Near-Infrared Spectroscopy for Prediction of Extubation Success after Neonatal Cardiac Surgery

Introduction: Reliable predictors of extubation readiness are needed and may reduce morbidity related to extubation failure. We aimed to examine the relationship between changes in pre-extubation near-infrared spectroscopy measurements from baseline and extubation outcomes after neonatal cardiac surgery. Materials and Methods: In this retrospective cross-sectional multi-centre study, a secondary analysis of prospectively collected data from neonates who underwent cardiac surgery at seven tertiary-care children’s hospitals in 2015 was performed. Extubation failure was defined as need for re-intubation within 72 hours of the first planned extubation attempt. Near-infrared spectroscopy measurements obtained before surgery and before extubation in patients who failed extubation were compared to those of patients who extubated successfully using t-tests. Results: Near-infrared spectroscopy measurements were available for 159 neonates, including 52 with single ventricle physiology. Median age at surgery was 6 days (range: 1–29 days). A total of 15 patients (9.4 %) failed extubation. Baseline cerebral and renal near-infrared spectroscopy measurements were not statistically different between those who were successfully extubated and those who failed, but pre-extubation cerebral and renal values were significantly higher in neonates who extubated successfully. An increase from baseline to time of extubation values in cerebral oximetry saturation by ≥ 5 % had a positive predictive value for extubation success of 98.6 % (95%CI: 91.1–99.8 %). Conclusion: Pre-extubation cerebral near-infrared spectroscopy measurements, when compared to baseline, were significantly associated with extubation outcomes. These findings demonstrate the potential of this tool as a valuable adjunct in assessing extubation readiness after paediatric cardiac surgery and warrant further evaluation in a larger prospective study

Utilization of inhaled nitric oxide after surgical repair of truncus arteriosus: A multicenter analysis

BackgroundElevated pulmonary vascular resistance (PVR) is common following repair of truncus arteriosus. Inhaled nitric oxide (iNO) is an effective yet costly therapy that is frequently implemented postoperatively to manage elevated PVR.ObjectivesWe aimed to describe practice patterns of iNO use in a multicenter cohort of patients who underwent repair of truncus arteriosus, a lesion in which recovery is often complicated by elevated PVR. We also sought to identify patient and center factors that were more commonly associated with the use of iNO in the postoperative period.DesignRetrospective cohort study.Setting15 tertiary care pediatric referral centers.PatientsAll infants who underwent definitive repair of truncus arteriosus without aortic arch obstruction between 2009 and 2016.InterventionsDescriptive statistics were used to demonstrate practice patterns of iNO use. Bivariate comparisons of characteristics of patients who did and did not receive iNO were performed, followed by multivariable mixed logistic regression analysis using backward elimination to identify independent predictors of iNO use.Main ResultsWe reviewed 216 patients who met inclusion criteria, of which 102 (46%) received iNO in the postoperative period: 69 (68%) had iNO started in the operating room and 33 (32%) had iNO initiated in the ICU. Median duration of iNO use was 4 days (range: 1‐21 days). In multivariable mixed logistic regression analysis, use of deep hypothermic circulatory arrest (odds ratio: 3.2; 95% confidence interval: 1.2, 8.4) and center (analyzed as a random effect, p = .02) were independently associated with iNO use.ConclusionsIn this contemporary multicenter study, nearly half of patients who underwent repair of truncus arteriosus received iNO postoperatively. Use of iNO was more dependent on individual center practice rather than patient characteristics. The study suggests a need for collaborative quality initiatives to determine optimal criteria for utilization of this important but expensive therapy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152533/1/chd12849_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152533/2/chd12849.pd

Insertion-deletions burden in copy number polymorphisms of the Tibetan population

BACKGROUND: Many studies have been conducted to identify either insertions-deletions (inDels) or copy number variations (CNVs) in humans, but few studies have been conducted to identify both of these forms coexisting in the same region. AIMS AND OBJECTIVES: To map the functionally significant sites within human genes that are likely to influence human traits and diseases. MATERIALS AND METHODS: In this report, we describe an inDel map in the 1051 Tibetan CNV regions obtained through CNV genotyping using Affymetrix Genome-wide single nucleotide polymorphism 6.0 chip. InDel polymorphisms in these copy number polymorphism regions were identified with a computational approach using the 2500 deoxyribonucleic acid sequences obtained from the 1000 Genome Project. RESULTS: The study identified a total of 95935 inDels that range from 1 bp to several bps in length which were found scattered across regulatory regions, exons and in introns of genes underlying the CNVs. A study on the distribution of inDels revealed that the majority of inDels were found in coding regions of the genome than the noncoding, while within the genes, inDels in intron regions were more followed by exonic regions and finally the regulatory regions. CONCLUSION: Study of inDels in CNV regions contribute to the enhanced understanding of the role played by the two variations and their collective influence on the genome. Further, a collection of these inDel genetic markers will aid in genetic mapping, further understanding of the phenotypic variability, identification of disease genes and in detecting novel CNVs

Astaxanthin and DHA supplementation ameliorates the proteomic profile of perinatal undernutrition-induced adipose tissue dysfunction in adult life

Abstract Maternal diet is an essential factor that directly and indirectly regulates fetal growth. Exposure to certain environmental conditions substantially impacts an individual's short- and long-term health. Adipose tissue dysfunction is a worldwide chronic disease caused by improper lipid build-up in adipose tissue leading to obesity. Therefore, it is the need of the hour to invent anti-obesity agents. As a keto–carotenoid, Astaxanthin (AsX) has been shown to have preventive effects against problems associated with obesity. A crucial role in the pathogenesis of obesity has been attributed to dietary polyunsaturated fatty acids. Adipose tissue plays a vital role in maintaining overall body homeostasis. Metabolic dysfunction of white adipocytes forms a critical step in the emergence of insulin resistance and related diseases. Here we aim to investigate the effect of AsX and Docosahexaenoic acid (DHA) supplementation on the proteomic profile of perinatal undernutrition-induced adipose tissue dysfunction in adult life using a rat model. The LC–MS/MS quantitative proteomics enabled us to identify differentially expressed proteins in perinatal undernourished but AsX and DHA-supplemented animal models. Data are available via ProteomeXchange with identifier PXD041772.This study explored biological roles, molecular functions of differentially expressed proteins, and pathways related to adipose tissue dysfunction induced by undernutrition and its effective modulation by AsX and DHA

Cigarette smoke induces metabolic reprogramming in lung cells

Cigarette smoking remains the leading cause of non-small cell lung carcinoma. Studies involving acute exposure of smoke on lung cells revealed induction of pre- cancerous state in lung cells. Recently few studies have reported the chronic effect of cigarette smoke in inducing cellular transformation. Yet no systemic study has been performed to understand the molecular alterations in lung cells due to cigarette smoke. Hence it is both important and necessary to study the chronic effect of cigarette smoke in a temporal setting to understand the molecular alterations. In this study, we carried out TMT based proteomic profiling of lung cells which were exposed to cigarette smoke condensate (CSC) for upto 12 months. We identified 2621 proteins in total, of which 145, 114, 87, 169 and 671 proteins were differentially expressed (p<0.05, 1.5 fold) in 2nd, 4th, 6th, 8th and 12th month respectively.Pathway analysis revealed enrichment of xenobiotic metabolism signaling for the first 8 months of smoke treatment, whereas continued exposure of smoke for 12 months revealed mitochondrial reprogramming in cells which includes dysregulation of oxidative phosphorylation machinery leading to enhanced reactive oxygen species and higher expression of enzymes involved in tricarboxylic acid cycle (TCA). In addition, chronic exposure of smoke led to overexpression of enzymes involved in glutamine metabolism, fatty acid degradation and lactate synthesis. This could possibly explain the availability of alternative source of carbon in TCA cycle apart from glycolytic pyruvate. Our data indicates that chronic exposure to cigarette smoke induces metabolic transformation in cells to support growth and survival

Annotation of the Zebrafish Genome through an Integrated Transcriptomic and Proteomic Analysis

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes

A multi-omic analysis of human naïve CD4+ T cells

Background: Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual. Results: Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome. Conclusions: We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter

Proteomic profiling of retinoblastoma by high resolution mass spectrometry

BACKGROUND: Retinoblastoma is an ocular neoplastic cancer caused primarily due to the mutation/deletion of RB1 gene. Due to the rarity of the disease very limited information is available on molecular changes in primary retinoblastoma. High throughput analysis of retinoblastoma transcriptome is available however the proteomic landscape of retinoblastoma remains unexplored. In the present study we used high resolution mass spectrometry-based quantitative proteomics to identify proteins associated with pathogenesis of retinoblastoma. METHODS: We used five pooled normal retina and five pooled retinoblastoma tissues to prepare tissue lysates. Equivalent amount of proteins from each group was trypsin digested and labeled with iTRAQ tags. The samples were analyzed on Orbitrap Velos mass spectrometer. We further validated few of the differentially expressed proteins by immunohistochemistry on primary tumors. RESULTS: We identified and quantified a total of 3587 proteins in retinoblastoma when compared with normal adult retina. In total, we identified 899 proteins that were differentially expressed in retinoblastoma with a fold change of ≥2 of which 402 proteins were upregulated and 497 were down regulated. Insulin growth factor 2 mRNA binding protein 1 (IGF2BP1), chromogranin A, fetuin A (ASHG), Rac GTPase-activating protein 1 and midkine that were found to be overexpressed in retinoblastoma were further confirmed by immunohistochemistry by staining 15 independent retinoblastoma tissue sections. We further verified the effect of IGF2BP1 on cell proliferation and migration capability of a retinoblastoma cell line using knockdown studies. CONCLUSIONS: In the present study mass spectrometry-based quantitative proteomic approach was applied to identify proteins differentially expressed in retinoblastoma tumor. This study identified the mitochondrial dysfunction and lipid metabolism pathways as the major pathways to be deregulated in retinoblastoma. Further knockdown studies of IGF2BP1 in retinoblastoma cell lines revealed it as a prospective therapeutic target for retinoblastoma. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12014-016-9128-7) contains supplementary material, which is available to authorized users