When One and One Gives More than Two: Challenges and Opportunities of Integrative Omics

Since the dawn of the post-genomic era a myriad of novel high-throughput technologies have been developed that are capable of measuring thousands of biological molecules at once, giving rise to various “omics” platforms. These advances offer the unique opportunity to study how individual parts of a biological system work together to produce emerging phenotypes. Today, many research laboratories are moving toward applying multiple omics platforms to analyze the same biological samples. In addition, network information of interacting molecules is being incorporated more and more into the analysis and interpretation of these multiple omics datasets, which provides novel ways to integrate multiple layers of heterogeneous biological information into a single coherent picture. Here, we provide a perspective on how such recent “integrative omics” efforts are likely going to shift biological paradigms once again, and what challenges lie ahead

Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study

With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations

A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments

<p>Abstract</p> <p>Background</p> <p>With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies.</p> <p>Results</p> <p>In this article, we describe a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models. A key feature of the model is the use of latent variables that represent quantities that can be combined across diverse platforms. We consider two methods for estimation of an index termed the probability of expression (POE). The first, reported in previous work by the authors, involves Markov Chain Monte Carlo (MCMC) techniques. The second method is a faster algorithm based on the expectation-maximization (EM) algorithm. The methods are illustrated with application to a meta-analysis of datasets for metastatic cancer.</p> <p>Conclusion</p> <p>The statistical methods described in the paper are available as an R package, metaArray 1.8.1, which is at Bioconductor, whose URL is <url>http://www.bioconductor.org/</url>.</p

Analysis of protein complexes through model‐based biclustering of label‐free quantitative AP‐MS data

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102630/1/msb201041.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102630/2/msb201041-sup-0001.pd

Analysis of hidden terminals effect on the performance of vehicular ad-hoc networks

Vehicular ad-hoc networks (VANETs) based on the IEEE 802.11p standard are receiving increasing attention for road safety provisioning. Hidden terminals, however, demonstrate a serious challenge in the performance of VANETs. In this paper, we investigate the effect of hidden terminals on the performance of one hop broadcast communication. The paper formulates an analytical model to analyze the effect of hidden terminals on the performance metrics such as packet reception probability (PRP), packet reception delay (PRD), and packet reception interval (PRI) for the 2-dimensional (2-D) VANET. To verify the accuracy of the proposed model, the analytical model-based results are compared with NS3 simulation results using 2-D highway scenarios. We also compare the analytical results with those from real vehicular network implemented using the commercial vehicle-to-everything (V2X) devices. The analytical results show high correlation with the results of both simulation and real network.This work was supported in part by IITP Grant through the Korean Government, under the development of wide area driving environment awareness and cooperative driving technology which are based on V2X wireless communication under grant R7117-19- 0164 and in part by the Center for Integrated Smart Sensors funded by the Ministry of Science, ICT & Future Planning as Global Frontier Project, South Korea (CISS-2019)

Plasma Protein and MicroRNA Biomarkers of Insulin Resistance: A Network-Based Integrative -Omics Analysis

Although insulin resistance (IR) is a key pathophysiologic condition underlying various metabolic disorders, impaired cellular glucose uptake is one of many manifestations of metabolic derangements in the human body. To study the systems-wide molecular changes associated with obesity-dependent IR, we integrated information on plasma proteins and microRNAs in eight obese insulin-resistant (OIR, HOMA-IR &gt; 2.5) and nine lean insulin-sensitive (LIS, HOMA-IR &lt; 1.0) normoglycemic males. Of 374 circulating miRNAs we profiled, 65 species increased and 73 species decreased in the OIR compared to the LIS subjects, suggesting that the overall balance of the miRNA secretome is shifted in the OIR subjects. We also observed that 40 plasma proteins increased and 4 plasma proteins decreased in the OIR subjects compared to the LIS subjects, and most proteins are involved in metabolic and endocytic functions. We used an integrative -omics analysis framework called iOmicsPASS to link differentially regulated miRNAs with their target genes on the TargetScan map and the human protein interactome. Combined with tissue of origin information, the integrative analysis allowed us to nominate obesity-dependent and obesity-independent protein markers, along with potential sites of post-transcriptional regulation by some of the miRNAs. We also observed the changes in each -omics platform that are not linked by the TargetScan map, suggesting that proteins and microRNAs provide orthogonal information for the progression of OIR. In summary, our integrative analysis provides a network of elevated plasma markers of OIR and a global shift of microRNA secretome composition in the blood plasma

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

Affinity purification coupled to mass spectrometry (AP-MS) represents a powerful and proven approach for the analysis of protein–protein interactions. However, the detection of true interactions for proteins that are commonly considered background contaminants is currently a limitation of AP-MS. Here using spectral counts and the new statistical tool, Significance Analysis of INTeractome (SAINT), true interaction between the serine/threonine protein phosphatase 5 (PP5) and a chaperonin, heat shock protein 90 (Hsp90), is discerned. Furthermore, we report and validate a new interaction between PP5 and an Hsp90 adaptor protein, stress-induced phosphoprotein 1 (STIP1; HOP). Mutation of PP5, replacing key basic amino acids (K97A and R101A) in the tetratricopeptide repeat (TPR) region known to be necessary for the interactions with Hsp90, abolished both the known interaction of PP5 with cell division cycle 37 homolog and the novel interaction of PP5 with stress-induced phosphoprotein 1. Taken together, the results presented demonstrate the usefulness of label-free quantitative proteomics and statistical tools to discriminate between noise and true interactions, even for proteins normally considered as background contaminants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83479/1/1508_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/83479/2/pmic_201000770_sm_SupplInfo.pd

A Metabolomic Analysis Of Thiol Response For Standard And Modified N-Acetyl Cysteine Treatment Regimens In Patients With Acetaminophen Overdose

Abstract N‐acetylcysteine (NAC) is an antidote to prevent acetaminophen (paracetamol‐APAP)‐induced acute liver injury (ALI). The 3‐bag licensed 20.25 h standard regimen, and a 12 h modified regimen, are used to treat APAP overdose. This study evaluated the redox thiol response and APAP metabolites, in patients with a single APAP overdose treated with either the 20.25 h standard or 12 h modified regimen. We used liquid chromatography tandem mass spectrometry to quantify clinically important oxidative stress biomarkers and APAP metabolites in plasma samples from 45 patients who participated in a randomized controlled trial (SNAP trial). We investigated the time course response of plasma metabolites at predose, 12 h, and 20.25 h post‐start of NAC infusion. The results showed that the 12 h modified regimen resulted in a significant elevation of plasma NAC and cysteine concentrations at 12 h post‐infusion. We found no significant alteration in the metabolism of APAP, mitochondrial, amino acids, and other thiol biomarkers with the two regimens. We examined APAP and purine metabolism in overdose patients who developed ALI. We showed the major APAP‐metabolites and xanthine were significantly higher in patients with ALI. These biomarkers correlated well with alanine aminotransferase activity at admission. Receiver operating characteristic analysis showed that at admission, plasma APAP‐metabolites and xanthine concentrations were predictive for ALI. In conclusion, a significantly higher redox thiol response with the modified NAC regimen at 12 h postdose suggests this regimen may produce greater antioxidant efficacy. At baseline, plasma APAP and purine metabolites may be useful biomarkers for early prediction of APAP‐induced ALI

Condensed ECM-based nanofilms on highly permeable PET membranes for robust cell-to-cell communications with improved optical clarity

The properties of a semipermeable porous membrane, including pore size, pore density, and thickness, play a crucial role in creating a tissue interface in a microphysiological system (MPS) because it dictates multicellular interactions between different compartments. The small pore-sized membrane has been preferentially used in an MPS for stable cell adhesion and the formation of tissue barriers on the membrane. However, it limited the applicability of the MPS because of the hindered cell transmigration via sparse through-holes and the optical translucence caused by light scattering through pores. Thus, there remain unmet challenges to construct a compartmentalized MPS without those drawbacks. Here we report a submicrometer-thickness (similar to 500 nm) fibrous extracellular matrix (ECM) film selectively condensed on a large pore-sized track-etched (TE) membrane (10 mu m-pores) in an MPS device, which enables the generation of functional tissue barriers simultaneously achieving optical transparency, intercellular interactions, and transmigration of cells across the membrane. The condensed ECM fibers uniformly covering the surface and 10 mu m-pores of the TE membrane permitted sufficient surface areas where a monolayer of the human induced pluripotent stem cell-derived brain endothelial cells is formed in the MPS device. The functional maturation of the blood-brain barrier (BBB) was proficiently achieved due to astrocytic endfeet sheathing the brain endothelial cells through 10 mu m pores of the condensed-ECM-coated TE (cECMTE) membrane. We also demonstrated the extravasation of human metastatic breast tumor cells through the human BBB on the cECMTE membrane. Thus, the cECMTE membrane integrated with an MPS can be used as a versatile platform for studying various intercellular communications and migration, mimicking the physiological barriers of an organ compartment

Analysis of protein complexes through model‐based biclustering of label‐free quantitative AP‐MS data

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102630/1/msb201041.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102630/2/msb201041-sup-0001.pd