Distinct epigenetic modulation of differentially expressed genes in the adult mouse brain following prenatal exposure to low-dose bisphenol A

Bisphenol A (BPA) is a common component in the manufacture of daily plastic consumer goods. Recent studies have suggested that prenatal exposure to BPA can increase the susceptibility of offspring to mental illness, although the underlying mechanisms remain unclear. In this study, we performed transcriptomic and epigenomic profiling in the adult mouse brain following prenatal exposure to low-dose BPA. We observed a sex-specific transcriptional dysregulation in the cortex, with more significant differentially expressed genes was observed in adult cortex from male offspring. Moreover, the upregulated genes primarily influenced neuronal functions, while the downregulated genes were significantly associated with energy metabolism pathways. More evidence supporting impaired mitochondrial function included a decreased ATP level and a reduced number of mitochondria in the cortical neuron of the BPA group. We further investigated the higher-order chromatin regulatory patterns of DEGs by incorporating published Hi-C data. Interestingly, we found that upregulated genes exhibited more distal interactions with multiple enhancers, while downregulated genes displayed relatively short-range interactions among adjacent genes. Our data further revealed decreased H3K9me3 signal on the distal enhancers of upregulated genes, whereas increased DNA methylation and H3K27me3 signals on the promoters of downregulated genes. In summary, our study provides compelling evidence for the potential health risks associated with prenatal exposure to BPA, and uncovers sex-specific transcriptional changes with a complex interplay of multiple epigenetic mechanisms.

Transcriptomic profiling and regulatory pathways of cardiac resident macrophages in aging

Cardiovascular diseases are an array of age-related disorders, and accumulating evidence suggests a link between cardiac resident macrophages (CRMs) and the age-related disorders. However, how does CRMs alter with aging remains elusive. In the present study, aged mice (20 months old) have been employed to check for their cardiac structural and functional alterations, and the changes in the proportion of CRM subsets as well, followed by sorting of CRMs, including C-C Motif Chemokine Receptor 2 (CCR2)+ and CCR2- CRMs, which were subjected to Smart-Seq. Integrated analysis of the Smart-Seq data with three publicly available single-cell RNA-seq datasets revealed that inflammatory genes were drastic upregulated for both CCR2+ and CCR2- CRMs with aging, but genes germane to wound healing were downregulated for CCR2- CRMs, suggesting the differential functions of these two subsets. More importantly, inflammatory genes involved in damage sensing, complement cascades, and phagocytosis were largely upregulated in CCR2- CRMs, implying the imbalance of inflammatory response upon aging. Our work provides a comprehensive framework and transcriptional resource for assessing the impact of aging on CRMs with a potential for further understanding cardiac aging.

Persistent organic pollutants dysregulate energy homeostasis in human ovaries in vitro

Exposure to persistent organic pollutants (POPs), such as dichlorodiphenyltrichloroethane (DDT) and polychlorinated biphenyls (PCBs), has historically been linked to population collapses in wildlife. Despite international regulations, these legacy chemicals are still currently detected in women of reproductive age, and their levels correlate with reduced ovarian reserve, longer time-to-pregnancy, and higher risk of infertility. However, the specific modes of action underlying these associations remain unclear. Here, we examined the effects of five commonly occurring POPs - hexachlorobenzene (HCB), p,p'-dichlorodiphenyldichloroethylene (DDE), 2,3,3',4,4',5-hexachlorobiphenyl (PCB156), 2,2',3,4,4',5,5'-heptachlorobiphenyl (PCB180), perfluorooctane sulfonate (PFOS) - and their mixture on human ovaries in vitro. We exposed human ovarian cancer cell lines COV434, KGN, and PA1 as well as primary ovarian cells for 24 h, and ovarian tissue containing unilaminar follicles for 6 days. RNA-sequencing of samples exposed to concentrations covering epidemiologically relevant levels revealed significant gene expression changes related to central energy metabolism in the exposed cells, indicating glycolysis, oxidative phosphorylation, fatty acid metabolism, and reactive oxygen species as potential shared targets of POP exposures in ovarian cells. Alpha-enolase (ENO1), lactate dehydrogenase A (LDHA), cytochrome C oxidase subunit 4I1 (COX4I1), ATP synthase F1 subunit alpha (ATP5A), and glutathione peroxidase 4 (GPX4) were validated as targets through qPCR in additional cell culture experiments in KGN. In ovarian tissue cultures, we observed significant effects of exposure on follicle growth and atresia as well as protein expression. All POP exposures, except PCB180, decreased unilaminar follicle proportion and increased follicle atresia. Immunostaining confirmed altered expression of LDHA, ATP5A, and GPX4 in the exposed tissues. Moreover, POP exposures modified ATP production in KGN and tissue culture. In conclusion, our results demonstrate the disruption of cellular energy metabolism as a novel mode of action underlying POP-mediated interference of follicle growth in human ovaries.

The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments

Haberlea rhodopensis, a resurrection species, is the only plant known to be able to survive multiple extreme environments, including desiccation, freezing temperatures, and long-term darkness. However, the molecular mechanisms underlying tolerance to these stresses are poorly studied. Here, we present a high-quality genome of Haberlea and found that ~ 23.55% of the 44,306 genes are orphan. Comparative genomics analysis identified 89 significantly expanded gene families, of which 25 were specific to Haberlea. Moreover, we demonstrated that Haberlea preserves its resurrection potential even in prolonged complete darkness. Transcriptome profiling of plants subjected to desiccation, darkness, and low temperatures revealed both common and specific footprints of these stresses, and their combinations. For example, PROTEIN PHOSPHATASE 2C (PP2C) genes were substantially induced in all stress combinations, while PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and GROWTH RESPONSE FACTOR 4 (GRF4) were induced only in darkness. Additionally, 733 genes with unknown functions and three genes encoding transcription factors specific to Haberlea were specifically induced/repressed upon combination of stresses, rendering them attractive targets for future functional studies. The study provides a comprehensive understanding of the genomic architecture and reports details of the mechanisms of multi-stress tolerance of this resurrection species that will aid in developing strategies that allow crops to survive extreme and multiple abiotic stresses.

Characterization of two distinct immortalized endothelial cell lines, EA.hy926 and HMEC-1, for in vitro studies: exploring the impact of calcium electroporation, Ca2+ signaling and transcriptomic profiles

BACKGROUND

Disruption of Ca2+ homeostasis after calcium electroporation (CaEP) in tumors has been shown to elicit an enhanced antitumor effect with varying impacts on healthy tissue, such as endothelium. Therefore, our study aimed to determine differences in Ca2+ kinetics and gene expression involved in the regulation of Ca2+ signaling and homeostasis, as well as effects of CaEP on cytoskeleton and adherens junctions of the established endothelial cell lines EA.hy926 and HMEC-1.

METHODS

CaEP was performed on EA.hy926 and HMEC-1 cells with increasing Ca2+ concentrations. Viability after CaEP was assessed using Presto Blue, while the effect on cytoskeleton and adherens junctions was evaluated via immunofluorescence staining (F-actin, α-tubulin, VE-cadherin). Differences in intracellular Ca2+ regulation ([Ca2+]i) were determined with spectrofluorometric measurements using Fura-2-AM, exposing cells to DPBS, ionomycin, thapsigargin, ATP, bradykinin, angiotensin II, acetylcholine, LaCl3, and GdCl3. Molecular distinctions were identified by analyzing differentially expressed genes and pathways related to the cytoskeleton and Ca2+ signaling through RNA sequencing.

RESULTS

EA.hy926 cells, at increasing Ca2+ concentrations, displayed higher CaEP susceptibility and lower survival than HMEC-1. Immunofluorescence confirmed CaEP-induced, time- and Ca2+-dependent morphological changes in EA.hy926's actin filaments, microtubules, and cell-cell junctions. Spectrofluorometric Ca2+ kinetics showed higher amplitudes in Ca2+ responses in EA.hy926 exposed to buffer, G protein coupled receptor agonists, bradykinin, and angiotensin II compared to HMEC-1. HMEC-1 exhibited significantly higher [Ca2+]i changes after ionomycin exposure, while responses to thapsigargin, ATP, and acetylcholine were similar in both cell lines. ATP without extracellular Ca2+ ions induced a significantly higher [Ca2+]i rise in EA.hy926, suggesting purinergic ionotropic P2X and metabotropic P2Y receptor activation. RNA-sequencing analysis showed significant differences in cytoskeleton- and Ca2+-related gene expression, highlighting upregulation of ORAI2, TRPC1, TRPM2, CNGA3, TRPM6, and downregulation of TRPV4 and TRPC4 in EA.hy926 versus HMEC-1. Moreover, KEGG analysis showed upregulated Ca2+ import and downregulated export genes in EA.hy926.

CONCLUSIONS

Our finding show that significant differences in CaEP response and [Ca2+]i regulation exist between EA.hy926 and HMEC-1, which may be attributed to distinct transcriptomic profiles. EA.hy926, compared to HMEC-1, displayed higher susceptibility and sensitivity to [Ca2+]i changes, which may be linked to overexpression of Ca2+-related genes and an inability to mitigate changes in [Ca2+]i. The study offers a bioinformatic basis for selecting EC models based on research objectives.

Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma

Cholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation patterns in each cell line. In addition, specific expression patterns with distinct biological functions and pathways involved were also observed in the PDPCs at the transcriptomic level. Furthermore, the drug-sensitivity results revealed that the PDPCs exhibited different responses to the six commonly used compounds. Our findings indicate that the established PDPCs can serve as novel in vitro reliable models to provide a crucial molecular basis for improving the understanding of tumorigenesis and its treatment.

Selection of goat β-casein derived ACE-inhibitory peptide SQPK and insights into its effect and regulatory mechanism on the function of endothelial cells

The angiotensin I-converting enzyme (ACE)-inhibitory peptide SQPK was selected by in silico digestion and virtual screening from goat β-casein, and its effect and regulatory mechanism on function of endothelial cells was further evaluated. The results showed that SQPK exhibited relatively good ACE inhibition capacity (IC50 = 452.7 μg/mL). Treatment with 25 μg/mL SQPK for 12 h significantly elevated nitric oxide (NO) production, stimulated eNOS expression (p < 0.05) and affected the transcriptomic profiling of EA. Hy926 cells. In particular, SQPK stimulated the expression of genes encoding inflammatory cytokines (CXCL1/2 and IL6) but depressed encoding mesenchymal markers (FN1 and CNN3). Furthermore, SQPK modified the expression of genes involved in endothelial-to-mesenchymal transition (EndMT). Therefore, the selected peptide SQPK may exert potential protective effects on the function of endothelial cells by inhibiting the EndMT.

Transcriptomic profiling of human granulosa cells between women with advanced maternal age with different ovarian reserve

BACKGROUND

Age-related diminished ovarian reserve (DOR) is not absolute. Some advanced maternal age (AMA) still have normal ovarian reserve (NOR) and often show better pregnancy outcomes. Exploring the transcriptomic profile of granulosa cells (GCs) in AMA could lead to new ideas for mitigating age-related diminished ovarian reserve.

AIM

This study aimed to analyze the transcriptomic profile of GCs in AMA with different ovarian reserve.

RESULTS

In total, 6273 statistically significant differential expression genes (DEGs) (|log2fc|> 1, q < 0.05) were screened from the two groups, among which 3436 genes were upregulated, and 2837 genes were downregulated in the DOR group. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, the potential functions of dysregulated genes in AMA with DOR or NOR were predicted. The GO enrichment analysis revealed that the DEGs were mainly enriched in obsolete oxidation-reduction process, mitochondrion, metal ion binding, ATP binding, etc. The KEGG pathway enrichment analysis revealed that the above-mentioned DEGs were mainly enriched in ferroptosis, regulation of actin cytoskeleton, oxidative phosphorylation, etc. Meanwhile, verification of the mRNA expression levels of DEGs revealed the possible involvement of "ferroptosis" in age-related diminished ovarian reserve.

CONCLUSIONS

From a new clinical perspective, we presented the first data showing the transcriptomic profile in GCs between AMA with different ovarian reserve. At the same time, we identified the role of ferroptosis in the GCs of AMA, providing a new biological basis for studying ovarian aging and improving pregnancy outcomes of AMA.

Thallium exposure interfered with heart development in embryonic zebrafish (Danio rerio): From phenotype to genotype

Thallium (Tl) is a rare trace metal element but increasingly detected in wastewater produced by coal-burning, smelting, and more recently, high-tech manufacturing industries. However, the adverse effects of Tl, especially cardiotoxicity, on aquatic biota remain unclear. In this study, zebrafish model was used to elucidate the effects and mechanisms of Tl(I) cardiotoxicity in developing embryos. Exposure of embryonic zebrafish to low-dose Tl(I) (25-100 μg/L) decreased heart rate and blood flow activity, and subsequently impaired swim bladder inflation and locomotive behavior of larvae. Following high-level Tl(I) administration (200-800 μg/L), embryonic zebrafish exhibited pericardial edema, incorrect heart looping, and thinner myocardial layer. Based on RNA-sequencing, Tl(I) altered pathways responsible for protein folding and transmembrane transport, as well as negative regulation of heart rate and cardiac jelly development. The gene expression of nppa, nppb, ucp1, and ucp3, biomarkers of cardiac damage, were significantly upregulated by Tl(I). Our findings demonstrate that Tl(I) at environmentally relevant concentrations interfered with cardiac development with respect to anatomy, function, and transcriptomic alterations. The cardiotoxic mechanisms of Tl(I) provide valuable information in the assessment of Tl-related ecological risk in freshwater environment.

Transcriptomic profiling reveals differential cellular response to copper oxide nanoparticles and polystyrene nanoplastics in perfused human placenta

The growing nanoparticulate pollution (e.g. engineered nanoparticles (NPs) or nanoplastics) has been shown to pose potential threats to human health. In particular, sensitive populations such as pregnant women and their unborn children need to be protected from harmful environmental exposures. However, developmental toxicity from prenatal exposure to pollution particles is not yet well studied despite evidence of particle accumulation in human placenta. Our study aimed to investigate how copper oxide NPs (CuO NPs; 10-20 nm) and polystyrene nanoplastics (PS NPs; 70 nm) impact on gene expression in ex vivo perfused human placental tissue. Whole genome microarray analysis revealed changes in global gene expression profile after 6 h of perfusion with sub-cytotoxic concentrations of CuO (10 µg/mL) and PS NPs (25 µg/mL). Pathway and gene ontology enrichment analysis of the differentially expressed genes suggested that CuO and PS NPs trigger distinct cellular response in placental tissue. While CuO NPs induced pathways related to angiogenesis, protein misfolding and heat shock responses, PS NPs affected the expression of genes related to inflammation and iron homeostasis. The observed effects on protein misfolding, cytokine signaling, and hormones were corroborated by western blot (accumulation of polyubiquitinated proteins) or qPCR analysis. Overall, the results of the present study revealed extensive and material-specific interference of CuO and PS NPs with placental gene expression from a single short-term exposure which deserves increasing attention. In addition, the placenta, which is often neglected in developmental toxicity studies, should be a key focus in the future safety assessment of NPs in pregnancy.

Integrated analysis of metabolomic and transcriptomic profiling reveals the effect of Buyang Huanwu decoction on Parkinson's disease in mice

BACKGROUND

Parkinson's disease (PD) is a common, complex, and chronic neurodegenerative disorder involved in multi-system. At present, medicine for PD has many limitations. Buyang Huanwu decoction (BHD), a famous traditional Chinese medicinal (TCM) formulae, is used in the treatment of PD clinically in China. However, the therapeutic mechanism is still unknown.

PURPOSE

We aimed to explore the pharmacological mechanism of BHD alleviating PD through an integrated liver metabolome and brain transcriptome analysis.

METHODS

The mice with PD were induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Behavioral tests and immunohistochemistry were used to evaluate the neuroprotective effects of BHD. The non-targeted metabolomics analysis was conducted to profile differentially accumulated metabolites (DAMs) in the liver using a UHPLC-Q-Exactive MS/MS method. The differentially expressed genes (DEGs) in the brain were investigated by transcriptomic analysis on an Illumina sequencing platform. The correlations of DAMs and DEGs were investigated using an integrated metabolomic and transcriptomic approach.

RESULTS

The results of behavioral tests and immunohistochemistry proved the alleviated effects of BHD on PD symptoms. A total of 14 and 36 DAMs were detected in the groups treated with low- (L group) and high-dose (H group) BHD respectively under the positive ion mode. Compared with the PD model group (M group), three enriched pathways including metabolic pathways, ABC transporters, and biosynthesis of amino acids were common in the L and H group. Transcriptomic analysis proved that BHD could regulate the expression of numerous genes, some of which were targeted by Ben-Ldopa such as Creb5, Gm45623, Ccer2, Cd180, Fosl2, Crip3, and Noxred1. Based on the integrated metabolomic and transcriptomic analysis, 7 metabolite-gene pairs were found in four comparisons, including C vs M, M vs P, M vs L, and M vs H, and 6 enriched pathways containing purine metabolism, glycine/serine/threonine metabolism, phenylalanine metabolism, carbon fixation in photosynthetic organisms, thiamine metabolism, and ABC transporters were overlapped.

CONCLUSIONS

Though the underlying pharmacological mechanism of BHD is still lacking, we provided evidence that BHD could improve dopaminergic neurons in MPTP-induced PD mice by regulating liver metabolism and brain transcriptome. The correlation between the liver and the brain was preliminarily revealed in this study.

Transcriptome profiling and bioinformatic analysis of the effect of ganoderic acid T prevents Sendai virus infection

Ganoderic acid T (GA-T) is an important triterpene of Ganoderma lucidum, which is utilized to treat viral infections. Sendai virus (SeV) is widely studied to determine the molecular biological characteristics of RNA viruses and employed to elucidate the mechanisms governing the innate immune response. However, the comprehensive mechanism governing the antiviral effects of GA-T against SeV infection remains unknown. In this study, SeV-infected host cells were treated with 16.3 μM GA-T, subsequently RNA-seq analysis was performed to screen the differentially expressed genes (DEGs). The RNA-seq data showed that GA-T treatment upregulated 934 DEGs and downregulated 1283 DEGs against viral infection, in particularly, IFNGR1, IL1A, and IL1R1 were upregulated, and mTOR, SMAD3, IFNL2 and IFNL3 were decreased. GO and KEGG analysis illustrated that DEGs were clustered in mTOR and IL-17 signalling pathways. Protein-protein interaction network analysis indicated the high degree of nodes, such as CXCL8, CSF2, CXCL1 and MYD88. Our results indicated that GA-T exerted its antiviral pharmacological effects through inhibition of the mTOR signalling pathway and adjustment of innate immunity system and the inflammatory response involving the IL-17 signalling pathway. Our results may help to elucidate the potential functions and underlying mechanisms governing the antiviral effects of GA-T.

Transcriptome profiling of a synergistic volumetric muscle loss repair strategy

Volumetric muscle loss overwhelms skeletal muscle's ordinarily capable regenerative machinery, resulting in severe functional deficits that have defied clinical repair strategies. In this manuscript we pair the early in vivo functional response induced by differing volumetric muscle loss tissue engineering repair strategies that are broadly representative of those explored by the field (scaffold alone, cells alone, or scaffold + cells) to the transcriptomic response induced by each intervention. We demonstrate that an implant strategy comprising allogeneic decellularized skeletal muscle scaffolds seeded with autologous minced muscle cellular paste (scaffold + cells) mediates a pattern of increased expression for several genes known to play roles in axon guidance and peripheral neuroregeneration, as well as several other key genes related to inflammation, phagocytosis, and extracellular matrix regulation. The upregulation of several key genes in the presence of both implant components suggests a unique synergy between scaffolding and cells in the early period following intervention that is not seen when either scaffolds or cells are used in isolation; a finding that invites further exploration of the interactions that could have a positive impact on the treatment of volumetric muscle loss.

Can biomarkers identified from the uterine fluid transcriptome be used to establish a noninvasive endometrial receptivity prediction tool? A proof-of-concept study

BACKGROUND

Embryo implantation in a receptive endometrium is crucial for successful pregnancy. Endometrial receptivity (ER) prediction tools based on endometrial transcriptome biomarkers by endometrial biopsy have been used to guide successful embryo implantation in in vitro fertilization (IVF) patients. However, no reliable noninvasive ER prediction method has been established, and one is greatly needed. We aimed to identify biomarkers from uterine fluid transcriptomic sequencing data for establishing noninvasive ER prediction tool and to evaluate its clinical application potential in patients undergoing IVF.

METHODS

The non-invasive RNA-seq based endometrial receptivity test (nirsERT) was established by analyzing transcriptomic profile of 144 uterine fluid specimens (LH + 5, LH + 7, and LH + 9) at three different receptive status from 48 IVF patients with normal ER in combination with random forest algorithm. Subsequently, 22 IVF patients who underwent frozen-thaw blastocyst transfer were recruited and analyzed the correlation between the predicted results of nirsERT and pregnancy outcomes.

RESULTS

A total of 864 ER-associated differentially expressed genes (DEGs) involved in biological processes associated with endometrium-embryo crosstalk, including protein binding, signal reception and transduction, biomacromolecule transport and cell-cell adherens junctions, were selected. Subsequently, a nirsERT model consisting of 87 markers and 3 hub genes was established using a random forest algorithm. 10-fold cross-validation resulted in a mean accuracy of 93.0%. A small cohort (n = 22) retrospective observation shows that 77.8% (14/18) of IVF patients predicted with a normal WOI had successful intrauterine pregnancies, while none of the 3 patients with a displaced WOI had successful pregnancies. One patient failed due to poor sequencing data quality.

CONCLUSIONS

NirsERT based on uterine fluid transcriptome biomarkers can predict the WOI period relatively accurately and may serve as a noninvasive, reliable and same cycle test for ER in reproductive clinics.

TRIAL REGISTRATION

Chinese Clinical Trial Registry: ChiCTR-DDD-17013375. Registered 14 November 2017, http://www.chictr.org.cn/index.aspx .

Accumulation and ecotoxicological effects induced by combined exposure of different sized polyethylene microplastics and oxytetracycline in zebrafish

Microplastics have been widely reported as carriers of antibiotics, yet studies investigating the combined ecotoxicology of microplastics and antibiotics on organisms is limited. In this study, different sized polystyrene plastics and oxytetracycline (OTC) were used to carry out a 30-day single and binary-combined exposure experiment of zebrafish, and the microplastics and OTC accumulation, liver histological alteration, biomarkers and transcriptomic response of zebrafish were evaluated. Our results indicated that 300 nm and 50 nm plastic particles increased the OTC accumulation in liver by 33.8% and 44.5%, respectively. Microplastics and OTC induced severe liver histological damage, and the damage is size-dependent, increasing with the decrease of microplastics sizes. The liver biomarkers indicated a different response pattern in single microplastics exposure and combined with OTC, single or co-exposure of 50 nm nano-plastics and OTC induced intense responses of integrated biomarker response values. The 50 nm nano-plastics, OTC and their combined exposure induced 1330, 2693 and 3965 significantly differentially expressed genes, respectively, in which the steroid biosynthesis pathway was significantly affected by all the three treatments. This study elucidated the size-dependent effects of microplastics and provided detailed data from histopathology to transcriptome profile, enhancing our understanding of the ecotoxicity of microplastics and OTC.

Minoxidil Regulates Aging-Like Phenotypes in Rat Cortical Astrocytes In Vitro

Mainly due to the slanted focus on the mechanism and regulation of neuronal aging, research on astrocyte aging and its modulation during brain aging is scarce. In this study, we established aged astrocyte culture model by long-term culturing. Cellular senescence was confirmed through SA-β-gal staining as well as through the examination of morphological, molecular, and functional markers. RNA sequencing and functional analysis of astrocytes were performed to further investigate the detailed characteristics of the aged astrocyte model. Along with aged phenotypes, decreased astrocytic proliferation, migration, mitochondrial energetic function and support for neuronal survival and differentiation has been observed in aged astrocytes. In addition, increased expression of cytokines and chemokine-related factors including plasminogen activator inhibitor -1 (PAI-1) was observed in aged astrocytes. Using the RNA sequencing results, we searched potential drugs that can normalize the dysregulated gene expression pattern observed in long-term cultured aged astrocytes. Among several candidates, minoxidil, a pyrimidine-derived anti-hypertensive and anti-pattern hair loss drug, normalized the increased number of SA-β-gal positive cells and nuclear size in aged astrocytes. In addition, minoxidil restored up-regulated activity of PAI-1 and increased mitochondrial superoxide production in aged astrocytes. We concluded that long term culture of astrocytes can be used as a reliable model for the study of astrocyte senescence and minoxidil can be a plausible candidate for the regulation of brain aging.

Transcriptional profiling of the developing rat ovary following intrauterine exposure to the endocrine disruptors diethylstilbestrol and ketoconazole

Exposure to endocrine-disrupting chemicals (EDCs) during development may cause reproductive disorders in women. Although female reproductive endpoints are assessed in rodent toxicity studies, a concern is that typical endpoints are not sensitive enough to detect chemicals of concern to human health. If so, measured endpoints must be improved or new biomarkers of effects included. Herein, we have characterized the dynamic transcriptional landscape of developing rat ovaries exposed to two well-known EDCs, diethylstilbestrol (DES) and ketoconazole (KTZ), by 3' RNA sequencing. Rats were orally exposed from day 7 of gestation until birth, and from postnatal day 1 until days 6, 14 or 22. Three exposure doses for each chemical were used: 3, 6 and 12 µg/kg bw/day of DES; 3, 6, 12 mg/kg bw/day of KTZ. The transcriptome changed dynamically during perinatal development in control ovaries, with 1137 differentially expressed genes (DEGs) partitioned into 3 broad expression patterns. A cross-species deconvolution strategy based on a mouse ovary developmental cell atlas was used to map any changes to ovarian cellularity across the perinatal period to allow for characterization of actual changes to gene transcript levels. A total of 184 DEGs were observed across dose groups and developmental stages in DES-exposed ovaries, and 111 DEGs in KTZ-exposed ovaries across dose groups and developmental stages. Based on our analyses, we have identified new candidate biomarkers for female reproductive toxicity induced by EDC, including Kcne2, Calb2 and Insl3.

Are we there yet? A machine learning architecture to predict organotropic metastases

BACKGROUND & AIMS

Cancer metastasis into distant organs is an evolutionarily selective process. A better understanding of the driving forces endowing proliferative plasticity of tumor seeds in distant soils is required to develop and adapt better treatment systems for this lethal stage of the disease. To this end, we aimed to utilize transcript expression profiling features to predict the site-specific metastases of primary tumors and second, to identify the determinants of tissue specific progression.

METHODS

We used statistical machine learning for transcript feature selection to optimize classification and built tree-based classifiers to predict tissue specific sites of metastatic progression.

RESULTS

We developed a novel machine learning architecture that analyzes 33 types of RNA transcriptome profiles from The Cancer Genome Atlas (TCGA) database. Our classifier identifies the tumor type, derives synthetic instances of primary tumors metastasizing to distant organs and classifies the site-specific metastases in 16 types of cancers metastasizing to 12 locations.

CONCLUSIONS

We have demonstrated that site specific metastatic progression is predictable using transcriptomic profiling data from primary tumors and that the overrepresented biological processes in tumors metastasizing to congruent distant loci are highly overlapping. These results indicate site-specific progression was organotropic and core features of biological signaling pathways are identifiable that may describe proliferative plasticity in distant soils.

cdev: a ground-truth based measure to evaluate RNA-seq normalization performance

Normalization of RNA-seq data has been an active area of research since the problem was first recognized a decade ago. Despite the active development of new normalizers, their performance measures have been given little attention. To evaluate normalizers, researchers have been relying on ad hoc measures, most of which are either qualitative, potentially biased, or easily confounded by parametric choices of downstream analysis. We propose a metric called condition-number based deviation, or cdev, to quantify normalization success. cdev measures how much an expression matrix differs from another. If a ground truth normalization is given, cdev can then be used to evaluate the performance of normalizers. To establish experimental ground truth, we compiled an extensive set of public RNA-seq assays with external spike-ins. This data collection, together with cdev, provides a valuable toolset for benchmarking new and existing normalization methods.

Lichenoid dysplasia is not a distinct pathological entity

OBJECTIVES

Oral Lichenoid Dysplasia (OLD) is a controversial histological term applied to lesions that display features of oral lichen planus (OLP) and oral epithelial dysplasia (OED). In this study we investigated the molecular profiles of OLD, OLP and OED to determine whether OLD exists as a distinct pathological entity.

MATERIALS AND METHODS

Samples from patients presenting with lesions diagnosed histologically as OLP, OLD or OED underwent RNA sequencing followed by differential gene expression, functional enrichment and network analysis, sparse partial least squares discriminant analysis, and immune cell phenotypic estimation.

RESULTS

Unsupervised clustering demonstrated a group of genes with high expression in OLP and OLD, and low expression in OED, predominantly involved in inflammatory processes. Many genes were significantly differentially expressed between either OLD or OLP and OED, but few between OLD and OLP. Functional enrichment showed significant pathways and ontologies related to inflammatory signalling and immune response between OLD or OLP and OED. Broad commonality was found between OLP and OLD in upregulation of specific immune system pathways. Classifying models discriminated histologically diagnosed OLD from OED based upon molecular data alone. Bioinformatic profiling showed that immune cell populations in OLP and OLD were consistent, and distinct from OED.

CONCLUSION

Molecular data shows that OLD is not a distinct pathological entity. Its transcriptomic and immunophenotypic profile is similar to OLP and distinct from OED. We recommend that oral lichenoid dysplasia not be used as a distinct pathological entity. Our data further supports exclusion of dysplasia in diagnosis of OLP.

Integration of transcriptome analysis with pathophysiological endpoints to evaluate cigarette smoke toxicity in an in vitro human airway tissue model

Exposure to cigarette smoke (CS) is a known risk factor in the pathogenesis of smoking-caused diseases, such as chronic obstructive pulmonary diseases (COPD) and lung cancer. To assess the effects of CS on the function and phenotype of airway epithelial cells, we developed a novel repeated treatment protocol and comprehensively evaluated the progression of key molecular, functional, and structural abnormalities induced by CS in a human in vitro air-liquid-interface (ALI) airway tissue model. Cultures were exposed to CS (diluted with 0.5 L/min, 1.0 L/min, and 4.0 L/min clean air) generated from smoking five 3R4F University of Kentucky reference cigarettes under the International Organization for Standardization (ISO) machine smoking regimen, every other day for 4 weeks (3 days per week, 40 min/day). By integrating the transcriptomics-based approach with the in vitro pathophysiological measurements, we demonstrated CS-mediated effects on oxidative stress, pro-inflammatory cytokines and matrix metalloproteinases (MMPs), ciliary function, expression and secretion of mucins, and squamous cell differentiation that are highly consistent with abnormalities observed in airways of smokers. Enrichment analysis on the transcriptomic profiles of the ALI cultures revealed key molecular pathways, such as xenobiotic metabolism, oxidative stress, and inflammatory responses that were perturbed in response to CS exposure. These responses, in turn, may trigger aberrant tissue remodeling, eventually leading to the onset of respiratory diseases. Furthermore, changes of a panel of genes known to be disturbed in smokers with COPD were successfully reproduced in the ALI cultures exposed to CS. In summary, findings from this study suggest that such an integrative approach may be a useful tool for identifying genes and adverse cellular events caused by inhaled toxicants, like CS.

Transcriptomic profiling of three-dimensional cholangiocyte spheroids long term exposed to repetitive Clonorchis sinensis excretory-secretory products

Background

Biliary tract infection with the carcinogenic human liver fluke, Clonorchis sinensis, provokes chronic inflammation, epithelial hyperplasia, periductal fibrosis, and even cholangiocarcinoma. Complications are proportional to the intensity and duration of the infection. In addition to mechanical irritation of the biliary epithelia from worms, their excretory-secretory products (ESPs) cause chemical irritation, which leads to inflammation, proliferation, and free radical generation.

Methods

A three-dimensional in vitro cholangiocyte spheroid culture model was established, followed by ESP treatment. This allowed us to examine the intrinsic pathological mechanisms of clonorchiasis via the imitation of prolonged and repetitive in vivo infection.

Results

Microarray and RNA-Seq analysis revealed that ESP-treated cholangiocyte H69 spheroids displayed global changes in gene expression compared to untreated spheroids. In ESP-treated H69 spheroids, 185 and 63 probes were found to be significantly upregulated and downregulated, respectively, corresponding to 209 genes (p < 0.01, fold change > 2). RNA-Seq was performed for the validation of the microarray results, and the gene expression patterns in both transcriptome platforms were well matched for 209 significant genes. Gene ontology analysis demonstrated that differentially expressed genes were mainly classified into immune system processes, the extracellular region, and the extracellular matrix. Among the upregulated genes, four genes (XAF1, TRIM22, CXCL10, and BST2) were selected for confirmation using quantitative RT-PCR, resulting in 100% similar expression patterns in microarray and RNA-Seq.

Conclusions

These findings broaden our understanding of the pathological pathways of liver fluke-associated hepatobiliary disorders and suggest a novel therapeutic strategy for this infectious cancer.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04717-2.

Functional characterization and transcriptomic profiling of a spheroid-forming midgut cell line from Helicoverpa zea (Lepidoptera: Noctuidae)

Insect cell lines have been frequently used in insect science research in recent years. Establishment of cell lines from specialized tissues like the lepidopteran midgut is expected to facilitate research efforts towards the understanding of uptake and metabolic properties, as well as the design of assays for use in pesticide discovery. However, the number of available lines from specialized tissues of insects and the level of understanding of the biological processes taking place in insect cells is far behind mammalian systems. In this study we examine two established cell lines of insect midgut origin, investigate their growth parameters and amenability to transfection and genetic manipulation, and test their potential to form spheroid-like 3D structures. Our results indicate that a midgut-derived cell line from Helicoverpa zea, RP-HzGUT-AW1, is amenable to genetic manipulation by transfection with a standard insect expression vector and has excellent ability to form spheroids. To further investigate the differentiation status of this line, we examined for expression of several candidate marker genes from different midgut cell types, enterocytes (ECs), Goblet cells (GCs), enteroendocrine cells (EEs) and intestinal stem cells (ISCs), indicating that both certain ISC and certain differentiated cell markers were present. To acquire a more detailed perspective of the differentiation landscape of the specific cells, we performed an RNAseq analysis of RP-HzGUT-AW1 grown either in 2D or 3D cultures. We hypothesize that RP-HzGUT-AW1 are in an "arrested" developmental stage between ISC and terminal differentiation. Furthermore, an enrichment of stress response and oxidoreductase genes was observed in the spheroid samples while no significant difference was evident in differentiation markers between cells grown in 2D and 3D. These results render RP-HzGUT-AW1 as the most well-characterized insect gut derived cell line so far, and lay the groundwork for future work investigating midgut cell lines application potential.

A connectivity map-based drug repurposing study and integrative analysis of transcriptomic profiling of SARS-CoV-2 infection

AIMS

The recent outbreak of COVID-19 has become a global health concern. There are currently no effective treatment strategies and vaccines for the treatment or prevention of this fatal disease. The current study aims to determine promising treatment options for the COVID-19 through a computational drug repurposing approach.

MATERIALS AND METHODS

In this study, we focus on differentially expressed genes (DEGs), detected in SARS-CoV-2 infected cell lines including "the primary human lung epithelial cell line NHBE" and "the transformed lung alveolar cell line A549". Next, the identified DEGs are used in the connectivity map (CMap) analysis to identify similarly acting therapeutic candidates. Furthermore, to interpret lists of DEGs, pathway enrichment and protein network analysis are performed. Genes are categorized into easily interpretable pathways based on their biological functions, and overrepresentation of each pathway is tested in comparison to what is expected randomly.

KEY FINDINGS

The results suggest the effectiveness of lansoprazole, folic acid, sulfamonomethoxine, tolnaftate, diclofenamide, halcinonide, saquinavir, metronidazole, ebselen, lidocaine and benzocaine, histone deacetylase (HDAC) inhibitors, heat shock protein 90 (HSP90) inhibitors, and many other clinically approved drugs as potent drugs against COVID-19 outbreak.

SIGNIFICANCE

Making new drugs remain a lengthy process, so the drug repurposing approach provides an insight into the therapeutics that might be helpful in this pandemic. In this study, pathway enrichment and protein network analysis are also performed, and the effectiveness of some drugs obtained from the CMap analysis has been investigated according to previous researches.

Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

BACKGROUND

Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling.

RESULTS

The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H₂O₂ (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H₂O₂-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H₂O₂ and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.

CONCLUSIONS

We speculated that drought-induced photosynthetic inhibition leads to H₂O₂ and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

Transcriptomic and metabolomic profiling reveals the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

BACKGROUND

Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear.

RESULTS

The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin).

CONCLUSION

These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.

RNA-Seq analysis reveals functionally relevant coding and non-coding RNAs in crossbred bull spermatozoa

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RNA-Seq analysis was done to characterize the transcriptome of crossbred bull spermatozoa.

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Among the 13,814 transcripts detected, 431 had FPKM > 1 and 13,673 had FPKM > 0 or < 1.

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Coding and non-coding RNAs account for 13,145 (95.15%) and 152 (1.1%), respectively.

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Sperm transcripts were mainly related to ribosome, oxidative phosphorylation and spliceosome pathways.

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qPCR analysis showed individual variations in transcriptional abundance of selected genes.

Sperm, which are believed to be transcriptionally and translationally inactive, synthesize RNA and proteins before there is gradual disappearance of the ribosome during chromatin compaction. Sperm transfer several functionally relevant transcripts to the oocyte, controlling maternal-zygotic transition and embryonic development. The present study was undertaken to profile and analyze sperm transcripts comprehensively using Next Generation Ribonucleic acid sequencing technology in Holstein Friesian x Tharparkar crossbred bulls. The results from global transcriptomic profiling revealed transcripts for 13,814 genes; of which 431 transcripts were expressed with >1 FPKM and 13,383 transcripts were expressed with >0 or <1 FPKM. The abundant mRNA transcripts of crossbred bull sperm were PRM1 and HMGB4. Gene ontology of transcripts with>1 FPKM revealed there was a major involvement in the structural constituent of ribosomes and translation. Results from pathway enrichment indicated the connection between ribosome, oxidative phosphorylation and spliceosome pathways and the transcripts of crossbred bull spermatozoa. The transcriptional abundance of selected genes, validated using RT-qPCR, indicated significant variations between bulls. Collectively, it may be inferred that the transcripts in crossbred bull sperm were heavily implicated in functions such as the structural constituent of ribosomes and translation, and pathways such as ribosome, oxidative phosphorylation and spliceosome. Further studies using larger sample sizes are required to understand the possible implications of transcriptomic variations on semen quality and fertility.

Molecular analysis of Chinese oesophageal squamous cell carcinoma identifies novel subtypes associated with distinct clinical outcomes

BACKGROUND

Oesophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer with a distinct incidence and prognosis. Molecular events driving ESCC subtypes and prognosis have not been established, and little is known regarding Chinese ESCC patients in Xinjiang, China.

METHODS

Here, we first integrated the genomic and transcriptomic data of 125 Chinese ESCC patients from Xinjiang Tumor Hospital (Urumqi, China). Two independent datasets of GSE53624 and The Cancer Genome Atlas (TCGA) ESCC were used to confirm the results of this study. DNA mutation and overall survival (OS) were analysed independently in the Chinese ESCC cohorts.

FINDINGS

Genomic analyses revealed a consistent mutation signatures and discordance among mutated genes across the different ESCC cohorts. In addition, transcriptomic profiling identified three Chinese ESCC subtypes associated with clinical and molecular attributes, including patient survival, lymph node status and genetic profile. Moreover, Chinese ESCC subtypes have distinct metabolic, inflammatory, metastatic, and cell proliferation features and unique potential therapeutics. Furthermore, the expression of cell cycle- and/or cell proliferation-related genes was higher in cyclin D1 (CCND1)-amplified tumours than in CCND1-normal tumours from Chinese ESCC patients, suggesting that CCND1 amplification promoted cell proliferation.

INTERPRETATION

Our findings provide a framework to facilitate the rational categorization of ESCC in Chinese patients and a foundation for new therapies.

FUNDING

This study was supported by the Research Fund of Key Laboratory of Xinjiang oncology (Grant no.2017D04006) and the Outstanding Youth Science and technology training project fund of Xinjiang, China (Grant no. 2017Q058).

Transcriptomic Analysis of the Cold-Pretreated Larimichthys crocea Showing Enhanced Growth Fitness in Cold Water

The large yellow croaker Larimichthys crocea is an economically important marine fish species endemic to China and East Asia. Ningde area of Fujian Province is a major L. crocea aquaculture and spawning center in China. L. crocea cultivated at the Zhoushan area appears to be popular but suffered high mortality in cold water during winter seasons. To reduce the mortality rate, we pretreated fish with cold shocks prior to shift to cold water. In this study, we show that cold-pretreated L. crocea 12 days after shift to cold water increase the viability by 5.77-fold compared to the unpretreated (live fish 75 versus 13, p value = 1.775e-06, n = 100). The highest loss of 31 out of 100 fish in the unpretreated group occurred in day 3 after temperature shift. To identify the pretreatment-induced transcriptional changes that may be attributed to cold-resistance and survival, we performed RNA-seq analysis of a total of 48 fish that were prior to and 48 h, 54 h, and 72 h after temperature shift in pretreated and unpretreated groups in sextuplicate. Transcriptomic profiling analysis indicates that pretreatment-induced transcriptional alterations of enzymes involved in FASI, β-oxidation, PUFA synthesis, oxidative phosphorylation, and molecular chaperones persisted after temperature shift, suggesting that these metabolic pathways may play a role in L. crocea cold-resistance and survival. Our study provides insights on how the pretreatment enhances the L. crocea growth fitness in cold water.

Toxicological effects of ambient fine (PM2.5-0.18) and ultrafine (PM0.18) particles in healthy and diseased 3D organo-typic mucocilary-phenotype models

The knowledge of the underlying mechanisms by which particulate matter (PM) exerts its health effects is still incomplete since it may trigger various symptoms as some persons may be more susceptible than others. Detailed studies realized in more relevant in vitro models are highly needed. Healthy normal human bronchial epithelial (NHBE), asthma-diseased human bronchial epithelial (DHBE), and COPD-DHBE cells, differentiated at the air-liquid interface, were acutely or repeatedly exposed to fine (i.e., PM_2.5-0.18, also called FP) and quasi-ultrafine (i.e., PM_0.18, also called UFP) particles. Immunofluorescence labelling of pan-cytokeratin, MUC5AC, and ZO-1 confirmed their specific cell-types. Baselines of the inflammatory mediators secreted by all the cells were quite similar. Slight changes of TNFα, IL-1β, IL-6, IL-8, GM-CSF, MCP-1, and/or TGFα, and of H3K9 histone acetylation supported a higher inflammatory response of asthma- and especially COPD-DHBE cells, after exposure to FP and especially UFP. At baseline, 35 differentially expressed genes (DEG) in asthma-DHBE, and 23 DEG in COPD-DHBE, compared to NHBE cells, were reported. They were involved in biological processes implicated in the development of asthma and COPD diseases, such as cellular process (e.g., PLA2G4C, NLRP1, S100A5, MUC1), biological regulation (e.g., CCNE1), developmental process (e.g., WNT10B), and cell component organization and synthesis (e.g., KRT34, COL6A1, COL6A2). In all the FP or UFP-exposed cell models, DEG were also functionally annotated to the chemical metabolic process (e.g., CYP1A1, CYP1B1, CYP1A2) and inflammatory response (e.g., EREG). Another DEG, FGF-1, was only down-regulated in asthma and specially COPD-DHBE cells repeatedly exposed. While RAB37 could help to counteract the down-regulation of FGF-1 in asthma-DHBE cells, the deregulation of FGR, WNT7B, VIPR1, and PPARGC1A could dramatically contribute to make it worse in COPD-DHBE cells. Taken together, these data contributed to support the highest effects of UFP versus FP and highest sensitivity of asthma- and notably COPD-DHBE versus NHBE cells.

Transcriptomic profiling of neural stem cell differentiation on graphene substrates

Graphene exhibits excellent mechanical strength, electrical conductivity and good biocompatibility, which make it a suitable candidate as a neural interfacing material in regenerative medicine and tissue engineering. Graphene is reported to promote both of neural stem cells (NSCs) proliferation and differentiation. However, the transcriptomes of 2D graphene-regulated NSC differentiation have not yet been investigated. To identify candidate genes, on which graphene may affect, we used next-generation RNA sequencing to analyze the transcriptome of NSCs differentiated for 21 days on a graphene substrate. These NSCs displayed highly enriched and differentially expressed genes compared with traditional cell culture in vitro. Of these, we identified motor protein genes that might regulate NSC differentiation, including cytoplasmic dynein and axonemal dynein genes, Ccdc108, Dnah5, and Dnah11. Furthermore, we analyzed the cell signaling pathway genes that might regulate NSC differentiation, and we constructed a protein-protein interaction network for the genes that are differentially expressed in NSCs on graphene compared to commercial tissue culture polystyrene substrates. We have identified genes potentially regulating the differentiation and migration of NSCs on graphene substrates, and our findings provide mechanistic evidence for the biological activities of graphene, especially in view of graphene-stem cell interactions.

Diffusible signal factor (DSF)-mediated quorum sensing modulates expression of diverse traits in Xanthomonas citri and responses of citrus plants to promote disease

Background

The gram-negative Xanthomonas genus contains a large group of economically important plant pathogens, which cause severe diseases on many crops worldwide. The diffusible signal factor (DSF) - mediated quorum sensing (QS) system coordinates expression of virulence factors in plant pathogenic Xanthomonas spp. However, the regulatory effects of this system during the Xanthomonas- plant interactions remain unclear from both the pathogen and host aspects.

Results

In this study, we investigated the in planta DSF- mediated QS regulon of X. citri subsp. citri (Xac), the causal agent of citrus canker. We also characterized the transcriptional responses of citrus plants to DSF-mediated Xac infection via comparing the gene expression patterns of citrus trigged by wild type Xac strain 306 with those trigged by its DSF- deficient (∆rpfF) mutant using the dual RNA-seq approach. Comparative global transcript profiles of Xac strain 306 and the ∆rpfF mutant during host infection revealed that DSF- mediated QS specifically modulates bacterial adaptation, nutrition uptake and metabolisms, stress tolerance, virulence, and signal transduction to favor host infection. The transcriptional responses of citrus to DSF-mediated Xac infection are characterized by downregulation of photosynthesis genes and plant defense related genes, suggesting photosynthetically inactive reactions and repression of defense responses. Alterations of phytohormone metabolism and signaling pathways were also triggered by DSF-mediated Xac infection to benefit the pathogen.

Conclusions

Collectively, our findings provide new insight into the DSF- mediated QS regulation during plant-pathogen interactions and advance the understanding of traits used by Xanthomonas to promote infection on host plants.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5384-4) contains supplementary material, which is available to authorized users.

Tlr7 deletion alters expression profiles of genes related to neural function and regulates mouse behaviors and contextual memory

The neuronal innate immune system recognizes endogenous danger signals and regulates neuronal development and function. Toll-like receptor 7 (TLR7), one of the TLRs that trigger innate immune responses in neurons, controls neuronal morphology. To further assess the function of TLR7 in the brain, we applied next generation sequencing to investigate the effect of Tlr7 deletion on gene expression in hippocampal and cortical mixed cultures and on mouse behaviors. Since previous in vivo study suggested that TLR7 is more critical for neuronal morphology at earlier developmental stages, we analyzed two time-points (4 and 18 DIV) to represent young and mature neurons, respectively. At 4 DIV, Tlr7 KO neurons exhibited reduced expression of genes involved in neuronal development, synaptic organization and activity and behaviors. Some of these Tlr7-regulated genes are also associated with multiple neurological and neuropsychiatric diseases. TLR7-regulated transcriptomic profiles differed at 18 DIV. Apart from neuronal genes, genes related to glial cell development and differentiation became sensitive to Tlr7 deletion at 18 DIV. Moreover, Tlr7 KO mice exhibited altered behaviors in terms of anxiety, aggression, olfaction and contextual fear memory. Electrophysiological analysis further showed an impairment of long-term potentiation in Tlr7 KO hippocampus. Taken together, these results indicate that TLR7 regulates neural development and brain function, even in the absence of infectious or pathogenic molecules. Our findings strengthen evidence for the role of the neuronal innate immune system in fine-tuning neuronal morphology and activity and implicate it in neuropsychiatric disorders.

Transcriptomic hallmarks of bone remodelling revealed by RNA-Seq profiling in blood of Arabian horses during racing training regime

The impact of exercises on young developing organisms is still of interest to researchers. Similarly like Thoroughbreds, Arabian horses competing at the race track. The high percent of lameness and loss of days in training are often the result of weakness in the condition of the musculoskeletal system. The objective of the presented study was to identify by RNA-Seq method, the possible skeletal system originating transcriptomic profile in peripheral blood of Arabian horses undergoing race training. Obtained results showed that one of the most significantly deregulated pathway involved in bone homeostasis was those involved in osteoclast differentiation. Among the significantly expressed molecules, we recognized twelve genes potentially involved in the metabolism of the skeletal system: BGLAP, CTSK, TYROBP, PDLIM7, SLC9B2, TWSG1, NOTCH2, IL6ST, VAV3, NFATc1, CLEC5A, TXLNG. The panel of identified genes should be evaluated as candidate biomarkers for bone homeostasis indicators of Arabians performing on race tracks to assess bone remodelling states during training for race track competitions.

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity

Background

Zucchini fruit is susceptible to chilling injury (CI), but the response to low storage temperature is cultivar dependent. Previous reports about the response of zucchini fruit to chilling storage have been focused on the physiology and biochemistry of this process, with little information about the molecular mechanisms underlying it. In this work, we present a comprehensive analysis of transcriptomic changes that take place after cold storage in zucchini fruit of two commercial cultivars with contrasting response to chilling stress.

Results

RNA-Seq analysis was conducted in exocarp of fruit at harvest and after 14 days of storage at 4 and 20 °C. Differential expressed genes (DEGs) were obtained comparing fruit stored at 4 °C with their control at 20 °C, and then specific and common up and down-regulated DEGs of each cultivar were identified. Functional analysis of these DEGs identified similarities between the response of zucchini fruit to low temperature and other stresses, with an important number of GO terms related to biotic and abiotic stresses overrepresented in both cultivars. This study also revealed several molecular mechanisms that could be related to chilling tolerance, since they were up-regulated in cv. Natura (CI tolerant) or down-regulated in cv. Sinatra (CI sensitive). These mechanisms were mainly those related to carbohydrate and energy metabolism, transcription, signal transduction, and protein transport and degradation. Among DEGs belonging to these pathways, we selected candidate genes that could regulate or promote chilling tolerance in zucchini fruit including the transcription factors MYB76-like, ZAT10-like, DELLA protein GAIP, and AP2/ERF domain-containing protein.

Conclusions

This study provides a broader understanding of the important mechanisms and processes related to coping with low temperature stress in zucchini fruit and allowed the identification of some candidate genes that may be involved in the acquisition of chilling tolerance in this crop. These genes will be the basis of future studies aimed to identify markers involved in cold tolerance and aid in zucchini breeding programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4500-9) contains supplementary material, which is available to authorized users.

Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass

Background

Heat stress is the primary abiotic stress limiting growth of cool-season grass species. The objective of this study was to determine molecular factors and metabolic pathways associated with superior heat tolerance in thermal bentgrass (Agrostis scabra) by comparative analysis of transcriptomic profiles with its co-generic heat-sensitive species creeping bentgrass (A. stolonifera).

Results

Transcriptomic profiling by RNA-seq in both heat-sensitive A. stolonifera (cv. ‘Penncross’) and heat-tolerant A. scabra exposed to heat stress found 1393 (675 up- and 718 down-regulated) and 1508 (777 up- and 731 down-regulated) differentially-expressed genes, respectively. The superior heat tolerance in A. scabra was associated with more up-regulation of genes in oxidative protection, proline biosynthesis, lipid hydrolysis, hemicellulose and lignin biosynthesis, compared to heat-sensitive A. stolonifera. Several transcriptional factors (TFs), such as high mobility group B protein 7 (HMGB7), dehydration-responsive element-binding factor 1a (DREB1a), multiprotein-bridging factor 1c (MBF1c), CCCH-domain containing protein 47 (CCCH47), were also found to be up-regulated in A. scabra under heat stress.

Conclusions

The unique TFs and genes identified in thermal A. scabra could be potential candidate genes for genetic modification of cultivated grass species for improving heat tolerance, and the associated pathways could contribute to the transcriptional regulation for superior heat tolerance in bentgrass species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4437-z) contains supplementary material, which is available to authorized users.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95

The mechanistic target of rapamycin (mTOR) and ryanodine receptor (RyR) signaling pathways regulate fundamental processes of neurodevelopment, and genetic mutations within these pathways have been linked to neurodevelopmental disorders. While previous studies have established that these signaling molecules are expressed in developing zebrafish, a detailed characterization of the ontogenetic profile of these signaling molecules is lacking. Thus, we evaluated the spatiotemporal expression of key transcripts in mTOR and RyR signaling pathways in wildtype zebrafish at 24, 72 and 120 hours post fertilization (hpf). We further determined whether transcriptional profiles of a subset of genes in both pathways were altered by exposure to PCB 95 (2,2′,3,5′,6-pentachlorobiphenyl), a pervasive environmental contaminant known to cause developmental neurotoxicity in mammalian systems via RyR-dependent mechanisms. Quantitative PCR revealed that transcription generally increased across development. Genes in the signaling pathway upstream of the mTORC1 complex, and the RyR-paralogs, ryr2a and ryr3, were robustly upregulated, and in situ hybridization of ryr3 coincided with a transcriptional shift from muscle to neuronal tissue after 24 hpf. Static waterborne exposure to PCB 95 beginning at 6 hpf significantly altered transcription of genes in both pathways. These changes were concentration- and time-dependent, and included downregulation of rptor, a member of the mTORC1 complex, at both 72 and 120 hpf, and increased transcript levels of the RyR paralog ryr2b and downstream target of RyR signaling, Wingless-type 2ba (wnt2ba) at 72 hpf. The detailed transcriptomic profiling of key genes within these two signaling pathways provides a baseline for identifying other environmental factors that modify normal spatiotemporal expression patterns of mTOR and RyR signaling pathways in the developing zebrafish, as illustrated here for PCB 95.

Identifying genomic targets for protein over-expression by "omics" analysis of Quiescent Escherichia coli cultures

Background

A cellular stress response is triggered upon induction of recombinant protein expression which feedback inhibits both growth as well as protein synthesis. In order to separate these two effects, it was decided to study “quiescent cultures” which continue to be metabolically active and express recombinant proteins even after growth cessation. The idea was to identify and up-regulate genes which are responsible for protein synthesis in the absence of growth. This would ensure that, even if growth were adversely affected post induction, there would be no attendant reduction in the protein expression capability of the cells. This strategy allowed us to design host strains, which did not grow better post induction but had significantly higher levels of protein expression.

Results

A quiescent Escherichia coli culture, which is able to sustain recombinant protein expression in the absence of growth, was analyzed by transcriptomic and proteomic profiling. Many genes involved in carbon utilization, biosynthesis of building blocks and stress protection were found to be up-regulated in the quiescent phase. Analysis of the global regulators showed that fis, which tends to get down-regulated as the cells enter stationary phase, remained up-regulated throughout the non-growing quiescent phase. The downstream genes regulated by fis like carB, fadB, nrfA, narH and queA were also up-regulated in the quiescent phase which could be the reason behind the higher metabolic activity and protein expression ability of these non-growing cells. To test this hypothesis, we co-expressed fis in a control culture expressing recombinant l-asparaginase and observed a significantly higher buildup of l-asparaginase in the culture medium.

Conclusions

This work represents an important breakthrough in the design of a superior host platform where a gene not directly associated with protein synthesis was used to generate a phenotype having higher protein expression capability. Many alternative gene targets were also identified which may have beneficial effects on expression ability.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0744-3) contains supplementary material, which is available to authorized users.

Transcriptomic dynamics in soybean near-isogenic lines differing in alleles for an aphid resistance gene, following infestation by soybean aphid biotype 2

BACKGROUND

Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed to investigate genome-wide changes in gene expressions of soybean near-isogenic lines (NILs) either with the Rag5 allele for resistance or the rag5 allele for susceptibility to the aphid following infestation with soybean aphid biotype 2.

RESULTS

The resistant (R)-NIL responded more rapidly to aphid infestation than the susceptible (S)-NIL, with differential expressions of 2496 genes during first 12 h of infestation (hai), compared to the aphid-free control. Although the majority of the differentially expressed genes (DEGs) in the R-NIL also responded to aphid infestation in S-NIL, overall the response time was longer and/or the magnitude of change was smaller in the S-NIL. In addition, 915 DEGs in R-NIL continued to be regulated at all time points (0, 6, 12, and 48 hai), while only 20 DEGs did so in S-NIL. Enriched gene ontology of the 2496 DEGs involved in plant defense responses including primary metabolite catalysis, oxidative stress reduction, and phytohormone-related signaling. By comparing R- vs. S-NIL, a total of 556 DEGs were identified. Of the 13 genes annotated in a 120-kb window of the Rag5 locus, two genes (Glyma.13 g190200 and Glyma.13 g190600) were differentially expressed (upregulated in S- or R-NIL), and another gene (Glyma.13 g190500) was induced up to 4-fold in the R-NIL at 6 and 12 h following aphid infestation.

CONCLUSIONS

This study strengthens our understanding of the defense dynamics in compatible and incompatible interactions of soybean and soybean aphid biotype 2. Several DEGs (e.g., Glyma.13 g190200, Glyma.13 g190500, and Glyma.13 g190600) near the Rag5 locus are strong candidate genes for further investigations.

Transcriptomic profiling and genetic analyses reveal novel key regulators of cellulase and xylanase gene expression in Penicillium oxalicum

BACKGROUND

The transition to a more environmentally friendly economy has prompted studies of modern biorefineries, including the utilization of low-value lignocellulose. The major challenge facing the widespread application of biorefineries is the high cost of enzymes that can efficiently hydrolyze recalcitrant cellulose to sugars. Penicillium oxalicum produces large amounts of plant-cell-wall-degrading enzymes, but their production is tightly controlled by complex regulatory networks, resulting in low yields of the native enzymes. Regulatory genes have been the targets of genetic engineering to improve enzyme production in microorganisms. In this study, we used transcriptomic profiling and genetic analyses to screen for and identify novel key regulators of cellulase and xylanase gene expression in P. oxalicum.

RESULTS

A comparative analysis of the transcriptomes of P. oxalicum HP7-1 on different carbon sources, including glucose, wheat bran, and wheat bran plus Avicel, identified 40 candidate genes regulating the expression of cellulolytic enzyme genes. Deletion mutants of 31 candidate genes were constructed in P. oxalicum ∆PoxKu70 and 11 resultant mutants showed significant changes in their filter-paper cellulase production compared with the parental strain ∆PoxKu70. Among these 11 mutants, ΔPoxCxrA, ΔPoxCxrB, and ΔPoxNsdD showed the most significant reduction in the enzyme production (96.8, 75.9, and 58.5%, respectively). Ten of these 11 genes are here reported to be involved in cellulase production for the first time. Further tests revealed that ΔPoxCxrA, ΔPoxCxrB, and ΔPoxNsdD displayed significantly reduced xylanase production, whereas ΔPoxCxrA produced negligible xylanase. Interestingly, ΔPoxCxrB and ΔPoxNsdD showed significantly increased β-glucosidase production. Real-time quantitative reverse transcription-PCR and an electrophoretic mobility shift assay (EMSA) showed that PoxCxrA, PoxCxrB, and PoxNsdD regulate the expression of one another, but the mode of regulation changes dynamically during the growth of fungal cells in the presence of cellulose. EMSA showed that PoxCxrA, PoxCxrB, and PoxNsdD directly bind the putative promoters of major cellulase and xylanase genes.

CONCLUSIONS

We have detected and identified three key new regulatory genes, PoxCxrA, PoxCxrB, and PoxNsdD, that directly and indirectly regulate the expression of cellulase and xylanase genes in P. oxalicum. This study provides novel insights into the regulatory mechanisms of fungal cellulase and xylanase gene expression.

A Transcriptomic Biomarker to Quantify Systemic Inflammation in Sepsis - A Prospective Multicenter Phase II Diagnostic Study

Development of a dysregulated immune response discriminates sepsis from uncomplicated infection. Currently used biomarkers fail to describe simultaneously occurring pro- and anti-inflammatory responses potentially amenable to therapy.

Marker candidates were screened by microarray and, after transfer to a platform allowing point-of-care testing, validated in a confirmation set of 246 medical and surgical patients. We identified up-regulated pathways reflecting innate effector mechanisms, while down-regulated pathways related to adaptive lymphocyte functions. A panel of markers composed of three up- (Toll-like receptor 5; Protectin; Clusterin) and 4 down-regulated transcripts (Fibrinogen-like 2; Interleukin-7 receptor; Major histocompatibility complex class II, DP alpha1; Carboxypeptidase, vitellogenic-like) described the magnitude of immune alterations. The created gene expression score was significantly greater in patients with definite as well as with possible/probable infection than with no infection (median (Q25/Q75): 80 (60/101)) and 81 (58/97 vs. 49 (27/66), AUC-ROC = 0.812 (95%-CI 0.755–0.869), p < 0.0001). Down-regulated lymphocyte markers were associated with prognosis with good sensitivity but limited specificity.

Quantifying systemic inflammation by assessment of both pro- and anti-inflammatory innate and adaptive immune responses provides a novel option to identify patients-at-risk and may facilitate immune interventions in sepsis.

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Pro- and anti-inflammatory signaling occurs simultaneously in the host response to infection.

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This response is currently monitored using biomarkers restricted to the pro-inflammatory component of innate immunity.

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We developed a biomarker panel consisting of 7 transcripts that can assess both facets at the point of care.

The concept that a selective, overwhelming systemic inflammation, the “Systemic Inflammatory Response Syndrome (SIRS)”, triggers organ failure subsequent to infection has lately been abandoned as it neglects parallel occurring anti-inflammatory responses or defects in the adaptive immune system.

The present findings suggest that a compound panel of nucleic acid biomarkers that was developed in independent training and verification cohorts and transferred to a point-of-care platform can more comprehensively describe the host response. Quantification of an enhanced innate immunity might inform studies of anti-inflammatory therapies, while measurement of derangements in specific immunity might guide strategies to restore immune effector functions.

Nitrogen deprivation-induced de novo transcriptomic profiling of the oleaginous green alga Botryococcus braunii 779

To assess the effect of nitrogen deprivation (ND), a moderately growing A-race Botryococcus braunii subisolate 779 was subjected to nitrogen deprivation for 3 days. De novo transcriptome was assembled and annotated by using Trinity software and Basic Local Alignment Search Tools (BLAST), respectively. Comparative analysis indicates that transcriptomes of A-races differ from those of B-races. Furthermore, majority of the homologous ESTs in A-race but not B-race transcriptomes were unknown sequences. Upon ND, level of photosynthetic transcripts, but not photosynthetic efficiency was downregulated. Unlike hydrocarbon contents, ESTs involved in hydrocarbon biosynthesis were not upregulated. Taken together, our results imply that A- and B-races belong to different B. braunii subspecies. Upon ND, excess photosynthetic transcripts are recycled for nitrogen; and hydrocarbon accumulation is not via de novo biosynthesis. Here we describe in details the data contents and analytic methodologies associated with the data uploaded to Gene Expression Omnibus (accession number GSE71296).

Transcriptional profiling of rat white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin

Polychlorinated dibenzodioxins are environmental contaminants commonly produced as a by-product of industrial processes. The most potent of these, 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), is highly lipophilic, leading to bioaccumulation. White adipose tissue (WAT) is a major site for energy storage, and is one of the organs in which TCDD accumulates. In laboratory animals, exposure to TCDD causes numerous metabolic abnormalities, including a wasting syndrome. We therefore investigated the molecular effects of TCDD exposure on WAT by profiling the transcriptomic response of WAT to 100μg/kg of TCDD at 1 or 4days in TCDD-sensitive Long-Evans (Turku/AB; L-E) rats. A comparative analysis was conducted simultaneously in identically treated TCDD-resistant Han/Wistar (Kuopio; H/W) rats one day after exposure to the same dose. We sought to identify transcriptomic changes coinciding with the onset of toxicity, while gaining additional insight into later responses. More transcriptional responses to TCDD were observed at 4days than at 1day post-exposure, suggesting WAT shows mostly secondary responses. Two classic AHR-regulated genes, Cyp1a1 and Nqo1, were significantly induced by TCDD in both strains, while several genes involved in the immune response, including Ms4a7 and F13a1 were altered in L-E rats alone. We compared genes affected by TCDD in rat WAT and human adipose cells, and observed little overlap. Interestingly, very few genes involved in lipid metabolism exhibited altered expression levels despite the pronounced lipid mobilization from peripheral fat pads by TCDD in L-E rats. Of these genes, the lipolysis-associated Lpin1 was induced slightly over 2-fold in L-E rat WAT on day 4.