Detect Changes In Expression Research Articles

Identification of Novel Candidate Targets for Fascaplysin through In Silico and In Vivo Analyses of Shared Targets among Structurally Similar Compounds

Background: The discovery of new drug targets is a critical and challenging aspect of drug development. Fascaplysin, a marine natural product, has shown potential in various biological applications, but identifying suitable protein targets for such compounds remains a complex task. Purpose: This study aims to identify new candidate protein targets for fascaplysin by analyzing the expected targets of structural analogs, utilizing both molecular docking analysis for prediction and in vivo experiments for validation. Methods: We utilized a public database to classify structurally similar analogs to fascaplysin into four groups based on their scaffold structures. The predicted protein targets were organized by scaffold structure and assessed for potential binding with fascaplysin through molecular docking analysis. In adult zebrafish, we employed quantitative polymerase chain reaction (qPCR) to detect expression changes in downstream signaling genes of the selected candidate targets, providing a predictive measure of interaction and biological effect. Results: A total of 93 common targets were identified across all groups, categorized based on protein characteristics. The molecular binding affinities between fascaplysin and 37 selected candidates, comprising 14 kinases and 23 receptors, were quantified. Molecular docking analyses highlighted MAPK8, MAP2K1, ERBB2, and JAK3 as novel drug target candidates. In adult zebrafish, fascaplysin modulated expression changes in downstream genes of these targets. This indicates the applicability of fascaplysin in treating diseases associated with these targets, revealing promising therapeutic potential. Conclusion: The in silico analysis method used in this study provides an efficient and cost-effective way to identify protein target candidates for drugs, using structural similarities and molecular docking to make the target validation process in drug development faster and easier. Integration of in vivo observations in adult zebrafish, specifically the modulation of downstream gene expression of candidate targets, complements in silico findings, enhancing the reliability of target identification. These results not only identify specific targets for fascaplysin but also establish a flexible framework that can be applied to other compounds, potentially expediting the drug discovery process.

Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement.

Mutations in MECP2 give rise to Rett syndrome (RTT), an X-linked neurodevelopmental disorder that results in broad cognitive impairments in females. While the exact etiology of RTT symptoms remains unknown, one possible explanation for its clinical presentation is that loss of MECP2 causes miswiring of neural circuits due to defects in the brain's capacity to respond to changes in neuronal activity and sensory experience. Here, we show that MeCP2 is phosphorylated at four residues in the mouse brain (S86, S274, T308, and S421) in response to neuronal activity, and we generate a quadruple knock-in (QKI) mouse line in which all four activity-dependent sites are mutated to alanines to prevent phosphorylation. QKI mice do not display overt RTT phenotypes or detectable gene expression changes in two brain regions. However, electrophysiological recordings from the retinogeniculate synapse of QKI mice reveal that while synapse elimination is initially normal at P14, it is significantly compromised at P20. Notably, this phenotype is distinct from the synapse refinement defect previously reported for Mecp2 null mice, where synapses initially refine but then regress after the third postnatal week. We thus propose a model in which activity-induced phosphorylation of MeCP2 is critical for the proper timing of retinogeniculate synapse maturation specifically during the early postnatal period.

A negative feedback loop centered on SMAD3 expression in transforming growth factor β1-induced corneal myofibroblast differentiation

SMAD3 downregulation is documented in transforming growth factor β1 (TGF-β1)-induced corneal fibroblasts differentiation to myofibroblasts (“fibroTOmyoDiff”) or corneal wound healing. However, the exact regulatory mechanism of TGF-β1/SMAD3 pathway in this context remains unclear. Here, we investigated the role and related mechanism of SMAD3 down-regulation in TGF-β1-induced human corneal fibroTOmyoDiff. By detecting expression changes of SMAD family during this process, we demonstrated that SMAD3 protein expression was dramatically decreased in the process and the decrease occurred mainly in SMAD3 gene transcription. Furthermore, SMAD3 overexpression using lentivirus infection and knockdown using sgRNA lentivirus infection or siRNAs revealed that SMAD3 overexpression enhanced TGF-β1-induced corneal fibroTOmyoDiff and vice versa. In addition, specific siRNAs and inhibitors targeting particular signaling pathway were used to figure out the intracellular signaling pathway regulating SMAD3, and the result showed that the decease of SMAD3 induced by TGF-β1 stimulation in human corneal fibroblasts (HCFs) was strikingly prevented by SMAD4 knockdown or p38 signaling inhibitor SB203580 treatment. Collectively, these results demonstrate that, in TGF-β1 induced corneal fibroTOmyoDiff, down-regulation of SMAD3 expression regulated by SMAD4 and p38 signaling pathways forms a negative feedback loop of TGFβ signaling to avoid excessive activation of the signaling, which suggest that SMAD3 may be a key target for corneal fibrosis treatment.

Gemcitabine Inhibits the Progression of Pancreatic Cancer by Restraining the WTAP/MYC Chain in an m6A-Dependent Manner.

Pancreatic cancer (PC) is a common malignant tumor of the digestive system, and its 5-year survival rate is only 4%. N6-methyladenosine (m6A) RNA methylation is the most common post-transcriptional modification and dynamically regulates cancer development, while its role in PC treatment remains unclear. We treated PC cells with gemcitabine and quantified the overall m6A level with m6A methylation quantification. Real-time quantitative reverse transcription polymerase chain reaction and Western blot analyses were used to detect expression changes of m6A regulators. We verified the m6A modification on the target genes through m6A-immunoprecipitation (IP), and further in vivo experiments and immunofluorescence (IF) assays were applied to verify regulation of gemcitabine on Wilms' tumor 1-associated protein (WTAP) and MYC. Gemcitabine inhibited the proliferation and migration of PC cells and reduced the overall level of m6A modification. Additionally, the expression of the "writer" WTAP was significantly downregulated after gemcitabine treatment. We knocked down WTAP in cells and found target gene MYC expression was significantly downregulated, m6A-IP also confirmed the m6A modification on MYC. Our experiments showed that m6A-MYC may be recognized by the "reader" IGF2BP1. In vivo experiments revealed gemcitabine inhibited the tumorigenic ability of PC cells. IF analysis also showed that gemcitabine inhibited the expression of WTAP and MYC, which displayed a significant trend of co-expression. Our study confirmed that gemcitabine interferes with WTAP protein expression in PC, reduces m6A modification on MYC and RNA stability, thereby inhibiting the downstream pathway of MYC, and inhibits the progression of PC.

Systematic profiling of subtelomeric silencing factors in budding yeast.

Subtelomeric gene silencing is the negative transcriptional regulation of genes located close to telomeres. This phenomenon occurs in a variety of eukaryotes with salient physiological implications, such as cell adherence, virulence, immune-system escape, and aging. The process has been widely studied in the budding yeast Saccharomyces cerevisiae, where genes involved in this process have been identified mostly on a gene-by-gene basis. Here, we introduce a quantitative approach to study gene silencing, that couples the classical URA3 reporter with GFP monitoring, amenable to high-throughput flow cytometry analysis. This dual silencing reporter was integrated into several subtelomeric loci in the genome, where it showed a gradual range of silencing effects. By crossing strains with this dual reporter at the COS12 and YFR057W subtelomeric query loci with gene-deletion mutants, we carried out a large-scale forward screen for potential silencing factors. The approach was replicable and allowed accurate detection of expression changes. Results of our comprehensive screen suggest that the main players influencing subtelomeric silencing were previously known, but additional potential factors underlying chromatin conformation are involved. We validate and report the novel silencing factor LGE1, a protein with unknown molecular function required for histone H2B ubiquitination. Our strategy can be readily combined with other reporters and gene perturbation collections, making it a versatile tool to study gene silencing at a genome-wide scale.

Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package

ABSTRACT Epimutations are rare alterations of the normal DNA methylation pattern at specific loci, which can lead to rare diseases. Methylation microarrays enable genome-wide epimutation detection, but technical limitations prevent their use in clinical settings: methods applied to rare diseases’ data cannot be easily incorporated to standard analyses pipelines, while epimutation methods implemented in R packages (ramr) have not been validated for rare diseases. We have developed epimutacions, a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/epimutacions.html). epimutacions implements two previously reported methods and four new statistical approaches to detect epimutations, along with functions to annotate and visualize epimutations. Additionally, we have developed an user-friendly Shiny app to facilitate epimutations detection (https://github.com/isglobal-brge/epimutacionsShiny) to non-bioinformatician users. We first compared the performance of epimutacions and ramr packages using three public datasets with experimentally validated epimutations. Methods in epimutacions had a high performance at low sample sizes and outperformed methods in ramr. Second, we used two general population children cohorts (INMA and HELIX) to determine the technical and biological factors that affect epimutations detection, providing guidelines on how designing the experiments or preprocessing the data. In these cohorts, most epimutations did not correlate with detectable regional gene expression changes. Finally, we exemplified how epimutacions can be used in a clinical context. We run epimutacions in a cohort of children with autism disorder and identified novel recurrent epimutations in candidate genes for autism. Overall, we present epimutacions a new Bioconductor package for incorporating epimutations detection to rare disease diagnosis and provide guidelines for the design and data analyses.

Changes in the expression of cancer- and metastasis-related genes and proteins after metformin treatment under different metabolic conditions in endometrial cancer cells

Research questionHyperinsulinemia and elevated estrogen levels are known risk factors for endometrial cancer (EC) development and are associated with obesity, type 2 diabetes mellitus (T2DM), insulin resistance, among others. Metformin, an insulin-sensitizing drug, displays anti-tumor effects in cancer patients, including EC, but the mechanism of action is still not completely understood. In the present study, the effects of metformin on gene and protein expression were investigated in pre- and postmenopausal EC in vitro models in order to identify candidates that are potentially involved in the drug's anti-cancer mechanism. DesignAfter treating the cells with metformin (0.1 and 1.0 mmol/L), changes in the expression of >160 cancer- and metastasis-related gene transcripts were evaluated with RNA arrays. A total of 19 genes and 7 proteins were selected for a follow-up expression analysis, including further treatment conditions, in order to evaluate the influence of hyperinsulinemia and hyperglycemia on metformin-induced effects. ResultsChanges in the expression of BCL2L11, CDH1, CDKN1A, COL1A1, PTEN, MMP9 and TIMP2 were analyzed on gene and protein level. The consequences resulting from the detected expression changes as well as the influence of varying environmental influences are discussed in detail. With the presented data, we contribute to a better understanding of the direct anti-cancer activity of metformin as well as its underlying mechanism of action in EC cells. ConclusionsAlthough further research will be necessary to confirm the data, the influence of different environmental settings on metformin-induced effects could be highlighted with the presented data. Additionally, gene and protein regulation were not similar in the pre- and postmenopausal in vitro models.

Translocator protein 18 kDa regulates retinal neuron apoptosis and pyroptosis in glaucoma

Glaucoma is the leading cause of blindness worldwide. However, our insufficient understanding of the pathogenesis of glaucoma has limited the development of effective treatments. Because recent research has highlighted the importance of non-coding RNAs (ncRNAs) in various diseases, we investigated their roles in glaucoma. Specifically, we detected expression changes of ncRNAs in cell and animal models of acute glaucoma. Further analysis revealed that the Ier2/miR-1839/TSPO axis was critical to cell loss and retinal damage. The knockdown of Ier2, the overexpression of miR-1839, and the silencing of TSPO effectively prevented retinal damage and cell loss. Furthermore, we found that the Ier2/miR-1839/TSPO axis regulated the pyroptosis and apoptosis of retinal neurons through the NLRP3/caspase1/GSDMD, cleaved-caspase3 pathways. In addition to high expression in the retina, TSPO expression was found to be significantly higher in the dorsal lateral geniculate nucleus (DLG) of the brain in the pathologically high intraocular pressure (ph-IOP) rat model, as well as in the peripheral blood mononuclear cells (PBMCs) of glaucoma patients with high IOP. These results indicate that TSPO, which is regulated by Ier2/miR-1839, plays an important role in the pathogenesis of glaucoma, and this study provides a theoretical basis and a new target for the diagnosis and treatment of glaucoma.

Transcriptome analysis indicates the involvement of herbicide-responsive and plant-pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti.

The continuous use of the herbicides contributes to the emergence of the resistant populations of numerous weed species that are tolerant to multiple herbicides with different modes of action (multiple resistance) which is provided by non-target-site resistance mechanisms. In this study, we addressed the question of rapid acquisition of herbicide resistance to pinoxaden (acetyl CoA carboxylase inhibitor) in Apera spica-venti, which endangers winter cereal crops and has high adaptation capabilities to inhabit many rural locations. To this end, de novo transcriptome of Apera spica-venti was assembled and RNA-sequencing analysis of plants resistant and susceptible to pinoxaden treated with this herbicide was performed. The obtained data showed that the prime candidate genes responsible for herbicide resistance were those encoding 3-ketoacyl-CoA synthase 12-like, UDP-glycosyltransferases (UGT) including UGT75K6, UGT75E2, UGT83A1-like, and glutathione S-transferases (GSTs) such as GSTU1 and GSTU6. Also, such highly accelerated herbicide resistance emergence may result from the enhanced constitutive expression of a wide range of genes involved in detoxification already before herbicide treatment and may also influence response to biotic stresses, which was assumed by the detection of expression changes in genes encoding defence-related proteins, including receptor kinase-like Xa21. Moreover, alterations in the expression of genes associated with methylation in non-treated herbicide-resistant populations were identified. The obtained results indicated genes that may be involved in herbicide resistance. Moreover, they provide valuable insight into the possible effect of resistance on the weed interaction with the other stresses by indicating pathways associated with both abiotic and biotic stresses. © 2023 Society of Chemical Industry.

Serial Gene Expression Profiling of Neural Stem Cells Shows Transcriptome Switch by Long-Term Physioxia from Metabolic Adaption to Cell Signaling Profile.

Oxygen is an essential factor in the cellular microenvironment with pivotal effects on neural development with a particular sensitivity of midbrain neural stem cells (NSCs) to high atmospheric oxygen tension. However, most experiments are still performed at atmospheric O2 levels (21%, normoxia), whereas mammalian brain tissue is physiologically exposed to substantially lower O2 tensions around 3% (physioxia). We here performed serial Affymetrix gene array analyses to detect expression changes in mouse fetal NSCs from both midbrain and cortical tissues when kept at physioxia compared to normoxia. We identified more than 400 O2-regulated genes involved in cellular metabolism, cell proliferation/differentiation, and various signaling pathways. NSCs from both regions showed a low number but high conformity of regulated genes (9 genes in midbrain vs. 34 in cortical NSCs; 8 concordant expression changes) after short-term physioxia (2 days) with metabolic processes and cellular processes being the most prominent GO categories pointing to cellular adaption to lower oxygen levels. Gene expression profiles changed dramatically after long-term physioxia (13 days) with a higher number of regulated genes and more diverse expression patterns when comparing the two NSC types (338 genes in midbrain vs. 121 in cortical NSCs; 75 concordant changes). Most prominently, we observed a reduction of hits in metabolic processes but an increase in biological regulation and signaling pointing to a switch towards signaling processes and stem cell maintenance. Our data may serve as a basis for identifying potential signaling pathways that maintain stem cell characteristics in cortical versus midbrain physioxic stem cell niches.

Enzalutamide Overcomes Dihydrotestosterone-Induced Chemoresistance in Triple- Negative Breast Cancer Cells via Apoptosis.

Triple-negative breast cancer is challenging to treat due to its heterogeneity and lack of therapeutic targets. Hence, systemic chemotherapy is still the mainstay in TNBC treatment. Unfortunately, patients commonly develop chemoresistance. Androgen signalling through its receptor is an essential player in breast cancer, where it has been shown to confer chemoresistance to TNBC cells. The objective of the study was to elucidate the mechanistic effects of enzalutamide in the chemoresponse of TNBC cells to doxorubicin through the apoptosis pathway. MDA-MB-231 and MDA-MB-453 cells were used as model systems of TNBC. Cell viability and apoptosis were investigated upon treatment of cells with doxorubicin in the presence of dihydrotestosterone (DHT) and/or enzalutamide. Caspase 3/7 activity and TUNEL assays were performed to assess the induction of apoptosis. The expression of apoptosis-regulatory genes was assayed by qPCR for the detection of expression changes. Enzalutamide decreased the viability of MDA-MB-231 and MDA-MB- 453 cells and reduced DHT-induced chemoresistance of both cell lines. It also increased the chemosensitivity towards doxorubicin in MDA-MB-231 cells. Increasing DNA degradation and caspase 3/7 activity were concomitant with these outcomes. Moreover, enzalutamide downregulated the expression of the anti-apoptosis genes, mcl1 and bcl2, in MDA-MB-231 cells, while increasing the expression of the pro-apoptotic gene bid. On the other hand, DHT upregulated the expression of the anti-apoptosis genes, mcl1 and bcl2, in both cell lines. DHT increased the expression of the anti-apoptosis genes mcl1 and bcl2 in the TNBC cells, presumably leading to cell survival via the prevention of doxorubicin-induced apoptosis. On the other hand, enzalutamide may sensitize the cells to doxorubicin through downregulation of the bid/bcl2/mcl1 axis that normally activates the executive caspases, caspase 3/7. The activities of the latter enzymes were apparent in DNA degradation at the late stages of apoptosis.

The κ-Opioid Receptor Agonist U50488H Ameliorates Neuropathic Pain Through the Ca2+/CaMKII/CREB Pathway in Rats

ObjectiveTo observe the ameliorative effect of kappa opioid receptor (KOR) agonist on rats with neuropathic pain (NP) and investigate the mechanism of action of the calcium ion (Ca2+)/calcium/calmodulin-dependent protein kinase II (CaMKII)/cyclic AMP response element-binding protein (CREB) pathway.MethodsA total of 40 Sprague Dawley rats were randomly divided into four groups: sham-operation group (Sham group), NP model group (NP group), NP + KOR agonist U50488H group (NU group) and NP + specific CaMKII antagonist (KN93) + U50488H group (NKU group). The thermal withdrawal latency (TWL) and mechanical withdrawal threshold (MWT) of each group of rats were determined. ELISA was applied to examine the changes in inflammatory factors and oxidative stress factors, and the apoptotic rate in dorsal root ganglia was observed using TUNEL staining. Ca2+ concentration, content of oxidative stress index ROS and the release of calcitonin gene-related peptide (CGRP) and N-methyl-D-aspartate receptor (NMDAR) in the dorsal root ganglia were measured by the immunofluorescence assay. Finally, Western blotting was performed to detect expression changes in the Ca2+/CaMKII/CREB pathway.ResultsThe KOR agonist U50488H could improve the values of TWL and MWT of NP the rats, inhibit inflammatory responses and relieve oxidative stress injury. Its mechanisms of action were associated with U50488H repression of Ca2+ influx, reduction of CGRP and NMDAR releases in the dorsal root ganglia and decreases in CaMKII and CREB phosphorylations in NP rats.ConclusionThe KOR agonist ameliorates NP through suppressing the activity of the Ca2+/CaMKII/CREB pathway.

Pharmacological targeting transient receptor potential canonical channel 6 modulates biological behaviors for cervical cancer HeLa and SiHA cell

BackgroundThis study aimed to observe the effect of transient receptor potential canonical channel 6 (TRPC6) antagonist 1-(β-[3-(4-method-phenyl) propoxy]-4-methoxyphenethyl)-1H-imidazole hydrate (SKF-96365) and its agonist 1-oleoyl-2-acetyl-sn-glycerol (OAG) on the proliferation of cervical cancer cell lines HeLa and SiHa, deoxyribonucleic acid (DNA) synthesis, cell migration, and TRPC6 expression.MethodReal-time quantitative polymerase chain reaction (RT-qPCR) and western blotting were used to detect the expression of TRPC6 in HeLa and SiHa cells. The tetrazolium salt 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, the 5-ethynyl -2'- deoxyuridine (EdU) fluorescence detection assay, and a scratch test were used to detect the changes of proliferation, DNA synthesis and cell migration of HeLa and SiHa cells after SKF 96,365 and OAG acted on HeLa and SiHa cells for different lengths of time. RT-qPCR was used to detect expression changes of TRPC6 SKF-96365 and OAG treated HeLa and SiHa cells.ResultsTRPC6 was expressed both in HeLa and SiHa cells. The MTT assay showed that after 24 h of SKF-96365 treatment, compared with the control group, the proliferation of HeLa and SiHa cells was inhibited, and there was a statistically significant difference (p < 0.05). After 24 h of OAG, compared with the control group, the proliferation of HeLa and SiHa cells had increased, and there was a statistically significant difference (p < 0.05). EdU fluorescence detection showed that SKF-96365 could inhibit the DNA synthesis of HeLa and SiHa cells, and OAG could promote the DNA synthesis of HeLa and SiHa cells (p < 0.05) in HeLa and SiHa cell lines.ConclusionThe high expression of calcium channel TRPC6 in HeLa and SiHa tissues may be related to the malignant behavior of cervical cancer cell lines HeLa and SiHa. This calcium channel may be a new target for the prevention and treatment of cervical cancer.

Identification of Phosphorus Stress Related Proteins in the Seedlings of Dongxiang Wild Rice (Oryza Rufipogon Griff.) Using Label-Free Quantitative Proteomic Analysis.

Phosphorus (P) deficiency tolerance in rice is a complex character controlled by polygenes. Through proteomics analysis, we could find more low P tolerance related proteins in unique P-deficiency tolerance germplasm Dongxiang wild rice (Oryza Rufipogon, DXWR), which will provide the basis for the research of its regulation mechanism. In this study, a proteomic approach as well as joint analysis with transcriptome data were conducted to identify potential unique low P response genes in DXWR during seedlings. The results showed that 3589 significant differential accumulation proteins were identified between the low P and the normal P treated root samples of DXWR. The degree of change was more than 1.5 times, including 60 up-regulated and 15 downregulated proteins, 24 of which also detected expression changes of more than 1.5-fold in the transcriptome data. Through quantitative trait locus (QTLs) matching analysis, seven genes corresponding to the significantly different expression proteins identified in this study were found to be uncharacterized and distributed in the QTLs interval related to low P tolerance, two of which (LOC_Os12g09620 and LOC_Os03g40670) were detected at both transcriptome and proteome levels. Based on the comprehensive analysis, it was found that DXWR could increase the expression of purple acid phosphatases (PAPs), membrane location of P transporters (PTs), rhizosphere area, and alternative splicing, and it could decrease reactive oxygen species (ROS) activity to deal with low P stress. This study would provide some useful insights in cloning the P-deficiency tolerance genes from wild rice, as well as elucidating the molecular mechanism of low P resistance in DXWR.

BRAF Mutations and Inflammatory Gene Expression in Myeloma Cells from Patients with Renal Dysfunction

BRAF Mutations and Inflammatory Gene Expression in Myeloma Cells from Patients with Renal Dysfunction

P–284 Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line

Abstract Study question The aim of the study was to identify new target proteins/pathways that are affected by metformin treatment in endometrial cancer cells in a proteomic approach. Summary answer The expression of 1,300 different proteins were investigated, of which 80 proteins with the most prominent changes were presented and some discussed in detail. What is known already The incidence of endometrial cancer (EC) has increased over the past years. Metabolic diseases such as obesity, type II diabetes mellitus (T2DM), and associated conditions (i.e. polycystic ovary syndrome (PCOS), insulin resistance) lead to elevated levels of circulating estrogens, which promote EC development and progression. Metformin, an insulin-sensitizing biguanide drug, commonly used in the treatment of T2DM, especially in obese patients, displayed anti-cancer effects in various cancer types, including EC. Different proteins and pathways have been suggested as potential targets, but the underlying mechanism of action of metformin’s anti-cancer activity is still not completely understood. Study design, size, duration In the present in vitro study, EC cells were cultured in 5.5 mmol/L glucose medium (supplemented with 10 nmol/L ß-estradiol (E2)) and treated with metformin (0.5 mmol/L), insulin (100 ng/mL), or remained untreated for 7 d. The expression of 1,300 different proteins was detected in cellular extracts in an affinity proteomic approach and compared between the treatment groups in order to identify potential target proteins and pathways that contribute to the anti-cancer effects of metformin. Participants/materials, setting, methods The study was carried out with the EC cell line HEC–1A that represents a postmenopausal model with low E2 sensitivity. Proteins were extracted, quantified with the BCA assay, and protein expression was analyzed using the scioDiscover antibody microarray. Differences in protein abundance between samples were presented as log2-fold changes (log2FC) with significance for samples that displayed |log2FC| ≥ 0.5 and adjusted p ≤ 0.05. Pathway analysis was carried out with the STRING and DAVID databases. Main results and the role of chance The data revealed that metformin and insulin targeted similar pathways in the present study and mostly acted on proteins related to proliferation, migration and tumor immune response. These pathways may be affected in a tumor-promoting as well as a tumor-suppressing way by either metformin treatment or insulin supplementation. Results for the 80 most affected proteins were presented and the consequences for the cells resulting from the detected expression changes were discussed in detail for several proteins. The presented data helps identify potential target proteins and pathways affected by metformin treatment in EC and allows for a better understanding of the mechanism of action of the biguanide drug’s anti-cancer activity. However, further investigations are necessary to confirm the observations and conclusions drawn from the presented data after metformin administration, especially for proteins that were regulated in a favorable way, i.e. AKT3, CCND2, CD63, CD81, GFAP, IL5, IL17A, IRF4, PI3, and VTCN1. Further proteins might be of interest, where metformin counteracted unfavorable effects that have been induced by hyperinsulinemia. Limitations, reasons for caution The results were obtained from an in vitro study with human cancer cell lines, and thus cannot be easily extrapolated to patients. Wider implications of the findings: In the context of a hyperinsulinemic environment, further proteins might be of interest, i.e. AMFR, CCND2, CD63, ERBB3, EZR, GFAP, IRF4, PI3, PLCG2, SORL1, VEGFA, VTCN1, SPP1, and TM9SF2. Here, a metformin-induced insulin-sensitization might be able to counteract unfavorable effects on protein expression profile that have been induced by hyperinsulinemia. Trial registration number Not applicable

Genetic diseases in the omics era

Accurate quantification of gene expression at RNA and protein levels has provided invaluable insight into the mechanisms of biological processes in health and disease. The so-called “-omics” technologies (transcriptomics, proteomics, but also epigenomics, etc.) enabled researchers to detect expression changes specifically associated with given biological states and, more recently, to establish their dynamics at a single-cell resolution in stem cell-based models. In this issue of Molecular Therapy, Djeddi et al.

Exploring the Impact of Cerebrovascular Disease and Major Depression on Non-diseased Human Tissue Transcriptomes.

BackgroundThe development of complex diseases is contributed by the combination of multiple factors and complicated interactions between them. Inflammation has recently been associated with many complex diseases and may cause long-term damage to the human body. In this study, we examined whether two types of complex disease, cerebrovascular disease (CVD) or major depression (MD), systematically altered the transcriptomes of non-diseased human tissues and whether inflammation is linked to identifiable molecular signatures, using post-mortem samples from the Genotype-Tissue Expression (GTEx) project.ResultsFollowing a series of differential expression analyses, dozens to hundreds of differentially expressed genes (DEGs) were identified in multiple tissues between subjects with and without a history of CVD or MD. DEGs from these disease-associated tissues—the visceral adipose, tibial artery, caudate, and spinal cord for CVD; and the hypothalamus, putamen, and spinal cord for MD—were further analyzed for functional enrichment. Many pathways associated with immunological events were enriched in the upregulated DEGs of the CVD-associated tissues, as were the neurological and metabolic pathways in DEGs of the MD-associated tissues. Eight gene-tissue pairs were found to overlap with those prioritized by our transcriptome-wide association studies, indicating a potential genetic effect on gene expression for circulating cytokine phenotypes.ConclusionCerebrovascular disease and major depression cause detectable changes in the gene expression of non-diseased tissues, suggesting that a possible long-term impact of diseases, lifestyles and environmental factors may together contribute to the appearance of “transcriptomic scars” on the human body. Furthermore, inflammation is probably one of the systemic and long-lasting effects of cerebrovascular events.

Coordinated action of human papillomavirus type 16 E6 and E7 oncoproteins on competitive endogenous RNA (ceRNA) network members in primary human keratinocytes

BackgroundmiRNAs and lncRNAs can regulate cellular biological processes both under physiological and pathological conditions including tumour initiation and progression. Interactions between differentially expressed diverse RNA species, as a part of a complex intracellular regulatory network (ceRNA network), may contribute also to the pathogenesis of HPV-associated cancer. The purpose of this study was to investigate the global expression changes of miRNAs, lncRNAs and mRNAs driven by the E6 and E7 oncoproteins of HPV16, and construct a corresponding ceRNA regulatory network of coding and non-coding genes to suggest a regulatory network associated with high-risk HPV16 infections. Furthermore, additional GO and KEGG analyses were performed to understand the consequences of mRNA expression alterations on biological processes.MethodsSmall and large RNA deep sequencing were performed to detect expression changes of miRNAs, lncRNAs and mRNAs in primary human keratinocytes expressing HPV16 E6, E7 or both oncoproteins. The relationships between lncRNAs, miRNAs and mRNAs were predicted by using StarBase v2.0, DianaTools-LncBase v.2 and miRTarBase. The lncRNA-miRNA-mRNA regulatory network was visualized with Cytoscape v3.4.0. GO and KEEG pathway enrichment analysis was performed using DAVID v6.8.ResultsWe revealed that 85 miRNAs in 21 genomic clusters and 41 lncRNAs were abnormally expressed in HPV E6/E7 expressing cells compared with controls. We constructed a ceRNA network with members of 15 lncRNAs – 43 miRNAs – 358 mRNAs with significantly altered expressions. GO and KEGG functional enrichment analyses identified numerous cancer related genes, furthermore we recognized common miRNAs as key regulatory elements in biological pathways associated with tumorigenesis driven by HPV16.ConclusionsThe multiple molecular changes driven by E6 and E7 oncoproteins resulting in the malignant transformation of HPV16 host cells occur, at least in part, due to the abnormal alteration in expression and function of non-coding RNA molecules through their intracellular competing network.

Bovine lactoferrin inhibits alveolar bone destruction in an orthodontic rat model with periodontitis

ObjectiveWe aimed to evaluate the effect of bovine lactoferrin (bLF) on alveolar bone destruction and remodelling under orthodontic force (OF) in periodontitis-affected rats. Material and methodsAfter establishing the periodontitis-affected rat model with lipopolysaccharides (LPS), the left maxillary first molars were moved orthodontically under a force of 0.2N. Based on saline or bLF gavage, 54 Sprague-Dawley (SD) rats were randomized into 5 groups: A (blank), P1 (LPS+OF+bLF), P2 (LPS+OF+saline), C1 (OF+bLF), and C2 (OF+saline). Animals were evaluated using micro-computed tomography (micro-CT) followed by haematoxylin and eosin (H&E) and tartrate-resistant acid phosphatase (TRAP) staining, and the LF level was determined using ELISA in the gingival crevicular fluid (GCF) of the experimental teeth. Immunohistochemistry helped to detect expression changes in RANKL, OPG and COX-2. ResultsMicro-CT results indicated that compared with group P2, trabecular number (Tb.N) and trabecular thickness (Tb.Th) in group P1 were higher and bone surface/bone volume (BS/BV) was lower on day 14, while trabecular separation (Tb.Sp) decreased significantly on Day 5 and Day 14 after bLF gavage (P<0.05). This was supported by changes in H&E and TRAP staining. bLF down-regulated RANKL level at both timepoints and up-regulated OPG level on Day 14 in periodontitis rats (P<0.05). The significant changes mentioned above were not observed between group C1 and C2 (P>0.05). No significant change in COX-2 levels were observed in any group (P>0.05). The lactoferrin level in GCF increased significantly after bLF gavage (P<0.05). ConclusionBovine lactoferrin inhibited LPS-induced bone destruction, but the bone healing effect was independent of orthodontic aseptic inflammatory bone remodelling.