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Sun Y, Huang ZL, Chen WX, Zhang YF, Lei HT, Huang QJ, Lun ZR, Qu LH, Zheng LL. GateView: A Multi-Omics Platform for Gene Feature Analysis of Virus Receptors within Human Normal Tissues and Tumors. Biomolecules 2024; 14:516. [PMID: 38785923 PMCID: PMC11118183 DOI: 10.3390/biom14050516] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Viruses are obligate intracellular parasites that rely on cell surface receptor molecules to complete the first step of invading host cells. The experimental method for virus receptor screening is time-consuming, and receptor molecules have been identified for less than half of known viruses. This study collected known human viruses and their receptor molecules. Through bioinformatics analysis, common characteristics of virus receptor molecules (including sequence, expression, mutation, etc.) were obtained to study why these membrane proteins are more likely to become virus receptors. An in-depth analysis of the cataloged virus receptors revealed several noteworthy findings. Compared to other membrane proteins, human virus receptors generally exhibited higher expression levels and lower sequence conservation. These receptors were found in multiple tissues, with certain tissues and cell types displaying significantly higher expression levels. While most receptor molecules showed noticeable age-related variations in expression across different tissues, only a limited number of them exhibited gender-related differences in specific tissues. Interestingly, in contrast to normal tissues, virus receptors showed significant dysregulation in various types of tumors, particularly those associated with dsRNA and retrovirus receptors. Finally, GateView, a multi-omics platform, was established to analyze the gene features of virus receptors in human normal tissues and tumors. Serving as a valuable resource, it enables the exploration of common patterns among virus receptors and the investigation of virus tropism across different tissues, population preferences, virus pathogenicity, and oncolytic virus mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
| | - Ling-Ling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Y.S.); (Z.-L.H.); (W.-X.C.); (Y.-F.Z.); (H.-T.L.); (Q.-J.H.); (Z.-R.L.)
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Schneider JL, Rowe JH, Garcia-de-Alba C, Kim CF, Sharpe AH, Haigis MC. The aging lung: Physiology, disease, and immunity. Cell 2021; 184:1990-2019. [PMID: 33811810 PMCID: PMC8052295 DOI: 10.1016/j.cell.2021.03.005] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023]
Abstract
The population is aging at a rate never seen before in human history. As the number of elderly adults grows, it is imperative we expand our understanding of the underpinnings of aging biology. Human lungs are composed of a unique panoply of cell types that face ongoing chemical, mechanical, biological, immunological, and xenobiotic stress over a lifetime. Yet, we do not fully appreciate the mechanistic drivers of lung aging and why age increases the risk of parenchymal lung disease, fatal respiratory infection, and primary lung cancer. Here, we review the molecular and cellular aspects of lung aging, local stress response pathways, and how the aging process predisposes to the pathogenesis of pulmonary disease. We place these insights into context of the COVID-19 pandemic and discuss how innate and adaptive immunity within the lung is altered with age.
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Affiliation(s)
- Jaime L Schneider
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Jared H Rowe
- Division of Hematology Boston Children's Hospital and Division of Pediatric Oncology Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Carolina Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Disease, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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Smith JC, Sausville EL, Girish V, Yuan ML, Vasudevan A, John KM, Sheltzer JM. Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract. Dev Cell 2020; 53:514-529.e3. [PMID: 32425701 PMCID: PMC7229915 DOI: 10.1016/j.devcel.2020.05.012] [Citation(s) in RCA: 276] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/26/2020] [Accepted: 05/12/2020] [Indexed: 01/06/2023]
Abstract
The factors mediating fatal SARS-CoV-2 infections are poorly understood. Here, we show that cigarette smoke causes a dose-dependent upregulation of angiotensin converting enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Using single-cell sequencing data, we demonstrate that ACE2 is expressed in a subset of secretory cells in the respiratory tract. Chronic smoke exposure triggers the expansion of this cell population and a concomitant increase in ACE2 expression. In contrast, quitting smoking decreases the abundance of these secretory cells and reduces ACE2 levels. Finally, we demonstrate that ACE2 expression is responsive to inflammatory signaling and can be upregulated by viral infections or interferon treatment. Taken together, these results may partially explain why smokers are particularly susceptible to severe SARS-CoV-2 infections. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive feedback loops that increase ACE2 levels and facilitate viral dissemination.
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Affiliation(s)
- Joan C Smith
- Google, Inc., New York City, NY 10011, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Erin L Sausville
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vishruth Girish
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Stony Brook University, Stony Brook, NY 11794, USA
| | - Monet Lou Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anand Vasudevan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kristen M John
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Hofstra University, Hempstead, NY 11549, USA
| | - Jason M Sheltzer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Abstract
Gene expression profiling of the host response to HIV infection has promised to fill the gaps in our knowledge and provide new insights toward vaccine and cure. However, despite 20 years of research, the biggest questions remained unanswered. A literature review identified 62 studies examining gene expression dysregulation in samples from individuals living with HIV. Changes in gene expression were dependent on cell/tissue type, stage of infection, viremia, and treatment status. Some cell types, notably CD4+ T cells, exhibit upregulation of cell cycle, interferon-related, and apoptosis genes consistent with depletion. Others, including CD8+ T cells and natural killer cells, exhibit perturbed function in the absence of direct infection with HIV. Dysregulation is greatest during acute infection. Differences in study design and data reporting limit comparability of existing research and do not as yet provide a coherent overview of gene expression in HIV. This review outlines the extraordinarily complex host response to HIV and offers recommendations to realize the full potential of HIV host transcriptomics.
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Choukrallah MA, Hoeng J, Peitsch MC, Martin F. Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice. BMC Genomics 2020; 21:291. [PMID: 32272900 PMCID: PMC7147004 DOI: 10.1186/s12864-020-6712-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/31/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and CS exposure are associated with transcriptional alterations in the lung. The current work aims to explore the interaction between age- and CS- associated transcriptomic perturbations and develop a transcriptomic clock able to predict the biological age and the impact of external factors on lung aging. RESULTS Our investigations revealed a substantial overlap between transcriptomic response to CS exposure and age-related transcriptomic alterations in the murine lung. Of particular interest is the strong upregulation of immunoglobulin genes with increased age and in response to CS exposure, indicating an important implication of B-cells in lung inflammation associated with aging and smoking. Furthermore, we used a machine learning approach based on Lasso regression to build a transcriptomic age model that can accurately predict chronological age in untreated mice and the deviations associated with certain exposures. Interestingly, CS-exposed-mice were predicted to be prematurely aged in contrast to mice exposed to fresh air or to heated tobacco products (HTPs). The accelerated aging rate associated with CS was reversed upon smoking cessation or switching to HTPs. Additionally, our model was able to predict premature aging associated with thoracic irradiation from an independent public dataset. CONCLUSIONS Aging and CS exposure share common transcriptional alteration patterns in the murine lung. The massive upregulation of B-cell restricted genes during these processes shed light on the contribution of cell composition and particularly immune cells to the measured transcriptomic signal. Through machine learning approach, we show that gene expression changes can be used to accurately monitor the biological age and the modulations associated with certain exposures. Our findings also suggest that the premature lung aging is reversible upon the reduction of harmful exposures.
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Affiliation(s)
| | - Julia Hoeng
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003, Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003, Neuchâtel, Switzerland
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Paul A, Sil J. Identification of Differentially Expressed Genes to Establish New Biomarker for Cancer Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1970-1985. [PMID: 29994718 DOI: 10.1109/tcbb.2018.2837095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The goal of the human genome project is to integrate genetic information into different clinical therapies. To achieve this goal, different computational algorithms are devised for identifying the biomarker genes, cause of complex diseases. However, most of the methods developed so far using DNA microarray data lack in interpreting biological findings and are less accurate in disease prediction. In the paper, we propose two parameters risk_factor and confusion_factor to identify the biologically significant genes for cancer development. First, we evaluate risk_factor of each gene and the genes with nonzero risk_factor result misclassification of data, therefore removed. Next, we calculate confusion_factor of the remaining genes which determines confusion of a gene in prediction due to closeness of the samples in the cancer and normal classes. We apply nondominated sorting genetic algorithm (NSGA-II) to select the maximally uncorrelated differentially expressed genes in the cancer class with minimum confusion_factor. The proposed Gene Selection Explore (GSE) algorithm is compared to well established feature selection algorithms using 10 microarray data with respect to sensitivity, specificity, and accuracy. The identified genes appear in KEGG pathway and have several biological importance.
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Kathuria H, Millien G, McNally L, Gower AC, Tagne JB, Cao Y, Ramirez MI. NKX2-1-AS1 negatively regulates CD274/PD-L1, cell-cell interaction genes, and limits human lung carcinoma cell migration. Sci Rep 2018; 8:14418. [PMID: 30258080 PMCID: PMC6158174 DOI: 10.1038/s41598-018-32793-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/13/2018] [Indexed: 12/20/2022] Open
Abstract
The function of most long noncoding RNAs (lncRNAs) is unknown. However, recent studies reveal important roles of lncRNAs in regulating cancer-related pathways. Human antisense lncRNA-NKX2-1-AS1 partially overlaps the NKX2-1/TTF1 gene within chromosomal region 14q13.3. Amplification of this region and/or differential expression of genes therein are associated with cancer progression. Herein we show higher levels of NKX2-AS1 and NKX2-1 in lung adenocarcinomas relative to non-tumor controls but no correlation between NKX2-1-AS1 and NKX2-1 levels across specimens, or with amplification of the 14q13.3 region, suggesting that NKX2-1-AS1 and NKX2-1 are independently regulated. Loss-and-gain of function experiments showed that NKX2-1-AS1 does not regulate NKX2-1 expression, or nearby genes, but controls genes in trans. Genes up-regulated by NKX2-1-AS1-knockdown belong to cell adhesion and PD-L1/PD-1 checkpoint pathways. NKX2-1-AS1 negatively regulates endogenous CD274/PD-L1, a known target of NKX2-1, and the transcriptional activity of -1kb-CD274 promoter-reporter construct. Furthermore, NKX2-1-AS1 interferes with NKX2-1 protein binding to the CD274-promoter, likely by NKX2-1 protein-NKX2-1-AS1 interactions. Finally, NKX2-1-AS1 negatively regulates cell migration and wound healing, but not proliferation or apoptosis. These findings support potential roles of NKX2-1-AS1 in limiting motility and immune system evasion of lung carcinoma cells, highlighting a novel mechanism that may influence tumorigenic capabilities of lung epithelial cells.
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Affiliation(s)
- Hasmeena Kathuria
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Guetchyn Millien
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Liam McNally
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Adam C Gower
- Clinical and Translational Science Institute, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Jean-Bosco Tagne
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Yuxia Cao
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Maria I Ramirez
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.
- Center for Translational Medicine, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.
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8
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Kuo CHS, Liu CY, Pavlidis S, Lo YL, Wang YW, Chen CH, Ko HW, Chung FT, Lin TY, Wang TY, Lee KY, Guo YK, Wang TH, Yang CT. Unique Immune Gene Expression Patterns in Bronchoalveolar Lavage and Tumor Adjacent Non-Neoplastic Lung Tissue in Non-Small Cell Lung Cancer. Front Immunol 2018; 9:232. [PMID: 29483918 PMCID: PMC5816075 DOI: 10.3389/fimmu.2018.00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022] Open
Abstract
Background The immune cells in the local environments surrounding non-small cell lung cancer (NSCLC) implicate the balance of pro- and antitumor immunity; however, their transcriptomic profiles remain poorly understood. Methods A transcriptomic microarray study of bronchoalveolar lavage (BAL) cells harvested from tumor-bearing lung segments was performed in a discovery group. The findings were validated (1) in published microarray datasets, (2) in an independent group by RT-qPCR, and (3) in non-diseased and tumor adjacent non-neoplastic lung tissue by immunohistochemistry and in BAL cell lysates by immunoblotting. Result The differential expression of 129 genes was identified in the discovery group. These genes revealed functional enrichment in Fc gamma receptor-dependent phagocytosis and circulating immunoglobulin complex among others. Microarray datasets analysis (n = 607) showed that gene expression of BAL cells of tumor-bearing lung segment was also the unique transcriptomic profile of tumor adjacent non-neoplastic lung of early stage NSCLC and a significantly gradient increase of immunoglobulin genes’ expression for non-diseased lungs, tumor adjacent non-neoplastic lungs, and tumors was identified (ANOVA, p < 2 × 10−16). A 53-gene signature was determined with significant correlation with inhibitory checkpoint PDCD1 (r = 0.59, p = 0.0078) among others, where the nine top genes including IGJ and IGKC were RT-qPCR validated with high diagnostic performance (AUC: 0.920, 95% CI: 0.831–0.985, p = 2.98 × 10−7). Increased staining and expression of IGKC revealed by immunohistochemistry and immunoblotting in tumor adjacent non-neoplastic lung tissues (Wilcoxon signed-rank test, p < 0.001) and in BAL cell lysates (p < 0.01) of NSCLC, respectively, were noted. Conclusion The BAL cells of tumor-bearing lung segments and tumor adjacent non-neoplastic lung tissues present a unique gene expression characterized by IGKC in relation to inhibitory checkpoints. Further study of humoral immune responses to NSCLC is warranted.
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Affiliation(s)
- Chih-Hsi Scott Kuo
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan.,Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Chien-Ying Liu
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Stelios Pavlidis
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Yu-Lun Lo
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yen-Wen Wang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Chih-Hung Chen
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - How-Wen Ko
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Fu-Tsai Chung
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tin-Yu Lin
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tsai-Yu Wang
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Kang-Yun Lee
- Division of Thoracic Medicine, Taipei Medical University Shuang Ho Hospital, New Taipei City, Taiwan
| | - Yi-Ke Guo
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Tzu-Hao Wang
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Cheng-Ta Yang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
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Budinger GRS, Kohanski RA, Gan W, Kobor MS, Amaral LA, Armanios M, Kelsey KT, Pardo A, Tuder R, Macian F, Chandel N, Vaughan D, Rojas M, Mora AL, Kovacs E, Duncan SR, Finkel T, Choi A, Eickelberg O, Chen D, Agusti A, Selman M, Balch WE, Busse P, Lin A, Morimoto R, Sznajder JI, Thannickal VJ. The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop. J Gerontol A Biol Sci Med Sci 2017; 72:1492-1500. [PMID: 28498894 PMCID: PMC5861849 DOI: 10.1093/gerona/glx090] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/10/2017] [Indexed: 12/31/2022] Open
Abstract
Death from chronic lung disease is increasing and chronic obstructive pulmonary disease has become the third leading cause of death in the United States in the past decade. Both chronic and acute lung diseases disproportionately affect elderly individuals, making it likely that these diseases will become more frequent and severe as the worldwide population ages. Chronic lung diseases are associated with substantial morbidity, frequently resulting in exercise limiting dyspnea, immobilization, and isolation. Therefore, effective strategies to prevent or treat lung disease are likely to increase healthspan as well as life span. This review summarizes the findings of a joint workshop sponsored by the NIA and NHLBI that brought together investigators focused on aging and lung biology. These investigators encouraged the use of genetic systems and aged animals in the study of lung disease and the development of integrative systems-based platforms that can dynamically incorporate data sets that describe the genomics, transcriptomics, epigenomics, metabolomics, and proteomics of the aging lung in health and disease. Further research was recommended to integrate benchmark biological hallmarks of aging in the lung with the pathobiology of acute and chronic lung diseases with divergent pathologies for which advanced age is the most important risk factor.
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Affiliation(s)
- GR Scott Budinger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Ronald A Kohanski
- Division of Aging Biology, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Weiniu Gan
- Division of Lung Diseases, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael S Kobor
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Luis A Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karl T Kelsey
- Departments of Epidemiology, Laboratory Medicine & Pathology, Brown University, Providence, Rhode Island
| | - Annie Pardo
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, México
| | - Rubin Tuder
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado at Denver Health Sciences Center, Denver, Colorado
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Navdeep Chandel
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Douglas Vaughan
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Mauricio Rojas
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ana L Mora
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Elizabeth Kovacs
- Department of Surgery, University of Colorado at Denver Health Sciences Center, Denver, Colorado
| | | | - Toren Finkel
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Augustine Choi
- Weill Cornell Medical College, Division of Pulmonary and Critical Care Medicine, Weill Department of Medicine, New York, New York
| | - Oliver Eickelberg
- Pulmonary Sciences and Critical Care Medicine, University of Colorado, Anschutz Medical Campus
| | - Danica Chen
- Program in Metabolic Biology, Nutritional Sciences & Toxicology, University of California, Berkeley, California
| | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Spain
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, México
| | - William E Balch
- Department of Chemical Physiology, Department of Cell and Molecular Biology, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California
| | - Paula Busse
- Division of Clinical Immunology, Department of Medicine, Mount Sinai School of Medicine, New York, New York
| | - Anning Lin
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Richard Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois
| | - Jacob I Sznajder
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
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10
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Paul A, Sil J, Mukhopadhyay CD. Gene selection for designing optimal fuzzy rule base classifier by estimating missing value. Appl Soft Comput 2017. [DOI: 10.1016/j.asoc.2017.01.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Dugo M, Cotroneo CE, Lavoie-Charland E, Incarbone M, Santambrogio L, Rosso L, van den Berge M, Nickle D, Paré PD, Bossé Y, Dragani TA, Colombo F. Human Lung Tissue Transcriptome: Influence of Sex and Age. PLoS One 2016; 11:e0167460. [PMID: 27902768 PMCID: PMC5130276 DOI: 10.1371/journal.pone.0167460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/15/2016] [Indexed: 12/04/2022] Open
Abstract
Background Sex and age strongly influence the pathophysiology of human lungs, but scarce information is available about their effects on pulmonary gene expression. Methods We followed a discovery-validation strategy to identify sex- and age-related transcriptional differences in lung. Results We identified transcriptional profiles significantly associated with sex (215 genes; FDR < 0.05) and age at surgery (217 genes) in non-involved lung tissue resected from 284 lung adenocarcinoma patients. When these profiles were tested in three independent series of non-tumor lung tissue from an additional 1,111 patients, we validated the association with sex and age for 25 and 22 genes, respectively. Among the 17 sex-biased genes mapping on chromosome X, 16 have been reported to escape X-chromosome inactivation in other tissues or cells, suggesting that this mechanism influences lung transcription too. Our 22 age-related genes partially overlap with genes modulated by age in other tissues, suggesting that the aging process has similar consequences on gene expression in different organs. Finally, seven genes whose expression was modulated by sex in non-tumor lung tissue, but no age-related gene, were also validated using publicly available data from 990 lung adenocarcinoma samples, suggesting that the physiological regulatory mechanisms are only partially active in neoplastic tissue. Conclusions Gene expression in non-tumor lung tissue is modulated by both sex and age. These findings represent a validated starting point for research on the molecular mechanisms underlying the observed differences in the course of lung diseases among men and women of different ages.
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Affiliation(s)
- Matteo Dugo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara E. Cotroneo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Matteo Incarbone
- Department of Surgery, San Giuseppe Hospital–MultiMedica, Milan, Italy
| | - Luigi Santambrogio
- Fondazione IRCCS Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Lorenzo Rosso
- Fondazione IRCCS Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - David Nickle
- Merck & Co. Inc., Rahway, NJ, United States of America
| | - Peter D. Paré
- University of British Columbia Center for Heart Lung Innovation and Institute for Heart and Lung Health, St. Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Institut Universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec, Canada
| | - Tommaso A. Dragani
- Department of Predictive and Preventive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- * E-mail:
| | - Francesca Colombo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Wang L, Wu N, Zhao TY, Li J. The potential biomarkers of drug addiction: proteomic and metabolomics challenges. Biomarkers 2016; 21:678-685. [PMID: 27328859 DOI: 10.1080/1354750x.2016.1201530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Drug addiction places a significant burden on society and individuals. Proteomics and metabolomics approaches pave the road for searching potential biomarkers to assist the diagnosis and treatment. This review summarized putative drug addiction-related biomarkers in proteomics and metabolomics studies and discussed challenges and prospects in future studies. Alterations of several hundred proteins and metabolites were reported when exposure to abused drug, which enriched in energy metabolism, oxidative stress response, protein modification and degradation, synaptic function and neurotrasmission, etc. Hsp70, peroxiredoxin-6 and α- and β-synuclein, as well as n-methylserotonin and purine metabolites, were promising as potential biomarker for drug addiction.
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Affiliation(s)
- Lv Wang
- a State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology , Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Ning Wu
- a State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology , Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Tai-Yun Zhao
- a State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology , Beijing Institute of Pharmacology and Toxicology , Beijing , China
| | - Jin Li
- a State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology , Beijing Institute of Pharmacology and Toxicology , Beijing , China
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Chen T, Chen L. Prediction of Clinical Outcome for All Stages and Multiple Cell Types of Non-small Cell Lung Cancer in Five Countries Using Lung Cancer Prognostic Index. EBioMedicine 2014; 1:156-66. [PMID: 26137522 PMCID: PMC4457348 DOI: 10.1016/j.ebiom.2014.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/16/2022] Open
Abstract
Lung cancer is a commonly diagnosed cancer. In this era of personalized medicine, genetic predictive models are becoming increasingly important. However, many current predictive models fail verification tests due to small sample sizes and institutional biases. We collected 17 gene expression datasets from public databases to generate our largest training and testing cohorts. After successfully eliminating institutional variations and merging multiple datasets, we generated a training cohort of 1073 and a testing cohort of 659. Using Siggenes, univariate and multivariate analyses, we identified seven gene signatures, and combined them with the clinical parameter age and stage to design the lung cancer prognostic index (LCPI). Using LCPI, we could differentiate lung cancer patients into three risk groups and predict patient survival probabilities at 10 and 15 year post-surgical resection. We extensively verified the predictive ability of LCPI for overall and recurrence free survival using 6 other datasets from five different countries.
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Affiliation(s)
- Tiehua Chen
- 4014S 1000 E, Salt Lake City, UT 84124, United States
| | - Luming Chen
- 4014S 1000 E, Salt Lake City, UT 84124, United States
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Harvey BG, Strulovici-Barel Y, Vincent TL, Mezey JG, Raviram R, Gordon C, Salit J, Tilley AE, Chung A, Sanders A, Crystal RG. High correlation of the response of upper and lower lobe small airway epithelium to smoking. PLoS One 2013; 8:e72669. [PMID: 24039793 PMCID: PMC3767732 DOI: 10.1371/journal.pone.0072669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/18/2013] [Indexed: 01/15/2023] Open
Abstract
The distribution of lung disease induced by inhaled cigarette smoke is complex, depending on many factors. With the knowledge that the small airway epithelium (SAE) is the earliest site of smoking-induced lung disease, and that the SAE gene expression is likely sensitive to inhaled cigarette smoke, we compared upper vs. lower lobe gene expression in the SAE within the same cigarette smokers to determine if the gene expression patterns were similar or different. Active smokers (n = 11) with early evidence of smoking-induced lung disease (normal spirometry but low diffusing capacity) underwent bronchoscopy and brushing of the upper and lower lobe SAE in order to compare upper vs lower lobe genome-wide and smoking-responsive gene expression by microarray. Cluster and principal component analysis demonstrated that, for each individual, the expression of the known SAE smoking-responsive genes were highly correlated in upper and lower lobe pairs, although, as expected, there were differences in the smoking-induced changes in gene expression from individual to individual. These observations support the concept that the heterogeneity observed among smokers in the anatomic distribution of smoking-induced disease are not secondary to the topographic differences in the effects of cigarette smoke on the airway epithelium.
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Affiliation(s)
- Ben-Gary Harvey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Yael Strulovici-Barel
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas L. Vincent
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Ramya Raviram
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Cynthia Gordon
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ann E. Tilley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Augustine Chung
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Abraham Sanders
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Ronald G. Crystal
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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Demidyuk IV, Shubin AV, Gasanov EV, Kurinov AM, Demkin VV, Vinogradova TV, Zinovyeva MV, Sass AV, Zborovskaya IB, Kostrov SV. Alterations in gene expression of proprotein convertases in human lung cancer have a limited number of scenarios. PLoS One 2013; 8:e55752. [PMID: 23409034 PMCID: PMC3567108 DOI: 10.1371/journal.pone.0055752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/30/2012] [Indexed: 11/18/2022] Open
Abstract
Proprotein convertases (PCs) is a protein family which includes nine highly specific subtilisin-like serine endopeptidases in mammals. The system of PCs is involved in carcinogenesis and levels of PC mRNAs alter in cancer, which suggests expression status of PCs as a possible marker for cancer typing and prognosis. The goal of this work was to assess the information value of expression profiling of PC genes. Quantitative polymerase chain reaction was used for the first time to analyze mRNA levels of all PC genes as well as matrix metalloproteinase genes MMP2 and MMP14, which are substrates of PCs, in 30 matched pairs of samples of human lung cancer tumor and adjacent tissues without pathology. Significant changes in the expression of PCs have been revealed in tumor tissues: increased FURIN mRNA level (p<0.00005) and decreased mRNA levels of PCSK2 (p<0.007), PCSK5 (p<0.0002), PCSK7 (p<0.002), PCSK9 (p<0.00008), and MBTPS1 (p<0.00004) as well as a tendency to increase in the level of PCSK1 mRNA. Four distinct groups of samples have been identified by cluster analysis of the expression patterns of PC genes in tumor vs. normal tissue. Three of these groups covering 80% of samples feature a strong elevation in the expression of a single gene in cancer: FURIN, PCSK1, or PCSK6. Thus, the changes in the expression of PC genes have a limited number of scenarios, which may reflect different pathways of tumor development and cryptic features of tumors. This finding allows to consider the mRNAs of PC genes as potentially important tumor markers.
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Affiliation(s)
- Ilya V Demidyuk
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
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Intra- and inter-individual variance of gene expression in clinical studies. PLoS One 2012; 7:e38650. [PMID: 22723873 PMCID: PMC3377725 DOI: 10.1371/journal.pone.0038650] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 05/11/2012] [Indexed: 01/29/2023] Open
Abstract
Background Variance in microarray studies has been widely discussed as a critical topic on the identification of differentially expressed genes; however, few studies have addressed the influence of estimating variance. Methodology/Principal Findings To break intra- and inter-individual variance in clinical studies down to three levels–technical, anatomic, and individual–we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of “inter-individual variable genes” were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduces/eliminates the effects of underestimated variance. Conclusions/Significance Our data demonstrated that correct variance evaluation is critical in selecting significant genes. If the degree of variance is underestimated, “noisy” genes are falsely identified as differentially expressed genes. These genes are the noise associated with biological interpretation, reducing the biological significance of the gene set. Our results also indicate that applying a higher number of fold change as the selection criteria reduces/eliminates the differences between distinct estimations of variance.
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17
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Implications for Powering Biomarker Discovery Studies. J Mol Diagn 2012; 14:130-9. [DOI: 10.1016/j.jmoldx.2011.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 10/03/2011] [Accepted: 10/25/2011] [Indexed: 12/18/2022] Open
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Michael D, Soi S, Cabera-Perez J, Weller M, Alexander S, Alevizos I, Illei G, Chiorini J. Microarray analysis of sexually dimorphic gene expression in human minor salivary glands. Oral Dis 2011; 17:653-61. [PMID: 21819492 DOI: 10.1111/j.1601-0825.2011.01816.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE We hypothesized that differential mRNA transcription between the sexes may be linked to the 9:1 female-to-male gender-related relative risk for the development of Sjögren's syndrome (SS), an autoimmune disease that leads to inflammation and dysfunction in the lachrymal and salivary glands. SUBJECTS AND METHODS RNA from minor salivary glands was collected from nine healthy volunteers (four men and five women) and analyzed using the Agilent 4 × 44K human microarray platform. Differential expression was confirmed by qRT-PCR. RESULTS Comparison of the transcriptome of minor salivary glands from normal male and female volunteers with that of salivary glands and secretory epithelia identified a number of gender, species, and tissue-specific gene expression patterns. These differences include, but are not limited to, a diverse set of genes involved in immune modulation, chemotactic control, inhibition of complement, metabolism, and neurogenesis. CONCLUSION Analysis of these changes provides insight into the protective and predisposing molecular factors that may be involved in the development of Sjögren's syndrome. Some of the gene changes observed in this study correlate with previously observed sexual dimorphisms in salivary gland function and also illustrate several new targets for further investigation.
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Affiliation(s)
- D Michael
- Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Center Drive, MD 20892, USA
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Chen X, Gorlov IP, Merriman KW, Weng SF, Foy M, Keener G, Amos CI, Spitz MR, Kimmel M, Gorlova OY. Association of smoking with tumor size at diagnosis in non-small cell lung cancer. Lung Cancer 2011; 74:378-83. [PMID: 21645942 DOI: 10.1016/j.lungcan.2011.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/22/2011] [Accepted: 04/20/2011] [Indexed: 01/17/2023]
Abstract
Tumor size at diagnosis (TSD) indirectly reflects tumor growth rate. The relationship between TSD and smoking is poorly understood. The aim of the study was to determine the relationship between smoking and TSD. We reviewed 1712 newly diagnosed and previously untreated non-small cell lung cancer (NSCLC) patients' electronic medical records and collected tumor characteristics. Demographic and epidemiologic characteristics were derived from questionnaires administered during personal interviews. Univariate and multivariate linear regression models were used to evaluate the relationship between TSD and smoking controlling for demographic and clinical factors. We also investigated the relationship between the rs1051730 SNP in an intron of the CHRNA3 gene (the polymorphism most significantly associated with lung cancer risk and smoking behavior) and TSD. We found a strong dose dependent relationship between TSD and smoking. Current smokers had largest and never smokers smallest TSD with former smokers having intermediate TSD. In the multivariate linear regression model, smoking status (never, former, and current), histological type (adenocarcinoma versus SqCC), and gender were significant predictors of TSD. Smoking duration and intensity may explain the gender effect in predicting TSD. We found that the variant allele of rs1051730 in CHRNA3 gene was associated with larger TSD of squamous cell carcinoma. In the multivariate linear regression model, both rs1051730 and smoking were significant predictors for the size of squamous carcinomas. We conclude that smoking is positively associated with lung tumor size at the moment of diagnosis.
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Affiliation(s)
- Xing Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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20
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Moré JM, Voelker DR, Silveira LJ, Edwards MG, Chan ED, Bowler RP. Smoking reduces surfactant protein D and phospholipids in patients with and without chronic obstructive pulmonary disease. BMC Pulm Med 2010; 10:53. [PMID: 20973980 PMCID: PMC2987951 DOI: 10.1186/1471-2466-10-53] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 10/25/2010] [Indexed: 01/21/2023] Open
Abstract
Background Pulmonary surfactant D (SP-D) has important regulatory functions for innate immunity and has been implicated as a biomarker for chronic obstructive pulmonary disease (COPD). We hypothesized that COPD patients would have reduced bronchoalveolar lavage (BAL) fluid SP-D levels compared to healthy smoking and non-smoking controls. Methods BAL SP-D and phospholipids were quantified and corrected for dilution in 110 subjects (65 healthy never smokers, 23 smokers with normal spirometry, and 22 smokers with COPD). Results BAL SP-D was highest in never smokers (mean 51.9 μg/mL ± 7.1 μg/mL standard error) compared to both smokers with normal spirometry (16.0 μg/mL ± 11.8 μg/mL) and subjects with COPD (19.1 μg/mL ± 12.9 μg/mL; P < 0.0001). Among smokers with COPD, BAL SP-D correlated significantly with FEV1% predicted (R = 0.43; P < 0.05); however, the strongest predictor of BAL SP-D was smoking status. BAL SP-D levels were lowest in current smokers (12.8 μg/mL ± 11.0 μg/mL), intermediate in former smokers (25.2 μg/mL ± 14.2 μg/mL; P < 0.008), and highest in never smokers. BAL phospholipids were also lowest in current smokers (6.5 nmol ± 1.5 nmol), intermediate in former smokers (13.1 nmol ± 2.1 nmol), and highest in never smokers (14.8 nmol ± 1.1 nmol; P < 0.0001). Conclusions These data suggest that smokers, and especially current smokers, exhibit significantly reduced BAL SP-D and phospholipids compared to nonsmokers. Our findings may help better explain the mechanism that leads to the rapid progression of disease and increased incidence of infection in smokers.
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Affiliation(s)
- Jayaji M Moré
- Department of Medicine, National Jewish Health, Denver, CO, USA
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21
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Ballard PL, Lee JW, Fang X, Chapin C, Allen L, Segal MR, Fischer H, Illek B, Gonzales LW, Kolla V, Matthay MA. Regulated gene expression in cultured type II cells of adult human lung. Am J Physiol Lung Cell Mol Physiol 2010; 299:L36-50. [PMID: 20382749 DOI: 10.1152/ajplung.00427.2009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alveolar type II cells have multiple functions, including surfactant production and fluid clearance, which are critical for lung function. Differentiation of type II cells occurs in cultured fetal lung epithelial cells treated with dexamethasone plus cAMP and isobutylmethylxanthine (DCI) and involves increased expression of 388 genes. In this study, type II cells of human adult lung were isolated at approximately 95% purity, and gene expression was determined (Affymetrix) before and after culturing 5 days on collagen-coated dishes with or without DCI for the final 3 days. In freshly isolated cells, highly expressed genes included SFTPA/B/C, SCGB1A, IL8, CXCL2, and SFN in addition to ubiquitously expressed genes. Transcript abundance was correlated between fetal and adult cells (r = 0.88), with a subset of 187 genes primarily related to inflammation and immunity that were expressed >10-fold higher in adult cells. During control culture, expression increased for 8.1% of expressed genes and decreased for approximately 4% including 118 immune response and 10 surfactant-related genes. DCI treatment promoted lamellar body production and increased expression of approximately 3% of probed genes by > or =1.5-fold; 40% of these were also induced in fetal cells. Highly induced genes (> or =10-fold) included PGC, ZBTB16, DUOX1, PLUNC, CIT, and CRTAC1. Twenty-five induced genes, including six genes related to surfactant (SFTPA/B/C, PGC, CEBPD, and ADFP), also had decreased expression during control culture and thus are candidates for hormonal regulation in vivo. Our results further define the adult human type II cell molecular phenotype and demonstrate that a subset of genes remains hormone responsive in cultured adult cells.
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Affiliation(s)
- Philip L Ballard
- Department of Pediatrics, University of California San Francisco, San Francisco, USA.
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Metabolic profiling reveals distinct variations linked to nicotine consumption in humans--first results from the KORA study. PLoS One 2008; 3:e3863. [PMID: 19057651 PMCID: PMC2588343 DOI: 10.1371/journal.pone.0003863] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 11/13/2008] [Indexed: 12/12/2022] Open
Abstract
Exposure to nicotine during smoking causes a multitude of metabolic changes that are poorly understood. We quantified and analyzed 198 metabolites in 283 serum samples from the human cohort KORA (Cooperative Health Research in the Region of Augsburg). Multivariate analysis of metabolic profiles revealed that the group of smokers could be clearly differentiated from the groups of former smokers and non-smokers. Moreover, 23 lipid metabolites were identified as nicotine-dependent biomarkers. The levels of these biomarkers are all up-regulated in smokers compared to those in former and non-smokers, except for three acyl-alkyl-phosphatidylcholines (e.g. plasmalogens). Consistently significant results were further found for the ratios of plasmalogens to diacyl-phosphatidylcolines, which are reduced in smokers and regulated by the enzyme alkylglycerone phosphate synthase (alkyl-DHAP) in both ether lipid and glycerophospholipid pathways. Notably, our metabolite profiles are consistent with the strong down-regulation of the gene for alkyl-DHAP (AGPS) in smokers that has been found in a study analyzing gene expression in human lung tissues. Our data suggest that smoking is associated with plasmalogen-deficiency disorders, caused by reduced or lack of activity of the peroxisomal enzyme alkyl-DHAP. Our findings provide new insight into the pathophysiology of smoking addiction. Activation of the enzyme alkyl-DHAP by small molecules may provide novel routes for therapy.
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Larsson O, Diebold D, Fan D, Peterson M, Nho RS, Bitterman PB, Henke CA. Fibrotic myofibroblasts manifest genome-wide derangements of translational control. PLoS One 2008; 3:e3220. [PMID: 18795102 PMCID: PMC2528966 DOI: 10.1371/journal.pone.0003220] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 08/20/2008] [Indexed: 11/19/2022] Open
Abstract
Background As a group, fibroproliferative disorders of the lung, liver, kidney, heart, vasculature and integument are common, progressive and refractory to therapy. They can emerge following toxic insults, but are frequently idiopathic. Their enigmatic propensity to resist therapy and progress to organ failure has focused attention on the myofibroblast–the primary effector of the fibroproliferative response. We have recently shown that aberrant beta 1 integrin signaling in fibrotic fibroblasts results in defective PTEN function, unrestrained Akt signaling and subsequent activation of the translation initiation machinery. How this pathological integrin signaling alters the gene expression pathway has not been elucidated. Results Using a systems approach to study this question in a prototype fibrotic disease, Idiopathic Pulmonary Fibrosis (IPF); here we show organized changes in the gene expression pathway of primary lung myofibroblasts that persist for up to 9 sub-cultivations in vitro. When comparing IPF and control myofibroblasts in a 3-dimensional type I collagen matrix, more genes differed at the level of ribosome recruitment than at the level of transcript abundance, indicating pathological translational control as a major characteristic of IPF myofibroblasts. To determine the effect of matrix state on translational control, myofibroblasts were permitted to contract the matrix. Ribosome recruitment in control myofibroblasts was relatively stable. In contrast, IPF cells manifested large alterations in the ribosome recruitment pattern. Pathological studies suggest an epithelial origin for IPF myofibroblasts through the epithelial to mesenchymal transition (EMT). In accord with this, we found systems-level indications for TGF-β -driven EMT as one source of IPF myofibroblasts. Conclusions These findings establish the power of systems level genome-wide analysis to provide mechanistic insights into fibrotic disorders such as IPF. Our data point to derangements of translational control downstream of aberrant beta 1 integrin signaling as a fundamental component of IPF pathobiology and indicates that TGF-β -driven EMT is one source for IPF myofibroblasts.
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Affiliation(s)
- Ola Larsson
- Pulmonary Division, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America.
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Abstract
Secretory leukocyte peptidase inhibitor (SLPI) belongs to the whey acidic protein four-disulfide core family of proteins, and has antimicrobial and antiprotease functions. SLPI is produced by the epithelial cells lining the respiratory, digestive, and reproductive tracts. Gene-targeting experiments in mice indicated that one function of SLPI is to protect proepithelin from elastase cleavage in wound healing. In addition to its antiprotease function, SLPI has an anti-inflammatory function through the modulation of nuclear factor-kappaB acting intracellularly, especially in macrophages. SLPI is also produced in cancer tissues, but its role in cancer is not well understood. SLPI genes are often upregulated under tumorigenic conditions. We found a negligible number of tumors in the lungs of SLPI knockout mice 20 or 40 weeks after administration of urethane, an interesting experimental model for investigating the function of SLPI in cancer. This review discusses the normal function of SLPI and its possible roles in cancer tissues.
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Affiliation(s)
- Toshihiro Nukiwa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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Roberts ES, Soucy NV, Bonner AM, Page TJ, Thomas RS, Dorman DC. Basal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium. Inhal Toxicol 2007; 19:941-9. [PMID: 17849278 DOI: 10.1080/08958370701513113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The nasal epithelium is an important target site for chemically induced toxicity and carcinogenicity. Experimental studies show that site-specific lesions can arise within the nasal respiratory or olfactory epithelium following the inhalation of certain chemicals. Moreover, gender differences in epithelial response are also reported. To better understand and predict gender differences in response of the nasal epithelium to inhaled xenobiotics, gene expression profiles from naive male and female Sprague-Dawley rats were constructed. Epithelial cells were manually collected from the nasal septum, naso- and maxillo-turbinates, and ethmoid turbinates of nine male and nine female rats. Gene expression analysis was performed using the Affymetrix Rat Genome 430 2.0 microarray. Surprisingly, there were few gender differences in gene expression. Gene ontology enrichment analysis identified several functional categories, including xenobiotic metabolism, cell cycle, apoptosis, and ion channel/transport, with significantly different expression between tissue types. These baseline data will contribute to our understanding of the normal physiology and selectivity of the nasal epithelial cells' response to inhaled environmental toxicants.
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Affiliation(s)
- Elizabeth S Roberts
- CIIT at the Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709-2137, USA
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26
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Misra V, Lee H, Singh A, Huang K, Thimmulappa RK, Mitzner W, Biswal S, Tankersley CG. Global expression profiles from C57BL/6J and DBA/2J mouse lungs to determine aging-related genes. Physiol Genomics 2007; 31:429-40. [PMID: 17726092 DOI: 10.1152/physiolgenomics.00060.2007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This study identified gene expression profiles that provided evidence for genomic mechanisms underlying the pathophysiology of aging lung. Aging lungs from C57BL/6 (B6) and DBA/2 (D2) mouse strains differ in physiology and morphometry. Lungs were harvested from B6 mice at 2, 18, and 26 mo and from D2 mice at 2 and 18 mo of age. Purified RNA was subjected to oligonucleotide microarray analyses, and differential expression analyses were performed for comparison of various data sets. A significant majority of differentially expressed genes were upregulated with aging in both strains. Aging D2 lungs uniquely exhibited upregulation in stress-response genes including xenobiotic detoxification cascades. In contrast, aging B6 lungs showed downregulation of heat shock-response genes. Age-dependent downregulation of genes common to both B6 and D2 strains included several collagen genes (e.g., Col1a1 and Col3a1). There was a greater elastin gene (Eln) expression in D2 mice at 2 mo, and Eln was uniquely downregulated with age in this strain. The matrix metalloproteinase 14 gene (Mmp14), critical to alveolar structural integrity, was also downregulated with aging in D2 mice only. Several polymorphisms in the regulatory and untranslated regions of Mmp14 were identified between strains, suggesting that variation in Mmp14 gene regulation contributes to accelerated aging of lungs in D2 mice. In summary, lungs of B6 and D2 mice age with variable rates at the gene expression level, and these quantifiable genomic differences provide a template for understanding the variability in age-dependent changes in lung structure and function.
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Affiliation(s)
- Vikas Misra
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Bock Axelsen J, Lotem J, Sachs L, Domany E. Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles. Proc Natl Acad Sci U S A 2007; 104:13122-7. [PMID: 17664417 PMCID: PMC1941809 DOI: 10.1073/pnas.0705824104] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have analyzed gene expression in different normal human tissues and different types of solid cancers derived from these tissues. The cancers analyzed include brain (astrocytoma and glioblastoma), breast, colon, endometrium, kidney, liver, lung, ovary, prostate, skin, and thyroid cancers. Comparing gene expression in each normal tissue to 12 other normal tissues, we identified 4,917 tissue-selective genes that were selectively expressed in different normal tissues. We also identified 2,929 genes that are overexpressed at least 4-fold in the cancers compared with the normal tissue from which these cancers were derived. The overlap between these two gene groups identified 1,340 tissue-selective genes that are overexpressed in cancers. Different types of cancers, including different brain cancers arising from the same lineage, showed differences in the tissue-selective genes they overexpressed. Melanomas overexpressed the highest number of brain-selective genes and this may contribute to melanoma metastasis to the brain. Of all of the genes with tissue-selective expression, those selectively expressed in testis showed the highest frequency of genes that are overexpressed in at least two types of cancer. However, colon and prostate cancers did not overexpress any testis-selective gene. Nearly all of the genes with tissue-selective expression that are overexpressed in cancers showed selective expression in tissues different from the cancers' tissue of origin. Cancers aberrantly expressing such genes may acquire phenotypic alterations that contribute to cancer cell viability, growth, and metastasis.
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Affiliation(s)
| | - Joseph Lotem
- Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leo Sachs
- Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
- To whom correspondence should be addressed. E-mail: or
| | - Eytan Domany
- Departments of *Physics of Complex Systems and
- To whom correspondence should be addressed. E-mail: or
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Van den Eynden GG, Van Laere SJ, Van der Auwera I, Gilles L, Burn JL, Colpaert C, van Dam P, Van Marck EA, Dirix LY, Vermeulen PB. Differential expression of hypoxia and (lymph)angiogenesis-related genes at different metastatic sites in breast cancer. Clin Exp Metastasis 2007; 24:13-23. [PMID: 17295094 DOI: 10.1007/s10585-006-9049-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 11/17/2006] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Breast cancer can metastasize via lymphatic and hematogenous pathways. Hypoxia and (lymph)angiogenesis are closely related processes that play a pivotal role in the tumor progression and metastasis. The aim of this study was to compare expression of hypoxia and (lymph)angiogenesis-related genes between primary breast tumors and metastases in different tissues. MATERIALS AND METHODS A gene list of 269 hypoxia and (lymph)angiogenesis-related genes was composed and validated using Onto-Express, Pathway-express and Ingenuity software. The expression of these genes was compared in microarray data of 62 samples of primary tumors and metastases of 31 patients with breast cancer retrieved from Gene Expression Omnibus. Similarity between samples was investigated using unsupervised hierarchical clustering analysis, principal component analysis and permutation testing. Differential gene expression between primary tumors and metastases and between metastases from different organs was analyzed using Kruskall-Wallis and Mann-Whitney statistics. RESULTS Unsupervised hierarchical cluster analysis demonstrated that hypoxia and (lymph)angiogenesis-related gene expression was more similar between samples from the same patient, than between samples from the same organ. Principal component analysis indicated that 22.7% and 7.0% of the total variation in the gene list was respectively patient and organ related. When differences in gene expression were studied between different organs, liver metastases seemed to differ most from the other secondary sites. Some of the best characterized molecules differentially expressed were VEGFA, PDGFRB, FGF4, TIMP1, TGFB-R1 and collagen 18A1 (precursor of endostatin). To confirm the results of these experiments at the protein level, immunohistochemical experiments were performed with antibodies for VEGFA and MMP-2. CONCLUSIONS Our results suggest that hypoxia and (lymph)angiogenesis-related gene expression is more dependent on the characteristics of the primary tumor than on the characteristics of the organs that bear the metastasis. However, when different organs are compared, the expression in liver metastases differs most from other metastatic sites and primary tumors, possibly due to organ-specific angiogenic and lymphangiogenic responses to metastasis-related hypoxia.
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Affiliation(s)
- Gert G Van den Eynden
- Translational Cancer Research Group (Lab Pathology, University of Antwerp/University Hospital Antwerp, Oncology Center, General Hospital, St.-Augustinus), Wilrijk, Antwerp 2610, Belgium
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Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinformatics 2006; 7:464. [PMID: 17059591 PMCID: PMC1624855 DOI: 10.1186/1471-2105-7-464] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 10/23/2006] [Indexed: 11/25/2022] Open
Abstract
Background Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the final measures of expression. One problem associated with these algorithms is that expression measurements for a particular sample are highly dependent on the set of samples used for normalization and results obtained by normalization with a different set may not be comparable. A related problem is that an organization producing and/or storing large amounts of data in a sequential fashion will need to either re-run the pre-processing algorithm every time an array is added or store them in batches that are pre-processed together. Furthermore, pre-processing of large numbers of arrays requires loading all the feature-level data into memory which is a difficult task even with modern computers. We utilize a scheme that produces all the information necessary for pre-processing using a very large training set that can be used for summarization of samples outside of the training set. All subsequent pre-processing tasks can be done on an individual array basis. We demonstrate the utility of this approach by defining a new version of the Robust Multi-chip Averaging (RMA) algorithm which we refer to as refRMA. Results We assess performance based on multiple sets of samples processed over HG U133A Affymetrix GeneChip® arrays. We show that the refRMA workflow, when used in conjunction with a large, biologically diverse training set, results in the same general characteristics as that of RMA in its classic form when comparing overall data structure, sample-to-sample correlation, and variation. Further, we demonstrate that the refRMA workflow and reference set can be robustly applied to naïve organ types and to benchmark data where its performance indicates respectable results. Conclusion Our results indicate that a biologically diverse reference database can be used to train a model for estimating probe set intensities of exclusive test sets, while retaining the overall characteristics of the base algorithm. Although the results we present are specific for RMA, similar versions of other multi-array normalization and summarization schemes can be developed.
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Affiliation(s)
- Simon Katz
- Gene Logic Inc., 610 Professional Dr, Gaithersburg, MD, 20876, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Johns Hopkins Bloomberg School of Health, 615 N Wolfe St, Baltimore, MD, 21205, USA
| | - Xue Lin
- Department of Applied Mathematics and Statistics, Johns Hopkins. University, 302 Whitehead Hall, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Mark Tripputi
- Gene Logic Inc., 610 Professional Dr, Gaithersburg, MD, 20876, USA
| | - Mark W Porter
- Gene Logic Inc., 610 Professional Dr, Gaithersburg, MD, 20876, USA
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Chambellan A, Cruickshank PJ, McKenzie P, Cannady SB, Szabo K, Comhair SAA, Erzurum SC. Gene expression profile of human airway epithelium induced by hyperoxia in vivo. Am J Respir Cell Mol Biol 2006; 35:424-35. [PMID: 16690988 PMCID: PMC2643263 DOI: 10.1165/rcmb.2005-0251oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hyperoxia leads to oxidative modification and damage of macromolecules in the respiratory tract with loss of biological functions. Given the lack of antioxidant gene induction with acute exposure to 100% oxygen, we hypothesized that clearance pathways for oxidatively modified proteins may be induced and serve in the immediate cellular response to preserve the epithelial layer. To test this, airway epithelial cells were obtained from individuals under ambient oxygen conditions and after breathing 100% oxygen for 12 h. Gene expression profiling identified induction of genes in the chaperone and proteasome-ubiquitin-conjugation pathways that together comprise an integrated cellular response to manage and degrade damaged proteins. Analyses also revealed gene expression changes associated with oxidoreductase function, cell cycle regulation, and ATP synthesis. Increased HSP70, protein ubiquitination, and intracellular ATP were validated in cells exposed to hyperoxia in vitro. Inhibition of proteasomal degradation revealed the importance of accelerated protein catabolism for energy production of cells exposed to hyperoxia. Thus, the human airway early response to hyperoxia relies predominantly upon induction of cytoprotective chaperones and the ubiquitin-proteasome-dependent protein degradation system to maintain airway homeostatic integrity.
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Affiliation(s)
- Arnaud Chambellan
- Institut du Thorax, INSERM U533, Faculté de Médecine, Nantes, France
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