Transcriptome Research Articles

Insights into Molecular Mechanism of Secondary Xylem Rapid Growth in Salix psammophila

Salix psammophila C. Wang & C. Y. Yang is an important windbreak and sand-fixing shrub species in Northwest China, with excellent characteristics such as resistance to drought, wind, and sand. S. psammophila needs to be stubbed flat after several years of growth to continue to grow, otherwise, its growth rate will slow down and even begin to die. To understand the genetic regulatory mechanism of secondary growth in S. psammophila, cell structure and transcriptome analysis were performed on the secondary xylem and secondary phloem of stems. The results showed that the secondary xylem and the secondary phloem of S. psammophila were well developed at 1, 2, and 3-year-old stages, and the secondary growth changes mainly occurred in the secondary xylem at the 2 to 3-year-old stage, with a faster growth rate. The CSE2 and CSE1 genes that regulate CSE (caffeoyl shikimate esterase) have high sequence similarity (92% and 93%) with the CSE2 and CSE1 genes of the genus Populus, respectively, and regulate lignin biosynthesis. Notably, the expression levels of these two genes decreased in the secondary xylem of 3-year-old S. psammophila, indicating that the rapid growth of S. psammophila may be related to lignin biosynthesis. Weighted gene co-expression network analysis (WGCNA) was utilized to screen candidate TFs and genes involved in the secondary growth processes of S. psammophila, which were categorized into six co-expression modules. A total of 79 genes were selected from these co-expression modules, and co-expression network maps of the genes were constructed. The results indicate that the secondary growth of S. psammophila was regulated by a TF regulatory network. Interestingly, PLATZ TFs were involved in the rapid secondary growth and stress tolerance in S. psammophila. This hints that S. psammophila may promote secondary growth by increasing stress tolerance.

Integration of metabolomics and transcriptomics reveals the mechanism of TMEM30A downregulation induced FSGS podocyte injury.

Podocyte injury plays a critical role in the pathogenesis and progression of focal and segmental glomerulosclerosis (FSGS). Transmembrane protein 30A (TMEM30A) downregulation participates in podocyte injury. This study aimed to identify the critical pathways and molecules associated with the downregulation of TMEM30A in the context of FSGS podocyte injury. In our study, we found TMEM30A and podocyte marker Synaptopodin were significantly downregulated in kidney tissues from patients with FSGS compared to those in normal controls. Using transcriptomic and metabolomic analyses, we characterized Tmem30a knockdown (KD) and normal mouse podocytes to identify differentially expressed genes and metabolites. Then, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) network were constructed, and the differentially expressed genes and metabolites were enriched into glycolytic pathway. Furthermore, we found the key glycolytic enzymes were downregulated in patients with FSGS, podocyte-specific Tmem30aLoxP/LoxP; NPHS2-Cre mice, and Tmem30a KD mouse podocytes. For rescue experiments, shTmem30a-resistant cDNA (resTmem30a) was created to intervene Tmem30a KD mouse podocytes. And we observed that podocyte-related molecules were downregulated in the Tmem30a KD group, along with glycolysis-related molecules, but the resTmem30a partially reversed this trend. Our findings clarified TMEM30A downregulation initiates podocyte injury by reducing glycolysis-related molecules (ALDOA, HK2, LDHA, and GAPDH) in FSGS and have implications for early diagnosis, prevention, and treatment.

GDH1-dependent α-ketoglutarate promotes HBV transcription by modulating histone methylations on the cccDNA minichromosome.

Hepatitis B virus (HBV) hijacks host cell metabolism, especially host glutamine metabolism, to support its replication. Glutamate dehydrogenase 1 (GDH1), a mitochondrial enzyme crucial for glutamine metabolism, can interact with histone demethylases to regulate gene expression through histone methylation. However, the mechanisms underlying GDH1-mediated glutamine metabolism reprogramming and the roles of key metabolites during HBV infection remain unclear. Transcriptomic and metabolomic analyses of HBV-infected cell were performed. Both HBV-infected cells and humanized liver chimeric mice were used to elucidate the effect of glutamine metabolism on HBV. HBV infection leads to the abnormal activation of glutamine metabolism, including upregulation of key enzymes and metabolites involved in glutamine metabolism. The viral core protein (HBc) mediates the translocation of GDH1 into the nucleus, where GDH1 activates covalently closed circular DNA (cccDNA) transcription by converting glutamate to α-ketoglutarate (αKG). Mechanistically, the promoting effect of GDH1-derived αKG on cccDNA transcription is independent of its conventional role. Rather, αKG directly interacts with the lysine-specific demethylase KDM4A and enhances KDM4A demethylase activity to regulate αKG-dependent histone demethylation, controlling cccDNA transcription. Our findings highlight the importance of glutamine metabolism in HBV transcription and suggest that glutamine deprivation is a potential strategy for silencing cccDNA transcription.

Targeting CXCL8 signaling sensitizes HNSCC to anlotinib by reducing tumor-associated macrophage-derived CLU.

Although nutrition-starvation therapy for malignancies such as HNSCC is highly desirable, the clinical outcomes remain disappointing. Understanding the spatial heterogeneity of glucose deficiency can reveal the molecular mechanisms regulating cancer metabolism and identify therapeutic targets to improve effective nutrient-starvation therapies. Multiple omics data from RNA-seq, proteomics and spatial transcriptome analyses of HNSCC samples were integrated to analyze the spatial heterogeneity of glucose deficiency. In vivo and in vitro CXCL8 and CLU expression levels in tumor cells were determined using qPCR, immunohistochemistry and ELISA. The ability of CLU from TAMs to respond to tumor-derived CXCL8 was assessed using RNA sequencing, siRNA silencing, immunofluorescence and CCK-8 assays. A mouse subcutaneous xenograft model was used to assess the outcomes of nutrition-starvation therapy combined with blockade of CXCL8 signaling. A set of genes that was significantly upregulated in HNSCC under conditions of glucose deficiency was identified using integrating multiple omics data analyses. The upregulated gene set was used to determine the glucose-deficient area according to transcriptome data of HNSCC, and CXCL8 was one of the most highly upregulated genes. The levels of both CXCL8 mRNA and its protein IL-8 in cancer cells under conditions of glucose deficiency were increased in an NF-κB-dependent manner. Supplementary IL-8 stimulated TAMs to synthesize CLU, and CLU counteracted oxidative stress in HNSCC cells under conditions of glucose deficiency. Moreover, pharmacological blockade of CXCL8 signaling (reparixin) sensitized HNSCC cells to nutrient-starvation therapy (anlotinib) in two xenograft models. Our results provide novel evidence of a feedback loop between cancer cells and TAMs in glucose-deficient regions. HNSCC-derived CXCL8 favors endogenous antioxidative processes and confers therapeutic resistance to nutrient-starvation therapies in HNSCC.

Identified Candidate Genes of Semen Trait in Three Pig Breeds Through Weighted GWAS and Multi-Tissue Transcriptome Analysis

High-quality semen is an essential factor for the success of artificial insemination, and revealing the genetic structure of pig semen traits helps improve semen quality. This study aimed to identify candidate genes associated with semen traits in three pig breeds (Duroc, Landrace, and Yorkshire) through weighted GWAS and multi-tissue transcriptome analysis. In this study, to identify candidate genes associated with semen traits in Duroc, Landrace, and Yorkshire, we performed weighted GWAS in four traits (sperm motility, sperm progressive motility, sperm abnormality rate, and total sperm count) using 936 pigs and multi-tissue transcriptome analysis using 34 tissues RNA-seq data of 5457 pigs from FarmGTEx. It was found that 16, 9, and 12 significant SNPs associated with semen traits were identified in Duroc, Landrace, and Yorkshire, with corresponding 7, 5, and 7 candidate genes in these three breeds, respectively, which may be involved in mammal spermatogenesis, testicular function, and male fertility. Moreover, we not only found the same candidate gene DNAI2 as in previous studies but also found two new candidate genes PNLDC1 and RSPH3, which were identified simultaneously in both Landrace and Yorkshire. By integrating the GWAS and multi-tissue transcriptome analysis results, we found that candidate genes associated with semen traits of three pig breeds were highly expressed in the testis tissue. The three genotypes of rs320928244 had significant effects on the expression of the DYNLT1 gene in the testis tissue of Landrace. These results together showed that these candidate genes were mainly related to sperm motility defects. This study helps deepen the understanding of the genetic basis of semen traits and provides a theoretical foundation for improving the semen quality of Duroc, Landrace, and Yorkshire breeds.

A Cytochrome P450 AaCP1 Is Required for Conidiation and Pathogenicity in the Tangerine Pathotype of Alternaria alternata

Citrus Alternaria brown spot caused by the necrotrophic fungal pathogen of the tangerine pathotype of Alternaria alternata causes yield losses in global tangerine production. In this study, we focus on a cytochrome P450 monooxygenase encoding gene, Aacp1, for its role in the sporulation, toxin production, and virulence of the tangerine pathotype of Alternaria alternata. Aacp1-deficient mutants (∆Aacp1) produced significantly fewer conidia than the wild-type strain. Chemical assays demonstrated that Aacp1 plays a negative role in resistance to oxidant stress and biosynthesis of ACT toxin. Virulence assays revealed that ΔAacp1 fails to induce necrotic lesions on detached Hongjv leaves. Transcriptomic analyses of WT and ΔAacp1 revealed that many metabolic process genes were regulated. Furthermore, our results revealed a previously unrecognized Aacp1 affected the expression of the gene encoding a naphthalene dioxygenase (AaNdo1) for sporulation and full virulence. Overall, this study revealed the diverse functions of cytochrome P450 monooxygenase in the phytopathogenic fungus.

Impact of m6A Modification and Transcript Quantity on mRNA Composition in Plant Stress Granules.

Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of N6-methyladenosine (m6A) in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In Lupinus angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen to investigate their localization within SGs and assess m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The m6A was observed only during the assembly of SGs. In mutants of Arabidopsis thaliana with reduced levels of m6A, ECT2 (reader of m6A) was not observed in SGs, and poly(A) RNA levels and the number of SGs were reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs.

Regulatory Mechanisms of EPA and DHA Proportions in a PUFA-Producing Microalga, Schizochytrium sp. ATCC 20888: From the Biosynthesis and Storage Distribution Aspects.

Schizochytrium sp. ATCC 20888 is an important species for industrial polyunsaturated fatty acids (PUFA) production. This study investigated the regulatory mechanisms affecting the proportions of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in terms of biosynthesis and storage distribution. EPA and DHA possessed different accumulation patterns: EPA proportion increased over time, while DHA peaked at 48 h. EPA was predominantly integrated into triacylglycerol during the logarithmic phase and phosphatidylcholine during the stationary phase. Transcriptome analysis revealed that EPA synthesis involved the fatty acid synthase-elongase/desaturase system, while DHA depended mainly on PUFA synthase. Key enzymes, including elongase ELOVL7, diacylglycerol acyltransferase (g10562), and lysophosphatidylcholine acyltransferases (g8836 and g7540), show a positive correlation with EPA yield, highlighting their roles in its biosynthesis and storage. Additionally, phosphopantetheine adenylyl transferase (PPAT/COASY) and ADP-ribosylation factor 1_2 (ARF1_2) were identified as potential regulators of PUFA proportions. This study provided insights for genetic optimization of PUFA production inSchizochytrium.

Manipulation of the brown glume and internode 1 gene leads to alterations in the colouration of lignified tissues, lignin content and pathogen resistance in wheat.

Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defence. Here, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike, with its localisation observed in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signalling pathway. The identification and functional characterisation of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defence against pathogen infection in wheat.

Distinct mechanisms of electroacupuncture and manual acupuncture in modulating hypothalamic GnRH–tanycyte unit function of polycystic ovary syndrome

Abstract Background Polycystic ovary syndrome (PCOS) is a complex neuroendocrine disorder characterized by dysregulation of the hypothalamus. Both electroacupuncture (EA) and manual acupuncture (MA) have demonstrated therapeutic efficacy in the treatment of PCOS through improvements in hypothalamic function. However, the underlying mechanisms remain poorly understood. Gonadotropin-releasing hormone (GnRH) neurons are pivotal in regulating hypothalamic endocrine function, whereas tanycyte, a specialized glial cell type, potentially contribute to this process. Methods A dihydrotestosterone (DHT)-induced PCOS-like mouse model was used to investigate the effects of acupuncture. Tissue clearing and three-dimensional (3D) imaging were employed to visualize the hypothalamic GnRH neuronal network and assess postacupuncture modifications. Transcriptome sequencing was performed to identify changes in the gene profiles associated with EA and MA. Rax-CreERT2 transgenic mice were utilized to investigate the molecular targets of EA in tanycytes. Results EA significantly alleviated neuroendocrine dysfunction in PCOS-like mice by restoring the density and coverage of GnRH axonal projections. MA displayed similar therapeutic effects but had less pronounced effects on GnRH axons. Transcriptome analysis revealed distinct mechanisms for these two approaches: EA primarily regulates neuroglial plasticity, whereas MA predominantly targets neurotransmitter regulation. Both EA and MA share a common therapeutic target in the integrin family. Functional studies in Rax-CreERT2 transgenic mice confirmed that Itgb1 plays a critical role in maintaining the balance of hypothalamic GnRH–tanycyte unit during EA treatment. Conclusions EA exerts therapeutic effects on PCOS by targeting hypothalamic GnRH–tanycyte unit, with Itgb1 identified as a key factor. MA primarily functions through neurotransmitter regulation. These findings highlight potential hypothalamic targets and provide new insights into the distinct mechanisms of EA and MA.

Integrated Transcriptomic and Metabolomic Analysis of Rat PASMCs Reveals the Underlying Mechanism for Pulmonary Arterial Hypertension.

Pulmonary arterial hypertension (PAH) is a kind of pulmonary vascular lesion characterized by vasoconstriction and reshaping of small pulmonary arteries, ultimately resulting in increased pulmonary artery pressure and pulmonary vascular resistance, and eventually leading to right ventricular failure and death. This study was aimed to construct a platelet-derived growth factor BB (PDGF-BB)-induced rat pulmonary artery smooth muscle cells (PASMCs) model and conduct a combined transcriptomic and metabolomic analysis to identify proliferation-related targets, thereby enhancing understanding of the pathogenesis underlying PAH. Rat PASMCs were isolated and cultured in the presence or absence of PDGF-BB for 24 hours. Cells were collected for transcriptomics and metabolomics investigations. A total of 1288 differentially expressed genes (572 up-regulated and 716 down-regulated) were identified in PDGF-BB-treated rat PASMCs compared to control cells. Subsequently, Gene ontology (GO) enrichment analysis revealed that 791 enriched GO terms were significantly enriched in PDGF-BB treated cells. Similarly, 294 differential metabolic pathways were enriched in PDGF-BB treated cells according to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA) were performed on the differentially expressed genes (DEGs). It turned out that 7219 gene sets were more enriched in PDGF-BB treated cells. In addition, a total of 28 secondary differential metabolites were identified in PDGF-BB-treated rat PASMCs compared to control cells (p-value < 0.05 and VIP > 1). We speculate that Mylk, Pla2g4a, Gucy1b1, Adcy8, Adcy4, Gucy1a2, Col3a1, and Plcb4 are potential targets for the treatment of PAH.

EGFR inhibition augments the therapeutic efficacy of the NAT10 inhibitor Remodelin in Colorectal cancer.

Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide, and treatment options for advanced CRC are limited. The regulatory mechanisms of aberrant NAT10-mediated N4-acetylcytidine (ac4C) modifications in cancer progression remains poorly understood. Consequently, an integrated transcriptomic analysis is necessary to fully elucidate the role of NAT10-mediated ac4C modifications in CRC progression. NAT10 expression levels were analyzed in CRC samples and compared with those in corresponding normal tissues. The potential mechanisms of NAT10 in CRC were investigated using RNA sequencing, RNA immunoprecipitation sequencing, and acetylated RNA immunoprecipitation sequencing. Additional in vivo and in vitro experiments, including CCK-8 assays, colony formation and mouse xenograft models, were conducted to explore the biological role of NAT10-mediated ac4C modifications. We also evaluated and optimized a potential treatment strategy targeting NAT10. We found that NAT10 is highly expressed in CRC samples and plays a pro-oncogenic role. NAT10 knockdown led to PI3K-AKT pathway inactivation, thereby inhibiting CRC progression. However, treatment with the NAT10 inhibitor Remodelin induced only a limited and reversible growth arrest in CRC cells. Further epigenetic and transcriptomic analysis revealed that NAT10 enhances the stability of ERRFI1 mRNA by binding to its coding sequence region in an ac4C-dependent manner. NAT10 knockdown decreased ERRFI1 expression, which subsequently activated the EGFR pathway and counteracted the inhibitory effects on CRC. Based on these findings, we demonstrated that dual inhibition of NAT10 and EGFR using Remodelin and the EGFR-specific monoclonal antibody cetuximab resulted in improved therapeutic efficacy compared to either drug alone. Moreover, we observed that 5-Fluorouracil promoted the interaction between NAT10 and UBR5, which increased the ubiquitin-mediated degradation of NAT10, leading to ERRFI1 downregulation and EGFR reactivation. Triple therapy with Remodelin, cetuximab, and 5-Fluorouracil enhanced tumor regression in xenograft mouse models of CRC with wild-type KRAS, NRAS and BRAF. Our study elucidated the mechanism underlying 5-Fu-induced NAT10 downregulation, revealing that NAT10 inhibition destabilizes ERRFI1 mRNA through ac4C modifications, subsequently resulting in EGFR reactivation. A triple therapy regimen of Remodelin, cetuximab, and 5-Fu showed potential as a treatment strategy for CRC with wild-type KRAS, NRAS and BRAF.

Human MAIT cell response profiles biased toward IL-17 or IL-10 are distinct effector states directed by the cytokine milieu

Mucosal-associated invariant T (MAIT) cells are unconventional T cells that mediate rapid antimicrobial immune responses to antigens derived from microbial riboflavin pathway metabolites presented by the evolutionarily conserved MR1 molecules. MAIT cells represent a large pre-expanded T cell subset in humans and are involved in both protective immunity and inflammatory immunopathology. However, what controls the functional heterogeneity of human MAIT cell responses is still largely unclear. Here, combining functional and transcriptomic analyses, we investigate how MAIT cell response programs are influenced by the cytokine milieu at the time of antigen recognition. Activation by MR1-presented antigen together with IL-12 induces intermediate levels of IFNγ and TNF, as well as a regulatory profile with substantial IL-10 production and elevated expression of TIM-3, LAG-3, and PD-1. Activation by the combination of antigen and IL-12 induces a c-MAF-dependent program required for IL-10 production. The MAIT cell-derived IL-10 mediates both autocrine and paracrine immune regulation. In contrast, coactivation of MAIT cells with IL-18 induces IL-17, GM-CSF, IFNγ, and TNF, without IL-10. Notably, IL-18 dominantly counteracts IL-10 expression. The activation states biased toward IL-10 or IL-17 production are reversible and do not represent stable subsets. Finally, MR1-restricted TCR-mediated activation without cytokine coactivation drives primarily granzyme B cytolytic arming. Altogether, these findings demonstrate that human MAIT cells adapt their functional effector response during antigen recognition to cytokine cues in the microenvironment, and identify programs biased toward either regulatory c-MAF-dependent IL-10 expression, or an inflammatory IL-17 and GM-CSF profile.

A plant endophytic bacterium Burkholderia seminalis strain 869T2 increases plant growth under salt stress by affecting several phytohormone response pathways.

Due to global warming and gradual climate change, plants are subjected to a wide range of environmental stresses, adversely affecting plant growth and production worldwide. Plants have developed various mechanisms to overpower these abiotic stresses, including salt stress, drought, and high light intensity. Apart from their own defense strategies, plants can get help from the beneficial endophytic bacteria inside host plants and assist them in enduring severe growth conditions. A previously isolated plant endophytic bacteria, Burkholderia seminalis 869T2, from vetiver grass can produce auxin, synthesize siderophore, and solubilize phosphate. The B. seminalis 869T2 can colonize inside host plants and increase the growth of bananas, Arabidopsis, and several leafy vegetables. We further demonstrated that different growth parameters of Arabidopsis and pak choi plants were significantly increased after inoculating the B. seminalis 869T2 under normal, salt, and drought stress conditions compared to the mock-inoculated plants. Both transcriptome analysis and quantitative real-time PCR results showed that expression levels of genes related to phytohormone signal transduction pathways, including auxin, gibberellin, cytokinin, and abscisic acid were altered in Arabidopsis plants after inoculated with the strain 869T2 under salt stress, in comparison to the mock-inoculated control with salt treatments. Furthermore, the accumulation levels of hydrogen peroxide (H2O2), electrolyte leakage (EL), and malondialdehyde (MDA) were lower in the 869T2-inoculated Arabidopsis and pak choi plants than in control plants under salt and drought stresses. The plant endophytic bacterium strain B. seminalis 869T2 may affect various phytohormone responses and reduce oxidative stress damage to increase salt and drought stress tolerances of host plants.

Unveiling Photoperiod-Responsive Regulatory Networks in Tropical Maize Through Transcriptome Analysis

Background/Objectives: Maize (Zea mays L.), a crop of worldwide importance, owes its adaptability to diverse environments to its genetic variation. However, tropical maize exhibits intrinsic photoperiod sensitivity, limiting its adaptability to temperate regions. Photoperiod sensitivity significantly affects the flowering time and other agronomic traits, but the underlying molecular mechanisms remain poorly understood. In this study, the aim is to elucidate the transcriptional regulatory networks mediating photoperiod responses in tropical maize inbred line Su65, providing insights into improving photoperiod adaptability. Methods: RNA-seq analysis was carried out to investigate photoperiod-responsive genes and pathways in tropical line Su65 exposed to varying photoperiod conditions. Differential expression analysis, functional enrichment, and the construction of protein–protein interaction (PPI) networks were carried out to investigate transcriptional dynamics. Additionally, qRT-PCR was employed to confirm the expression patterns of key candidate genes and generate detailed temporal expression profiles. Results: A total of 1728 differentially expressed genes (DEGs) were identified, with significant enrichment in pathways such as stress responses, redox homeostasis, and secondary metabolite biosynthesis. A set of new key hub genes (such as Zm00001d048531, Zm00001d018821, Zm00001d034892, etc.) were identified through PPI network analysis. Temporal expression profiling of ZmPHYB1, ZmPHYC1, ZmFKF2, ZmGI2, and ZmPRR37a, the key genes involved in circadian rhythms, revealed distinct regulatory patterns of photoperiod-sensitive genes at different time points, highlighting their roles in flowering time regulation and developmental transitions. Conclusions: In this study, critical molecular networks underlying photoperiod sensitivity in tropical maize are uncovered and a foundation is provided for improving photoperiod adaptability through genetic improvement. By integrating RNA-seq and qRT-PCR, the research offers valuable insights into transcriptional dynamics and their role in maize development under photoperiodic regulation.

Cellular senescence induced by cholesterol accumulation is mediated by lysosomal ABCA1 in APOE4 and AD

BackgroundCellular senescence, a hallmark of aging, has been implicated in Alzheimer’s disease (AD) pathogenesis. Cholesterol accumulation is known to drive cellular senescence; however, its underlying mechanisms are not fully understood. ATP-binding cassette transporter A1 (ABCA1) plays an important role in cholesterol homeostasis, and its expression and trafficking are altered in APOE4 and AD models. However, the role of ABCA1 trafficking in cellular senescence associated with APOE4 and AD remains unclear.MethodsWe examined the association between cellular senescence and ABCA1 expression in human postmortem brain samples using transcriptomic, histological, and biochemical analyses. Unbiased proteomic screening was performed to identify the proteins that mediate cellular ABCA1 trafficking. We created ABCA1 knock out cell lines and mouse models to validate the role of ABCA1 in cholesterol-induced mTORC1 activation and senescence. Additionally, we used APOE4-TR mice and induced pluripotent stem cell (iPSC) models to explore cholesterol-ABCA1-senescence pathways.ResultsTranscriptomic profiling of the human dorsolateral prefrontal cortex from the Religious Order Study/Memory Aging Project (ROSMAP) cohort revealed the upregulation of cellular senescence transcriptome signatures in AD, which correlated with ABCA1 expression and oxysterol levels. Immunofluorescence and immunoblotting analyses confirmed increased lipofuscin-stained lipids and ABCA1 expression in AD brains and an association with mTOR phosphorylation. Discovery proteomics identified caveolin-1, a sensor of cellular cholesterol accumulation, as a key promoter of ABCA1 endolysosomal trafficking. Greater caveolin-1 expression was observed in APOE4-TR mouse models and AD human brains. Oxysterol induced mTORC1 activation and senescence were regulated by ABCA1 lysosomal trapping. Treatment of APOE4-TR mice with cyclodextrin reduced brain oxysterol levels, ABCA1 lysosome trapping, mTORC1 activation, and attenuated senescence and neuroinflammation markers. In human iPSC-derived astrocytes, the reduction of cholesterol by cyclodextrin attenuated inflammatory responses.ConclusionsOxysterol accumulation in APOE4 and AD induced ABCA1 and caveolin-1 expression, contributing to lysosomal dysfunction and increased cellular senescence markers. This study provides novel insights into how cholesterol metabolism accelerates features of brain cellular senescence pathway and identifies therapeutic targets to mitigate these processes.

Integrated transcriptomic and metabolomic analyses reveal critical gene regulatory network in response to drought stress in Dendrobium nobile Lindl

Abstract Background Dendrobium nobile Lindl belongs to the genus Dendrobium of the orchid family and is a valuable herbal medicine. Drought stress severely affects the growth of D. nobile Lindl; however, the specific regulatory mechanisms have not yet been elucidated. Results In the present study, we conducted a combined transcriptome and metabolome analysis of D. nobile Lindl stems under different drought stress conditions. Global transcriptomic changes were detected in Dendrobium under different drought stress conditions. KEGG enrichment analysis showed that the DEGs were enriched in plant hormone signal transduction; cutin, suberin, and wax biosynthesis; starch and sucrose metabolism; and the biosynthesis of various plant secondary metabolites. The differentially abundant metabolites (DAMs) detected using STEM analysis were enriched in pathways associated with glucosinolate biosynthesis and cyanoamino acid metabolism. We constructed a regulatory network for the drought tolerance of Dendrobium by weighted gene co-expression analysis. Conclusions The results showed that arginine and proline metabolism, glucosinolate biosynthesis and tyrosine metabolism pathways participated in regulating drought stress in D. nobile Lindl. Our study provides a theoretical basis for studying the drought resistance mechanisms in Dendrobium.

Increased distribution of carbon metabolic flux during de novo cytidine biosynthesis via attenuation of the acetic acid metabolism pathway in Escherichia coli.

Acetic acid, a by-product of cytidine synthesis, competes for carbon flux from central metabolism, which may be directed either to the tricarboxylic acid (TCA) cycle for cytidine synthesis or to overflow metabolites, such as acetic acid. In Escherichia coli, the acetic acid synthesis pathway, regulated by the poxB and pta genes, facilitates carbon consumption during cytidine production. To mitigate carbon source loss, the CRISPR-Cas9 gene-editing technique was employed to knock out the poxB and pta genes in E. coli, generating the engineered strains K12ΔpoxB and K12ΔpoxBΔpta. After 39h of fermentation in 500 mL shake flasks, the cytidine yields of strains K12ΔpoxB and K12ΔpoxBΔpta were 1.91 ± 0.04g/L and 18.28 ± 0.22g/L, respectively. Disruption of the poxB and pta genes resulted in reduced acetic acid production and glucose consumption. Transcriptomic and metabolomic analyses revealed that impairing the acetic acid metabolic pathway in E. coli effectively redirected carbon flux toward cytidine biosynthesis, yielding a 5.26-fold reduction in acetate metabolism and an 11.56-fold increase in cytidine production. These findings provide novel insights into the influence of the acetate metabolic pathway on cytidine biosynthesis in E. coli.

Multiomic Analysis Provided Insights into the Responses of Carbon Sources by Wood-Rotting Fungi Daldinia carpinicola

Daldinia carpinicola is a newly identified species of wood-rotting fungi, with substantial aspects of its biology and ecological function yet to be clarified. A Nanopore third-generation sequencer was employed for de novo genome assembly to examine the genetic characteristics. The genome consisted of 35.93 Mb in 46 contigs with a scaffold N50 of 4.384 Mb. Glycoside hydrolases and activities enzymes accounted for a large proportion of the 522 identified carbohydrate-active enzymes (CAZymes), suggesting a strong wood degradation ability. Phylogenetic and comparative analysis revealed a close evolutionary relationship between D. carpinicola and D. bambusicola. D. carpinicola and Hypoxylon fragiforme exhibited significant collinear inter-species genome alignment. Based on transcriptome and metabolomic analyses, D. carpinicola showed a greater ability to utilize sucrose over sawdust as a carbon source, enhancing its growth by activating glycolysis/gluconeogenesis and the citrate cycle. However, compared with sucrose, sawdust as a carbon source activated D. carpinicola amino acid biosynthesis and the production of various secondary metabolites, including diterpenoid, indole alkaloid, folate, porphyrin, and biotin metabolism. The study establishes a theoretical basis for research and applications in biological processes, demonstrating a strategy to modulate the production of secondary metabolites by altering its carbon sources in D. carpinicola.

Immune microenvironment spatial landscapes of tertiary lymphoid structures in gastric cancer

BackgroundTertiary lymphoid structures (TLS) correlate with tumour prognosis and immunotherapy responses in gastric cancer (GC) studies. However, understanding the complex and diverse immune microenvironment within TLS requires comprehensive analysis.MethodsWe examined the prognostic impact of TLS within the tumour core (TC) of 59 GC patients undergoing immunotherapy. Multispectral fluorescence imaging was employed to evaluate variations in immune cell infiltration across different TLS sites among 110 GC patients, by quantifying immune cell density and spatial characteristics. We also generated a single-cell transcriptomic atlas of TLS-positive (n = 4) and TLS-negative (n = 8) microenvironments and performed spatial transcriptomics (ST) analysis on two samples.ResultsTLS presence in the TC significantly correlated with improved immune-related overall survival (P = 0.049). CD8+LAG-3−PD-1+TIM-3−, CD4+PD-L1+, and CD4+FoxP3− T cell densities were significantly higher in the TLS within TC compared to tumour and stromal regions. Immune cells within TLS exhibited closer intercellular proximity than those outside TLS. Five key density and spatial characteristics of immune cells within TLS in the TC were selected to develop the Density and Spatial Score risk model. Single-cell RNA sequencing revealed strong intercellular interactions in the presence of TLS within the microenvironment. However, TLS-absent environment facilitated tumour cell interactions with immune cells through MIF- and galectin-dependent pathways, recruiting immunosuppressive cells. ST analysis confirmed that T and B cells co-localise within TLS, enhancing immune response activation compared to cancer nests and exerting a strong anti-tumour effect.ConclusionsTLS presence facilitates frequent cell-to-cell communication, forming an active immune microenvironment, highlighting the prognostic value of TLS.