Papers by Shankar Subramaniam
... Mano R. Maurya, Department of Bioengineering, University of California San Diego, La Jolla, C... more ... Mano R. Maurya, Department of Bioengineering, University of California San Diego, La Jolla, CA. Shankar Subramaniam, San Diego Supercomputer Center, Department of Bioengineering, Department of Chemistry & Biochemistry, University of California San Diego, La Jolla ...
... Mano R. Maurya, Department of Bioengineering, University of California San Diego, La Jolla, C... more ... Mano R. Maurya, Department of Bioengineering, University of California San Diego, La Jolla, CA. Daniel M. Tartakovsky, Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA. ...
... Mano R. Maurya 1 , TaiJung Choi 2 , Daniel M. Tartakovsky 2 and Shankar Subramaniam 3 , (1)De... more ... Mano R. Maurya 1 , TaiJung Choi 2 , Daniel M. Tartakovsky 2 and Shankar Subramaniam 3 , (1)Department of Bioengineering, University of California San Diego, La Jolla, CA, (2)Department of Mechanical and Aerospace Engineering, University of California, San Diego, La ...
Cell
an outstanding example of subcellular compartmentalization as a strategy to optimize function ( .
PloS one, 2015
Altered extrahepatic bile ducts, gut, and cardiovascular anomalies constitute the variable phenot... more Altered extrahepatic bile ducts, gut, and cardiovascular anomalies constitute the variable phenotype of biliary atresia (BA). To identify potential susceptibility loci, Caucasian children, normal (controls) and with BA (cases) at two US centers were compared at >550000 SNP loci. Systems biology analysis was carried out on the data. In order to validate a key gene identified in the analysis, biliary morphogenesis was evaluated in 2-5-day post-fertilization zebrafish embryos after morpholino-antisense oligonucleotide knockdown of the candidate gene ADP ribosylation factor-6 (ARF6, Mo-arf6). Among 39 and 24 cases at centers 1 and 2, respectively, and 1907 controls, which clustered together on principal component analysis, the SNPs rs3126184 and rs10140366 in a 3' flanking enhancer region for ARF6 demonstrated higher minor allele frequencies (MAF) in each cohort, and 63 combined cases, compared with controls (0.286 vs. 0.131, P = 5.94x10-7, OR 2.66; 0.286 vs. 0.13, P = 5.57x10-7,...
Cellular responses to inputs that vary both temporally and spatially are determined by complex re... more Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway� entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid / that allows
Since their inception nearly three decades ago, cybernetic models have been used to analyze the d... more Since their inception nearly three decades ago, cybernetic models have been used to analyze the dynamic control of metabolism based off of goals relevant to an organism's functioning. In the case of single cellular organisms, goals like the maximization of carbon uptake rate or growth rate have shown much success in predicting phenomena like dynamic intracellular fluxes, gene knockout behavior and hysteresis effects in chemostat cultures. The goal of this work is to take this existing framework for modeling single-celled organisms and modify it appropriately to describe more complex mammalian metabolic networks. A key step in this process is finding an appropriate description of the metabolic objectives of these cells or cellular subsystems. The focus of study in this work is the response of eicosanoid metabolism in RAW 264.7 macrophages to lipopolysaccharide (LPS), a biochemical marker of bacterial infection. Eicosanoids are a diverse group of molecules derived from the oxidati...
Complement C5 is a 189 kDa protein synthesized in liver as a single-chain precursor molecule. The... more Complement C5 is a 189 kDa protein synthesized in liver as a single-chain precursor molecule. The precursor molecule is then cleaved to a disulfide linked two-chain glycoprotein consisting of a 115 kDa (C5α) and a 75 kDa N-terminal (C5β) chain. C5 is present in all the three known complement activation pathways: classical, alternative and lectin. C5α chain is cleaved by C5 convertases, which are formed during the complement activation process, to form C5a (74 a.a long) and C5α' chain (925 a.a long). C5α' chain and C5β chain (655 a.a. long) together form C5b. C5a is a major anaphylotoxin involved in chemotaxis of neutrophils and release of pro-inflammatory cytokines. These functions of C5a require binding to its receptor, C5aR. C5b sequentially recruits C6, C7, C8 and C9 in a non-enzymatic manner to form the terminal complement complex (TCC, also called membrane attack complex or MAC). TCC forms a lytic pore in the target membrane and kills the pathogen. While the functions o...
Properdin is currently the only known positive regulator of complement activation and stabilizes ... more Properdin is currently the only known positive regulator of complement activation and stabilizes the alternative pathway C3 convertase (C3bBb). It is composed of multiple identical protein subunits, with each subunit carrying a separate ligand-binding site. Previous reports suggest that properdin function depends on multiple interactions between its subunits and its ligands. Properdin recognizes several pathogen- or damage/danger-associated molecular patterns (PAMPs and DAMPs, respectively) on foreign and apoptotic cells. Once bound, it initiates and propagates the complement response by attracting fluid-phage C3b to recognize surfaces and fostering de novo convertase assembly, and by stabilizing C3 convertase complexes (C3bBbfP). Therefore, it is central to continuous deposition of the activated complement fragment C3b on the surfaces of the pathogens, which it achieves by preventing the dissociation of the Bb catalytic subunit from the inherently labile C3bBb complexes.
Gastroenterology, 2015
ABSTRACT In the setting where two individuals are genetically similar, epigenetic mechanisms coul... more ABSTRACT In the setting where two individuals are genetically similar, epigenetic mechanisms could account for discordance in the presence or absence of non-alcoholic fatty liver disease (NAFLD). This study investigated if serum microRNAs (miRs) could explain discordance in NAFLD. This is a cross-sectional analysis of a prospective cohort study of 40 (n=80) twin-pairs residing in Southern California. All participants underwent a standardised research visit, liver MRI using proton-density fat fraction to quantify fat content and miR profiling of their serum. Among the 40 twin-pairs, there were 6 concordant for NAFLD, 28 were concordant for non-NAFLD and 6 were discordant for NAFLD. The prevalence of NAFLD was 22.5% (18/80). Within the six discordant twins, a panel of 10 miRs differentiated the twin with NAFLD from the one without. Two of these miRs, miR-331-3p and miR-30c, were also among the 21 miRs that were different between NAFLD and non-NAFLD groups (for miR-331-3p: 7.644±0.091 vs 8.057±0.071, respectively, p=0.004; for miR-30c: 10.013±0.126 vs 10.418±0.086, respectively, p=0.008). Both miRs were highly heritable (35.9% and 10.7%, respectively) and highly correlated with each other (R=0.90, p=2.2×10(-16)) suggesting involvement in a common mechanistic pathway. An interactome analysis of these two miRs showed seven common target genes. Using a novel human twin-study design, we demonstrate that discordancy in liver fat content between the twins can be explained by miRs, and that they are heritable. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
Lipids are crucial for the life of the cell. Many lipid-derived metabolites play a vital role in ... more Lipids are crucial for the life of the cell. Many lipid-derived metabolites play a vital role in the regulation and control of various cellular functions and in the pathophysiology of many diseases. The LIPID MAPS consortium (www.lipidmaps.org) has developed methods to quantitatively measure the composition of lipids and its metabolites in RAW 264.7 macrophage cells. Time-course data in response to treatment with KDO2 lipid A (a lipopolysaccharide analogue) has been collected. Recently, we have developed a novel two steps approach to estimating rate parameters using temporal data. First, a constrained least squares-based optimization (the Matlab optimization functions lsqlin) is used to compute good initial guesses for the parameter values. Second, a generalized constrained nonlinear optimization (Matlab optimization function fmincon) is used to estimate the parameters. The combined use of both functions makes the overall process computationally efficient. We have used this approach...
We have used continuum electrostatic methods to investigate the role of electrostatic interaction... more We have used continuum electrostatic methods to investigate the role of electrostatic interactions in the structure, function, and pH-dependent stability of the fungal Rhizomucor mieheilipase (RmL) family. We identify a functionally important electrostatic network which includes residues S144, D203, H257, Y260, H143, Y28, R80, and D91 (residue numbering is from RmL). This network consists of residues belonging to the catalytic triad (S144, D203, H257), residues located in proximity to the active site (Y260), residues stabilizing the geometry of the active site (Y28, H143), and residues located in the lid (D91) or close to the first hinge (R80). The lid and the first hinge are associated with the interfacial activation of lipases, where an R-helical lid opens up by rotating around two hinge regions. All network residues are well conserved in a set of 12 lipase homologues, and 6 of the network residues are located in sequence motifs. We observe that the effects of modeled mutations R8...
Oncogene
Glioblastoma can originate from terminally differentiated astrocytes and neurons, which can dedif... more Glioblastoma can originate from terminally differentiated astrocytes and neurons, which can dedifferentiate to a stem cell-like state upon transformation. In this study, we confirmed that transformed dedifferentiated astrocytes and neurons acquired a stem/progenitor cell state, although they still retained gene expression memory from their parental cell. Transcriptional network analysis on these cells identified upregulated genes in three main pathways: Wnt signaling, cell cycle and focal adhesion with the gene Spp1, also known as osteopontin (OPN) serving as a key common node connecting these three pathways. Inhibition of OPN blocked the formation of neurospheres, affected the proliferative capacity of transformed neurons and reduced the expression levels of neural stem cell markers. Specific inhibition of OPN in both murine and human glioma tumors prolonged mice survival. We conclude that OPN is an important player in dedifferentiation of cells during tumor formation, hence its in...
BMC research notes, 2015
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on th... more Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on the skeletal muscle. Severe muscle wasting, chronic inflammation and fibrosis characterize dystrophic muscle. Here we identify dysregulated pathways in DMD utilizing a co-expression network approach as described in Weighted Gene Co-expression Network Analysis (WGCNA). Specifically, we utilize WGCNA's "preservation" statistics to identify gene modules that exhibit a weak conservation of network topology within healthy and dystrophic networks. Preservation statistics rank modules based on their topological metrics such as node density, connectivity and separability between networks. Raw data for DMD was downloaded from Gene Expression Omnibus (GSE6011) and suitably preprocessed. Co-expression networks for each condition (healthy and dystrophic) were generated using the WGCNA library in R. Preservation of healthy network edges was evaluated with respect to dystrophic muscle and ...
Gut, Jan 22, 2015
In the setting where two individuals are genetically similar, epigenetic mechanisms could account... more In the setting where two individuals are genetically similar, epigenetic mechanisms could account for discordance in the presence or absence of non-alcoholic fatty liver disease (NAFLD). This study investigated if serum microRNAs (miRs) could explain discordance in NAFLD. This is a cross-sectional analysis of a prospective cohort study of 40 (n=80) twin-pairs residing in Southern California. All participants underwent a standardised research visit, liver MRI using proton-density fat fraction to quantify fat content and miR profiling of their serum. Among the 40 twin-pairs, there were 6 concordant for NAFLD, 28 were concordant for non-NAFLD and 6 were discordant for NAFLD. The prevalence of NAFLD was 22.5% (18/80). Within the six discordant twins, a panel of 10 miRs differentiated the twin with NAFLD from the one without. Two of these miRs, miR-331-3p and miR-30c, were also among the 21 miRs that were different between NAFLD and non-NAFLD groups (for miR-331-3p: 7.644±0.091 vs 8.057±...
2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, 2010
microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biolog... more microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biology approach to predict the regulatory network of miRNAs among the most down-regulated genes by the lipopolysaccharides (LPS) treatment in the macrophage RAW267.4 cell line. We combine the proteome and transcriptome data sets to define 200 target genes that are significantly down-regulated by the LPS treatment. We perform the profiling of over 300 miRNAs with the RNA-Seq method. Using the complementary binding rule between the seed sequences of profiled miRNAs and the 3'UTRs of target genes, we predict genes involved in mobility, metabolism, and oxidative phosphorylation as the top targets of miRNA negative regulation.
Complement C3 is the central component of the human complement system. It is ~186 kDa in size, co... more Complement C3 is the central component of the human complement system. It is ~186 kDa in size, consisting of an α-chain (~110 kDa) and a β-chain (~75 kDa) that are connected by cysteine bridges. C3 in its native form is inactive. Cleavage of C3 into C3b (~177 kDa) and C3a (~9 kDa) is a crucial step in the complement activation cascade, which can be initiated by one or more of the three distinct pathways, called alternative, classical and lectin complement pathways. In the alternative pathway, hydrated C3 (C3(H20)) recruits complement factor B (fB), which is then cleaved by complement factor D (fD) to result in formation of the minor form of C3-convertase (C3(H20)Bb) that cleaves C3 into C3a and C3b. A small percent of the resulting C3b is rapidly deposited (opsonization through covalent bond) in the immediate vicinity of the site of activation (e.g. pathogen surface) and now forms the major form of C3-convertase (C3bBb), thereby creating an efficient cycle of C3 cleavage. Properdin,...
Vaccine, 2015
Vaccines have drastically reduced the mortality and morbidity of many diseases. However, vaccines... more Vaccines have drastically reduced the mortality and morbidity of many diseases. However, vaccines have historically been developed empirically, and recent development of vaccines against current pandemics such as HIV and malaria has been met with difficulty. The advent of high-throughput technologies, coupled with systems biological methods of data analysis, has enabled researchers to interrogate the entire complement of a variety of molecular components within cells, and characterize the myriad interactions among them in order to model and understand the behavior of the system as a whole. In the context of vaccinology, these tools permit exploration of the molecular mechanisms by which vaccines induce protective immune responses. Here we review the recent advances, challenges, and potential of systems biological approaches in vaccinology. If the challenges facing this developing field can be overcome, systems vaccinology promises to empower the identification of early predictive signatures of vaccine response, as well as novel and robust correlates of protection from infection. Such discoveries, along with the improved understanding of immune responses to vaccination they impart, will play an instrumental role in development of the next generation of rationally designed vaccines.
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Papers by Shankar Subramaniam