Changes In Gene Expression Profiles Research Articles

Integrating metabolomics and metatranscriptomics to explore the formation pathway of aroma-active volatile phenolics and metabolic profile during industrial radish paocai fermentation

The aroma profile of industrial Sichuan paocai is formed and regulated by complex physiological and biochemical reactions and microbial metabolism, but little is known so far. In this study, we comprehensively analyzed the changes of metabolic profile and gene expression profile, mainly explored the formation pathways of two skeleton aroma-active compounds, 4-ethylphenol and 4-ethylguaiacol, and verified the pathways at multiple levels. The results showed that a total of 136 volatile metabolites and 560 non-volatile metabolites were identified in the whole fermentation process. The types and concentrations of metabolites in paocai were higher than those in brine, and gradually converged with fermentation. Differential analysis of metabolism and transcription levels were both enriched in three pathways: amino acid metabolism, phenylpropanoid metabolism and lipid metabolism. Among them, 4-ethylphenol and 4-ethylguaiacol, the products of the phenylpropanoid metabolism, were converted from p-coumaric acid and ferulic acid in plant cell walls, respectively. Under the action of decarboxylase produced by yeast (such as Debaryomyces Hansenii) and lactic acid bacteria (such as Lactobacillus versmoldensis), intermediate metabolites vinylphenols were produced, and the intermediate metabolites further produce the final products under the action of vinylphenol reductase. The key gene copy number, enzyme activity, and metabolite concentration in the pathways were detected to provide stronger evidence for the formation pathways. This study provided meaningful new insights for the development of aroma-producing enzymes and further guidance for the flavor improvement of industrial paocai.

Investigating the change in gene expression profile of blood mononuclear cells post-laparoscopic sleeve gastrectomy in Chinese obese patients.

Laparoscopic sleeve gastrectomy (LSG) is a sustainable technique that effectively treats morbid obesity. However, the molecular mechanisms underlying the improvement of metabolic health following this process warrants more investigation. This study investigates LSG-related molecules and uses bulk RNA-sequencing high-throughput analysis to unravel their regulatory mechanisms. Peripheral blood mononuclear cells (PBMC) were collected from ten obese patients with BMI ≥ 32.5 kg/m2 in the Department of General Surgery of Kunming First People's Hospital. After LSG, patients were followed up for one month, and blood samples were retaken. Blood samples from ten patients before and after LSG and bulk RNA-Seq data were analyzed in this study. LSG-associated gene expression was detected by weighted gene coexpression network analysis (WGCNA) and differential analysis. Subsequently, essential signature genes were identified using logistic least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and single-sample gene set enrichment analysis (ssGSEA) were utilized to reveal the potential functions of the target genes. Furthermore, the Pearson correlation of signature genes with leptin and lipocalin was also explored. Finally, we constructed a robust endogenous RNA (ceRNA) network based on miRWalk and starBase databases. We identified 18 overlapping genes from 91 hub genes, and 165 differentially expressed mRNAs (DE-mRNA), which were revealed to be significantly associated with immune cells, immune response, inflammatory response, lipid storage, and localization upon functional enrichment analysis. Three signature genes, IRF1, NFKBIA, and YRDC, were identified from the 18 overlapping genes by LASSO and SVM-REF algorithms. The logistic regression model based on the three signature genes highlighted how robustly they discriminated between samples. ssGSEA indicated these genes to be involved in lipid metabolism and degradation pathways. Moreover, leptin levels were significantly reduced in patients undergoing LSG, and NFKBIA significantly negatively correlated with leptin. Finally, we identified how the long non-coding RNA (lncRNA) ATP2B1-AS1 regulated the expression of the signature genes by competitively binding to six microRNAs (miRNAs), which were hsa-miR-6509-5p, hsa-miR-330-5P, hsa-miR-154-5P, hsa-miR-145-5P, hsa-miR4726-5P and hsa-miR-134-5P. This study identified three critical regulatory genes significantly differentiated between patients before and after LSG treatment and highlighted their potentially crucial role after bariatric surgery. This provides novel insights to increase our understanding of the underlying mechanisms of weight loss and associated metabolic improvement after bariatric surgery.

Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican

Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.

Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria.

The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum and the mosquito vector that transmits the parasite has led to dramatic losses in endemic Hawaiian forest bird species. Understanding how mechanisms of disease immunity to avian malaria may evolve is critical as climate change facilitates increased disease transmission to high elevation habitats where malaria transmission has historically been low and the majority of the remaining extant Hawaiian forest bird species now reside. Here, we compare the transcriptomic profiles of highly susceptible Hawai'i 'amakihi (Chlorodrepanis virens) experimentally infected with P. relictum to those of uninfected control birds from a naïve high elevation population. We examined changes in gene expression profiles at different stages of infection to provide an in-depth characterization of the molecular pathways contributing to survival or mortality in these birds. We show that the timing and magnitude of the innate and adaptive immune response differed substantially between individuals that survived and those that succumbed to infection, and likely contributed to the observed variation in survival. These results lay the foundation for developing gene-based conservation strategies for Hawaiian honeycreepers by identifying candidate genes and cellular pathways involved in the pathogen response that correlate with a bird's ability to recover from malaria infection.

Pre-Diabetes-Linked miRNA miR-193b-3p Targets PPARGC1A, Disrupts Metabolic Gene Expression Profile and Increases Lipid Accumulation in Hepatocytes: Relevance for MAFLD.

Distinct plasma microRNA profiles associate with different disease features and could be used to personalize diagnostics. Elevated plasma microRNA hsa-miR-193b-3p has been reported in patients with pre-diabetes where early asymptomatic liver dysmetabolism plays a crucial role. In this study, we propose the hypothesis that elevated plasma hsa-miR-193b-3p conditions hepatocyte metabolic functions contributing to fatty liver disease. We show that hsa-miR-193b-3p specifically targets the mRNA of its predicted target PPARGC1A/PGC1α and consistently reduces its expression in both normal and hyperglycemic conditions. PPARGC1A/PGC1α is a central co-activator of transcriptional cascades that regulate several interconnected pathways, including mitochondrial function together with glucose and lipid metabolism. Profiling gene expression of a metabolic panel in response to overexpression of microRNA hsa-miR-193b-3p revealed significant changes in the cellular metabolic gene expression profile, including lower expression of MTTP, MLXIPL/ChREBP, CD36, YWHAZ and GPT, and higher expression of LDLR, ACOX1, TRIB1 and PC. Overexpression of hsa-miR-193b-3p under hyperglycemia also resulted in excess accumulation of intracellular lipid droplets in HepG2 cells. This study supports further research into potential use of microRNA hsa-miR-193b-3p as a possible clinically relevant plasma biomarker for metabolic-associated fatty liver disease (MAFLD) in dysglycemic context.

The Effect of Long-Term Inorganic Iodine on Intrathyroidal Iodothyronine Content and Gene Expression in Mice with Graves' Hyperthyroidism.

Background: The main molecular mechanism underlying acute suppression of iodine organification in normal thyroids after an excessive iodine load, that is, the Wolff-Chaikoff effect, is assumed to be suppression of iodine oxidation and iodothyronine synthesis. However, the mechanism underlying chronic antithyroid action of inorganic iodine in Graves' disease is not fully understood. Using a mouse model of Graves' hyperthyroidism, we examined changes in iodothyronine content and gene expression profiles in the thyroid glands after inorganic iodine loading. Materials and Methods: Graves' hyperthyroidism was induced and maintained in BALB/c mice by repeated immunizations of recombinant adenovirus expressing the human thyrotropin (TSH) receptor A-subunit. Hyperthyroid mice were left untreated (GD-C; n = 8) or treated with inorganic iodine for 12 weeks (GD-NaI; n = 8). We used unimmunized BALB/c mice as a control group (n = 10). In each mouse, serum thyroxine (T4) levels were measured with enzyme-linked immunosorbent assay (ELISA) at 4-week intervals. The intrathyroidal iodothyronine content and gene expression levels were, respectively, evaluated by mass spectrometry and RNA sequencing (RNA-seq) at the end of the experimental period. Results: Serum T4 levels in the GD-C group remained higher than in the control group, whereas those in the GD-NaI group declined to normal levels during the experimental period. Intrathyroidal triiodothyronine (T3), reverse T3 (rT3), and T4 contents in the GD-C group were higher than the control group, and rT3 and T4 were further increased in the GD-NaI group. The observed alterations in iodothyronine levels in the thyroid and sera may be explained by altered expression levels of genes for iodothyronine biosynthetic molecules, their transporter, and deiodinases. Conclusion: In this mouse model of hyperthyroidism, higher intrathyroidal accumulation of T4 and reduced gene expression data of iodothyronine transporters in the GD-NaI group suggest that chronic antithyroid action of iodine in Graves' disease involves suppression of hormone secretion.

Transcriptomics analysis of ethanol treatment of male Aedes aegypti reveals a small set of putative radioprotective genes.

Introduction: Sterile Insect Technique (SIT) is based on releasing sterilized male insects into wild insect populations to compete for mating with wild females. Wild females mated with sterile males will produce inviable eggs, leading to a decline in population of that insect species. Sterilization with ionizing radiation (x-rays) is a commonly used mechanism for sterilization of males. Since irradiation can cause damage to both, somatic and germ cells, and can severely reduce the competitiveness of sterilized males relative to wild males, means to minimize the detrimental effects of radiation are required to produce sterile, competitive males for release. In an earlier study, we identified ethanol as a functional radioprotector in mosquitoes. Methods: Here, we used Illumina RNA-seq to profile changes in gene expression of male Aedes aegypti mosquitoes fed on 5% ethanol for 48hours prior to receiving a sterilizing x-ray dose, compared to males fed on water prior to sterilization. Results: RNA-seq revealed a robust activation of DNA repair genes in both ethanol-fed and water-fed males after irradiation, but surprisingly few differences in gene expression between ethanol-fed and water-fed males regardless of radiation treatment. Discussion: While differences in gene expression due to ethanol exposure were minimal, we identified a small group of genes that may prime ethanol-fed mosquitoes for improved survivability in response to sterilizing radiation.

Characterization of pathological remodeling in the chronic atrioventricular block cynomolgus monkey heart.

We studied time course of pathological remodeling occurring in the cynomolgus monkey hearts against persistent atrioventricular block condition (n = 10). The atrioventricular block induced the ventricular and atrial dilation followed by the ventricular hypertrophy. Interstitial fibrosis in the ventricle was also observed along with gradual increases in the plasma angiotensin II and aldosterone concentrations. These adaptations were associated with the changes in gene expression profiling reflecting fibrosis and hypertrophy. Atrioventricular block reduced the ventricular rate and cardiac output, but the ejection fraction and stroke volume increased, whereas the cardiac output was gradually restored to its basal level. Systolic/diastolic blood pressure after the atrioventricular block was kept equal to or lower than that before the block, according with lack of increase in the plasma catecholamine levels. Chronic atrioventricular block gradually prolonged the QRS width and JT interval, leading to the QT interval prolongation in conscious state. 10mg/kg of dl-sotalol hydrochloride induced torsade de pointes (TdP) in 6 out of 10 animals by 15months. Animals showing longer QTcF under anesthesia after the atrioventricular block developed dl-sotalol-induced TdP earlier. No marked difference was observed in pharmacokinetics of dl-sotalol between 1 and 7months after the atrioventricular block. Each TdP spontaneously terminated, reflecting a monkey's relatively small "effective size of the heart (=∛(left ventricular weight)/wavelength of reentry)". These fundamental knowledge will help better utilize the chronic atrioventricular block monkeys as an in vivo proarrhythmia model for detecting drug-induced TdP.

Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco.

Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.

New murine model of alcoholic hepatitis in obesity-induced metabolic-associated fatty liver disease.

Metabolic-associated fatty liver disease (MAFLD) and alcoholic hepatitis (AH) are among the most prevalent liver diseases worldwide, and their coexistence is common in clinical practice. However, currently established models of MAFLD-AH coexistence do not fully replicate their pathological characteristics and require sophisticated experimental techniques. Therefore, we aimed to develop an easily replicable model that mimics obesity-induced MAFLD-AH in patients. Our goal was to establish a murine model that replicates MAFLD and AH coexistence, resulting in significant liver injury and inflammation. To this end, we administered a single ethanol gavage dose to ob/ob mice on a chow diet. The administration of a single dose of ethanol led to elevated serum transaminase levels, increased liver steatosis, and apoptosis in ob/ob mice. Furthermore, ethanol binge caused a significant increase in oxidative stress in ob/ob mice, as measured via 4-hydroxynonenal. Importantly, the single dose of ethanol also markedly exacerbated liver neutrophil infiltration and upregulated the hepatic mRNA expression of several chemokines and neutrophil-related proteins, including Cxcl1, Cxcl2, and Lcn2. Whole-liver transcriptomic analysis revealed that ethanol-induced changes in gene expression profile shared similar features with AH and MAFLD. In ob/ob mice, a single dose of ethanol binge caused significant liver injury and neutrophil infiltration. This easy-to-replicate murine model successfully mimics the pathological and clinical features of patients with coexisting MAFLD and AH and closely resembles the transcriptional regulation seen in human disease.

Hepatic Polarized Differentiation Promoted the Maturity and Liver Function of Human Embryonic Stem Cell-Derived Hepatocytes via Activating Hippo and AMPK Signaling Pathways.

Hepatocytes exhibit a multi-polarized state under the in vivo physiological environment, however, human embryonic stem cell-derived hepatocytes (hEHs) rarely exhibit polarity features in a two-dimensional (2D) condition. Thus, we hypothesized whether the polarized differentiation might enhance the maturity and liver function of hEHs. In this study, we obtained the polarized hEHs (phEHs) by using 2D differentiation in conjunct with employing transwell-based polarized culture. Our results showed that phEHs directionally secreted albumin, urea and bile acids, and afterward, the apical membrane and blood-bile barrier (BBIB) were identified to form in phEHs. Moreover, phEHs exhibited a higher maturity and capacitity of cellular secretory and drug metabolism than those of non-phEHs. Through transcriptome analysis, it was found that the polarized differentiation induced obvious changes in gene expression profiles of cellular adhesion and membrane transport in hEHs. Our further investigation revealed that the activation of Hippo and AMPK signaling pathways made contributions to the regulation of function and cellular polarity in phEHs, further verifying that the liver function of hEHs was closely related with their polarization state. These results not only demonstrated that the polarized differentiation enhanced the maturity and liver function of hEHs, but also identified the molecular targets that regulated the polarization state of hEHs.

Changes in the gene expression and gut microbiome to the infection of decapod iridescent virus 1 in Cherax quadricarinatus

As a new emerging viral pathogen, Decapod iridescent virus 1 (DIV1) seriously threatens crustacean farming in recent years. However, limited research progresses have been made on the immune mechanism between host and viral factors in response to DIV1 infection. In the current study, a natural occurrence of DIV1 infection with obvious clinical signs was found in farmed redclaw crayfish Cherax quadricarinatus, and confirmed by nested PCR detection and histopathological examination. Besides, gene expression profiles were analyzed after being challenged with DIV1, and results showed that 27 immune related genes were upregulated compared with the control group. Moreover, the gut microbiota from healthy and DIV1-infected crayfish were investigated by 16S rDNA high-throughput sequencing. Results showed that significant differences in the microbial composition and function were observed after DIV1 challenge. Furthermore, we discovered that changes in gene expression profiles were correlated with microbiota alterations under DIV1 challenge. Taken together, our findings will provide new insights into the immune response mechanism of DIV1 infection in crustaceans.

МИТОХОНДРИАЛЬНО-НАПРАВЛЕННЫЙ АНТИОКСИДАНТ SKQ1 РЕГУЛИРУЕТ СИГНАЛЬНУЮ СИСТЕМУ KEAP1/NRF2/ARE И АПОПТОЗ В ЛЕЙКОЦИТАХ КРОВИ ПРИ ОКИСЛИТЕЛЬНОМ СТРЕССЕ

This study demonstrated that hyperoxia induced (0.5 MPa, 90 min) oxidative stress decreased mRNA level of Nrf2 transcription factor and Nrf2 induced genes encoding antioxidant enzymes (SOD1, CAT, GPx4) in leukocytes of rat blood. The change in gene expression profiles in hyperoxia was accompanied by disbalance of antioxidant enzyme activities in the leukocytes – activation of superoxide dismutase, and inhibition of catalase, glutathione peroxidase. The administration of SkQ1 (50 nmol/kg during 5 days) significantly increased mRNA level of Nrf2 transcription factor and Nrf2 induced genes encoding antioxidant enzymes SOD2 and GPx4 and nor malized the transcriptional activity of the SOD1 and CAT genes in the leukocytes under the hyperoxia induced oxidative stress. Catalase and glutathione peroxidase activity in the leukocytes increased concurrently with reversion of superoxide dismutase activity to the control level. The protective effect of SkQ1 in hyperoxia induced oxidative stress may be realized via direct antioxidant activity and the stimulation of the Keap1/Nrf2/ARE defense system. Administration of SkQ1 in extremely low amounts (50 nmol/kg for 5 days) effectively inhibits the accumulation of lipid peroxidation molecular products, normalizes the structural state of lymphocyte membranes and the level of their apoptosis under the condition of physiological standard and oxidative stress.

Anti-mesothelin immunotoxin induces mesothelioma eradication, anti-tumor immunity, and the development of tertiary lymphoid structures

LMB-100 is a recombinant immunotoxin composed of a Fab linked to a toxin. It kills cells expressing human mesothelin (hMSLN), which is highly expressed on the surface of mesothelioma and many other cancer cells. Clinically, we observed some patients had delayed responses to an anti-hMSLN immunotoxin treatment, suggesting the induction of anti-tumor immunity. We aimed to develop a mouse model to investigate whether immunotoxin alone can induce anti-tumor immunity and to study the mechanism of this immunity. An immunocompetent transgenic mouse was used to grow mouse mesothelioma AB1 cells expressing hMSLN in the peritoneal cavity. Mice were treated with LMB-100, and mice with complete responses (CRs) were rechallenged with tumor cells to determine whether anti-tumor immunity developed. Changes in gene expression profiles were evaluated by Nanostring, and changes in cytokines and chemokines were checked by protein arrays. The distribution of various immune cells was assessed by immunohistochemistry. Our results show that the mice with tumor reached CRs and developed anti-tumor immunity after LMB-100 treatment alone. The primary response requires CD8+ T cells, CD4+ T cells, and B cells. Transcriptional profiling shows that LMB-100 treatment reshapes the tumor immune microenvironment by upregulating chemotaxis signals. LMB-100 treatment upregulates genes associated with tertiary lymphoid structures (TLS) development and induces TLS formation in tumors. In sum, immunotoxin-mediated cell death induces anti-tumor immunity and the development of TLS, which provides insights into how immunotoxins cause tumor regressions.

Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy

Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.

Early changes in gene expression profiles in AML patients during induction chemotherapy

BackgroundElucidation of the genetic mechanisms underlying treatment response to standard induction chemotherapy in AML patients is warranted, in order to aid in risk-adapted treatment decisions as novel treatments are emerging. In this pilot study, we explored the treatment-induced expression patterns in a small cohort of AML patients by analyzing differential gene expression (DGE) over the first 2 days of induction chemotherapy.MethodsBlood samples were collected from ten AML patients at baseline (before treatment initiation) and during the first 2 days of treatment (Day 1; approximately 24 h, and Day 2; approximately 48 h after treatment initiation, respectively) and RNA was extracted for subsequent RNA sequencing. DGE between time points were assessed by pairwise analysis using the R package edgeR version 3.18.1 in all patients as well as in relation to treatment response (complete remission, CR, vs non-complete remission, nCR). Ingenuity Pathway Analysis (Qiagen) software was used for pathway analysis and visualization.ResultsAfter initial data quality control, two patients were excluded from further analysis, resulting in a final cohort of eight patients with data from all three timepoints. DGE analysis demonstrated activation of pathways with genes directly or indirectly associated with NF-κB signaling. Significant activation of the NF-κB pathway was seen in 50% of the patients 2 days after treatment start, while iNOS pathway effects could be identified already after 1 day. nCR patients displayed activation of pathways associated with cell cycle progression, oncogenesis and anti-apoptotic behavior, including the STAT3 pathway and Salvage pathways of pyrimidine ribonucleotides. Notably, a significant induction of cytidine deaminase, an enzyme responsible for the deamination of Ara-C, could be observed between baseline and Day 2 in the nCR patients but not in patients achieving CR.ConclusionsIn conclusion, we show that time-course analysis of gene expression represents a feasible approach to identify relevant pathways affected by standard induction chemotherapy in AML patients. This poses as a potential method for elucidating new drug targets and biomarkers for categorizing disease aggressiveness and evaluating treatment response. However, more studies on larger cohorts are warranted to elucidate the transcriptional basis for drug response.

Abstract 12021: Investigation of the Role of Long Non-Coding RNA H19 on Endothelial to Mesenchymal Transition in Aortic Valve Stenosis

Background: Endothelial to mesenchymal transition (EndMT) is a transdifferentiation process of cells that is associated with the development of aortic valve stenosis (AVS) in adulthood. It was shown that long non-coding RNAs are dysregulated in this process and might play a crucial role in EndMT-mediated AVS. Here we aim to elucidate the role of long non-coding RNA H19 (LncRNA H19) in the pathogenesis of EndMT-related AVS. Methods and Results: RNA sequencing of aortic valve tissue explanted from AVS-patients with coronary artery disease (CAD) revealed that H19 was significantly dysregulated. EndMT was induced in vitro in vascular and valvular endothelial cells (VECs) via TNFα and TGFß+IL1ß stimulation and expression of endothelial marker genes vWF and eNOS and mesenchymal marker genes αSMA , SM22 , Vimentin and SNAI2 was confirmed by RT-qPCR. Loss of function of H19 followed by EndMT induction demonstrated distinct changes in gene expression profile and protein levels which were detected by qRT-PCR, immunoblotting, and immunofluorescence. Further experiments indicate that loss of H19 may promote EndMT. Functional assays in vascular and valvular endothelial cells suggested that H19 is a critical regulator of angiogenic sprouting and migration. To unveil the specific molecular signature in angiogenesis a RT 2 profiler array was performed to identify the regulation of angiogenesis with 84 angiogenesis-related genes. Our assay revealed JAG1 as a potential dysregulated candidate with a 4.43-fold regulation. Further molecular mechanism will be investigated via identification of binding partners and downstream targets of H19 in EndMT by using primary cells and VECs. Conclusion: Our data suggests that H19 might play a role in EndMT in context of AVS. Further investigation by using a murine model of AVS should confirm the H19-mediated of EndMT in the development of AVS.

Differential expression of immune-regulatory proteins C5AR1, CLEC4A and NLRP3 on peripheral blood mononuclear cells in early-stage non-small cell lung cancer patients

Changes in gene expression profiling of peripheral blood mononuclear cells (PBMC) appear to represent the host’s response to the cancer cells via paracrine signaling. We speculated that protein expression on circulating T-lymphocytes represent T-lymphocyte trafficking before infiltration into the tumor microenvironment. The possibility of using protein expression on circulating T-lymphocytes as a biomarker to discriminate early-stage non-small cell lung cancer (NSCLC) was explored. Four independent PBMC gene expression microarray datasets (GSE12771, GSE13255, GSE20189 and GSE3934) were analyzed. We selected C5AR1, CLEC4A and NLRP3 based on their significant protein expression in tumor-infiltrating lymphocytes, but not in normal lymphoid tissue. A validation study using automated flow cytometry was conducted in 141 study participants including 76 treatment-naive early-stage non-small cell lung cancer patients (NSCLC), 12 individuals with non-malignant pulmonary diseases, and 53 healthy individuals. Median ratios of C5AR1, CLEC4A and NLRP3 specific antibody staining to CD3 positive cells in early-stage NSCLC patients compared to healthy controls were 0.014 [0–0.37] vs. 0.01 [0–0.07, p = 0.13], 0.03 [0–0.87] vs. 0.02 [0–0.13, p = 0.10] and 0.19 [0–0.60] vs. 0.09 [0.02–0.31, p < 0.0001], respectively. Median fluorescence intensity (MFI) of CD3+C5AR1+, CD3+CLEC4A+ and CD3+NLRP3+ expression in early-stage NSCLC patients compared to healthy volunteers was 185 [64.2–4801] vs. 107.5 [27–229, p < 0.0001], 91.2 [42.4–2355] vs. 71.25 [46.2–103, p = 0.0005], and 1585 [478–5224] vs. 758.5 [318–1976, p < 0.0001], respectively. NLRP3:CD3 ratio, CD3+C5AR1+, CD3+CLEC4A+ and CD3+NLRP3+ MFI were significantly higher in early-stage NSCLC than healthy volunteers with an area under the ROC curve of 0.69–0.76. The CD3+NLRP3+ MFI provided the most distinguishable expression at 71.5% sensitivity and 70% specificity. Furthermore, CD3+NLRP3+ MFI potentially discriminated between early-stage NSCLC from malignant-mimic inflammation and infection pulmonary disease. Further validation in various pulmonary inflammatory disease might be warranted. Our proof-of-principle findings strengthen the hypothesis that malignancies generate distinctive protein expression fingerprints on circulating T-lymphocytes.

Comparative Transcriptome Analysis Reveals the Key Genes Involved in Lipid Deposition in Pekin Ducks (Anas platyrhynchos domesticus)

There are differences in lipid deposition in fatty-type (FT) and lean-type (LT) ducks. Fatty ducks have a higher rate of sebum and abdominal fat, lower meat yield and hepatic lipid contents than LT ducks. However, the underlying changes in gene expression profiles regarding the lipid deposition between FT and LT ducks have not yet been clarified. To identify the differentially expressed genes in the liver, sebum, and abdominal fat between both ducks, we identified the gene expression profiles in the liver, sebum, and abdominal fat derived from FT and LT ducks by comparing the multistage transcriptomes. Our results showed that there were 622, 1536, and 224 differentially expressed genes (DEGs) in the liver, sebum, and abdominal fat between the FT and LT ducks, respectively. KEGG enrichment showed that the DEGs related to lipid metabolism were enriched in the biosynthesis of unsaturated fatty acid, glycerolipid and fatty acid metabolism in the liver; and were enriched in the fatty acid metabolism, fatty acid biosynthesis, glycerolipid metabolism, linoleic acid metabolism, and the PPAR signaling pathway in the sebum. There was no pathway related to a lipid metabolism enriched in abdominal fat. A gene functional analysis showed that the DEGs involved in adipogenesis were found to be upregulated. In contrast, those involved in lipolysis were downregulated in the liver and serum of FT ducks. The DEGs showed that ATP-binding cassette sub-family G member 8 (ABCG8), fatty acid synthase (FASN), and phospholipid transfer protein (PLTP) were highly expressed in the liver of FT ducks, and acyl-CoA synthetase long-chain family member3 (ACSL3), ACSL5, ACSL6, 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (AGPAT1), AGPAT9, ELOVL fatty acid elongase 6 (ELVOL6), fatty acid desaturase 1 (FADS1), FADS2, monoacylglycerol O-acyltransferase 1 (MOGAT1), serine/threonine kinase 17a (STK17A), and serine/threonine kinase 39 (STK39) were highly expressed in the sebum of FT ducks. A weighted correlation network analysis (WGCNA) of the DEGs showed ABCG8, FADS2, ACSL5, and ELOVL6 positively correlated with hepatic fatty acid synthesis, and AGPAT1, STK17A, STK32A, FADS1, and ACSL3 positively correlated with lipid deposition in the sebum. In summary, ABCG8 might be the key gene for the reduced hepatic lipid deposition in FT Pekin ducks, and FADS2, ACSL5, ELOVL6, AGPAT1, STK17A, STK32A, FADS1, and ACSL3 were the key genes for lipid deposition in the sebum of FT Pekin ducks. Our results provide new insights into the transcriptome regulation in lipid deposition of Pekin ducks and will be helpful for duck breeding.

The allelopathic effect of para-hydroxybenzoic acid on the gene expression of photosynthesis and respiration in Solanum lycopersicum

As an important economically and nutritionally valuable vegetable, tomato has been planted everywhere worldwide, which has resulted in a succession cropping obstacle due to the shortage of farmland. The effects of plant allelopathy, one of the major obstacles to succession cropping, has not been fully defined or explored, especially on plant gene expression profile changes. In this study, the high-throughput sequencing technology was used to analysis the gene expression in tomato leaves treated with the Para-hydroxybenzoic acid (PHBA), an important allelochemical, that was found to have the highest content in the soil of succession cropped tomatoes. We found the expression of genes related to respiration, photosynthesis, starch and sucrose metabolism, amino acid metabolism, pyrimidine metabolism, and ROS metabolism was changed in response to PHBA treatment. Our study on the allelopathic effects of PHBA on photosynthesis and respiration in Solanum lycopersicum has provided a solid evidence for the negative effect of allelochemical on the transcriptomic profiles needed for normal physiological activities of succession cropped tomato, thus will be beneficial for improving our knowledge of the mechanism of plant allelopathy.