Extracellular Processes Research Articles

Considerable Bacterial Community Structure Coupling with Extracellular Electron Transfer at Karst Area Stone in Yunnan, China

ABSTRACTNearly all karst stones have partial dark and light color sections under the same condition. In this study, 24662 operational taxonomic units (OTUs) were examined from karst stones surface samples. Dark samples showed higher abundance of 18,115 OTUs (73.5%) and containing clustered bacterial communities, as indicated by the results of principal component and cluster analyses. Additionally, heatmap analysis showed microorganisms distinction between different color samples and 19 genera of electroactive microorganisms gathered in the dark samples. Furthermore, iron manganese oxides were detected as the main mineral composition difference. Notably, dark samples exhibited remarkable photoelectrochemical activity in response to visible light. Under sunlight, both microorganisms and minerals displayed close relationship with extracellular electron transfer process, which enhanced the understanding for microorganism-–mineral interactions in natural karst environments.

Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation.

The catalytic activity of trypsin-like serine proteases is in many cases regulated by conformational changes initiated by binding of physiological modulators to exosites located distantly from the active site. A trypsin-like serine protease of particular interest is urokinase-type plasminogen activator (uPA), which is involved in extracellular tissue remodeling processes. Herein, we used hydrogen/deuterium exchange mass spectrometry (HDXMS) to study regulation of activity in the catalytic domain of the murine version of uPA (muPA) by two muPA specific monoclonal antibodies. Using a truncated muPA variant (muPA16-243), containing the catalytic domain only, we show that the two monoclonal antibodies, despite binding to an overlapping epitope in the 37s and 70s loops of muPA16-243, stabilize distinct muPA16-243 conformations. Whereas the inhibitory antibody, mU1 was found to increase the conformational flexibility of muPA16-243, the stimulatory antibody, mU3, decreased muPA16-243 conformational flexibility. Furthermore, the HDXMS data unveil the existence of a pathway connecting the 70s loop to the active site region. Using alanine scanning mutagenesis, we further identify the 70s loop as an important exosite for the activation of the physiological uPA substrate plasminogen. Thus, the data presented here reveal important information about dynamics in uPA by demonstrating how various ligands can modulate uPA activity by mediating long-range conformational changes. Moreover, the results provide a possible mechanism of plasminogen activation.

Urinary metalloproteinases and tissue inhibitors of metalloproteinases as potential early biomarkers for renal fibrosis in children with nephrotic syndrome.

In chronic glomerulopathies, renal fibrosis (RF) results from extracellular matrix remodeling processes regulated by matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP). We assessed urinary (u-) and serum (s-) MMP-1, -2, -9, TIMP-1, -2 concentrations and MMP-1, -2, -9/TIMP-1, -2 ratios in children with nephrotic syndrome. Steroid-dependent and steroid-resistant nephrotic patients (SDNS-Ps and SRNS-Ps, respectively) were compared with respect to measured parameters. The correlations of measured parameters with magnitude of proteinuria and histopathological diagnosis were determined.The study comprised of 39 children with nephrotic syndrome and 20 healthy controls. Twenty-three patients had SDNS and 16 ones—SRNS. The concentrations MMPs and TIMPs were measured using enzyme-linked immunosorbent assay.In nephrotic patients, higher u-MMP-1, -2, -9/creatinine ratios and u-TIMP-1, -2/creatinine ratios were observed as compared with controls. Nephrotic children were also characterized by lower MMP-1, -2, -9/TIMP-1 ratios. In SRNS-Ps, u-MMP-2/creatinine ratio and u-TIMP-1/creatinine ratio were higher as compared with SDNS-Ps. Magnitude of proteinuria correlated positively with u-MMP-2/creatinine ratio and negatively with u-MMP-2/TIMP-1. In minimal change disease (MCD) patients as compared with those with other glomerulopathies, there was higher u-MMP-2/TIMP-1 ratio. No significant differences in s-MMPs, s-TIMPs, and s-MMPs/TIMPs ratios between nephrotic patients and controls were observed.Children with nephrotic syndrome are characterized by increased u-fibrotic biomarkers excretions. U-MMP-1, -2, -9 excretions and u-MMP-2/TIMP-1 ratio may become potential early biomarkers for RF. SRNS-Ps, those with heavier proteinuria and other than MCD glomerulopathies, seem to be more susceptible to early RF.

Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1.

Shewanella oneidensis MR-1 can transfer electrons from the intracellular environment to the extracellular space of the cells to reduce the extracellular insoluble electron acceptors (Extracellular Electron Transfer, EET). Benefiting from this EET capability, Shewanella has been widely used in different areas, such as energy production, wastewater treatment, and bioremediation. Genome-wide proteomics data was used to determine the active proteins involved in activating the EET process. We identified 1012 proteins with decreased expression and 811 proteins with increased expression when the EET process changed from inactivation to activation. We then networked these proteins to construct the active protein networks, and identified the top 20 key active proteins by network centralization analysis, including metabolism- and energy-related proteins, signal and transcriptional regulatory proteins, translation-related proteins, and the EET-related proteins. We also constructed the integrated protein interaction and transcriptional regulatory networks for the active proteins, then found three exclusive active network motifs involved in activating the EET process—Bi-feedforward Loop, Regulatory Cascade with a Feedback, and Feedback with a Protein–Protein Interaction (PPI)—and identified the active proteins involved in these motifs. Both enrichment analysis and comparative analysis to the whole-genome data implicated the multiheme c-type cytochromes and multiple signal processing proteins involved in the process. Furthermore, the interactions of these motif-guided active proteins and the involved functional modules were discussed. Collectively, by using network-based methods, this work reported a proteome-wide search for the key active proteins that potentially activate the EET process.

The Role of Galectins as Modulators of Metabolism and Inflammation.

Galectins are β-galcotosid-binding lectins. The function of galectins varies with their tissue-specific and subcellular location, and their binding to carbohydrates makes them key players in several intra- and extracellular processes where they bind to glycosylated proteins and lipids. In humans, there are 12 identified galectins, some with tissue-specific distribution. Galectins are found inside cells and in the nucleus, cytosol, and organelles, as well as extracellularly. Galectin-1, -2, -3, -4, -7, -8, -9, and -12 can all induce T-cell apoptosis and modulate inflammation. In the context of metabolic control and loss of the same in, for example, diabetes, galectin-1, -2, -3, -9, and -12 are especially interesting. This review presents information on galectins relevant to the control of inflammation and metabolism and the potential to target galectins for therapeutic purposes.

Роль генов фиброгенеза в формировании подверженности к коронарному атеросклерозу

To study associations between genes of different functional classes, including fibrogenesis genes, with coronary atherosclerosis and specific features of its course. We included in this study 404 patients with confirmed chronic ischemic heart disease (IHD) who had undergone coronary artery bypass grafting. Two groups of participants were distinguished - those with (n=188) and without (n=216) history of myocardial infarction (MI). Control group consisted of inhabitants of the Siberia region (n=285). Associations were analyzed using 48 single nucleotide polymorphisms (SNP) located in genes earlier determined as associated with diseases of the cardiovascular continuum (diabetes mellitus, MI, atherosclerosis). Multiplex genotyping was performed using mass spectrometry. For statistical analyses we used Statistica v8.0 and R-language with "stats" and "genetics" packages. We identified several genetic markers contributing to susceptibility to development of atherosclerosis. Same markers were identified as determinants of the character of the course of atherosclerotic disease. Risk of development of atherosclerosis was higher in carriers of the following genotypes: TT of ITGB5 gene (rs1007856) - by 1.6 times (OR=1.59; р=0.0153); GG of ITGA4 gene - by 1.85 times (OR=1.85; р=0.0016); GG of IGFBP7 gene (rs11133482) - by 2.4 times (OR=2.36; р=0.0031). The following genotypes were identified as protective against MI and determining stable course of the disease: AA of TLR4 gene (rs4986790) (OR=0.47; р=0.0104).; CC of LDLR gene (rs2738446) (OR=0,53; р=0.0041); GG of OAS1 gene (rs1131454) (OR=0.50; р=0.0274). Susceptibility to coronary atherosclerosis and prognosis of disease progression were found to be associated with polymorphism of certain genes, involved in metabolism of the extracellular matrix and processes of fibrogenesis (ADAMDEC1, ITGA4, ITGB5, CDKN2B-AS1, IGFBP7), lipid metabolism (LDLR), immune system functioning (TLR4, OAS1) and DNA repair (LIG1).

Insights into the generation of monoclonal antibody acidic charge variants during Chinese hamster ovary cell cultures.

Charge variation is one of the most important heterogeneities during monoclonal antibody (mAb) manufacturing and this study presents insights into the generation of acidic charge variants during cell culture processes. Since acidic variants generate both intracellularly and extracellularly, main charge fraction collected by weak cation exchange chromatography (WCX) was incubated in harvested cell supernatant (HCS) to simulate and investigate the extracellular process firstly. It is found that the main fraction was degraded rapidly into acidic variants rather than basic variants extracellularly, and the degradation sites were located in both Fab and Fc fragments indicated by papain digestion. Besides, certain process parameters were investigated as their potential roles in the extracellular process. As a result, media composition showed significant influence on degradation while culture time point did not, suggesting that the extracellular process was a spontaneous process without enzyme catalysis. Additionally, kinetics study reveals that the extracellular process was a pseudo first-order reaction. The E app value (21.59kcal/mol) estimated from the Arrhenius equation suggests that the extracellular degradation might be mainly attributed to asparagine deamidation. Furthermore, we established an acidic variants generation model, indicating that the extracellular process plays a dominant role in modulating the final acidic variant level. This study provides better understanding for controlling product heterogeneity in mAb manufacturing.

Degradation of tropoelastin and skin elastin by neprilysin

Neprilysin is also known as skin fibroblast-derived elastase, and its up-regulation during aging is associated with impairments of the elastic fiber network, loss of skin elasticity and wrinkle formation. However, information on its elastase activity is still limited. The aim of this study was to investigate the degradation of fibrillar skin elastin by neprilysin and the influence of the donor's age on the degradation process using mass spectrometry and bioinformatics approaches. The results showed that cleavage by neprilysin is dependent on previous damage of elastin. While neprilysin does not cleave young and intact skin elastin well, it degrades elastin fibers from older donors, which may further promote aging processes. With regards to the cleavage behavior of neprilysin, a strong preference for Gly at P1 was found, while Gly, Ala and Val were well accepted at P1′ upon cleavage of tropoelastin and skin elastin. The results of the study indicate that the progressive release of bioactive elastin peptides by neprilysin upon skin aging may enhance local tissue damage and accelerate extracellular matrix aging processes.

Visible Light Enhanced Extracellular Electron Transfer between a Hematite Photoanode and Pseudomonas aeruginosa

Exploring the interplay between sunlight, semiconducting minerals, and microorganisms in nature has attracted great attention in recent years. Here we report for the first time the investigation of the interaction between a hematite photoelectrode and Pseudomonas aeruginosa PAO1 under visible light irradiation. Hematite is the most abundant mineral on earth, with a band gap of 2.0 eV. A hematite electrode was electrochemically deposited on fluorine-doped tin oxide (FTO). It was thoroughly characterized by environmental scanning electron microscopy (ESEM), Raman, and UV–Vis spectroscopy, and its prompt response to visible light was determined by linear sweep voltammetry (LSV). Notably, under light illumination, the hematite electrode immersed in a live cell culture was able to produce 240% more photocurrent density than that in the abiotic control of the medium, suggesting a photoenhanced extracellular electron transfer process occurring between hematite and PAO1. Different temperatures of LSV measurements showed bioelectrochemical activity in the system. Furthermore, I–t curves under various conditions demonstrated that both a direct and an indirect electron transferring process occurred between the hematite photoanode and PAO1. Moreover, the indirect electron transferring route was more dominant, which may be mainly attributed to the pyocyanin biosynthesized by PAO1. Our results have expanded our understanding in that in addition to Geobacter and Shewanella it has been shown that more microorganisms are able to perform enhanced extracellular electron transfer with semiconducting minerals under sunlight in nature.

The diversity, distribution and function of N-acyl-homoserine lactone (AHL) in industrial anaerobic granular sludge

Although AHL-mediated quorum sensing (QS) signaling has been proved to be ecologically important in biofilm formation and aerobic granulation process, the biological role of AHL in anaerobic granule has not been experimentally investigated. In this paper, we explored the AHL level in 10 full-scale industrial anaerobic granular bioreactors and detected a total of 4 kinds of AHLs. C8-HSL and C10-HSL were indicated to be the potentially universal QS signal molecules in anaerobic granules and involved in extracellular polymeric substance (EPS) production and granulation process. The add-back experiments further supported the hypothesis that C8-HSL and C10-HSL might play an important role in facilitating anaerobic granulation through regulation of EPS synthesis. 12 Microorganisms might be regulated by AHL to play an important role in EPS production. This study provides a foundation for exploring the function of AHL in anaerobic granular systems, which may shed light on advanced AHL-based anaerobic granulation strategy.

Is perceived long term stress related to the acute stress reaction?

Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) can cause heart failure, and this study aims to identify genes and transcription factors (TFs) associated with DCM and ICM.Gene expression dataset GSE42955 was generated from GEO database, and it contained 12 DCM, 12 ICM, and 5 control samples. Differentially expressed genes (DEGs) were identified between DCM (or ICM) and controls. Gene functions were investigated, and their associations were analyzed using Enrichmentmap plugin in Cytoscape. Protein-protein interactions (PPIs) between DEGs were determined, and DEGs with high degree were defined as key DEGs. Potential TFs of key DEGs were predicted using iRegulon plugin. Common DEGs were found, and their functional interactions were investigated using GeneMANIA.A total of 362 and 300 DEGs were respectively identified for DCM and ICM in comparison with controls, and these DEGs mainly participated in similar functions about extracellular region, membrane, immune process, and defense response. PPI networks were respectively constructed for DCM and ICM, and 26 key DEGs (e.g. CXCL10, IL6, TLR3, and VCAM1) were found, which might be targeted by 35 TFs (e.g. IRF1). Besides, 47 common up-regulated DEGs were found, which participated in 14 pathways like Apoptosis, Collagen formation, as well as 127 common down-regulated DEGs that involved in 20 pathways like Adaptive immune system, Interferon γ signaling (e.g. IRF1, VCAM1), and Toll-like receptor signaling pathway (e.g. CXCL10, IL6, TLR3).DCM and ICM may share similar mechanism, and TFs (e.g. IRF1) play crucial roles in their development via regulating gene expression.

Engineered M13 Nanofiber Accelerates Ischemic Neovascularization by Enhancing Endothelial Progenitor Cells.

Dysfunction or loss of blood vessel causes several ischemic diseases. Although endothelial progenitor cells (EPCs) are a promising source for cell-based therapy, ischemia-induced pathophysiological condition limits the recovery rate by causing drastic cell death. To overcome this issue, we attempted to develop a cell-targeted peptide delivery and priming system to enhance EPC-based neovascularization using an engineered M13 bacteriophage harboring nanofibrous tubes displaying ~2700 multiple functional motifs. The M13 nanofiber was modified by displaying RGD, which is an integrin-docking peptide, on the minor coat protein, and by mutilayering SDKP motifs, which are the key active sites for thymosin β4, on the major coat protein. The engineered M13 nanofiber dramatically enhanced ischemic neovascularization by activating intracellular and extracellular processes such as proliferation, migration, and tube formation in the EPCs. Furthermore, transplantation of the primed EPCs with the M13 nanofiber harboring RGD and SDKP facilitated functional recovery and neovascularization in a murine hindlimb ischemia model. Overall, this study demonstrates the effectiveness of the M13 nanofiber-based novel peptide delivery and priming strategy in promoting EPC bioactivity and neovessel regeneration. To our knowledge, this is first report on M13 nanofibers harboring dual functional motifs, the use of which might be a novel strategy for stem and progenitor cell therapy against cardiovascular ischemic diseases.

The in situ spectral methods for examining redox status of c-type cytochromes in metal-reducing/oxidizing bacteria

The membrane-associated c-type cytochromes (c-Cyts) have been well known as the key enzymes mediating extracellular electron transfer to terminal electron acceptors, resulting in biogeochemical elemental transformation, contaminant degradation, and nutrient cycling. Although c-Cyts-mediated metal reduction or oxidation have been mainly investigated with the purified proteins of metal reducing/oxidizing bacteria, the in vivo behavior of c-Cyts is still unclear, given the difficulty in measuring the proteins of intact cells. Fortunately, the in situ spectroscopy would be ideal for measuring the reaction kinetics of c-Cyts in intact cells under noninvasive physiological conditions. It can also help the establishment of kinetic/thermodynamic models of extracellular electron transfer processes, which are essential to understand the electron transfer mechanisms at the molecular scale. This review briefly summarizes the current advances in spectral methods for examining the c-Cyts in intact cells of dissimilatory metal reducing bacteria and Fe(II)-oxidizing bacteria.

Prognostic value and molecular correlates of a CT image-based quantitative pleural contact index in early stage NSCLC

To evaluate the prognostic value and molecular basis of a CT-derived pleural contact index (PCI) in early stage non-small cell lung cancer (NSCLC). We retrospectively analysed seven NSCLC cohorts. A quantitative PCI was defined on CT as the length of tumour-pleura interface normalised by tumour diameter. We evaluated the prognostic value of PCI in a discovery cohort (n = 117) and tested in an external cohort (n = 88) of stage I NSCLC. Additionally, we identified the molecular correlates and built a gene expression-based surrogate of PCI using another cohort of 89 patients. To further evaluate the prognostic relevance, we used four datasets totalling 775 stage I patients with publically available gene expression data and linked survival information. At a cutoff of 0.8, PCI stratified patients for overall survival in both imaging cohorts (log-rank p = 0.0076, 0.0304). Extracellular matrix (ECM) remodelling was enriched among genes associated with PCI (p = 0.0003). The genomic surrogate of PCI remained an independent predictor of overall survival in the gene expression cohorts (hazard ratio: 1.46, p = 0.0007) adjusting for age, gender, and tumour stage. CT-derived pleural contact index is associated with ECM remodelling and may serve as a noninvasive prognostic marker in early stage NSCLC. • A quantitative pleural contact index (PCI) predicts survival in early stage NSCLC. • PCI is associated with extracellular matrix organisation and collagen catabolic process. • A multi-gene surrogate of PCI is an independent predictor of survival. • PCI can be used to noninvasively identify patients with poor prognosis.

Gene expression profiling in patients with polymyalgia rheumatica before and after symptom-abolishing glucocorticoid treatment

BackgroundThe pathophysiology, including the impact of gene expression, of polymyalgia rheumatica (PMR) remains elusive. We profiled the gene expression in muscle tissue in PMR patients before and after glucocorticoid treatment.MethodsGene expression was measured using Affymetrix Human Genome U133 Plus 2.0 arrays in muscle biopsies from 8 glucocorticoid-naive patients with PMR and 10 controls before and after prednisolone-treatment for 14 days. For 14 genes, quantitative real-time PCR (qRT-PCR, n = 9 in both groups) was used to validate the microarray findings and to further investigate the expression of genes of particular interest.ResultsPrednisolone normalized erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) in PMR patients. A total of 165 putatively clinically relevant, differentially expressed genes were identified (cut-off: fold difference > ±1.2, difference of mean > 30, and p < 0.05); of these, 78 genes differed between patients and controls before treatment, 131 genes responded to treatment in a given direction only in patients, and 44 fulfilled both these criteria. In 43 of the 44 genes, treatment counteracted the initial difference. Functional clustering identified themes of biological function, including regulation of protein biosynthesis, and regulation of transcription and of extracellular matrix processes. Overall, qRT-PCR confirmed the microarray findings: Microarray-detected group differences were confirmed for 9 genes in 17 of 18 comparisons (same magnitude and direction of change); lack of group differences in microarray testing was confirmed for 5 genes in 8 of 10 comparisons. Before treatment, using qRT-PCR, expression of interleukin 6 (IL-6) was found to be 4-fold higher in patients (p < 0.05).ConclusionsThis study identifies genes in muscle, the expression of which may impact the pathophysiology of PMR. Moreover, the study adds further evidence of the importance of IL-6 in the disease. Follow-up studies are needed to establish the exact pathophysiological relevance of the identified genes.The study was retrospectively listed on the ISRCTN registry with study ID ISRCTN69503018 and date of registration the 26th of July 2017.

Exclusive Extracellular Bioreduction of Methyl Orange by Azo Reductase-Free Geobacter sulfurreducens.

Azo dyes are a class of recalcitrant organic pollutants causing severe environmental pollution. For their biodecolorization, the azo reductase system was considered as the major molecular basis in bacteria. However, the intracellular localization of azo reductase limits their function for efficient azo dye decolorization. This limitation may be circumvented by electrochemically active bacteria (EAB) which is capable of extracellular respiration. To verify the essential role of extracellular respiration in azo dye decolorization, Geobacter sulfurreducens PCA, a model EAB, was used for the bioreduction of methyl orange (MO), a typical azo dye. G. sulfurreducens PCA efficiently reduced MO into amines. Kinetic results showed that G. sulfurreducens PCA had the highest decolorization efficiency among the currently known MO reducing bacteria. Electrons from acetate oxidization by this strain were transferred by the respiratory chain to MO. The mass and electron balances, fluorescent probing and proteinase K treatment experimental results indicate that the biodecolorization of MO by G. sulfurreducens PCA is an exclusive extracellular process. OmcB, OmcC and OmcE were identified as the key outer-membrane proteins for the extracellular MO reduction. This work deepens our understanding of EAB physiology and is useful for the decontamination of environments polluted with azo dyes. The contribution of extracellular respiration to pollutants reduction will broaden the environmental applications of EAB.

Extracellular polymeric substances are transient media for microbial extracellular electron transfer.

Microorganisms exploit extracellular electron transfer (EET) in growth and information exchange with external environments or with other cells. Every microbial cell is surrounded by extracellular polymeric substances (EPS). Understanding the roles of three-dimensional (3D) EPS in EET is essential in microbiology and microbial exploitation for mineral bio-respiration, pollutant conversion, and bioenergy production. We have addressed these challenges by comparing pure and EPS-depleted samples of three representative electrochemically active strains viz Gram-negative Shewanella oneidensis MR-1, Gram-positive Bacillus sp. WS-XY1, and yeast Pichia stipites using technology from electrochemistry, spectroscopy, atomic force microscopy, and microbiology. Voltammetry discloses redox signals from cytochromes and flavins in intact MR-1 cells, whereas stronger signals from cytochromes and additional signals from both flavins and cytochromes are found after EPS depletion. Flow cytometry and fluorescence microscopy substantiated by N-acetylglucosamine and electron transport system activity data showed less than 1.5% cell damage after EPS extraction. The electrochemical differences between normal and EPS-depleted cells therefore originate from electrochemical species in cell walls and EPS. The 35 ± 15-nm MR-1 EPS layer is also electrochemically active itself, with cytochrome electron transfer rate constants of 0.026 and 0.056 s-1 for intact MR-1 and EPS-depleted cells, respectively. This surprisingly small rate difference suggests that molecular redox species at the core of EPS assist EET. The combination of all the data with electron transfer analysis suggests that electron "hopping" is the most likely molecular mechanism for electrochemical electron transfer through EPS.

Visualization of extracellular DNA released during border cell separation from the root cap.

Root border cells are programmed to separate from the root cap as it penetrates the soil environment, where the cells actively secrete >100 extracellular proteins into the surrounding mucilage. The detached cells function in defense of the root tip by an extracellular trapping process that also requires DNA, as in mammalian white blood cells. Trapping in animals and plants is reversed by treatment with DNase, which results in increased infection. The goal of this study was to evaluate the role of DNA in the structural integrity of extracellular structures released as border cells disperse from the root tip upon contact with water. DNA stains including crystal violet, toluidine blue, Hoechst 33342, DAPI, and SYTOX green were added to root tips to visualize the extracellular mucilage as it absorbed water and border cell populations dispersed. DNase I was used to assess structural changes occurring when extracellular DNA was degraded. Complex masses associated with living border cells were immediately evident in response to each stain, including those that are specific for DNA. Treating with DNase I dramatically altered the appearance of the extracellular structures and their association with border cells. No extracellular DNA was found in association with border cells killed by freezing or high-speed centrifugation. This observation is consistent with the hypothesis that, as with border cell extracellular proteins, DNA is secreted by living cells. DNA is an integral component of border cell extracellular traps.

Abstract 5902: Roles of tumor microenvironment in pancreatic cancer progression

Abstract Although it has been recognized that tumor microenvironment plays a pivotal role in cancer progression, little is known about how differences of microenvironment affect malignant characteristics of cancer cells. In the present study, we tried to investigate the roles of pancreatic tumor microenvironment by use of several mouse inoculation models. First, human pancreatic cancer SUIT-2 cells (parental cells) were inoculated into pancreas orthotopically or into subcutaneous tissue ectopically. In order to expose cancer cells to each microenvironment for long period, processes of inoculation and extraction of cancer cells from primary tumor were repeated. After 3 circles of inoculation, cancer cells were collected from primary tumors in each model and established as distinct cancer cell lines, that is, 3P cells from pancreas in the orthotopic model and 3sc cells from subcutaneous tissue in the ectopic model, respectively. Orthotopic inoculation of these established cells revealed that the 3sc cells, and more prominently the 3P cells, showed higher tumorigenicity in vivo than parental cells. In addition, the 3P cells specifically exhibited low E-cadherin expression and high invasiveness, suggesting that the 3P cells possessed the highest malignant characteristics. Next, gene expression profiles in these cells were examined. RNA-sequence analysis demonstrated that distinct signaling pathways were activated in the 3P or 3sc cells. Pathways associated with extracellular matrix disassembly or collagen catabolic process were commonly activated in the 3P and 3sc cells. On the other hand, pathways including stem cell development or axon guidance were activated only in the 3P cells. These findings suggested that interactions between cancer cells and pancreatic microenvironment are necessary to obtain highly malignant traits. We are currently focusing upon some molecules, which are expressed specifically in the 3P cells, and figuring out their roles in pancreatic cancer progression. Finally, we also tried to uncover the underlying mechanisms of developing highly malignant 3P cells. Two processes are expected to be involved; small fractions of highly malignant cancer cells were adapted to pancreatic microenvironment (“selection”) or parental cells were affected by pancreatic microenvironment (“education”). To address this hypothesis, several clones within the parental SUIT-2 cells were isolated and inoculated as described previously. Individual clones varied in their tumor-forming ability, indicating that heterogeneity is present amongst the parental cells. However, we found that the gene expression profile in each clone was altered after in vivo orthotopic inoculation, suggesting that pancreatic microenvironment may have influence on phenotype of cancer cells. Based on these observations, we postulated that not only “selection” process but “education” process is involved in establishment of highly malignant cancer cells. Citation Format: Kei Takahashi, Shogo Ehata, Daizo Koinuma, Kohei Miyazono. Roles of tumor microenvironment in pancreatic cancer progression [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 5902. doi:10.1158/1538-7445.AM2017-5902

Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture

Extracellular vesicles (EVs) are involved in intercellular communication and affect processes including immune and antiviral responses. Blood serum, a common cell culture medium component, is replete with EVs and must be depleted prior to EV-related experiments. The extent to which depletion processes deplete non-EV particles is incompletely understood, but depleted serum is associated with reduced viability and growth in cell culture. Here, we examined whether serum depleted by two methods affected HIV-1 replication. In cell lines, including HIV-1 latency models, increased HIV-1 production was observed, along with changes in cell behavior and viability. Add-back of ultracentrifuge pellets (enriched in EVs but possibly other particles) rescued baseline HIV-1 production. Primary cells were less sensitive to serum depletion processes. Virus produced under processed serum conditions was more infectious. Finally, changes in cellular metabolism, surface markers, and gene expression, but not miRNA profiles, were associated with depleted serum culture. In conclusion, depleted serum conditions have a substantial effect on HIV-1 production and infectivity. Dependence of cell cultures on “whole serum” must be examined carefully along with other experimental variables, keeping in mind that the effects of EVs may be accompanied by or confused with those of closely associated or physically similar particles.