan. 3Division of Pulmonary Oncology and Inter- mutation is recognized as a good predictor for the initial efficacy of ventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memo- EGFR-TKI treatments, in which the response rates and disease control 4 rial Hospital, Linkou, Taoyuan, Taiwan. Department of Thoracic Surgery, Chang rates are 60%–70% and 85%–95%, respectively. These TKIs are Gung Memorial Hospital, Linkou, Taoyuan, Taiwan. 5National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan. 6School of associated with a median progression-free survival (PFS) time of – – Medical Laboratory Science and Biotechnology, Taipei Medical University, 9 14 months compared with 5 7 months for platinum-based Taipei, Taiwan. 7Division of Chest Medicine, Department of Internal Medicine, chemotherapy (7). Unfortunately, patients treated with first/second- Taichung Veterans General Hospital, Taichung, Taiwan. 8Faculty of Medicine, generation EGFR-TKIs eventually develop acquired resistance to these 9 School of Medicine, National Yang-Ming University, Taipei, Taiwan. Department agents after a median of 10–16 months that most commonly (50%– of Cell and Molecular Biology, College of Medicine, Chang Gung University, 60% of cases) results from a secondary mutation at position 790 in Taoyuan, Taiwan. 10Molecular Medicine Research Center, Chang Gung Univer- sity, Taoyuan, Taiwan. 11Liver Research Center, Chang Gung Memorial Hospital, EGFR (T790M; refs. 8, 9). Osimertinib, a third-generation irreversible – Linkou, Taoyuan, Taiwan. 12Research Center for Food and Cosmetic Safety, EGFR-TKI that selectively inhibits both EGFR-TKI sensitizing and College of Human Ecology, Chang Gung University of Science and Technology, EGFR T790M–resistance mutations (10), obtained FDA-accelerated Taoyuan, Taiwan. approval in November 2015. Recent studies have also shown that Note: Supplementary data for this article are available at Clinical Cancer osimertinib improves both the median PFS (18.9 vs. 10.2 months) and Research Online (http://clincancerres.aacrjournals.org/). overall survival (OS; 38.6 vs. 31.8 months) compared with first- € T.-F. Hsiao and C.-L. Wang contributed equally to this article. generation EGFR-TKIs in patients with treatment-na ve, EGFR muta- tion–positive (exon 19 deletion or L858R) advanced NSCLC (11, 12), Corresponding Author: Chia-Jung Yu, Chang Gung University, No. 259 Wenhua fi 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan. Phone: 886-3211-8800, ext. 3424; suggesting that osimertinib will be a new standard of care in rst-line Fax: 886-3211-8042; E-mail: [email protected] EGFR-mutated NSCLC. T790M can be evaluated via either a tissue rebiopsy or circulating cell-free tumor DNA in the plasma, and its Clin Cancer Res 2020;XX:XX–XX evaluation is currently mandatory after progression to first/second- doi: 10.1158/1078-0432.CCR-19-3972 generation EGFR-TKIs (13). However, neither cancer progression nor Ó2020 American Association for Cancer Research. an improvement in the patient's OS is correlated with EGFR AACRJournals.org | OF1 Downloaded from clincancerres.aacrjournals.org on September 29, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst March 10, 2020; DOI: 10.1158/1078-0432.CCR-19-3972 Hsiao et al. Hospital (Linkou, Taoyuan, Taiwan; approval number: 99-3738B and Translational Relevance 99-3671B). This study was conducted in accordance with the Decla- Mutated EGFR is a predictor of the initial treatment efficacy of ration of Helsinki and Good Clinical Practice. Written informed EGFR–tyrosine kinase inhibitors (TKI) in advanced lung adeno- consent was received from all patients before collection. For the carcinoma (ADC). Unfortunately, neither EGFR mutations nor discovery phase, malignant pleural effusion (MPE) from 23 patients molecular markers can accurately monitor cancer progression or with advanced lung ADC with EGFR mutations who received EGFR- predict patient survival. EGFR-TKI susceptibility associated bio- TKI–targeted therapy with or without following chemotherapy regi- markers to benefit patients with lung ADC are in high demand. mens were included. PE from 10 patients with tuberculosis (TB) Pleural effusion (PE) has been recognized as a promising source for represents benign pulmonary disease. These 33 patients' PEs were biomarker discovery. By integrating PE proteomic and tissue divided into four groups (Fig. 1A; Supplementary Table S2): MPE genomic analyses, we herein identified soluble cadherin-3 (sCDH3) obtained prior to treatment (before treatment, BT group) from 11 as a marker for monitoring first/second-generation EGFR-TKI patients who achieved partial response (PR) for at least 6 months, MPE resistance in real time. Cadherin-3 (CDH3) knockdown enhances obtained on the day of failure from 8 patients who received EGFR-TKI EGFR-TKI sensitivity in ADC cells. Importantly, the baseline treatment followed by chemotherapy [progressive disease; PD (TþC)], serum sCDH3 level is associated with progression-free survival in MPE obtained on the day of failure from 4 patients who received patients with ADC who received EGFR-TKI therapy and with EGFR-TKI treatment [PD (T)], and PE from 10 patients with TB. For overall survival in patients with non–small cell lung cancer the verification phase, these 33 PEs used in the discovery phase were (NSCLC). Our results establish a biomarker dataset for EGFR- included in ELISA. To determine the sCDH3 level via ELISA, serum TKI resistance and prognosis. This study significantly advances the samples were obtained from 272 treatment-na€ve NSCLC patients development of a liquid biopsy to benefit patients with NSCLC and (baseline) and 57 healthy controls (Table 1). Specifically, 23 MPE and provides new insights into EGFR-TKI resistance in lung ADC. 76 serum samples from patients with ADC with mutated EGFR and who received first/second-generation EGFR-TKIs were collected between 2009 and 2016. Among these 272 patients with NSCLC, serum samples collected 1 month (29 Æ 8 days) after EGFR-TKI mutations. This suggests that even in patients with the same EGFR treatment from 43 patients with ADC (28 PR and 15 non-PR) with mutation status, the event of acquiring resistance and the timing of EGFR mutations were included to examine alterations in sCDH3 levels resistance are heterogeneous and unpredictable. To improve the upon EGFR-TKI treatment. To detect
Load more

Recommended publications
  • New CDH3 Mutation in the First Spanish Case of Hypotrichosis with Juvenile Macular Dystrophy, a Case Report
    Blanco-Kelly et al. BMC Medical Genetics (2017) 18:1 DOI 10.1186/s12881-016-0364-5 CASEREPORT Open Access New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report Fiona Blanco-Kelly1,2, Luciana Rodrigues-Jacy da Silva1, Iker Sanchez-Navarro1, Rosa Riveiro-Alvarez1,2, Miguel Angel Lopez-Martinez1, Marta Corton1,2 and Carmen Ayuso1,2,3* Abstract Background: CDH3 on 16q22.1 is responsible for two rare autosomal recessive disorders with hypotrichosis and progressive macular dystrophy: Hypotrichosis with Juvenile Macular Dystrophy and Ectodermal Dysplasia, Ectrodactyly and Macular Dystrophy. We present a new case of Hypotrichosis with Juvenile Macular Dystrophy. Case presentation: A Spanish male born in 1998 from non-consanguineous healthy parents with a suspected diagnosis of Keratosis Follicularis Spinulosa Decalvans and Retinitis Pigmentosa Inversa referred to our Genetics Department (IIS-Fundación Jiménez Díaz). Molecular study of ABCA4 was performed, and a heterozygous missense p.Val2050Leu variant in ABCA4 was found. Clinical revision reclassified this patient as Hypotrichosis with Juvenile Macular Dystrophy. Therefore, further CDH3 sequencing was performed showing a novel maternal missense change p.Val205Met (probably pathogenic by in silico analysis), and a previously reported paternal frameshift c.830del;p.Gly277Alafs*20, thus supporting the clinical diagnosis.. Conclusions: This is not only the first Spanish case with this clinical and molecular diagnosis, but a new mutation has been described in CDH3. Moreover, this work reflects the importance of joint assessment of clinical signs and evaluation of pedigree for a correct genetic study approach and diagnostic. Keywords: Macular dystrophy, CDH3, Hypotrichosis, Syndromic retinal dystrophy, Case report Background Dysplasia, Ectrodactyly and Macular Dystrophy (EEM, The CDH3 gene, on16q22.1, encodes for P-cadherin, OMIM: 225280) [18].
    [Show full text]
  • Human N-Cadherin / CD325 / CDH2 Protein (His & Fc Tag)
    Human N-Cadherin / CD325 / CDH2 Protein (His & Fc Tag) Catalog Number: 11039-H03H General Information SDS-PAGE: Gene Name Synonym: CD325; CDHN; CDw325; NCAD Protein Construction: A DNA sequence encoding the human CDH2 (NP_001783.2) (Met 1-Ala 724) was fused with the C-terminal polyhistidine-tagged Fc region of human IgG1 at the C-terminus. Source: Human Expression Host: HEK293 Cells QC Testing Purity: > 70 % as determined by SDS-PAGE Endotoxin: Protein Description < 1.0 EU per μg of the protein as determined by the LAL method Cadherins are calcium dependent cell adhesion proteins, and they preferentially interact with themselves in a homophilic manner in Stability: connecting cells. Cadherin 2 (CDH2), also known as N-Cadherin (neuronal) (NCAD), is a single-pass tranmembrane protein and a cadherin containing ℃ Samples are stable for up to twelve months from date of receipt at -70 5 cadherin domains. N-Cadherin displays a ubiquitous expression pattern but with different expression levels between endocrine cell types. CDH2 Asp 160 Predicted N terminal: (NCAD) has been shown to play an essential role in normal neuronal Molecular Mass: development, which is implicated in an array of processes including neuronal differentiation and migration, and axon growth and fasciculation. The secreted recombinant human CDH2 is a disulfide-linked homodimeric In addition, N-Cadherin expression was upregulated in human HSC during protein. The reduced monomer comprises 813 amino acids and has a activation in culture, and function or expression blocking of N-Cadherin predicted molecular mass of 89.9 kDa. As a result of glycosylation, it promoted apoptosis. During apoptosis, N-Cadherin was cleaved into 20- migrates as an approximately 114 and 119 kDa band in SDS-PAGE under 100 kDa fragments.
    [Show full text]
  • The N-Cadherin Interactome in Primary Cardiomyocytes As Defined Using Quantitative Proximity Proteomics Yang Li1,*, Chelsea D
    © 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs221606. doi:10.1242/jcs.221606 TOOLS AND RESOURCES The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics Yang Li1,*, Chelsea D. Merkel1,*, Xuemei Zeng2, Jonathon A. Heier1, Pamela S. Cantrell2, Mai Sun2, Donna B. Stolz1, Simon C. Watkins1, Nathan A. Yates1,2,3 and Adam V. Kwiatkowski1,‡ ABSTRACT requires multiple adhesion, cytoskeletal and signaling proteins, The junctional complexes that couple cardiomyocytes must transmit and mutations in these proteins can cause cardiomyopathies (Ehler, the mechanical forces of contraction while maintaining adhesive 2018). However, the molecular composition of ICD junctional homeostasis. The adherens junction (AJ) connects the actomyosin complexes remains poorly defined. – networks of neighboring cardiomyocytes and is required for proper The core of the AJ is the cadherin catenin complex (Halbleib and heart function. Yet little is known about the molecular composition of the Nelson, 2006; Ratheesh and Yap, 2012). Classical cadherins are cardiomyocyte AJ or how it is organized to function under mechanical single-pass transmembrane proteins with an extracellular domain that load. Here, we define the architecture, dynamics and proteome of mediates calcium-dependent homotypic interactions. The adhesive the cardiomyocyte AJ. Mouse neonatal cardiomyocytes assemble properties of classical cadherins are driven by the recruitment of stable AJs along intercellular contacts with organizational and cytosolic catenin proteins to the cadherin tail, with p120-catenin β structural hallmarks similar to mature contacts. We combine (CTNND1) binding to the juxta-membrane domain and -catenin β quantitative mass spectrometry with proximity labeling to identify the (CTNNB1) binding to the distal part of the tail.
    [Show full text]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • The Urothelial Cell Line Urotsa Transformed by Arsenite and Cadmium Display Basal Characteristics Associated with Muscle Invasive Urothelial Cancers
    University of North Dakota UND Scholarly Commons Pathology Faculty Publications Department of Pathology 12-14-2018 The Urothelial Cell Line UROtsa Transformed by Arsenite and Cadmium Display Basal Characteristics Associated with Muscle Invasive Urothelial Cancers Zachary E. Hoggarth Danyelle B. Osowski Brooke A. Freeberg Scott H. Garrett University of North Dakota, [email protected] Mary Ann Sens University of North Dakota, [email protected] See next page for additional authors Follow this and additional works at: https://commons.und.edu/path-fac Recommended Citation Hoggarth, Zachary E.; Osowski, Danyelle B.; Freeberg, Brooke A.; Garrett, Scott H.; Sens, Mary Ann; Zhou, Xudong; Zhang, Ke K.; and Somji, Seema, "The Urothelial Cell Line UROtsa Transformed by Arsenite and Cadmium Display Basal Characteristics Associated with Muscle Invasive Urothelial Cancers" (2018). Pathology Faculty Publications. 1. https://commons.und.edu/path-fac/1 This Article is brought to you for free and open access by the Department of Pathology at UND Scholarly Commons. It has been accepted for inclusion in Pathology Faculty Publications by an authorized administrator of UND Scholarly Commons. For more information, please contact [email protected]. Authors Zachary E. Hoggarth, Danyelle B. Osowski, Brooke A. Freeberg, Scott H. Garrett, Mary Ann Sens, Xudong Zhou, Ke K. Zhang, and Seema Somji This article is available at UND Scholarly Commons: https://commons.und.edu/path-fac/1 RESEARCH ARTICLE The urothelial cell line UROtsa transformed by arsenite and cadmium display basal characteristics associated with muscle invasive urothelial cancers Zachary E. Hoggarth, Danyelle B. Osowski, Brooke A. Freeberg, Scott H. Garrett, Donald A.
    [Show full text]
  • And MUC1 in Mammary Epithelial Cells
    Linköping University Post Print Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells Stina Petersson, E. Shubbar, M. Yhr, A. Kovacs and Charlotta Enerbäck N.B.: When citing this work, cite the original article. The original publication is available at www.springerlink.com: Stina Petersson, E. Shubbar, M. Yhr, A. Kovacs and Charlotta Enerbäck, Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells, 2011, Breast Cancer Research and Treatment, (125), 1, 13-25. http://dx.doi.org/10.1007/s10549-010-0820-4 Copyright: Springer Science Business Media http://www.springerlink.com/ Postprint available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-63954 1 Loss of ICAM-1 signaling induces psoriasin (S100A7) and MUC1 in mammary epithelial cells Petersson S1, Shubbar E1, Yhr M1, Kovacs A2 and Enerbäck C3 Departments of 1Clinical Genetics and 2Pathology, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden; 3Department of Clinical and Experimental Medicine, Division of Cell Biology and Dermatology, Linköping University, SE-581 85 Linköping, Sweden E-mail: [email protected] E-mail: maria.yhr@ clingen.gu.se E-mail: [email protected] E-mail: [email protected] Correspondence: Stina Petersson, Department of Clinical Genetics, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden E-mail: [email protected] 2 Abstract Psoriasin (S100A7), a member of the S100 gene family, is highly expressed in high-grade comedo ductal carcinoma in situ (DCIS), with a higher risk of local recurrence. Psoriasin is therefore a potential biomarker for DCIS with a poor prognosis.
    [Show full text]
  • Adherens Junctions, Desmosomes and Tight Junctions in Epidermal Barrier Function Johanna M
    14 The Open Dermatology Journal, 2010, 4, 14-20 Open Access Adherens Junctions, Desmosomes and Tight Junctions in Epidermal Barrier Function Johanna M. Brandner1,§, Marek Haftek*,2,§ and Carien M. Niessen3,§ 1Department of Dermatology and Venerology, University Hospital Hamburg-Eppendorf, Hamburg, Germany 2University of Lyon, EA4169 Normal and Pathological Functions of Skin Barrier, E. Herriot Hospital, Lyon, France 3Department of Dermatology, Center for Molecular Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany Abstract: The skin is an indispensable barrier which protects the body from the uncontrolled loss of water and solutes as well as from chemical and physical assaults and the invasion of pathogens. In recent years several studies have suggested an important role of intercellular junctions for the barrier function of the epidermis. In this review we summarize our knowledge of the impact of adherens junctions, (corneo)-desmosomes and tight junctions on barrier function of the skin. Keywords: Cadherins, catenins, claudins, cell polarity, stratum corneum, skin diseases. INTRODUCTION ADHERENS JUNCTIONS The stratifying epidermis of the skin physically separates Adherens junctions are intercellular structures that couple the organism from its environment and serves as its first line intercellular adhesion to the cytoskeleton thereby creating a of structural and functional defense against dehydration, transcellular network that coordinate the behavior of a chemical substances, physical insults and micro-organisms. population of cells. Adherens junctions are dynamic entities The living cell layers of the epidermis are crucial in the and also function as signal platforms that regulate formation and maintenance of the barrier on two different cytoskeletal dynamics and cell polarity.
    [Show full text]
  • Coexisting Proinflammatory and Antioxidative Endothelial Transcription Profiles in a Disturbed Flow Region of the Adult Porcine Aorta
    Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta Anthony G. Passerini*†‡, Denise C. Polacek*‡, Congzhu Shi*, Nadeene M. Francesco*, Elisabetta Manduchi§, Gregory R. Grant§, William F. Pritchard¶, Steven Powellʈ, Gary Y. Chang*†, Christian J. Stoeckert, Jr.§**, and Peter F. Davies*†,††‡‡ *Institute for Medicine and Engineering, Departments of †Bioengineering, ††Pathology and Laboratory Medicine, and **Genetics, and §Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104; ¶U.S. Food and Drug Administration, Rockville, MD 20852; and ʈAstraZeneca Pharmaceuticals, Mereside Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom Edited by Louis J. Ignarro, University of California School of Medicine, Los Angeles, CA, and approved December 22, 2003 (received for review September 15, 2003) In the arterial circulation, regions of disturbed flow (DF), which are with protective profiles of gene expression (e.g., antioxidative, characterized by flow separation and transient vortices, are suscep- antiinflammatory, and͞or antiproliferative) when compared to the tible to atherogenesis, whereas regions of undisturbed laminar flow absence of flow (7–11, 13, 14, 17, 19) and selected examples of the (UF) appear protected. Coordinated regulation of gene expression by protective genes have been shown to be expressed in endothelium endothelial cells (EC) may result in differing regional phenotypes that in vivo (14, 19). A small number of microarray studies comparing either favor or inhibit atherogenesis. Linearly amplified RNA from EC gene expression between DF and UF conditions in vitro have freshly isolated EC of DF (inner aortic arch) and UF (descending been conducted (15, 16); however, transcriptional profiling in vivo thoracic aorta) regions of normal adult pigs was used to profile has been limited by the small sample size available within hemo- differential gene expression reflecting the steady state in vivo.By dynamic regions of interest.
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • Minimal 16Q Genomic Loss Implicates Cadherin-11 in Retinoblastoma
    Minimal 16q Genomic Loss Implicates Cadherin-11 in Retinoblastoma Mellone N. Marchong,1,2 Danian Chen,1,6 Timothy W. Corson,1,3 Cheong Lee,1 Maria Harmandayan,1 Ella Bowles,1 Ning Chen,5 and Brenda L. Gallie1,2,3,4,5 1Divisions of Cancer Informatics and Cellular and Molecular Biology, Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada; Departments of 2Medical Biophysics, 3Molecular and Medical Genetics, and 4Ophthalmology, University of Toronto, Toronto, Ontario, Canada; 5Retinoblastoma Solutions, Toronto, Ontario, Canada; and 6Department of Ophthalmology, West China Hospital, Faculty of Medicine, Sichuan University, Chengdu, People’s Republic of China Abstract compared with normal adult human retina. Our analyses Retinoblastoma is initiated by loss of both RB1 alleles. implicate CDH11, but not CDH13, as a potential tumor Previous studies have shown that retinoblastoma suppressor gene in retinoblastoma. (Mol Cancer Res tumors also show further genomic gains and losses. We 2004;2(9):495–503) now define a 2.62 Mbp minimal region of genomic loss of chromosome 16q22, which is likely to contain tumor suppressor gene(s), in 76 retinoblastoma tumors, using Introduction loss of heterozygosity (30 of 76 tumors) and quantitative Retinoblastoma is the most common intraocular tumor in multiplex PCR (71 of 76 tumors). The sequence-tagged children. Mutations of both alleles (M1 and M2) of the RB1 site WI-5835 within intron 2 of the cadherin-11 (CDH11) gene at chromosome 13q14 are necessary (1) for retinoblastoma gene showed the highest frequency of loss (54%, 22 of tumor initiation but not sufficient for malignant transformation 41 samples tested).
    [Show full text]
  • Cell Adhesion Molecules in Normal Skin and Melanoma
    biomolecules Review Cell Adhesion Molecules in Normal Skin and Melanoma Cian D’Arcy and Christina Kiel * Systems Biology Ireland & UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +353-1-716-6344 Abstract: Cell adhesion molecules (CAMs) of the cadherin, integrin, immunoglobulin, and selectin protein families are indispensable for the formation and maintenance of multicellular tissues, espe- cially epithelia. In the epidermis, they are involved in cell–cell contacts and in cellular interactions with the extracellular matrix (ECM), thereby contributing to the structural integrity and barrier for- mation of the skin. Bulk and single cell RNA sequencing data show that >170 CAMs are expressed in the healthy human skin, with high expression levels in melanocytes, keratinocytes, endothelial, and smooth muscle cells. Alterations in expression levels of CAMs are involved in melanoma propagation, interaction with the microenvironment, and metastasis. Recent mechanistic analyses together with protein and gene expression data provide a better picture of the role of CAMs in the context of skin physiology and melanoma. Here, we review progress in the field and discuss molecular mechanisms in light of gene expression profiles, including recent single cell RNA expression information. We highlight key adhesion molecules in melanoma, which can guide the identification of pathways and Citation: D’Arcy, C.; Kiel, C. Cell strategies for novel anti-melanoma therapies. Adhesion Molecules in Normal Skin and Melanoma. Biomolecules 2021, 11, Keywords: cadherins; GTEx consortium; Human Protein Atlas; integrins; melanocytes; single cell 1213. https://doi.org/10.3390/ RNA sequencing; selectins; tumour microenvironment biom11081213 Academic Editor: Sang-Han Lee 1.
    [Show full text]
  • Mapping Transmembrane Binding Partners for E-Cadherin Ectodomains
    Mapping transmembrane binding partners for E-cadherin ectodomains Omer Shafraza, Bin Xieb, Soichiro Yamadaa, and Sanjeevi Sivasankara,b,1 aDepartment of Biomedical Engineering, University of California, Davis, CA 95616; and bBiophysics Graduate Group, University of California, Davis, CA 95616 Edited by Barry Honig, Howard Hughes Medical Institute, Columbia University, New York, NY, and approved October 28, 2020 (received for review May 22, 2020) We combine proximity labeling and single molecule binding assays proteins that directly interact with a transmembrane bait would to discover transmembrane protein interactions in cells. We first be positioned in close proximity to both the bait’s ectodomain screen for candidate binding partners by tagging the extracellular and cytoplasmic regions. Consequently, if the proximity-based and cytoplasmic regions of a “bait” protein with BioID biotin ligase labeling enzyme was fused to both the bait’s extracellular and and identify proximal proteins that are biotin tagged on both their cytoplasmic regions, identifying transmembrane proteins that extracellular and intracellular regions. We then test direct binding are biotinylated in both regions would enable us to narrow interactions between proximal proteins and the bait, using single down the list of possible binding partners for subsequent AFM molecule atomic force microscope binding assays. Using this ap- binding measurements. Furthermore, an integrated extracellu- proach, we identify binding partners for the extracellular region lar and cytoplasmic BioID measurement would significantly of E-cadherin, an essential cell–cell adhesion protein. We show that increase the precision of the screen by dramatically reducing the desmosomal proteins desmoglein-2 and desmocollin-3, the focal the number of false positive hits.
    [Show full text]