DOCSLIB.ORG

Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases That Correlates with Prolonged Survival

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases That Correlates with Prolonged Survival Published OnlineFirst January 17, 2020; DOI: 10.1158/1078-0432.CCR-19-2184 CLINICAL CANCER RESEARCH | TRANSLATIONAL CANCER MECHANISMS AND THERAPY Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases that Correlates with Prolonged Survival Kolja Pocha1, Andreas Mock1,2,3,4, Carmen Rapp1, Steffen Dettling1, Rolf Warta1,4, Christoph Geisenberger1, Christine Jungk1, Leila R. Martins5, Niels Grabe6, David Reuss7,8, Juergen Debus4,9, Andreas von Deimling4,7,8, Amir Abdollahi4,9, Andreas Unterberg1, and Christel C. Herold-Mende1,4 ABSTRACT ◥ Purpose: To provide a better understanding of the interplay of three surfactant metabolism-related genes (SFTPA1, SFTPB, between the immune system and brain metastases to advance and NAPSA) was closely associated with TIL numbers. Their therapeutic options for this life-threatening disease. expression was not only prognostic in brain metastasis but also Experimental Design: Tumor-infiltrating lymphocytes (TIL) in primary lung adenocarcinoma. Correlation with scRNA-seq were quantified by semiautomated whole-slide analysis in data revealed that brain metastases with high expression of brain metastases from 81 lung adenocarcinomas. Multi-color surfactant genes might originate from tumor cells resembling staining enabled phenotyping of TILs (CD3, CD8, and FOXP3) alveolar type 2 cells. Methylome-based estimation of immune cell on a single-cell resolution. Molecular determinants of the fractions in primary lung adenocarcinoma confirmed a positive extent of TILs in brain metastases were analyzed by transcrip- association between lymphocyte infiltration and surfactant tomics in a subset of 63 patients. Findings in lung adenocarci- expression. Tumors with a high surfactant expression displayed noma brain metastases were related to published multi-omic atranscriptomicprofile of an inflammatory microenvironment. primary lung adenocarcinoma The Cancer Genome Atlas data Conclusions: The expression of surfactant metabolism-related (n ¼ 230) and single-cell RNA-sequencing (scRNA-seq) data genes (SFTPA1, SFTPB,andNAPSA)defines an inflamed subtype (n ¼ 52,698). of lung adenocarcinoma brain metastases characterized by high Results: TIL numbers within tumor islands was an independent abundance of TILs in close vicinity to tumor cells, a prolonged prognostic marker in patients with lung adenocarcinoma brain survival, and a tumor microenvironment which might be more metastases. Comparative transcriptomics revealed that expression accessible to immunotherapeutic approaches. Introduction histologically be divided into two groups: small-cell lung cancer and non–small cell lung cancer (NSCLC). NSCLC can be further sub- Lung cancer is the most common type of cancer worldwide and the divided into subtypes, the most frequent being adenocarcinoma (2, 3). most common cause of cancer-related death (1, 2). Lung cancer can Lung adenocarcinoma also accounts for the largest histologic subset of brain metastases (4). Of note, brain metastases are even more frequent than primary brain tumors (5). Patients with brain metastases have a 1Division of Experimental Neurosurgery, Department of Neurosurgery, poor median overall survival of 7–13 months (6). Treatment is usually Heidelberg University Hospital, Heidelberg, Germany. 2Department of Medical multimodal and consists of systemic chemotherapy combined with Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg 3 microsurgery, stereotactic radiosurgery, and/or radiotherapy (7). University Hospital, Heidelberg, Germany. Department of Translational Medical There is increasing evidence for the role of the host immune system Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany. 4German Cancer in cancer development, suppression, and recurrence (8). In colorectal Consortium (DKTK), Heidelberg, Germany. 5Division of Applied Functional cancer for instance, the quantification of tumor-infiltrating lympho- Genomics, German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, cytes (TIL) has become a valid prognostic marker for patient survival Germany. 6Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, and is believed to be superior to the tumor–node–metastasis classi- 7 University of Heidelberg, Heidelberg, Germany. Department of Neuropathol- fication (9). Many studies have since confirmed the prognostic power ogy, Institute of Pathology, Heidelberg University Hospital, Heidelberg, of immune cell infiltrates in a large number of cancer types. The Germany. 8Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Institute of Pathology, Heidelberg University Hospital, Heidel- positive effect of cytotoxic T cells and Th1 T cells on survival has been berg, Germany. 9Department of Radiation Oncology, University of Heidelberg, shown; however, the influence of intratumoral Th2, Th17, and reg- Heidelberg, Germany. ulatory T cells (Tregs) on survival is less clear (10). In patients with Note: Supplementary data for this article are available at Clinical Cancer lung adenocarcinoma with high overall T-cell counts and high cyto- Research Online (http://clincancerres.aacrjournals.org/). toxic T-cell counts, prolonged survival has been observed (11). Tregs, K. Pocha and A. Mock contributed equally to this article. on the other hand, seem to impair prognosis (12). However, in addition to quantity, the spatial distribution of immune Corresponding Author: Christel C. Herold-Mende, Heidelberg University cells and their vicinity to tumor cells in terms of localization within Hospital, INF 400, Heidelberg 69120, Germany. Phone: 4962-2156-6405; Fax: 4962-2156-33979; E-mail: [email protected] tumor islands or retention in the tumor stroma (13, 14) and the differences between primary tumors and subsequent metastases must Clin Cancer Res 2020;26:2231–43 be taken into account. It has been shown that infiltration with cytotoxic doi: 10.1158/1078-0432.CCR-19-2184 T cells decreases from primary lung cancer to metastases (15, 16). Ó2020 American Association for Cancer Research. Nevertheless, data on the impact of T-cell infiltration on survival in AACRJournals.org | 2231 Downloaded from clincancerres.aacrjournals.org on September 29, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst January 17, 2020; DOI: 10.1158/1078-0432.CCR-19-2184 Pocha et al. informed consent was obtained from all patients in accordance with Translational Relevance the Declaration of Helsinki and its later amendments. Immunotherapies have become a powerful addition to the established therapies in metastatic non–small cell lung cancer. Immunofluorescence staining Given the dismal prognosis of brain metastases in these patients Tumor tissue was snap-frozen in liquid nitrogen–cooled isopentane it is essential to identify subsets of patients that have a tumor immediately after resection. Frozen tissues were cut into 5–7 mm slices, microenvironment that might be more accessible to immunother- acetone-fixed, and stored at À80C until staining. Immunofluorescent apeutic approaches. We provide evidence that a fraction of lung staining was performed using anti-CD3 (Dako, A0452), anti-CD8 adenocarcinoma brain metastases is indeed characterized by higher (Clone YTC182.20, Abcam, Ab60076), and anti-FOXP3 (Clone 236A/ tumor-infiltrating lymphocyte numbers and is in close association E7, Abcam, Ab20034) as described previously (27). DAPI (Invitrogen, with an inflamed microenvironment and high expression of sur- D1306) was used to counterstain the nuclei. The incubation time was factant genes. 1 hour, and this was followed by three washing steps. Secondary antibodies, including anti-rabbit Alexa Fluor 647 (Life Technologies, A21245), anti-rat Alexa Fluor 488 (Life Technologies, A11006), and anti-mouse Alexa Fluor 555 (Life Technologies, A31570) were then brain metastasis remain controversial, with some studies suggesting a applied for 1 hour, and this was followed by three washing steps. þ þ þ favorable role for CD3 , CD8 , and CD45R0 T cells (17) and other Tumor cells were labeled using anti-pan cytokeratin (Progen, 61835; studies showing no benefit (18, 19). Dako, M0630) staining in combination with an antibody labeling kit Understanding the interplay between the immune system and (Thermo Fisher Scientific, Z25002). Isotype controls were rabbit IgG cancer cells is becoming even more critical in patients with brain (Dako, X0936), IgG2b (eBioscience, 14-4031), and IgG1 (Abcam, metastases as checkpoint inhibitor therapies are on the rise for ab91353). The antibody characteristics are listed in Supplementary treating lung adenocarcinoma (20). Knowledge about the immune Table S1. microenvironment in primary lung cancer cannot be extrapolated to include brain metastases, because of specialized resident immune Semi-automated quantification of T-cell infiltration and stromal cells, including microglia and astrocytes (21–23), and Following immunofluorescent staining, whole-slide images were physical restriction by the blood–brain barrier (24). Genomic generated for all 81 tumor samples using an automated microscope alterations between primary lung cancer and brain metastasis, as (Olympus IX51 equipped with a F-View II camera, both Olympus) at well as their connection to the immune system are the subject of 20-fold magnification with the cellSens Software (Olympus). Tissue- ongoing research (25). Other data suggest that the amount of T-cell Quest Software (version 4.0.1.0137, TissueGnostics GmbH)
Load more

Recommended publications
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Evaluation of the NOD/SCID Xenograft Model for Glucocorticoid-Regulated
    Bhadri et al. BMC Genomics 2011, 12:565 http://www.biomedcentral.com/1471-2164/12/565 RESEARCHARTICLE Open Access Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia Vivek A Bhadri1,3, Mark J Cowley2, Warren Kaplan2, Toby N Trahair1,3 and Richard B Lock1* Abstract Background: Glucocorticoids such as prednisolone and dexamethasone are critical drugs used in multi-agent chemotherapy protocols used to treat acute lymphoblastic leukemia (ALL), and response to glucocorticoids is highly predictive of outcome. The NOD/SCID xenograft mouse model of ALL is a clinically relevant model in which the mice develop a systemic leukemia which retains the fundamental biological characteristics of the original disease. Here we report a study evaluating the NOD/SCID xenograft mouse model to investigate glucocorticoid- induced gene expression. Cells from a glucocorticoid-sensitive xenograft derived from a child with B-cell precursor ALL were inoculated into NOD/SCID mice. When highly engrafted the mice were randomized into groups of 4 to receive dexamethasone 15 mg/kg by intraperitoneal injection or vehicle control. Leukemia cells were harvested from mice spleens at 0, 8, 24 or 48 hours thereafter, and gene expression analyzed on Illumina WG-6_V3 chips, comparing all groups to time 0 hours. Results: The 8 hour dexamethasone-treated timepoint had the highest number of significantly differentially expressed genes, with fewer observed at the 24 and 48 hour timepoints, and with minimal changes seen across the time-matched controls. When compared to publicly available datasets of glucocorticoid-induced gene expression from an in vitro cell line study and from an in vivo study of patients with ALL, at the level of pathways, expression changes in the 8 hour xenograft samples showed a similar response to patients treated with glucocorticoids.
    [Show full text]
  • (COPD) and Lung Cancer by Means of Cell Specific
    UNDERSTANDING SHARED PATHOGENESIS BETWEEN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND LUNG CANCER BY MEANS OF CELL SPECIFIC GENOMICS CLARA EMILY GREEN A thesis submitted to the University of Birmingham for the degree of DOCTOR OF PHILOSOPHY The Institute of Inflammation and Ageing College of Medical and Dental Sciences University of Birmingham February 2018 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Introduction COPD (Chronic Obstructive Pulmonary Disease) and lung cancer are related conditions associated with inflammation. Relatively little focus has been given to the endothelium, through which inflammatory cells transmigrate to reach the lung. We sought to determine if coding and non-coding alterations in pulmonary endothelium exist in COPD and lung cancer. Methods Patients with and without COPD undergoing thoracic surgery were recruited. Pulmonary Endothelial Cells were isolated from lung and tumour and extracted RNA (ribonucleic acid) used for miRNA (micro-RNA) and mRNA (messenger RNA) microarrays. Ingenuity pathway analysis (IPA) was also carried out. Results 2071 genes and 43 miRNAs were significantly upregulated in COPD. 4 targets were validated by quantitative polymerase chain reaction, of which miR-181b-3p was chosen for functional validation.
    [Show full text]
  • A Dissertation Entitled the Androgen Receptor
    A Dissertation entitled The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit Submitted to the Graduate Faculty as partial fulfillment of the requirements for the PhD Degree in Biomedical science Dr. Manohar Ratnam, Committee Chair Dr. Lirim Shemshedini, Committee Member Dr. Robert Trumbly, Committee Member Dr. Edwin Sanchez, Committee Member Dr. Beata Lecka -Czernik, Committee Member Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo August 2011 Copyright 2011, Mesfin Gonit This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit As partial fulfillment of the requirements for the PhD Degree in Biomedical science The University of Toledo August 2011 Prostate cancer depends on the androgen receptor (AR) for growth and survival even in the absence of androgen. In the classical models of gene activation by AR, ligand activated AR signals through binding to the androgen response elements (AREs) in the target gene promoter/enhancer. In the present study the role of AREs in the androgen- independent transcriptional signaling was investigated using LP50 cells, derived from parental LNCaP cells through extended passage in vitro. LP50 cells reflected the signature gene overexpression profile of advanced clinical prostate tumors. The growth of LP50 cells was profoundly dependent on nuclear localized AR but was independent of androgen. Nevertheless, in these cells AR was unable to bind to AREs in the absence of androgen.
    [Show full text]
  • Identification of Potential Key Genes in Gastric Cancer Using Bioinformatics Analysis
    178 BIOMEDICAL REPORTS 12: 178-192, 2020 Identification of potential key genes in gastric cancer using bioinformatics analysis WEI WANG1, YING HE2, QI ZHAO3, XIAODONG ZHAO3 and ZHIHONG LI1 1Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700; 2Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610075; 3Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, P.R. China Received October 5, 2019; Accepted January 27, 2020 DOI: 10.3892/br.2020.1281 Abstract. Gastric cancer (GC) is one of the most common types results of the present study suggest that FN1, COL1A1, INHBA of cancer worldwide. Patients must be identified at an early and CST1 may be potential biomarkers and therapeutic targets stage of tumor progression for treatment to be effective. The for GC. Additional studies are required to explore the potential aim of the present study was to identify potential biomarkers value of ATP4A and ATP4B in the treatment of GC. with diagnostic value in patients with GC. To examine potential therapeutic targets for GC, four Gene Expression Introduction Omnibus (GEO) datasets were downloaded and screened for differentially expressed genes (DEGs). Gene Ontology Gastric cancer (GC) is a malignant tumor that originates and Kyoto Encyclopedia of Genes and Genomes (KEGG) in the epithelium of the gastric mucosa and is one of the analyses were subsequently performed to study the func- most common types of malignant tumors in the world (1). tion and pathway enrichment of the identified DEGs. A According to GLOBOCAN 2018, there were >1,000,000 new protein-protein interaction (PPI) network was constructed.
    [Show full text]
  • Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
    Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades.
    [Show full text]
  • Research Article Identification of Key Genes and Pathways in Triple-Negative Breast Cancer by Integrated Bioinformatics Analysis
    Hindawi BioMed Research International Volume 2018, Article ID 2760918, 10 pages https://doi.org/10.1155/2018/2760918 Research Article Identification of Key Genes and Pathways in Triple-Negative Breast Cancer by Integrated Bioinformatics Analysis Pengzhi Dong ,1 Bing Yu,2 Lanlan Pan,1 Xiaoxuan Tian ,1 and Fangfang Liu 3 1 Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China 2Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300100, China 3Department of Breast Pathology and Research Laboratory, Key Laboratory of Breast Cancer Prevention and Terapy (Ministry of Education), National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China Correspondence should be addressed to Fangfang Liu; [email protected] Received 14 March 2018; Revised 15 June 2018; Accepted 4 July 2018; Published 2 August 2018 Academic Editor: Robert A. Vierkant Copyright © 2018 Pengzhi Dong et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Purpose. Triple-negative breast cancer refers to breast cancer that does not express estrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (Her2). Tis study aimed to identify the key pathways and genes and fnd the potential initiation and progression mechanism of triple-negative breast cancer (TNBC). Methods. We downloaded the gene expression profles of GSE76275 from Gene Expression Omnibus (GEO) datasets. Tis microarray Super-Series sets are composed of gene expression data from 265 samples which included 67 non-TNBC and 198 TNBC.
    [Show full text]
  • Regulation of the Glucocorticoid Receptor Via a BET
    RESEARCH ARTICLE Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer Neel Shah1,2, Ping Wang3, John Wongvipat1, Wouter R Karthaus1, Wassim Abida4, Joshua Armenia1, Shira Rockowitz3, Yotam Drier5, Bradley E Bernstein5, Henry W Long6, Matthew L Freedman6, Vivek K Arora7, Deyou Zheng3, Charles L Sawyers1,8* 1Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, United States; 2The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States; 3Department of Neurology, Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, United States; 4Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, United States; 5Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, United States; 6Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States; 7Division of Medical Oncology, Washington University School of Medicine, St Louis, United States; 8Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States Abstract In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of androgen receptor (AR) blockade by the glucocorticoid receptor (GR). In contrast to fixed genomic alterations, here we show that GR-mediated antiandrogen resistance is *For correspondence: [email protected] adaptive and reversible due to regulation of GR expression by a tissue-specific enhancer. GR expression is silenced in prostate cancer by a combination of AR binding and EZH2-mediated Competing interest: See repression at the GR locus, but is restored in advanced prostate cancers upon reversion of both page 15 repressive signals.
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]
  • Insights Into MYC Biology Through Investigation of Synthetic Lethal Interactions with MYC Deregulation
    Insights into MYC biology through investigation of synthetic lethal interactions with MYC deregulation Mai Sato Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Mai Sato All Rights Reserved ABSTRACT Insights into MYC biology through investigation of synthetic lethal interactions with MYC deregulation Mai Sato MYC (or c-myc) is a bona fide “cancer driver” oncogene that is deregulated in up to 70% of human tumors. In addition to its well-characterized role as a transcription factor that can directly promote tumorigenic growth and proliferation, MYC has transcription-independent functions in vital cellular processes including DNA replication and protein synthesis, contributing to its complex biology. MYC expression, activity, and stability are highly regulated through multiple mechanisms. MYC deregulation triggers genome instability and oncogene-induced DNA replication stress, which are thought to be critical in promoting cancer via mechanisms that are still unclear. Because regulated MYC activity is essential for normal cell viability and MYC is a difficult protein to target pharmacologically, targeting genes or pathways that are essential to survive MYC deregulation offer an attractive alternative as a means to combat tumor cells with MYC deregulation. To this end, we conducted a genome-wide synthetic lethal shRNA screen in MCF10A breast epithelial cells stably expressing an inducible MYCER transgene. We identified and validated FBXW7 as a high-confidence synthetic lethal (MYC-SL) candidate gene. FBXW7 is a component of an E3 ubiquitin ligase complex that degrades MYC. FBXW7 knockdown in MCF10A cells selectively induced cell death in MYC-deregulated cells compared to control.
    [Show full text]
  • Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis
    Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis by Valbona Luga A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy, Department of Molecular Genetics, University of Toronto © Copyright by Valbona Luga, 2013 Tumour-Stroma Signalling in Cancer Cell Motility and Metastasis Valbona Luga Doctor of Philosophy Department of Molecular Genetics University of Toronto 2013 Abstract The tumour-associated stroma, consisting of fibroblasts, inflammatory cells, vasculature and extracellular matrix proteins, plays a critical role in tumour growth, but how it regulates cancer cell migration and metastasis is poorly understood. The Wnt-planar cell polarity (PCP) pathway regulates convergent extension movements in vertebrate development. However, it is unclear whether this pathway also functions in cancer cell migration. In addition, the factors that mobilize long-range signalling of Wnt morphogens, which are tightly associated with the plasma membrane, have yet to be completely characterized. Here, I show that fibroblasts secrete membrane microvesicles of endocytic origin, termed exosomes, which promote tumour cell protrusive activity, motility and metastasis via the exosome component Cd81. In addition, I demonstrate that fibroblast exosomes activate autocrine Wnt-PCP signalling in breast cancer cells as detected by the association of Wnt with Fzd receptors and the asymmetric distribution of Fzd-Dvl and Vangl-Pk complexes in exosome-stimulated cancer cell protrusive structures. Moreover, I show that Pk expression in breast cancer cells is essential for fibroblast-stimulated cancer cell metastasis. Lastly, I reveal that trafficking in cancer cells promotes tethering of autocrine Wnt11 to fibroblast exosomes. These studies further our understanding of the role of ii the tumour-associated stroma in cancer metastasis and bring us closer to a more targeted approach for the treatment of cancer spread.
    [Show full text]
  • Integrative Methods for the Analysis of Genome Wide Association Studies
    INTEGRATIVE METHODS FOR THE ANALYSIS OF GENOME WIDE ASSOCIATION STUDIES A DISSERTATION SUBMITTED TO THE DEPARTMENT OF COMPUTER SCIENCE AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Marc A. Schaub June 2012 © 2012 by Marc Andreas Schaub. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/qt820xd3631 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Serafim Batzoglou, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Atul Butte I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. David Dill Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Abstract Genome Wide Association Studies (GWAS) have identified over 4,500 common vari- ants in the human genome that are statistically associated with diseases and other phenotypical traits.
    [Show full text]