Specific Cell Lines Research Articles

Gold nanoparticle‑mediated delivery of paclitaxel and nucleic acids for cancer therapy (Review).

Paclitaxel is a potent antineoplastic agent, but poor solubility and resistance have limited its use. Gold nanoparticles (AuNPs) are widely studied as drug carriers because they can be engineered to prevent drug insolubility, carry nucleic acid payloads for gene therapy, target specific tumor cell lines, modulate drug release and amplify photothermal therapy. Consequently, the conjugation of paclitaxel with AuNPs to improve antiproliferative and pro-apoptotic potency may enable improved clinical outcomes. There are currently a number of different AuNPs under development, including simple drug or nucleic acid carriers and targeted AuNPs that are designed to deliver therapeutic payloads to specific cells. The current study reviewed previous research on AuNPs and the development of AuNP-based paclitaxel delivery.

A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines.

Cancer is a heterogeneous and complex disease and one of the leading causes of death worldwide. The high tumor heterogeneity between individuals affected by the same cancer type is accompanied by distinct molecular and phenotypic tumor profiles and variation in drug treatment response. In silico modeling of cancer as an aberrantly regulated system of interacting signaling molecules provides a basis to enhance our biological understanding of disease progression, and it offers the means to use computer simulations to test and optimize drug therapy designs on particular cancer types and subtypes. This sets the stage for precision medicine: the design of treatments tailored to individuals or groups of patients based on their tumor-specific molecular cancer profiles. Here, we show how a relatively large manually curated logical model can be efficiently enhanced further by including components highlighted by a multi-omics data analysis of data from Consensus Molecular Subtypes covering colorectal cancer. The model expansion was performed in a pathway-centric manner, following a partitioning of the model into functional subsystems, named modules. The resulting approach constitutes a middle-out modeling strategy enabling a data-driven expansion of a model from a generic and intermediate level of molecular detail to a model better covering relevant processes that are affected in specific cancer subtypes, comprising 183 biological entities and 603 interactions between them, partitioned in 25 functional modules of varying size and structure. We tested this model for its ability to correctly predict drug combination synergies, against a dataset of experimentally determined cell growth responses with 18 drugs in all combinations, on eight cancer cell lines. The results indicate that the extended model had an improved accuracy for drug synergy prediction for the majority of the experimentally tested cancer cell lines, although significant improvements of the model’s predictive performance are still needed. Our study demonstrates how a tumor-data driven middle-out approach toward refining a logical model of a biological system can further customize a computer model to represent specific cancer cell lines and provide a basis for identifying synergistic effects of drugs targeting specific regulatory proteins. This approach bridges between preclinical cancer model data and clinical patient data and may thereby ultimately be of help to develop patient-specific in silico models that can steer treatment decisions in the clinic.

The EBiSC iPSC bank for disease studies

The European Bank for induced Pluripotent Stem Cells (EBiSC), a non-profit repository for storage, banking, Quality Control (QC) and subsequent distribution of research-grade human induced Pluripotent Stem Cell (iPSC) lines, has centralised iPSC lines generated internationally across >35 disease areas and made them available to users via the EBiSC Catalogue, for research use (cells.ebisc.org/). Comprehensive datasets are accessible prior to purchase detailing the disease background of the original tissue sample, background of iPSC reprogramming and cell line characterisation data. EBiSC also performs robust QC screening to ensure supply of reliable, well-characterised iPSC lines, compliant with ISO9001:2015 principles. Whole Genome Sequencing data for specific iPSC lines can be downloaded from the European Genome Archive, subject to application to the EBiSC Data Access Committee. The EBiSC Access and Use Agreement, required to be completed prior to shipping, can be downloaded from the website along with specific Cell Line Information Packs; together these documents clarify how EBiSC lines can be used for research and detail any specific Third Party Obligations and/or restrictions for use which may apply. A protocol for how to culture and monitor iPSC lines including implementation of routine cell line screening is also available. A second project phase will continue collecting iPSC lines generated internationally, provide iPSC derived differentiated products using improved automation strategies for upscaling and develop the current services provided by EBiSC, including iPSC reprogramming, gene-editing and characterisation.

Cytotoxicity and genotoxicity of Hevea brasiliensis latex C-serum DCS sub-fraction as anticancer agents

Dialysed latex C-serum supernatant (DCS) sub-fraction from the rubber tree (Hevea brasiliensis) was reported to exert significant anti-proliferative effect on specific cancer cell lines, especially in human triple negative breast cancer (MDA-MB-231) and human liver carcinoma (HepG2) cells. In the present study, two human non-cancer origin cell lines, MCF-10A (human breast epithelial cells) and HDFa (human adult dermal fibroblast cells), showed least susceptibility when treated with DCS sub-fraction at concentration range 0–100 µg/mL using 2,5-diphenyl tetrazolium bromide (MTT) assay. Genotoxicity of DCS sub-fraction was assessed through Ames test, in vitro mouse lymphoma assay, and in vitro micronucleus assay. All genotoxicity experiments were tested with the presence and absence of S9 mixture as metabolic activation system. Ames test results showed negative result of mutagenicity as no clear dose-dependent relationship was observed despite mutagenic potential was detected in frame shift-based TA98 and TA1535 Salmonella typhimurium strains. Mouse lymphoma assay produced non-linear dose-dependent effect in experiments without the presence of S9. Meanwhile, experiment with the presence of S9 resulted in an inverse effect of the dose-dependent relationship. In micronucleus assay, the dose-dependent cytotoxicity effect of DCS sub-fraction showed no correlation with the increase number of cells containing micronuclei but appeared to be time-dependent. In conclusion, DCS sub-fraction showed no significant positive results in genotoxicity assays. In vivo genotoxicity assays should be conducted to ensure the safe use of DCS sub-fraction in further exploration for biological applications.

Synergistic Drug Combination Prediction by Integrating Multiomics Data in Deep Learning Models.

Intrinsic and acquired drug resistance is a major challenge in cancer therapy. Synergistic drug combinations could help to overcome drug resistance. However, the number of possible drug combinations is enormous, and it is infeasible to experimentally screen all drug combinations with limited resources. Therefore, computational models to predict and prioritize effective drug combinations are important for combination therapy discovery. Compared with existing models, we propose a novel deep learning model, AuDNNsynergy, to predict the synergy of pairwise drug combinations by integrating multiomics data. Specifically, three autoencoders are trained using the gene expression, copy number, and genetic mutation data of tumor samples from The Cancer Genome Atlas (TCGA). Then the gene expression, copy number, and mutation of individual cancer cell lines are coded using the three trained autoencoders. The physicochemical features of individual drugs and the encoded omics data of individual cancer cell lines are used as the input features of a deep neural network that predicts the synergy score of given pairwise drug combinations against the specific cancer cell lines. The comparison results showed the proposed AuDNNsynergy model outperforms, specifically in terms of rank correlation metric, four state-of-the-art approaches, namely, DeepSynergy, Gradient Boosting Machines, Random Forests, and Elastic Nets.

The Identification of a Novel Unsymmetrical Azine as an Apoptosis Inducer in Colorectal Cancer.

Defects in the physiological mechanisms of apoptosis are one of the pivotal factors implicated in carcinogenesis. Thus, the development of novel compounds that target various apoptotic pathways has provided promising anticancer therapeutic opportunities. This study explores the cytotoxic effects of a novel unsymmetrical azine against specific cancer cell lines and investigates the mechanism of cytotoxicity. Molecular modeling was used to test the binding affinity of four new unsymmetrical azines to a model of an apoptosis inhibitor protein (XIAP). The compound with the highest binding affinity, C4, was further tested on different cell lines. Real-time Polymerase Chain Reaction (PCR) and Transmission Electron Microscope (TEM) were used to study apoptosis induction biochemically and morphologically. In comparison to cisplatin as a control, the compound C4 exhibited notable cytotoxicity against all tested cancer cell lines, especially the human colorectal carcinoma cell line (HCT-116). Furthermore, C4-treated cells demonstrated marked overexpression of the pro-apoptotic proteins Bax and caspase-3 as well as the tumor suppressor p53. On the other hand, the expression of the anti-apoptotic protein Bcl-2 was inhibited. On TEM examination, C4-treated HCT-116 cells showed classical structural signs of apoptosis. This study identifies a novel azine (C4), which induces remarkable cytotoxicity against the colorectal carcinoma cell line, mediated through apoptosis induction. These novel insights suggest C4 as a promising therapeutic agent in colorectal cancer.

Oxyresveratrol Inhibits IL-1β-Induced Inflammation via Suppressing AKT and ERK1/2 Activation in Human Microglia, HMC3

Oxyresveratrol (OXY), a major phytochemical component derived from several plants, has been proved to have several pharmacological properties. However, the role of OXY in regulating neuroinflammation is still unclear. Here, we focused mainly on the anti-neuroinflammatory effects at the cellular level of OXY in the interleukin-1 beta (IL-1β)-stimulated HMC3 human microglial cell line. We demonstrated that OXY strongly decreased the release of IL-6 and MCP-1 from HMC3 cells stimulated with IL-1β. Nevertheless, IL-1β could not induce the secretion of TNF-α and CXCL10 in this specific cell line, and that OXY did not have any effects on reducing the basal level of these cytokines in the sample culture supernatants. The densitometry analysis of immunoreactive bands from Western blot clearly indicated that IL-1β does not trigger the nuclear factor-kappa B (NF-κB) signaling. We discovered that OXY exerted its anti-inflammatory role in IL-1β-induced HMC3 cells by suppressing IL-1β-induced activation of the PI3K/AKT/p70S6K pathway. Explicitly, the presence of OXY for only 4 h could strongly inhibit AKT phosphorylation. In addition, OXY had moderate effects on inhibiting the activation of ERK1/2. Results from immunofluorescence study further confirmed that OXY inhibited the phosphorylation of AKT and ERK1/2 MAPK upon IL-1β stimulation in individual cells. These findings suggest that the possible anti-inflammatory mechanisms of OXY in IL-1β-induced HMC3 cells are mainly through its ability to suppress the PI3K/AKT/p70S6K and ERK1/2 MAPK signal transduction cascades. In conclusion, our study provided accumulated data that OXY is able to suppress IL-1β stimulation signaling in human microglial cells, and we believe that OXY could be a probable pharmacologic agent for altering microglial function in the treatment of neuroinflammation.

Abstract 4960: Sox2, Oct4, and Nanog expression for identification of ovarian cancer tumor initiating cells

Abstract High Grade Serous Ovarian Cancer (HGSOC) is the most lethal gynecological disease in women, with over 70% of advanced stage disease relapsing within 18 months. Recent studies suggest that tumor-initiating cells (TICs) support tumor heterogeneity, chemoresistance, and relapse in HGSOC. Identification of TICs has traditionally relied on expression of surface markers such as CD133, CD44, and CD117 and/or enzymes such as aldehyde dehydrogenase (ALDH). Unfortunately, these markers are often cell type specific and not reproducible across patient samples. More reliable markers of TICs may include stem cell transcription factors such as Sox2, Oct4, and Nanog that function to support long-term self-renewal, multipotency, and quiescence, although these factors have not been comprehensively evaluated in ovarian cancer. We have previously shown that ovarian cancer cells cultured in 3D spheroid-supporting conditions have enhanced expression of Sox2, Oct4, and Nanog and are more tumorigenic than cells cultured in 2D as a monolayer. We hypothesize that Sox2, Oct4, and Nanog support spheroid formation, chemotherapy resistance, and tumorigenicity more reliably than traditional TIC markers. To investigate this hypothesis we evaluated five HGSOC cell lines (CAOV3/CAOV4/OV90/OVCAR4/OVCAR8), two undefined serous lines (ACI23, OVCAR5) and one non-serous line (SKOV3) in 2D vs 3D conditions and quantitated Sox2, Oct4, and Nanog expression, spheroid formation, chemotherapy resistance and tumorigenicity. Our data show that OVCAR4, OVCAR5, and OVCAR8 had the highest expression of Sox2, Oct4, and Nanog in 3D conditions and at least half of the cell lines had enriched expression of all three factors after chemotherapy treatment. A correlation analysis of the traditional TIC markers shows that the surface marker CD133 positively correlated with expression of Sox2, Oct4, and Nanog. Analysis of TCGA data shows that Sox2, Oct4, and Nanog are prone to amplification or gain of function events in 21%, 4%, and 7% of patients, respectively, and these patients are significantly more likely to have recurrent disease. Overall our findings suggest that Sox2, Oct4, and Nanog correlate with TIC features and may be more reliable markers for the identification of cells with enhanced tumor-initiation capacity and drug resistance. Our data further clarify specific ovarian cancer cell lines that have greater dependence on these factors. More reliable and consistent identification of ovarian TICs will improve our understanding of TIC biology and enable the design of therapies to overcome chemotherapy resistance and disease relapse. Citation Format: Mikella Robinson, Samuel F. Gilbert, Logan J. Alexander, Samuel E. Green, Omar Lujano-Olazaba, Omid Patrus, Jennifer A. Waters, Jacqueline M. Lara, Carrie D. House. Sox2, Oct4, and Nanog expression for identification of ovarian cancer tumor initiating cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4960.

Abstract 1012: Determinants of immune evasion in MET driven lung cancer

Abstract PURPOSE: The 5' ectonucleotidase (NT5E) encodes for the CD73 membrane protein that converts the extracellular AMP into adenosine (Ado), an immunosuppressive nucleoside that generates anti-inflammatory responses by stimulating T cell anergy. We aimed to analyze CD73 expression across non-small cell lung cancer (NSCLC) and explore its role in immunomodulation and its predictive value to immunotherapy (ICI). METHODS: We analyzed CD73 (NT5E) expression across lung adenocarcinoma samples from The Cancer Genome Atlas (TCGA) and determined top co-expressed genes or correlations with alterations in lung cancer (LC) driver genes. Correlations were validated in specific cancer cell lines using appropriate treatments to activate or inhibit selected pathways. A CRISPR-Cas9 CD73-knockout cell line model was generated to explore direct regulation of extracellular Ado production, as well as impact on secreted cytokines. Finally, we performed staining of CD73 and other immune-related molecules (CD8+ TILs, PD-L1, STING) in a pilot cohort of NSCLC patients (n=35) treated with first line ICI +/- chemotherapy at the DFCI. RESULTS: TCGA analysis revealed strong correlation between MET and CD73 expression and identified MET altered tumors, either by MET exon 14 skipping mutations (METex14) or MET amplification, as being enriched for high CD73 expression (p=0.03). Functional assays using LC cell lines showed that MET activation increases CD73 expression at a transcriptional and protein level by using qPCR, western-blot and flow-cytometry. Additional adenosinergic-related molecules, including the adenosine receptor A2BR (ADORA2B), were co-regulated in parallel with CD73, defining a specific phenotype. In our pilot cohort of patients, CD73 high expression (2+) was found in 20% of lung tumors, mostly adenocarcinomas, whereas 50% were negative (0+) for CD73 expression. CD73 was positively associated with high CD8+ (p= 0.02). Clinical outcomes are being evaluated to elucidate the potential role of CD73 as a predictive marker to ICI. CONCLUSIONS: MET altered tumors and LC cell lines express high levels of CD73 and other adenosinergic-related molecules, representing a potential mechanism of immune evasion and target for immunotherapy. The potential predictive role of CD73 expression in a larger cohort of patients treated with immune checkpoint inhibition (ICI) will be performed. Citation Format: Maria Saigi, Ryohei Yoshida, Erik H Knelson, Navin R Mahadevan, Amir Vajdi, Israel Cañadas, Tran C Thai, Mark M. Awad, Montse Sánchez-Céspedes, David A Barbie. Determinants of immune evasion in MET driven lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1012.

Abstract 1935: The NEDD8 and EGFR pathways are independent therapeutic targets in colorectal cancer

Abstract Colorectal cancer (CRC) develops and progresses through an accumulation of genetic and epigenetic alterations in multiple molecular pathways. Currently, targeted therapies combined with standard chemotherapy are the first-line therapy for metastatic CRC; nevertheless, the effectiveness of these drugs is limited by primary and acquired resistance. Since pathways are highly interconnected, the development of rational combinations of targeted therapies can be exploited to circumvent resistance mechanisms. As a possible alternative pathway for CRC treatment, an attractive option is the blockade of the NEDD8-ubiquitin like protein conjugation pathway. We previously found that the NEDD8-inhibitor pevonedistat has significant in vitro and in vivo activity on a subset of CRCs. However, the in vivo response is limited to tumor stabilization rather than regression, highlighting the need for therapeutic combinations. When the optimal drug combination cannot be readily predicted, functional genetic screens represent a powerful tool for unbiased exploration. We therefore carried out a synthetic lethality screening with an shRNA library covering 200 genes associated with FDA-approved drugs. The screening was aimed at identifying shRNAs that would be depleted only in the presence of pevonedistat: such constructs were expected to target genes that could harbor synergistic effects with NEDD8 inhibition. After shRNA library transduction, CRC cell lines were grown in the absence or presence of low-dose pevonedistat; Next Generation Sequencing and bioinformatics analysis allowed comparing the transduced library repertoire with or without pevonedistat, and identifying candidate synthetic lethal genes. The screening results revealed a strong, pevonedistat-dependent depletion of constructs targeting different tyrosine kinases (i.e. EGFR, BRAF, FYN and FLT4) in specific CRC cell lines (CAR1, WIDR, LIM2099 and DIFI, respectively). Firstly, we focused on the remarkable drop-out of EGFR-targeting shRNAs in CAR1 cells, which represent a subgroup of aggressive tumors refractory to cetuximab treatment, despite the lack of currently known markers of resistance. We discovered an independent and additive effect of anti-EGFR drugs (cetuximab and lapatinib) combined with pevonedistat, which was then validated in vitro on further cell lines (HCA7 and HROC69) and in vivo on HCA7-transplanted mice. Furthermore, we considered the depletion of constructs targeting BRAF, a member of EGFR pathway, observed in WIDR BRAF-mutant cells: we found an additive effect of BRAF inhibitor vemurafenib and pevonedistat in reducing in vitro cell growth. Altogether our results suggest that the concomitant pharmacological inhibition of NEDD8 and EGFR-pathway could be a novel effective approach to treat clinically aggressive CRCs, worthy of further characterization. Citation Format: Federica Invrea, Alessandro Carugo, Consalvo Petti, Cristopher Bristow, Michael Peoples, Carlotta Cancelliere, Alessia Corrado, Alberto Bardelli, Claudio Isella, Giulio F. Draetta, Enzo Medico. The NEDD8 and EGFR pathways are independent therapeutic targets in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1935.

Identification, Purification and Molecular Characterization of Chondrosin, a New Protein with Anti-tumoral Activity from the Marine Sponge Chondrosia Reniformis Nardo 1847.

Chondrosia reniformis is a common marine demosponge showing many peculiarities, lacking silica spicules and with a body entirely formed by a dense collagenous matrix. In this paper, we have described the identification of a new cytotoxic protein (chondrosin) with selective activity against specific tumor cell lines, from C. reniformis, collected from the Liguria Sea. Chondrosin was extracted and purified using a salting out approach and molecular weight size exclusion chromatography. The cytotoxic fractions were then characterized by two-dimensional gel electrophoresis and mass spectrometry analysis and matched the results with C. reniformis transcriptome database. The procedure allowed for identifying a full-length cDNA encoding for a 199-amino acids (aa) polypeptide, with a signal peptide of 21 amino acids. The mature protein has a theoretical molecular weight of 19611.12 and an IP of 5.11. Cell toxicity assays showed a selective action against some tumor cell lines (RAW 264.7 murine leukemia cells in particular). Cell death was determined by extracellular calcium intake, followed by cytoplasmic reactive oxygen species overproduction. The in silico modelling of chondrosin showed a high structural homology with the N-terminal region of the ryanodine receptor/channel and a short identity with defensin. The results are discussed suggesting a possible specific interaction of chondrosin with the Cav 1.3 ion voltage calcium channel expressed on the target cell membranes.

Silica-Based Nanoparticles for Biomedical Applications: From Nanocarriers to Biomodulators.

Silica-based nanoparticles (SNPs) are a classic type of material employed in biomedical applications because of their excellent biocompatibility and tailorable physiochemical properties. Typically, SNPs are designed as nanocarriers for therapeutics delivery, which can address a number of intrinsic drawbacks of therapeutics, including limited bioavailability, short circulation lifetime, and unfavorable biodistribution. To improve the delivery efficiency and spatiotemporal precision, tremendous efforts have been devoted to engineering the physiochemical properties of SNPs, including particle size, morphology, and mesostructure, as well as conjugating targeting ligands and/or "gatekeepers" to endow improved cell selectivity and on demand release profiles. Despite significant progress, the biologically inert nature of the bare silica framework has largely restricted the functionalities of SNPs, rendering conventional SNPs mainly as nanocarriers for targeted delivery and controlled release. To meet the requirements of next generation nanomedicines with improved efficacy and precision, new insights on the relationship between the physiochemical properties of SNPs and their biological behavior are highly valuable. Meanwhile, a conceptual shift from a simple spatiotemporal control mechanism to a more sophisticated biochemistry and signaling pathway modulation would be of great importance.In this Account, an overview of our recent contribution to the field is presented, wherein SNPs with rationally designed nanostructures and nanochemistry are applied as nanocarriers (defined as "nanomaterials being used as a transport module for another substance" according to Wikipedia) and/or biomodulators (defined as "any material that modifies a biological response" according to Wiktionary). This Account encompasses two main sections. In the first section, we focus on the conventional nanocarriers concept with new insights on the design principles of the nanostructures. We present examples to demonstrate the engineering of pore geometry, surface topology, and asymmetry of nanoparticles to achieve enhanced drug, gene, and protein delivery efficiency. The contribution of surface roughness of SNPs on improving the cellular uptake efficiency, adhesion property, and DNA transfection capacity is particularly highlighted. In the second section, we discuss novel SNPs designed as biomodulators to regulate intracellular microenvironment and cell signaling, such as the oxidative stress and glutathione levels for improving the anticancer efficacy of therapeutics and mRNA transfection in specific cell lines. The interplay between the nanoparticles, biological system, and drugs is discussed. We further discuss how to engineer the composition of SNPs to modulate metal hemostasis to realize inherent anticancer activity. Two typical examples, including modulating copper signaling for tumor vasculature targeted therapy and controlling iron signaling for macrophage polarization based immunotherapy, are presented to highlight the unique advantages of SNPs as nanosized therapeutics in comparison to molecular drugs. Moreover, utilizing these two examples, we showcase the possibility of designing SNPs with intrinsic pharmaceutical activity to indirectly control tumor growth without inducing significant cytotoxicity, thus alleviating the biosafety concerns of nanomedicines. At the end of this Account, we discuss our personal perspectives on the promises, opportunities, and issues in engineered SNPs as nanocarriers as well as their transition toward biomodulators. With a major focus on the latter scenario, the current status and possible future directions are outlined.

Coibamide A Targets Sec61 to Prevent Biogenesis of Secretory and Membrane Proteins.

Coibamide A (CbA) is a marine natural product with potent antiproliferative activity against human cancer cells and a unique selectivity profile. Despite promising antitumor activity, the mechanism of cytotoxicity and specific cellular target of CbA remain unknown. Here, we develop an optimized synthetic CbA photoaffinity probe (photo-CbA) and use it to demonstrate that CbA directly targets the Sec61α subunit of the Sec61 protein translocon. CbA binding to Sec61 results in broad substrate-nonselective inhibition of ER protein import and potent cytotoxicity against specific cancer cell lines. CbA targets a lumenal cavity of Sec61 that is partially shared with known Sec61 inhibitors, yet profiling against resistance conferring Sec61α mutations identified from human HCT116 cells suggests a distinct binding mode for CbA. Specifically, despite conferring strong resistance to all previously known Sec61 inhibitors, the Sec61α mutant R66I remains sensitive to CbA. A further unbiased screen for Sec61α resistance mutations identified the CbA-resistant mutation S71P, which confirms nonidentical binding sites for CbA and apratoxin A and supports the susceptibility of the Sec61 plug region for channel inhibition. Remarkably, CbA, apratoxin A, and ipomoeassin F do not display comparable patterns of potency and selectivity in the NCI60 panel of human cancer cell lines. Our work connecting CbA activity with selective prevention of secretory and membrane protein biogenesis by inhibition of Sec61 opens up possibilities for developing new Sec61 inhibitors with improved drug-like properties that are based on the coibamide pharmacophore.

Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis

The pro-inflammatory mediator receptor activator of nuclear factor-kappa B ligand (RANKL) plays a significant role in the development of rheumatoid arthritis; however, its role in inflammatory bowel disease is unknown. Genome-wide association meta-analysis for Crohn’s disease (CD) identified a variant near the TNFSF11 gene that encodes RANKL and CD risk allele increased expression of RANKL in specific cell lines. This study aims to elucidate if the RANKL inhibitor denosumab can reduce the severity of experimental colitis and modify the gut microbiota composition using murine dinitrobenzenesulfonic acid (DNBS)-experimental model of colitis mimicking CD. In colitic conditions, denosumab treatment significantly decreased the pro-inflammatory cytokines IL-6, IL-1β, and TNF-α within the colonic mucosa. Moreover, colitis was accompanied by disruption of gut microbiota, and preventative treatment with denosumab modulated this disruption. Denosumab treatment also modified the alpha- and beta diversity of colonic mucosa and fecal microbiota. These results provide a rationale for considering denosumab as a future potential therapy in CD; however, more detailed experimental and clinical studies are warranted.

Where are G-quadruplexes located in the human transcriptome?

It has been demonstrated that RNA G-quadruplexes (G4) are structural motifs present in transcriptomes and play important regulatory roles in several post-transcriptional mechanisms. However, the full picture of RNA G4 locations and the extent of their implication remain elusive. Solely computational prediction analysis of the whole transcriptome may reveal all potential G4, since experimental identifications are always limited to specific conditions or specific cell lines. The present study reports the first in-depth computational prediction of potential G4 region across the complete human transcriptome. Although using a relatively stringent approach based on three prediction scores that accounts for the composition of G4 sequences, the composition of their neighboring sequences, and the various forms of G4, over 1.1 million of potential G4 (pG4) were predicted. The abundance of G4 was computationally confirmed in both 5′ and 3′UTR as well as splicing junction of mRNA, appreciate for the first time in the long ncRNA, while almost absent of most of the small ncRNA families. The present results constitute an important step toward a full understanding of the roles of G4 in post-transcriptional mechanisms.

Folate decorated epigallocatechin-3-gallate (EGCG) loaded PLGA nanoparticles; in-vitro and in-vivo targeting efficacy against MDA-MB-231 tumor xenograft.

Epigallocatechin-3-gallate (EGCG), a major polyphenolic constituent of green tea exhibits significant anti-cancer potential over a wide range of cancer cells. We have developed folate peptide decorated PLGA-NPs loaded with EGCG (FP-EGCG-NPs) to bind folate receptor (FR) specific breast cancer cell lines and evaluated their efficacy in pre-clinical studies. EGCG loaded PLGA nanoparticles (EGCG-NPs) were characterised for size, surface morphology, surface charge, encapsulation efficacy and in-vitro drug release kinetics. Cellular uptake and in-vitro cytotoxicities of free drug, folate peptide conjugated and unconjugated EGCG-NPs were investigated against FR positive MDA-MB-231 and MCF-7 cells. The conjugated nanoparticles exhibited promising cytotoxic potentials as well as significantly high cellular internalisation in MDA-MB-231 cells as compared to unconjugated one. It also ensured longer half life, higher plasma concentration, favourably high apoptotic potential and significantly high mitochondrial depolarization effect as compared to free EGCG. The loaded nanoparticles were radiolabeled with technetium-99m and their tumor selectivity in MDA-MB-231 tumor bearing nude mice was investigated by scintigraphic imaging study. Finally in-vivo therapeutic efficacy studies in tumor bearing nude mice were also done to evaluate the efficacy of the formulation for cancer treatment.

The effect of SLA expression on genetically-engineered pig renal cells on the human T cell xenoresponse

Abstract Background Xenotransplantation using genetically-engineered (GE) pig organs offers an unlimited supply of organs for patients with end-stage organ failure. Disrupting the porcine GGTA1/CMAH/β4GalNT2 genes (TKO) markedly reduces binding of human natural anti-pig antibodies in human to carbohydrate antigens expressed on the pig organ. However, more evident have demonstrated that T cell responses play a major role in xenogeneic rejection, and that immunosuppression alone is likely incapable of completely suppressing these responses. The object of this study is at an organ-specific level to evaluate human T cell-mediated response against GE pig renal microvascular endothelial cells (RMEC) with or without swine leukocyte antigen (SLA) class I or II. Methods Primary RMEC were isolated from the GGTA1/CMAH knockout (DKO) pigs, and immortalized using Lenti-SV40 T. The gene editing was performed to create specific TKO RMEC cell lines expressing SLA class II. Stimulation of human T cell activation or proliferation by RMEC was performed flow cytometry-based mixed lymphocyte reaction (MLR). Results The specific GE cells lacking carbohydrates or expressing SLA class I or II were confirmed. MLR data shows that human CD4+ T cell proliferation by CD31+ RMEC was higher than that by fibroblast-like renal cells (RC), and was significantly inhibited by immunosuppressive drugs. Furthermore, both of CD69+ and CD25+ T cells were significantly enhanced by RMEC with expression of SLA class I and II compared with SLA class I alone. Conclusion Porcine RMEC express SLA class I/II and known costimulatory molecules and have the ability to simulate human T cell proliferation. RMEC will be a useful reagent for the further study of xenotransplantation.

VirusCircBase: a database of virus circular RNAs.

Circular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.

REPIC: a database for exploring the N6-methyladenosine methylome

The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples of 49 studies, covering 61 cell lines or tissues in 11 organisms. REPIC allows users to query N6-methyladenosine (m6A) modification sites by specific cell lines or tissue types. In addition, it integrates m6A/MeRIP-seq data with 1418 histone ChIP-seq and 118 DNase-seq data tracks from the ENCODE project in a modern genome browser to present a comprehensive atlas of m6A methylation sites, histone modification sites, and chromatin accessibility regions. REPIC is accessible at https://repicmod.uchicago.edu/repic.

Contaminated and misidentified cell lines commonly use in cancer research.

Cell line authentication is important for credibility concern and scientific reproducibility. Authenticated cancer cell lines retain the properties of the cancers of origin and serve valuable resources for medical research. Experimental results commonly will be validated in more than one cell line to avoid specific cell line effect not generalizable to the disease on the whole. The use of appropriate and verified cell lines would therefore be very important in preclinical studies of translational research, bridging basic research to clinics.