Variation in stability of endogenous reference genes in fallopian tubes and endometrium from healthy and ectopic pregnant women

Validating Reference Gene Expression Stability in Human Ovarian Follicles, Oocytes, Cumulus Cells, Ovarian Medulla, and Ovarian Cortex Tissue

Human ovarian cells are phenotypically very different and are often only available in limited amounts. Despite the fact that reference gene (RG) expression stability has been validated in oocytes and other ovarian cells from several animal species, the suitability of a single universal RG in the different human ovarian cells and tissues has not been determined. The present study aimed to validate the expression stability of five of the most used RGs in human oocytes, cumulus cells, preantral follicles, ovarian medulla, and ovarian cortex tissue. The selected genes were glyceraldehyde 3-phosphate dehydrogenase (GAPDH), beta-2-microglobulin (B2M), large ribosomal protein P0 (RPLP0), beta-actin (ACTB), and peptidylprolyl isomerase A (PPIA). Overall, the stability of all RGs differed among ovarian cell types and tissues. NormFinder identified ACTB as the best RG for oocytes and cumulus cells, and B2M for medulla tissue and isolated follicles. The combination of two RGs only marginally increased the stability, indicating that using a single validated RG would be sufficient when the available testing material is limited. For the ovarian cortex, depending on culture conditions, GAPDH or ACTB were found to be the most stable genes. Our results highlight the importance of assessing RGs for each cell type or tissue when performing RT-qPCR analysis.

Fallopian tube epithelial cells express androgen receptor and have a distinct hormonal responsiveness when compared with endometrial epithelium

STUDY QUESTION

How does steroid receptor expression, proliferative activity and hormone responsiveness of the fallopian tube (FT) epithelium compare to that of the endometrial epithelium?

SUMMARY ANSWER

Proliferative indices, hormone receptor expression-scores and in vitro response to oestrogen and androgens of the human FT demonstrate a distinct pattern from the matched endometrium.

WHAT IS KNOWN ALREADY

The FT epithelium exists as a continuum of the endometrium, and both express steroid hormone receptors. The ovarian steroid hormones regulate cyclical proliferation and regeneration of the endometrium, but their effects on steroid hormone receptor expression and proliferation in the FT have not yet been fully elucidated.

STUDY DESIGN, SIZE, DURATION

We included women with proven fertility, undergoing hysterectomy and bilateral salpingo-oophorectomy for benign, gynaecological conditions at Liverpool Women's NHS Foundation Trust. They had no known endometrial or tubal pathology and were not on hormonal treatments for at least 3 months preceding sample collection in this prospective observational study (conducted between 2010 and 2018). A full-thickness sample of the endometrium and a sample from the FT were collected from each woman.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The differential protein and mRNA levels of steroid hormone receptors, oestrogen receptors α and β, androgen receptor (AR) and progesterone receptor (PR), and the proliferative marker (Ki67) of the endometrium and the FT tissue samples from 47 healthy women undergoing surgery (37 premenopausal and 10 postmenopausal) were investigated using immunohistochemistry and quantitative real-time PCR. The comparative responsiveness to oestrogen and androgen of the endometrium and the fimbrial end of the FT was analysed using an in vitro short-term explant culture model. The endpoints assessed in the explants were the changes in mRNA and protein levels for AR, PR and the epithelial proliferative index after 24 h treatment with oestradiol (E2) or dihydrotestosterone (DHT).

MAIN RESULTS AND THE ROLE OF CHANCE

The premenopausal endometrial functionalis glands (FG) displayed the well-known cyclic variation in cellular proliferation and steroid receptor scores. Compared with the endometrial FG, the matched FT epithelium (both fimbrial or isthmic ends) displayed a significantly lower proportion of cells expressing Ki67 (2.8% ± 2.2%, n = 18 vs 30.0% ± 26.3%, n = 16, P = 0.0018, respectively) accompanied with a significantly higher AR immunoscores (6.7 ± 2.7, n = 16 vs 0.3 ± 1.0, n = 10, P = 0.0136). The proportion of cells expressing Ki67 and the AR immunoscores of the FT epithelium correlated positively with endometrial luminal epithelium (r = 0.62, P = 0.005, and r = 0.68, P = 0.003, respectively). In vitro experiments suggested the tubal explants to be apparently less responsive to E2 yet more sensitive to DHT compared with the matched endometrium explants.

LIMITATIONS, REASONS FOR CAUTION

The short-term in vitro nature of the tissue explant cultures used in the study may not be representative of how different anatomical regions of the endometrium and FT behave in vivo. Our study included a high proportion of older premenopausal women with a regular menstrual cycle, which may therefore affect extrapolation of findings to a younger group.

WIDER IMPLICATIONS OF THE FINDINGS

Advancing our understanding of tubal and endometrial epithelial cell function has important implications for the diagnosis and treatment of diseases such as infertility, ectopic pregnancy, endometriosis and cancer.

STUDY FUNDING/COMPETING INTEREST(S)

The work included in this article was funded by Wellbeing of Women project grants RG1073 and RG2137 (D.K.H.) and Wellbeing of Women Entry-Level Scholarship ELS706 (A.M). A.M. was also supported by an NIHR ACF fellowship grant. Further support received from Liverpool Women's Hospital NHS Trust (S.M.), University of Liverpool (E.B. and A.W.). All authors declare there are no conflicts of interest.

TRIAL REGISTRATION NUMBER

N/A.

Selection and verification of the combination of reference genes for RT-qPCR analysis in rat adrenal gland development

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is commonly used for gene expression analysis, and the accuracy of its results depends greatly on chosen reference genes. Adrenal gland is the core of the occurrence and development of fetal-originated adult diseases. Its dysplasia or dysfunction may increase susceptibility to adult disease, which has apparent sex differences. To explore the optimal combination of reference genes for RT-qPCR in female and male rats adrenal development, we selected seven reference genes (GAPDH, β-actin, etc.), and use RT-qPCR to detect genes expression during different stages of rats adrenal development under physiological conditions. Then we analysed data using GeNorm, NormFinder and BestKeeper to select the optimal combination of reference genes. Further, we used the intrauterine growth retardation (IUGR) model of rat caused by prenatal caffeine exposure (PCE) to verify the stability and accuracy of the selected combination of reference genes under physiological conditions. The results showed that TBP + β-actin could be the optimal combination of reference genes for fetal rat adrenals under physiological conditions, without obvious sex differences. In infancy and adolescence, the optimal combination of reference genes for adrenals had sex differences, and females were GAPDH + β-actin, while males were GAPDH + SDHA. In PCE model, the optimal combination of reference genes was consistent with physiological conditions. Using combination of reference genes to analyze target genes can improve the accuracy of the results. In summary, this study provided reliable combination of reference genes for RT-qPCR and experimental supports for researches on adrenal development.

Towards deep phenotyping pregnancy: a systematic review on artificial intelligence and machine learning methods to improve pregnancy outcomes

Objective

Development of novel informatics methods focused on improving pregnancy outcomes remains an active area of research. The purpose of this study is to systematically review the ways that artificial intelligence (AI) and machine learning (ML), including deep learning (DL), methodologies can inform patient care during pregnancy and improve outcomes.

Materials and methods

We searched English articles on EMBASE, PubMed and SCOPUS. Search terms included ML, AI, pregnancy and informatics. We included research articles and book chapters, excluding conference papers, editorials and notes.

Results

We identified 127 distinct studies from our queries that were relevant to our topic and included in the review. We found that supervised learning methods were more popular (n = 69) than unsupervised methods (n = 9). Popular methods included support vector machines (n = 30), artificial neural networks (n = 22), regression analysis (n = 17) and random forests (n = 16). Methods such as DL are beginning to gain traction (n = 13). Common areas within the pregnancy domain where AI and ML methods were used the most include prenatal care (e.g. fetal anomalies, placental functioning) (n = 73); perinatal care, birth and delivery (n = 20); and preterm birth (n = 13). Efforts to translate AI into clinical care include clinical decision support systems (n = 24) and mobile health applications (n = 9).

Conclusions

Overall, we found that ML and AI methods are being employed to optimize pregnancy outcomes, including modern DL methods (n = 13). Future research should focus on less-studied pregnancy domain areas, including postnatal and postpartum care (n = 2). Also, more work on clinical adoption of AI methods and the ethical implications of such adoption is needed.

Selection of Suitable Reference Genes for qPCR Gene Expression Analysis of HepG2 and L02 in Four Different Liver Cell Injured Models

Quantitative real-time PCR (qPCR) has become a widely used approach to analyze the expression level of selected genes. However, owing to variations in cell types and drug treatments, a suitable reference gene should be selected according to special experimental design. In this study, we investigated the expression level of ten candidate reference genes in hepatoma carcinoma cell (HepG2) and human hepatocyte cell line (L02) treated with ethanol (EtOH), hydrogen peroxide (H₂O₂), acetaminophen (APAP), and carbon tetrachloride (CCl₄), respectively. To analyze raw cycle threshold values (Cp values) from qPCR run, three reference gene validation programs, including Bestkeeper, geNorm, and NormFinder, were used to evaluate the stability of ten candidate reference genes. The results showed that TATA-box binding protein (TBP) and tubulin beta 2a (TUBB2a) presented the highest stability for normalization under different treatments and were regarded as the most suitable reference genes of HepG2 and L02. In addition, this study not only identified the most stable reference genes of each treatment, but also suggested that β-actin (ACTB), glyceraldehade-3-phosphate dehydrogenase (GAPDH), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ), and beta-2 microglobulin (B2M) were the least stable reference genes in HepG2 and L02. This work was the first report to systematically explore the stability of reference genes in injured models of HepG2 and L02.

Selection of Endogenous Control Reference Genes for Studies on Type 1 or Type 2 Endometrial Cancer

A panel of 32 candidate reference genes was used to identify the most stable genes for gene normalisation in quantitative RT-PCR studies using endometrial biopsies obtained from women with endometrial cancer (type 1 or type 2) and without cancer (controls). RNA from the biopsies was isolated, examined for purity and quality, and then reverse transcribed into cDNA before being subjected to real-time qRT-PCR analysis in triplicate within the TaqMan gene Expression Assay kit. The most 'stable' endogenous control genes were then identified using the geNorm qbase + 2 and NormFinder software packages. PSMC4, PUM1 and IPO8 were identified as the best reference genes combination for type 1 endometrial cancer (grades 1, 2 and 3), whereas for type 2 endometrial cancer (serous and carcinosarcoma), UBC, MRPL19, PGK1 and PPIA were the best reference genes combination. We conclude that the use of these normaliser combinations should provide accurate interpretation of gene expression at the transcript level in endometrial cancer studies especially for types 1 and 2 cancers.

Evaluation of reference genes for gene expression studies in human brown adipose tissue

Human brown adipose tissue (BAT) has during the last 5 year been subjected to an increasing research interest, due to its putative function as a target for future obesity treatments. The most commonly used method for molecular studies of human BAT is the quantitative polymerase chain reaction (qPCR). This method requires normalization to a reference gene (genes with uniform expression under different experimental conditions, e.g. similar expression levels between human BAT and WAT), but so far no evaluation of reference genes for human BAT has been performed. Two different microarray datasets with samples containing human BAT were used to search for genes with low variability in expression levels. Seven genes (FAM96B, GNB1, GNB2, HUWE1, PSMB2, RING1 and TPT1) identified by microarray analysis, and 8 commonly used reference genes (18S, B2M, GAPDH, LRP10, PPIA, RPLP0, UBC, and YWHAZ) were selected and further analyzed by quantitative PCR in both BAT containing perirenal adipose tissue and subcutaneous adipose tissue. Results were analyzed using 2 different algorithms (Normfinder and geNorm). Most of the commonly used reference genes displayed acceptably low variability (geNorm M-values <0.5) in the samples analyzed, but the novel reference genes identified by microarray displayed an even lower variability (M-values <0.25). Our data suggests that PSMB2, GNB2 and GNB1 are suitable novel reference genes for qPCR analysis of human BAT and we recommend that they are included in future gene expression studies of human BAT.

Validation of endogenous control reference genes for normalizing gene expression studies in endometrial carcinoma

Real-time quantitative RT-PCR (qRT-PCR) is a powerful technique used for the relative quantification of target genes, using reference (housekeeping) genes for normalization to ensure the generation of accurate and robust data. A systematic examination of the suitability of endogenous reference genes for gene expression studies in endometrial cancer tissues is absent. The aims of this study were therefore to identify and evaluate from the thirty-two possible reference genes from a TaqMan(®) array panel their suitability as an internal control gene. The mathematical software packages geNorm qBasePLUS identified Pumilio homolog 1 (Drosophila) (PUM1), ubiquitin C (UBC), phosphoglycerate kinase (PGK1), mitochondrial ribosomal protein L19 (MRPL19) and peptidylpropyl isomerase A (cyclophilin A) (PPIA) as the best reference gene combination, whilst NormFinder identified MRPL19 as the best single reference gene, with importin 8 (IPO8) and PPIA being the best combination of two reference genes. BestKeeper ranked MRPL19 as the most stably expressed gene. In addition, the study was validated by examining the relative expression of a test gene, which encodes the cannabinoid receptor 1 (CB1). A significant difference in CB1 mRNA expression between malignant and normal endometrium using MRPL19, PPIA, and IP08 in combination was observed. The use of MRPL19, IPO8 and PPIA was identified as the best reference gene combination for the normalization of gene expression levels in endometrial carcinoma. This study demonstrates that the arbitrary selection of endogenous control reference genes for normalization in qRT-PCR studies of endometrial carcinoma, without validation, risks the production of inaccurate data and should therefore be discouraged.

Identification and validation of suitable reference genes for RT-qPCR analysis in mouse testis development

RT-qPCR is a commonly used method for evaluating gene expression; however, its accuracy and reliability are dependent upon the choice of appropriate reference gene(s), and there is limited information available on suitable reference gene(s) that can be used in mouse testis at different stages. In this study, using the RT-qPCR method, we investigated the expression variations of six reference genes representing different functional classes (Actb, Gapdh, Ppia, Tbp, Rps29, Hprt1) in mice testis during embryonic and postnatal development. The expression stabilities of putative reference genes were evaluated using five algorithms: geNorm, NormFinder, Bestkeeper, the comparative delta C(t) method and integrated tool RefFinder. Analysis of the results showed that Ppia, Gapdh and Actb were identified as the most stable genes and the geometric mean of Ppia, Gapdh and Actb constitutes an appropriate normalization factor for gene expression studies. The mRNA expression of AT1 as a test gene of interest varied depending upon which of the reference gene(s) was used as an internal control(s). This study suggested that Ppia, Gapdh and Actb are suitable reference genes among the six genes used for RT-qPCR normalization and provide crucial information for transcriptional analyses in future studies of gene expression in the developing mouse testis.

Endocannabinoid regulation in human endometrium across the menstrual cycle

Humans produce endogenous cannabinoids (endocannabinoids), a group of molecules that activate the same receptors as tetrahydrocannabinol. Endocannabinoids play important roles in reproduction in multiple species, but data in human endometrium are limited. Because endocannabinoids such as anandamide (AEA) and 2-arachidonoyl glycerol (2-AG) often act within tissues as paracrine factors, their effects can be modulated by changes in expression of locally produced synthetic and degradative/oxidative enzymes. The objective of this study was to localize and quantify expression of these key synthetic and degradative/oxidative enzymes for AEA and 2-AG in human endometrium throughout the menstrual cycle. Key synthetic enzymes include N-arachidonyl-phosphatidylethanolamine phospholipase-D (NAPE-PLD), diacylglycerol-lipase a (DAGL-α, and DAGL-β. Key degradative enzymes include fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL); cyclooxygenase 2 (COX2) is an oxidative enzyme. Endometrial samples were collected in 49 regularly cycling, normal women. Protein localization and expression were achieved by immunohistochemistry and messenger RNA (mRNA) expression by real-time reverse transcriptase polymerase chain reaction. No significant cycle-dependent mRNA expression was observed except that of COX2 (P = .002), which demonstrated maximum expression in the proliferative phase. During the secretory phase, NAPE-PLD protein had increased expression in luminal (P = .001), stromal (P = .007), and glandular (P = .04) epithelia, while FAAH had increased glandular (P = .009) and luminal (P = .01) expression. Increased expression in glandular epithelia was identified for MAGL (P = .03). The COX2 had increased luminal expression during the early secretory phase (P < .0001). In conclusion, maximal expression of degradatory/oxidative enzymes in the secretory phase may foster decreased endocannabinoid tone during implantation.

Expression of adiponectin, leptin, and their receptors in ovarian endometrioma

OBJECTIVE

To evaluate the expression of leptin, leptin receptor (ObR), adiponectin, and adiponectin receptor (AdipoR) in ovarian endometriomas compared with normal endometrium, and to analyze relationships among adipokines and their receptors.

DESIGN

Experimental study.

SETTING

A clinic for the treatment of endometriosis and basic research laboratories.

PATIENT(S)

Forty-four women with endometriosis and 42 age-matched women with no laparoscopic evidence of endometriosis as control subjects.

INTERVENTION(S)

Endometrial tissue samples were obtained during laparoscopic surgery.

MAIN OUTCOME MEASURE(S)

Immunohistochemical staining for leptin, ObR, adiponectin, and AdipoR was performed with the use of tissue microarray. Clinical characteristics were reviewed from the patient's medical records. The effect of leptin on the expression of adiponectin was evaluated in endometriotic cell line using real-time reverse-transcription polymerase chain reaction.

RESULT(S)

Positive expression rates of leptin and ObR were significantly higher in ovarian endometrioma compared with normal endometrium, but those of adiponectin and AdipoR were similar (ovarian endometrioma vs. normal endometrium, respectively: leptin 100% vs. 59.5%; ObR 72.7% vs. 33.3%; adiponectin 31.8% vs. 42.9%; AdipoR 88.6% vs. 73.8%). Expression of adipokines and their receptors did not show any correlation with disease stage. A positive correlation was found between expression of ObR and adiponectin (correlation coefficient 0.488; P=.001). Leptin treatment in endometriotic cells induced mRNA expression of adiponectin.

CONCLUSION(S)

These data suggest that leptin and its receptor are induced in ovarian endometriomas, and that the leptin/ObR system regulates adiponectin gene expression in endometriotic cells.