A mutation in transmembrane protein 135 impairs lipid metabolism in mouse eyecups

Aging is a significant factor in the development of age-related diseases but how aging disrupts cellular homeostasis to cause age-related retinal disease is unknown. Here, we further our studies on transmembrane protein 135 (Tmem135), a gene involved in retinal aging, by examining the transcriptomic profiles of wild-type, heterozygous and homozygous Tmem135 mutant posterior eyecup samples through RNA sequencing (RNA-Seq). We found significant gene expression changes in both heterozygous and homozygous Tmem135 mutant mouse eyecups that correlate with visual function deficits. Further analysis revealed that expression of many genes involved in lipid metabolism are changed due to the Tmem135 mutation. Consistent with these changes, we found increased lipid accumulation in mutant Tmem135 eyecup samples. Since mutant Tmem135 mice have similar ocular pathologies as human age-related macular degeneration (AMD) eyes, we compared our homozygous Tmem135 mutant eyecup RNA-Seq dataset with transcriptomic datasets of human AMD donor eyes. We found similar changes in genes involved in lipid metabolism between the homozygous Tmem135 mutant eyecups and AMD donor eyes. Our study suggests that the Tmem135 mutation affects lipid metabolism as similarly observed in human AMD eyes, thus Tmem135 mutant mice can serve as a good model for the role of dysregulated lipid metabolism in AMD.

Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach

Esophageal carcinoma (EsC) is a member of the cancer group that occurs in the esophagus; globally, it is known as one of the fatal malignancies. In this study, we used gene expression analysis to identify molecular biomarkers to propose therapeutic targets for the development of novel drugs. We consider EsC associated four different microarray datasets from the gene expression omnibus database. Statistical analysis is performed using R language and identified a total of 1083 differentially expressed genes (DEGs) in which 380 are overexpressed and 703 are underexpressed. The functional study is performed with the identified DEGs to screen significant Gene Ontology (GO) terms and associated pathways using the Database for Annotation, Visualization, and Integrated Discovery repository (DAVID). The analysis revealed that the overexpressed DEGs are principally connected with the protein export, axon guidance pathway, and the downexpressed DEGs are principally connected with the L13a-mediated translational silencing of ceruloplasmin expression, formation of a pool of free 40S subunits pathway. The STRING database used to collect protein-protein interaction (PPI) network information and visualize it with the Cytoscape software. We found 10 hub genes from the PPI network considering three methods in which the interleukin 6 (IL6) gene is the top in all methods. From the PPI, we found that identified clusters are associated with the complex I biogenesis, ubiquitination and proteasome degradation, signaling by interleukins, and Notch-HLH transcription pathway. The identified biomarkers and pathways may play an important role in the future for developing drugs for the EsC.

Identification of a Key Glioblastoma Candidate Gene, FUBP3, Based on Weighted Gene Co-expression Network Analysis

Background: Glioblastoma multiforme (GBM) is the most common aggressive malignant brain tumor. However, the molecular mechanism of glioblastoma formation is still poorly understood. To identify candidate genes that may be connected to glioma growth and development, weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network between gene sets and clinical characteristics. We also explored the function of the key candidate gene.Methods: Two GBM datasets were selected from GEO Datasets. The R language was used to identify differentially expressed genes. WGCNA was used to construct a gene co-expression network in the GEO glioblastoma samples. A custom Venn diagram website was used to find the intersecting genes. The GEPIA website was used for survival analysis to determine the significant gene, FUBP3. OS,DSS, and PFI analyses, based on the UCSC Cancer Genomics Browser, were performed to verify the significance of FUBP3. Immunohistochemistry was performed to evaluate the expression of FUBP3 in glioblastoma and adjacent normal tissue. KEGG and GO enrichment analyses were used to reveal possible functions of FUBP3. Microenvironment analysis was used to explore the relationship between FUBP3 and immune infiltration. Immunohistochemistry was performed to verify the results of the microenvironment analysis.Results: GSE70231 and GSE108474 were selected from GEO Datasets, then 715 and 694 differentially expressed genes (DEGs) from GSE70231 and GSE108474, respectively, were identified. We then performed weighted gene co-expression network analysis (WGCNA) and identified the most downregulated gene modules of GSE70231 and GSE108474, and 659 and 3915 module genes from GSE70231 and GSE108474, respectively, were selected. Five intersection genes (FUBP3, DAD1, CLIC1, ABR, and DNM1) were calculated by Venn diagram. FUBP3 was then identified as the only significant gene by survival analysis using the GEPIA website. OS, DSS, and PFI analyses verified the significance of FUBP3. Immunohistochemical analysis revealed FUBP3 expression in GBM and adjacent normal tissue. KEGG and GO analyses uncovered the possible function of FUBP3 in GBM. Tumor microenvironment analysis showed that FUBP3 may be connected to immune infiltration, and immunohistochemistry identified a positive correlation between immune cells (CD4+ T cells, CD8+ T cells, and macrophages) and FUBP3.Conclusion: FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression. Therefore, interventions involving FUBP3 and its regulatory pathway may be a new approach for GBM treatment.

A Detailed Gene Expression Map of Giardia Encystation

Giardia intestinalis is an intestinal protozoan parasite that causes diarrheal infections worldwide. A key process to sustain its chain of transmission is the formation of infectious cysts in the encystation process. We combined deep RNAseq of a broad range of encystation timepoints to produce a high-resolution gene expression map of Giardia encystation. This detailed transcriptomic map of encystation confirmed a gradual change of gene expression along the time course of encystation, showing the most significant gene expression changes during late encystation. Few genes are differentially expressed early in encystation, but the major cyst wall proteins CWP-1 and -2 are highly up-regulated already after 3.5 h encystation. Several transcription factors are sequentially up-regulated throughout the process, but many up-regulated genes at 7, 10, and 14 h post-induction of encystation have binding sites in the upstream regions for the Myb2 transcription factor, suggesting that Myb2 is a master regulator of encystation. We observed major changes in gene expression of several meiotic-related genes from 10.5 h of encystation to the cyst stage, and at 17.5 h encystation, there are changes in many different metabolic pathways and protein synthesis. Late encystation, 21 h to cysts, show extensive gene expression changes, most of all in VSP and HCMP genes, which are involved in antigenic variation, and genes involved in chromatin modifications. This high-resolution gene expression map of Giardia encystation will be an important tool in further studies of this important differentiation process.

Associations of PYGO2 and PRDM9 Genes Single Nucleotide Polymorphisms with Idiopathic Azoospermia in Iranian Population

Background One cause of infertility is azoospermia which affects about 1% of men in the general population. Non-obstructive azoospermia can be due to genetic disorders. Pygo2 and PRDM9 are two genes involved in spermatogenesis process. The aim of this study was to assess two single nucleotide polymorphism (SNPs) rs61758740, rs61758741 and rs2973631, rs1874165 in these genes respectively. Methods In this case-control study, a total of 100 Iranian patients with idiopathic azoospermia and 100 fertile control subjects were genotyped for Pygo2 rs61758740 and rs61758741 and PRDM9 rs2973631 polymorphism using Tetra-ARMS PCR. PRDM9 rs1874165 polymorphism was assessed by PCR-RFLP method. LH, FSH and testosterone concentrations were measured with electrochemical luminescence (ECL) method. Results Our data indicated a significant increase only in the FSH and LH hormone levels of patients which suggest that the cause of azoospermia is not pre-testicular. rs61758740 (T>C) polymorphism in Pygo2 gene was associated with increased risk of azoospermia (OR, 2.359; 95% Cl (1.192 – 4.666); p= 0.012). Also based on dominant model analysis in rs2973631 of PRDM9 gene, we identified a significant gene frequency difference between cases and control in dominant, recessive and codominant models but dominant, codominant and overdominant models was confirmed for rs1874165. Conclusion Our findings provide evidence for an association between Pygo2 and RDM9 genetic variation and idiophatic azoospermia in Iranian populations. Therefore, SNPs of these genes can be cosidered as a risk factor for male infertility.

Genetic predispositions moderate the effectiveness of tobacco excise taxes

Background Tobacco consumption is one of the leading causes of preventable death. In this study, we analyze whether someone’s genetic predisposition to smoking moderates the response to tobacco excise taxes. Methods We interact polygenic scores for smoking behavior with state-level tobacco excise taxes in longitudinal data (1992-2016) from the US Health and Retirement Study (N = 12,058). Results Someone’s genetic propensity to smoking moderates the effect of tobacco excise taxes on smoking behavior along the extensive margin (smoking vs. not smoking) and the intensive margin (the amount of tobacco consumed). In our analysis sample, we do not find a significant gene-environment interaction effect on smoking cessation. Conclusions When tobacco excise taxes are relatively high, those with a high genetic predisposition to smoking are less likely (i) to smoke, and (ii) to smoke heavily. While tobacco excise taxes have been effective in reducing smoking, the gene-environment interaction effects we observe in our sample suggest that policy makers could benefit from taking into account the moderating role of genes in the design of future tobacco control policies.

The behavioral effects of gestational and lactational benzo[a]pyrene exposure vary by sex and genotype in mice with differences at the Ahr and Cyp1a2 loci

Benzo[a]pyrene (BaP) is a polycyclic aromatic hydrocarbon (PAH) and known carcinogen in the Top 10 on the United States' list of priority pollutants. Humans are exposed through a variety of sources including tobacco smoke, grilled foods and fossil fuel combustion. Recent studies of children exposed to higher levels of PAHs during pregnancy and early life have identified numerous adverse effects on the brain and behavior that persist into school age and adolescence. Our studies were designed to look for genotype and sex differences in susceptibility to gestational and lactational exposure to BaP using a mouse model with allelic differences in the aryl hydrocarbon receptor and the xenobiotic metabolizing enzyme CYP1A2. Pregnant dams were exposed to 10 mg/kg/day of BaP in corn oil-soaked cereal or the corn oil vehicle alone from gestational day 10 until weaning at postnatal day 25. Neurobehavioral testing began at P60 using one male and one female per litter. We found main effects of sex, genotype and treatment as well as significant gene x treatment and sex x treatment interactions. BaP-treated female mice had shorter latencies to fall in the Rotarod test. High-affinity AhrbCyp1a2(-/-) mice had greater impairments in Morris water maze. Interestingly, poor-affinity AhrdCyp1a2(-/-) mice also had deficits in spatial learning and memory regardless of treatment. We believe our findings provide future directions in identifying human populations at highest risk of early life BaP exposure, because our model mimics known human variation in our genes of interest. Our studies also highlight the value of testing both males and females in all neurobehavioral studies.

CTAG1A expression associates with survival in triple negative breast cancer.

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of cancer/testis antigen 1A, encoded by CTAG1A when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, CTAG1A expression was correlated with distant metastasis-free survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. CTAG1A may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

PNCK expression associates with survival in triple negative breast cancer.

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of pregnancy up-regulated non-ubiquitously expressed CaM kinase, encoded by PNCK when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, PNCK expression was correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. PNCK may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

STK25 expression associates with survival in triple negative breast cancer.

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of serine/threonine kinase 25, encoded by STK25 when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, STK25 expression was correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. STK25 may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.