Use Of Microarray Analysis Research Articles

Fetal reduction for everyone?

Infertility treatments have benefited millions of couples to have their own children; however, the complication of multiple pregnancies with their increased morbidity and mortality has created significant problems. Fetal reduction (FR) was developed to ameliorate these issues. Over 30 years of publications show that FR has been highly successful in substantially reducing both mortality and morbidity. As with most radically new techniques, initial cases were in the "nothing to lose" category. With experience, indications liberalize, and quality of life issues increase as a proportion of cases. Overall risks for twins are not twice as those for singletons, but they are approximately 4- to 5-fold higher. In experienced hands, the combination of genetic testing by CVS followed by FR has made most multiples behave statistically as if they were originally the lower number. The use of microarray analysis to better determine fetal genetic health before deciding on which fetus(es) to keep or reduce further improves pediatric outcomes. With increasing experience and lower average starting numbers, the proportion of FRs to a singleton has increased considerably. Twins to a singleton FR now constitute an increasing proportion of cases performed. Data on such cases show improved outcomes, and we believe FR should be at least discussed and offered to all patients with a dichorionic twin pregnancy or higher. eSET is not a panacea because of the resultant monochorionic twins.

VP06.12: The use of microarray analysis for prenatal diagnosis in King Faisal Specialist Hospital

VP06.12: The use of microarray analysis for prenatal diagnosis in King Faisal Specialist Hospital

Chromosomal microarray analysis in the investigation of prenatally diagnosed congenital heart disease

Chromosomal microarray analysis has emerged as a primary diagnostic tool in prenatally diagnosed congenital heart disease and other structural anomalies in clinical practice. Our study aimed to investigate the diagnostic yield of microarray analysis as a first-tier test for chromosomal abnormalities in fetuses with both isolated and nonisolated congenital heart disease and to identify the association of different pathogenic chromosomal abnormalities with different subgroups of congenital heart disease. Retrospective data from 217 pregnancies that were diagnosed with congenital heart disease between 2011 and 2016 were reviewed. All pregnancies were investigated with the use of microarray analysis during the study period. Classification of chromosomal abnormalities was done based on American College of Medical Genetics and Genomics guidelines into (1) pathogenic chromosomal abnormalities that included numeric chromosomal abnormalities (aneuploidy and partial aneuploidy) and pathogenic copy number variants (22q11.2 deletion and other microdeletions/microduplications), (2) variants of uncertain significance, and (3) normal findings. Our study found a detection rate for pathogenic chromosomal abnormalities (numeric and pathogenic copy number variants) of 36.9% in pregnancies (n=80) that were diagnosed prenatally with congenital heart disease who underwent invasive testing with chromosomal microarray. The detection rate for numeric abnormalities was 29.5% (n=64) and for pathogenic copy number variants was 7.4% (n=16) of which 4.2% were 22q11.2 deletion and 3.2% were other pathogenic copy number variants, most of which theoretically could have been missed by the use of conventional karyotype alone. Pathogenic copy number variants were most common in conotruncal defects (19.6%; 11/56) that included 42.9% in cases of interrupted aortic arch, 23.8% in cases of tetralogy of Fallot, 13.3% in cases of transposition of the great arteries, and 8.3% in cases of double outlet right ventricle. Of these changes, 81.8% were 22q11.2 deletion, and 18.2% were other microdeletions/microduplications. After conotruncal defects, pathogenic copy number variants were most common in right ventricular outflow tract and left ventricular outflow tract groups (8% and 2.2%, respectively) in which none were 22q11.2 deletion. Pathogenic chromosomal abnormalities (numeric and pathogenic copy number variants) detected by chromosomal microarray analysis were significantly more common in the nonisolated congenital heart disease group (64.5%; n=49) compared with the isolated group (22%; n=31; P<.001). In pregnancies that were diagnosed with congenital heart disease and had undergone diagnostic genetic testing, our study showed that chromosomal microarray analysis has an added value in the detection of pathogenic chromosomal abnormalities compared with conventional karyotype, particularly in cases of pathogenic copy number variants. This yield is influenced not only by the type of congenital heart disease but also by the presence of extracardiac anomalies.

Genes regulating programmed cell death are significantly upregulated in porcine immature oocytes

Abstract Correct maturation of the oocyte is crucial for further fertilization and embryogenesis. It comprises of both nuclear and cytoplasmic maturation, during which the proteins, nutrients and mRNAs are assembled. Cumulus cells are connected with the oocyte via gap-junctions, which enable bi-directional transfer of molecules, forming cumulus-oocyte complex (COC). The expression pattern in CCs is thought to resemble the genes expressed in the oocyte. The CCs surrounding the gamete of high developmental competence have an increased expression of apoptotic markers. Therefore, our aim in this study was to determine whether any apoptosis-related genes are upregulated in porcine oocytes before or after IVM. We isolated COCs from 45 pubertal crossbred gilts, performed brilliant cresyl blue (BCB) staining and analyzed the gene expression pattern in oocytes before and after IVM with the use of microarray analysis. The results include 419 differentially expressed transcripts, 25 of which belong to „regulation of apoptosis” and „regulation of cell death” GO BP terms. This set of genes includes BCLAF1, EIF2AK3, KLF10, MIF, MAP3K1, NOTCH2, TXNIP and APP, all of which have been upregulated in immature porcine oocytes. Our results suggest that they play part in porcine oocyte maturation and could be used as potential markers of female gamete’s developmental competence. This knowledge could serve as a basis to improve ART in pigs.

Axenfeld‐Rieger syndrome: Further clinical and array delineation of four unrelated patients with a 4q25 microdeletion

Axenfeld-Rieger syndrome (ARS) is an autosomal dominant disorder with variable expressivity. It is characterized by dysgenesis of the anterior segment of the eye together with dental, cardiac, and umbilical anomalies. There is a high incidence of secondary high tension glaucoma. It is a genetically heterogeneous condition due to deletion or mutations of FOXC1 (6p25) or PITX2 (4q25). We report on four unrelated patients with overlapping microdeletions encompassing PITX2 at 4q25. We compare the genotypes and phenotypes of these newly described ARS patients and discuss the involvement of contiguous genes. Patients 1, 2, and 3 had mild learning difficulties, not typically seen in patients with ARS. We implicate the adjacent neuronally expressed genes; NEUROG2, UGT8, NDST3, and PRSS12 as potentially causal. Our findings support the use of microarray analysis in ARS patients for full prognostic information in infants presenting with ARS-like phenotypes.

A biological study of differentiation and hypertrophy of chondrocytes in human cervical OPLL with the use of microarray analysis

A biological study of differentiation and hypertrophy of chondrocytes in human cervical OPLL with the use of microarray analysis

FlyPrimerBank: An Online Database for Drosophila melanogaster Gene Expression Analysis and Knockdown Evaluation of RNAi Reagents

The evaluation of specific endogenous transcript levels is important for understanding transcriptional regulation. More specifically, it is useful for independent confirmation of results obtained by the use of microarray analysis or RNA-seq and for evaluating RNA interference (RNAi)-mediated gene knockdown. Designing specific and effective primers for high-quality, moderate-throughput evaluation of transcript levels, i.e., quantitative, real-time PCR (qPCR), is nontrivial. To meet community needs, predefined qPCR primer pairs for mammalian genes have been designed and sequences made available, e.g., via PrimerBank. In this work, we adapted and refined the algorithms used for the mammalian PrimerBank to design 45,417 primer pairs for 13,860 Drosophila melanogaster genes, with three or more primer pairs per gene. We experimentally validated primer pairs for ~300 randomly selected genes expressed in early Drosophila embryos, using SYBR Green-based qPCR and sequence analysis of products derived from conventional PCR. All relevant information, including primer sequences, isoform specificity, spatial transcript targeting, and any available validation results and/or user feedback, is available from an online database (www.flyrnai.org/flyprimerbank). At FlyPrimerBank, researchers can retrieve primer information for fly genes either one gene at a time or in batch mode. Importantly, we included the overlap of each predicted amplified sequence with RNAi reagents from several public resources, making it possible for researchers to choose primers suitable for knockdown evaluation of RNAi reagents (i.e., to avoid amplification of the RNAi reagent itself). We demonstrate the utility of this resource for validation of RNAi reagents in vivo.

Age related changes in gene expression within the cochlea of C57BL/6J mice.

Hearing loss as a unique symptom is highly prevalent in the elderly and while there exists several pathologies that would result in age related hearing loss (ARHL), most agree it is multifactorial with environmental, metabolic and genetic components. However, no research to date has discovered a definitive genetic cause. This paper describes the use of microarray to address this issue. The left cochlea of laboratory aged C57BL6J mice at 4, 15 and 45 weeks was extracted from pooled, agematched animals and the RNA extracted for use in microarray analysis. The contralateral cochlea was also removed and used for immunohistochemical analysis. Microarray revealed 116 genes to be up or down regulated between young and old animals, the most prominent being prolactin (108.2 fold increase) and growth hormone (43.94 fold increase). The prolactin inhibitor calcitonin was also down regulated over 2 fold. Immunohistochemistry revealed prolactin to be weakly expressed within the spiral ganglion, whilst its receptor was widely distributed throughout the cochlea. This is the first study demonstrating the cochlea as a site for extrapituitary prolactin expression and that this expression is related to age. Combined with the widespread distribution of prolactin receptor, there may be implications for prolactin's role in ARHL.

Immunological Tolerance Monitoring in Solid Organ Transplantation

In organ transplantation, achieving an operational tolerance is the ultimate goal. However, inducing this tolerance with a minimal dose of anti-rejection drugs can only be safely achieved when guided by biomarkers reflecting the immune reactivity in patients. We review recently described biomarkers and assays for the identification of patients for their risk of organ rejection and their suitability for drug weaning. The clinical assessment of tolerance has been attempted with immunological tools, including the analysis of immune cell subsets, regulatory T cells, ELISPOT, and trans-vivo delayed-type hypersensitivity assays. These methods are promising tools for diagnosis; however, their ability to determine the presence and persistence of responsiveness to their transplant is not available. As the omics technologies advance, comprehensive and high-throughput biomarker studies have become more accessible, more affordable, and more customizable. Validating the use of microarray analysis has important implications for monitoring patients for the development of tolerance following transplantation as well as for determining the mechanisms by which tolerance is induced and maintained. Finally, collaborative efforts are needed to design and perform prospective multicenter trials to validate the identified biomarkers across different laboratories.

Mismatch between transcriptomic and histopathologic picture of canine lymphomas

Lymphoma is one of the most common malignant tumours occurring in dogs. Since there is a constant need for new, more comprehensive laboratory diagnostic tools which permit the precise determination of many tumour-related factors we decided to verify whether the use of microarray analysis could be helpful in classifying lymphomas. The study was performed on samples collected from 7 dogs in which multicentric lymphoma was recognized. Among this group we were able to identify one sub-cluster of transcriptionally similar tumours, which completely differed in terms of the histopathological examination. Among them there were one diffuse large B cell lymphoma, one diffuse macronucleolated medium-sized cell lymphoma and one pleomorphic mixed small and large T-cell lymphoma. The lymphomas belonging to the sub-cluster differed from other analysed tumours in the expression of more than 100 genes of which only 18 were described earlier in regard to lymphomas.

Genomic disorders on chromosome 22

Chromosome 22, the first human chromosome to be completely sequenced, is prone to genomic alterations. Copy-number variants (CNVs) are common because of an enrichment of low-copy repeat sequences that precipitate a high frequency of nonallelic homologous misalignments and unequal recombination during meiosis. Among these is one of the most common multiple anomaly syndromes in humans and the most common microdeletion syndrome, velocardiofacial syndrome (VCFS), also known as 22q11.2 deletion syndrome and DiGeorge syndrome. This review will focus on the recent literature dealing with both the molecular and clinical aspects of chromosome 22 genomic variations. Although the literature covering this area is expansive, the majority is descriptive or analytical of the problems presented by these genomic disorders, and there is little evidence of translational research including treatment outcomes. With the increased use of microarray analysis in both research and clinical practice, variations in CNVs are becoming elucidated. Genomic analysis continues to characterize genes and gene effect. Research on the COMT gene continues to yield interesting findings, including a possible sex-mediated effect because of its regulatory role with estrogen. There is a small amount of treatment outcome data relevant to neuropsychiatric disorders in VCFS, but based on small samples and short-term follow-up. Although hundreds of studies in the past year have focused on genomic disorders of chromosome 22, little progress has been made in the implementation of translational research, even for more common disorders including VCFS.

Molecular profiling of synovial joints: Use of microarray analysis to identify factors that direct the development of the knee and elbow

Synovial joints develop from the interzone, a dense layer of mesenchymal progenitor cells that marks the site of the future joint. During the morphogenic events that follow, joints attain their distinct shape and organization. The molecular mechanisms controlling the initial specification of synovial joints has been studied, but the question of how individual joints attain the specific structure required for their unique functions remains largely unresolved. Here, we use microarray analysis to compare knee and elbow formation to identify factors involved in the development of specific joints. The knee is enriched for the hindlimb patterning genes Hoxc9, Hoxc10, and Tbx4 and for Tgfbi, Rspo2, and Sfrp2, factors involved in transforming growth factor-beta/bone morphogenetic protein (TGFβ/BMP) and Wnt signaling. Consistent with these findings, we show that TGFβ signaling directs knee morphogenesis, and is necessary for meniscus development. The tissue surrounding the elbow is highly enriched for genes involved in muscle specification and differentiation, and in splotch-delayed muscleless mutants, elbow, but not knee morphogenesis is disrupted. Our results suggest there are fundamental differences in how individual joints develop after interzone formation. Our microarray analyses provides a new resource for further investigation of the pathways involved in the morphogenesis of specific synovial joints.

Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos

BackgroundIn the field of mouse genetics the advent of technologies like microarray based expression profiling dramatically increased data availability and sensitivity, yet these advanced methods are often vulnerable to the unavoidable heterogeneity of in vivo material and might therefore reflect differentially expressed genes between mouse strains of no relevance to a targeted experiment. The aim of this study was not to elaborate on the usefulness of microarray analysis in general, but to expand our knowledge regarding this potential “background noise” for the widely used Illumina microarray platform surpassing existing data which focused primarily on the adult sensory and nervous system, by analyzing patterns of gene expression at different embryonic stages using wild type strains and modern transgenic models of often non-isogenic backgrounds.ResultsWild type embryos of 11 mouse strains commonly used in transgenic and molecular genetic studies at three developmental time points were subjected to Illumina microarray expression profiling in a strain-by-strain comparison. Our data robustly reflects known gene expression patterns during mid-gestation development. Decreasing diversity of the input tissue and/or increasing strain diversity raised the sensitivity of the array towards the genetic background. Consistent strain sensitivity of some probes was attributed to genetic polymorphisms or probe design related artifacts.ConclusionOur study provides an extensive reference list of gene expression profiling background noise of value to anyone in the field of developmental biology and transgenic research performing microarray expression profiling with the widely used Illumina microarray platform. Probes identified as strain specific background noise further allow for microarray expression profiling on its own to be a valuable tool for establishing genealogies of mouse inbred strains.

Prenatal genetic diagnosis using microarray analysis in fetuses with congenital heart defects

To evaluate the use of microarray analysis as a tool for the detection of submicroscopic chromosomal aberrations in prenatal diagnosis. Twelve consecutive singleton fetuses with congenital heart defects but normal karyotype and normal fluorescence in situ hybridization results for the DiGeorge region were examined for chromosomal aberrations by genomic microarray analysis. Results were confirmed by fluorescence in situ hybridization and quantitative real time-polymerase chain reaction. At 1 Mb resolution, potentially causal copy number variations were identified in 3 out of 12 fetuses (25%) comprising a 9 Mb q terminal deletion on chromosome 15, a 3.5 Mb duplication in the critical region for the Potocki-Lupski syndrome on chromosome 17 and a mosaic trisomy 7. At higher resolution, aberrations with uncertain significance were identified in a further three cases (25%). In our study, the application of microarray analysis in prenatal testing proved to be a valuable tool for the identification of submicroscopic chromosomal aberrations where conventional cytogenetic methods failed. Selection of appropriate resolution was found to be critical to obtain reliable, diagnostically conclusive data.

HHGF Overexpression in Myoblast Sheets Enhances Their Angiogenic Potential in Rat Chronic Heart Failure

After severe myocardial infarction (MI), heart failure results from ischemia, fibrosis, and remodeling. A promising therapy to enhance cardiac function and induce therapeutic angiogenesis via a paracrine mechanism in MI is myoblast sheet transplantation. We hypothesized that in a rat model of MI-induced chronic heart failure, this therapy could be further improved by overexpression of the antiapoptotic, antifibrotic, and proangiogenic hepatocyte growth factor (HGF) in the myoblast sheets. We studied the ability of wild type (L6-WT) and human HGF-expressing (L6-HGF) L6 myoblast sheet-derived paracrine factors to stimulate cardiomyocyte, endothelial cell, or smooth muscle cell migration in culture. Further, we studied the autocrine effect of hHGF-expression on myoblast gene expression profiles by use of microarray analysis. We induced MI in Wistar rats by left anterior descending coronary artery (LAD) ligation and allowed heart failure to develop for 4 weeks. Thereafter, we administered L6-WT (n = 15) or L6-HGF (n = 16) myoblast sheet therapy. Control rats (n = 13) underwent LAD ligation and rethoracotomy without therapy, and five rats underwent a sham operation in both surgeries. We evaluated cardiac function with echocardiography at 2 and 4 weeks after therapy, and analyzed cardiac angiogenesis and left ventricular architecture from histological sections at 4 weeks. Paracrine mediators from L6-HGF myoblast sheets effectively induced migration of cardiac endothelial and smooth muscle cells but not cardiomyocytes. Microarray data revealed that hHGF-expression modulated myoblast gene expression. In vivo, L6-HGF sheet therapy effectively stimulated angiogenesis in the infarcted and non-infarcted areas. Both L6-WT and L6-HGF therapies enhanced cardiac function and inhibited remodeling in a similar fashion. In conclusion, L6-HGF therapy effectively induced angiogenesis in the chronically failing heart. Cardiac function, however, was not further enhanced by hHGF expression.

Evolving applications of microarray analysis in prenatal diagnosis

Evaluation of copy number variation by microarray analysis has significant advantages over standard metaphase karyotyping and is quickly becoming the primary means of postnatal genetic evaluation for neonates and infants with dysmorphic features or cognitive difficulties. Before this technology is routinely used for prenatal diagnosis, further evaluation of its value and the clinical dilemmas it may introduce requires further study. This article reviews the recent literature on array technology use in prenatal diagnosis. The use of microarray analysis for routine prenatal diagnosis is still being investigated. Use in certain prenatal situations such as the fetus with structural anomalies or those who are stillborn appears to add important, clinically relevant information. There are a broad range of array designs available and recent research has focused on the appropriate design for prenatal testing. Patient counseling may occasionally be difficult because of the uncertain phenotype associated with some array findings. We present a brief overview of microarray technology including benefits and limitations. Previous research regarding use of microarray in prenatal diagnosis including specific scenarios of anomalous fetuses and abnormal karyotype is reviewed. Current guidelines and the authors' recommendations are presented.

STAT1 Is a Master Regulator of Pancreatic β-Cell Apoptosis and Islet Inflammation

Cytokines produced by islet-infiltrating immune cells induce β-cell apoptosis in type 1 diabetes. The IFN-γ-regulated transcription factors STAT1/IRF-1 have apparently divergent effects on β-cells. Thus, STAT1 promotes apoptosis and inflammation, whereas IRF-1 down-regulates inflammatory mediators. To understand the molecular basis for these differential outcomes within a single signal transduction pathway, we presently characterized the gene networks regulated by STAT1 and IRF-1 in β-cells. This was done by using siRNA approaches coupled to microarray analysis of insulin-producing cells exposed or not to IL-1β and IFN-γ. Relevant microarray findings were further studied in INS-1E cells and primary rat β-cells. STAT1, but not IRF-1, mediates the cytokine-induced loss of the differentiated β-cell phenotype, as indicated by decreased insulin, Pdx1, MafA, and Glut2. Furthermore, STAT1 regulates cytokine-induced apoptosis via up-regulation of the proapoptotic protein DP5. STAT1 and IRF-1 have opposite effects on cytokine-induced chemokine production, with IRF-1 exerting negative feedback inhibition on STAT1 and downstream chemokine expression. The present study elucidates the transcriptional networks through which the IFN-γ/STAT1/IRF-1 axis controls β-cell function/differentiation, demise, and islet inflammation.

Inflammation and Innate Immune Response Against Viral Infections in Marine Fish

Viral infections in fish are common in both natural and cultured fish populations and the spread of infectious disease is a serious threat to both natural ecosystems and commercial exploitations. A significant body of studies have addressed the host response to viral infection including the efficacy of DNA vaccines however we still have a fragmented vision of both pathologies associated with viral infection and the immune response to those across fish species. Many studies have concentrated upon freshwater fish including the zebrafish (Danio rerio) and the Rainbow trout (Oncorhynchus mykiss) whereas the majority of marine fish studies address the Atlantic salmon (Salmo salar). Here we provide a comprehensive review concentrating upon the salient pathological features of the most common viral infections including examples of the Betanodaviruses, Birnaviruses, Rhabdoviruses and the Isavirus in cultured fish with emphasis where possible upon non-salmonid cold water adapted marine species. In parallel we review the current state of the art mainly in reference to gene expression studies describing the host innate immune response concentrating upon the inflammatory response and its relationship toward anti-viral immunity in fish. Due to the complexity of the observed responses and the limitations of candidate gene expression studies to describe global biological processes, recent efforts in the use of microarray analysis for the study of the anti-viral response have been highlighted including members of the Pleuronectiform and the Perciform families. Finally we review the potential of the zebrafish to become a significant biological model in the elucidation of the molecular mechanisms underlying the piscine immune response to viral infection.

Is Gene Expression Profiling of Head and Neck Cancers Ready for the Clinic?

One of the major challenges in the head and neck oncology clinic is the need to identify biomarkers and/or gene expression signatures that complement, strengthen and increase the sensitivity and specificity of the current clinicopathologic analyses. Microarray analysis of head and neck tumors has demonstrated that the combined influence of many genes or biomarkers can make superior identifiers and/or predictors of tumor behavior and patient outcome. Here, an update of the recent literature on the prognostic and predictive value of microarrays for patients with head and neck squamous cell carcinomas is presented. Microarray technology has the potential for improved decision-making and corroboration within the clinical setting. However, further integration, standardization, validation and research are required before the use of microarray analysis is ready for routine clinical management of head and neck squamous cell carcinomas.

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