Rapid detection of fetal aneuploidy using proteomics approaches on amniotic fluid supernatant

An exhaustive review of the metaheuristic algorithms for search and optimization: taxonomy, applications, and open challenges

As the world moves towards industrialization, optimization problems become more challenging to solve in a reasonable time. More than 500 new metaheuristic algorithms (MAs) have been developed to date, with over 350 of them appearing in the last decade. The literature has grown significantly in recent years and should be thoroughly reviewed. In this study, approximately 540 MAs are tracked, and statistical information is also provided. Due to the proliferation of MAs in recent years, the issue of substantial similarities between algorithms with different names has become widespread. This raises an essential question: can an optimization technique be called 'novel' if its search properties are modified or almost equal to existing methods? Many recent MAs are said to be based on 'novel ideas', so they are discussed. Furthermore, this study categorizes MAs based on the number of control parameters, which is a new taxonomy in the field. MAs have been extensively employed in various fields as powerful optimization tools, and some of their real-world applications are demonstrated. A few limitations and open challenges have been identified, which may lead to a new direction for MAs in the future. Although researchers have reported many excellent results in several research papers, review articles, and monographs during the last decade, many unexplored places are still waiting to be discovered. This study will assist newcomers in understanding some of the major domains of metaheuristics and their real-world applications. We anticipate this resource will also be useful to our research community.

The Use of Proteomics in Assisted Reproduction

Despite the explosive increase in the use of Assisted Reproductive Technologies (ART) over the last 30 years, their success rates remain suboptimal. Proteomics is a rapidly-evolving technology-driven science that has already been widely applied in the exploration of human reproduction and fertility, providing useful insights into its physiology and leading to the identification of numerous proteins that may be potential biomarkers and/or treatment targets of a successful ART pregnancy. Here we present a brief overview of the techniques used in proteomic analyses and attempt a comprehensive presentation of recent data from mass spectrometry-based proteomic studies in humans, regarding all components of ARTs, including the male and female gamete, the derived zygote and embryo, the endometrium and, finally, the ART offspring both pre- and postnatally.

The Applications of Genetic Algorithms in Medicine

A great wealth of information is hidden amid medical research data that in some cases cannot be easily analyzed, if at all, using classical statistical methods. Inspired by nature, metaheuristic algorithms have been developed to offer optimal or near-optimal solutions to complex data analysis and decision-making tasks in a reasonable time. Due to their powerful features, metaheuristic algorithms have frequently been used in other fields of sciences. In medicine, however, the use of these algorithms are not known by physicians who may well benefit by applying them to solve complex medical problems. Therefore, in this paper, we introduce the genetic algorithm and its applications in medicine. The use of the genetic algorithm has promising implications in various medical specialties including radiology, radiotherapy, oncology, pediatrics, cardiology, endocrinology, surgery, obstetrics and gynecology, pulmonology, infectious diseases, orthopedics, rehabilitation medicine, neurology, pharmacotherapy, and health care management. This review introduces the applications of the genetic algorithm in disease screening, diagnosis, treatment planning, pharmacovigilance, prognosis, and health care management, and enables physicians to envision possible applications of this metaheuristic method in their medical career.].

Non-invasively collected amniotic fluid as a source of possible biomarkers for premature rupture of membranes investigated by proteomic approach

PURPOSE

Preterm delivery is one of the main causes of perinatal morbidity and mortality and it accounts for 75 % of perinatal mortality and more than half of the long-term morbidity. We applied a proteomic approach based on mass spectrometry (MS) for biomarkers discovery of preterm premature rupture of membranes (pPROM) by investigating amniotic fluid (AF) invasively and non-invasively collected.

METHODS

Amniotic fluid was obtained from vagina of women with pPROM (group 1), PROM at term (group 2) and by genetic amniocentesis (group 3). Pre-fractionated AF proteome was analyzed through matrix assisted laser desorption ionization-time of flight (MALDI-TOF) MS. The characterization of proteins/peptides of interest was obtained by high performance liquid chromatography-electrospray tandem MS.

RESULTS

Three peptides overexpressed in pPROM and able to discriminate the groups 1 and 2 were detected. One peptide was identified as the fragment Gly452LAVPDGPLGLPPKPro466 of the protein KIAA1522, expressed by fetal brain and liver. This peptide was overexpressed in a patient of the group 3, completely asymptomatic at the time of the amniocentesis, who later developed pPROM.

CONCLUSION

Amniotic fluid invasively and non-invasively collected can be analyzed by MALDI-TOF MS to obtain proteomic profiles. Proteomic analysis identified a peptide with promising diagnostic capability for pPROM.

Preliminary proteomic-based identification of a novel protein for Down's syndrome in maternal serum

Prenatal screening for Down's syndrome (DS) is in need of improvement. As a powerful platform, proteomics techniques could also be used for identification of new biomarkers for DS screening. In this case-control proteome study, pregnant women were diagnosed prenatally by karyotype analysis from amniotic fluid (AF). Maternal serum samples were collected from six pregnancies with fetuses affected by DS and six pregnancies with normal fetuses. First, we used two-dimensional electrophoresis and mass spectrometry to identify the different levels of expression of proteins in maternal serum between the DS and control groups in the second trimester. Second, we used bioinformatics to analyze the proteins by DAVID. Then, the interesting candidates were further tested by enzyme-linked immunosorbent assay (ELISA). Twenty-nine proteins were successfully identified in maternal serum obtained from pregnancies with fetuses affected by DS. The top five proteins up-regulated were serotransferrin (TF), alpha-1b-glycoprotein (A1BG), desmin (DES), alpha-1-antitrypsin (SERPINA1) and ceruloplasmin (CP), while serum amyloid P-component (APCS) was the most down-regulated protein. These 29 proteins were categorized based on binding, catalytic activity and enzyme regulator activity. The biological roles were involved in biological regulation, metabolic processes, cellular processes and response to a stimulus. Based on ELISA, the median concentrations of CP and complement factor B (CFB) were 332.3 and 412.3 ng/mL, respectively. The concentrations of CP and CFB were significantly higher in the DS group than in the control group ( P < 0.05). In conclusion, proteomic approaches offer the possibility of further improving the performance of DS screening and our identification of up- and down-regulated proteins may lead to new candidates for DS screening.

Proteomic analysis of amniotic fluid for the diagnosis of fetal aneuploidies

Advances in technologies associated with mass spectrometry-based proteomic techniques have added a new dimension to the field of biomedical research. Most of the existing research on human gestation has focused on the application of these high-throughput methodologies in the study of amniotic fluid. In cases of fetal aneuploidies, the use of proteomic platforms has contributed to the identification of relevant protein biomarkers that could potentially change early diagnosis and treatment. The current article focuses on studies of normal amniotic fluid using proteomic technologies and describes alterations noted in the amniotic fluid proteome in the presence of fetal aneuploidies.

Application of proteomics for the identification of biomarkers in amniotic fluid: are we ready to provide a reliable prediction?

Proteomics-based identification of biomarkers for fetal abnormalities and pregnancy complications in amniotic fluid (AF) has made significant progress in the past 5 years. This is attributed mainly to advances in mass spectrometry-based proteomic technologies that enable new strategies for discovering biomarkers from complex biological fluids in a high-throughput and sensitive manner. These markers, although they still need to be verified, are diagnostic and may in the future provide targets for therapeutic intervention. In the current review we focus on the emergence of proteomics as a major platform technology in studying AF and developing biomarkers for fetal aneuploidies and pregnancy-related disorders.

A rapid and sensitive prenatal diagnosis of familial amyloidotic polyneuropathy ATTR Val30Met by mass spectrometry

OBJECTIVE

To make a prenatal diagnosis of familial amyloidotic polyneuropathy (FAP) by mass spectrometry with the amniotic fluid.

METHODS

Amniotic-fluid samples of three non-FAP pregnant women and six amniotic-fluid samples of fetal mice whose mother was a heterozygotic FAP amyloidgenic transthyretin (ATTR) Val30Met gene carrier were collected. Electro spray ionization mass spectrometry (ESI-MS) was employed to identify and quantitatively measure the molecular weight of the human transthyretin (TTR) in the amniotic fluid.

RESULTS

TTR was detected in the amniotic fluid of all the human samples. In four of the six fetuses of the transgenic mice, human TTR Val30Met was detected. The other two samples showed only mouse TTR without human TTR Val30Met. DNA analysis revealed that the four fetuses were TTR Val30Met positive, but two were negative. The data from the DNA analysis and ESI-MS showed a 100% concordance.

CONCLUSION

Mass spectrometry analysis of the amniotic fluid might be a useful tool to make a prenatal diagnosis of FAP ATTR Val30Met.

Proteomic technologies for prenatal diagnostics: advances and challenges ahead

Proteomics-based identification of biomarkers for fetal abnormalities in maternal plasma, amniotic fluid and reproductive fluids has made significant progress in the past 5 years. This is attributed mainly to advances in various technology platforms associated with mass spectrometry-based techniques. As these techniques are highly sensitive and require only small quantities of body fluids, it is hoped that they will pave the way for the development of effective noninvasive approaches, without subjecting the developing fetus to the same degree of harm as current invasive procedures (e.g., amniocentesis). It is possible that these developments will include same-day analyses, thereby permitting rapid intervention when necessary. To date, a host of body fluids, such as maternal serum and plasma, amniotic fluid, cervical fluid, vaginal fluid, urine, saliva or fetal material, such as placental trophoblast, fetal membranes or cord blood, have been used successfully in the quest to develop markers for a number of pregnancy-related pathologies. In the current review update we focus on the emergence of proteomics as a major platform technology in studying various types of fetal conditions and developing markers for pregnancy-related disorders, such fetal aneuploidy, preterm birth, preeclampsia, intra-amniotic infection and fetal stress. Should the development of these markers be successful, then it is to be envisaged that proteomic approaches will become standard of care for a number of disease conditions associated with feto-maternal health.

Application of proteomics for diagnosis of fetal aneuploidies and pregnancy complications

Proteomic technologies represent new strategies towards high-throughput, simultaneous analysis of thousands of biological molecules leading to the discovery of biomarkers for early diagnosis, prognosis and prediction of pregnancy outcome. Proteomics have additional relevance in understanding pathophysiology and the development of molecularly targeted therapeutics. Comparison of normal human amniotic fluid proteome with that coming from pregnancies carrying fetuses with chromosomal abnormalities facilitated the detection of panels of potential biomarkers for prenatal detection of fetal aneuploidies. Candidate biomarkers for the early prediction of preeclampsis are also available, while four biomarkers (defensins-2 and -1, calgranulin-C, and calgranulin-A), which were called the "MR score", can quickly and accurately detect potentially dangerous infections and predict premature birth. Researchers remain hopeful that proteomic studies will allow for the identification of either one protein marker or of a panel of markers for prenatal detection of fetal aneuploidies and pregnancy complications that could be usefully employed for diagnostic purposes or improvement of the current screening methods. For maximum predictive power however, biomarkers should be selected for further comparative analysis of expression and structural modifications in large numbers of samples from chromosomally normal and abnormal pregnancies obtained from different populations.

Prenatal diagnosis: update on invasive versus noninvasive fetal diagnostic testing from maternal blood

The modern obstetrics care includes noninvasive prenatal diagnosis testing such as first trimester screening performed between 11 and 14 weeks' gestation and second trimester screening performed between 15 and 20 weeks. In these screening tests, biochemical markers are measured in the maternal blood with or without ultrasound for fetal nuchal translucency with reported accuracy of up to 90%. Invasive procedures, including amniocentesis or chorionic villi sampling, are used to achieve over 99% accuracy. During these procedures direct fetal material is examined and, therefore, these tests are highly accurate with the caveat of a small risk for pregnancy loss. Much research now focuses on other noninvasive highly accurate and risk-free tests that will identify fetal material in the maternal blood. Fetal cells and fetal DNA/RNA provide fetal information but are hard to find in an overwhelming background of maternal cells and in the absence of specific fetal cell markers. The most experience has been accumulated with fetal rhesus and fetal sex determination from maternal blood, with an accuracy of up to 100% by using gene sequences that are absent from maternal blood. Although not clinically applicable yet, fetal cells, fetal DNA/RNA and fetal proteomics in combination with cutting edge technology are described to prenatally diagnose aneuploidies and single-gene disorders.

Proteomic profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry

OBJECTIVE

Simultaneous analysis of the protein composition of biological fluids is now possible. Such an approach can be used to identify biological markers of disease and to understand the pathophysiology of disorders that have eluded classification, diagnosis, and treatment. The purpose of this study was to analyze the differences in protein composition of the amniotic fluid of patients in preterm labor.

STUDY DESIGN

Amniotic fluid was obtained by amniocentesis from three groups of women with preterm labor and intact membranes: (1) women without intra-amniotic infection/inflammation (IAI) who delivered at term, (2) women without IAI who delivered a preterm neonate, and (3) women with IAI. Intra-amniotic infection was defined as a positive amniotic fluid culture for microorganisms. Intra-amniotic inflammation was defined as an elevated amniotic fluid interleukin (IL)-6 (> or =2.3 ng/mL). Two-dimensional (2D) chromatography was used for analysis. The first dimension separated proteins by isoelectric point, while the second, by the degree of hydrophobicity. 2D protein maps were generated using different experimental conditions (reducing agents as well as protein concentration). The maps were used to discern subsets of isoelectric point/hydrophobicity containing differentially expressed proteins. Protein identification of differentially expressed fractions was conducted with mass spectrometry. Enzyme-linked immunosorbent assays (ELISA) as well as surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS)-based on-chip antibody capture immunoassays were also used for confirmation of a specific protein that was differentially expressed.

RESULTS

(1) Amniotic fluid protein composition can be analyzed using a combination of 2D liquid chromatography and mass spectrometry for the identification of proteins differentially expressed in patients in preterm labor. (2) While total insulin-like growth factor-binding protein-1 (IGFBP-1) concentration did not change, IGFBP-1 fragments at about 13.5 kDa were present in patients with IAI. (3) Proteins that were over-expressed in group 1 included von Ebner gland protein precursor, IL-7 precursor, apolipoprotein A1, tropomyosin sk1 (TPMsk1) fragment, ribosomal protein S6 kinase alpha-3, and alpha-1-microglobulin/bikunin precursor (AMBP). (4) Proteins that were over-expressed in group 3 included fibrinopeptide B, transferrin, major histocompatibility complex (MHC) class 1 chain-related A antigen fragment, transcription elongation factor A, sex-determining region Y (SRY) box 5 protein, Down syndrome critical region 2 protein (DSCR2), and human peptide 8 (HP8). (5) One protein, retinol-binding protein, was over-expressed in women who delivered preterm, regardless of the presence of IAI.

CONCLUSIONS

A combination of techniques involving 2D chromatography, mass spectrometry, and immunoassays allows identification of proteins that are differentially regulated in the amniotic fluid of patients with preterm labor. Specifically, the amount of the IGFBP-1 fragments at approximately 13.5 kDa was found to be increased in patients with IAI, while the amount of the intact form of IGFBP-1 was decreased.

Mass spectrometry-based proteomics in reproductive medicine

The emergence of powerful mass spectrometry-based proteomic techniques has added a new dimension to the field of biomedical research. Application of these high throughput methodologies in pregnancy-related pathology has contributed to the comprehension of the underlying pathophysiologies and the successful identification of relevant protein biomarkers that can potentially change early diagnosis and treatment of several medical conditions related to human pregnancy. Most of the existing research on human reproduction and gestation has focused on follicular fluid, cervical/vaginal fluid, and amniotic fluid. Although proteome technologies in reproductive medicine research are not as yet widely applied, characterization of the proteome of reproductive fluids can be expected to significantly improve maternal healthcare. This article aims to summarize the applications of mass spectrometry based technology on the most important and specific biological fluids related to reproduction and gestation.

Post-genomics studies and their application to non-invasive prenatal diagnosis

Non-invasive prenatal diagnosis (NIPD) offers the opportunity to eliminate completely the risky procedures of amniocentesis and chorionic villus sampling. The development of NIPD tests has largely centred around the isolation and analysis of fetal cells in the maternal circulation and the analysis of free fetal DNA in maternal plasma. Both of these techniques offer difficult technical challenges, and at the current moment in time the use of free fetal DNA is the simplest and most effective method of defining paternally inherited fetal genes for diagnosis. Post-genomics technologies that explore the proteins (proteomics) and transcripts (transcriptomics) released by the placenta into the maternal circulation offer new opportunities to identify genes and their protein products that are key diagnostic markers of disease (in particular Down syndrome), and might replace the current screening markers in use for prediction of risk of Down syndrome. In the ideal situation, these markers are sufficiently diagnostic not to require invasive sampling of fetal genetic material. Post-genomics techniques might also offer better opportunities for defining fetal cell-specific markers that might enhance their isolation from maternal blood samples. This review describes progress in these studies, particularly those funded by the Special Non-invasive Advances in Fetal and Neonatal Evaluation (SAFE) Network of Excellence.

Proteomic profile determination of autosomal aneuploidies by mass spectrometry on amniotic fluids

BACKGROUND

Prenatal diagnosis of chromosomal abnormalities by cytogenetic analysis is time-consuming, expensive, and requires highly qualified technicians. Rapid diagnosis of aneuploidies followed by reassurance of women with normal results can be performed by molecular analysis of uncultured foetal cells. In the present study, we developed a proteomic fingerprinting approach coupled with a statistical classification method to improve diagnosis of aneuploidies, including trisomies 13, 18, and 21, in amniotic fluid samples.

RESULTS

The proteomic spectra obtained from 52 pregnant women were compiled, normalized, and mass peaks with mass-to-charge ratios between 2.5 and 50 kDa identified. Peak information was combined together and analysed using univariate statistics. Among the 208 expressed protein peaks, 40 differed significantly between aneuploid and non aneuploid samples, with AUC diagnostic values ranging from 0.71 to 0.91. Hierarchical clustering, principal component analysis and support vector machine (SVM) analysis were performed. Two class predictor models were defined from the training set, which resulted in a prediction accuracy of 92.3% and 96.43%, respectively. Using an external and independent validation set, diagnostic accuracies were maintained at 87.5% and 91.67%, respectively.

CONCLUSION

This pilot study demonstrates the potential interest of protein expression signature in the identification of new potential biological markers that might be helpful for the rapid clinical management of high-risk pregnancies.

Overview and introduction to clinical proteomics

As the field of clinical proteomics progresses, discovery of disease biomarkers becomes paramount. However, the immediate challenges are to establish standard operating procedures for both clinical specimen handling and reduction of sample complexity and to increase the ability to detect proteins and peptides present in low amounts. The traditional concept of a disease biomarker is shifting toward a new paradigm, namely, that an ensemble of proteins or peptides would be more efficient than a single protein/peptide in the diagnosis of disease. Because clinical proteomics usually requires easy access to well-defined fresh clinical specimens (including morphologically consistent tissue and properly pretreated body fluids of sufficient quantity), biorepository systems need to be established. Here, we address these questions and emphasize the necessity of developing various microdissection techniques for tissue specimens, multidimensional fractionation for body fluids, and other related techniques (including bioinformatics), tools which could become integral parts of clinical proteomics for disease biomarker discovery.

Bioinformatics approaches in clinical proteomics

Protein expression profiling is increasingly being used to discover, validate and characterize biomarkers that can potentially be used for diagnostic purposes and to aid in pharmaceutical development. Correct analysis of data obtained from these experiments requires an understanding of the underlying analytic procedures used to obtain the data, statistical principles underlying high-dimensional data and clinical statistical tools used to determine the utility of the interpreted data. This review summarizes each of these steps, with the goal of providing the nonstatistician proteomics researcher with a working understanding of the various approaches that may be used by statisticians. Emphasis is placed on the process of mining high-dimensional data to identify a specific set of biomarkers that may be used in a diagnostic or other assay setting.

Human body fluid proteome analysis

The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.

Proteomic analysis of amniotic fluid in pregnancies with Down syndrome

Proteomic analysis is widely used for the detection of diagnostic markers. In the present study amniotic fluid supernatants (AFS) from pregnancies with Down syndrome (DS) fetuses and from chromosomally normal fetuses in the 17th week of gestation were analyzed by 2-DE. Gel comparison revealed significant differences in the two groups. Spots with different expression levels were excised and proteins were identified by MALDI-MS and nano-ESI-MS/MS. Splicing factor arginine/serine-rich 4 (SFRS4; Q08170) was present only in AFS from DS fetuses and completely absent in the control group. Quantitative differences were detected for alpha-1-microglobulin (AMBP; P02760), collagen alpha 1 (I) chain (CO1A1; P02452), collagen alpha 1 (III) chain (CO3A1; P02461), collagen alpha 1 (V) chain d (CO5A1; P20908), and basement membrane-specific heparin sulfate proteoglycan core protein (PGBM; P98160). These proteins were increased in cases with DS, whereas protein IBP-1 (P08833) was decreased by 40% compared with chromosomally normal fetuses. Four proteins, CO1A1, CO3A1, CO5A1, and PGBM, appeared as fragments. As differentially expressed proteins were present in all pregnancies with DS tested, they may represent useful potential markers for prenatal diagnosis. However, for protein biomarkers to be of any clinical utility, systematic analysis of the maternal serum should be conducted.

Proteomics, Part II: The Emerging Role of Proteomics Over Genomics in Spontaneous Preterm Labor/Birth

Conventional wisdom holds that complications of immature organ systems such as respiratory distress syndrome, intraventricular hemorrhage, necrotizing enterocolitis, and bronchopulmonary dysplasia are the primary causes of the high neonatal morbidity and mortality attendant preterm delivery. However, recent evidence suggests that a major cause of prematurity-associated neonatal pathology is the fetal and neonatal response to inflammation/infection. Although functional genomics offered the promise of providing answers to many of these questions, the identification of the genes intrinsic to human parturition proved to be a difficult task. Proteomic profiling of the amniotic fluid (AF) provides a precise means for detection of inflammation by revealing the presence of 4 biomarkers (defensins-2 and -1, calgranulin-C, and calgranulin-A) that are highly predictive of intrauterine inflammation (MR score). The MR score is especially useful as it presents a gradient of disease activity progressing from "absent" to "mild" to "severe" inflammation. Thus, it provides the ability to identify patients who may benefit from interventions in utero in a modern diagnostic-therapeutic framework.

TARGET AUDIENCE

Obstetricians & Gynecologists, Family Physicians.

LEARNING OBJECTIVES

After completion of this article, the reader should be able to explain that the cause or causes of preterm delivery are still unknown, recall that functional genomics has not given the answer to these causes, and state that proteomic profiling of amniotic fluid, through mass-restricted (MR) scoring, may be predictive of intrauterine inflammation and allow for potential diagnosis and potential therapy.