Alcohol Use Disorders Are Associated With a Unique Impact on Airway Epithelial Cell Gene Expression

BACKGROUND

Alcohol use disorders (AUDs) and cigarette smoking both increase risk for the development of community-acquired pneumonia (CAP), likely through adverse effects on proximal airway mucociliary clearance and pathogen recognition. Smoking-related alterations on airway gene expression are well described, but little is known about the impact of AUDs. We measured gene expression in human airway epithelial cells (AECs), hypothesizing that AUDs would be associated with novel differences in gene expression that could alter risk for CAP.

METHODS

Bronchoscopy with airway brushings was performed in participants with AUDs and controls to obtain AECs. An AUD Identification Test was used to define AUD. RNA was extracted from AECs, and mRNA expression data were collected on an Agilent micro-array. Differential expression analyses were performed on the filtered and normalized data with correction for multiple testing. Enrichment analyses were performed using clusterProfiler.

RESULTS

Expression data from 19 control and 18 AUD participants were evaluated. After adjustment for smoking, AUDs were associated with significant differential expression of 520 AEC genes, including genes for ribosomal proteins and genes involved in protein folding. Enrichment analyses indicated significant differential expression of 24 pathways in AUDs, including those implicated in protein targeting to membrane and viral gene expression. Smoking-associated AEC gene expression differences mirrored previous reports, but differed from those associated with AUDs.

CONCLUSIONS

AUDs have a distinct impact on AEC gene expression that may influence proximal airway function independent of smoking. Alcohol-associated alterations may influence risk for CAP through modifying key mechanisms important in protecting proximal airway integrity.

TLR3 Deficiency Leads to a Dysregulation in the Global Gene-Expression Profile in Murine Oviduct Epithelial Cells Infected with Chlamydia muridarum

Chlamydia trachomatis replicates primarily in the epithelial cells lining the genital tract and induces the innate immune response by triggering cellular pathogen recognition receptors (PRRs). Our previous studies showed that Toll-like receptor 3 (TLR3) is expressed in murine oviduct epithelial (OE) cells, is the primary PRR triggered by C. muridarum (Cm) early during infection to induce IFN-β synthesis, and that TLR3 signaling regulates the chlamydial induced synthesis of a plethora of other innate inflammatory modulators including IL-6, CXCL10, CXCL16 and CCL5. We also showed that the expression of these cytokines induced by Chlamydia was severely diminished during TLR3 deficiency; however, the replication of Chlamydiain TLR3 deficient OE cells was more robust than in WT cells. These data suggested that TLR3 had a biological impact on the inflammatory response to Chlamydia infection; however, the global effects of TLR3 signaling in the cellular response to Chlamydia infection in murine OE cells has not yet been investigated. To determine the impact of TLR3 signaling on Chlamydia infection in OE cell at the transcriptome level, we infected wild-type (OE-WT) and TLR3-deficient (OE-TLR3KO) cells with Cm, and performed transcriptome analyses using microarray. Genome-wide expression and ingenuity pathway analysis (IPA) identified enhanced expression of host genes encoding for components found in multiple cellular processes encompassing: (1) pro-inflammatory, (2) cell adhesion, (3) chemoattraction, (4) cellular matrix and small molecule transport, (5) apoptosis, and (6) antigen-processing and presentation. These results support a role for TLR3 in modulating the host cellular responses to Cm infection that extend beyond inflammation and fibrosis, and shows that TLR3 could serve a potential therapeutic target for drug and/or vaccine development.

Prenatal diagnosis of Pallister-Killian syndrome in pregnancy with normal CVS result and abnormal ultrasound findings in the second trimester

OBJECTIVE

To highlight importance of detailed ultrasound examination in fetuses with known normal karyotype (and micro-array result) from CVS. In case of markedly abnormal ultrasound result repeated karyotyping by amniocentesis should be considered. Sample should be analyzed by routine cytogenetic techniques, however also micro-array and targeted FISH should be added in order to achieve most accurate diagnosis.

CASE REPORT

We report prenatal diagnosis of Pallister-Killian Syndrome (PKS) at 18 gestational weeks. The mother asked us for second opinion scan in our centre due to finding of seven soft markers of chromosomal defects in fetus with normal CVS result. Our examination revealed asymmetrical fetal growth, normohydramnion, spastic fetal movements and several abnormalities: nuchal edema, mild bilateral hydronephrosis, omphalocoele and facial anomalies. We asked for targeted genetic analysis for PKS. Amniocentesis with repeated genetic analysis confirmed PKS (80% mosaicism of tetrasomy 12p).

CONCLUSION

Diagnosis of PKS led mother to terminate pregnancy.

From genome to function by studying eQTLs

Genome-wide association studies (GWASs) have shown a large number of genetic variants to be associated with complex diseases. The identification of the causal variant within an associated locus can sometimes be difficult because of the linkage disequilibrium between the associated variants and because most GWAS loci contain multiple genes, or no genes at all. Expression quantitative trait locus (eQTL) mapping is a method used to determine the effects of genetic variants on gene expression levels. eQTL mapping studies have enabled the prioritization of genetic variants within GWAS loci, and have shown that trait-associated single nucleotide polymorphisms (SNPs) often function in a tissue- or cell type-specific manner, sometimes having downstream effects on completely different chromosomes. Furthermore, recent RNA-sequencing (RNA-seq) studies have shown that a large repertoire of transcripts is available in cells, which are actively regulated by (trait-associated) variants. Future eQTL mapping studies will focus on broadening the range of available tissues and cell types, in order to determine the key tissues and cell types involved in complex traits. Finally, large meta-analyses will be able to pinpoint the causal variants within the trait-associated loci and determine their downstream effects in greater detail. This article is part of a Special Issue entitled: From Genome to Function.

FAM70B as a Novel Prognostic Marker for Cancer Progression and Cancer-Specific Death in Muscle-Invasive Bladder Cancer

Purpose

To validate whether FAM70B, which was found in our micro-array profiling as a prognostic marker for cancer survival, could accurately predict prognosis in patients with muscle-invasive bladder cancer (MIBC).

Materials and Methods

A total of 124 patients with MIBC were enrolled in this study. The FAM70B expression level was analyzed by real-time polymerase chain reaction by using RNA from tumor tissues. The prognostic effect of FAM70B was evaluated by Kaplan-Meier analysis and a multivariate Cox regression model.

Results

Kaplan-Meier estimates showed a significant difference in progression-free survival (log-rank test, p=0.011) and cancer-specific survival (log-rank test, p=0.017) according to FAM70B gene expression level. By multivariate Cox regression analysis, high FAM70B expression was predictive of cancer progression (hazard ratio [HR], 2.115, p=0.013) and cancer-specific death (HR, 1.925; p=0.033). In the subgroup analysis, high expression of FAM70B was associated with poor cancer-specific survival, progression-free survival, and overall survival in the patients who underwent cystectomy (log-rank test, p=0.013, p=0.036, p=0.005, respectively). In the chemotherapy group, FAM70B expression was associated with cancer-specific survival and progression-free survival (log-rank test, p=0.013, p=0.042, respectively). Moreover, high FAM70B expression was associated with shorter cancer-specific survival in localized or locally advanced tumor stages (log-rank test, p=0.016).

Conclusions

We confirmed the significance of FAM70B as a prognostic marker in a validation cohort. Therefore, we propose that the FAM70B gene could be used to more precisely predict cancer progression and cancer-specific death in patients with MIBC.

Effect of gamma-aminobutyric acid on the gene expression of Huh-7 cell lines

AIM: To investigate role of gamma aminobutyric acid (GABA) in Huh-7 cell expression.

METHODS: Huh-7 cell lines were co-cultured with 10 μmol/L GABA for 24 h, and then mRNA was extracted from the cells to reversely transcribe into cDNA. The cDNA profile was analyzed using microarray assay.

RESULTS: Forty one differentially expressed genes were screened, of which 16 were up-regulated while 11 were down-regulated significantly. The above genes were mainly involved in cell proliferation, apoptosis and immunologic function, and functions of other genes remained unknown.

CONCLUSION: Differentially expressed profiles under the action of GABA are successfully screened using microarray technique, indicating that GABA may participate in regulation of liver cell function.