Changes In Epithelial Gene Expression Research Articles

Proton Pump Inhibitors Modulate Gene Expression Profile in Esophageal Mucosa and Microbiome.

Proton pump inhibitors (PPIs) are commonly used to manage children with upper gastrointestinal symptoms and without a formal diagnosis. We investigated the effect of PPIs on esophageal mucosal transcriptome and active microbiota in children with normal esophagi. Furthermore, we examined whether the differences in host esophageal mucosal gene expression were driven by an underlying esophageal epithelial cell type composition. Using metatranscriptomics, the host transcriptional and active microbial profiles were captured from 17 esophageal biopsy samples (PPI naïve [PPI-], n = 7; PPI exposed [PPI+], n = 10) collected from children without any endoscopic and histologic abnormalities in their esophagus (normal esophagus). Deconvolution computational analysis was performed with xCell to assess if the observed epithelial gene expression changes were related to the cell type composition in the esophageal samples. The median (IQR) age of our cohort was 14 years (12-16) with female (63%) preponderance. Both groups were similar in terms of their demographics and clinical features. Compared with PPI-, the PPI+ had upregulation of 27 genes including the MUC genes. The cell type composition was similar between the PPI- and PPI+ groups. Prevotella sp and Streptococcus sp were abundant in PPI+ group. In children with normal esophagus, PPI exposure can be associated with upregulation of esophageal mucosal homeostasis and epithelial cell function genes in a cell-type independent manner, and an altered esophageal microbiome. Additional studies are warranted to validate our findings and to investigate the causal effect of PPIs on the normal esophageal epithelium and microbial communities.

Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia.

SummaryIntestinal homeostasis is underpinned by LGR5+ve crypt-base columnar stem cells (CBCs), but following injury, dedifferentiation results in the emergence of LGR5−ve regenerative stem cell populations (RSCs), characterized by fetal transcriptional profiles. Neoplasia hijacks regenerative signaling, so we assessed the distribution of CBCs and RSCs in mouse and human intestinal tumors. Using combined molecular-morphological analysis, we demonstrate variable expression of stem cell markers across a range of lesions. The degree of CBC-RSC admixture was associated with both epithelial mutation and microenvironmental signaling disruption and could be mapped across disease molecular subtypes. The CBC-RSC equilibrium was adaptive, with a dynamic response to acute selective pressure, and adaptability was associated with chemoresistance. We propose a fitness landscape model where individual tumors have equilibrated stem cell population distributions along a CBC-RSC phenotypic axis. Cellular plasticity is represented by position shift along this axis and is influenced by cell-intrinsic, extrinsic, and therapeutic selective pressures.

Gut/Oral Bacteria Variability May Explain the High Efficacy of Green Tea in Rodent Tumor Inhibition and Its Absence in Humans.

Consumption of green tea (GT) and GT polyphenols has prevented a range of cancers in rodents but has had mixed results in humans. Human subjects who drank GT for weeks showed changes in oral microbiome. However, GT-induced changes in RNA in oral epithelium were subject-specific, suggesting GT-induced changes of the oral epithelium occurred but differed across individuals. In contrast, studies in rodents consuming GT polyphenols revealed obvious changes in epithelial gene expression. GT polyphenols are poorly absorbed by digestive tract epithelium. Their metabolism by gut/oral microbial enzymes occurs and can alter absorption and function of these molecules and thus their bioactivity. This might explain the overall lack of consistency in oral epithelium RNA expression changes seen in human subjects who consumed GT. Each human has different gut/oral microbiomes, so they may have different levels of polyphenol-metabolizing bacteria. We speculate the similar gut/oral microbiomes in, for example, mice housed together are responsible for the minimal variance observed in tissue GT responses within a study. The consistency of the tissue response to GT within a rodent study eases the selection of a dose level that affects tumor rates. This leads to the theory that determination of optimal GT doses in a human requires knowledge about the gut/oral microbiome in that human.

Association of Bone Morphogenetic Protein 6 With Exocrine Gland Dysfunction in Patients With Sjögren's Syndrome and in Mice

Primary Sjögren's syndrome (SS) is characterized by autoimmune activation and loss of function in secretory epithelia. The present study was undertaken to investigate and characterize changes in the epithelia associated with the loss of gland function in primary SS. To identify changes in epithelial gene expression, custom microarrays were probed with complementary RNA (cRNA) isolated from minor salivary glands (MSGs) of female patients with primary SS who had low focus scores and low salivary flow rates, and the results were compared with those obtained using cRNA from the MSGs of sex-matched healthy volunteers. The effect of bone morphogenetic protein 6 (BMP-6) on salivary gland function was tested using adeno-associated virus-mediated gene transfer to the salivary glands of C57BL/6 mice. A significant increase in expression of BMP-6 was observed in RNA isolated from SS patients compared with healthy volunteers. Overexpression of BMP-6 locally in the salivary or lacrimal glands of mice resulted in the loss of fluid secretion as well as changes in the connective tissue of the salivary gland. Assessment of the fluid movement in either isolated acinar cells from mice overexpressing BMP-6 or a human salivary gland cell line cultured with BMP-6 revealed a loss in volume regulation in these cells. Lymphocytic infiltration in the submandibular gland of BMP-6 vector-treated mice was increased. No significant changes in the production of proinflammatory cytokines or autoantibodies associated with SS (anti-Ro/SSA and anti-La/SSB) were found after BMP-6 overexpression. In addition to identifying BMP-6 expression in association with xerostomia and xerophthalmia in primary SS, the present results suggest that BMP-6-induced salivary and lacrimal gland dysfunction in primary SS is independent of the autoantibodies and immune activation associated with the disease.

Abstract B07: Nasal epithelial gene expression profiles reflect dynamic biological response to smoking cessation

Abstract Rationale: There are few indicators of which cigarette smokers are at highest risk for developing lung cancer and COPD, and it is unclear why individuals remain at risk for decades after smoking-cessation. The kinetics of gene-expression alterations upon smoking-cessation might delineate distinct biological processes that are activated in response to and during recovery from tobacco smoke exposure. Furthermore, differences in this response or recovery might be associated with disease risk. We therefore sought to determine whether the kinetics of gene-expression alterations upon smoking-cessation could be detected in readily collected nasal epithelium. Methods: Nasal epithelial brushings were obtained from 8 active smokers enrolled in smoking-cessation programs. Brushings were obtained at baseline and at 4, 8, 16, and 24-weeks after smoking-cessation. Urine cotinine or exhaled carbon monoxide was used to assess tobacco abstinence. RNA extracted from the nasal brushings was processed and hybridized to Gene 1.0 ST Arrays. Gene expression changes associated with smoking-cessation were identified with a linear mixed effects model. Functional enrichment was determined using DAVID. Gene Set Enrichment Analysis (GSEA) was used to determine the relationship of nasal epithelial gene-expression changes associated with smoking-cessation to previous cross-sectional bronchial and nasal airway gene expression datasets of current, longer-term former and never smokers and to a previous published dataset of in-vitro exposure of cultured bronchial epithelial cells (NHBE) to cigarette smoke (CS). Results: The expression levels of 78 genes were associated with short-term smoking-cessation (FDR q<0.05, FC ≥ 1.75), with 6 genes up-regulated and 72 genes down-regulated with tobacco abstinence. A majority of the changes occur within 1-2 months of quitting. These genes were enriched in functional categories including oxidoreductase activity and metabolism of xenobiotic (p<0.05). Genes that decreased with smoking-cessation were enriched for genes whose expression levels in the airway datasets were higher in current smokers relative to never smokers or longer-term former smokers (FDR <10−3). Genes increased in active smokers that reversed with smoking-cessation were enriched among genes that are induced followed 15 minutes in-vitro exposure of NHBE to CS (FDR <5*10−3). Conclusion: Nasal epithelial gene expression profiles reflect the host response to smoking-cessation and are concordant with reversible changes identified in an independent bronchial airway dataset. Genes that reverse rapidly after smoking-cessation are inversely related to gene expression differences induced by acute cigarette smoke exposure in-vitro; suggesting that aspects of the gene-expression response to tobacco smoke both occur and reverse with rapid kinetics upon smoking. We have further found that genes with different biological functions revert to baseline with different dynamics following smoking-cessation. These data suggest that the smoking-induced field of injury can be measured non-invasively in nasal epithelium and leveraged to understand the kinetics of the reversible impact of smoking. These minimally invasive tools can be applied in population studies to assess the physiological impact of alternate tobacco products and other inhaled environmental exposures. Citation Format: Kahkeshan Hijazi, Bozena Malyszko, Xiaohui Zhang, Gang Liu, Yuriy Alekseyev, Yves-Martine Dumas, Louise Hertsgaard, Joni Jenson, Cindy Rohde, Dorothy K Hatsukami, Stephen S. Hecht, Daniel R Brooks, George O’Connor, Marc Lenburg, Katrina Steiling, Avrum Spira. Nasal epithelial gene expression profiles reflect dynamic biological response to smoking cessation. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B07.

Time Course Gene Expression Using Laser Capture Microscopy-Extracted Bile Ducts, but Not Hepatic Parenchyma, Reveals Acute Alpha-Naphthylisothiocyanate Toxicity

Acute toxic responses to a 50-mg/kg oral dose of 1-naphthylisothiocyanate (ANIT) were evaluated by microarray analysis of laser capture-microdissected rat biliary epithelium or hepatic parenchyma obtained 2 and 6 hours postdose. Distinct differences in gene expression patterns between biliary epithelium and hepatic parenchyma were noted at the 2-hour postdose time point, where 375 genes were altered in biliary epithelium but only 38 genes were altered in hepatic parenchyma. Endoplasmic reticulum stress genes were uniquely expressed in biliary epithelial cells at 2 hours postdose. By 6 hours postdose, 620 genes were altered in biliary epithelium, but only 32 genes were altered in hepatic parenchyma. In biliary epithelium, expression of genes involved in the unfolded protein response had decreased compared with the 2-hour time point, while expression of genes involved in protein degradation such as proteasome-ubquination pathways and cell death pathways had increased. At this same time, hepatic parenchymal gene expression changed little. Within 6 hours following oral exposure to ANIT, prior to morphologic changes, specific biliary epithelial gene expression changes, indicative of a vigorous unfolded protein response with protein destruction and cell death pathway activation were noted, in contrast to minor changes in the hepatic parenchyma.

CDNA array analysis of cag pathogenicity island-associated Helicobacter pylori epithelial cell response genes.

Helicobacter pylori strains containing the cag pathogenicity island (PAI) induce NF-kappaB activation and interleukin-8 secretion in gastric epithelial cells. The aim of this study was to investigate changes in epithelial gene expression induced by cag PAI-positive and -negative strains of H. pylori using high-density cDNA array hybridization technology. Radio-labeled cDNA prepared from H. pylori-infected Kato 3 gastric epithelial cells was hybridized to high-density cDNA arrays to identify changes in epithelial gene expression compared to noninfected controls. In vivo expression of selected, differentially expressed genes was examined by reverse transcription-PCR analysis of H. pylori-positive and -negative gastric mucosa. Screening of ca. 57,800 cDNAs identified 208 known genes and 48 novel genes and/or expressed sequence tags of unknown function to be differentially expressed in Kato 3 cells following H. pylori infection. Marked differences in gene expression profiles were observed following cag PAI-positive and cag PAI-negative infection with 15 novel cDNAs and 92 known genes being differentially expressed. H. pylori was found to change the expression of genes encoding growth factors and cytokine/chemokines and their receptors, apoptosis proteins, transcription factors and metalloprotease-disintegrin proteins (ADAMs), and tissue inhibitors of metalloproteinases. Gastric differential expression of selected known genes (amphiregulin and ADAM 10) and a novel gene (HPYR1) was confirmed in vivo in patients with H. pylori infection. Confirmation of the in vivo expression of selected genes demonstrates the usefulness of this approach for investigating pathogen-induced changes in host gene expression.

Colon of interleukin 10 deficient mice shows idghly specific changes in epithelial gene expression during inflammation

Colon of interleukin 10 deficient mice shows idghly specific changes in epithelial gene expression during inflammation

Monitoring gastric epithelial gene expression changes induced by Helicobacter pylori

Monitoring gastric epithelial gene expression changes induced by Helicobacter pylori

DISTINCT CHANGES IN INTESTINAL EPITHELIAL GENE EXPRESSION UPON METHOTREXATE TREATMENT

Introduction. Structure, function and differentiation of the intestinal epithelium are severely affected in patients receiving cytostatic drugs. Especially in pediatric patients, major side effects like malabsorption and malnutrition are of great concern. Little is known about effects of cytostatics on gene expression in the intestinal epithelium and about the mechanisms that mediate the mucosal damage and regeneration. Aim. In order to get insight in the functional capacities of intestinal epithelium during tissue damage and subsequent regeneration, we focussed on rats treated with methotrexate (MTX) as a model to investigate quantitavely the changes in epithelium specific gene expression. Methods. Rats were injected i.v. with a single dose of MTX (30 mg/kg). Up to 10 days after treatment rats were sacrificed and jejunal segments were removed and processed for histological and biochemical analysis. Gene expression of cell type specific differentiation markers was quantified at the level of mRNA, protein and enzyme activity using Northern blots, Western blots and enzyme assays, respectively. Results. Histologically, mucosal damage resulted in villus shortening at day 1 that increased to almost complete villus atrophy at day 4. During day 1 to day 4, enterocyte markers carbamoyl phosphate synthese (CPS) and sucrase-isomaltase (SI) decreased one after another to undetectable levels, whereas the enterocyte marker intestinal fatty acid binding protein (iFABP) increased to 120% of control values. In these tissue samples, expression of the mucin MUC2, a goblet cell marker, increased 1.5-fold. Furthermore, expression of chromogranin A (chromA), a marker for differrentiated entero-endocrine cells, decreased 2.5-fold during villus shortening. Expression of lysozyme, a marker for Paneth cells, increased 3-fold at day 2. The crypt villus architecture was regenerated at day 6. During regeneration, expression of all differentiation markers returned to normal values. Expression patterns of mRNA, protein and enzyme activity of each marker gene were parallel during the course of the experiment. Conclusions. Our results indicate a distinct effects of MTX on gene expression in different intestinal epithelial cell types. Decreased expression of CPS and SI together with an increased expression of iFABP after MTX treatment, suggests selective changes in enterocyte metabolism during damage and regeneration. Furthermore, goblet cells and Paneth cells contribute to increased synthesis of the cytoprotective molecules, MUC2 and lysozyme, during epithelial damage. Since effects of MTX parallelled at the different levels of expression, changes in epithelial gene expression seem to be mainly regulated at pretranslational level.