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Results for “transcriptome analysis”

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PubMed2026

Transcriptomic and network analyses identify epigenetic regulators of drug-tolerant persister (DTP) subsets in EGFR-mutant HCC827 non-small cell lung cancer.

BACKGROUND: The clinical efficacy of osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), in EGFR-mutant non-small cell lung cancer (NSCLC) is limited by the inevitable acquired resistance. Drug-tolerant persister (DTP) cells, which survive initial therapy, are considered a key reservoir for this resistance. Understanding the molecular characteristics of DTPs is essential for developing strategies to prevent relapse. OBJECTIVE: This study aimed to characterize the transcriptomic landscape of osimertinib-tolerant DTP cells and identify key epigenetic regulators associated with the DTP phenotype in EGFR-mutant HCC827 NSCLC cells through integrated transcriptomic and network analyses. METHODS: We established an in vitro model of osimertinib tolerance using an EGFR-mutant (exon 19 deletion) HCC827 NSCLC cell line. Parental HCC827 cells and DTP subsets were subjected to transcriptomic analysis by RNA sequencing (RNA-seq). Differentially expressed genes were identified, followed by bioinformatics analyses, including Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analyses to identify key biological processes driving the DTP phenotype. Key findings were validated using quantitative real-time PCR (qPCR). RESULTS: Osimertinib treatment induced a morphologically distinct DTP population. Transcriptomic profiling revealed a marked shift in gene expression compared to parental cells. Functional enrichment analysis showed significant upregulation of epigenetic pathways. PPI network analysis identified a core module of eight hub genes, including histone deacetylases (HDAC5, HDAC9), sirtuins (SIRT1, SIRT2), and histone acetyltransferase (KAT2B). qPCR confirmed increased expression of HDAC5, HDAC9, and SIRT1. CONCLUSION: Epigenetic reprogramming accompanies the transition to an osimertinib-tolerant state in EGFR-mutant HCC827 cells. Targeting HDACs and sirtuins may represent a promising strategy to eliminate DTP subpopulations and delay or prevent acquired resistance.

Drug-tolerant persister↗

PubMed2003

Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway.

Type III secretion systems (TTSSs) are utilized by numerous bacterial pathogens to inject effector proteins directly into host cells. Using a whole-genome microarray, we investigated the conditions and regulatory factors that control the expression of the Pseudomonas aeruginosa TTSS. The transcriptional response of known TTSS genes indicates a hierarchical pattern of expression in which a set of secretion apparatus and regulatory genes is constitutively expressed. Further analysis of genes coordinately regulated with those encoding the TTSS led to the identification of a signaling pathway that originates from a membrane-associated adenylate cyclase and controls TTSS gene expression. Transcriptome analysis of mutants lacking the ability to synthesize cAMP or the cAMP binding protein Vfr implicated this pathway in the global regulation of host-directed virulence determinants, including the TTSS.

Adenylyl Cyclases↗

PubMed2025

Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal.

While the key aspects of genetic evolution and their clinical implications in clear cell renal-cell carcinoma (ccRCC) are well-documented, how genetic features co-evolve with the phenotype and tumor microenvironment (TME) remains elusive. Here, through joint genomic-transcriptomic analysis of 243 samples from 79 patients recruited to the TRACERx Renal study, we identify pervasive non-genetic intratumor heterogeneity, with over 40% not attributable to genetic alterations. By integrating tumor transcriptomes and phylogenetic structures, we observe convergent evolution to specific phenotypic traits, including cell proliferation, metabolic reprogramming and overexpression of putative cGAS-STING repressors amid high aneuploidy. We also uncover a co-evolution between the tumor and the T cell repertoire, as well as a longitudinal shift in the TME from an anti-tumor to an immunosuppressive state, linked to the acquisition of recurrently late ccRCC drivers 9p loss and SETD2 mutations. Our study reveals clinically-relevant and hitherto underappreciated non-genetic evolution patterns in ccRCC.

Journal Article↗

PubMed2025

Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1.

Improving wheat drought resilience and water use efficiency (WUE) is critical for sustaining productivity under increasing water scarcity. Here, we integrate genome-wide association study (GWAS), expression quantitative trait locus (eQTL) mapping, population-transcriptome analysis, and summary-data-based mendelian randomization (SMR), followed by functional validation using indexed EMS mutants and transgenic lines, to systematically identify key WUE regulators. GWAS across water conditions in 228 accessions identifies 73 quantitative trait loci (QTLs) for WUE-traits. Transcriptome profiling of 110 diverse accessions reveals 28 drought-responsive modules. eQTL mapping uncovers 146,966 regulatory variants, including condition-specific hotspots associated with key drought-related pathways. Integrative analysis underscores 85 high-confidence candidate genes, notably TaMYB7-A1. Overexpression of TaMYB7-A1 enhances photosynthesis, WUE, root development, and grain yield under drought condition by activating TaPIP2;2-B1 (water transport), TaRD20-D1 (stomatal regulation), and TaABCB4-B1 (root growth), reflecting reduced water loss and improved physiological resilience. Our study presents a comprehensive regulatory map and robust targets for wheat drought adaptation and resilient cultivar breeding.

Triticum↗

PubMed2003

A new tool for rheumatology: large-scale analysis of gene expression.

Large-scale analysis of gene expression with cDNA arrays is spreading over many biological fields, including rheumatology. In this report, we wish to explain the principle and main advantages of this tool in the context of our discipline. Until 1995, analysis of gene expression was conducted for a few genes at a time but DNA chips now allow one to monitor the expression of thousands of genes in a single experiment and analyze the transcriptome, i.e. the whole of the transcripts in a given cell or tissue. Whatever the platform used (macro- or microarrays, oligo-chips), this technology rests upon the hybridization of i) a set of cDNA clones tethered to a solid support (nylon or glass) as probes, and ii) labelled cDNAs that are reverse-transcribed from bulk mRNAs extracted from a cell or tissue sample as a target. The end result is information on the relative abundance of every mRNA between two or more samples. The transcriptome analysis has two main objectives in rheumatology: i) identifying a gene expression profile that is a hallmark of a pathology and using it for a diagnostic or prognostic purpose, and ii) gathering genes with similar changes of expression, which allows one to specify the identity of novel proteins involved in a well-known intracellular cascade of regulation or even to identify new cascades.

Arthritis, Rheumatoid↗

PubMed2000

[Cancer genome or the development of molecular portraits of tumors].

The rapid development of cancer genomics is due to important progresses in oncogenesis, human genome sequencing and emergence of new technologies in genome and transcriptome analysis. In this context, the aim of the French program 'Cartes d'Identites des Tumeurs--Molecular Portraits of Tumors' is to build a public data base containing a pan genome assessment of genome and transcriptome alterations in the major types of tumors as well as in relevant normal cells and experimental models. Data mining is done in the context of genome annotations and clinical and biological informations attached to the enrolled samples. The goal of the program is to define new tests useful for diagnostic procedures in clinical laboratories and new targets for biological treatments of tumors.

France↗

PubMed2026

Stage-specific remodeling of wingless-related integration sites (WNT) signaling during oocyte-to-embryo transition in pigs.

The WNT signaling pathway is a central regulator of cell polarity, adhesion, cytoskeletal dynamics, and lineage specification during early embryonic development. Although its roles have been extensively studied in murine and human models, the temporal regulation and pathway architecture of WNT signaling during early porcine development remain poorly defined. Here, we performed a comprehensive transcriptomic analysis to characterize WNT pathway dynamics across key stages of pig in vitro development, including immature oocytes (IMO), mature oocytes (MO), zygotes (ZY), cleaved embryos (2-4 cells; CL), and blastocysts (BL). Global analyses revealed major transcriptomic transitions (FDR <0.05; |Fold Change| ≥2) during oocyte maturation and blastocyst formation, whereas zygotes and cleaved embryos exhibited highly similar expression profiles. Module-based and gene-level analyses showed that oocyte maturation is associated with increased expression of extracellular WNT antagonists and components of the β-catenin destruction complex, together with selective regulation of Frizzled receptors, consistent with tight control of canonical WNT signaling at the MII stage. Following fertilization, this inhibitory configuration was partially relieved, alongside transient upregulation of specific WNT ligands, transcriptional mediators, and adhesion-related components during zygotic genome activation and early cleavage. At the blastocyst stage, WNT signaling became increasingly associated with planar cell polarity and epithelial organization modules. Together, the data reveal a highly dynamic and stage-specific restructuring of WNT signaling during early porcine development. Our findings indicate that precise temporal modulation-rather than uniform activation-of WNT pathway components accompanies the porcine oocyte-to-embryo transition, providing a molecular framework to better understand early developmental regulation and offering insights relevant to reproductive biotechnology and developmental biology.

Wnt Signaling Pathway↗

PubMed2025

Drought recovery in plants triggers a cell-state-specific immune activation.

All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organism, yet stress recovery is understudied. To investigate how plants recover from drought, we examine a fine-scale time series of RNA sequencing starting 15 min after rehydration following moderate drought. We reveal that drought recovery is a rapid process involving the activation of thousands of recovery-specific genes. To capture these rapid recovery responses in different Arabidopsis thaliana (A. thaliana) leaf cell types, we perform a single-nucleus transcriptome analysis at the onset of drought recovery, identifying a cell type-specific transcriptional state developing independently across cell types. To further validate the cell-type specific transcriptional changes observed during drought recovery, we employ spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH), revealing anatomical localization of recovery-induced gene expression programs across Arabidopsis leaf tissues. Furthermore, we reveal a recovery-induced activation of the immune system that occurs autonomously, and which enhances pathogen resistance in vivo in A. thaliana, wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Since rehydration promotes microbial proliferation and thereby increases the risk of infection, the activation of drought recovery-induced immunity may be crucial for plant survival in natural environments. These findings indicate that drought recovery coincides with a preventive defense response, unraveling the complex regulatory mechanisms that facilitate stress recovery in different plant cell types.

Arabidopsis↗

PubMed2026

COMMD9-regulated endothelial cell abnormality-induced hypercoagulability is associated with Budd-Chiari syndrome.

BACKGROUND: Budd-Chiari syndrome (BCS) presents diagnostic and treatment challenges owing to its insidious onset. Genetic variants associated with BCS vary geographically; in Asian populations, the condition is primarily caused by membranous obstruction composed of endothelial cells (ECs). A better understanding of the genetic pathogenesis of membranous BCS may offer new insights into disease mechanisms. METHODS: This study employed whole-exome sequencing to identify candidate genes responsible for EC abnormalities in 485 patients with membranous BCS and 329 patients with vascular malformations (VaMs). Functional investigations were conducted to validate the selected genes in vitro and in vivo. RESULTS: Whole-exome data revealed that the frequency of variants in the vascular function-related KLHDC2 exceeded that of JAK2 in BCS. Knockdown of KLHDC2 promoted adhesion and suppressed proliferation of ECs. In addition, 92 genes enriched for rare variants overlapped between BCS and VaMs. Systems biology analysis revealed two gene clusters, including COMMD9, enriched in proteins intolerant to loss-of-function mutations. Furthermore, suppression of COMMD9 impaired EC migration and tube formation, inhibited subintestinal angiogenic sprouting in zebrafish, and elevated EC adhesion. Transcriptomic analysis linked COMMD9 to EC abnormalities via the PI3K-Akt pathway. Commd9 knockdown promoted venous hypercoagulability in vivo following drug or ligation-induced stenosis. CONCLUSIONS: These findings indicate that multiple rare genetic variants, particularly in COMMD9, are involved in the development of membranous BCS by regulating hypercoagulability induced by EC abnormalities. These findings may help guide future clinical research towards improved understanding and treatment of BCS.

Budd–Chiari syndrome↗

PubMed2025

Effect of acupuncture on brain microenvironment in rats with post-stroke limb spasticity based on single-cell transcriptome sequencing technology.

OBJECTIVE: To investigate the possible mechanisms by which acupuncture improves post-stroke limb spasticity using single-cell sequencing technology. METHODS: Thirty-two rats were randomly assigned to four groups: Control, Sham, Model, and Acupuncture. The middle cerebral artery occlusion (MCAO) model was established, and the acupuncture groups received acupuncture treatment. After treatment, brain morphological changes and the degree of neurological impairment were assessed. The effect of acupuncture on the proportion of brain cell types in the ischemic penumbra of MCAO rats was analyzed using single-cell transcriptomics, and the expression and enrichment of differentially expressed genes were examined. Finally, selected differential genes were validated by Western blot and quantitative real-time polymerase chain reaction. RESULTS: Triphenyltetrazolium chloride staining showed that the infarct area in MCAO rats was significantly reduced after acupuncture. Garcia scoring, hematoxylin-eosin staining, Nissl staining, and terminal deoxynucleotidyl transferase dUTP nick end labeling demonstrated that acupuncture reduced brain damage. Enzyme-linked immunosorbent assay results showed that acupuncture significantly decreased serum inflammatory factors, including interleukin-1 beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α). Single-cell transcriptome analysis revealed marked changes in cell type proportions between the Acupuncture and Model groups. A total of 207 differential genes were identified, including 157 upregulated and 50 downregulated genes. Analysis of macrophage-specific differential genes in the ischemic penumbra showed enrichment in Gene Ontology terms such as Ras protein signal transduction and regulation of GTPase activity, and Kyoto Encyclopedia of Genes and Genomes pathways including lysosome, axon guidance, and mitogen-activated protein kinase signaling. S100a8 and leukocyte specific transcript 1 (LST1) were identified as key differential genes. CONCLUSION: These findings suggest that the key differential genes S100a8 and LST1 may alleviate post-stroke limb spasticity by regulating the inflammatory response in the ischemic penumbra.

Animals↗

PubMed2026

Interaction analysis of miRNA and mRNA reveals the regulatory mechanism of immune response in golden pompano (Trachinotus ovatus) spleen to Streptococcus iniae infection.

Streptococcus iniae is a major warm-water pathogen that cause high mortality and severe economic losses in golden pompano industry. In the present study, we performed the mRNA-miRNA integrated transcriptomic analysis of spleen of golden pompano challenged with S. iniae to explore the possible regulatory mechanism to bacterial infection. In total, we excavated 5072 DEGs, of which 2765 up-regulated and 2307 down-regulated genes. KEGG enrichment analysis indicated that the DEGs were primarily enriched in immune-related pathways, such as proteasome, cytokine-cytokine receptor interaction, p53 signaling pathway, lysosome, phagosome, Herpes simplex virus 1 infection. Additionally, a protein-protein interaction (PPI) network was constructed to extract hub genes. And the result showed that 4 hub genes, comprising cd4, il10, tnfsf2, myd88, may play vital roles in response to S. iniae infection. Furthermore, a total of 46 differentially expressed miRNAs (DEMs) were identified, containing 23 known and 23 novel DEMs. By integrating mRNA and miRNA joint analysis, we established a miRNA-mRNA regulatory network, including 12 miRNAs and 14 genes. Among them, novel-miR-357 were identified as a multi-target hub miRNA. These results provide important insights into the molecular regulatory mechanisms of immune response and inflammation processes in the defense of golden pompano against S. iniae infection.

Integrative interaction↗

PubMed2026

Extracellular vesicle miR-93-5p cargo regulates glomerular endothelial cell damage in Alport syndrome.

Modulation of miRNA expression in glomerular cells is associated with renal disease. Here, we investigated the role of miR-93-5p in mitigating glomerular damage in Alport syndrome and whether the disease-modifying activity of extracellular vesicles from human amniotic fluid stem cells (hAFSC-EVs) is mediated by their miR-93-5p cargo. We identified downregulation of miR-93-5p specifically in glomerular endothelial cells in Alport syndrome along disease progression. Silencing of miR-93-5p in hAFSC-EVs changed the transcriptomic and proteomic profile, regulating EV disease-modifying activity. Compared with naive hAFSC-EVs, silenced hAFSC-EVs did not rescue glomerular endothelial function in vitro and did not restore kidney function in vivo. We established that hAFSC-EVs regulate VEGFR1 and VEGFR2 signaling by miR-93-5p cargo transfer, highlighting that miR-93-5p can restore glomerular endothelial cell biology. Spatial transcriptomics analysis of hAFSC-EV-injected kidneys showed that these EVs can reverse pathways altered during disease progression by stimulating proregenerative processes, specifically in the glomerulus, by regulating miR-93-5p targets. Alteration of glomerular endothelial cell transcriptomics and miR-93-5p targets was also confirmed in biopsies of patients with Alport syndrome using spatial molecular imaging. We demonstrated the critical role of miR-93-5p in glomerular endothelial cells and the capability of hAFSC-EVs to regulate miR-93-5p and its targets in Alport syndrome.

Humans↗

PubMed2002

Laser capture microdissection of Plasmodium falciparum liver stages for mRNA analysis.

Plasmodium falciparum liver-stages are important targets for vaccine-induced protective immune responses and prophylactic treatment against malaria. Little is known of the gene expression profile of malaria parasites during their development inside hepatocytes. The sequencing of the P. falciparum genome and the development of DNA microarray technology give new opportunities to identify genes expressed during the development of Plasmodium. However, transcriptome analysis cannot currently be applied to the hepatic stages, due to difficulties in obtaining sufficient amounts of parasite material that lie among the large excess of host cell RNA. Here, we describe the isolation of liver-stages by a modified laser capture microdissection approach applied to human hepatocyte cultures infected with P. falciparum. RT-PCR amplification of several P. falciparum transcripts demonstrated the high quality of the RNA recovered after microdissection. This approach should enable analyses of P. falciparum transcriptome during its hepatic development and substantially assist the identification of new therapeutic and vaccine targets.

Animals↗

PubMed2025

Genomic and stress resistance characterization of Lactiplantibacillus plantarum GX17, a potential probiotic for animal feed applications.

UNLABELLED: Lactobacilli, recognized as beneficial bacteria within the human body, are celebrated for their multifaceted probiotic functions, including the regulation of intestinal flora, enhancement of body immunity, and promotion of nutrient absorption. This study comprehensively analyzed the genotypic and phenotypic characteristics of Lactiplantibacillus plantarum (L. plantarum) strains isolated from the intestines of healthy chicks and assessed their potential as probiotics. The assembled genome consists of 29,521,986 bp, and a total of 1,771 coding sequences (CDSs) were predicted. Based on the entire genome sequence analysis, 50 stress resistance genes and seven virulence factors were identified. The results of the phenotypic experiments showed that the strain had good resistance to high temperature, low temperature, acid, alkali, salt, artificial gastrointestinal fluid, and strong antioxidant capacity. Additionally, transcriptomic analysis confirmed that under stress conditions, the expression levels of key genes were significantly upregulated. Therefore, the phenotypic characteristics of L. plantarum GX17 align well with its genotypic features, demonstrating promising probiotic properties. This strain holds great potential as a probiotic candidate, and further investigation into its beneficial effects on human health is warranted. IMPORTANCE: In humans, Lactiplantibacillus plantarum may synergize with host microbiota to ameliorate dysbiosis-related pathologies, enhance immunomodulation, and facilitate micronutrient bioavailability. For livestock, its application could improve feed conversion ratios, suppress enteric pathogens through competitive exclusion, and mitigate antibiotic overuse, "a critical strategy in One Health frameworks." Further investigations into strain-specific mechanisms (e.g., postbiotic metabolites, quorum sensing regulation) are warranted to translate these genomic-phenotypic advantages into sustainable health solutions across species.

Probiotics↗

PubMed2026

Exogenous ABA enhances cold tolerance of Rhododendron yedoense var. poukhanense under subzero temperature: integrating physiology, transcriptome, and proteome.

Low temperature limits the growth and ornamental value of evergreen shrubs. Rhododendron yedoense var. poukhanense, an important ornamental shrub from Northeast China, frequently suffers freezing damage during winter. While exogenous abscisic acid (ABA) enhances cold tolerance in many plants, its molecular mechanisms at subzero temperatures remain poorly understood in non-model species lacking chromosome-level reference genomes. This study investigated the effects of exogenous ABA on freezing tolerance in R. yedoense var. poukhanense at -4 °C using an integrated physiological, transcriptomic, and proteomic approach. Cutting seedlings were subjected to four treatments: CK (22°C control), A (22°C + ABA), LT (-4°C), and ALT (-4°C + ABA). Photosynthetic pigments, osmotic regulation substances, antioxidant enzyme activities, and malondialdehyde (MDA) content were measured. Transcriptome sequencing and quantitative proteomics were performed, and transcriptome data were validated by quantitative real-time PCR (qRT-PCR) of 15 selected genes. ABA pretreatment reduced visible cold injury severity, partially preserved photosynthetic pigments, decreased MDA content by 28.7%, and promoted recovery of catalase (+43.6%), superoxide dismutase (+31.1%), and peroxidase (+20.0%) activities under freezing stress. Transcriptome analysis revealed 8, 444 differentially expressed genes (DEGs) in LT versus CK and 6, 481 DEGs in ALT versus CK, representing a 23% reduction in transcriptional reprogramming scope attributable to ABA priming. The ALT versus LT comparison identified only 1, 690 additional DEGs, indicating that most cold-responsive genes were pre-activated during the ABA priming phase. Proteome analysis identified 1, 461 differentially expressed proteins (DEPs) in ALT versus CK. Integrated analysis revealed extensive post-transcriptional regulation, with transcript-protein concordance of only 1.0-4.1%, and co-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in both omics layers. qRT-PCR validation confirmed high reliability of the transcriptome data (R2 = 0.8500). These findings demonstrate that exogenous ABA enhances freezing tolerance through multi-layered molecular regulation encompassing transcriptional buffering, translational reprogramming, and functional reallocation from photosynthesis to stress protection. This study provides the first integrated physiology-transcriptome-proteome framework for ABA-mediated freezing tolerance in an evergreen ornamental shrub and offers theoretical support for ABA-based winter protection strategies.

Rhododendron yedoense var. Poukhanense↗

PubMed2026

Cold-adapted RNA polymerase from Pseudomonas phage Njord improves synthesis of therapeutic mRNA.

An RNA polymerase identified in the genome of Pseudomonas phage Njord offers a promising tool for the synthesis of mRNA and other therapeutic nucleic acids. Originating from a marine microbial ecosystem, Njord RNAP transcribes RNA at high yield even under low temperature conditions. Key properties of the enzyme relevant to mRNA synthesis are presented including transcriptional fidelity, promoter specificity, incorporation of modified nucleotides, and the impurity profile of the RNA. Specific attention is given to the formation of contaminating double-stranded RNA (dsRNA) species. Analysis of transcription reactions shows that DNA-templated promoter-independent transcription is a major source of detectable dsRNA impurities and that Njord RNAP displays a minimal level of this activity. Consistent with the known inflammatory role of dsRNA in synthetic mRNA, transcriptomic analysis of cell culture and a live animal study demonstrates that mRNA synthesized with Njord RNAP elicits only a minimal immune response. This natural enzyme enables efficient mRNA synthesis at ambient temperature and produces transcripts essentially free of dsRNA, offering significant potential to streamline mRNA manufacturing processes.

DNA-Directed RNA Polymerases↗

PubMed2025

Multi-omics analyses provide insights into the molecular basis for salt tolerance of Phyla nodiflora.

The perennial herbaceous plant, Phyla nodiflora (Verbenaceae), which possesses natural resistance to multiple abiotic stresses, is widely used as a pioneer species in island ecological restoration. Due to the lack of information about its genome, the mechanism underlying its tolerance to environmental stresses, such as salinity, is almost entirely unknown. Here, we report on the high-quality genome of P. nodiflora that is 403.07 Mb in size, and which was assembled and anchored onto 18 pseudo-chromosomes. Genomic synteny revealed that P. nodiflora underwent two whole genome duplication events, which promoted the expansion of genes related to environmental adaptation and the biosynthesis of secondary metabolites. An integrated genomic and transcriptomic analysis suggested that salt stress tolerance in P. nodiflora is associated with the expansion and activated expression of genes related to abscisic acid (ABA) homeostasis and signaling. The expansion of ZEP family genes may contribute to the consistent increase in ABA levels under salt stress. Lysine acetylomic analysis revealed that exposure to salt led to widespread protein deacetylation, with these proteins primarily involved in signal transduction, carbohydrate transport and metabolism, and transcription regulation. Deacetylation of glutathione S-transferase increased enzymatic activities in response to salt-induced oxidative stress. Collectively, the genomic, transcriptomic, and lysine acetylomic analyses provide profound insight into the molecular basis of the adaptation of P. nodiflora to salt stress, and will be helpful to engineer salt-tolerant plants for ecological restoration.

Salt Tolerance↗

PubMed2001

Microarray analysis of nicotine-induced changes in gene expression in endothelial cells.

Cigarette smoking causes vascular endothelial dysfunction and is a major risk factor for cardiovascular diseases. Nicotine, a major constituent of cigarette smoke, has been shown to alter gene expression in endothelial cells; however, the regulatory pathways involved remain to be defined. We hypothesized that there might be distinct pathways that could be identified by systematic transcriptome analysis. Using the cDNA microarray approach, we ascertained the expression of over 4,000 genes in human coronary artery endothelial cells and identified a number of nicotine-modulated genes encoding a protein involving in signal transduction or transcriptional regulation. Among these were phosphatidylinositol phosphate kinase and diacylglycerol kinase, which are regulators of the inositol phospholipid pathway. Changes were also detected for transcription factors cAMP response element binding protein and nuclear factor-kappaB, of which the activities of both have been previously shown to be altered in nicotine-stimulated cells. The data from this study are relevant to understanding the mechanisms underlying the pathophysiological effect of nicotine and smoking, particularly on endothelial function and pathogenesis of atherosclerosis.

Cells, Cultured↗