RNA-seq Technique Research Articles

UniLIVER: a human liver cell atlas for data-driven cellular state mapping.

The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://lifeome.net/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a novel machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of "variant" cellular states analogy to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the "deviated" states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte "intermediate" states significantly indicate poor prognosis. Besides, we find the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues.

RNA sequencing reveals key factors modulating TNFα-stimulated odontoblast-like differentiation of dental pulp stem cells.

Inflammation is a complex host response to harmful infections or injuries, playing both beneficial and detrimental roles in tissue regeneration. Notably, clinical dentinogenesis associated with caries development occurs within an inflammatory environment. Reparative dentinogenesis is closely linked to intense inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs) into the dentin lineage. Understanding how inflammatory responses influence DPSCs is essential for elucidating the mechanisms underlying dentin and pulp regeneration. Given the limited data on this process, a broad approach is employed here to gain a deeper understanding of the complex mechanisms involved and to identify downstream signaling targets. This study aims to investigate the role of inflammation and the complement receptor C5L2 in the odontoblastic differentiation of DPSCs and the associated transcriptomic changes using poly-A RNA sequencing (RNA-seq). RNA-seq techniques provide insight into the transcriptome of a cell, offering higher coverage and greater resolution of its dynamic nature. Following inflammatory stimulation, DPSCs exhibit significantly altered gene profiles, including marked upregulation of key odontogenic genes, highlighting the critical role of inflammation in dentinogenesis. We demonstrate that TNFα-treated odontoblast-like differentiating DPSCs, under C5L2 modulation, exhibit significant differential gene expression and transcriptomic changes. The data presented may provide new avenues for experimental approaches to uncover pathways in dentinogenesis by identifying specific transcription factors and gene profiles.

RNA-seq shows Angiopoietin-like 4 promotes hepatocellular carcinoma progression by inducing M2 polarization of tumor-associated macrophages.

Hepatocellular carcinoma (HCC) represents a particularly aggressive form of cancer, characterized by its rapid progression and a complex interplay with the surrounding immune cellular environment. The primary objective of this study was to comprehensively investigate the role of ANGPTL4 in the context of HCC, utilizing RNA sequencing (RNA-seq) techniques to explore its impact on the M2 polarization of tumor-associated macrophages (TAM) and to uncover potential mechanisms driving HCC progression. To achieve this, we performed a transcriptome analysis of HCC cell lines, alongside cells obtained after co-culturing these lines with macrophages. By comparing gene expression profiles between the experimental groups exposed to ANGPTL4 and control groups, we aimed to identify specific molecular pathways associated with ANGPTL4's function. In addition to gene expression analysis, we employed flow cytometry to assess the polarization status of TAM. Furthermore, we utilized immunohistochemistry to evaluate the distribution of macrophages within HCC tissues and to quantify the expression levels of M2 macrophage markers. The results derived from RNA-seq analysis were particularly revealing; treatment with ANGPTL4 led to a significant upregulation of genes linked to M2 polarization, notably including CD206 and Arg1. In subsequent experimental observations, it became evident that ANGPTL4 not only facilitated the M2 polarization of macrophages but also enhanced the proliferation and migratory capacity of HCC cells through the upregulation of these same cytokines.

Dissection of Gene Expression at the Single-Cell Level: scRNA-seq.

Sequencing approaches that allowed for a better resolution of the transcriptome have been a major goal in the transcriptomics field since the development of RNA-seq techniques. While RNA-seq provides gene expression data from one entire sample in bulk, single-cell analysis allows for a better characterization of gene expression associated to specific cell types. Single-cell RNA-seq(scRNA-seq) is a reliable technique to unravel transcriptomic features of the tissues of interest dissociated at a single-cell level. The main feature of the single-cell technique is its ability to generate barcoded individual cells that allow for tracking the origin of thousands to millions of transcripts and reveal new cell types associated to diseases and different cell types and states. In this chapter, we discuss how scRNA-seq has become the gold standard to deepen the understanding of the gene expression with single-cell resolution.

Ribo-seq and RNA-seq analyses enrich the regulatory network of tomato fruit cracking

Tomato (Solanum lycopersicum L.), one of the most widely grown vegetable crops in the world, faces cracking problems before and after harvest. Fruit cracking reduces the commercial value and seriously affects the economic performance of the fruits by affecting the appearance and quality of the fruit. Clarifying the molecular mechanism underlying tomato fruit cracking is of great importance for selecting and breeding cracking-resistant varieties. At present, research on the molecular mechanism of tomato fruit cracking has made progress, but few studies have been conducted to explore the genes related to fruit cracking regulation using combined multi-omics analysis. We applied Ribo-seq (ribosome analysis sequencing) and RNA-seq (RNA-sequencing) techniques to uncover potential fruit cracking regulatory genes and improve the regulatory network of fruit cracking using extremely cracking-resistant (CR) and cracking-susceptible (CS) tomato genotypes. Combining these two sets of histological data and translation efficiency, 41 genes were identified to be associated with fruit cracking. The genes played functions on hormone synthesis (e.g. Solyc09g089580.4, Solyc07g049530.3), reactive oxygen species regulation (e.g. Solyc08g080940.3), cell wall metabolism (e.g. Solyc04g071070.2, Solyc03g123630.4), aquaporins activity (e.g. Solyc03g096290.3, Solyc10g083880.2), cuticle and wax composition, as well as mineral elements transport (e.g. Solyc10g006660.3, Solyc01g057770.3), while 10 of them were transcription factors (TF) (e.g. Solyc05g015850.4, Solyc08g078190.2). Based on the investigation of the interaction relationship between these genes, the synergistic regulation of multi-gene tomato fruit cracking was predicted. This study suggests that the synergistic action of transcription and translation is an important molecular mechanism in regulating tomato fruit cracking.

A systems biology approach unveils different gene expression control mechanisms governing the immune response genetic program in peripheral blood mononuclear cells exposed to SARS-CoV-2.

COVID-19 and other pandemic viruses continue being important for public health and the global economy. Therefore, it is essential to explore the pathogenesis of COVID-19 more deeply, particularly its association with inflammatory and antiviral processes. In this study, we used the RNA-seq technique to analyze mRNA and non-coding RNA profiles of human peripheral blood mononuclear cells (PBMCs) from healthy individuals after SARS-CoV-2 in vitro exposure, to identify pathways related to immune response and the regulatory post-transcriptional mechanisms triggered that can serve as possible complementary therapeutic targets. Our analyses show that SARS-CoV-2 induced a significant regulation in the expression of 790 genes in PBMCs, of which 733 correspond to mRNAs and 57 to non-coding RNAs (lncRNAs). The immune response, antiviral response, signaling, cell proliferation and metabolism are the main biological processes involved. Among these, the inflammatory response groups the majority of regulated genes with an increase in the expression of chemokines involved in the recruitment of monocytes, neutrophils and T-cells. Additionally, it was observed that exposure to SARS-CoV-2 induces the expression of genes related to the IL-27 pathway but not of IFN-I or IFN-III, indicating the induction of ISGs through this pathway rather than the IFN genes. Moreover, several lncRNA and RNA binding proteins that can act in the cis-regulation of genes of the IL-27 pathway were identified. Our results indicate that SARS-CoV-2 can regulate the expression of multiple genes in PBMCs, mainly related to the inflammatory and antiviral response. Among these, lncRNAs establish an important mechanism in regulating the immune response to the virus. They could contribute to developing severe forms of COVID-19, constituting a possible therapeutic target.

Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response.

Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.

CTIM-18. HIGH LEVEL OF MUTATIONAL LOAD AND DIVERSITY OF TUMOR INFILTRATING T LYMPHOCYTES ARE FAVORABLE PROGNOSTIC MARKERS FOR CANCER SURVIVAL IN CHILDREN WITH RECURRENT MEDULLOBLASTOMA DURING ADOPTIVE CELLULAR THERAPY

Abstract BACKGROUND Adoptive cellular therapy (ACT) has shown remarkable efficacy in some patients with solid tumors, resulting in durable complete responses. A key mechanism behind this success is the targeting of neoantigens by T cells. There is culminating evidence that tumor-infiltrating lymphocytes (TILs) have a major effect on the clinical attributes of human cancer and can influence the tumor response to various therapy regimens. We have been sequencing RNA isolated from patient’s tumors to evaluate their mutational burden and identify tumor-specific neoantigens. Additionally, we have identified the entire repertoire of tumor-infiltrating lymphocytes in patients with recurrent medulloblastoma. METHODS Total tumor RNA was extracted from resected brain tumor specimens and after we applied in-house bulk RNA-Seq and TCR-Seq techniques using rapid amplification of cDNA ends (RACE) technology with the addition of a common adapter at the 5’ end. RESULTS & CONCLUSIONS Analysis of the 22 tumor tissues revealed that the frequency of non-synonymous mutations varied dramatically more than 10-fold among patients with recurrent medulloblastoma undergoing adoptive cellular therapy (Re-MATCH protocol, FDA IND BB-14058). Patients with shorter overall survival exhibited non-synonymous mutation frequencies between 0.113 and 0.335 mutations per megabase (Mb). Children with prolonged overall survival had higher mutation frequencies, ranging from 0.6 to 1.1 mutations per Mb. These findings highlight the potential of using mutational burden as a biomarker for patient selection and treatment customization, ultimately aiming to improve outcomes in ACT for recurrent medulloblastoma. Up to 2000 unique TCR clones were found among TIL populations in patients who responded well to ACT. Patients with poor outcomes had significantly lower TCR diversity, with only 10-40 unique TCR clones among TILs. The correlation between TCR diversity among TILs and clinical outcomes in pediatric brain tumors underscores the importance of a diverse T cell repertoire for the success of ACT.

Data normalization of plasma miRNA profiling from patients with COVID-19

When using the reverse-transcription quantitative polymerase chain reaction (RT-qPCR) technique for quantitative assessment of microRNA (miRNA) expression, normalizing data using a stable endogenous gene is essential; however, no universally adequate reference gene exists. Therefore, in this study, we aimed to determine, via the RNA-Seq technique, the most adequate endogenous normalizer for the expression assessment of plasma miRNAs in patients with coronavirus disease 2019 (COVID-19). Two massive sequencing procedures were performed (a) to identify differentially expressed miRNAs between patients with COVID-19 and healthy volunteers (n = 12), and (b) to identify differentially expressed miRNAs between patients with severe COVID-19 and those with mild COVID-19 (n = 8). The endogenous normalizer candidates were selected according to the following criteria: (1) the miRNA must have a fold regulation = 1; (2) the miRNA must have a p-value > 0.990; and (3) the miRNAs that were discovered the longest ago should be selected. Four miRNAs (hsa-miR-34a-3p, hsa-miR-194-3p, hsa-miR-17-3p, and hsa-miR-205-3p) met all criteria and were selected for validation by RT-qPCR in a cohort of 125 patients. Of these, only hsa-miR-205-3p was eligible endogenous normalizers in the context of COVID-19 because their expression was stable between the compared groups.

R2R3-MYB transcription factor GmMYB68 is involved in the accumulation of soybean isoflavones

We aimed to investigate the regulatory function of the soybean transcription factor R2R3-MYB (GmMYB68) in isoflavone biosynthesis. Through comprehensive subcellular and chromosomal localization analyses, we found that GmMYB68 was predominantly localized to the nucleus and mapped to chromosome Gm04. Notably, SSR markers near this gene significantly correlated with seed isoflavone content. GmMYB68 overexpression markedly increased isoflavone contents, confirming its positive role in regulating isoflavone synthesis. GmMYB68 also played a crucial role in the response of soybean to abiotic stress. Using RNA-seq and yeast one-hybrid techniques, we discovered an intricate interaction between GmMYB68 and key isoflavone biosynthesis genes GmCHS7 and GmCHS8. These findings provide novel insights into the mechanisms underlying isoflavone biosynthesis. Furthermore, using yeast two-hybrid experiments, we identified proteins interacting with GmMYB68, suggesting roles in the synthesis of physiologically active compounds and abiotic stress response. We not only elucidated the regulatory mechanisms of GmMYB68 in isoflavone biosynthesis and abiotic stress response but also constructed a molecular network encompassing GmMYB68, GmCHS7, and GmCHS8. This network provides a theoretical basis for a better understanding of and strategies for improving soybean isoflavone biosynthesis.

Overexpression of the persimmon ABA receptor DkPYL3 gene alters fruit development and ripening in transgenic tomato

Abscisic acid (ABA) is a crucial plant hormone that regulates various aspects of plant development. However, the specific function of the ABA receptor PYL in fruit development has not been fully understood. In this study, we focused on DkPYL3, a member of the ABA receptor subfamily Ⅰ in persimmon, which exhibited high expression levels in fruit, particularly during the young fruit and turning stages. Through yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), protein inhibition assays, and RNA-seq techniques, we identified and characterized the DkPYL3 protein, which was found to inhibit the activity of protein phosphatase type 2 C (PP2C). By heterologous overexpressing (OE) persimmon DkPYL3 in tomatoes, we investigated the impact of the DkPYL3 gene on fruit development and ripening. DkPYL3-OE upregulated the expression of genes related to chlorophyll synthesis and development, leading to a significant increase in chlorophyll content in young fruit. Several fruit quality parameters were also affected by DkPYL3 expression, including sugar content, single fruit weight, and photosynthesis rate. Additionally, fruits overexpressing DkPYL3 exhibited earlier ripening and higher levels of carotenoids and flavonoids compared to wild-type fruits. These results demonstrate the pivotal role of DkPYL3 in ABA-mediated young fruit development, ripening onset, and fruit quality in transgenic tomatoes.

Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency.

Growing evidence suggests that activity-dependent gene expression is crucial for neuronal plasticity and behavioral experience. Enhancer RNAs (eRNAs), a class of long noncoding RNAs, play a key role in these processes. However, eRNAs are highly dynamic and are often present at lower levels than their corresponding mRNAs, making them difficult to detect using total RNA-seq techniques. Nascent RNA sequencing, which separates nascent RNAs from the steady-state RNA population, has been shown to increase the ability to detect activity-induced eRNAs with a higher signal-to-noise ratio. However, there is a lack of bioinformatic tools or pipelines for detecting eRNAs utilizing nascent RNA-seq and other multiomics data sets. In this study, we addressed this gap by developing a novel bioinformatic framework, e-finder, for finding eRNAs and have made it available to the scientific community. Additionally, we reanalyzed our previous nascent RNA sequencing data and compared them with total RNA-seq data to identify activity-regulated RNAs in neuronal cell populations. Using H3K27 acetylome data, we characterized activity-dependent eRNAs that drive the transcriptional activity of the target genes. Our analysis identified a subset of eRNAs involved in mediating synapse organization, which showed increased activity-dependent transcription after the potassium chloride stimulation. Notably, our data suggest that nascent RNA-seq with an enriched H3K27ac signal exhibits high resolution to identify potential eRNAs in response to membrane depolarization. Our findings uncover the role of the eRNA-mediated gene activation network in neuronal systems, providing new insights into the molecular processes characterizing neurological diseases.

An in-depth study of anthocyanin synthesis in the exocarp of virescens and nigrescens oil palm: metabolomic and transcriptomic analysis.

Oil palm (Elaeis guineensis Jacq.) is a very important tropical woody oil plant with high commercial and ornamental value. The exocarp of the oil palm fruit is rich in anthocyanosides and proanthocyanidins, which not only give it a bright colour, but also mark the maturity of the fruit. The study of the dynamic change pattern of anthocyanoside content and important anthocyanoside metabolism-related regulatory genes during oil palm ripening is conducive to the improvement of the ornamental value of oil palm and the determination of the optimal harvesting period of the fruits. We analyzed the virescens oil palm (AS) and nigrescens oil palm (AT) at 95 days (AS1, AT1), 125 days (AS2, AT2) and 185 days (AS3, AT3) after pollination were used as experimental materials for determining the changes in the total amount of anthocyanins as well as their metabolomics and transcriptomics studies by using the LC-MS/MS technique and RNA-Seq technique. The results showed that the total anthocyanin content decreased significantly from AS1 (119µg/g) to AS3 (23µg/g), and from AT1 (1302µg/g) to AT3 (170µg/g), indicating a clear decreasing trend during fruit development. Among them, the higher flavonoids in AS and AT included anthocyanins such as peonidin-3-O-rutinoside (H35), pelargonidin-3-O-rutinoside (H21), and cyanidin-3-O-glucoside (H7), as well as condensed tannins such as procyanidin B2 (H47), procyanidin C1 (H49), and procyanidin B3 (H48). Notably, nine genes involved in the anthocyanin biosynthetic pathway exhibited up-regulated expression during the pre-development stage of oil palm fruits, particularly during the AS1 and AT1 periods. These genes include: Chalcone synthase (CHS; LOC105036364); Flavanone 3-hydroxylase (F3H; LOC105054663); Dihydroflavonol 4-reductase (DFR; LOC105040724, LOC105048473); Anthocyanidin synthase (ANS; LOC105035842), UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT; LOC105039612); Flavonoid 3',5'-hydroxylase (F3'5'H; LOC105036086, LOC105044124, LOC105045493). In contrast, five genes demonstrated up-regulated expression as the fruits developed, specifically during the AS3 and AT3 periods. These genes include: Chalcone synthase (CHS; LOC105036921, LOC105035716); Chalcone isomerase (CHI; LOC105045978); UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT; LOC105046326); Flavonoid 3'-hydroxylase (F3'H; LOC105036086). Most of differentially expressed genes exhibited up-regulation during the early stages of fruit development, which may contribute to the elevated anthocyanin content observed in oil palm fruits of both types during the pre-developmental period. Furthermore, the expression levels of most genes were found to be higher in the AT fruit type compared to the AS fruit type, suggesting that the differential expression of these genes may be a key factor underlying the differences in anthocyanoside production in the exocarp of oil palm fruits from these two fruit types. The findings of this study provide a theoretical foundation for the identification and characterization of genes involved in anthocyanin synthesis in oil palm fruits, as well as the development of novel variations using molecular biology approaches.

Neddylation signaling inactivation by tetracaine hydrochloride suppresses cell proliferation and alleviates vemurafenib-resistance of melanoma

Tetracaine, a local anesthetic, exhibits potent cytotoxic effects on multiple cancer; however, the precise underlying mechanisms of its anti-cancer activity remain uncertain. The anti-cancer activity of tetracaine was found to be the most effective among commonly used local anesthetics in this study. After tetracaine treatment, the differentially expressed genes in melanoma cells were identified by the RNAseq technique and enriched in the lysosome signaling pathway, cullin family protein binding, and proteasome signaling pathway through Kyoto Encyclopedia of Genes and Genomes. Additionally, the ubiquitin-like neddylation signaling pathway, which is hyperactivated in melanoma, could be abrogated due to decreased NAE2 expression after tetracaine treatment. The neddylation of the pro-oncogenic Survivin, which enhances its stability, was significantly reduced following treatment with tetracaine. The activation of neddylation signaling by NEDD8 overexpression could reduce the antitumor efficacy of tetracaine in vivo and in vitro. Furthermore, vemurafenib-resistant melanoma cells showed higher level of neddylation, and potential substrate proteins undergoing neddylation modification were identified through immunoprecipitation and mass spectrometry. The tetracaine treatment could reduce drug resistance via neddylation signaling pathway inactivation in melanoma cells. These findings demonstrate that tetracaine effectively inhibits cell proliferation and alleviates vemurafenib resistance in melanoma by suppressing the neddylation signaling pathway, providing a promising avenue for controlling cancer progression.Graphical

Genome-Wide Identification and Expression Analysis of the Cys2His2 Zinc Finger Protein Gene Family in Flammulina filiformis.

Zinc finger proteins (ZFPs) are essential transcription factors in eukaryotes, particularly the extensively studied C2H2 family, which is known for its involvement in various biological processes. This research provides a thorough examination and analysis of the C2H2-ZFP gene family in Flammulina filiformis. Using bioinformatics tools, 58 FfC2H2-ZFP genes spread across 11 chromosomes were identified and scrutinized in detail for their gene structures, protein characteristics, and phylogenetic relationships. The study of phylogenetics and synteny sheds light on the evolutionary relationships among C2H2-ZFPs in F. filiformis and other fungi, revealing a complex evolutionary past. The identification of conserved cis-regulatory elements in the gene promoter regions suggests intricate functionalities, particularly in the developmental and stress response pathways. By utilizing RNA-seq and qRT-PCR techniques, the expression patterns of these genes were explored across different developmental stages and tissues of F. filiformis, unveiling distinct expression profiles. Notably, significant expression variations were observed in the stipe elongation region and pilei of various sizes, indicating potential roles in fruiting body morphogenesis. This study enhances our knowledge of the C2H2-ZFP gene family in F. filiformis and lays the groundwork for future investigations into their regulatory mechanisms and applications in fungal biology and biotechnology.

Transcriptomics and metabolomics analyses of graphene oxide toxicity on porcine alveolar macrophages

Graphene oxide (GO) is a type of nanomaterial widely used in tissue engineering, photocatalysis, and biomedicine. GO has been found to produce adverse effects on a broad range of cells and tissues. However, the molecular mechanisms underlying GO toxicity still remain to be explored. In this study, using porcine alveolar macrophages as a study model, we explored the toxic effects of GO and performed genome-wide detection of genes and metabolites associated with GO exposure using RNA-seq and liquid chromatograph mass spectrometer techniques. GO exposure significantly inhibited cell viability and induced apoptosis and oxidative stress in porcine alveolar macrophages. Further, GO exposure promoted cellular inflammation by upregulating the expression of pro-inflammatory cytokines (IL-6, IL-8, and IL-12). Transcriptomic analysis of GO-exposed cells revealed 424 differentially expressed genes. Functional enrichment analysis showed that the differentially expressed genes were significantly enriched in the pathways of Ribosome and oxidative phosphorylation (OXPHOS). In addition, metabolic analysis identified 203 differential metabolites, and these metabolites were significantly enriched in biosynthesis of cofactors, purine metabolism, and nucleotide metabolism. Integrative analyses of transcriptome and metabolome showed that OXPHOS was the most significantly enriched pathway and the involved genes were downregulated. This study revealed the toxic effects of GO on porcine alveolar macrophages and provided global insights to the metabolomic and transcriptomic alterations related to GO exposure. The results contributed to our understanding of the molecular mechanism of GO, and may further promote the detection of biomarkers for the prediction and control of GO toxicity.

Integrative transcriptomics and proteomics analysis provide a deep insight into goose astrovirus-host interactions during GAstV infection

Goose astrovirus (GAstV) is a newly discovered astrovirus. GAstV causes gout and death in 4- to -16-day-old goslings. For the past few years, fatal gout, the cardinal clinical symptom of gosling infected with GAstV, has been spreading rapidly in some goose Chinese farms, which caused continuous economic losses to the goose breeding industry in China. Currently, several underlying mechanisms involved in viral replication, inflammatory reaction, virions release, and viral pathogenesis of GAstV remain to be elucidated. In this study, we explored the mechanisms of GAstV-host interactions, the transcriptome and proteome profiles of GAstV-infected LMH cells were sequenced by RNA-seq and data-independent acquisition (DIA) techniques, respectively, and followed using an integrative analysis. Compared with uninfected LMH cells, a total of 322 differentially expressed genes (DEG) (195 up-regulated, 127 down-regulated) and 36 differentially expressed proteins (DEP) (31 up-regulated, 5 down-regulated) were detected. Nine DEGs were randomly selected for further validation by quantitative real-time polymerase chain reaction (qPCR). Through GO and KEGG enrichment analysis, DEG and DEP were significantly enriched in several important cellular signaling pathways, including MAPK, PI3K-Akt, cAMP, chemokine, calcium, phospholipase D, Ras, TNF, IL-17, Rap1, NF-kappa B signaling pathways, indicating that GAstV affects cell growth and immune signaling. This study provided an overview of changes in transcriptome and proteome profiles of GAstV-infected LMH cells, therefore, providing a crucial basis to further explore the mechanisms of GAstV-host interactions.

The Concerted Function of a Novel Class of Transcription Factors, ZBFs, in Light, Jasmonate and Abscisic Acid Signaling Pathways.

Several classes of transcription factors have been investigated in light signaling pathways that bind to the Light Responsive Elements (LREs) present in the promoters of light regulatory genes for transcriptional regulation. Some of these transcription factors have been shown to be binding to numerous promoters through genome-wide ChIP-on-chip (ChIP-chip) studies. Furthermore, through the integration of ChIP-seq and RNA-seq techniques, it has been demonstrated that a transcription factor modifies the expression of numerous genes with which it interacts. However, the mode of action of these transcription factors and their dependency on other regulators in the pathway has just started to be unraveled. In this review article, we focus on a particular class of transcription factors, ZBF (Z-box Binding Factor), and their associated partners within the same or other classes of transcription factors and regulatory proteins during photomorphogenesis. Moreover, we have further made an attempt to summarize the cross talk of these transcription factors with jasmonic acid, abscisic acid and salicylic acid mediated defense signaling pathways. This review offers an in-depth insight into the manner in which ZBFs and their interactors reshape cellular functions and plant behavior. The underlying principles not only contribute to a comprehensive understanding but also establish a framework for analyzing the interplay between early developmental events and hormone signaling, a regulation orchestrated by the ZBF family.

Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection

Long noncoding RNAs (lncRNAs) are crucial regulators of various biological processes. However, it remains unclear how lncRNAs can be involved in the immune response to Nocardia seriolae invasion in largemouth bass (Micropterus salmoides). Here we leveraged the whole transcriptome RNA-seq technique to screen lncRNAs associated with the head kidney infected with Nocardia seriolae. A total of 5,661 lncRNAs were identified, comprising 2,427 known lncRNAs and 3,234 novel lncRNAs. Among these, 531 lncRNAs were found to be differentially expressed, with 213 showing increased expression and 318 showing reduced expression. In these differentially expressed lncRNAs, 176 lncRNAs may have cis-regulatory relationships with 243 protein-coding genes. For example, MSTRG.17818.1, MSTRG.10160.1 target mapk1 and rela, respectively, thereby regulating gene expression. We then exploited Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to analyze the enrichment of target genes of lncRNAs. These target genes were found to be significantly enriched in immune signaling pathways, including RIG-I-like receptor signaling and Toll-like receptor signaling. Furthermore, we harnessed a total of 12 mRNAs, 33 miRNAs, and 167 lncRNAs to construct two lncRNA-miRNA-mRNA network maps. CeRNA maps revealed that some lncRNAs can competitively bind to the same miRNA and affect the expression of immune-related genes. For instance, MSTRG.13668.1 and MSTRG.5180.1 can simultaneously bind to mir-155–5p to increase irak4 expression. These findings suggest that lncRNAs may participate in the immune response process of infected largemouth bass with Nocardia seriolae. Overall, this work presents a thorough lncRNAs expression profile of Nocardia seriolae-infected largemouth bass and offers insights into the ceRNA regulatory processes that influence fish's immune response to bacterial infections.

Prediction Model for Therapeutic Responses in Ovarian Cancer Patients using Paclitaxel-resistant Immune-related lncRNAs.

Ovarian cancer (OC) is the deadliest malignant tumor in women with a poor prognosis due to drug resistance and lack of prediction tools for therapeutic responses to anti- cancer drugs. The objective of this study was to launch a prediction model for therapeutic responses in OC patients. The RNA-seq technique was used to identify differentially expressed paclitaxel (PTX)- resistant lncRNAs (DE-lncRNAs). The Cancer Genome Atlas (TCGA)-OV and ImmPort database were used to obtain immune-related lncRNAs (ir-lncRNAs). Univariate, multivariate, and LASSO Cox regression analyses were performed to construct the prediction model. Kaplan- meier plotter, Principal Component Analysis (PCA), nomogram, immune function analysis, and therapeutic response were applied with Genomics of Drug Sensitivity in Cancer (GDSC), CIBERSORT, and TCGA databases. The biological functions were evaluated in the CCLE database and OC cells. The RNA-seq defined 186 DE-lncRNAs between PTX-resistant A2780-PTX and PTXsensitive A2780 cells. Through the analysis of the TCGA-OV database, 225 ir-lncRNAs were identified. Analyzing 186 DE-lncRNAs and 225 ir-lncRNAs using univariate, multivariate, and LASSO Cox regression analyses, 9 PTX-resistant immune-related lncRNAs (DEir-lncRNAs) acted as biomarkers were discovered as potential biomarkers in the prediction model. Single-cell RNA sequencing (scRNA-seq) data of OC confirmed the relevance of DEir-lncRNAs in immune responsiveness. Patients with a low prediction score had a promising prognosis, whereas patients with a high prediction score were more prone to evade immunotherapy and chemotherapy and had poor prognosis. The novel prediction model with 9 DEir-lncRNAs is a valuable tool for predicting immunotherapeutic and chemotherapeutic responses and prognosis of patients with OC.