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1.  Improved asymmetry prediction for siRNAs 
The FEBS journal  2014;281(1):320-330.
In the development of RNA interference (RNAi) therapeutics, merely selecting short, interfering RNA (siRNA) sequences that are complementary to the messenger RNA (mRNA) target does not guarantee target silencing. Current algorithms for selecting siRNAs rely on many parameters, one of which is asymmetry, often predicted through calculation of the relative thermodynamic stability of the two ends of the siRNA. However, we have previously shown that highly-active siRNA sequences are likely to have particular nucleotides at each 5’-end, independent of their thermodynamic asymmetry. Here, we describe an algorithm for predicting highly active siRNA sequences based only on these two asymmetry parameters. The algorithm uses end sequence nucleotide preferences and predicted thermodynamic stabilities, each weighted based on training data from the literature, to rank the probability that an siRNA sequence will have high or low activity. The algorithm successfully predicts weakly- and highly-active sequences for enhanced green fluorescent protein (EGFP) and protein kinase R (PKR). Use of these two parameters in combination improves the prediction of siRNA activity over current approaches for predicting asymmetry. Going forward, we anticipate that this approach to siRNA asymmetry prediction will be incorporated into the next generation of siRNA selection algorithms.
PMCID: PMC3924726  PMID: 24393396
asymmetry; siRNA; EGFP; PKR
2.  Human Milk Galectin-3 Binding Protein and Breastfeeding-Associated HIV Transmission 
Analysis of milk from 247 HIV-infected Zambian mothers showed that Galectin-3 Binding Protein (Gal3BP) concentrations were significantly higher among HIV-infected mothers who transmitted HIV through breastfeeding (6.51±2.12 ug/mL) than among non-transmitters but were also correlated with higher milk and plasma HIV RNA copies/ml and lower CD4+ cell counts. The association between Gal3BP and postnatal transmission was attenuated after adjustment for milk and plasma HIV load and CD4+ cell counts. This suggests that although milk Gal3BP is a marker of advanced maternal disease, it does not independently modify transmission risk.
PMCID: PMC3907473  PMID: 23899964
HIV transmission; breastfeeding; Galectin-3 Binding Protein; oral transmission
3.  Primary Neuron/Astrocyte Co-Culture on Polyelectrolyte Multilayer Films: A Template for Studying Astrocyte-Mediated Oxidative Stress in Neurons** 
Advanced functional materials  2008;18(2):294-301.
We engineered patterned co-cultures of primary neurons and astrocytes on polyelectrolyte multilayer (PEM) films without the aid of adhesive proteins/ligands to study the oxidative stress mediated by astrocytes on neuronal cells. A number of studies have explored engineering co-culture of neurons and astrocytes predominantly using cell lines rather than primary cells owing to the difficulties involved in attaching primary cells onto synthetic surfaces. To our knowledge this is the first demonstration of patterned co-culture of primary neurons and astrocytes for studying neuronal metabolism. In our study, we used synthetic polymers, namely poly(diallyldimethylammoniumchloride) (PDAC) and sulfonated poly(styrene) (SPS) as the polycation and polyanion, respectively, to build the multilayers. Primary neurons attached and spread preferentially on SPS surfaces, while primary astrocytes attached to both SPS and PDAC surfaces. SPS patterns were formed on PEM surfaces, either by microcontact printing SPS onto PDAC surfaces or vice-versa, to obtain patterns of primary neurons and patterned co-cultures of primary neurons and astrocytes. We further used the patterned co-culture system to study the neuronal response to elevated levels of free fatty acids as compared to the response in separated monoculture by measuring the level of reactive oxygen species (ROS; a widely accepted marker of oxidative stress). The elevation in the ROS levels was observed to occur earlier in the patterned co-culture system than in the separated monoculture system. The results suggest that this technique may provide a useful tool for engineering neuronal co-culture systems, that may more accurately capture neuronal function and metabolism, and thus could be used to obtain valuable insights into neuronal cell function and perhaps even the pathogenesis of neurodegenerative diseases.
PMCID: PMC4229016  PMID: 25400537
4.  Curcumin-induced upregulation of the anti-tau cochaperone BAG2 in primary rat cortical neurons 
Neuroscience letters  2013;554:10.1016/j.neulet.2013.09.008.
Alzheimer’s disease (AD) is a progressive, neurodegenerative disease characterized by extracellular deposits of amyloid beta (Aβ) protein and intracellular neurofibrillary tangles of hyperphosphorylated tau protein. Various studies suggest that the tau tangle pathology, which lies downstream to Aβ pathology, is essential to produce AD-associated clinical phenotype and thus treatments targeting tau pathology may prevent or delay disease progression effectively. In this context, our present study examined three polyphenol compounds (curcumin, EGCG and resveratrol) for their possible activity against two endogenous proteins (BAG2 and LAMP1) that are shown to play a vital role in clearing tau tangles from neurons. Human epidemiological and animal data suggest potential positive effects of these polyphenols against AD. Here, primary rat cortical neurons treated with these polyphenols significantly up-regulated BAG2 levels at different concentrations, while only EGCG upregulated LAMP1 levels, although at higher concentrations. Importantly, curcumin doubled BAG2 levels at low micromolar concentrations that are clinically relevant. In addition, curcumin also downregulated levels of phosphorylated tau, which may be potentially attributed to the curcumin-induced upregulation in BAG2 levels in the neurons. The present results demonstrate novel activity of polyphenol curcumin in up-regulating an anti-tau cochaperone BAG2 and thus, suggest probable benefit of curcumin against AD-associated tauopathy.
PMCID: PMC3825752  PMID: 24035895
Alzheimer’s disease; tau; polyphenol; curcumin; BAG2
5.  Palmitate induces transcriptional regulation of BACE1 and presenilin by STAT3 in neurons mediated by astrocytes 
Experimental neurology  2013;248:482-490.
Deregulation of calcium has been implicated in neurodegenerative diseases, including Alzheimer’s disease (AD). Previously, we showed that saturated free-fatty acid, palmitate, causes AD-like changes in primary cortical neurons mediated by astrocytes. However, the molecular mechanisms by which conditioned media from astrocytes cultured in palmitate induces AD-like changes in neurons are unknown. This study demonstrates that this condition media from astrocytes elevates calcium level in the neurons, which subsequently increases calpain activity, a calcium-dependent protease, leading to enhance p25/Cdk5 activity and phosphorylation and activation of the STAT3 (signal transducer and activator of transcription) transcription factor. Inhibiting calpain or Cdk5 significantly reduces the upregulation in nuclear level of pSTAT3, which we found to transcriptionally regulate both BACE1 and presenilin-1, the latter is a catalytic subunit of γ-secretase. Decreasing pSTAT3 levels reduced the mRNA levels of both BACE1 and presenilin-1 to near control levels. These data demonstrate a signal pathway leading to the activation of STAT3, and the generation of the amyloid peptide. Thus, our results suggest that STAT3 is an important potential therapeutic target of AD pathogenesis.
PMCID: PMC3787872  PMID: 23968646
Alzheimer’s disease; fatty acids; calcium; STAT3; BACE1; presenilin-1
6.  Ensemble Classification of Cancer Types and Biomarker Identification 
Drug development research  2012;73(7):414-419.
Cancer classification is an important step in biomarker identification. Developing machine learning methods that correctly predict cancer subtypes/types can help in identifying potential cancer biomarkers. In this commentary, we presented ensemble classification approach and compared its performance with single classification approaches. Additionally, the application of cancer classification in identifying biomarkers for drug design was discussed.
PMCID: PMC4162531  PMID: 25221378
cancer classification; gene expression; ensemble; biomarker; drug design
7.  Early Phosphoproteomic Changes in the Mouse Spleen During Deoxynivalenol-Induced Ribotoxic Stress 
Toxicological Sciences  2013;135(1):129-143.
The trichothecene mycotoxin deoxynivalenol (DON) targets the innate immune system and is of public health significance because of its frequent presence in human and animal food. DON-induced proinflammatory gene expression and apoptosis in the lymphoid tissue have been associated with a ribotoxic stress response (RSR) that involves rapid phosphorylation of mitogen-activated protein kinases (MAPKs). To better understand the relationship between protein phosphorylation and DON’s immunotoxic effects, stable isotope dimethyl labeling–based proteomics in conjunction with titanium dioxide chromatography was employed to quantitatively profile the immediate (≤ 30min) phosphoproteome changes in the spleens of mice orally exposed to 5mg/kg body weight DON. A total of 90 phosphoproteins indicative of novel phosphorylation events were significantly modulated by DON. In addition to critical branches and scaffolds of MAPK signaling being affected, DON exposure also altered phosphorylation of proteins that mediate phosphatidylinositol 3-kinase/AKT pathways. Gene ontology analysis revealed that DON exposure affected biological processes such as cytoskeleton organization, regulation of apoptosis, and lymphocyte activation and development, which likely contribute to immune dysregulation associated with DON-induced RSR. Consistent with these findings, DON impacted phosphorylation of proteins within diverse immune cell populations, including monocytes, macrophages, T cells, B cells, dendritic cells, and mast cells. Fuzzy c-means clustering analysis further indicated that DON evoked several distinctive temporal profiles of regulated phosphopeptides. Overall, the findings from this investigation can serve as a template for future focused exploration and modeling of cellular responses associated with the immunotoxicity evoked by DON and other ribotoxins.
PMCID: PMC3748769  PMID: 23811945
ribotoxic stress response; phosphorylation; quantitative proteomics; trichothecene mycotoxin; deoxynivalenol.
8.  Inhibition of SPT reduces Aβ and tau hyperphosphorylation in a mouse model, a safe therapeutic strategy for Alzheimer’s disease 
Neurobiology of aging  2013;34(8):2037-2051.
The contribution of the autosomal dominant mutations to the etiology of familial Alzheimer’s disease (AD) is well characterized. However, the molecular mechanisms contributing to sporadic AD are less understood. Increased ceramide levels have been evident in AD patients. We previously reported that increased ceramide levels, regulated by increased serine palmitoyltransferase (SPT), directly mediate amyloid β (Aβ) levels. Therefore, we inhibited SPT in an AD mouse model (TgCRND8) through subcutaneous administration of L-cylcoserine (LCS). The cortical Aβ42 and hyperphosphorylated tau levels were down regulated with the inhibition of SPT/ceramide. Positive correlations were observed between cortical SPT, ceramide and Aβ42 levels. With no evident toxic effects observed, inhibition of SPT could be a safe therapeutic strategy to ameliorate the AD pathology. We previously observed that miR-137, -181c, -9 and 29a/b post-transcriptionally regulate SPT levels, and the corresponding miRNA levels in the blood sera are potential diagnostic biomarkers for AD. Here, we observe a negative correlation between cortical Aβ42 and sera Aβ42, and a positive correlation between cortical miRNA levels and sera miRNA levels suggesting their potential as non-invasive diagnostic biomarkers.
PMCID: PMC3651806  PMID: 23528227
Alzheimer’s disease; serine palmitoyltransferase; inhibition; amyloid beta; tau hyperphosphorylation; microRNA
9.  The Accumulation of Versican in the Nodules of Benign Prostatic Hyperplasia 
The Prostate  2009;69(2):149-158.
Proteoglycans, a complex group of extracellular matrix (ECM) molecules, are elevated in benign prostatic hyperplasia (BPH). Versican is a stromal proteoglycan present in prostate tissue. Versican expression is elevated in tissues with increased proliferation. Based on these observations, we determined the extent and distribution of versican expression in prostates with BPH.
The involvement of versican in BPH nodules was compared with levels in non-nodular transition (TZ) and peripheral zone (PZ) tissues from 18 human prostate glands using immunohistochemistry, Northern blots and/or QRTPCR to localize versican and quantify versican mRNA transcript levels, and Western blots to assess gene product levels.
Increased versican immunoreactivity was observed in the stroma of BPH nodules. Higher steady state levels of versican variants V0, V1, and V3 mRNA transcript and gene product were detected in the nodular tissues than in the non-nodular TZ or PZ parenchyma.
These results suggest that versican may play a role in nodule formation in BPH.
PMCID: PMC4092210  PMID: 18819099
Prostate hyperplasia; proteoglycans; extracellular matrix; versican
10.  Cell Adhesion on Polyelectrolyte Multilayer Coated Polydimethylsiloxane Surfaces with Varying Topographies 
Tissue engineering  2007;13(8):2105-2117.
This article demonstrates that the micro-topography of the surface with respect to the pattern size and pitch influences cell adhesion and proliferation. Extensive research has shown the dependence of cell proliferation on substrate chemistry, but the influence of substrate topography on cell attachment has only recently been appreciated. To evaluate the effect of substrate physical properties (i.e., periodic microstructures) on cell attachment and morphology, we compared the response of several cell types (fibroblasts, HeLa, and primary hepatocytes) cultured on various polydimethylsiloxane (PDMS) patterns. PDMS has been used as an artificial construct to mimic biological structures. Although PDMS is widely used in biomedical applications, membrane technology, and microlithography, it is difficult to maintain cells on PDMS for long periods, and the polymer has proved to be a relatively inefficient substrate for cell adhesion. To improve adhesion, we built polyelectrolyte multilayers (PEMs) on PDMS surfaces to increase surface wettability, thereby improving attachment and spreading of the cells. Micrographs demonstrate the cellular response to physical parameters, such as pattern size and pitch, and suggest that surface topography, in part, regulates cell adhesion and proliferation. Therefore, varying the surface topography may provide a method to influence cell attachment and proliferation for tissue-engineering applications.
PMCID: PMC4059019  PMID: 17518734
11.  Application of Metabolic Flux Analysis to Identify the Mechanisms of Free Fatty Acid Toxicity to Human Hepatoma Cell Line 
Biotechnology and bioengineering  2008;99(2):399-410.
Chronic exposure to elevated levels of free fatty acids (FFAs) has been shown to cause cell death (lipotoxicity), but the underlying mechanisms of lipotoxicity in hepatocytes remain unclear. We have previously shown that the saturated FFAs cause much greater toxicity to human hepatoma cells (HepG2) than the unsaturated ones (Srivastava and Chan, 2007). In this study, metabolic flux analysis (MFA) was applied to identify the metabolic changes associated with the cytotoxicity of saturated FFA. Measurements of the fluxes revealed that the saturated FFA, palmitate, was oxidized to a greater extent than the non-toxic oleate and had comparatively less triglyceride synthesis and reduced cystine uptake. Although fatty acid oxidation had a high positive correlation to the cytotoxicity, inhibitor experiments indicated that the cytotoxicity was not due to the higher fatty acid oxidation. Application of MFA revealed that cells exposed to palmitate also had a consistently reduced flux of glutathione (GSH) synthesis but greater de novo ceramide synthesis. These predictions were experimentally confirmed. In silico sensitivity analyses identified that the GSH synthesis was limited by the uptake of cysteine. Western blot analyses revealed that the levels of the cystine transporter xCT, but not that of the GSH-synthesis enzyme glutamylcysteine synthase (GCS), were reduced in the palmitate cultures, suggesting the limitation of cysteine import as the cause of the reduced GSH synthesis. Finally, supplementing with N-acetyl L-cysteine (NAC), a cysteine-provider whose uptake does not depend on xCT levels, reduced the FFA-toxicity significantly. Thus, the metabolic alterations that contributed to the toxicity and suggested treatments to reduce the toxicity were identified, which were experimentally validated.
PMCID: PMC4059351  PMID: 17615559
metabolism; free fatty acid; toxicity; ceramide; glutathione; cystine transporter
12.  Involvement of astroglial ceramide in palmitic acid-induced Alzheimer-like changes in primary neurons 
The European journal of neuroscience  2007;26(8):2131-2141.
A high-fat diet has been shown to significantly increase the risk of the development of Alzheimer’s disease (AD), a neurodegenerative disease histochemically characterized by the accumulation of amyloid beta (Aβ) protein in senile plaques and hyperphosphorylated tau in neurofibrillary tangles. Previously, we have shown that saturated free fatty acids (FFAs), palmitic and stearic acids, caused increased amyloidogenesis and tau hyperphosphorylaion in primary rat cortical neurons. These FFA-induced effects observed in neurons were found to be mediated by astroglial FFA metabolism. Therefore, in the present study we investigated the basic mechanism relating astroglial FFA metabolism and AD-like changes observed in neurons. We found that palmitic acid significantly increased de-novo synthesis of ceramide in astroglia, which in turn was involved in inducing both increased production of the Aβ protein and hyperphosphorylation of the tau protein. Increased amyloidogenesis and hyperphoshorylation of tau lead to formation of the two most important pathophysiological characteristics associated with AD, Aβ or senile plaques and neurofibrillary tangles, respectively. In addition to these pathophysiological changes, AD is also characterized by certain metabolic changes; abnormal cerebral glucose metabolism is one of the distinct characteristics of AD. In this context, we found that palmitic acid significantly decreased the levels of astroglial glucose transporter (GLUT1) and down-regulated glucose uptake and lactate release by astroglia. Our present data establish an underlying mechanism by which saturated fatty acids induce AD-associated pathophysiological as well as metabolic changes, placing ‘astroglial fatty acid metabolism’ at the center of the pathogenic cascade in AD.
PMCID: PMC4059364  PMID: 17908174
Alzheimer’s disease; astroglia; ceramide; fat; rat
13.  Using Dynamic Gene Module Map Analysis To Identify Targets That Modulate Free Fatty Acid Induced Cytotoxicity 
Biotechnology progress  2007;24(1):29-37.
The objective of this study was to identify pathways that regulate the cytotoxicity induced by free fatty acids (FFAs) in human hepatoblastoma cells (HepG2/C3A). Gene expression profiles of HepG2/C3A cells were obtained at three time points, after 24, 48, and 72 h of exposure to different types of FFA. Saturated fatty acid (palmitate) was found to be cytotoxic. The pathways activated by the different FFAs at the different time points were identified using global gene module map analysis. Unsaturated FFAs exerted transcriptional regulation mainly within the first 24 h, whereas saturated FFA, palmitate, regulated energy production pathways, such as the electron transport chain (ETC) and tricarboxylic acid cycle, within the first 24 h. In the next 24 h, palmitate up-regulated 36 cell death relevant pathways and down-regulated several protective pathways, such as the pentose phosphate pathway and glutathione-related pathways. In the final 24 h, the FFAs did not induce significant transcriptional regulation. We hypothesized that palmitate induced cytotoxicity by first perturbing metabolic pathways in the initial 24 h, resulting in changes to factors, such as metabolites or signaling molecules, which subsequently triggered cell death relevant pathways in the next 24 h. The uptake and release of 27 metabolites were measured to further elucidate the metabolic changes in the first 24 h. It was determined that ketone bodies such as β-hydroxybutyrate and acetoacetate were important in separating the toxic from the nontoxic phenotypes. A regression model was used to identify the genes relevant to these metabolites. Some of the genes identified to be important were experimentally validated. It was found that ETC genes such as NADH dehydrogenase and succinate dehydrogenase were involved in palmitate induced cytotoxicity.
PMCID: PMC4059368  PMID: 18052188
14.  A multi-layer inference approach to reconstruct condition-specific genes and their regulation 
Bioinformatics  2013;29(12):1541-1552.
An important topic in systems biology is the reverse engineering of regulatory mechanisms through reconstruction of context-dependent gene networks. A major challenge is to identify the genes and the regulations specific to a condition or phenotype, given that regulatory processes are highly connected such that a specific response is typically accompanied by numerous collateral effects. In this study, we design a multi-layer approach that is able to reconstruct condition-specific genes and their regulation through an integrative analysis of large-scale information of gene expression, protein interaction and transcriptional regulation (transcription factor-target gene relationships). We establish the accuracy of our methodology against synthetic datasets, as well as a yeast dataset. We then extend the framework to the application of higher eukaryotic systems, including human breast cancer and Arabidopsis thaliana cold acclimation. Our study identified TACSTD2 (TROP2) as a target gene for human breast cancer and discovered its regulation by transcription factors CREB, as well as NFkB. We also predict KIF2C is a target gene for ER−/HER2− breast cancer and is positively regulated by E2F1. The predictions were further confirmed through experimental studies.
Availability: The implementation and detailed protocol of the layer approach is available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3673221  PMID: 23610368
15.  Tunable Resistive m-dPEG Acid Patterns on Polyelectrolyte Multilayers at Physiological Conditions: Template for Directed Deposition of Biomacromolecules 
This paper describes a new class of salt-responsive poly(ethylene glycol) (PEG) self-assembled monolayers (SAMs) on top of polyelectrolyte multilayer (PEMs) films. PEM surfaces with poly(diallyldimethylammonium chloride) as the topmost layer are chemically patterned by microcontact printing (μCP) oligomeric PEG molecules with an activated carboxylic acid terminal group (m-dPEG acid). The resistive m-d-poly(ethylene glycol) (m-dPEG) acid molecules on the PEMs films were subsequently removed from the PEM surface with salt treatment, thus converting the nonadhesive surfaces into adhesive surfaces. The resistive PEG patterns facilitate the directed deposition of various macromolecules such as polymers, dyes, colloidal particles, proteins, liposomes, and nucleic acids. Further, these PEG patterns act as a universal resist for different types of cells (e.g., primary cells, cell lines), thus permitting more flexibility in attaching a wide variety of cells to material surfaces. The patterned films were characterized by optical microscopy and atomic force microscopy (AFM). The PEG patterns were removed from the PEM surface at certain salt conditions without affecting the PEM films underneath the SAMs. Removal of the PEG SAMs and the stability of the PEM films underneath it were characterized with ellipsometry and optical microscopy. Such salt- and pH-responsive surfaces could lead to significant advances in the fields of tissue engineering, targeted drug delivery, materials science, and biology.
PMCID: PMC4040536  PMID: 18052083
16.  Global Protein Phosphorylation Dynamics during Deoxynivalenol-Induced Ribotoxic Stress Response in the Macrophage 
Toxicology and applied pharmacology  2013;268(2):201-211.
Deoxynivalenol (DON), a trichothecenemycotoxin produced by Fusarium that commonly contaminates food, is capable of activating mononuclear phagocytes of the innate immune system via a process termed the ribotoxic stress response (RSR). To encapture global signaling events mediating RSR, we quantified the early temporal (≤30 min) phosphoproteome changes that occurred in RAW 264.7 murine macrophage during exposure to a toxicologically relevant concentration of DON (250 ng/mL). Large-scale phosphoproteomic analysis employing stable isotope labeling of amino acids in cell culture (SILAC) in conjunction with titanium dioxide chromatography revealed that DON significantly upregulated or downregulated phosphorylation of 188 proteins at both known and yet-to-be functionally characterized phosphosites. DON-induced RSR is extremely complex and goes far beyond its prior known capacity to inhibit translation and activate MAPKs. Transcriptional regulation was the main target during early DON-induced RSR, covering over 20 percent of the altered phosphoproteins as indicated by Gene Ontology annotation and including transcription factors/cofactors and epigenetic modulators. Other biological processes impacted included cell cycle, RNA processing, translation, ribosome biogenesis, monocyte differentiation and cytoskeleton organization. Some of these processes could be mediated by signaling networks involving MAPK-, NFκB-, AKT- and AMPK-linked pathways. Fuzzy c-means clustering revealed that DON-regulated phosphosites could be discretely classified with regard to the kinetics of phosphorylation/dephosphorylation. The cellular response networks identified provide a template for further exploration of the mechanisms of trichothecenemycotoxins and other ribotoxins, and ultimately, could contribute to improved mechanism-based human health risk assessment.
PMCID: PMC4041276  PMID: 23352502
Ribotoxic stress response; phosphorylation; quantitative proteomics; trichothecenemycotoxin; deoxynivalenol
17.  Endothelial deletion of ADAM17 in mice results in defective remodeling of the semilunar valves and cardiac dysfunction in adults 
Mechanisms of development  2013;130(0):272-289.
Global inactivation of the metalloproteinase ADAM17 during mouse development results in perinatal lethality and abnormalities of the heart, including late embryonic cardiomegaly and thickened semilunar and atrioventricular valves. These defects have been attributed in part to a lack of ADAM17-mediated processing of HB-EGF, as absence of soluble HB-EGF results in similar phenotypes. Because valvular mesenchymal cells are largely derived from cardiac endothelial cells, we generated mice with a floxed Adam17 allele and crossed these animals with Tie2-Cre transgenics to focus on the role of endothelial ADAM17 in valvulogenesis. We find that although hearts from late-stage embryos with ablation of endothelial ADAM17 appear normal, an increase in valve size and cell number is evident, but only in the semilunar cusps. Unlike Hbegf−/− valves, ADAM17-null semilunar valves do not differ from controls in acute cell proliferation at embryonic day 14.5 (E14.5), suggesting compensatory processing of HB-EGF. However, levels of the proteoglycan versican are significantly reduced in mutant hearts early in valve remodeling (E12.5). After birth, aortic valve cusps from mutants are not only hyperplastic but also show expansion of the glycosaminoglycan-rich component, with the majority of adults exhibiting aberrant compartmentalization of versican and increased deposition of collagen. The inability of mutant outflow valve precursors to transition into fully mature cusps is associated with decreased postnatal viability, progressive cardiomegaly, and systolic dysfunction. Together, our data indicate that ADAM17 is required in valvular endothelial cells for regulating cell content as well as extracellular matrix composition and organization in semilunar valve remodeling and homeostasis.
PMCID: PMC3622831  PMID: 23354118
Valve; metalloproteinase; proteoglycan; echocardiography; endothelial; extracellular matrix
18.  Quantitative, solution-phase profiling of multiple transcription factors in parallel 
Analytical and bioanalytical chemistry  2013;405(8):2461-2468.
Transcription factors are regulatory proteins that bind to specific sites of chromosomal DNA to enact responses to intracellular and extracellular stimuli. Transcription factor signalling networks are branched and interconnected so that any single transcription factor can activate many different genes and one gene can be activated by a combination of different transcription factors. Thus, trying to characterize a cellular response to a stimulus by measuring the level of only one transcription factor potentially ignores important simultaneous events that contribute to the response. Hence, parallel measurements of transcription factors are necessary to capture the breadth of valuable information about cellular responses that would not be obtained by measuring only a single transcription factor. We have sought to develop a new, scalable, flexible, and sensitive approach to analysis of transcription factor levels that complements existing parallel approaches. Here, we describe proof-of-principle analyses of purified human transcription factors and breast cancer nuclear extracts. Our assay can successfully quantify transcription factors in parallel with ~10-fold better sensitivity than current techniques. Sensitivity of the assay can be further increased by 200-fold through the use of PCR for signal amplification.
PMCID: PMC3582790  PMID: 23361227
Transcription Factors; Parallel; DNA binding activity; Magnetic Beads separation; Breast Cancer
19.  Palmitate-activated astrocytes via SPT increase BACE1 in primary neurons by SMases 
Neurobiology of aging  2012;34(2):540-550.
Astrocytes play a critical role in neurodegenerative diseases, including Alzheimer’s disease (AD). Previously, we showed that saturated free-fatty acid, palmitate (PA), upregulates BACE1 level and amyloidogenesis in primary rat neurons mediated by astrocytes. However, the molecular mechanisms by which conditioned media from PA-treated astrocytes upregulates BACE1 level in neurons are unknown. This study demonstrates that serine palmitoyltransferase (SPT) in the astrocytes increases ceramide levels, which enhances the release of cytokines that mediate the activation of neural and acidic sphingomyelinase (N-SMase and A-SMase) in the neurons, to propagate the deleterious effects of palmitate, i.e. BACE1 upregulation. In support of the relevance of SPT in AD, our lab recently measure and found SPT levels to be significantly upregulated in AD brains as compared to controls (Geekiyanage and Chan, 2011). Cytokines, namely TNFα and IL-1β, released into the conditioned media of PA-treated astrocytes activate N-SMase and A-SMase in the neurons. Neutralizing the cytokines in the PA-treated astrocyte conditioned media reduced BACE1 upregulation. However, inhibiting SPT in the astrocytes decreased the levels of both TNFα and IL-1β in the conditioned media, which in turn reduced the SMase activities and BACE1 level in primary neurons. Thus, our results suggest that the activation of the astrocytes by PA is mediated by SPT, and the activated astrocytes increases BACE1 level in the neurons, the latter is mediate by the SMases.
PMCID: PMC3459302  PMID: 22727944
Alzheimer’s disease; Fatty acid; Sphingomyelinase; Serine palmitoyltransferase; Ceramide; TNFα; IL-1β
20.  Cleavage of Hyaluronan is Impaired in Aged Dermal Wounds 
Changes in extracellular matrix (ECM) are one of many components that contribute to impaired wound healing in aging. This study examined the effect of age on the glycosaminoglycan hyaluronan (HA) in normal and wounded dermis from young (4–6 month-old) and aged (22–24 month-old) mice. HA content and size was similar in the normal dermis of young and aged mice. Dermal explants labeled with [3H]-glucosamine showed decreased generation of smaller forms of HA in aged explants relative to young explants. Aged mice exhibited delayed wound repair compared with young mice with the greatest differential at 5 days. Expression of hyaluronan synthase (HAS) 2,3 and hyaluronidase (HYAL) 1-3 mRNA in wounds of young and aged mice was similar. There was a trend toward decreased HYAL protein expression in aged wound dermis, which was accompanied by changes in detectable HYAL activity. Total HA content was similar in young and aged wound dermis. There was significantly less HA in the lower MW range (~250 kDa and smaller) in 5-day wound dermis, but not 9-day wound dermis, from aged mice relative to young mice. We propose that decreased cleavage of HA is an additional component of impaired dermal wound healing in aging.
PMCID: PMC3570623  PMID: 23022999
Wound healing; Dermis; Age; Mice; Hyaluronan; Hyaluronan Synthase; Hyaluronidase
21.  A Classification Framework Applied to Cancer Gene Expression Profiles 
Journal of healthcare engineering  2013;4(2):10.1260/2040-2295.4.2.255.
Classification of cancer based on gene expression has provided insight into possible treatment strategies. Thus, developing machine learning methods that can successfully distinguish among cancer subtypes or normal versus cancer samples is important. This work discusses supervised learning techniques that have been employed to classify cancers. Furthermore, a two-step feature selection method based on an attribute estimation method (e.g., ReliefF) and a genetic algorithm was employed to find a set of genes that can best differentiate between cancer subtypes or normal versus cancer samples. The application of different classification methods (e.g., decision tree, k-nearest neighbor, support vector machine (SVM), bagging, and random forest) on 5 cancer datasets shows that no classification method universally outperforms all the others. However, k-nearest neighbor and linear SVM generally improve the classification performance over other classifiers. Finally, incorporating diverse types of genomic data (e.g., protein-protein interaction data and gene expression) increase the prediction accuracy as compared to using gene expression alone.
PMCID: PMC3873740  PMID: 23778014
classification; cancer; feature selection; gene expression; machine learning; supervised learning
22.  Time Controlled Release of Arabinofuranosylcytosine (Ara-C) from Agarose Hydrogels using Layer-by-Layer Assembly: An In Vitro Study 
Journal of biomaterials science. Polymer edition  2011;23(0):10.1163/092050610X552221.
Experimentally induced axonal regeneration is compromised by glial scar formation arising from leptomeningeal fibroblasts cells in and around the hydrogel scaffold implanted for nerve repair. Strategies are needed to prevent such fibroblastic reactive cell layer formation for enhanced axonal regeneration. Here, we implement the technique of layer-by-layer assembled degradable, hydrogen bonded multilayers on agarose hydrogels to incorporate an anti-mitotic drug (1-β-D-arabinofuranosylcytosine (Ara-C)) within the agarose hydrogels. We show controlled release of Ara-C under physiological conditions over a period of days. The concentrations of Ara-C released from agarose at the different time points were sufficient to inhibit fibroblast growth in vitro, while not adversely affecting the viability of the neuronal cells.
PMCID: PMC3873741  PMID: 21294967
Time controlled release; agarose; Ara-C; layer-by-layer assembly; reactive cell layer; nerve repair
23.  Oligomerization of the transmembrane domain of IRE1α in SDS micelles 
IRE1α (Inositol-requiring enzyme 1 α), an endoplasmic reticulum (ER)-resident sensor for mammalian unfolded protein response, is a type I transmembrane protein which has a bifunctional enzyme containing kinase and RNase domains. Although the luminal domain and cytosolic domain of IRE1α are thought to play crucial roles in regulating the protein activity, no functional and structural studies of the transmembrane domain exist thus far. Herein, using CD spectroscopy, we report that the transmembrane domain of the IRE1α is alpha helical in a membrane-like environment. In addition, SDS-PAGE and FRET analyses support that the transmembrane domain forms oligomers in SDS micelles. Thus, the study would provide insights into how the transmembrane domain plays a role in regulating the IRE1α protein activity.
PMCID: PMC3489956  PMID: 23041190
endoplasmic reticulum; transmembrane domain; dimerization; IRE1α
Nano LIFE  2012;2(3):1241005-.
The development of nanoscale delivery vehicles for siRNAs is a current topic of considerable importance. However, little is understood about the exact trafficking mechanisms for siRNA-vehicle complexes across the plasma membrane and into the cytoplasm. While some information can be gleaned from studies on delivery of plasmid DNA, the different delivery requirements for these two vehicles makes drawing specific conclusions a challenge. However, using chemical inhibitors of different endocytosis pathways, studies on which endocytotic pathways are advantageous and deleterious for the delivery of nucleic acid drugs are emerging. Using this information as a guide, it is expected that the future development of effective siRNA delivery vehicles and therapeutics will be greatly improved.
PMCID: PMC3743083  PMID: 23956796
RNA interference; siRNA; pDNA; nanoparticles; therapeutics; endocytosis
25.  Design of siRNA Therapeutics from the Molecular Scale 
While protein-based therapeutics is well-established in the market, development of nucleic acid therapeutics has lagged. Short interfering RNAs (siRNAs) represent an exciting new direction for the pharmaceutical industry. These small, chemically synthesized RNAs can knock down the expression of target genes through the use of a native eukaryotic pathway called RNA interference (RNAi). Though siRNAs are routinely used in research studies of eukaryotic biological processes, transitioning the technology to the clinic has proven challenging. Early efforts to design an siRNA therapeutic have demonstrated the difficulties in generating a highly-active siRNA with good specificity and a delivery vehicle that can protect the siRNA as it is transported to a specific tissue. In this review article, we discuss design considerations for siRNA therapeutics, identifying criteria for choosing therapeutic targets, producing highly-active siRNA sequences, and designing an optimized delivery vehicle. Taken together, these design considerations provide logical guidelines for generating novel siRNA therapeutics.
PMCID: PMC3749788  PMID: 23976875
siRNA therapeutic; RNAi; liver cancer; siRNA design; delivery vehicle design

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