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Peptide Pattern of Amniotic Fluid and Its LITHUANIAN UNIVERSITY OF HEALTH SCIENCES MEDICAL ACADEMY Egl Machtejevien PEPTIDE PATTERN OF AMNIOTIC FLUID AND ITS CORRELATION WITH PROTEIN COMPOSITION OF FETAL MEMBRANES: THE SEARCH FOR NEW POTENTIAL BIOMARKERS TO PREDICT PRETERM PREMATURE RUPTURE OF MEMBRANES Doctoral dissertation Biomedical Sciences, Medicine (06B) Kaunas, 2013 1 This doctoral dissertation was carried out at the Lithuanian University of Health Sciences in 2008–2012. Scientific Supervisor !"#$%& '"%& (<*+& ,#-+.*+& /+01+34516.& 891*:3+.1+.& ;.1<6"41*=& #$& >6+-*:& Sciences, Biomedical Sciences, Medicine – 06B) 2 TABLE OF CONTENTS ABBREVIATIONS ....................................................................................... 5 1. INTRODUCTION ................................................................................... 7 2. AIM AND TASKS OF THE STUDY ...................................................... 9 2.1. Aim of the study ........................................................................... 9 2.2. Tasks of the study ......................................................................... 9 3. NOVELTY OF THE RESEARCH ........................................................... 9 4. REVIEW OF THE LITERATURE ......................................................... 10 4.1. “Omics” technologies ...................................................................... 10 4.1.1. Human genome ........................................................................ 10 4.1.2. Transcriptome .......................................................................... 11 4.1.3. Proteome ................................................................................... 12 4.2. Fetal membranes ............................................................................. 20 4.2.1. The amniochorionic extracellular matrix proteins ................... 20 4.2.2. Matrix metalloproteinases ....................................................... 21 4.2.3. Tissue inhibitors of metalloproteinases ................................... 22 4.3. Physiology of amniotic fluid ........................................................... 22 4.3.1. Composition of amniotic fluid ................................................. 22 4.3.2. Regulation of amniotic fluid volume ....................................... 23 4.4. Amniotic fluid proteome ................................................................. 24 4.4.1. The normal human amniotic fluid proteome ........................... 24 4.4.2. Gestational age-dependent changes ......................................... 26 4.4.3. Clinical applications of amniotic fluid proteomics .................. 28 4.5. Human plasma proteome ................................................................. 33 4.6. Methods of proteomic analysis of amniotic fluid ............................ 34 4.6.1. Gel electrophoresis .................................................................. 35 4.6.2. Protein arrays ........................................................................... 35 4.6.3. Liquid chromatography ........................................................... 37 4.7. Preterm premature rupture of the membranes ................................. 46 4.7.1. Definitions and incidence ...................................................... 46 4.7.2. Risk factors ............................................................................ 47 4.7.3. Etiology and pathophysiology ............................................... 50 4.7.4. Diagnosis ............................................................................... 53 4.7.5. Prediction of preterm premature rupture of membranes ....... 56 5. PATIENTS, BIOLOGICAL SAMPLES AND METHODOLOGY ....... 58 5.1. Patients ............................................................................................ 58 3 5.2. Biological samples ........................................................................... 60 5.3. The analytical system ...................................................................... 62 5.4. Database searching and confidence of proteins identification ........ 65 5.5. Ethical aspects ................................................................................. 66 6. RESULTS AND DISCUSSION ............................................................. 67 6.1. Peptides and proteins identified in amniotic fluid ........................... 70 6.2. Characterization of amniotic fluid proteome ................................... 80 6.3. Comparison of the amniotic fluid proteome with previous publications ............................................................................................. 82 6.4. Gestational age-dependent changes in the amniotic fluid proteome ................................................................................................. 84 6.5. Fetal membranes proteome .............................................................. 88 6.5.1. Comparison of proteome from fetal membranes of patients with PPROM and term labor with intact membranes ........................ 89 6.5.2. Comparison of proteome from the fetal membranes and amniotic fluid of patients with PPROM and term labor with intact membranes ......................................................................................... 97 6.6. Comparison of biological samples peptidome and proteome from patients with preterm premature rupture of membranes ................ 98 7. CONCLUSIONS ................................................................................... 101 8. BENEFITS OF THE RESEARCH AND POTENTIAL FOR THE FUTURE .................................................................................. 102 9. LIST OF ORIGINAL PUBLICATIONS .............................................. 104 10. REFERENCES .................................................................................... 106 ACKNOWLEGMENTS ........................................................................... 120 4 ABBREVIATIONS 2DE two dimensional electrophoresis 2D LC/MS two dimensional liquid chromatography mass spectrometry 2D PAGE two dimensional polyacrylamide gel electrophoresis AC amniocentesis AF amniotic fluid AFI amniotic fluid index AFP alpha-fetoprotein CVF cervico-vaginal fluid Da dalton (the unified atomic mass unit) DNA deoxyribonucleic acid ECM extracellular matrix ELISA enzyme-linked immuno sorbent assay ESI electrospray ionization fFN fetal fibronectin FN false negative FP false positive G group group of amniotic fluid samples from patients at 16–18 week of gestation with intact membranes (obtained during prenatal genetic amniocentesis) HLUHS Hospital of the Lithuanian University of Health Sciences HPLC high performance liquid chromatography HPPP Human Plasma Proteome Project HUPO Human Proteome Organization IAI intraamniotic infection IEC ion exchange chromatography IUI intrauterine infection Ig immunogloblin IGFBP-1 insulin-like growth factor-binding protein 1 IL interleukins LC liquid chromatography MALDI-TOF matrix assisted laser desorption/ionization time-of-flight MD multidimensional MDG Millennium development goal MMP matrix metalloproteinases MR mass restricted MS mass spectrometry m/z mass-to-charge ratio 5 PCR polymerase chain reaction pI isoelectric point (the pH at which a protein carries no net electrical charge or net charge is zero) ppm parts per million PPROM preterm premature rupture of membranes PROM premature rupture of membranes PTD preterm delivery PTL preterm labor Q-TOF quadrupole time-of-flight R group group of amniotic fluid samples from patients with preterm premature rupture of membranes RAM restricted access material RNR ribonucleic acid RP reverse phase SD standard deviation SELDI-TOF surface-enhanced laser desorption/ionization time-of-flight SCX strong cation exchange SPE solid phase extraction TIMP tissue inhibitor of metalloproteinase Z group group of amniotic fluid samples from patients with term pregnancies and intact membranes (obtained during cesarean section) 6 1. INTRODUCTION The Millennium Development Goals (MDGs) were set in 2000 by the United Nations. MDG-4 targets a two-thirds reduction of under 5 years children deaths between 1990 and 2015 [1]. While under age of 5 mortality rates are improving in many countries worldwide, neonatal mortality rates (deaths in the first 28 days of life) have shown much less progress. Neonatal deaths now account for more than 42% of under-5 deaths [2,3]. Com- plications of preterm birth are the leading direct cause of neonatal mortality, accounting for an estimated 27% of the almost four million neonatal deaths every year, and act as a risk factor for many neonatal deaths due to multiple causes, particularly infections [3]. Therefore, achievement of MDG-4 is strongly influenced by progress in reducing neonatal deaths. Since preterm birth is the leading cause of these deaths, therefore progress is dependent on achieving of evidence-based interventions to prevent preterm delivery; also to improve survival for preterm newborns. Preterm premature rupture of membranes (abbreviated as PPROM) is defined as the rupture of fetal membranes before the onset of labor before 37 weeks of gestation. PPROM occurs in 2% to 5% of pregnancies and is the most common cause of preterm birth, present in 25% to 40% of cases, and can result in significant neonatal morbidity and mortality [4,5,6]. According to the Lithuanian Medical Data of Births 1616 (5.6%) newborns were born prematurely in Lithuania in 2011 [7]. Epidemiological and clinical studies have identified a number of factors associated with increased risk for
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