Genome-wide Gene Expression Profiling Research Articles

The Myc-associated zinc finger protein epigenetically controls expression of interferon-γ-stimulated genes by recruiting STAT1 to chromatin

The MYC-Associated Zinc Finger Protein (MAZ) plays important roles in chromatin organization and gene transcription regulation. Dysregulated expression of MAZ causes diseases, such as glioblastoma, breast cancer, prostate cancer, and liposarcoma. Previously, it has been reported that MAZ controls the proinflammatory response in colitis and colon cancer via STAT3 signaling, suggesting that MAZ is involved in regulating immunity-related pathways. However, the molecular mechanism underlying this regulation remains elusive. Here, we investigate the regulatory effect of MAZ on interferon-gamma (IFN-γ)-stimulated genes via STAT1, a protein that plays an essential role in immune responses to viral, fungal, and mycobacterial pathogens. We demonstrate that about 80% of occupied STAT1-binding sites colocalize with occupied MAZ-binding sites in HAP1/K562 cells after IFN-γ stimulation. MAZ depletion significantly reduces STAT1 binding in the genome. By analyzing genome-wide gene expression profiles in the RNA-Seq data, we show that MAZ depletion significantly suppresses a subset of the immune response genes, which include the IFN-stimulated genes IRF8 and Absent in Melanoma 2. Furthermore, we find that MAZ controls expression of the immunity-related genes by changing the epigenetic landscape in chromatin. Our study reveals an important role for MAZ in regulating immune-related gene expression.

Bioactives and metabolites of Tetrastigma hemsleyanum root extract alleviate DSS-induced ulcerative colitis by targeting the SYK protein in the B cell receptor signaling pathway

Tetrastigma hemsleyanum is an endemic Chinese herb with a wide range of pharmacological activities, including anti-inflammatory, antiviral, antioxidant, antitumor, and immunomodulatory activities. However, the effect and mechanisms of the anti-inflammatory activity of T. hemsleyanum root extract against dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) have not yet been fully investigated. This study aimed to explore the therapeutic effect and molecular mechanisms of T. hemsleyanum root extract in DSS-induced UC mice and knockdown cells. T. hemsleyanum root extract was obtained and analyzed by high-performance liquid chromatography (HPLC). The therapeutic effects of T. hemsleyanum root extract on DSS-induced UC mice were evaluated by the disease activity index (DAI) score, colon length, serum inflammatory cytokines and oxidant/antioxidant levels, and histopathological features of the ileum and colon. Genome-wide gene expression profiles of ileal and colonic tissues were collected by transcriptomics, and signaling pathways were analyzed by the KEGG database. UC-related pathways were uploaded to the STRING database, then the protein-protein interactions (PPIs) were determined by Cytoscape, and the enriched genes were evaluated by real-time quantitative PCR (qPCR). The protein-ligand complexes were docked by AutoDock, and the genes were knocked down in Caco-2cells by shRNA. The non-targeted metabolomic profiling of ileal contents was analyzed by ultra-high-performance liquid chromatography (UHPLC), and gut microflora were sequenced by an Illumina MiSeq System. Ten components that alleviated UC symptoms in mice by decreasing the DAI and serum inflammatory cytokines and oxidant levels, promoting intestinal development, and increasing serum antioxidant levels were identified in T. hemsleyanum root extract. T. hemsleyanum root extract activated the B cell receptor signaling pathway in the colon tissue of UC mice, in which two components, rutin and astragaline, bound to the spleen tyrosine kinase (SYK) protein but also restored gut microflora diversity and increased the proportion of probiotics. Furthermore, metabolites of T. hemsleyanum root extract were involved in vitamin metabolism, fatty acid metabolism, and ferroptosis. The rutin and astragaline components of T. hemsleyanum root extract, by binding to SYK protein, activated the B cell receptor signaling pathway and restored gut microflora diversity to alleviate UC symptoms in mice.

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.

A variety of computational methods have been developed to identify functionally related gene modules from genome-wide gene expression profiles. Integrating the results of these methods to identify consensus modules is a promising approach to produce more accurate and robust results. In this application note, we introduce COMMO, the first web server to identify and analyze consensus gene functionally related gene modules from different module detection methods. First, COMMO implements eight state-of-the-art module detection methods and two consensus clustering algorithms. Second, COMMO provides users with mRNA and protein expression data for 33 cancer types from three public databases. Users can also upload their own data for module detection. Third, users can perform functional enrichment and two types of survival analyses on the observed gene modules. Finally, COMMO provides interactive, customizable visualizations and exportable results. With its extensive analysis and interactive capabilities, COMMO offers a user-friendly solution for conducting module-based precision medicine research. COMMO web is available at https://commo.ncpsb.org.cn/, with the source code available on GitHub: https://github.com/Song-xinyu/COMMO/tree/master.

BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells.

The BloodChIP Xtra database (http://bloodchipXtra.vafaeelab.com/) facilitates genome-wide exploration and visualization of transcription factor (TF) occupancy and chromatin configuration in rare primary human hematopoietic stem (HSC-MPP) and progenitor (CMP, GMP, MEP) cells and acute myeloid leukemia (AML) cell lines (KG-1, ME-1, Kasumi1, TSU-1621-MT), along with chromatin accessibility and gene expression data from these and primary patient AMLs. BloodChIP Xtra features significantly more datasets than our earlier database BloodChIP (two primary cell types and two cell lines). Improved methodologies for determining TF occupancy and chromatin accessibility have led to increased availability of data for rare primary cell types across the spectrum of healthy and AML hematopoiesis. However, there is a continuing need for these data to be integrated in an easily accessible manner for gene-based queries and use in downstream applications. Here, we provide a user-friendly database based around genome-wide binding profiles of key hematopoietic TFs and histone marks in healthy stem/progenitor cell types. These are compared with binding profiles and chromatin accessibility derived from primary and cell line AML and integrated with expression data from corresponding cell types. All queries can be exported to construct TF-gene and protein-protein networks and evaluate the association of genes with specific cellular processes.

Cyhexatin causes developmental toxic effects by disrupting endocrine system and inducing behavioral inhibition, apoptosis and DNA hypomethylation in zebrafish (Danio rerio) larvae

Cyhexatin (CYT), an organotin acaricide, is extensively utilized in developing countries to mitigate plant diseases caused by mites and minimize agricultural crop losses. However, the comprehensive mechanisms underlying the developmental stage of non-target organisms remain largely unexplored. In this study, zebrafish embryos were firstly exposed to CYT (0.06, 0.12, and 0.20 ng/mL, referred to as CYTL, CYTM, and CYTH, respectively) from 2 hpf (hours post fertilization) to 30 dpf (days post fertilization). No developmental toxicity was observed in the CYTL and CYTM groups, except for induced deformed phenotypes in the CYTM group at 120 hpf. However, exposure to CYTH resulted in significant reductions in spontaneous movement (24 hpf), heart rate (48 hpf), hatching rate (48 and 72 hpf), body weight (30 dpf), whole body length (30 dpf), and locomotion (30 dpf). Additionally, CYTH exposure induced morphological malformations, including spinal curvature, pericardial edema, and tail curvature in zebrafish larvae. Moreover, CYTH treatment induced apoptosis, increased reactive oxygen species (ROS) production, and resulted in significant reductions in free T3, cholesterol, estradiol, and testosterone levels in zebrafish larvae, while free T4 levels were increased. RNA-Seq analysis indicated that CYTH exposure led to significant alterations in the genome-wide gene expression profiles of zebrafish, particularly in the thyroid hormone and steroid biosynthesis signaling pathways, indicating endocrine disruption. Furthermore, CYTH exposure induced global DNA hypomethylation, reduced S-adenosylmethionine (SAM) levels and the SAM/S-adenosylhomocysteine (SAH) ratio, elevated SAH levels, and suppressed the mRNA expression of DNA methyltransferases (DNMTs) while also downregulating DNMT1 at both the gene and protein levels in zebrafish larvae. Overall, this study partially elucidated the developmental toxicity and endocrine disruption caused by CYT in zebrafish, providing evidence of the environmental hazards associated with this acaricide.

Circulating short chain fatty acids and fatigue in patients with head and neck cancer: A longitudinal prospective study

Fatigue among patients with head and neck cancer (HNC) has been associated with higher inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory and immunoregulatory effects. Therefore, this study aimed to examine the association between SCFAs and fatigue among patients with HNC undergoing treatment with radiotherapy with or without concurrent chemotherapy. Plasma SCFAs and the Multidimensional Fatigue Inventory-20 were collected prior to and one month after the completion of treatment in 59 HNC patients. The genome-wide gene expression profile was obtained from blood leukocytes prior to treatment. Lower butyrate concentrations were significantly associated with higher fatigue (p = 0.013) independent of time of assessment, controlling for covariates. A similar relationship was observed for iso/valerate (p = 0.025). Comparison of gene expression in individuals with the top and bottom 33% of butyrate or iso/valerate concentrations prior to radiotherapy revealed 1,088 and 881 significantly differentially expressed genes, respectively (raw p < 0.05). The top 10 Gene Ontology terms from the enrichment analyses revealed the involvement of pathways related to cytokines and lipid and fatty acid biosynthesis. These findings suggest that SCFAs may regulate inflammatory and immunometabolic responses and, thereby, reduce inflammatory-related symptoms, such as fatigue.

RNA-Pol II Transcription Elongation Factor FpRtfA Is Required for Virulence and Secondary Metabolism in Fusarium pseudograminearum

The soil-borne pathogen Fusarium pseudograminearum is capable of causing a highly destructive crown disease in wheat. The purpose of this study was to characterize the biological functions, such as of virulence and secondary metabolites (SMs), of a putative RNA-Pol II transcription elongation factor, FpRtfA, in F. pseudograminearum. The current study revealed that the deletion of FpRtfA reduced radial growth compared to wild type in F. pseudograminearum. In addition, FpRtfA was found important to conidiation and response to metal ions and oxidative stress. More importantly, the virulence to the wheat stem base or head was decreased when FpRtfA was deleted. Using genome-wide gene expression profiling, FpRtfA was found to regulate several processes related to the above phenotype, such as the carbohydrate metabolic process, and the response to oxidative stress and oxidoreductase activity, especially for SMs. Further, we proved that FpRtfA exerts its regulatory effect on the virulence of pathogens by modulating the expression of the PKS gene, but not the generation of DON. In conclusion, FpRtfA has important roles in growth, asexual development, and the response to metal ions and oxidative stress. More importantly, FpRtfA is required for SMs and full virulence in F. pseudograminearum.

A global view of transcriptome dynamics during flower development in Capsicum annuum L.

An analysis of genome-wide gene expression profiles during floral organ development can provide important clues about the molecular basis of gene functions and developmental processes. In this study, we analyzed the transcriptome data of 36 samples obtained during floral organ development from pepper ‘6421’ and detected 30 016 genes that were expressed in at least one sample. K-means clustering analysis was used to classify the data into 16 clusters based on the similarities between the dynamic expression profiles of genes. Of these, 15 clusters exhibited notable up-regulation or down-regulation trends in different developmental stages or tissues of floral organs. We identified transcription factors expressed at the early, medium, and late stages of bud development (F1, F5, F9). Transcription factor families such as AP2-ERF, MADS-box, MYB, bHLH, and NAC showed significant levels of enrichment. In comparison with genes expressed in vegetative tissues at different stages, certain genes were specifically up-regulated during flower development; among these, the number of genes specifically up-regulated during the stamen (Sta10) and bud tetrad development (F4) stages was the highest. Through extensive studies of the ABCDE model of flower development in Arabidopsis, we identified 17 ABCDE model candidate genes in pepper, most of which were up-regulated at specific stages of flower bud development. The expression data provided in this study is the most comprehensive dataset available for pepper to date and will serve as a resource for identifying the functions of many specific genes involved in flower development in pepper and other Solanaceae plants.

Pathway-level multi-omics analysis of the molecular mechanisms underlying the toxicity of long-term tacrolimus exposure

Tacrolimus (TAC)-based treatment is associated with nephrotoxicity and hepatotoxicity; however, the underlying molecular mechanisms responsible for this toxicity have not been fully explored. This study elucidated the molecular processes underlying the toxic effects of TAC using an integrative omics approach. Rats were sacrificed after 4 weeks of daily oral TAC administration at a dose of 5 mg/kg. The liver and kidney underwent genome-wide gene expression profiling and untargeted metabolomics assays. Molecular alterations were identified using individual data profiling modalities and further characterized by pathway-level transcriptomics-metabolomics integration analysis. Metabolic disturbances were mainly related to an imbalance in oxidant-antioxidant status, as well as in lipid and amino acid metabolism in the liver and kidney. Gene expression profiles also indicated profound molecular alterations, including in genes associated with a dysregulated immune response, proinflammatory signals, and programmed cell death in the liver and kidney. Joint-pathway analysis indicated that the toxicity of TAC was associated with DNA synthesis disruption, oxidative stress, and cell membrane permeabilization, as well as lipid and glucose metabolism. In conclusion, our pathway-level integration of transcriptome and metabolome and conventional analyses of individual omics profiles, provided a more comprehensive picture of the molecular changes resulting from TAC toxicity. This study also serves as a valuable resource for subsequent investigations aiming to understand the mechanism underlying the molecular toxicology of TAC.

In Vivo Genome-Wide Gene Expression Profiling Reveals That Haemophilus influenzae Purine Synthesis Pathway Benefits Its Infectivity within the Airways.

Haemophilus influenzae is a human-adapted bacterial pathogen that causes airway infections. Bacterial and host elements associated with the fitness of H. influenzae within the host lung are not well understood. Here, we exploited the strength of in vivo-omic analyses to study host-microbe interactions during infection. We used in vivo transcriptome sequencing (RNA-seq) for genome-wide profiling of both host and bacterial gene expression during mouse lung infection. Profiling of murine lung gene expression upon infection showed upregulation of lung inflammatory response and ribosomal organization genes, and downregulation of cell adhesion and cytoskeleton genes. Transcriptomic analysis of bacteria recovered from bronchoalveolar lavage fluid samples from infected mice showed a significant metabolic rewiring during infection, which was highly different from that obtained upon bacterial in vitro growth in an artificial sputum medium suitable for H. influenzae. In vivo RNA-seq revealed upregulation of bacterial de novo purine biosynthesis, genes involved in non-aromatic amino acid biosynthesis, and part of the natural competence machinery. In contrast, the expression of genes involved in fatty acid and cell wall synthesis and lipooligosaccharide decoration was downregulated. Correlations between upregulated gene expression and mutant attenuation in vivo were established, as observed upon purH gene inactivation leading to purine auxotrophy. Likewise, the purine analogs 6-thioguanine and 6-mercaptopurine reduced H. influenzae viability in a dose-dependent manner. These data expand our understanding of H. influenzae requirements during infection. In particular, H. influenzae exploits purine nucleotide synthesis as a fitness determinant, raising the possibility of purine synthesis as an anti-H. influenzae target. IMPORTANCE In vivo-omic strategies offer great opportunities for increased understanding of host-pathogen interplay and for identification of therapeutic targets. Here, using transcriptome sequencing, we profiled host and pathogen gene expression during H. influenzae infection within the murine airways. Lung pro-inflammatory gene expression reprogramming was observed. Moreover, we uncovered bacterial metabolic requirements during infection. In particular, we identified purine synthesis as a key player, highlighting that H. influenzae may face restrictions in purine nucleotide availability within the host airways. Therefore, blocking this biosynthetic process may have therapeutic potential, as supported by the observed inhibitory effect of 6-thioguanine and 6-mercaptopurine on H. influenzae growth. Together, we present key outcomes and challenges for implementing in vivo-omics in bacterial airway pathogenesis. Our findings provide metabolic insights into H. influenzae infection biology, raising the possibility of purine synthesis as an anti-H. influenzae target and of purine analog repurposing as an antimicrobial strategy against this pathogen.

Differentiated Embryonic Neurospheres from Familial Alzheimer's Disease Model Show Innate Immune and Glial Cell Responses.

Proteins involved in the Alzheimer's disease (AD), such as amyloid precursor protein (APP) and presenilin-1 (PS1), play critical roles in early development of the central nervous system (CNS), as well as in innate immune and glial cell responses. Familial AD is associated with the presence of APPswe and PS1dE9 mutations. However, it is still unknown whether these mutations cause deficits in CNS development of carriers. We studied genome-wide gene expression profiles of differentiated neural progenitor cells (NPCs) from wild-type and APPswe/PS1dE9 mouse embryo telencephalon. The occurrence of strong innate immune and glial cell responses in APPswe/PS1dE9 neurospheres mainly involves microglial activation, inflammatory mediators and chemokines. APPswe/PS1dE9 neurospheres augmented up to 100-fold CCL12, CCL5, CCL3, C3, CX3CR1, TLR2 and TNF-alpha expression levels, when compared to WT neurospheres. Expression levels of the glia cell marker GFAP and microglia marker Iba-1 were up to 20-fold upregulated in APPswe/PS1dE9 neurospheres. The secretome of differentiated APPswe/PS1dE9 NPCs revealed enhanced chemoattraction of peripheral blood mononuclear cells. When evaluating the inferred protein interaction networks constructed from the array data, an improvement in astrocyte differentiation in APPswe/PS1dE9 neurosphereswas evident in view ofincreased GFAPexpression. Transgenic NPCs differentiated into neural phenotypes presented expression patterns of cytokine, glial cells, and inflammatory mediators characteristic of APPswe/PS1dE9 adult animals. Consequently, the neurogenic niche obtained from differentiation of embryonic APPswe/PS1dE9 neurospheres spontaneously presents several alterations observed in adult ADbrains. Finally, our data strengthen pathophysiological hypotheses that propose an early neurodevelopmental origin for familial AD.

Pathogenicity and Transcriptomic Analyses of Two "Candidatus Liberibacter asiaticus" Strains Harboring Different Types of Phages.

"Candidatus Liberibacter asiaticus" is one of the putative causal agents of citrus Huanglongbing (HLB), a highly destructive disease threatening the global citrus industry. Several types of phages had been identified in "Ca. Liberibacter asiaticus" strains and found to affect the biology of "Ca. Liberibacter asiaticus." However, little is known about the influence of phages in "Ca. Liberibacter asiaticus" pathogenicity. In this study, two "Ca. Liberibacter asiaticus" strains, PYN and PGD, harboring different types of phages were collected and used for pathogenicity analysis in periwinkle (Catharanthus roseus). Strain PYN carries a type 1 phage (P-YN-1), and PGD harbors a type 2 phage (P-GD-2). Compared to strain PYN, strain PGD exhibited a faster reproduction rate and higher virulence in periwinkle: leaf symptoms appeared earlier, and there was a stronger inhibition in the growth of new flush. Estimation of phage copy numbers by type-specific PCR indicated that there are multiple copies of phage P-YN-1 in strain PYN, while strain PGD carries only a single copy of phage P-GD-2. Genome-wide gene expression profiling revealed the lytic activity of P-YN-1 phage, as evidenced by the unique expression of genes involved in lytic cycle, which may limit the propagation of strain PYN and lead to a delayed infection in periwinkle. However, the activation of genes involved in lysogenic conversion of phage P-GD-1 indicated it could reside within the "Ca. Liberibacter asiaticus" genome as a prophage form in strain PGD. Comparative transcriptome analysis showed that the significant differences in expression of virulence factor genes, including genes associated with pathogenic effectors, transcriptional factors, the Znu transport system, and the heme biosynthesis pathway, could be another major determinant of virulence variation between two "Ca. Liberibacter asiaticus" strains. This study expanded our knowledge of "Ca. Liberibacter asiaticus" pathogenicity and provided new insights into the differences in pathogenicity between "Ca. Liberibacter asiaticus" strains. IMPORTANCE Citrus Huanglongbing (HLB), also called citrus greening disease, is a highly destructive disease threatening citrus production worldwide. "Candidatus Liberibacter asiaticus" is one of the most common putative causal agents of HLB. Phages of "Ca. Liberibacter asiaticus" have recently been identified and found to affect "Ca. Liberibacter asiaticus" biology. Here, we found that "Ca. Liberibacter asiaticus" strains harboring different types of phages (type 1 or type 2) showed different levels of pathogenicity and multiplication patterns in the periwinkle plant (Catharanthus roseus). Transcriptome analysis revealed the possible lytic activity of type 1 phage in a "Ca. Liberibacter asiaticus" strain, which could limit the propagation of "Ca. Liberibacter asiaticus" and lead to the delayed infection in periwinkle. The heterogeneity in the transcriptome profiles, particularly the significant differences in expression of virulence factors genes, could be another major determinant of difference in virulence observed between the two "Ca. Liberibacter asiaticus" strains. These findings improved our understanding of "Ca. Liberibacter asiaticus"-phage interaction and provided insight into "Ca. Liberibacter asiaticus" pathogenicity.

Gene Co-Expression Analysis of Multiple Brain Tissues Reveals Correlation of FAM222A Expression with Multiple Alzheimer's Disease-Related Genes.

Alzheimer's disease (AD) is the most common form of dementia in the elderly marked by central nervous system (CNS) neuronal loss and amyloid plaques. FAM222A, encoding an amyloid plaque core protein, is an AD brain atrophy susceptibility gene that mediates amyloid-β aggregation. However, the expression interplay between FAM222A and other AD-related pathway genes is unclear. Our goal was to study FAM222A's whole-genome co-expression profile in multiple tissues and investigate its interplay with other AD-related genes. We analyzed gene expression correlations in Genotype-Tissue Expression (GTEx) tissues to identify FAM222A co-expressed genes and performed functional enrichment analysis on identified genes in CNS system. Genome-wide gene expression profiling identified 673 genes significantly correlated with FAM222A (p <  2.5×10-6) in 48 human tissues, including 298 from 13 CNS tissues. Functional enrichment analysis revealed that FAM222A co-expressed CNS genes were enriched in multiple AD-related pathways. Gene co-expression network analysis for identified genes in each brain region predicted other disease associated genes with similar biological function. Furthermore, co-expression of 25 out of 31 AD-related pathways genes with FAM222A was replicated in brain samples from 107 aged subjects from the Aging, Dementia and TBI Study. This gene co-expression study identified multiple AD-related genes that are associated with FAM222A, indicating that FAM222A and AD-associated genes can be active simultaneously in similar biological processes, providing evidence that supports the association of FAM222A with AD.

Abstract LB036: IRF8 regulates tumor cell sensitivity to intrinsic ferroptosis by repressing p53

Abstract Tumor cell resistance to ferroptosis, which is a recently discovered CTL induced cell death pathway, remains incompletely understood. We report here that interferon regulatory factor 8 (IRF8) functions as a regulator of tumor cell intrinsic ferroptosis. Genome-wide gene expression profiling identified ferroptosis pathway as an IRF8-regulated pathway in tumor cells. IRF8.KO tumor cells are resistant to intrinsic ferroptosis induction and also exhibit decreased ferroptosis in response to tumor specific CTL killing. Loss of IRF8 increases p53 express in tumor cells and knocking out Tp53 in IRF8.KO cells restored tumor cell sensitivity to intrinsic ferroptosis induction. We were able to show that treating tumor-bearing mice with IRF8-encoding plasmid NTC9385R-mIRF8 encapsulated in a DOTAP-cholesterol lipid nanoparticle significantly reduced tumor growth and increased the percentage of dead cells in the tumor. Our data therefore determine that IRF8 represses p53 expression to maintain tumor cell sensitivity to intrinsic ferroptosis. Citation Format: Dakota Poschel, Mercy Kehinde-Ige, John Klement, Dafeng Yang, Alyssa Merting, Natasha Savage, Huidong Shi, Kebin Liu. IRF8 regulates tumor cell sensitivity to intrinsic ferroptosis by repressing p53 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB036.

Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis

Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfishes represent a good example of metamorphosis in teleost fishes. During metamorphosis of flatfish, organ regression and neoformation occur, with one of the most notable changes being the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic to a post-metamorphic stage. We identified 29,019 differentially accessible chromatin regions and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profiles, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis in flatfish species.

Abstract 3927: Genome-wide screening and validation of molecular targets and biomarkers for lung cancer

Abstract The number of lung cancer patients who respond well to currently available standard therapies is still small, new molecular targeted therapies with companion diagnostics are eagerly needed. We have been developing new molecular therapies targeting oncoproteins with their cancer biomarkers as follows, i) To identify strongly expressed genes in 120 lung cancers by genome-wide gene expression profile analysis, ii) To verify the candidate genes for their scarce expression in 23 normal organs, iii) To validate the clinicopathological significance of their protein expression by tissue microarray covering about 400 lung cancers (non-small cell lung cancers (NSCLCs) and SCLCs), iv) To examine their importance in the growth and/or invasion of cancer cells by siRNA, small molecule inhibitor, cell permeable peptides targeting their function and/or antibody assays, and v) To analyze the oncogenic function of the target molecules. By this system, we identified 50 oncoproteins and selected a LSERT (lung cancer-specific receptor tyrosine kinase) as a candidate. Immunocytochemical and immunohistochemical analyses confirmed that LSERT protein was expressed in cytoplasm and cytoplasmic membrane of lung cancer cells, but it was hardly expressed in normal lung cells. Strong LSERT expression was associated with poorer prognosis for surgically-treated NSCLC patients, and it was an independent prognostic factor. Exogenous expression of LSERT increased the cell growth and invasion probably through its elevated kinase activity and subsequent phosphorylation of downstream proteins. Inhibition of LSERT expression by siRNAs or treatment with anti-LSERT antibody suppressed the growth of lung cancer cells. Our genome-wide screening might be a useful approach to identify target molecules for developing new therapeutics and diagnostics. LSERT could be a candidate cancer biomarker and therapeutic target for lung cancer. Citation Format: Yataro Daigo, Atsushi Takano, Yusuke Nakamura. Genome-wide screening and validation of molecular targets and biomarkers for lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3927.

Integrated analysis of genome-wide gene expression and DNA methylation profiles reveals candidate genes in ovary endometriosis.

The incidence of endometriosis (EMs), a common disease in gynecology, has increased over the years. Women suffer from the symptoms caused by EMs, such as chronic pelvic pain, dysmenorrhea, and infertility. However, the etiology and pathophysiology of EMs remain unclear. This study aimed to identify candidate genes of endometriosis through integrated analysis of genome-wide gene expression and DNA methylation profiles. Eutopic and ectopic endometrial tissues were collected from patients who were diagnosed as ovarian EMs. Genome-wide methylation profiling identified 17551 differentially methylated loci, with 9777 hypermethylated and 7774 hypomethylated loci. Differentially methylated loci were mainly concentrated in the gene body and intergenic regions. Genome-wide gene expression profiling identified 1837 differentially expressed genes (DEGs), with 1079 genes upregulated and 758 downregulated in ectopic groups. Integrated analysis revealed that DNA methylation was negatively correlated to gene expression in most genomic regions, such as exon, 3'UTR, 5'UTR, and promoter. We also identified promoter-related (53 downregulated and 113 upregulated) and enhancer-related DMGs (212 downregulated and 232 upregulated), which were significantly correlated to the gene expression. Further validation of the top-ranked genes belonging to differentially methylated genes (DMGs) and DEGs revealed that TMEM184A, GREM2, SFN, KIR3DX1, HPGD, ESR1, BST2, PIK3CG and RNASE1 were significant candidate genes in ovarian endometriosis. Our study revealed the significance of DNA methylation in the gene expression in ovary endometriosis, which provides new insights and a molecular foundation for understanding the underlying mechanisms of endometriosis.

The global regulator FpLaeB is required for the regulation of growth, development, and virulence in Fusarium pseudograminearum.

Fusarium pseudograminearum is a soil-borne pathogen that is capable of causing a highly destructive crown disease in wheat. Secondary metabolites (SMs), especially deoxynivalenol (DON), are the primary virulence factors during infection. Here, we characterised the global regulator FpLaeB, an orthologue of LaeB protein function, to regulate the SM in Aspergillus nidulans. Through the utility of the gene targeting approach, we found that the vegetative growth of the FpLaeB deletion mutant was drastically reduced compared to that of the wild type. FpLaeB was also important for conidiation because the FpLaeB deletion mutant formed fewer conidia in induced medium. In addition, the sensitivity of the FpLaeB deletion mutant to the cell wall integrity inhibitor was decreased, while its growth was more severely inhibited by the cell membrane inhibitor sodium dodecyl sulfate (SDS) than that of the wild type. More importantly, the virulence was decreased when the FpLaeB deletion mutant was inoculated onto the wheat stem base or head. Through genome-wide gene expression profiling, FpLaeB was found to regulate several processes related to the above phenotypes such as the carbohydrate metabolic process, which is an integral and intrinsic component of membranes, especially SMs. Furthermore, the generation of DON was impaired in the FpLaeB deletion mutant via ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay. These results showed that FpLaeB plays an important role in the growth, development, and maintenance of the cell wall, and in membrane integrity. More importantly, FpLaeB is required for SMs and full virulence in F. pseudograminearum.

Genome-Wide Gene Expression Profiling Reveals the Direct Effect of Dienogest on Ovarian Endometriotic Stromal Cells

Endometriosis affects up to 10% of women of reproductive age, causing dysmenorrhea, chronic pelvic pain, and infertility. The current key drug for endometriosis is dienogest, a progestin with high specificity for the progesterone receptor. To reveal the direct anti-endometriotic effect of dienogest on ovarian endometriotic cells, we investigated the genome-wide gene expression profiles of ovarian endometriotic stromal cells with (Dienogest group) or without dienogest treatment (Control group) and compared the groups’ gene expression profiles. We performed a gene ontology (GO) analysis and Ingenuity pathway analysis using these data. To validate the microarray data, we performed real-time RT-PCRs and immunohistochemistry for the differentially expressed genes between the two groups. Of 647 genes differentially expressed between the two groups, 314 genes were upregulated and 333 were downregulated in the Dienogest group versus the Control group. The GO analysis showed that the regulation of macrophage chemotaxis, the collagen catabolic process, and the proteoglycan biosynthetic process are the main biological processes closely associated with the differentially expressed genes. We identified 20 canonical pathways that were most significantly differentially expressed in the Dienogest group versus the Control group. We observed that matrix metalloproteinases (MMPs) are the genes in these pathways that are most closely associated with dienogest treatment. Of components involved in the regulation of macrophage chemotaxis, colony-stimulating factor 1 and macrophage-stimulating 1 are potential upstream regulators of MMPs and were observed herein to be suppressed by dienogest. Our results suggest that dienogest may thus exert its anti-endometriotic effect by directly suppressing MMPs.

Gene expression profiling of nasal inflammation induced by diesel particles using an in vivo system

Korean diesel particulate matter 20 (KDP20) is a pollutant comprising a complex mixture of carbon and chemical irritants. Although particulate matter and nasal inflammation are strongly associated, the underlying molecular mechanism based on systematic transcriptome analysis remains unknown. In this study, genome-wide gene expression profiles of mouse nasal tissues were determined following exposure to KDP20 for 5 and 10 days and compared with those of the control (n = 4/group). We identified 758 significant differentially expressed genes (DEGs) and classified them as 5-day-specific, 10-day-specific, and common among groups based on their expression patterns. The terms “regulation of alpha-beta T cell differentiation,” “macrophage differentiation,” and “cell adhesion mediated by integrin” were significantly enriched in each group. Receiver operating characteristic analysis revealed six genes as potential predictive biomarkers. The differential expression of these six genes was validated using quantitative RT-PCR (n = 3/group). Furthermore, a possible mechanism for nasal inflammation was suggested through the binding analysis between metal ions and genes. The genes identified in this study may play important roles in regulating the mechanism of nasal inflammation induced by diesel particles, especially immune cell regulation, and may function as markers for diesel particle-induced nasal inflammation.