Table SI. Significantly Differentially Expressed Mrnas of GSE19089 Data Series with the Criteria of Adjusted P<0.05 Andlogfc
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An Overview of the Kallikrein Gene Families in Humans and Other Species: Emerging Candidate Tumour Markers૾
Clinical Biochemistry 36 (2003) 443–452 An overview of the kallikrein gene families in humans and other species: Emerging candidate tumour markers૾ George M. Yousefa,b, Eleftherios P. Diamandisa,b,* aDepartment of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada bDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Abstract Kallikreins are serine proteases with diverse physiologic functions. They are represented by multigene families in many animal species, especially in rat and mouse. Recently, the human kallikrein gene family has been fully characterized and includes 15 members, tandemly localized on chromosome 19q13.4. A new definition has now been proposed for kallikreins, which is not based on function but, rather, on close proximity and structural similarities. In this review, we summarize available information about kallikreins in many animal species with special emphasis on human kallikreins. We discuss the common structural features of kallikreins at the DNA, mRNA and protein levels and overview their evolutionary history. Kallikreins are expressed in a wide range of tissues including the salivary gland, endocrine or endocrine-related tissues such as testis, prostate, breast and endometrium and in the central nervous system. Most, if not all, genes are under steroid hormone regulation. Accumulating evidence indicates that kallikreins are involved in many pathologic conditions. Of special interest is the potential role of kallikreins in the central nervous system. In addition, many kallikreins seem to be candidate tumor markers for many malignancies, especially those of endocrine-related organs. © 2003 The Canadian Society of Clinical Chemists. All rights reserved. Keywords: Kallikrein; Tumor markers; Cancer biomarkers; Prostate cancer; Breast cancer; Ovarian cancer; Alzheimer’s disease; Serine proteases; Chromosome 19; Kallikrein evolution; Rodent kallikreins; Hormonally regulated genes 1. -
The Correlation of Keratin Expression with In-Vitro Epithelial Cell Line Differentiation
The correlation of keratin expression with in-vitro epithelial cell line differentiation Deeqo Aden Thesis submitted to the University of London for Degree of Master of Philosophy (MPhil) Supervisors: Professor Ian. C. Mackenzie Professor Farida Fortune Centre for Clinical and Diagnostic Oral Science Barts and The London School of Medicine and Dentistry Queen Mary, University of London 2009 Contents Content pages ……………………………………………………………………......2 Abstract………………………………………………………………………….........6 Acknowledgements and Declaration……………………………………………...…7 List of Figures…………………………………………………………………………8 List of Tables………………………………………………………………………...12 Abbreviations….………………………………………………………………..…...14 Chapter 1: Literature review 16 1.1 Structure and function of the Oral Mucosa……………..…………….…..............17 1.2 Maintenance of the oral cavity...……………………………………….................20 1.2.1 Environmental Factors which damage the Oral Mucosa………. ….…………..21 1.3 Structure and function of the Oral Mucosa ………………...….……….………...21 1.3.1 Skin Barrier Formation………………………………………………….……...22 1.4 Comparison of Oral Mucosa and Skin…………………………………….……...24 1.5 Developmental and Experimental Models used in Oral mucosa and Skin...……..28 1.6 Keratinocytes…………………………………………………….….....................29 1.6.1 Desmosomes…………………………………………….…...............................29 1.6.2 Hemidesmosomes……………………………………….…...............................30 1.6.3 Tight Junctions………………………….……………….…...............................32 1.6.4 Gap Junctions………………………….……………….….................................32 -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Loss of Keratin 13 in Oral Carcinoma in Situ: a Comparative Study of Protein and Gene Expression Levels Using Paraffin Sections
Modern Pathology (2012) 25, 784–794 784 & 2012 USCAP, Inc. All rights reserved 0893-3952/12 $32.00 Loss of keratin 13 in oral carcinoma in situ: a comparative study of protein and gene expression levels using paraffin sections Hiroko Ida-Yonemochi1,2,3, Satoshi Maruyama3, Takanori Kobayashi3, Manabu Yamazaki1, Jun Cheng1 and Takashi Saku1,3 1Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; 2Division of Anatomy and Cell Biology of the Hard Tissue, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan and 3Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, Niigata, Japan Immunohistochemical loss of keratin (K)13 is one of the most valuable diagnostic criteria for discriminating carcinoma in situ (CIS) from non-malignancies in the oral mucosa while K13 is stably immunolocalized in the prickle cells of normal oral epithelium. To elucidate the molecular mechanism for the loss of K13, we compared the immunohistochemical profiles for K13 and K16 which is not expressed in normal epithelia, but instead enhanced in CIS, with their mRNA levels by in-situ hybridization in formalin-fixed paraffin sections prepared from 23 CIS cases of the tongue, which were surgically removed. Reverse transcriptase-PCR was also performed using RNA samples extracted from laser-microdissected epithelial fragments of the serial paraffin sections in seven of the cases. Although more enhanced expression levels for K16 were confirmed at both the protein and gene levels in CIS in these seven cases, the loss of K13 was associated with repressed mRNA levels in four cases, but not in the other three cases. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Supplementary Material Contents
Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration ......................................................................................................... -
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Florida State University Libraries Faculty Publications The Department of Biomedical Sciences 2010 Functional Intersection of the Kallikrein- Related Peptidases (KLKs) and Thrombostasis Axis Michael Blaber, Hyesook Yoon, Maria Juliano, Isobel Scarisbrick, and Sachiko Blaber Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] Article in press - uncorrected proof Biol. Chem., Vol. 391, pp. 311–320, April 2010 • Copyright ᮊ by Walter de Gruyter • Berlin • New York. DOI 10.1515/BC.2010.024 Review Functional intersection of the kallikrein-related peptidases (KLKs) and thrombostasis axis Michael Blaber1,*, Hyesook Yoon1, Maria A. locus (Gan et al., 2000; Harvey et al., 2000; Yousef et al., Juliano2, Isobel A. Scarisbrick3 and Sachiko I. 2000), as well as the adoption of a commonly accepted Blaber1 nomenclature (Lundwall et al., 2006), resolved these two fundamental issues. The vast body of work has associated 1 Department of Biomedical Sciences, Florida State several cancer pathologies with differential regulation or University, Tallahassee, FL 32306-4300, USA expression of individual members of the KLK family, and 2 Department of Biophysics, Escola Paulista de Medicina, has served to elevate the importance of the KLKs in serious Universidade Federal de Sao Paulo, Rua Tres de Maio 100, human disease and their diagnosis (Diamandis et al., 2000; 04044-20 Sao Paulo, Brazil Diamandis and Yousef, 2001; Yousef and Diamandis, 2001, 3 Program for Molecular Neuroscience and Departments of 2003; -
Toward Unraveling the Complexity of Simple Epithelial Keratins in Human Disease
Toward unraveling the complexity of simple epithelial keratins in human disease M. Bishr Omary, … , Pavel Strnad, Shinichiro Hanada J Clin Invest. 2009;119(7):1794-1805. https://doi.org/10.1172/JCI37762. Review Series Simple epithelial keratins (SEKs) are found primarily in single-layered simple epithelia and include keratin 7 (K7), K8, K18–K20, and K23. Genetically engineered mice that lack SEKs or overexpress mutant SEKs have helped illuminate several keratin functions and served as important disease models. Insight into the contribution of SEKs to human disease has indicated that K8 and K18 are the major constituents of Mallory-Denk bodies, hepatic inclusions associated with several liver diseases, and are essential for inclusion formation. Furthermore, mutations in the genes encoding K8, K18, and K19 predispose individuals to a variety of liver diseases. Hence, as we discuss here, the SEK cytoskeleton is involved in the orchestration of several important cellular functions and contributes to the pathogenesis of human liver disease. Find the latest version: https://jci.me/37762/pdf Review series Toward unraveling the complexity of simple epithelial keratins in human disease M. Bishr Omary,1 Nam-On Ku,1,2 Pavel Strnad,3 and Shinichiro Hanada1,4 1Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA. 2Department of Biomedical Sciences, Graduate School, Yonsei University, Seoul, Republic of Korea. 3Department of Internal Medicine I, University Medical Center Ulm, Ulm, Germany. 4Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, Japan. Simple epithelial keratins (SEKs) are found primarily in single-layered simple epithelia and include keratin 7 (K7), K8, K18–K20, and K23. -
Disease-Causing Keratin Mutations and Cytoskeletal Dysfunction In
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ermatology and Venereology, +-./ D& 6 6()*) :>*$"*7$()$ :=>!?<7!*7""'7?<*$7( , ,,, 7*(+)?*/ ,## 22# E F , ,,, 7*(+)?*1 In memory of my mother Tienguep Josephine, To my father & My Children “An idea that is developed and put into action is more important than an idea that exists only as an idea” (Buddha) “Judge your success by what you had to give up in order to achieving (get) it” (Dalai Lama) List of papers included This thesis is based on the following papers, herein referred to by their Roman numerals. I. Chamcheu JC, Virtanen M, Navsaria H, Bowden PE, Vahlquist A and Törmä H (2010) Epidermolysis bullosa simplex due to KRT5 mutations: mutation-related differences in cellular fragility and the protective effects of trimethylamine N-oxide in cultured primary keratinocytes. *British Journal of Dermatology, 162(5): 980-989. II. -
Activation Profiles and Regulatory Cascades of the Human Kallikrein-Related Peptidases Hyesook Yoon
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2008 Activation Profiles and Regulatory Cascades of the Human Kallikrein-Related Peptidases Hyesook Yoon Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES ACTIVATION PROFILES AND REGULATORY CASCADES OF THE HUMAN KALLIKREIN-RELATED PEPTIDASES By HYESOOK YOON A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Fall Semester, 2008 The members of the Committee approve the dissertation of Hyesook Yoon defended on July 10th, 2008. ________________________ Michael Blaber Professor Directing Dissertation ________________________ Hengli Tang Outside Committee Member ________________________ Brian Miller Committee Member ________________________ Oliver Steinbock Committee Member Approved: ____________________________________________________________ Joseph B. Schlenoff, Chair, Department of Chemistry and Biochemistry The Office of Graduate Studies has verified and approved the above named committee members. ii ACKNOWLEDGMENTS I would like to dedicate this dissertation to my parents for all your support, and my sister and brother. I would also like to give great thank my advisor, Dr. Blaber for his patience, guidance. Without him, I could never make this achievement. I would like to thank to all the members in Blaber lab. They are just like family to me and I deeply appreciate their kindness, consideration and supports. I specially like to thank to Mrs. Sachiko Blaber for her endless guidance and encouragement. I would like to thank Dr Jihun Lee, Margaret Seavy, Rani and Doris Terry for helpful discussions and supports. -
A Multiparametric Serum Kallikrein Panel for Diagnosis of Non ^ Small
Imaging, Diagnosis, Prognosis A Multiparametric Serum Kallikrein Panel for Diagnosis of Non ^ Small Cell Lung Carcinoma Chris Planque,1, 2 Lin Li,3 Yingye Zheng,3 Antoninus Soosaipillai,1, 2 Karen Reckamp,4 David Chia,5 Eleftherios P. Diamandis,1, 2 and Lee Goodglick5 Abstract Purpose: Human tissue kallikreins are a family of15 secreted serine proteases.We have previous- ly shown that the expression of several tissue kallikreins is significantly altered at the transcription- al level in lung cancer. Here, we examined the clinical value of 11members of the tissue kallikrein family as potential biomarkers for lung cancer diagnosis. Experimental Design: Serum specimens from 51 patients with non ^ small cell lung cancer (NSCLC) and from 50 healthy volunteers were collected. Samples were analyzed for11kallikreins (KLK1, KLK4-8, and KLK10-14) by specific ELISA. Data were statistically compared and receiver operating characteristic curves were constructed for each kallikrein and for various combinations. Results: Compared with sera from normal subjects, sera of patients with NSCLC had lower levels of KLK5, KLK7, KLK8, KLK10, and KLK12, and higher levels of KLK11, KLK13, and KLK14. Expres- sion of KLK11and KLK12 was positively correlated with stage.With the exception of KLK5, expres- sion of kallikreins was independent of smoking status and gender. KLK11, KLK12, KLK13, and KLK14 were associated with higher risk of NSCLC as determined by univariate analysis and con- firmed by multivariate analysis.The receiver operating characteristic curve of KLK4, KLK8, KLK10, KLK11,KLK12, KLK13, and KLK14 combined exhibited an area under the curve of 0.90 (95% con- fidence interval, 0.87-0.97). -
Gene Expression Predictors of Breast Cancer Outcomes
GENE EXPRESSION PREDICTORS OF BREAST CANCER OUTCOMES Erich Huang2, Skye H Cheng1, Holly Dressman2, Jennifer Pittman5, Mei-Hua Tsou1, Cheng-Fang Horng1, Andrea Bild2, Edwin S Iversen4,5, Ming Liao5, Chii-Ming Chen1, Mike West5, Joseph R Nevins2,6 and Andrew T Huang1,3 1Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan 2Department of Molecular Genetics and Microbiology, Duke University Medical Center 3Department of Medicine, Duke University Medical Center 4Department of Biostatistics and Bioinformatics, Duke University Medical Center 5Institute of Statistics and Decision Sciences, Duke University 6Howard Hughes Medical Institute SUMMARY Background The integration of currently accepted risk factors with genomic data carries the promise of focusing the practice of medicine on the individual patient. Such integration requires interpreting the complex, multivariate patterns in gene expression data, and evaluating their capacity to improve clinical predictions. We do this here, in a study of predicting nodal metastatic states and relapse for breast cancer patients. Methods DNA microarray data from samples of primary breast tumors were analyzed using non-linear statistical analyses to evaluate multiple patterns of interactions of groups of genes that have predictive value, at the individual patient level, with respect to lymph node metastasis and cancer recurrence. Findings We identify aggregate patterns of gene expression (metagenes) that associate with lymph node status and recurrence, and that are capable of honestly predicting outcomes in individual patients with about 90% accuracy. The identified metagenes define distinct groups of genes, suggesting different biological processes underlying these two characteristics of breast cancer. Initial external validation comes from similarly accurate predictions of nodal status of a small sample in a quite distinct population group.