Cell Adhesion Processes Research Articles

Identification of the potential crucial genes in invasive ductal carcinoma using bioinformatics analysis.

Invasive ductal carcinoma (IDC) is a common histological type of breast cancer. The aim of this study was to identify the potential crucial genes associated with IDC and to provide valid biological information for further investigations. The gene expression profiles of GSE10780 which contained 42 histologically normal breast tissues and 143 IDC tissues were downloaded from the GEO database. Functional and pathway enrichment analysis of differentially expressed genes (DEGs) were performed and protein-protein interaction (PPI) network was analyzed using Cytoscape. In total, 999 DEGs were identified, including 667 up-regulated and 332 down-regulated DEGs. Gene ontology analysis demonstrated that most DEGs were significantly enriched in mitotic cell cycle, adhesion and protein binding process. Through PPI network analysis, a significant module was screened out, and the top 10 hub genes, CDK1, CCNB1, CENPE, CENPA, PLK1, CDC20, MAD2L1, HIST1H2BK, KIF2C and CCNA2 were identified from the PPI network. The expression levels of the 10 genes were validated in Oncomine database. KIF2C, MAD2L1 and PLK1 were associated with the overall survival. And we used cBioPortal to explore the genetic alterations of hub genes and potential drugs. In conclusion, the present study identified DEGs between normal and IDC samples, which could improve our understanding of the molecular mechanisms in the development of IDC, and these candidate genes might be used as therapeutic targets for IDC.

Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis

Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a false discovery rate <5% were detected in patients versus controls. Upregulated genes clustered in immunologic, cell adhesion, and keratin-related processes. Interestingly, 676 deregulated non-coding genes were detected, 257 of which were classified as antisense genes. Sense genes expressed opposite of these antisense genes were also deregulated in 42% of the observed sense-antisense gene pairs. The majority of the antisense genes had a similar effect sizes in an independent North American dataset with three genes (CTBP1-AS2, OTUD6B-AS1, and AGAP2-AS1) exceeding the study-wide Bonferroni-corrected P-value (PBonf < 0.0023, Pcombined= 1.1× 10-9, 1.4× 10-8, 1.7× 10-6, respectively). In this study, we highlight that together with coding genes, (antisense) long non-coding RNAs are deregulated in skin tissue of systemic sclerosis patients suggesting a novel class of genes involved in pathogenesis of systemic sclerosis.

Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans

The dramatic increase in membrane proteome complexity is arguably one of the most pivotal evolutionary events that underpins the origin of multicellular animals. However, the origin of a significant number of membrane families involved in metazoan development has not been clarified. In this study, we have manually curated the membrane proteomes of 22 metazoan and 2 unicellular holozoan species. We identify 123,014 membrane proteins in these 24 eukaryotic species and classify 86% of the dataset. We determine 604 functional clusters that are present from the last holozoan common ancestor (LHCA) through many metazoan species. Intriguingly, we show that more than 70% of the metazoan membrane protein families have a premetazoan origin. The data show that enzymes are more highly represented in the LHCA and expand less than threefold throughout metazoan species; in contrast to receptors that are relatively few in the LHCA but expand nearly eight fold within metazoans. Expansions related to cell adhesion, communication, immune defence, and developmental processes are shown in conjunction with emerging biological systems, such as neuronal development, cytoskeleton organization, and the adaptive immune response. This study defines the possible LHCA membrane proteome and describes the fundamental functional clusters that underlie metazoan diversity and innovation.

Modification of titanium alloys surface properties by plasma electrolytic oxidation (PEO) and influence on biological response.

Surface characteristics can mediate biological interaction improving or affecting the tissue integration after implantation of a biomaterial. Features such as topography, wettability, surface energy and chemistry can be key determinants for interactions between cells and materials. Plasma electrolytic oxidation (PEO) is a technique used to control this kind of parameters by the addition of chemical species and the production of different morphologies on the surfaces of titanium and its alloys. With the purpose to improve the biological response, surfaces of c.p titanium and Ti6Al4V were modified by using PEO. Different electrolytes, voltages, current densities and anodizing times were tested in order to obtain surfaces with different characteristics. The obtained materials were characterized by different techniques such as X-ray diffraction (XRD), scanning electron microscopy (SEM) and glow discharge optical emission spectroscopy (GDOES). Wettability of the obtained surfaces were measured and the corresponding surface energies were calculated. Superhydrophilic surfaces with contact angles of about 0 degrees were obtained without any other treatment but PEO and this condition in some cases remains stable after several weeks of anodizing; crystal phase composition (anatase-rutile) of the anodic surface appears to be critical for obtaining this property. Finally, in order to verify the biological effect of these surfaces, osteoblast were seeded on the samples. It was found that cell behavior improves as SFE (surface free energy) and coating porosity increases whereas it is affected negatively by roughness. Techniques for surface modification allow changes in the coatings such as surface energy, roughness and porosity. As a consequence of this, biological response can be altered. In this paper, surfaces of c.p Ti and Ti6Al4V were modified by using plasma electrolytic oxidation (PEO) in order to accelerate the cell adhesion process.

Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy.

BackgroundGingivo-buccal squamous cell carcinoma (GBSCC) is one of the most common oral cavity cancers in India with less than 50% patients surviving past 5 years. Here, we report a whole transcriptome profile on a batch of GBSCC tumours with diverse tobacco usage habits. The study provides an entire landscape of altered expression with an emphasis on searching for targets with therapeutic potential.MethodsWhole transcriptomes of 12 GBSCC tumours and adjacent normal tissues were sequenced and analysed to explore differential expression of genes. Expression changes were further compared with those in TCGA head and neck cohort (n = 263) data base and validated in an independent set of 10GBSCC samples.ResultsDifferentially expressed genes (n = 2176) were used to cluster the patients based on their tobacco habits, resulting in 3 subgroups. Immune response was observed to be significantly aberrant, along with cell adhesion and lipid metabolism processes. Different modes of immune evasion were seen across 12 tumours with up-regulation or consistent expression of CD47, unlike other immune evasion genes such as PDL1, FUT4, CTLA4 and BTLA which were downregulated in a few samples. Variation in infiltrating immune cell signatures across tumours also indicates heterogeneity in immune evasion strategies. A few actionable genes such as ITGA4, TGFB1 and PTGS1/COX1 were over expressed in most samples.ConclusionThis study found expression deregulation of key immune evasion genes, such as CD47 and PDL1, and reasserts their potential as effective immunotherapeutic targets for GBSCC, which requires further clinical studies. Present findings reiterate the idea of using transcriptome profiling to guide precision therapeutic strategies.

Impaired Expression of Focal Adhesion Kinase in Mesenchymal Stromal Cells from Low-Risk Myelodysplastic Syndrome Patients.

The pathogenic role of mesenchymal stromal cells (MSCs) in myelodysplastic syndromes (MDS) development and progression has been investigated by numerous studies, yet, it remains controversial in some aspects (1, 2). In the present study, we found distinct features of MSCs from low-risk (LR)-MDS stromal microenvironment as compared to those from healthy subjects. At the molecular level, focal adhesion kinase, a key tyrosine kinase in control of cell proliferation, survival, and adhesion process, was found profoundly suppressed in expression and activation in LR-MDS MSC. At a functional level, LR-MDS MSCs showed impaired growth and clonogenic capacity, which were independent of cellular senescence and apoptosis. The pro-adipogenic differentiation and attenuated osteogenic capacity along with reduced SDF-1 expression could be involved in creating an unfavorable microenvironment for hematopoiesis. In conclusion, our experiments support the theory that the stromal microenvironment is fundamentally altered in LR-MDS, and these preliminary data offer a new perspective on LR-MDS pathophysiology.

Abstract 4485: Identification and characterization of novel RACK1 binding partners that may modulate the elongation phase of protein synthesis

Abstract RACK1 (Receptor for Activated C Kinase 1) is a member of the tryptophan-aspartate (WD-repeat) family of proteins. By functioning as a scaffold protein, RACK1 is involved in regulating many different signalling pathways in cells, including cell proliferation and cell migration. Interestingly, RACK1 has been identified as a central component of the ribosomal machinery, specifically located on the 40S ribosomal subunit close to the mRNA exit channel where it makes contact with other ribosomal proteins. Importantly, it is believed that in this position, RACK1 can recruit a series of kinases and phosphatases as well as functioning to regulate the translation and the synthesis of particular cohorts of proteins. Moreover, RACK1 plays a central role in influencing the location of the translation machinery. Using 2D and 3D models of colon cancer cell lines, together with Click-IT chemistry and Mass Spectrometry analysis, we were able to identify a series of proteins, including newly synthesized proteins, that interact with RACK1. We identified proteins involved in cell cycle control, metabolism and protein synthesis. As expected, we have found a number of proteins that are involved in cell migration and a number of proteins that are mediators of the cell adhesion process. Interestingly, some of the most highly scored interacting proteins were those involved in protein synthesis. Of those, we identified several elongation factors as being novel RACK1 binding partners. Elongation factors are a class of proteins directly involved in the elongation phase of protein synthesis. Along with this primary function, these factors have different important roles in cells, such as influencing cytoskeleton remodelling and activation of growth and proliferation pathways. Elongation factors have been found to be upregulated in many different types of cancer. We have confirmed the interaction between RACK1 and several of these elongation factors and we have determined that many of these are dysregulated in colon cancer. We have established that the activity of these elongation factors is regulated by a combination of stress conditions and growth factor stimulations. We have determined that RACK1 plays a central role in scaffolding these proteins to promote proliferation and migration in our colon cancer cell models. Collectively, these results provide a novel and interesting role for RACK1 in the modulation of the elongation phase of protein synthesis. We are now investigating the subcellular location of these factors in response to different stimuli and asking how is RACK1 involved in their localization downstream of IGF-I and integrin signalling. Characterizing and mapping the interaction between these proteins and RACK1, both in cells and tissue, may lead to the design of novel therapeutic approaches in colon cancer. Citation Format: Beatrice Malacrida, Rasmus K. Flygaard, Catríona M. Dowling, John C. Coffey, Lasse B. Jenner, Patrick A. Kiely. Identification and characterization of novel RACK1 binding partners that may modulate the elongation phase of protein synthesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4485. doi:10.1158/1538-7445.AM2017-4485

Identification of extracellular matrix protein 1 as a potential plasma biomarker of ESCC by proteomic analysis using iTRAQ and 2D-LC-MS/MS.

This study was aimed to conduct a proteomics profiling analysis on plasma obtained from ESCC patients with the goal of identifying appropriate plasma protein biomarkers in the progression of ESCC. Plasma from 28 ESCC patients and 28 healthy controls (HC) were analyzed by iTRAQ combined with 2D-LC-MS/MS. ProteinPilot software was used to identify the differentially expressed plasma proteins in ESCC compared to HC. Western blot was performed to verify the expression of selected proteins in 37 independent ESCC patients and 37 HC. Transwell and MTT assays were used to detect the biological function of ECM1 protein in vitro. Nineteen (four upregulated and fifteen downregulated) proteins were identified as differentially expressed between ESCC and HC (p<0.05). Biological functions of these proteins are involved in cell adhesion, cell apoptosis and metabolic processes, visual perception and immune response. Of these, extracellular matrix 1 (ECM1) and lumican (LUM) were selected further confirmation by Western blot (p<0.05), which were consistent with the iTRAQ results. Furthermore, the migration ability of EC9706 cell line after overexpressing ECM1 was increased significantly (p<0.05). The proliferation ability of HUVEC cell was enhanced when treated with the culture supernatants of EC9706 overexpressed ECM1(p<0.05). This proteome analysis indicate that ECM1 is a potential novel plasma protein biomarker for the detection of primary ESCC and evaluation of neoplasms progression.

Zebrafish exposure to environmentally relevant concentration of depleted uranium impairs progeny development at the molecular and histological levels.

Uranium is an actinide naturally found in the environment. Anthropogenic activities lead to the release of increasing amounts of uranium and depleted uranium (DU) in the environment, posing potential risks to aquatic organisms due to radiological and chemical toxicity of this radionucleide. Although environmental contaminations with high levels of uranium have already been observed, chronic exposures of non-human species to levels close to the environmental quality standards remain scarcely characterized. The present study focused on the identification of the molecular pathways impacted by a chronic exposure of zebrafish to 20 μg/L of DU during 10 days. The transcriptomic effects were evaluated by the use of the mRNAseq analysis in three organs of adult zebrafish, the brain the testis and the ovaries, and two developmental stages of the adult fish progeny, two-cells embryo and four-days larvae. The results highlight generic effects on the cell adhesion process, but also specific transcriptomic responses depending on the organ or the developmental stage investigated. The analysis of the transgenerational effects of DU-exposure on the four-day zebrafish larvae demonstrate an induction of genes involved in oxidative response (cat, mpx, sod1 and sod2), a decrease of expression of the two hatching enzymes (he1a and he1b), the deregulation of the expression of gene coding for the ATPase complex and the induction of cellular stress. Electron microscopy analysis of skeletal muscles on the four-days larvae highlights significant histological impacts on the ultrastructure of both the mitochondria and the myofibres. In addition, the comparison with the transcriptomic data obtained for the acetylcholine esterase mutant reveals the induction of protein-chaperons in the skeletal muscles of the progeny of fish chronically exposed to DU, pointing towards long lasting effects of this chemical in the muscles. The results presented in this study support the hypothesis that a chronic parental exposure to an environmentally relevant concentration of DU could impair the progeny development with significant effects observed both at the molecular level and on the histological ultrastructure of organs. This study provides a comprehensive transcriptomic dataset useful for ecotoxicological studies on other fish species at the molecular level. It also provides a key DU responsive gene, egr1, which may be a candidate biomarker for monitoring aquatic pollution by heavy metals.

Gangliosides: Structures, Biosynthesis, Analysis, and Roles in Cancer.

Gangliosides are acidic glycosphingolipids containing one or more sialic acid residues. They are essential compounds at the outer leaflet of the plasma membrane, where they interact with phospholipids, cholesterol, and transmembrane proteins, forming lipid rafts. They are involved in cell adhesion, proliferation, and recognition processes, as well as in the modulation of signal transduction pathways. These functions are mainly governed by the glycan moiety, and changes in the structures of gangliosides occur under pathological conditions, particularly in neuro-ectoderm-derived cancers. With the progress in mass spectrometry analysis of gangliosides, their role in cancer progression can be now investigated in more detail. In this review we summarize the current knowledge on the biosynthesis of gangliosides and their role in cancers, together with the recent development of cancer immunotherapy targeting gangliosides.

Developmental features of cotton fibre middle lamellae in relation to cell adhesion and cell detachment in cultivars with distinct fibre qualities

BackgroundCotton fibre quality traits such as fibre length, strength, and degree of maturation are determined by genotype and environment during the sequential phases of cotton fibre development (cell elongation, transition to secondary cell wall construction and cellulose deposition). The cotton fibre middle lamella (CFML) is crucial for both cell adhesion and detachment processes occurring during fibre development. To explore the relationship between fibre quality and the pace at which cotton fibres develop, a structural and compositional analysis of the CFML was carried out in several cultivars with different fibre properties belonging to four commercial species: Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum.ResultsCotton fibre cell adhesion, through the cotton fibre middle lamella (CFML), is a developmentally regulated process determined by genotype. The CFML is composed of de-esterified homogalacturonan, xyloglucan and arabinan in all four fibre-producing cotton species: G. hirsutum, G. barbadense, G. herbaceum and G. arboreum. Conspicuous paired cell wall bulges are a feature of the CFML of two G. hirsutum cultivars from the onset of fibre cell wall detachment to the start of secondary cell wall deposition. Xyloglucan is abundant in the cell wall bulges and in later stages pectic arabinan is absent from these regions.ConclusionsThe CFML of cotton fibres is re-structured during the transition phase. Paired cell wall bulges, rich in xyloglucan, are significantly more evident in the G. hirsutum cultivars than in other cotton species.

Recurrently deregulated lncRNAs in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) cells often invade the portal venous system and subsequently develop into portal vein tumour thrombosis (PVTT). Long noncoding RNAs (lncRNAs) have been associated with HCC, but a comprehensive analysis of their specific association with HCC metastasis has not been conducted. Here, by analysing 60 clinical samples’ RNA-seq data from 20 HCC patients, we have identified and characterized 8,603 candidate lncRNAs. The expression patterns of 917 recurrently deregulated lncRNAs are correlated with clinical data in a TCGA cohort and published liver cancer data. Matched array data from the 60 samples show that copy number variations (CNVs) and alterations in DNA methylation contribute to the observed recurrent deregulation of 235 lncRNAs. Many recurrently deregulated lncRNAs are enriched in co-expressed clusters of genes related to cell adhesion, immune response and metabolic processes. Candidate lncRNAs related to metastasis, such as HAND2-AS1, were further validated using RNAi-based loss-of-function assays. Thus, we provide a valuable resource of functional lncRNAs and biomarkers associated with HCC tumorigenesis and metastasis.

Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes.

Focal adhesion kinase (FAK) is a multidomain protein (FERM-kinase-FAT) with important signaling functions in the regulation of cell-substrate adhesions. Its inactive, autoinhibited form is recruited from the cytoplasm to the plasma membrane, where it becomes activated at PIP2 enriched regions. To elucidate the molecular basis of activation, we performed a systematic screening of binding orientations of FAK's autoinhibited FERM-kinase complex, as well as of the dissociated FERM and kinase domains alone, on model plasma membranes using coarse-grained scFix MARTINI simulations, partially corroborated by atomistic MD simulations. The proteins adopted many more different orientations than previously thought. The presence of PIP2 tuned and narrowed the complex map of competing interfacial orientations. The dissociated FERM domain most frequently interacted with the membrane through its autoinhibitory interface rather than with the "basic patch" residues. These findings suggest a PIP2-dependent activation mechanism in which membrane binding of the dissociated FERM domain competes with the rebinding of the kinase domain. This competition could promote FAK autophosphorylation on Y397 and subsequent Src binding. The orientation of peripheral proteins at membranes is crucial to understand cell adhesion processes and is furthermore required to exploit steered molecular dynamics to predict how tensile forces might switch their active states.

Abstract B56: RNA-seq analysis of prostate cancer samples from Hispanic patients reveal progressive characteristics in Gleason patterns

Abstract Background. One of the prognostic markers widely used in clinic to predict survival in prostate cancer (PC) patients is the Gleason score. Differences have been observed in biochemical progression-free and overall survival in patients with different Gleason scores. Because each Gleason represents a different state of tumor progression, we decided to characterize expression profiles and pathways in Gleason 3, 4 and 5 in order to explore the tumor biology context in each pattern, and thus determine possible prognosis biomarkers in PC. Methods. We extracted RNA from normal and malignant formalin-fixed paraffin-embedded tissues from radical prostatectomy samples of Colombian patients and analyzed expression using data generated with next generation sequencing methods. Pathway analysis was done with MetaCore. Results. Eleven gene networks (7 genes) were common between all Gleason scores and represented cellular processes possibly involved with damage of the prostatic tissue including: cell adhesion, cytoskeleton remodeling and metabolism of phosphatidyl compounds. According to the analysis in Gleason pattern 3, the principal pathways were associated with cytoskeleton remodeling, gap junctions signaling and regulation of cell adhesion. These pathways could contribute to de-differentiation process experienced by cells towards tumor transformation in early stages of progression. Also, signaling of epithelial-to-mesenchymal transition (EMT) were observed, this findings could suggests not only cytoskeleton remodeling during de-differentiation, but also appearance of metastatic cells in this Gleason pattern. On the other hand, the action of the Androgen Receptor (AR) is suggested by protein-protein interactions characterized by rapid activation of signaling cascades of proliferation, cell growth and survival, via MAPK and PI3K/AKT. The latter in turn induces AR overexpression through control of regulatory protein MDM-2 and optimizes binding of AR to promoter/enhancer regions over its target genes. Also, AR inhibits WNT signaling via interaction with B-catenin. However, AR is a LEF-1/TCF transcriptional target, which is activated by WNT/B-catenin signaling. The pathways identified in Gleason pattern 4 were similar to those of Gleason 3, with a more significant participation of pathways leading to cytoskeleton remodeling, regulation of cell adhesion molecules and of EMT. In addition, there is ligand-independent activation of AR, wherein activating mutations, splicing variants and activation by other signaling cascades, may lead to directed transactivation of target genes in a deregulated manner. Further, NGF/TrkA/PI3K-mediated signaling may lead to inhibition of apoptosis and survival of these cells. Finally, pathways analysis in Gleason pattern 5 showed that the most significant was cell adhesion and ECM remodeling, which favors the metastatic process and regulation of cell motility and adhesion, processes aided by migration and angiogenesis signaling pathways. Likewise, AR activation and downstream signaling has an important role, transactivating transcription factors, which together lead to cell proliferation, inhibition of apoptosis, expression of tumor growth factors, regulation of cell adhesion molecules and from inflammatory response. The latter is reflected in another pathway identified, as is the antigen presentation by MHC class II. Conclusion. The pathways identified by different Gleason patterns exhibit progression of localized prostate tumors into metastatic ones, where there is cell growth and dysregulation in signaling pathways at the beginning, and then, as they progress, they acquire the ability to migrate and to regulate AR signaling through different mechanisms so that allows AR to be a central regulator in PC. Citation Format: Natalia L. Acosta, Melody C. Baddoo, Alba L. Combita, Rodolfo Varela, Jorge Mesa, Maria C. Sanabria-Salas, Jovanny Zabaleta. RNA-seq analysis of prostate cancer samples from Hispanic patients reveal progressive characteristics in Gleason patterns. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr B56.

Genome-wide screen identifies a novel prognostic signature for breast cancer survival.

Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion, cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.

PCR analysis of the absolute number of copies of human chromosome 18 transcripts in liver and HepG2 cells

Using reverse transcription in conjunction with the quantitative real-time PCR or digital droplet PCR, the transcriptome profiling of human chromosome 18 has been carried out in liver hepatocytes and hepatoblastoma cells (HepG2 cell line) in terms of the absolute number of each transcript per cell. The transcript abundance varies within the range of 0.006 to 9635 and 0.011 to 4819 copies per cell for HepG2 cell line and hepatocytes, respectively. The expression profiles for genes of chromosome 18 in hepatocytes and HepG2 cells were found to significantly correlate: the Spearman's correlation coefficient was equal to 0.81. The distribution of frequency of transcripts over their abundance was bimodal for HepG2 cells and unimodal for liver hepatocytes. Bioinformatic analysis of the differential gene expression has revealed that genes of chromosome 18, overexpressed in HepG2 cells compared to hepatocytes, are associated with cell division and cell adhesion processes. It is assumed that the enhanced expression of those genes in HepG2 cells is related to the proliferation activity of cultured cells. The differences in transcriptome profiles have to be taken into account when modelling liver hepatocytes with cultured HepG2 cells.

High expression of RAB43 predicts poor prognosis and is associated with epithelial-mesenchymal transition in gliomas

The Ras-related GTP-binding protein (RAB) family plays an important role in regulating signal transduction and cellular processes including vesicle transport, cytoskeleton formation and membrane trafficking. More recently, several RAB members have been reported to promote tumorigenesis in many types of cancers. However, the clinical significance and potential function of RAB43 in gliomas remain unclear. Herein, we found that RAB43 was upregulated and positively correlated with the grade of progression in glioma patients by insilico analysis and immunohistochemistry (IHC). Patients with high RAB43 displayed worse clinical outcomes in comparison to those with low RAB43. RAB43 was also highly expressed in mesenchymal and G3subtypes, and isocitrate dehydrogenase1 (IDH1) wild-type gliomas. Moreover, transcriptomic analyses via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that RAB43‑related gene sets were mainly involved in the regulation of cell adhesion and cell migration processes. Further investigation indicated that RAB43 downregulation significantly suppressed the migratory and invasive ability of glioma cells, as well as decreased the expression of epithelial-mesenchymal transition (EMT) markers (N-cadherin, vimentin and Snail). In conclusion, a high level of RAB43 was significantly associated with the malignant phenotypes of gliomas, which suggests that RAB43 may serve as a novel biomarker and a potential therapeutic target for gliomas.

Bio-active molecules modified surfaces enhanced mesenchymal stem cell adhesion and proliferation

Surface modification of the substrate as a component of in vitro cell culture and tissue engineering, using bio-active molecules including extracellular matrix (ECM) proteins or peptides derived ECM proteins can modulate the surface properties and thereby induce the desired signaling pathways in cells. The aim of this study was to evaluate the behavior of human bone marrow mesenchymal stem cells (hBM-MSCs) on glass substrates modified with fibronectin (Fn), collagen (Coll), RGD peptides (RGD) and designed peptide (R-pept) as bio-active molecules. The glass coverslips were coated with fibronectin, collagen, RGD peptide and R-peptide. Bone marrow mesenchymal stem cells were cultured on different substrates and the adhesion behavior in early incubation times was investigated using scanning electron microscopy (SEM) and confocal microscopy. The MTT assay was performed to evaluate the effect of different bio-active molecules on MSCs proliferation rate during 24 and 72 h. Formation of filopodia and focal adhesion (FA) complexes, two steps of cell adhesion process, were observed in MSCs cultured on bio-active molecules modified coverslips, specifically in Fn coated and R-pept coated groups. SEM image showed well adhesion pattern for MSCs cultured on Fn and R-pept after 2 h incubation, while the shape of cells cultured on Coll and RGD substrates indicated that they might experience stress condition in early hours of culture. Investigation of adhesion behavior, as well as proliferation pattern, suggests R-peptide as a promising bio-active molecule to be used for surface modification of substrate in supporting and inducing cell adhesion and proliferation.

Lipid glycosylation: a primer for histochemists and cell biologists.

Glycolipids are glycoconjugates that are predominantly found on the extracellular surface of cells ranging from bacteria to men. In bacteria and plants, glycoglycerolipids represent the main glycolipid species. Ceramides as carrier for glycans, termed glycosphingolipids (GSLs), are characteristic for vertebrates and insects. The glycan part is involved in a variety of biological activities including cell adhesion and initiation of signaling. Most of these functions rest on two basic principles: (1) GSLs spontaneously contribute to organize lipid rafts in biological membranes, thereby forming functional complexes ('glycosynapses') with receptor proteins and ion channels and (2) their glycans are bound by receptors like galectins (protein-glycan recognition) or cognate glycans (glycan-glycan recognition). This interaction modulates cell adhesion, differentiation and growth processes. Besides their contribution to normal cell behavior, GSL expression patterns also influence disease processes by inducing cellular malfunctions when aberrant, as highlighted by inherited disorders of GSL metabolism like sphingolipidoses. Altered GSL patterns are also associated with common neurological diseases, autoimmune diseases and cancer. With respect to infections, various GSL-presented glycans are attachment sites for bacteria and viruses as well as primary targets for bacterial toxins. This review provides an introduction to GSL structures, their nomenclature and metabolism. Building on this, normal and pathological functions of GSL will be surveyed.

Identification of non-coding and coding RNAs in porcine endometrium

One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes. In addition, our results showed that the differentially expressed genes (IL1R, FGF9, DUPS10, DUPS4, CD14 and MAP4K4) in MAPK pathway, and lncRNAs of XLOC_2604764 and XLOC_2604756 may play a vital role in regulating embryo implantation. Besides, we investigated the lncRNA-ssc-miR-132-mRNA interactions, aiming to explain the regulatory networks of coding and non-coding genes that contributes to the establishment of the maternal pregnancy.