Bioinformatics Analysis Reveals Novel Differentially Expressed Genes Between Ectopic and Eutopic Endometrium in Women with Endometriosis

Background

Endometriosis is one of the chronic and prevalent diseases among women. There is limited knowledge about its pathophysiology at the cellular and molecular levels, causing a lack of a definite cure for this disease. In this study, differentially expressed genes (DEGs) between ectopic and paired eutopic endometrium in women with endometriosis were analyzed through bioinformatics analysis for better understanding of the molecular pathogenesis of endometriosis.

Methods

Gene expression data of ectopic and paired eutopic endometrium were taken from the Gene Expression Omnibus database. DEGs were screened by the Limma package in R with considering specific criteria. Then, the protein-protein interaction network was reconstructed between DEGs. The fast unfolding clustering algorithm was used to find sub-networks (modules). Finally, the three most relevant modules were selected and the functional and pathway enrichment analyses were performed for the selected modules.

Results

A total of 380 DEGs (245 up-regulated and 135 down-regulated) were identified in the ectopic endometrium and compared with paired eutopic endometrium. The DEGs were predominantly enriched in an ensemble of genes encoding the extracellular matrix and associated proteins, metabolic pathways, cell adhesions and the innate immune system. Importantly, DPT, ASPN, CHRDL1, CSTA, HGD, MPZ, PED1A, and CLEC10A were identified as novel DEGs between the human ectopic tissue of endometrium and its paired eutopic endometrium.

Conclusion

The results of this study can open up a new window to better understanding of the molecular pathogenesis of endometriosis and can be considered for designing new treatment modalities.

Interactions dietary components with expression level of breast cancer-related genes

Background

Dietary components can influence the effects of genetic background in breast cancer (BC). This review study aimed to investigate the effect of dietary components on the expression level of BC-related genes.

Methods

In this narrative review, Embase, PubMed, PsycInfo, and the Cochrane databases were used to collect the related papers with interactions of BC, genetics, and dietary intake. Appropriate keywords such as BC, gene expression, mutation, nutrient, and diet (alone and together) were applied for data collection.

Results

The association of BC with some genes including the BC1 gene (BRCA1), the human epidermal growth factor receptor 2 (HER2), and the fat mass and obesity-associated (FTO) gene can be affected by dietary components. Moderate B12 supplementation may be protective against BC in people with the inherited mutation of BRCA. The olive oil may have a protective effect against BC through several mechanisms such as suppressing HER-2 expression. Furthermore, high glycemic index foods may increase the risk of BC by the activation of the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway and the up-regulation of FTO gene expression.

Conclusion

There are interactions between BC, BC-related genes, and dietary intake. Dietary components such as macronutrients, micronutrients, and phytochemicals may regulate the expression level of BC-related genes. Further longitudinal studies are needed to confirm the associations between BC-related genes and diet and to discover the underlying mechanisms.

Unraveling the Complex Interactions between the Fat Mass and Obesity-Associated (FTO) Gene, Lifestyle, and Cancer

Carcinogenesis is a complicated process and originates from genetic, epigenetic, and environmental factors. Recent studies have reported a potential critical role for the fat mass and obesity-associated (FTO) gene in carcinogenesis through different signaling pathways such as mRNA N6-methyladenosine (m6A) demethylation. The most common internal modification in mammalian mRNA is the m6A RNA methylation that has significant biological functioning through regulation of cancer-related cellular processes. Some environmental factors, like physical activity and dietary intake, may influence signaling pathways engaged in carcinogenesis, through regulating FTO gene expression. In addition, people with FTO gene polymorphisms may be differently influenced by cancer risk factors, for example, FTO risk allele carriers may need a higher intake of nutrients to prevent cancer than others. In order to obtain a deeper viewpoint of the FTO, lifestyle, and cancer-related pathway interactions, this review aims to discuss upstream and downstream pathways associated with the FTO gene and cancer. The present study discusses the possible mechanisms of interaction of the FTO gene with various cancers and provides a comprehensive picture of the lifestyle factors affecting the FTO gene as well as the possible downstream pathways that lead to the effect of the FTO gene on cancer.

The effect of FTO rs9939609 polymorphism on the association between colorectal cancer and dietary fiber

Background

Gene polymorphisms may explain the controversy on the association between colorectal cancer (CRC) and dietary fibers. The purpose of this study was to investigate the effect of fat mass and obesity-associated (FTO) rs9939609 polymorphism on the association between colorectal cancer and dietary fiber.

Methods

This case-control study was conducted on 160 CRC cases and 320 healthy controls in Tehran, Iran. The participants' food intake was assessed using a semi-quantitative food frequency questionnaire (FFQ). The frequency of rs9939609 FTO polymorphism in the case and control groups was determined using the tetra-primer amplification refractory mutation (tetra-ARMS) method.

Results

In the participants with the TT genotype of the FTO rs9939609, the cases had higher BMI and lower intake of dietary fiber compared to the controls (P = 0.01). Among A allele carriers of FTO rs9939609 polymorphism, the cases had higher BMI (P = 0.04) and lower intake of total fiber (P = 0.02) and soluble fiber (P = 0.02). An inverse association was found between CRC and dietary fiber intake among those with the AA/AT FTO rs9939609 genotype after adjusting for age, sex, smoking, alcohol consumption, physical activity, BMI, and calorie intake (OR = 0.9, CI 95%:0.84-0.92, P < 0.05).

Conclusion

This study found a link between higher dietary fiber consumption and a lower risk of CRC in A-allele carriers of FTO rs9939609 polymorphism. Future studies are needed to identify the underlying mechanisms of the association between CRC and dietary fibers in people with different FTO genotypes.

A comprehensive bioinformatic analysis revealed novel MicroRNA biomarkers of Parkinson's disease

Parkinson's disease (PD) is categorized as a neurodegenerative disorder. Different studies have focused on the role of microRNAs (miRNAs) on PD progression. Due to its complexity in initiation and progression, a considerable requirement has arisen to identify novel miRNA biomarkers in a noninvasive manner. In silico analysis has been used to select differentially expressed miRNAs (DE-miRNAs) and key pathways in this disease. In this manner, several data sets of different neurodegenerative diseases have been analyzed to purify the findings of the present study. Totally, 15 DE miRNAs showed significant changes compared to healthy controls and other neurodegenerative diseases. Then, the targets of the miRNAs were predicted through miRTarBase and TargetScan databases. Besides, enrichment analysis was implemented for predicted target genes. Most of the target genes were enriched in the TRAIL signaling pathway, Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, protein serine/threonine kinase activity, and Cytoplasm. Moreover, a protein-protein interaction network was constructed to find the most key DE miRNAs and targets in this disease. The results of the present study may help researchers shed light on the discovery of novel biomarkers for PD.

Interactions of Colorectal Cancer, Dietary Fats, and Polymorphisms of Arachidonate Lipoxygenase and Cyclooxygenase Genes: A Literature Review

Objective

Genetics and dietary factors play important roles in the development of colorectal cancer (CRC). However, the underlying mechanisms of the interactions between CRC, gene polymorphisms, and dietary fat are unclear. This review study investigated the effects of polymorphisms of arachidonate lipoxygenase (ALOX) and cyclooxygenase (COX) genes in the association between CRC and dietary fat.

Methods

All the related papers published from 2000 to 2022 were collected from different databases such as PubMed, Science Direct, Scopus, and Cochran using related keywords such as colorectal cancer, ALOX, COX, polymorphism, and dietary fat. Non-English and unrelated documents were excluded.

Results

Some single-nucleotide polymorphisms (SNPs) in the ALOX and COX genes, such as rs2228065, rs6413416, and rs4986832 in the ALOX gene, and rs689465 in the COX gene may play significant roles in the association between the risk of CRC and dietary fats. SNPs of ALOX and COX genes may influence the effects of dietary fatty acids on the risk of CRC.

Conclusion

Some polymorphisms of the ALOX and COX genes may have important roles in the effects of dietary fat on the risk of CRC. If future studies confirm these results, dietary recommendations for preventing colorectal cancer may be personalized based on the genotype of the ALOX and COX genes.

Search for Cosmic-Ray Electron and Positron Anisotropies with Seven Years of Fermi Large Area Telescope Data

The Large Area Telescope on board the Fermi Gamma-ray Space Telescope has collected the largest ever sample of high-energy cosmic-ray electron and positron events since the beginning of its operation. Potential anisotropies in the arrival directions of cosmic-ray electrons or positrons could be a signature of the presence of nearby sources. We use almost seven years of data with energies above 42 GeV processed with the Pass 8 reconstruction. The present data sample can probe dipole anisotropies down to a level of 10^{-3}. We take into account systematic effects that could mimic true anisotropies at this level. We present a detailed study of the event selection optimization of the cosmic-ray electrons and positrons to be used for anisotropy searches. Since no significant anisotropies have been detected on any angular scale, we present upper limits on the dipole anisotropy. The present constraints are among the strongest to date probing the presence of nearby young and middle-aged sources.

Intrauterine administration of hCG immediately after oocyte retrieval and the outcome of ICSI: a randomized controlled trial

STUDY QUESTION

Does the intrauterine administration of hCG immediately after oocyte retrieval in antagonist cycles with ICSI and fresh embryo transfer (ET) influence the implantation rate or chemical and clinical pregnancy rates?

SUMMARY ANSWER

The intrauterine administration of hCG after oocyte retrieval increases the implantation rate and chemical and clinical pregnancy rates.

WHAT IS KNOWN ALREADY

Over half of IVF/ICSI cycles fail due to implantation failure. Intrauterine administration of hCG, a few minutes before ET, increased the implantation and pregnancy rates in most but not in all studies. The effect of intrauterine administration of hCG, after oocyte retrieval, has not yet been studied.

STUDY DESIGN, SIZE, DURATION

The study was a parallel, triple-blind randomized clinical trial (RCT) performed from September 2015 to February 2016, in a university hospital. We recruited women undergoing antagonist ovarian stimulation, ICSI and ET. For an effect size of 0.2, power of 80% at a significance level of 0.05, we needed 150 participants. Accounting for a 7% dropout rate, a total of 160 women was considered appropriate. A computer-generated randomization list with a block size of 4, with 1:1 allocation was used. The treatment allocation was placed in a sealed, opaque, envelope and picked up consecutively. Immediately after oocyte retrieval, patients in the intervention and control groups were treated with intrauterine injection of hCG and saline, respectively. Participants underwent ET on Day 3. A beta-hCG test was done at 2 weeks. If positive, three transvaginal-ultrasonographies (TVSs) were done at 3, 4 and 10 weeks after ET. The participants were called up thereafter and questioned about the continuity of their pregnancy.

PARTICIPANTS/MATERIALS, SETTING, METHOD

Of 1990 women attending the infertility clinic of our university hospital, 508 were IVF/ICSI candidates during the study period, and 245 of the patients on an antagonist cycle met the criteria to be invited into our trial. Inclusion criteria were normal ovarian reserve, age ≤41, undergoing ICSI, and fresh ET and normal TSH and prolactin. Uncontrolled chronic disease, severe hydrosalpinx, severe endometriosis, morphologic embryo deficiencies, non-obstructive azospermia and high risk of severe ovarian hyperstimulation syndrome were criteria for exclusion. After taking an informed consent, a total of 158 participants were recruited, of which 80 were randomly allocated to receive intrauterine 500 IU hCG in up to 0.5 ml normal saline and 78 to receive intrauterine 0.5 ml normal saline immediately after oocyte retrieval, during general anaesthesia. ICSI was performed conventionally. The 4-8 cell embryos were transferred on the third day after oocyte retrieval. Implantation rate, chemical and clinical pregnancy rates were analysed and compared between the two groups.

MAIN RESULTS AND THE ROLE OF CHANCE

Patients' demographic and baseline characteristics were comparable. The clinical results showed statistically significant differences between the two groups regarding the biochemical pregnancy rate (59.2 versus 31.3%; P = 0.001; odds ratio (OR) = 1.88; 95% CI, 1.26-2.82; risk difference (RD) = 27.8; 95% CI, 11.2-42.3), implantation rate (37 versus 17%; P = 0.012; OR = 2.29; 95% CI, 1.02-5.14; RD = 20.2; 95% CI, 5.4-33.8), clinical pregnancy rate (50.7 versus 16.4%; P < 0.001; OR = 3.08; 95% CI, 1.71-5.55; RD = 34.3; 95% CI, 18.7-47.6) and ongoing pregnancy rate (40.1 versus 13.4%; P = 0.001; OR = 3.04; 95% CI, 1.55-5.93; RD = 27.4; 95% CI, 12.7-40.6). The abortion and ectopic pregnancy rates were not statistically different between the two groups.

LIMITATIONS, REASONS FOR CAUTION

The insertion of an intrauterine insemination catheter and the injection of a small amount of saline into the uterine cavity (without hCG) may also have some impact on implantation. This effect could be studied by comparing this intervention with another study group without any intrauterine injection.There are no specific side effects mentioned in the literature for the intrauterine administration of hCG, neither were any observed in our study, but it is best to be cautious about probable side effects, because this type of intervention is relatively new and experimental, and deserves more studies before being entered into routine clinical practice.

WIDER IMPLICATIONS OF THE FINDINGS

Intrauterine administration of hCG immediately after oocyte pick up increases its effectiveness; however, further investigations are required before this procedure can be recommended for clinical practice.

STUDY FUNDING/COMPETING INTERESTS

This study was supported by the Women's Health Research Center, Tabriz University of Medical Sciences, Iran. No external funds were used. The authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

IRCT201206165485N4.

TRIAL REGISTRATION DATE

2 September 2015.

DATE OF FIRST PATIENT'S ENROLMENT

2 September 2015.

Study of antimicrobial effects of vancomycin loaded PLGA nanoparticles against enterococcus clinical isolates

Researchers have demonstrated that antimicrobial agents in nanoparticle (NP) forms have better activities. Vancomycin (VCM), as a glycopeptide antibiotic with antimicrobial activity against gram positive bacteria, is poorly absorbed from the intestinal tract. Enterococcus is a genus of bacteria that became resistant to a wide range of antibiotics in last decades, and cause severe infections in hospitalized patients. This paper describes preparation of VCM--loaded poly (lactic-co-glycolic acid) (PLGA) NPs and compares the antimicrobial effects with drug solution against clinical Enterococcus isolates. VCM-loaded PLGA NPs were fabricated by W1/O/W2 solvent evaporation method. The comparison of obtained Minimum Inhibitory Concentration (MIC) values showed a significant decrease in the antimicrobial effect of VCM -loaded NPs. Results also indicated that the potency of the NPs against VCM resistant isolates of Enterococcus was less than VCM susceptible isolates. The reduced antimicrobial effect of formulated NPs in invitro condition is perhaps related to the strong electrostatic linkage between hydrophilic drug (VCM) and hydrophobic polymer (PLGA) that lead to the slow release of the antibiotic from polymeric NPs.

Steric restrictions on the binding of large metal ions to serum transferrin

Apotransferrin in 0.1 M N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid at 25 degrees C and pH 7.4 was titrated with acidic solutions of Lu3+, Tb3+, and Eu3+. Metal binding at the two specific metal-binding sites of transferrin was followed from changes in the difference UV spectra at 245 nm. The binding of Tb3+ was also followed from changes in the fluorescence emission spectrum at 549 nm. Apotransferrin was titrated with solutions containing varying ratios of the metal ion and the competitive chelating agent nitrilotriacetic acid, and metal-transferrin binding constants were calculated by nonlinear least-squares fits of the absorbance as a function of titrant added. The sequential carbonate-independent equilibrium constants for the binding of two metal ions are log KM1 = 11.08 and log KM2 = 7.93 for Lu3+, log KM1 = 11.20 and log KM2 = 7.61 for Tb3+, and log KM1 = 9.66 and log KM2 = 7.27 for Eu3+. Titrations of both C-terminal and N-terminal monoferric transferrins indicate that all of these metal ions bind more strongly to the C-terminal binding site. The trend in log K values as a function of the lanthanide ionic radius has been evaluated both by plots of log K versus the metal ion charge/radius ratio and by linear free-energy relationships in which binding constants for complexes of the larger lanthanides are plotted versus the binding constants for complexes with the smallest lanthanide, Lu3+. Both methods indicate that there is a sharp drop in the binding constants for the C-terminal binding site for metals larger than Tb3+. This decrease is attributed to a steric hindrance to the binding of the larger cations. The steric effect is not as strong for metal binding at the N-terminal site. As a result, the selectivity for binding to the C-terminal site, which is quite high for the smaller lanthanides, drops sharply on going from Tb3+ to Nd3+.

Binding of monovalent anions to human serum transferrin

Serum transferrin is the protein whose primary function is to bind iron and transport it through the blood. Apotransferrin has two specific metal-binding sites that bind a variety of metal ions in addition to the ferric ion. The distinguishing feature of the transferrins is that a "synergistic" bicarbonate anion is bound along with the metal ion to form a stable Fe(3+)-CO3-Tf ternary complex. Previous research has shown that apotransferrin will also bind divalent anions such as phosphate and sulfate. Difference UV spectroscopy has now been used to show that a series of monovalent anions bind weakly to apotransferrin. Equilibrium constants for the binding of chloride, perchlorate, bromide, fluoride and Hepes have been calculated. A reaction scheme for the binding of anions is proposed which predicts that the binding of the nonsynergistic anions to apotransferrin will interfere with metal binding by competing directly with the binding of the synergistic bicarbonate anion. Difference UV data are presented which demonstrate this type of competition between nonsynergistic anions and Tb3+. Competition from the nonsynergistic anions follows the order HPO4(2-) > SO4(2-) approximately F- > ClO4- approximately Cl- approximately Br-. Speciation calculations have been performed to determine the concentrations of anion-apotransferrin complexes in Hepes and Tris buffers and in human serum and to estimate the extent to which competition from anions in the buffer will interfere with metal-binding to apotransferrin.