Similar Gene Expression Levels Research Articles

Comparison of P-glycoprotein gene expression of two Haemonchus contortus isolates from Yucatan, Mexico, with resistant or susceptible phenotype to ivermectin in relation to a susceptible reference strain

The variability in the expression of different P-glycoprotein (P-gp) genes in parasitic nematodes of ruminants such as Haemonchus contortus (Hco-pgp) may be caused by different factors including nematode biology, geographical region and anthelmintic pressure. This study analysed the relative expression level of 10 P-gp genes in two H. contortus (Hco-pgp) field isolates from Yucatan, Mexico: 1) PARAISO (IVM-resistant) and 2) FMVZ-UADY (IVM-susceptible). These isolates were compared with a susceptible reference isolate from Puebla, Mexico, namely “CENID-SAI”. In all cases H. contortus adult males were used. The Hco-pgp genes (1, 2, 3, 4, 9, 10, 11, 12, 14 and 16) were analysed for each isolate using the RT-qPCR technique. The Hco-pgp expressions were pairwise compared using the 2-ΔΔCt method and a t-test. The PARAISO isolate showed upregulation compared to the CENID-SAI isolate for Hco-pgp 1, 3, 9, 10 and 16 (P < 0.05), and the PARAISO isolate showed upregulation vs. FMVZ-UADY isolate for Hco-pgp 2 and 9 (P < 0.05), displaying 6.58- and 5.93-fold differences (P < 0.05), respectively. In contrast, similar Hco-pgp gene expression levels were recorded for FMVZ-UADY and CENID-SAI isolates except for Hco-pgp1 (P <0.1), which presented a significant upregulation (6.08-fold). The relative expression of Hco-pgp allowed confirming the IVM-resistant status of the PARAISO isolate and the IVM-susceptible status of the FMVZ-UADY isolate when compared to the CENID-SAI reference isolate. Therefore, understanding the association between the Hco-pgp genes expression of H. contortus and its IVM resistance status could help identifying the genes that could be used as molecular markers in the diagnosis of IVM resistance. However, it is important to consider the geographic origin of the nematode isolate and the deworming history at the farm of origin.

Engineered Gold and Silica Nanoparticle-Incorporated Hydrogel Scaffolds for Human Stem Cell-Derived Cardiac Tissue Engineering.

Electrically conductive biomaterials and nanomaterials have demonstrated great potential in the development of functional and mature cardiac tissues. In particular, gold nanomaterials have emerged as promising candidates due to their biocompatibility and ease of fabrication for cardiac tissue engineering utilizing rat- or stem cell-derived cardiomyocytes (CMs). However, despite significant advancements, it is still not clear whether the enhancement in cardiac tissue function is primarily due to the electroconductivity features of gold nanoparticles or the structural changes of the scaffold resulting from the addition of these nanoparticles. To address this question, we developed nanoengineered hydrogel scaffolds comprising gelatin methacrylate (GelMA) embedded with either electrically conductive gold nanorods (GNRs) or nonconductive silica nanoparticles (SNPs). This enabled us to simultaneously assess the roles of electrically conductive and nonconductive nanomaterials in the functionality and fate of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Our studies revealed that both GNR- and SNP-incorporated hydrogel scaffolds exhibited excellent biocompatibility and similar cardiac cell attachment. Although the expression of sarcomere alpha-actinin did not significantly differ among the conditions, a more organized sarcomere structure was observed within the GNR-embedded hydrogels compared to the nonconductive nanoengineered scaffolds. Furthermore, electrical coupling was notably improved in GNR-embedded scaffolds, as evidenced by the synchronous calcium flux and enhanced calcium transient intensity. While we did not observe a significant difference in the gene expression profile of human cardiac tissues formed on the conductive GNR- and nonconductive SNP-incorporated hydrogels, we noticed marginal improvements in the expression of some calcium and structural genes in the nanomaterial-embedded hydrogel groups as compared to the control condition. Given that the cardiac tissues formed atop the nonconductive SNP-based scaffolds (used as the control for conductivity) also displayed similar levels of gene expression as compared to the conductive hydrogels, it suggests that the electrical conductivity of nanomaterials (i.e., GNRs) may not be the sole factor influencing the function and fate of hiPSC-derived cardiac tissues when cells are cultured atop the scaffolds. Overall, our findings provide additional insights into the role of electrically conductive gold nanoparticles in regulating the functionalities of hiPSC-CMs.

Cutaneous burn injury represents a major risk factor for the development of traumatic ectopic bone formation following blast-related extremity injury

Blast-related traumatic heterotopic ossification (tHO) impacts clinical outcomes in combat-injured patients, leading to delayed wound healing, inflammatory complications, and reduced quality of life. Blast injured patients often have significant burns. This study investigated whether a partial thickness thermal burn injury exacerbates blast-related tHO in a clinically relevant polytrauma animal model. Adult male Sprague Dawley rats were subjected to an established model involving a whole-body blast overpressure exposure (BOP), complex extremity trauma followed by hind limb amputation (CET) followed by the addition of a 10 % total body surface area (TBSA) second degree thermal burn (BU). Micro-CT scans on post-operative day 56 showed a significant increase in HO volume in the CET + BU as compared to the CET alone injury group (p < .0001; 22.83 ± 3.41 mm3 vs 4.84 ± 5.77 mm3). Additionally, CET + BU concomitant with BOP significantly increased HO (p < .0001; 34.95 ± 7.71 mm3) as compared to CET + BU alone, confirming BOP has a further synergistic effect. No HO was detectable in rats in the absence of CET. Serum analysis revealed similar significant elevated (p < .0001) levels of pro-inflammatory markers (Cxcl1 and Il6) at 6 h post-injury (hpi) in the CET + BU and BOP + CET + BU injury groups as compared to naïve baseline values. Real-time qPCR demonstrated similar levels of chondrogenic and osteogenic gene expression in muscle tissue at the site of injury at 168 hpi in both the CET + BU and BOP+CET + BU injury groups. These results support the hypothesis that a 10 % TBSA thermal burn markedly enhances tHO following acute musculoskeletal extremity injury in the presence and absence of blast overpressure. Furthermore, the influence of BOP on tHO cannot be accounted for either in regards to systemic inflammation induced from remote injury or inflammatory-osteo-chondrogenic expression changes local to the musculoskeletal trauma, suggesting that another mechanism beyond BOP and BU synergistic effects are at play. Therefore, these findings warrant future investigations to explore other mechanisms by which blast and burn influence tHO, and testing prophylactic measures to mitigate the local and systemic inflammatory effects of these injuries on development of HO.

Differential induction of defense genes in hexaploid wheat roots by the plant-parasitic nematodes Pratylenchus neglectus and P. thornei.

Pratylenchus neglectus and P. thornei are among the most destructive root lesion nematodes of wheat in the Pacific Northwest, United States of America and throughout the world. The aim of this study was to determine whether both nematode species were similar in their ability to induce defense genes in roots of wheat genotype Scarlet, and whether a combination of both species induced a different pattern of gene induction than each species alone. The long-term aspect of the research was to identify nematode-inducible promoters for deploying defense genes in roots in breeding programs. The root transcriptomes of genotype Scarlet were obtained after a one-week infection period with each nematode species separately, or both species combined. Root defense gene expression was induced for all three treatments relative to the no-nematode control, but P. thornei affected expression to a greater extent compared to P. neglectus. The species combination induced the highest number of defense genes. This result was not predicted from nematode enumeration studies, in which P. thornei colonization was substantially lower than that of P. neglectus, and the nematode combination did not show a significant difference. Quantitative real time polymerase chain reaction (qRT-PCR) assays for Dehydrin2, Glucan endo-1,3-beta-glucosidase, 1-cys-Peroxiredoxin, Pathogenesis-related protein 1 and Late embryogenesis-abundant proteins 76 and group 3 authenticated the induction observed in the transcriptome data. In addition, a near-isogenic line of Scarlet harboring genetic resistance to fungal soilborne pathogens, called Scarlet-Rz1, showed similar or higher levels of defense gene expression compared to fungus-susceptible Scarlet in qRT-PCR assays. Finally, transcriptome expression patterns revealed nematode-inducible promoters that are responsive to both P. neglectus and P. thornei.

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2

Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.

Utilizing Autoencoders for Analysis and Classification of Microscopic in Situ Hybridization Images

Currently, analysis of microscopic In Situ Hybridization (ISH) images is done manually by experts. Precise evaluation and classification of such microscopic images can ease experts' work and reveal further insights about the data. In this work, we propose a deep-learning workflow to detect and classify areas of microscopic images with similar levels of gene expression. Analysis of the data is done by employing a type of ANN – Deep Learning Autoencoders – suitable for unsupervised learning. The model's performance is optimised by balancing the latent layers' length and complexity and fine-tuning hyperparameters. The results are validated by adapting the mean-squared error (MSE) metric and comparison to expert's evaluation. Reconstruction of the whole-scale microscopic images is used to summarise and visualise the results.

Exploring the expression and potential function of follicle stimulating hormone receptor in extragonadal cells related to abdominal aortic aneurysm.

Follicle stimulating hormone (FSH) is identified to play a role in postmenopausal disease and hypothesized to affect abdominal aortic aneurysm (AAA) onset/progression in postmenopausal women. We aimed to detect FSHR gene expression in AAA tissue and cell types involved in AAA formation. FSH stimulation of human umbilical cord endothelial cells (HUVECs), smooth muscle cells (HUCs) and PMA-differentiated macrophages to assess gene expression of FSHR and various markers. Human macrophages activated with various stimuli were assessed for FSHR gene expression. AAA dataset, AAA tissue samples and AAA-derived smooth muscle cells (SMC) obtained from elderly female donors were assessed for FSHR gene expression. AAA-SMCs were stimulated with FSH to assess its effect on gene expression. Lastly, oxidized low-density-lipoprotein (ox-LDL) uptake and abundance of cell surface protein markers were assessed by flow cytometry after FSH stimulation of human monocytes. FSH stimulation showed similar levels of gene expression in HUVECs and HUCs. Only ACTA2 was downregulated in HUCs. In PMA-differentiated macrophages, gene expression of inflammation markers was unchanged after FSH stimulation. FSHR gene expression was found to be low in the AAA datasets. Female AAA-SMCs show occasional FSHR gene expression at a very low level, yet stimulation with FSH did not affect gene expression of SMC- or inflammation markers. FSH stimulation did not impact ox-LDL uptake or alter cell surface protein expression in monocytes. While FSHR gene expression was detected in human testis tissue, it was below quantification level in all other investigated cell types, even upon activation of macrophages with various stimuli. Despite previous reports, we did not detect FSHR gene expression in various extragonadal cell types, except in occasional female AAA-SMCs. No clear effect on cell activation was observed upon FSH stimulation in any cell type. Our data suggest that a direct effect of FSH in AAA-related extragonadal cells is unlikely to influence AAA.

The pathogenetic basis for a disease continuum in early- and late-onset ataxia-dystonia supports a unified genetic diagnostic approach

Genetically inherited ataxic disorders are classified by their age of disease presentation into early- and late-onset ataxia (EOA and LOA, presenting before or after the 25th year-of-life). In both disease groups, comorbid dystonia co-occurs frequently. Despite overlapping genes and pathogenetic features, EOA, LOA and dystonia are considered as different genetic entities with a separate diagnostic approach. This often leads to diagnostic delay. So far, the possibility of a disease continuum between EOA, LOA and mixed ataxia-dystonia has not been explored in silico. In the present study, we analyzed the pathogenetic mechanisms underlying EOA, LOA and mixed ataxia-dystonia. We analyzed the association of 267 ataxia genes with comorbid dystonia and anatomical MRI lesions in literature. We compared anatomical damage, biological pathways, and temporal cerebellar gene expression between EOA, LOA and mixed ataxia-dystonia. The majority (≈65%) of ataxia genes were associated with comorbid dystonia in literature. Both EOA and LOA gene groups with comorbid dystonia were significantly associated with lesions in the cortico-basal-ganglia-pontocerebellar network. EOA, LOA and mixed ataxia-dystonia gene groups were enriched for biological pathways related to nervous system development, neural signaling and cellular processes. All genes revealed similar cerebellar gene expression levels before and after 25 years of age and during cerebellar development. In EOA, LOA and mixed ataxia-dystonia gene groups, our findings show similar anatomical damage, underlying biological pathways and temporal cerebellar gene expression patterns. These findings may suggest the existence of a disease continuum, supporting the diagnostic use of a unified genetic approach.

Adipose and Bone Marrow Derived-Mesenchymal Stromal Cells Express Similar Tenogenic Expression Levels when Subjected to Mechanical Uniaxial Stretching In Vitro.

The present study was conducted to determine whether adipose derived mesenchymal stromal cells (AD-MSCs) or bone marrow derived-MSCs (BM-MSCs) would provide superior tenogenic expressions when subjected to cyclical tensile loading. The results for this would indicate the best choice of MSCs source to be used for cell-based tendon repair strategies. Both AD-MSCs and BM-MSCs were obtained from ten adult donors (N = 10) and cultured in vitro. At passaged-2, cells from both groups were subjected to cyclical stretching at 1 Hz and 8% of strain. Cellular morphology, orientation, proliferation rate, protein, and gene expression levels were compared at 0, 24, and 48 hours of stretching. In both groups, mechanical stretching results in similar morphological changes, and the redirection of cell alignment is perpendicular to the direction of stretching. Loading at 8% strain did not significantly increase proliferation rates but caused an increase in total collagen expression and tenogenic gene expression levels. In both groups, these levels demonstrated no significant differences suggesting that in a similar loading environment, both cell types possess similar tenogenic potential. In conclusion, AD-MSCs and BM-MSCs both demonstrate similar tenogenic phenotypic and gene expression levels when subjected to cyclic tensile loading at 1 Hz and 8% strain, thus, suggesting that the use of either cell source may be suitable for tendon repair.

Rapid response of osmotic stress transcription factor 1 (OSTF1) expression to salinity challenge in gills of marine euryhaline milkfish (Chanos chanos).

Euryhaline teleosts can survive in environments with different salinities. Cortisol is an important hormone for acclimation to seawater (SW) of euryhaline teleosts. Osmotic stress transcription factor 1 (OSTF1), also called the transforming growth factor-beta stimulated clone 22 domain 3 (tsc22d3), was first reported in tilapia as an acute response gene and protein under hyperosmotic stress, and it is regulated by cortisol. To date, most studies on OSTF1 have focused on freshwater inhabitants, such as tilapia, medaka, and catadromous eel. The expression of OSTF1 and the correlation between OSTF1 and cortisol in marine inhabitant euryhaline teleosts, to our knowledge, remain unclear. This study reveals the changes in the expression levels of branchial OSTF1, plasma cortisol levels, and their correlation in the marine inhabitant milkfish with ambient salinities. The two sequences of milkfish TSC22D3 transcripts were classified as OSTF1a and OSTF1b. Both genes were expressed universally in all detected organs and tissues but were the most abundant in the liver. Similar gene expression levels of ostf1a and ostf1b were found in SW- and fresh water (FW)-acclimated milkfish gills, an important osmoregulatory organ. Within 12 hours of being transferred from FW to SW, the gene expression level of ostf1b increased significantly (4 folds) within 12 h, whereas the expression level of ostf1a remained constant. Moreover, cortisol levels increased rapidly after being transferred to a hyperosmotic environment. After an intraperitoneal injection of cortisol, the gene expression levels of ostf1a and ostf1b were elevated. However, under hyperosmotic stress, ostf1a gene expression remained stable. Overall, the results revealed that ostf1b was the primary gene in milkfish responding to hypertonic stress, and cortisol concentration increased after the transfer of milkfish from FW to SW. Furthermore, cortisol injection increased the expression of ostf1a and ostf1b. As a result, factors other than cortisol may activate ostf1b in milkfish gills in response to an environmental salinity challenge.

Proliferation and Differentiation of Intestinal Caco-2 Cells Are Maintained in Culture with Human Platelet Lysate Instead of Fetal Calf Serum

Cell lines are widely used as in vitro model systems and substitute for animal experiments. The frequently used Caco-2 cell line is considered to reflect characteristics of differentiated intestinal epithelium. However, the need to culture the cells with fetal calf serum (FCS) induces a high variability, risk of contamination and is ethically disputed. We tested the culture of Caco-2 cells with human platelet lysate (PL) instead of FCS. We compared cell viability and differentiation by measuring ATP levels, gene and protein expression of specific markers in total cell extracts, brush border membrane vesicles (BBM) and lipid rafts (LR). Cell viability was slightly enhanced in cells grown with PL compared to FCS. The cells differentiated to an intestinal phenotype like the cells cultured in FCS, as indicated by the similar gene expression levels of hexose and protein transport proteins and the structural protein VILLIN. BBM showed a comparable distribution of the intestinal hydrolases, indicating a maintained cell membrane polarity. The distribution of the marker protein FLOTILLIN-2 in LR was also similar. We conclude that PL is an exquisite and suitable replacement for FCS in the culture of Caco-2 cells that can eliminate many disadvantages incurred due to the use of FCS.

Optimized alginate-based 3D printed scaffolds as a model of patient derived breast cancer microenvironments in drug discovery

The cancer microenvironment influences tumor progression and metastasis and is pivotal to consider when designing in vivo-like cancer models. Current preclinical testing platforms for cancer drug development are mainly limited to 2D cell culture systems that poorly mimic physiological environments and traditional, low throughput animal models. The aim of this work was to produce a tunable testing platform based on 3D printed scaffolds (3DPS) with a simple geometry that, by extracellular components and response of breast cancer reporter cells, mimics patient-derived scaffolds (PDS) of breast cancer. Here, the biocompatible polysaccharide alginate was used as base material to generate scaffolds consisting of a 3D grid containing periostin and hydroxyapatite. Breast cancer cell lines (MCF7 and MDA-MB-231) produced similar phenotypes and gene expression levels of cancer stem cell, epithelial–mesenchymal transition, differentiation and proliferation markers when cultured on 3DPS and PDS, contrasting conventional 2D cultures. Importantly, cells cultured on 3DPS and PDS showed scaffold-specific responses to cytotoxic drugs (doxorubicin and 5-fluorouracil) that were different from 2D cultured cells. In conclusion, the data presented support the use of a tunable alginate-based 3DPS as a tumor model in breast cancer drug discovery.

Transcriptome analysis provides a blueprint of coral egg and sperm functions.

BackgroundReproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data.MethodsHere, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes?ResultsWe show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization.

Biomarker data from KATHERINE: A phase III study of adjuvant trastuzumab emtansine (T-DM1) versus trastuzumab (H) in patients with residual invasive disease after neoadjuvant therapy for HER2-positive breast cancer.

502 Background: The phase 3 KATHERINE study (NCT01772472) compared adjuvant T-DM1 versus H in patients with residual invasive breast cancer after neoadjuvant chemotherapy plus HER2-targeted therapy. Here we report exploratory analyses of the relationship between invasive disease-free survival (IDFS) and biomarkers potentially related to response. Methods: Formalin fixed paraffin-embedded tissue samples were collected before neoadjuvant treatment and/or at surgery. Surgical samples were used for analyses, except when only pre-treatment samples were available (~20% of cases). DNA was derived to identify PIK3CA hotspot mutations and gene expression (RNA) analysis was used to detect HER2, PD-L1, CD8 and predefined immune signatures including 3-gene, 5-gene, Teffector, chemokine signaling, and checkpoint inhibitor signatures. RNA analysis was adjusted for tumor content and expression levels were dichotomized at the median into low (≤) and high (&gt;) groups. The effect of treatment and biomarkers on IDFS was assessed. Results: PIK3CA mutation (mut) status was available from 1363 (91.7%) patients. T-DM1 IDFS benefit was independent of PIK3CA mut status (mut: HR 0.54; 95%CI 0.23–0.90; non-mut: HR 0.48; 95%CI 0.35–0.65) and no impact of PIK3CA mut was observed within either treatment arm. Gene expression data were available from 1059 (71.3%) patients. Similar gene expression levels were observed between treatment arms, but, unlike the surgical samples (n = 815), the pre-treatment samples (n = 244) were not representative of the ITT population. Thus, subsequent analyses were based on surgical samples (H n = 398; T-DM1 n = 417). Consistent treatment benefit with T-DM1 vs H was observed across the single-gene and immune gene-signature subgroups as in the ITT population. High vs low HER2 expression was associated with worse outcome (HR 2.02; 95% CI 1.32–3.11) within the H arm, but not within the T-DM1 arm (HR 1.01; 95% CI 0.56–1.83). High vs low PD-L1 expression was associated with better outcome within the H arm (HR 0.66; 95% CI 0.44–1.00) but not within the T-DM1 arm (HR 1.05; 95% CI 0.59–1.87). Similar trends were observed in the checkpoint inhibitor subgroups. Conclusions: These exploratory analyses provide the first data on the relationship between biomarker expression in residual disease after HER2-targeted therapy and outcomes. PIK3CA mut status did not influence outcomes with H or T-DM1. T-DM1 benefit appeared to be independent of all biomarkers assessed. Clinical trial information: NCT01772472 .

Metabolic flux and functional potential of microbial community in an acidogenic dynamic membrane bioreactor

In this study, a laboratory-scale acidogenic dynamic membrane bioreactor (DMBR) was operated with or without alginate immobilization under various hydraulic retention times. The interactions between biofilm formation, metabolic flux and predicted functional genes were investigated in the DMBR. Regardless of the alginate immobilization, hydrogen yield was increased after biofilm was formed on a supporting material. Metabolic flux shifts from homoacetogenic to hydrogenic pathways along with biofilm formation was confirmed by flux balance analysis for metabolites. KEGG ortholog count prediction of functional genes from microbial consortia using bioinformatics package (PICRUSt). Predicted enzymes showed similar levels of functional gene expression regardless of the immobilization status. PICRUSt result showed strong evidence of the functional relationship among hydrogen production, biofilm formation, and metabolic pathway. Taken together, this study provides to estimate characteristics of biofilm formation changes and to better understand the microbial metabolism of DMBR.

Patterns of systemic and local inflammation in patients with asthma hospitalised with influenza.

Patients with asthma are at risk of hospitalisation with influenza, but the reasons for this predisposition are unknown. A prospective observational study of adults with PCR-confirmed influenza in 11 UK hospitals, measuring nasal, nasopharyngeal and systemic immune mediators and whole-blood gene expression. Of 133 admissions, 40 (30%) had previous asthma; these were more often female (70% versus 38.7%, OR 3.69, 95% CI 1.67-8.18; p=0.0012), required less mechanical ventilation (15% versus 37.6%, Chi-squared 6.78; p=0.0338) and had shorter hospital stays (mean 8.3 versus 15.3 days, p=0.0333) than those without. In patients without asthma, severe outcomes were more frequent in those given corticosteroids (OR 2.63, 95% CI 1.02-6.96; p=0.0466) or presenting >4 days after disease onset (OR 5.49, 95% CI 2.28-14.03; p=0.0002). Influenza vaccination in at-risk groups (including asthma) were lower than intended by national policy and the early use of antiviral medications were less than optimal. Mucosal immune responses were equivalent between groups. Those with asthma had higher serum interferon (IFN)-α, but lower serum tumour necrosis factor, interleukin (IL)-5, IL-6, CXCL8, CXCL9, IL-10, IL-17 and CCL2 levels (all p<0.05); both groups had similar serum IL-13, total IgE, periostin and blood eosinophil gene expression levels. Asthma diagnosis was unrelated to viral load, IFN-α, IFN-γ, IL-5 or IL-13 levels. Asthma is common in those hospitalised with influenza, but may not represent classical type 2-driven disease. Those admitted with influenza tend to be female with mild serum inflammatory responses, increased serum IFN-α levels and good clinical outcomes.

Determination of Fat Accumulation Reduction by Edible Fatty Acids and Natural Waxes In Vitro.

Natural edible waxes mixed with plant oils, containing high levels of unsaturated fatty acids (FAs), are known as oleogels. Oleogels are used for replacing saturated FAs in animal-derived food with unsaturated FAs. However, the health effects of edible waxes are not yet clearly defined. The purpose of this study was to investigate the effect of FAs and natural waxes on the adipogenesis in 3T3-L1 cells. The 3T3-L1 cells were differentiated and treated with FAs and waxes. These FAs [Palmitic acid (PA), Stearic acid (SA), Oleic acid (OA), Linoleic acid (LA), and Alpha-linolenic acid (ALA)] and waxes [beeswax (BW) and carnauba wax (CW)] were prepared at varying concentrations, and cell toxicity, triglyceride accumulation, lipid droplets size, and distribution inside of cells were determined. Adipogenic gene expression including PPARγ, FASN, C/EBPα, SREBP-1, and CPT-1 was determined. Results showed that increasing the concentration of FAs and waxes led to a decrease in the adipocyte cells viability and metabolic performance. SA showed the highest level of triglyceride accumulation (p<0.05), whereas ALA showed the lowest (p<0.05). Both BW and CW at 3.0 ppm showed significantly higher lipid accumulation than in the control and other groups (p<0.05). ALA had significantly downregulated adipogenic gene expression levels, excluding those of CPT-1, compared to the other treatment groups (p<0.05). Moreover, BW demonstrated similar adipogenic gene expression levels as ALA compared to CW. Consequently, ALA and BW may have health benefits by reducing adipogenesis and can be used in processed meat.

Detection of condition-specific marker genes from RNA-seq data with MGFR.

The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines.

N-glycome inheritance from cells to extracellular vesicles in B16 melanomas.

We investigated the correlation between metastatic behaviors of tumor cells and asparagine‐linked glycosylation (N‐glycosylation) of tumor‐derived extracellular vesicles (EVs). Three mouse melanoma B16 variants with distinct metastatic potentials show similar gene expression levels and enzymatic activities of glycosyltransferases involved in N‐glycosylation. All melanoma variants and EVs have nearly identical profiles of de‐sialylated N‐glycans. The major de‐sialylated N‐glycan structures of cells and EVs are core‐fucosylated, tetra‐antennary N‐glycans with β1,6‐N‐acetylglucosamine branches. A few N‐glycans are extended by N‐acetyllactosamine repeats. Sialylation of these N‐glycans may generate cell‐type‐specific N‐glycomes on EVs. Taken together, melanoma‐derived EVs show high expression of tumor‐associated N‐glycans, and the core structure profile is inherited during multiple selection cycles of B16 melanomas and from tumor cells to EVs.

Abstract 3995: Exploring non-small cell lung carcinoma cell lines' sensitivity to neratinib

Abstract Introduction: Lung cancer is the second most common diagnosed malignancy and accounts for the biggest number of cancer related deaths worldwide. Despite increased health warnings associated with habits, such as smoking, ten year survival rates for lung cancer in the UK remain similar to those seen in the 1970's. In the USA, the 5 year survival rates dramatically reduce with late disease stage, from 49 percent at Stage 1A to 5 percent at Stage IIIB. Mutations in epidermal growth factor receptor (EGFR) appears to be quite common in lung cancer. ERBB2 mutations also appear, albeit at lower frequency. In addition, ERBB2 amplifications have also been reported, particularly in tumors that have become resistant to EGFR-TKIs. Neratinib is an orally available tyrosine kinase inhibitor that irreversibly binds and inhibits EGFR, ERBB2 and ERBB4 receptor tyrosine kinases. This study aimed to characterize in detail the expression profile of genes downstream of the EGFR family members in two NSCLC cell lines and their differential sensitivity to neratinib. Materials and Methods: A549 (adenocarcinoma), a cell line with intermediate sensitivity to gefitnib, and SKMES-1 (squamous cell carcinoma) NSCLC cell lines were purchased from American Tissue Culture Collection (ATCC). Cytotoxicity was assessed using an MTT assay. Changes in gene expression in response to neratinib were quantified by next generation sequencing using AmpliSeq technology and analysed using Ingenuity pathway analysis (IPA) software. Results: SKMES-1 lung cancer cells were found to be more sensitive to neratinib than A549 cancer cells. Both cell lines exhibited similar low gene expression levels of ERBB2. SKMES-1 cancer cells showed higher gene expression profiles for the remaining HER family members, EGFR, ERBB3 and ERBB4, compared to the A549 cancer cells. IPA analysis showed that in SKMES-1 cells treated with neratinib differentially expressed genes were associated with inhibition of Akt and ERK pathways and their signal transduction whereas, this was not seen in the A549 cells. Conclusions: This study has shown that although these two NSCLC cell lines have similar gene expression levels of ERBB2, there is a difference in profile amongst the other receptor family members. EGFR and ERBB4 mRNA transcript levels were twice as high in SK-MES-1 compared to A549. This variance in the ERBB family gene expression profile may account for the differing sensitivities these cell lines have to neratinib. Further analysis indicates that Akt/ERK signal transduction was inhibited in SKMES-1 cells treated with neratinib though the exact mechanism for this remains unknown. Citation Format: Sioned Owen, Dafydd A. Dart, Alshad S. Lalani, Francesca Avogadri-Connors, Richard P. Bryce, Wen G. Jiang. Exploring non-small cell lung carcinoma cell lines' sensitivity to neratinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3995.