Protein ANalysis THrough Evolutionary Relationships Research Articles

Expression Profiling of Human Schlemm's Canal Endothelial Cells From Eyes With and Without Glaucoma.

Ocular hypertension is a major risk factor for glaucoma and the inner wall of Schlemm's canal (SC) endothelia participates in the regulation of aqueous humor outflow resistance. This study aimed to identify differentially expressed genes in primary cultures of SC cells from glaucoma patients. This study examined SC samples from three glaucoma cases and four controls. Schlemm's canal cells were isolated from eight different postmortem human eyes. Total RNA was extracted, labeled, and hybridized to Illumina HumanWG-6 BeadChips containing probes for approximately 47,000 human transcripts. After extracting the data using Illumina GenomeStudio software, the data were normalized and analyzed using the R package limma in Bioconductor. Using Protein ANalysis THrough Evolutionary Relationships (PANTHER) software, gene ontology analysis of highly expressed genes was executed in controls and glaucoma groups separately. Pathway analysis was performed with differentially expressed genes using WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). Selected genes were validated using droplet digital PCR (ddPCR). Gene ontology analysis indicated similar functional categories in cases and controls. Differential analysis identified a total of 113 genes with at least 2-fold expression changes in cases. Pathway analysis indicated significant enrichment of genes in cell adhesion, heparin binding, glycosaminoglycan binding, filopodium, and extracellular matrix remodeling. Eighteen selected genes with differential expression were successfully validated using ddPCR. This study represents the first genome-wide expression study of human primary SC cells from glaucoma patients and provides a potential list of targets regulating SC cell stiffness and pore formation, eventually the outflow resistance in glaucoma individuals.

Altered exosomal protein expression in the serum of NF-κB knockout mice following skeletal muscle ischemia-reperfusion injury.

BackgroundThe NF-κB signaling pathway plays a role in local and remote tissue damage following ischemia-reperfusion (I/R) injury to skeletal muscles. Evidence suggests that exosomes can act as intercellular communicators by transporting active proteins to remote cells and may play a role in regulating inflammatory processes. This study aimed to profile the exosomal protein expression in the serum of NF-κB knockout mice following skeletal muscle ischemia-reperfusion injury.ResultsTo investigate the potential changes in protein expression mediated by NF-κB in secreted exosomes in the serum following I/R injury, the levels of circulating exosomal proteomes in C57BL/6 and NF-κB−/− mice were compared using two dimensional differential in-gel electrophoresis (2-DE), liquid chromatography tandem mass spectrometry (LC-MS/MS), and proteomic analysis. In C57BL/6 mice, the levels of circulating exosomal proteins, including complement component C3 prepropeptide, PK-120 precursor, alpha-amylase one precursor, beta-enolase isoform 1, and adenylosuccinate synthetase isozyme 1, increased following I/R injury. However, in the NF-κB−/− mice, the expression of the following was upregulated in the exosomes: protease, serine 1; glyceraldehyde-3-phosphate dehydrogenase-like isoform 1; glyceraldehyde-3-phosphate dehydrogenase; and pregnancy zone protein. In contrast, the expression of apolipoprotein B, complement component C3 prepropeptide, and immunoglobulin kappa light chain variable region was downregulated in NF-κB−/− mice. Bioinformatic annotation using the Protein Analysis Through Evolutionary Relationships (PANTHER) database revealed that the expression of the exosomal proteins that participate in metabolic processes and in biological regulation was lower in NF-κB−/− mice than in C57BL/6 mice, whereas the expression of proteins that participate in the response to stimuli, in cellular processes, and in the immune system was higher.ConclusionsThe data presented in this study suggest that NF-κB might regulate exosomal protein expression at a remote site via circulation following I/R injury.

Proteomic analysis of cerebrospinal fluid: toward the identification of biomarkers for gliomas.

Gliomas are the most common primary brain tumors in adults and, despite advances in the understandings of glioma pathogenesis in the genetic era, they are still ineradicable, justifying the need to develop more reliable diagnostic and prognostic biomarkers for this malignancy. Because changes in cerebrospinal fluid (CSF) are suggested to be capable of sensitively reflecting pathological processes, e.g., neoplastic conditions, in the central nervous system, CSF has been deemed a valuable source for potential biomarkers screening in this era of proteomics. This systematic review focused on the proteomic analysis of glioma CSF that has been published to date and identified a total of 19 differentially expressed proteins. Further functional and protein-protein interaction assessments were performed by using Protein Analysis Through Evolutionary Relationships (PANTHER) website and Ingenuity Pathway Analysis (IPA) software, which revealed several important protein networks (e.g., IL-6/STAT-3) and four novel focus proteins (IL-6, galanin (GAL), HSPA5, and WNT4) that might be involved in glioma pathogenesis. The concentrations of these focus proteins were subsequently determined by enzyme-linked immunosorbent assay (ELISA) in an independent set of CSF and tumor cyst fluid (CF) samples. Specifically, glioblastoma (GBM) CF had significantly lower GAL, HSPA5, and WNT4 levels than CSF from different grades of glioma. In contrast, IL-6 level was significantly higher in GBM CF when compared with CSF and, among different CSF groups, was highest in GBM CSF. Therefore, these candidate protein biomarkers, identified from both the literatures and in silico analysis, may have potentials in clinical diagnosis, prognosis evaluation, treatment response monitoring, and novel therapeutic targets identification for patients with glioma.

Biomechanical regulation of leptin expression in vascular smooth muscle both in vivo and in vitro: a novel vascular‐proteomic and physiological approach (866.9)

Hypertension is considered one of the major risk factors in developing cardiovascular diseases. Hemodynamic abnormality in hypertension is associated with structural and functional alterations which are mainly mediated via leptin. Molecular mechanisms associated with leptin‐mediated blood vessels remodeling both in vivo and in vitro have not been fully elucidated. In this study, we investigated the effect of partial portal vein ligation (PPVL) on leptin expression in vascular smooth muscle (VSMC) and secretion. We used blood vessels organ culture under mechanical stretch in order to investigate molecular mechanisms of leptin‐induced VSMC remodeling. Data showed that leptin expression and ROS production significantly increased in VSMC after 7 and 14 days post PPVL. A significant increase in serum leptin levels was observed in PPVL. Exposing the blood vessels to mechanical stretch (mimicking hypertension) significantly increased nuclear translocation of GATA‐4 and NFAT which were attenuated by the co‐administration of an anti‐leptin receptor antibody and the RhoA inhibitor C3. In addition, vascular‐proteomics platform was performed assessing differential proteome/systems biology profile between stretched and unstretched blood vessels to investigate the underlying mechanisms involved in vascular hypertrophy. A differential display of proteins were identified (7 proteins were upregulated vs. 12 downregulated) using PANTHER (Protein Analysis Through Evolutionary Relationships) system and Pathway Studio 8. Our results indicate that the activation of GATA‐4 & ROS production plays a pivotal role in hypertension signaling, leading to leptin synthesis and VSMC hypertrophy.Grant Funding Source: Supported by CNRS and MPP at AUB

Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention

We hypothesized that genetic variation affects responsiveness to 17-alpha hydroxyprogesterone caproate (17P) for recurrent preterm birth prevention. Women of European ancestry with ≥1 spontaneous singleton preterm birth at <34 weeks' gestation who received 17P were recruited prospectively and classified as a 17P responder or nonresponder by the difference in delivery gestational age between 17P-treated and -untreated pregnancies. Samples underwent whole exome sequencing. Coding variants were compared between responders and nonresponders with the use of the Variant Annotation, Analysis, and Search Tool (VAAST), which is a probabilistic search tool for the identification of disease-causing variants, and were compared with a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway candidate gene list. Genes with the highest VAAST scores were then classified by the online Protein ANalysis THrough Evolutionary Relationships (PANTHER) system into known gene ontology molecular functions and biologic processes. Gene distributions within these classifications were compared with an online reference population to identify over- and under- represented gene sets. Fifty women (9 nonresponders) were included. Responders delivered 9.2 weeks longer with 17P vs 1.3 weeks' gestation for nonresponders (P < .001). A genome-wide search for genetic differences implicated the NOS1 gene to be the most likely associated gene from among genes on the KEGG candidate gene list (P < .00095). PANTHER analysis revealed several over-represented gene ontology categories that included cell adhesion, cell communication, signal transduction, nitric oxide signal transduction, and receptor activity (all with significant Bonferroni-corrected probability values). We identified sets of over-represented genes in key processes among responders to 17P, which is the first step in the application of pharmacogenomics to preterm birth prevention.

Trichostatin A protects against cisplatin-induced ototoxicity by regulating expression of genes related to apoptosis and synaptic function

ObjectiveAlthough inhibition of histone deacetylases (HDACs) has been shown to protect against cisplatin-induced hearing loss, the underlying mechanism is still poorly understood. In the present study, we aim to investigate the protective effect of trichostatin A (TSA), a specific inhibitor of HDACs, on cisplatin-induced ototoxicity and to determine the differentially expressed genes involved in this process. MethodsThe basilar membrane of the cochlea was isolated from 3-day newborn Wistar rats. Organotypic cultures were treated with 150μM cisplatin or 200nM TSA. For combination treatment, cells were pre-incubated with TSA for 1h, followed by TSA plus cisplatin treatment. Rhodamine-phalloidin staining was used to label hair cells, and immunocytochemistry with an anti-neurofilament-200 antibody was applied to label spiral ganglion neurons (SGNs). Global expression profile microarray analysis was used to identify differentially expressed genes. Molecular function and signal pathway analysis were performed using a protein analysis through evolutionary relationships (PANTHER) classification system. Real-time quantitative PCR (qPCR) was carried out for data validation. ResultsSevere loss of hair cells and SGNs occurred after 48h of cisplatin incubation, while TSA significantly increased the number of hair cells and SGNs in the combination treatment group (P<0.05). Compared with control, expression of 71 genes were up-regulated and 383 genes were down-regulated upon cisplatin treatment. Addition of TSA induced the up-regulation of 1387 genes and down-regulation of 1226 genes as compared with cisplatin administration alone. After cisplatin treatment, we observed significant down-regulation of mRNA for several genes related to synaptic function genes, including Camk2a, Camk2b, Vglut1, Snap25 and Rab3b, whereas pretreatment with TSA elevated mRNA levels of these genes. TSA greatly decreased expression of genes related to the calcium signaling pathway (Capn1 and Capn2) and apoptosis signaling pathway (Tnfrsf1a and Tp53), while addition of TSA significantly reduced levels of Tnfrsf1a and Tp53 compared with cisplatin alone (P<0.01). ConclusionsOur results suggested that TSA might protect against cisplatin-induced ototoxicity via mediating expression of genes responsible for regulating apoptosis, intracellular calcium homeostasis, neurotransmitter synthesis and release, and synaptic plasticity.

Proteomic Profiling and Interactome Analysis of ER-Positive/HER2/neuNegative Invasive Ductal Carcinoma of the Breast: Towards Proteomics Biomarkers

Breast cancer, especially ER positive/HER2/neu negative IDC, is the predominant subtype of invasive ductal carcinoma. Although proteomic approaches have been used towards biomarker discovery in clinical breast cancer, ER positive/HER2/neu negative IDC is the least studied subtype. To discover biomarkers, as well as to understand the molecular events associated with disease progression of estrogen receptor positive/HER2/neu negative subtype of invasive ductal carcinoma, differential protein expression profiling was performed by using LC-MS(E) (MS at elevated energy). A total of 118 proteins were identified, of which 26 were differentially expressed. These identified proteins were functionally classified and their interactions and coexpression were analyzed by using bioinformatic tools PANTHER (Protein Analysis THrough Evolutionary Relationships) and STRING (Search Tool for the Retrieval of Interacting Genes). These proteins were found to be upregulated and were involved in cytoskeletal organization, calcium binding, and stress response. Interactions of annexin A5, actin, S100 A10, glyceraldehyde 3 phosphate dehydrogenase, superoxide dismutase 1, apolipoprotein, fibrinogen, and heat shock proteins were prominent. Differential expression of these proteins was validated by two-dimensional gel electrophoresis and Western blot analysis. The cluster of these proteins may serve as a signature profile for estrogen receptor positive/ HER2/neu negative subtype.

SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways

Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a protein- or gene-centric fashion. Unfortunately, proteome-wide analysis of non-synonymous single-nucleotide variations (nsSNVs) is not easy to perform because information on nsSNVs and functionally important sites are not well integrated both within and between databases and their search engines. We have developed SNVDis that allows evaluation of proteome-wide nsSNV distribution in functional sites, domains and pathways. More specifically, we have integrated human-specific data from major variation databases (UniProtKB, dbSNP and COSMIC), comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved Domain Database (CDD) and pathway information from Protein ANalysis THrough Evolutionary Relationships (PANTHER) and mapped all of them in a uniform and comprehensive way to the human reference proteome provided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, which are extracted from a number of different sources, provides a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out whether there is an over- or under-representation of nsSNVs in specific domains, pathways or user-defined protein lists. The underlying datasets are updated once every 3months. SNVDis is freely available at http://hive.biochemistry.gwu.edu/tool/snvdis.

Heuristic Methods for Finding Pathogenic Variants in Gene Coding Sequences

These are exciting times, with a plethora of new technologies that are expediting discovery of the genetic underpinnings of human disease. Comprehensive resequencing of the human genome is now feasible and affordable, allowing each person's entire genetic makeup to be revealed. The major focus of

Investigation of serum proteome alterations in human glioblastoma multiforme

Glioblastoma multiforme (GBM) or grade IV astrocytoma is the most common and lethal adult malignant brain tumor. The present study was conducted to investigate the alterations in the serum proteome in GBM patients compared to healthy controls. Comparative proteomic analysis was performed employing classical 2DE and 2D-DIGE combined with MALDI TOF/TOF MS and results were further validated through Western blotting and immunoturbidimetric assay. Comparison of the serum proteome of GBM and healthy subjects revealed 55 differentially expressed and statistically significant (p <0.05) protein spots. Among the identified proteins, haptoglobin, plasminogen precursor, apolipoprotein A-1 and M, and transthyretin are very significant due to their functional consequences in glioma tumor growth and migration, and could further be studied as glioma biomarkers and grade-specific protein signatures. Analysis of the lipoprotein pattern indicated elevated serum levels of cholesterol, triacylglycerol, and low-density lipoproteins in GBM patients. Functional pathway analysis was performed using multiple software including ingenuity pathway analysis (IPA), protein analysis through evolutionary relationships (PANTHER), database for annotation, visualization and integrated discovery (DAVID), and GeneSpring to investigate the biological context of the identified proteins, which revealed the association of candidate proteins in a few essential physiological pathways such as intrinsic prothrombin activation pathway, plasminogen activating cascade, coagulation system, glioma invasiveness signaling, and PI3K signaling in B lymphocytes. A subset of the differentially expressed proteins was applied to build statistical sample class prediction models for discrimination of GBM patients and healthy controls employing partial least squares discriminant analysis (PLS-DA) and other machine learning methods such as support vector machine (SVM), Decision Tree and Naïve Bayes, and excellent discrimination between GBM and control groups was accomplished.

DNMT1: An emerging target in the treatment of invasive urinary bladder cancer

ObjectivesMore than 14,000 people die from invasive urothelial carcinoma (iUC) of the urinary bladder each year in the USA, and more effective therapies are needed. Naturally occurring canine iUC very closely resembles the disease in humans and serves as a highly relevant translational model for novel therapy of human iUC. Work was undertaken to identify new targets for anticancer therapy in dogs with the goal of translating successful therapeutic strategies into humans with iUC. Materials and methodsMicroarray expression analyses were conducted on mRNA extracted from canine normal bladder (n = 4) and iUC tissues (n = 4) using Genome Array 1.0 and analyzed by GeneSpring GX 11, with the stringency of P < 0.02 and a ≥2-fold change. The genes thus identified were further analyzed for functional and pathway analysis using Protein ANalysis THrough Evolutionary Relationships (PANTHER) Classification System. In selecting genes for further study, consideration was given for evidence of a role of the gene in human iUC. From these analyses, DNA methyltransferase 1 (DNMT1) was selected for further study. Immunohistochemistry (IHC) of canine normal bladder and iUC tissues was performed to confirm the microarray expression analyses. The effects of targeting DNMT1 in vitro was assessed through MTT assay and Western blot of canine iUC cells treated with 5-azacitidine (5-azaC) and trichostatin A (TSA). ResultsDNMT1 was expressed in 0 of 6 normal canine bladder samples and in 10 of 22 (45%) canine iUC samples. The proliferation of canine iUC cells was inhibited by 5-azaC (at concentrations ≥5 μm) and by TSA (at concentrations ≥0.1 μm). Western blot results were supportive of DNMT1-related effects having a role in the antiproliferative activity. ConclusionsMicroarray expression analyses on canine tissues identified DNMT1 as a potentially “targetable” gene. Expression of DNMT1 in canine iUC was confirmed by IHC, and in vitro studies confirmed that drugs that inhibit DNMT1 have antiproliferative effects. These findings are similar to those recently reported in human iUC and are also in line with results of a preclinical (prehuman) trial of 5-azaC in dogs with naturally occurring iUC. DNMT1 has excellent potential as a target for iUC therapy in humans.

Abstract 1048: DNMT1: An emerging target in the treatment of invasive urinary bladder cancer

Abstract Introduction: More than 14,000 people die from invasive transitional cell carcinoma (InvTCC) of the urinary bladder each year in the US, and more effective therapies are needed. Naturally-occurring canine InvTCC very closely resembles the disease in humans and serves as a highly relevant translational model for novel therapy of human InvTCC. Work was undertaken to identify new entry points for anticancer therapy in dogs with the goal of translating successful therapeutic strategies into humans with InvTCC. Methods: Microarray expression analyses were conducted on canine normal bladder from dogs with no urinary tract disease (n=4) and InvTCC tissues (n=4) using Genome Array 1.0 and analyzed by GeneSpring GX 11, with the stringency of p &amp;lt; 0.02 and a ≥2-fold change. The genes thus identified were further analyzed for functional and pathway analysis using PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System. In selecting genes for further study, consideration was also given for evidence of a role of the gene in human InvTCC. From these analyses, DNA methyltransferase 1 (DNMT1) was selected for further study. Immunohistochemistry (IHC) of canine normal bladder and InvTCC tissues was performed to confirm the microarray expression analyses. The effects of targeting DNMT1 in vitro was assessed through MTT assay and Western blot of canine InvTCC cells treated with 5-azacitidine (5-azaC) and trichostatin A (TSA). Results: DNMT1 was expressed in 0 of 6 normal canine bladder samples and in 10 of 22 (45%) canine InvTCC samples. The proliferation of canine InvTCC cells was inhibited by 5-azaC (at concentrations &amp;gt; 5µM) and by TSA (at concentrations &amp;gt; 0.1µM). Western blot results were supportive of DNMT1-related effects having a role in the antiproliferative activity. Discussion and Conclusions: Microarray expression analyses on canine tissues identified DNMT1 as a potentially “targetable” gene. Expression of DNMT1 in canine InvTCC was confirmed by IHC, and in vitro studies confirmed that drugs that inhibit DNMT1 have antiproliferative effects. These findings are similar to those recently reported by Wu et al. (Cancer, 2011) in human InvTCC. These findings are also in line with results of a pre-clinical (pre-human) trial of 5-azaC in dogs with naturally-occurring InvTCC, in which remission or cancer control occurred in 72% of dogs. In conclusion, DNMT1 has excellent potential as a target for InvTCC therapy in humans. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1048. doi:1538-7445.AM2012-1048

Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response

Vivax malaria is the most widely distributed human malaria resulting in 80-300 million clinical cases every year. It causes severe infection and mortality but is generally regarded as a benign disease and has not been investigated in detail. The present study aimed to perform human serum proteome analysis in a malaria endemic area in India to identify potential serum biomarkers for vivax malaria and understand host response. The proteomic analysis was performed on 16 age and gender matched subjects (vivax patients and control) in duplicate. Protein extraction protocols were optimized for large coverage of the serum proteome and to obtain high-resolution data. Identification of 67 differentially expressed and statistically significant (Student's t-test; p<0.05) protein spots was established by MALDI-TOF/TOF mass spectrometry. Many of the identified proteins such as apolipoprotein A and E, serum amyloid A and P, haptoglobin, ceruloplasmin, and hemopexin are interesting from a diagnostic point of view and could further be studied as potential serum biomarkers. The differentially expressed serum proteins in vivax malaria identified in this study were subjected to functional pathway analysis using multiple software, including Ingenuity Pathway Analysis (IPA), Protein ANalysis THrough Evolutionary Relationships (PANTHER) and Database for Annotation, Visualization and Integrated Discovery (DAVID) functional annotation tool for better understanding of the biological context of the identified proteins, their involvement in various physiological pathways and association with disease pathogenesis. Functional pathway analysis of the differentially expressed proteins suggested the modulation of multiple vital physiological pathways, including acute phase response signaling, complement and coagulation cascades, hemostasis and vitamin D metabolism pathway due to this parasitic infection. This article is part of a Special Issue entitled: Proteomics: The clinical link.

Gene Expression Profiling of Early-Phase Sjögren's Syndrome in C57BL/6.NOD-Aec1Aec2Mice Identifies Focal Adhesion Maturation Associated with Infiltrating Leukocytes

Despite considerable efforts, the molecular and cellular events in lacrimal gland tissues initiating inflammatory responses leading to keratoconjunctivitis sicca (KCS), autoimmunity, and Sjögren's syndrome (SjS) have yet to be defined. To determine whether altered glandular homeostasis occurs before the onset of autoimmunity, a temporal transcriptome study was carried out in an animal model of primary SjS. Using oligonucleotide microarrays, gene expression profiles were generated for lacrimal glands of C57BL/6.NOD-Aec1Aec2 mice 4 to 20 weeks of age. Pairwise analyses identified genes differentially expressed, relative to their 4-week expression, during the development of SjS-like disease. Statistical analyses defined differentially and coordinately expressed gene sets. The PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification system was used to define annotated biological processes or functions. Temporal transcript expression profiles of C57BL/6.NOD-Aec1Aec2 lacrimal glands before, or concomitant with, the first appearance of inflammatory cells revealed a highly restricted subset of differentially expressed genes encoding interactive extracellular matrix proteins, fibronectin, integrins, and syndecans. In contrast, genes encoding interepithelial junctional complex proteins defined alterations in tight junctions (TJ), adherens, desmosomes, and gap junctions, suggesting perturbations in the permeability of the paracellular spaces between epithelial barriers. Correlating with this were gene sets defining focal adhesion (FA) maturation and Ras/Raf-Mek/Erk signal transduction. Immunohistochemically, FAs were associated with infiltrating leukocytes and not with lacrimal epithelial cells. For the first time, FA maturations are implicated as initial biomarkers of impending autoimmunity in lacrimal glands of SjS-prone mice. Changes in TJ complex genes support an increased movement of cells through paracellular spaces.

암세포주와 공동 배양된 인간 지방 조직 유래 중간엽 줄기 세포의 유전자 발현 분석

중간엽 줄기 세포는 다분화능을 가지고 있으며 골수, 지방, 태반, 치아속질, 윤활막, 편도 및 가슴샘 등 인체의 다양한 조직에서 분리된다. 중간엽 줄기세포는 조직의 항상성을 조절하며 다분화능, 분리와 조작의 용이함, 암세포로의 화학주성 및 면역 반응 조절 등의 특징을 가지고 있어서 재생 의학, 암 치료 및 식대주 질환(GVHD) 등에 이용할 수 있는 세포치료제로 주목 받고 있다. 하지만 주위 세포와 조직을 지지하고 조절하는 특징과 관련하여 중간엽 줄기세포가 혈관 생성을 촉진하고 성장인자를 분비하며 암세포를 공격하는 면역 반응을 억제함으로써 암의 진행을 촉진시킨다는 사실 또한 보고 되고 있다. 이러한 사실들로 인해 중간엽 줄기세포의 임상 적용이 제한되고 있다. 본 연구에서는 어떠한 기전을 통해서 중간엽 줄기세포가 암의 진행을 촉진하는 지지 세포로 기능하는지를 밝히기 위해서 인체 지방 조직에서 유래한 중간엽 줄기세포를 두 개의 암세포주(H460, U87MG)와 각각 공동 배양하고 microarray를 이용해서 암세포와 공동 배양되지 않은 중간엽 줄기세포와 유전자의 발현을 비교하였다. 두 암세포주와 공동배양에서 공통적으로 2배 이상 차이 나는 유전자를 DAVID (Database for Annotation, Visualization and Integrated Discovery)와 PANTHER (Protein ANalysis THrough Evolutionary Relationships)를 이용해 분석하였으며 생물학적 과정, 분자적 기능, 세포의 구성 성분, 단백질의 종류, 질병과 인체 조직 그리고 신호전달에 관련된 정보를 획득하였다. 이를 통해서 암세포는 중간엽 줄기세의 분화, 증식, 에너지 대사, 세포의 구조 및 분비기능을 조절하여 유전자의 발현 양상을 암 연관 섬유모세포(cancer associated fibroblast)와 유사한 세포로 변형 시킨다는 사실을 알 수 있었다. 본 연구의 결과는 중간엽 줄기세포를 이용한 임상 치료제의 효과와 안정성을 개선하는데 응용될 수 있을 것이다. Mesenchymal stem cells (MSC) are multipotent and can be isolated from diverse human tissues including bone marrow, fat, placenta, dental pulp, synovium, tonsil, and the thymus. They function as regulators of tissue homeostasis. Because of their various advantages such as plasticity, easy isolation and manipulation, chemotaxis to cancer, and immune regulatory function, MSCs have been considered to be a potent cell source for regenerative medicine, cancer treatment and other cell based therapy such as GVHD. However, relating to its supportive feature for surrounding cell and tissue, it has been frequently reported that MSCs accelerate tumor growth by modulating cancer microenvironment through promoting angiogenesis, secreting growth factors, and suppressing anti-tumorigenic immune reaction. Thus, clinical application of MSCs has been limited. To understand the underlying mechanism which modulates MSCs to function as tumor supportive cells, we co-cultured human adipose tissue derived mesenchymal stem cells (ASC) with cancer cell lines H460 and U87MG. Then, expression data of ASCs co-cultured with cancer cells and cultured alone were obtained via microarray. Comparative expression analysis was carried out using DAVID (Database for Annotation, Visualization and Integrated Discovery) and PANTHER (Protein ANalysis THrough Evolutionary Relationships) in divers aspects including biological process, molecular function, cellular component, protein class, disease, tissue expression, and signal pathway. We found that cancer cells alter the expression profile of MSCs to cancer associated fibroblast like cells by modulating its energy metabolism, stemness, cell structure components, and paracrine effect in a variety of levels. These findings will improve the clinical efficacy and safety of MSCs based cell therapy.

Current and Future Therapeutic Targets of Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic systematic autoimmune disease which affects about 1% of the population world wide. This article aimed to identify current therapeutic targets for RA based on data from the literature and drug target related databases. Identified targets were further analysed using a powerful bioinformatics tool, PANTHER (Protein ANalysis THrough Evolutionary Relationships). Additionally, we explored future possible therapeutic targets for RA and discussed the possibility of discovering novel drugs with improved efficacy and reduced toxicity for RA treatment. Data on current clinical drugs for RA treatment were extracted from the US Food and Drugs Administration (FDA) website. Candidate targets of RA were extracted from three online databases: Drugbank, Therapeutic Target Database (TTD) and Potential Drug Target Database (PDTD). A total of 95 clinical protein targets for RA have been identified and were analysed using the PANTHER Classification System. According to the PANTHER analysis, most commonly involved pathways in current RA targeting includes inflammation mediated by chemokine and cytokine signalling pathways, angiogenesis, p53 pathway, de novo purine biosynthesis, T-cell activation, apoptosis signalling pathway and vascular endothelial growth factor (VEGF) receptor signalling pathway. Accordingly, current clinical agents for the treatment of RA mainly include corticosteroids, non-steriodal anti-inflammatory drugs (NSAIDs) and disease-modifying antirheumatic drugs (DMARDs). In addition, a number of investigational targets for RA have been identified and many novel drugs for RA therapy are under investigation. Current approaches to handle RA aim to ameliorate inflammation, to relieve pain, and most importantly to protect the cartilage, joints and bones from further damage by blocking proinflammatory molecules and inhibit the production of matrix-degrading factors. New drugs for RA with improved efficacy and safety should be developed.

MicroRNA alterations in Barrett′s esophagus, esophageal adenocarcinoma, and esophageal adenocarcinoma cell lines following cranberry extract treatment: Insights for chemoprevention

Background:Aberrant expression of small noncoding endogenous RNA molecules known as microRNAs (miRNAs) is documented to occur in multiple cancer types including esophageal adencarcinoma (EAC) and its only known precursor, Barrett's esophagus (BE). Recent studies have linked dysregulation of specific miRNAs to histological grade, neoplastic progression and metastatic potential.Materials and Methods:Herein, we present a summary of previously reported dysregulated miRNAs in BE and EAC tissues as well as EAC cell lines and evaluate a cranberry proanthocyanidin rich extract's (C-PAC) ability to modulate miRNA expression patterns of three human EAC cell lines (JHEso-Ad-1, OE33 and OE19).Results:A review of 13 published studies revealed dysregulation of 87 miRNAs in BE and EAC tissues, whereas 52 miRNAs have been reported to be altered in BE or EAC cell lines, with 48% overlap with miRNA changes reported in tissues. We report for the first time C-PAC–induced modulation of five miRNAs in three EAC cell lines resulting in 26 validated gene targets and identification of key signaling pathways including p53, angiogenesis, T-cell activation and apoptosis. Additionally, mutiple cancer related networks were ideintified as modulated by C-PAC utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Analysis Through Evolutionary Relationships (PANTHER), and MetaCore analysis tools.Conclusions:Study results support the cancer inhibitory potential of C-PAC is in part attributable to C-PAC's ability to modify miRNA profiles within EAC cells. A number of C-PAC–modulated miRNAs have been been identified as dysregulated in BE and EAC. Further insights into miRNA dysregulation and modulation by select cancer preventive agents will support improved targeted interventions in high-risk cohorts.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb.org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.

Biocompatibility of peritoneal dialysis solutions determined by genomics of human leucocytes: a cross-over study.

Sir, Peritoneal dialysis (PD) is based on passive movement of water and soluble molecules across the peritoneum. In continuous ambulatory peritoneal dialysis (CAPD), the patient's abdomen is filled with a dialysate fluid introducing an osmotic gradient driven by electrolytes and glucose, or macromolecules such as icodextrin. Biocompatibility of PD fluids is the most important criterion to enable long-term dialysis without introducing clinically significant changes in the functional characteristics of the peritoneum and systemic inflammatory effects [1]. The effects of biocompatibility on clinical outcome include changes in the physiology of cell populations constituting the peritoneal cavity (leucocyte, mesothelial and endothelial cells, and fibroblasts) and the gene expression of peripheral blood mononuclear cells (PBMCs) triggering alterations in cytokine, chemokine and growth factor networks, upregulation of proinflammatory and profibrotic pathways, and induction of carbonyl and oxidative stress [2–4]. Our study objective was to compare the genome-wide gene expression signature of PBMCs of PD patients using glucose-based (GBF) and icodextrin-based peritoneal fluids (IBF) to allow a direct comparison of biocompatibility relevant intracellular processes with respect to the PD fluid used. This pilot study should give us first insights into the alterations in gene expression of leucocytes triggered by different PD fluids and should provide an informative basis for future research. Therefore, we conducted a random cross-over study in five stable ESRD patients being treated with CAPD between 4 and 18 months (demographic data are provided on our laboratory homepage in Table ​Table11 (http://www.meduniwien.ac.at/nephrogene/data/pd/)). Blood samples (10 ml) were collected immediately after a 4- to 6-h dwell of GBF (Physioneal® 40, Glucose 2.27% w/v, 395 mOsmol/l) and an overnight dwell of IBF (Extraneal®, icodextrin 7.5%, 284 mOsmol/l) [study approved by the local Institutional review board (Ethical Committee # EK-318/06, see http://ohrp.cit.nih.gov/search/asearch.asp)]. Oligoarrays were obtained from the Stanford University Functional Genomics core facility. All microarray experiment protocols can be found on the Stanford University webpage at http://cmgm.stanford.edu/pbrown/protocols/index.html. Stratagene Universal human reference RNA was used as a reference. Raw data files as well as the MIAME checklist are available at our laboratory webpage. Table 1 Biological processes separating IBF- and GBF-treated patient groups as derived on the level of PBMC differential gene expression A paired t-test (P < 0.05) of log-transformed expression values was used to evaluate differences between IBF and GBF treatment. Differentially expressed genes (DEGs) were hierarchically clustered and graphically represented using the MultiExperiment Viewer (MeV) (Pearson correlation, complete linkage) [5]. DEGs were furthermore analysed with respect to their molecular functions, biological processes and interaction partner using gene ontology terms (GO-Terms), PANTHER (Protein ANalysis THrough Evolutionary Relationships) ontologies and Online Predicted Human Interaction Database (OPHID). A total of 124 genes (fold change over two, 34 up-regulated and 90 down-regulated in the IBF group) were identified as being significantly differentially expressed in PBMCs comparing patients under IBF and GBF usage (Figure 1 online on our homepage). A total of 27 up-regulated genes assigned to IBF treatment and 81 up-regulated genes associated with GBF treatment could be classified according to PANTHER ontologies (Table ​(Table1).1). A number of the genes up-regulated in the course of IBF usage were found to be involved in immune response and inflammatory processes. Genes up-regulated by GBF usage in contrast are found to be assigned to development and signal transduction processes. Our study provides full genome differential gene expression profiles of PBMCs after peritoneal dialysis on a genome-wide scale comparing GBF and IBF peritoneal dialysis fluids confirming the differential involvement of inflammation. A limitation of our study is the small sample size of five CAPD patients. Therefore, we used a random cross-over design and computed a paired t-test. These pilot data suggest reduced inflammation and consequently an improved biocompatibility of GBF peritoneal fluids compared with IBF fluids. Certainly, further evaluation in larger studies is needed.

Molecular network of the comprehensive multiple sclerosis brain-lesion proteome

Background A recent proteomics study of multiple sclerosis (MS) lesion-specific proteome profiling clearly revealed a pivotal role of coagulation cascade proteins in chronic active demyelination. However, among thousands of proteins examined, nearly all of remaining proteins are yet to be characterized in terms of their implications in MS brain-lesion development. Methods By the systems biology approach using four different pathway analysis tools of bioinformatics, we studied molecular networks and pathways of the proteome dataset of acute plaques, chronic active plaques (CAP), and chronic plaques (CP). Results The database search on Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein analysis through evolutionary relationships (PANTHER) indicated the relevance of extracellular matrix (ECM)–mediated focal adhesion and integrin signaling to CAP and CP proteome. KeyMolnet disclosed a central role of the complex interaction among diverse cytokine signaling pathways in brain-lesion development at all disease stages, as well as a role of integrin signaling in CAP and CP. Ingenuity pathway analysis (IPA) identified the network constructed with a wide range of ECM components, such as collagen, type I α1, type I α2, type VI α2, type VI α3, fibronectin 1, fibulin 2, laminin α1, vitronectin, and heparan sulfate proteoglycan, as one of the networks highly relevant to CAP proteome. Conclusions Although four distinct platforms produced diverse results, they commonly suggested a role of ECM and integrin signaling in development of chronic lesions of MS. These in silico observations indicate that the selective blockade of the interaction between ECM and integrins in brain lesions in situ would be a target for therapeutic intervention in MS.