Changes In Transcript Expression Research Articles

Genetic and functional adaptations and alcohol-biased signaling in the mediodorsal thalamus of alcohol dependent mice.

Alcohol Use Disorder (AUD) is a significant health concern characterized by an individual's inability to control alcohol intake. With alcohol misuse increasing and abstinence rates declining, leading to severe social and health consequences, it is crucial to uncover effective treatment strategies for AUD by focusing on understanding neuroadaptations and cellular mechanisms. The mediodorsal thalamus (MD) is a brain region essential for cognitive functioning and reward-guided choices. However, the effects of alcohol (ethanol) dependence on MD neuroadaptations and how dependence alters MD activity during choice behaviors for alcohol and a natural reward (sucrose) are not well understood. Adult C57BL/6J mice treated with chronic intermittent ethanol (CIE) exposure were used to assess genetic and functional adaptations in the MD. Fiber photometry-based recordings of GCaMP6f expressed in the MD of C57BL/6J mice were acquired to investigate in vivo neural adaptations during choice drinking sessions for alcohol (15%) and either water or sucrose (3%). There were time-dependent changes in cFos and transcript expression during acute withdrawal and early abstinence. Differentially expressed genes were identified in control mice across different circadian time points and when comparing control and alcohol dependent mice. Gene Ontology enrichment analysis of the alcohol-sensitive genes revealed disruption of genes that control glial function, axonal myelination, and protein binding. CIE exposure also increased evoked firing in MD cells at 72 hours of withdrawal. In alcohol-dependent male and female mice that show increased alcohol drinking and preference for alcohol over water, we observed an increase in alcohol intake and preference for alcohol when mice were given a choice between alcohol and sucrose. Fiber photometry recordings demonstrated that MD activity is elevated during and after licking bouts for alcohol, water, and sucrose, and the signal for alcohol is significantly higher than that for water or sucrose during drinking. The elevated signal during alcohol bouts persisted in alcohol dependent mice. These findings demonstrate that CIE causes genetic and functional neuroadaptations in the MD and that alcohol dependence enhances alcohol-biased behaviors, with the MD uniquely responsive to alcohol, even in dependent mice.

Functional knockout of the Oatp1d1 membrane transporter affects toxicity of diclofenac in zebrafish embryos

Organic anion transporting polypeptides (OATPs) facilitate the cellular uptake of a large number of compounds. Zebrafish Oatp1d1 matches the functional capabilities of human OATP orthologs, particularly in hormone and drug transport. It is highly expressed in the liver and later stages of embryonic development, indicating its critical role in zebrafish physiology and development. Data from previous in vitro analyses have shown a high affinity of zebrafish Oatp1d1 for pharmaceuticals and xenobiotics, providing the basis for further in vivo studies on its defence and developmental functions. Using CRISPR-Cas9 technology, we have generated an Oatp1d1 zebrafish mutant that has highly reduced Oatp1d1 expression in embryos and adult tissues compared to wild type (WT). The absence of Oatp1d1 was confirmed using custom-made antibodies. To evaluate its ecotoxicological relevance, mutant and WT embryos were exposed to increasing concentrations of diclofenac, an NSAID known for its wide and frequent use, environmental pseudo-persistence and ecological implications. WT embryos showed developmental delays and malformations such as spinal curvature, cardiac edema and blood pooling at higher diclofenac concentrations, whereas the Oatp1d1 mutant embryos showed marked resilience, with milder developmental defects and delayed toxic effects. These observations suggest that the absence of Oatp1d1 impedes the efficient entry of diclofenac into hepatocytes, thereby slowing its biotransformation into potentially more toxic metabolites. In addition, the changes in transcript expression of other uptake transporters revealed a highly probable and complex network of compensatory mechanisms. Therefore, the results of this study point to the importance of Oatp1d1-mediated transport of diclofenac, as demonstrated for the first time in vivo using an Oatp1 deficient zebrafish line. Finally, our data indicates that the compensatory role of other transporters with overlapping substrate preferences needs to be considered for a reliable understanding of the physiological and/or defensive role(s) of membrane transporters.

Expression of WNT Signaling Genes in the Dorsolateral Prefrontal Cortex in Schizophrenia.

Gene expression alterations in postmortem schizophrenia tissue are well-documented and are influenced by genetic, medication, and epigenetic factors. The Wingless/Integrated (WNT) signaling pathway, critical for cell growth and development, is involved in various cellular processes including neurodevelopment and synaptic plasticity. Despite its importance, WNT signaling remains understudied in schizophrenia, a disorder characterized by metabolic and bioenergetic defects in cortical regions. In this study, we examined the gene expression of 10 key WNT signaling pathway transcripts: IQGAP1, CTNNβ1, GSK3β, FOXO1, LRP6, MGEA5, TCF4, βTRC, PPP1Cβ, and DVL2 in the dorsolateral prefrontal cortex (DLPFC) using postmortem tissue from schizophrenia subjects (n = 20, 10 males, 10 females) compared to age, pH, and postmortem interval (PMI)-matched controls (n = 20, 10 males, 10 females). Employing the R-shiny application Kaleidoscope, we conducted in silico "lookup" studies from published transcriptomic datasets to examine cell- and region-level expression of these WNT genes. In addition, we investigated the impact of antipsychotics on the mRNA expression of the WNT genes of interest in rodent brain transcriptomic datasets. Our findings revealed no significant changes in region-level WNT transcript expression; however, analyses of previously published cell-level datasets indicated alterations in WNT transcript expression and antipsychotic-specific modulation of certain genes. These results suggest that WNT signaling transcripts may be variably expressed at the cellular level and influenced by antipsychotic treatment, providing novel insights into the role of WNT signaling in the pathophysiology of schizophrenia.

Abstract 5831: The TLE1 transcriptional and epigenetic machinery contributes to EGFR targeted therapy resistance in human lung adenocarcinoma

Abstract In human lung adenocarcinoma that carry Epidermal Growth Factor Receptor (EGFR) sensitizing mutations, targeting the EGFR pathway with the use of EGFR tyrosine kinase inhibitors (EGFR-TKIs) has emerged as a promising therapeutic strategy providing initial clinical benefit to many patients. Unfortunately, resistance to EGFR-TKIs eventually develops leading to disease progression. In addition to genetic mutations, transcriptional and epigenetic mediated changes in gene expression remain an important mechanism contributing to EGFR-TKI resistance. Here, we report a novel function of the transcriptional corepressor Transducin-Like Enhancer of Split-1 (TLE1) in mediating EGFR-TKI resistance in EGFR mutant LUAD cells through its survival promoting gene transcriptional program. In EGFR mutant, EGFR TKI sensitive LUAD cells, sole activation of the TLE1 nuclear function attenuates EGFR TKI sensitivity with concomittant reduction of EGFR-TKI-mediated apoptosis. Conversely, downregulation of endogenous TLE1 expression via siRNAs/shRNAs and deletion of TLE1 gene via CRISPR-Cas9 in EGFR-mutant, EGFR-TKI resistant cells partially restore EGFR-TKI sensitivity via induction of EGFR-TKI apoptosis. Mechanistically, the anti-apoptosis promoting gene transcriptional program of TLE1 is dependent on its functional interaction with the transcriptional repressor HES-1, a downstream Notch target which has been associated with relapse in LUAD patients following EGFR-TKI treatment. Collectively, these studies indicate the TLE1 corepressor as a determinant of resistance to EGFR targeted therapy and raise the possibility that inhibiting TLE1 nuclear function may serve as an adjuct therapy to circumvent EGFR-TKI resistance. Citation Format: Hector Ramos Biliran, Xin Yao, Nasir Roberts, Prince Iheukwumere, Renwei Chen, Ma. Carmela Dela Cruz. The TLE1 transcriptional and epigenetic machinery contributes to EGFR targeted therapy resistance in human lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5831.

Biological effects of diesel exhaust inhalation. III cardiovascular function

Objective Inhalation of diesel exhaust (DE) has been shown to be an occupational hazard in the transportation, mining, and gas and oil industries. DE also contributes to air pollution, and therefore, is a health hazard to the general public. Because of its effects on human health, changes have been made to diesel engines to reduce both the amounts of particulate matter and volatile fumes they generate. The goal of the current study was to examine the effects of inhalation of diesel exhaust. Materials and Methods The study presented here specifically examines the effects of exposure to 0.2 and 1.0 mg/m3 DE or filtered air (6h/d for 4 d) on measures of peripheral and cardio-vascular function, and biomarkers of heart and kidney dysfunction in male rats. A Tier 2 engine used in oil and gas fracking operations was used to generate the diesel exhaust. Results Exposure to 0.2 mg/m3 DE resulted in an increase in blood pressure 1d following the last exposure, and increases in dobutamine-induced cardiac output and stroke volume 1 and 27d after exposure. Changes in peripheral vascular responses to norepinephrine and acetylcholine were minimal as were changes in transcript expression in the heart and kidney. Exposure to 1.0 mg/m3 DE did not result in major changes in blood pressure, measures of cardiac function, peripheral vascular function or transcript expression. Discussion and Conclusions Based on the results of this study, we suggest that exposure to DE generated by a Tier 2 compliant diesel engine generates acute effects on biomarkers indicative of cardiovascular dysfunction. Recovery occurs quickly with most measures of vascular/cardiovascular function returning to baseline levels by 7d following exposure.

Response of soil microbial glycoside hydrolase family 6 cellulolytic population to lignocellulosic biochar reveals biochar stability toward microbial degradation.

Biochar produced from lignocellulosic biomass offers an opportunity to recycle waste into a valuable soil amendment. The application of biochar has been proposed to mitigate climate change by sequestering carbon in the soil. However, the field impact of biochar treatment on the cellulolytic microbial populations involved in the earlier steps of cellulose degradation is poorly understood. A field trial spanning three consecutive crop cycles of Zea mays was conducted in a degraded tropical Ultisol of Peninsular Malaysia. The soil was amended with two contrasting biochar made from oil palm kernel shells (pyrolyzed at 400°C) and rice husks (gasified at 800°C) with or without fertilizer supplementation. Soil samples were taken at each harvesting stage and analyzed for total organic carbon, labile active organic carbon, total cellulase, and β-glucosidase. Microbial glycoside hydrolase family 6 (GH6) cellulase genes and transcripts, involved in the early steps of cellulose degradation, were quantified from the extracted soil deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), respectively. Total organic carbon, labile active organic carbon, and β-glucosidase activity were significantly increased, while no effect on total cellulase activity was found. Both biochars stimulated the total population (DNA-derived) abundance of soil microorganisms harboring the GH6 cellulase genes. The biochar amendment did not affect the active population (RNA-derived) of the GH6 cellulolytic community, showing no significant changes in transcript expression. This indirectly corroborates the role of biochar as a potential carbon sequester in the soil.

Nrf1 is not a direct target gene of SREBP1, albeit both are integrated into the rapamycin-responsive regulatory network in human hepatoma cells.

The essential role of protein degradation by ubiquitin-proteasome system is exerted primarily for maintaining cellular protein homeostasis. The transcriptional activation of proteasomal genes by mTORC1 signaling depends on Nrf1, but whether this process is directly via SREBP1 remains elusive. In this study, our experiment evidence revealed that Nrf1 is not a direct target of SREBP1, although both are involved in the rapamycin-responsive regulatory networks. Closely scrutinizing two distinct transcriptomic datasets unraveled no significant changes in transcriptional expression of Nrf1 and almost all proteasomal subunits in either siSREBP2-silencing cells or SREBP1-∕-MEFs, when compared to equivalent controls. However, distinct upstream signaling to Nrf1 dislocation by p97 and its processing by DDI1/2, along with downstream proteasomal expression, may be monitored by mTOR signaling, to various certain extents, depending on distinct experimental settings in different types of cells. Our further evidence has been obtained from DDI1-∕-(DDI2insC) cells, demonstrating that putative effects of mTOR on the rapamycin-responsive signaling to Nrf1 and proteasomes may also be executed partially through a DDI1/2-independent mechanism, albeit the detailed regulatory events remain to be determined.

Neural adaption in midbrain GABAergic cells contributes to high-fat diet-induced obesity.

Overeating disorders largely contribute to worldwide incidences of obesity. Available treatments are limited. Here, we discovered that long-term chemogenetic activation of ventrolateral periaqueductal gray (vlPAG) GABAergic cells rescue obesity of high-fat diet-induced obesity (DIO) mice. This was associated with the recovery of enhanced mIPSCs, decreased food intake, increased energy expenditure, and inguinal white adipose tissue (iWAT) browning. In vivo calcium imaging confirmed vlPAG GABAergic suppression for DIO mice, with corresponding reduction in intrinsic excitability. Single-nucleus RNA sequencing identified transcriptional expression changes in GABAergic cell subtypes in DIO mice, highlighting Cacna2d1 as of potential importance. Overexpressing CACNA2D1 in vlPAG GABAergic cells of DIO mice rescued enhanced mIPSCs and calcium response, reversed obesity, and therefore presented here as a potential target for obesity treatment.

The Ig Superfamily Ligand B7H6 Subjects Activated T Cells to NK Cell Surveillance and Limits CAR T Cell Persistence

Understanding the mechanisms that regulate T cell immunity is critical for the development of effective therapies for diseases associated with T cell dysfunction. Co-inhibitory ‘checkpoint molecules’ are tightly connected to T cell activation and balance excessive or prolonged immune activation by suppressing clonal expansion. Previous studies have suggested that NK cells might also suppress lymphocyte expansion, but the specific ligands enabling T cell recognition by natural cytotoxicity receptors (NCRs) remain unknown. In this study, we describe the physiological expression of the immunoglobulin superfamily ligand B7H6 on activated T cells and elucidated the functional and clinical implication of its recognition by autologous NK cells. In a targeted proteomics screen for mediators of NK cell recognition on T cells, we identified the Ig superfamily ligand B7H6 ( NCR3LG1) to be highly expressed by T cells upon activation. We show that, unlike other checkpoint molecules, B7H6 mediates NKp30-dependent recognition and subsequent cytolysis of activated T cells by autologous NK cells. Time-resolved deep RNA-sequencing of anti-CD3/CD28-stimulated peripheral blood-derived T cells from n=24 human donors revealed that NCR3LG1 transcript expression changes dynamically upon stimulation and that B7H6 surface protein recognition by NK cells initiates Granzyme B-mediated ‘fratricide’ as early as 8 hours post T cell stimulation. Genomic knockout of NCR3LG1 rendered activated T cells resistant to NK cell-mediated killing without affecting their viability or proliferative capacity. By analyzing transcriptomic profiles of 313,303 CD8+ and 283.930 CD4+ T cells in datasets of multiple sclerosis (MS, n = 62 patients), inflammatory bowel disease (IBD, n = 4 patients), hepatitis B virus infection (HBV, n = 23 patients) and 9 different cancer entities (n = 47 patients), we found a conserved B7H6+ T cell population that is prevalent in the tissue and blood of most individuals at 1-5% frequency. In line with our experimental data, B7H6 positivity was coupled to a highly activated cell state of T cells. Considering CAR T cell manufacturing involves robust activation and clonal expansion, we hypothesized the B7H6-NKp30 axis is a yet unknown, but relevant factor in limiting CAR T cell persistence. Clinical-grade CD19.CD28.4-1BBzeta-CAR T cell products as well as circulating CAR T cells in lymphoma patients indeed uniformly expressed NCR3LG1 transcripts and B7H6 surface protein and were lysed by autologous NK cells in vitro. We then co-injected CD19.CAR T cells and patient-autologous NK cells in leukemia-engrafted mice and observed reduced CAR T cell persistence in the peripheral blood of mice with NK cell co-injection. Co-injection of NK cells further increased tumor burden and resulted in significantly decreased survival in leukemia-bearing mice treated with CD19-recognizing CAR-T cells, while these effects could be minimized by NKp30 antibody blockade or prior genetic editing of NCR3LG1 on CAR T cells. Given the physiological coupling T cell activation and B7H6 expression, any T cell-directed immunotherapy regimen might trigger the B7H6-NKp30-cytolysis mechanism. We therefore analyzed tissue of patients that were treated with nivolumab and ipilimumab (NCT03416244). In contrast to the previous notion of largely tumor-targeting NK cell function, we observed an increased NK cell abundance in patients that failed to respond to treatment. Notably, we found both B7H6+ CD8+ and CD4+ T cells in situ and that their abundance and a high NK/T ratio was associated with reduced progression-free survival (PFS), even in initial clinical responders, and experimentally deducted a NKp30 dependent cytolysis of these T cells. Together, our data demonstrates a mechanism that couples T cell expansion to eventual clearance by NK cells. This concept differs from the previously known immune checkpoints, as those molecules act through intracellular downstream signaling in T cells. We show that NK cell surveillance via B7H6 counteracts anti-tumor activity of CAR-T cells in vivo and that the genetic or antibody-mediated inhibition of B7H6 enhances T cell persistence. We therefore suggest an alternative immune checkpoint that limits T cell expansion and persistence in physiological and cellular engineering contexts. Targeting the B7H6-NKp30 axis may offer a means to modulate T cell immunity across multiple disease entities.

Low-concentration exogenous 3-indoleacetic acid improves fruit-setting rate of Marsdenia tenacissima by inhibiting the expression of embryo abortion-related genes

Marsdenia tenacissima is a medicinal plant characterized by many flowers, few fruits, and a low fruit-setting rate. Exogenous auxins can improve the fruit-setting rate of plants; however, their impacts on M. tenacissima and regulatory mechanisms remain unclear. In this study, we conducted a field experiment to determine the fruit-setting rate, seed-setting rate, fruit size, and changes in transcriptional expression of related genes by spraying 10 and 50 mg·L-1 of 3-indoleacetic acid (IAA). The control plants were sprayed with distilled water. Our results indicated that the fruit-setting rate was 0.15 when treated with 10 mg·L-1 of IAA, which was 2.76-fold higher than that of the control. Compared with that of the control, the number of differentially expressed genes (DEGs) regulated by 10 mg·L-1 of IAA was 28.6-fold higher than that regulated by 50 mg·L-1 of IAA. These DEGs were closely related to hormone metabolism and fruit development. By transcriptome analysis, spraying 10 mg·L-1 of IAA increased the expressions of STP6, MYB17, and LAX3 and reduced those of CXE18, ILR1-like 3, and SAUR50; this possibly affected the ovule, embryo, and fruit development, thereby elevating the fruit-setting rate of M. tenacissima. Our results indicated that low IAA concentration increased the fruit-setting rate of M. tenacissima, providing theoretical and practical support for promoting the seed yield of M. tenacissima.

Transcriptome analysis reveals molecular signature and cell-type difference of Homo sapiens endothelial-to-mesenchymal transition.

Endothelial-to-mesenchymal transition (EndoMT), a specific form of epithelial-to-mesenchymal transition, drives a growing number of human (Homo sapiens) pathological conditions. This emerging knowledge opens a path to discovering novel therapeutic targets for many EndoMT-associated disorders. Here, we constructed an atlas of the endothelial-cell transcriptome and demonstrated EndoMT-induced global changes in transcriptional gene expression. Our gene ontology analyses showed that EndoMT could be a specific checkpoint for leukocyte chemotaxis, adhesion, and transendothelial migration. We also identified distinct gene expression signatures underlying EndoMT across arterial, venous, and microvascular endothelial cells. We performed protein-protein interaction network analyses, identifying a class of highly connected hub genes in endothelial cells from different vascular beds. Moreover, we found that the short-chain fatty acid acetate strongly inhibits the transcriptional program of EndoMT in endothelial cells from different vascular beds across tissues. Our results reveal the molecular signature and cell-type difference of EndoMT across distinct tissue- and vascular-bed-specific endothelial cells, providing a powerful discovery tool and resource value. These results suggest that therapeutically manipulating the endothelial transcriptome could treat an increasing number of EndoMT-associated pathological conditions.

P02.03.A INTEGRATIVE (EPI)GENETIC ANALYSIS OF INVASION-PROMOTING GENES IN HIGH-GRADE GLIOMA CELLS

Abstract BACKGROUND DNA methylation-based analyses of brain tumors including glioma is currently the gold standard for diagnostic classification. Aberrant epigenetic alterations can lead to inappropriate gene expression and thereby promote tumorigenesis. Glioblastoma (GBM), CNS WHO grade 4, is characterized by a very diffuse infiltrative growth into the adjacent brain parenchyma. Due to these highly invasive but also genetically heterogeneous and plastic cellular phenotypes, standard treatment, including maximum resection, radio- and chemotherapy, has limited efficacy. It can be assumed that intertumoral or molecular heterogeneity of gliomas on transcriptional level is caused by altered epigenetic changes within the individual tumor cells. Considering this, we hypothesize that tumor cell invasion being one of the critical hallmarks of highly malignant gliomas goes along with altered DNA methylation status and following from this changes in invasion-promoting transcript expression. MATERIAL AND METHODS We performed several in vitro screening approaches to describe the genetic, epigenetic and transcriptional status of invasion glioma cells. Within our first approach, we isolated fractions of glioma cells with increased invasive properties and performed Illumina® array-based methylation profiling as well as RNA sequencing analysis to identify methylation-driven, invasion-associated gene sets. During a second approach, the inducible CRISPR/Cas9 Synergistic Activation Mediator (SAM) system and a genome-wide sgRNA library were introduced in a serum-free glioma cell line. During CRISPR/Cas9 SAM mediated single-gene activation cells were subjected to a transwell invasion assay and sgRNA representation within the invasive glioma cell fraction was determined by next-generation-sequencing (NGS). RESULTS In this study, we integrated Illumina HumanMethylation850K methylation data, RNA-sequencing data and invasion-promoting sgRNA representation data. By systemic screening we identified an invasion-promoting gene signature and the correlating promotor DNA-methylation status. Future studies will be directed to further investigate the impact of identified genes in invasion of high-grade glioma cells. CONCLUSION This integrative experimental approach complements existing genome-wide inhibitory screens as well as incorporates for the first time DNA-methylation profiles and transcriptome analysis with gene-sets identified by CRISPR/Cas9 activation screen and thereby holds the potential to identify novel invasion-essential candidate genes.

The Selective LAT1 Inhibitor JPH203 Enhances Mitochondrial Metabolism and Content in Insulin-Sensitive and Insulin-Resistant C2C12 Myotubes.

Population data have shown an association between higher circulating branched-chain amino acids (BCAA) and the severity of insulin resistance in people with diabetes. While several studies have assessed BCAA metabolism as a potential target for regulation, less attention has been paid to the role of L-type amino acid transporter 1 (LAT1), the primary transporter of BCAA in skeletal muscle. The aim of this study was to assess the impact of JPH203 (JPH), a LAT1 inhibitor, on myotube metabolism in both insulin-sensitive and insulin-resistant myotubes. C2C12 myotubes were treated with or without 1 μM or 2 μM JPH for 24 h with or without insulin resistance. Western blot and qRT-PCR were used to assess protein content and gene expression, respectively. Mitochondrial and glycolytic metabolism were measured via Seahorse Assay, and fluorescent staining was used to measure mitochondrial content. BCAA media content was quantified using liquid chromatography-mass spectrometry. JPH at 1 μM (but not 2 μM) increased mitochondrial metabolism and content without inducing changes in mRNA expression of transcripts associated with mitochondrial biogenesis or mitochondrial dynamics. Along with increased mitochondrial function, 1μM treatment also reduced extracellular leucine and valine. JPH at 2 μM reduced pAkt signaling and increased extracellular accumulation of isoleucine without inducing changes in BCAA metabolic genes. Collectively, JPH may increase mitochondrial function independent of the mitochondrial biogenic transcription pathway; however, high doses may reduce insulin signaling.

Quantitative Analysis of Isoform Switching in Cancer.

Over the past 8 years, multiple studies examined the phenomenon of isoform switching in human cancers and discovered that isoform switching is widespread, with hundreds to thousands of such events per cancer type. Although all of these studies used slightly different definitions of isoform switching, which in part led to a rather poor overlap of their results, they all leveraged transcript usage, a proportion of the transcript's expression in the total expression level of the parent gene, to detect isoform switching. However, how changes in transcript usage correlate with changes in transcript expression is not sufficiently explored. In this article, we adopt the most common definition of isoform switching and use a state-of-the-art tool for the analysis of differential transcript usage, SatuRn, to detect isoform switching events in 12 cancer types. We analyze the detected events in terms of changes in transcript usage and the relationship between transcript usage and transcript expression on a global scale. The results of our analysis suggest that the relationship between changes in transcript usage and changes in transcript expression is far from straightforward, and that such quantitative information can be effectively used for prioritizing isoform switching events for downstream analyses.

Modulation of cellular transcriptome and proteome composition by azidohomoalanine—implications on click chemistry–based secretome analysis

The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry–based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15–39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale.Key messagesAzide-containing amino acid analogs affect gene expression profiles.Azide-containing amino acid analogs influence cellular proteome.Azidohomoalanine labeling induces cellular stress and apoptotic pathways.Secretome consists of proteins with dysregulated expression profiles.

Cellulase mediated stress triggers the mutations of oleaginous yeast Trichosporon cutaneum with super-large spindle morphology and high lipid accumulation.

Accumulation of intracellular lipid bodies in oleaginous yeast cells is highly restricted by their natural intracellular space. Here we show a cellulase mediated adaptive evolution with ultra-centrifugation fractionation of oleaginous yeast Trichosporon cutaneum to obtain the favorable cell structure for lipid accumulation. Cellulase was added to the wheat straw hydrolysate during long-term adaptive evolution for disruption of cell wall integrity of T. cutaneum cells. The cellulase, together with ultracentrifugation force, triggered multiple mutations and transcriptional expression changes of the functional genes associated with cell wall integrity and lipid synthesis metabolism. The fractionated mutant T. cutaneum YY52 demonstrated the heavily weakened cell wall and high lipid accumulation by the super-large expanded spindle cells (two orders of magnitude greater than the parental). A record-high lipid production by T. cutaneum YY52 was achieved (55.4±0.5gL-1 from wheat straw and 58.4±0.1gL-1 from corn stover). This study not only obtained an oleaginous yeast strain with industrial application potential for lipid production but also provided a new method for generation of mutant cells with high intracellular metabolite accumulation.

Establishment of a lipopolysaccharide-induced inflammation model of human fetal colon cells.

Inflammatory bowel disease (IBD) is a global health problem and there are few cell models for IBD at present. To culture a human fetal colon (FHC) cell line in vitro and establish an FHC cell inflammation model that meets the requirements for high expression of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). FHC cells were cultured with various concentrations of Escherichia coli lipopolysaccharide (LPS) in appropriate media for 0.5, 1, 2, 4, 8, 16 and 24h to stimulate an inflammatory reaction. The viability of FHC cells was detected by a Cell Counting Kit-8 (CCK-8) assay. The transcriptional levels and protein expression changes of IL-6 and TNF-α in FHC cells were detected by Quantitative Real‑Time Polymerase Chain Reaction (qRT-PCR) and Enzyme‑Linked Immunosorbent Assay (ELISA), respectively. Appropriate stimulation conditions were selected (i.e., LPS concentration and treatment time), based on changes in cell survival rate, and IL-6 and TNF-α expression levels. An LPS concentration higher than 100µg/mL or a treatment time longer than 24h resulted in morphological changes and decreased cell survival. By contrast, expression levels of IL-6 and TNF-α significantly increased within 24h when LPS concentration lower than 100µg/mL and peaked at 2h, whilst maintaining cell morphology and viability in FHC cells. The treatment of FHC cells with 100µg/mL LPS within 24h was optimal in terms of stimulating IL-6 and TNF-α expression.

Single cell molecular alterations reveal target cells and pathways of conditioned fear memory.

Recent evidence indicates that hippocampus is important for conditioned fear memory (CFM). Though few studies consider the roles of various cell types' contribution to such a process, as well as the accompanying transcriptome changes during this process. The purpose of this study was to explore the transcriptional regulatory genes and the targeted cells that are altered by CFM reconsolidation. A fear conditioning experiment was established on adult male C57 mice, after day 3 tone-cued CFM reconsolidation test, hippocampus cells were dissociated. Using single cell RNA sequencing (scRNA-seq) technique, alterations of transcriptional genes expression were detected and cell cluster analysis were performed and compared with those in sham group. Seven non-neuronal and eight neuronal cell clusters (including four known neurons and four newly identified neuronal subtypes) has been explored. Among them, CA subtype 1 has characteristic gene markers of Ttr and Ptgds, which is speculated to be the outcome of acute stress and promotes the production of CFM. The results of KEGG pathway enrichment indicate the differences in the expression of certain molecular protein functional subunits in long-term potentiation (LTP) pathway between two types of neurons (DG and CA1) and astrocytes, thus providing a new transcriptional perspective for the role of hippocampus in the CFM reconsolidation. More importantly, the correlation between the reconsolidation of CFM and neurodegenerative diseases-linked genes is substantiated by the results from cell-cell interactions and KEGG pathway enrichment. Further analysis shows that the reconsolidation of CFM inhibits the risk-factor genes App and ApoE in Alzheimer's Disease (AD) and activates the protective gene Lrp1. This study reports the transcriptional genes expression changes of hippocampal cells driven by CFM, which confirm the involvement of LTP pathway and suggest the possibility of CFM-like behavior in preventing AD. However, the current research is limited to normal C57 mice, and further studies on AD model mice are needed to prove this preliminary conclusion.

Sex differences in the transcriptome of extracellular vesicles secreted by fetal neural stem cells and effects of chronic alcohol exposure

BackgroundPrenatal alcohol (ethanol) exposure (PAE) results in brain growth restriction, in part, by reprogramming self-renewal and maturation of fetal neural stem cells (NSCs) during neurogenesis. We recently showed that ethanol resulted in enrichment of both proteins and pro-maturation microRNAs in sub-200-nm-sized extracellular vesicles (EVs) secreted by fetal NSCs. Moreover, EVs secreted by ethanol-exposed NSCs exhibited diminished efficacy in controlling NSC metabolism and maturation. Here we tested the hypothesis that ethanol may also influence the packaging of RNAs into EVs from cell-of-origin NSCs.MethodsSex-specified fetal murine iso-cortical neuroepithelia from three separate pregnancies were maintained ex vivo, as neurosphere cultures to model the early neurogenic niche. EVs were isolated by ultracentrifugation from NSCs exposed to a dose range of ethanol. RNA from paired EV and cell-of-origin NSC samples was processed for ribosomal RNA-depleted RNA sequencing. Differential expression analysis and exploratory weighted gene co-expression network analysis (WGCNA) identified candidate genes and gene networks that were drivers of alterations to the transcriptome of EVs relative to cells.ResultsThe RNA content of EVs differed significantly from cell-of-origin NSCs. Biological sex contributed to unique transcriptome variance in EV samples, where > 75% of the most variant transcripts were also sex-variant in EVs but not in cell-of-origin NSCs. WGCNA analysis also identified sex-dependent enrichment of pathways, including dopamine receptor binding and ectoderm formation in female EVs and cell-substrate adhesion in male EVs, with the top significant DEGs from differential analysis of overall individual gene expressions, i.e., Arhgap15, enriched in female EVs, and Cenpa, enriched in male EVs, also serving as WCGNA hub genes of sex-biased EV WGCNA clusters. In addition to the baseline RNA content differences, ethanol exposure resulted in a significant dose-dependent change in transcript expression in both EVs and cell-of-origin NSCs that predominantly altered sex-invariant RNAs. Moreover, at the highest dose, ~ 73% of significantly altered RNAs were enriched in EVs, but depleted in NSCs.ConclusionsThe EV transcriptome is distinctly different from, and more sex-variant than, the transcriptome of cell-of-origin NSCs. Ethanol, a common teratogen, results in dose-dependent sorting of RNA transcripts from NSCs to EVs which may reprogram the EV-mediated endocrine environment during neurogenesis.

Whole exome and transcript profiling of liver following aflatoxin B1 exposure in rats.

We recently developed a rat whole exome sequencing (WES) panel and used it to evaluate early somatic mutations in archival liver tissues from F344/N rats exposed to the hepatocarcinogen, Aflatoxin B1 (AFB1), a widely studied, potent mutagen and hepatocarcinogen associated with hepatocellular carcinoma (HCC). Rats were exposed to 1 ppm AFB1 in feed for 14, 90 and 90 days plus a recovery 60-day, non-exposure period (150-day) time point. Isolated liver DNA was exome sequenced. We identified 172 sequence variants across all time points, of which 101 were non-synonymous variants. Well-annotated genes carried a diverse set of 29 non-synonymous mutations at 14-days, increasing to 39 mutations at 90-days and then decreasing to 33 mutations following the 60-day recovery. Gene Set Enrichment Analysis conducted on previously reported, available RNA expression data of the same exome sequenced archival samples identified altered transcripts in pathways associated with malignant transformation. These included HALLMARK gene sets associated with cell proliferation (MYC Targets Version 1 and Version 2, E2F targets), cell cycle (G2M checkpoint, mitotic spindle), cell death (apoptosis), and DNA damage (DNA repair, UV response Up, Reactive oxygen species) pathways. DriverNet Impact analysis integrated exome-seq and expression data to reveal somatic mutations in Mcm8, Bdp1 and Cct6a that may drive cancer formation. Connectivity with transcript expression changes identified these genes as the top-ranked candidate driver genes associated with hepatocellular transformation. In conclusion, exome sequencing revealed early somatic mutations that may play a role in cancer cell transformation that are translatable to aflatoxin-induced HCC.