Expression of MSX1, HOXA11 and TP53I3 in the endometrium associated with the onset of pregnancy after repeated failed IVF attempts in patients with tubo-peritoneal factor infertility

Relevance. The success of the in vitro fertilisation (IVF) program, among other factors, depends on the readiness of the endometrium to accept the embryo. It is believed that this is possible during the so-called implantation window, the timing of which can be shifted under the influence of various factors. Evaluation of endometrial receptivity and the implantation window based on analysis of endometrial gene expression before embryo transfer is a promising approach for predicting the likelihood of pregnancy in IVF programs. Aim. To construct a classifier based on the expression of endometrial genes for predicting the outcome of an IVF program in patients with tubal-peritoneal infertility factor and repeated failed IVF attempts in history. Materials and methods. Before the IVF program, a genome-wide transcriptome profiling of endometrial samples of 15 women with tubal-perioneal infertility factor and repeated unsuccessful IVF attempts in history was carried out using Affymetrix arrays. Potential genes capable of classifying IVF program outcomes were selected, after which the expression of these genes was analyzed by qPCR-RT in the endometrium of 47 women to construct IVF outcome classifiers based on the expression of pairs or triples of genes. Results. A classifier based on the expression of the triple of genes MSX1 (HOX7), HOXA11, and TP53I3 made it possible to determine the onset of pregnancy in an IVF program with a sensitivity of 73% and a specificity of 71% with an area under the ROC-curve (AUC) of 0.738 (95% confidence interval 0.5770.898). Earlier, a relationship was found between the expression of these genes and receptivity of the endometrium, which suggests that these genes play a role in the onset of the implantation window. Conclusions. The use of a classifier based on the genes MSX1 (HOX7), HOXA11, and TP53I3 can determine the readiness of the endometrium to accept an embryo and create an individual prognosis of the outcome of an IVF program in women with tubal-peritoneal infertility factor and repeated failed IVF attempts in history.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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MUC1 and E-cadherin immunohistochemistry of endometrium cannot predict the outcome of in vitro fertilization: A case-control study

F1000Research ◽

10.12688/f1000research.17929.1 ◽

2019 ◽

Vol 8 ◽

pp. 162

Author(s):

Saumitra Chakravarty ◽

Mohammed Kamal

Keyword(s):

Gene Expression ◽

Case Control Study ◽

Case Control ◽

Endometrial Receptivity ◽

Ivf Outcome ◽

Predictive Tool ◽

Control Study ◽

Signal Intensities ◽

E Cadherin

Background: Although in vitro fertilization (IVF) has played a major role in the management of infertility, its failure rate is still 60-80% and most of the causes failure are unknown. Therefore, a histomorphology-based predictive tool to forecast IVF outcome that utilizes expression data of certain cellular adhesion molecules in endometrium pertaining to successful implantation might provide the theoretical basis to develop a low-cost laboratory investigation suited for low to middle income countries as opposed to the expensive gene expression based tools like endometrial receptivity array. In this study, mucin 1 (MUC1) and E-cadherin immunohistochemistry of endometrium from aspiring IVF women were analyzed to see if there is any correlation between signal intensities and endometrial receptivity in terms of IVF outcome. Methods: This was a case-control study conducted among women of reproductive age with infertility who underwent IVF at the Centre for Assisted Reproduction (CARe), Dhaka between March and December 2017. Endometrial biopsy samples were collected and routine histological as well as immunohistochemical analysis was performed on those samples at the Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka. A total of 21 patients, 17 cases (IVF failure) and four controls (IVF success), were included in the study by consecutive convenient sampling. Relevant history and medical records of each of the patients were also obtained accordingly. Results: No statistically significant correlation was found between IVF outcomes and the signal intensities in endometrium produced by MUC1 and E-cadherin immunohistochemistry. Conclusions: Despite the fact that this study did not find any statistically significant correlation between endometrial immunohistochemistry of MUC1 and E-cadherin and IVF outcome, further studies may incorporate gene expression arrays to supplement or revise those findings.

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Expression and significance of miR-30d-5p and SOCS1 in patients with recurrent implantation failure during implantation window

Reproductive Biology and Endocrinology ◽

10.1186/s12958-021-00820-2 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yuhao Zhao ◽

Dongmei He ◽

Hong Zeng ◽

Jiefeng Luo ◽

Shuang Yang ◽

...

Keyword(s):

Endometrial Biopsy ◽

Endometrial Receptivity ◽

Leukaemia Inhibitory Factor ◽

In Vitro Fertilisation ◽

Control Group ◽

Implantation Failure ◽

Recurrent Implantation Failure ◽

Tissue Samples ◽

Implantation Window

Abstract Background Poor endometrial receptivity is a major factor that leads to recurrent implantation failure. However, the traditional method cannot accurately evaluate endometrial receptivity. Various studies have indicated that microRNAs (miRNAs) are involved in multiple processes of embryo implantation, but the role of miRNAs in endometrial receptivity in patients with recurrent implantation failure (RIF) remains elusive. In the present study, we investigated the presence of pinopodes and the roles of miR-30d-5p, suppressor of cytokine signalling 1 (SOCS1) and the leukaemia inhibitory factor (LIF) pathway in women with a history of RIF during the implantation window. Methods Endometrial tissue samples were collected between January 2018 to June 2019 from two groups of women who underwent in vitro fertilisation and embryo transfer (IVF-ET) or frozen ET. The RIF group included 20 women who underwent ≥ 3 ETs, including a total of ≥ 4 good-quality embryos, without pregnancy, whereas the control group included 10 women who had given birth at least once in the past year. An endometrial biopsy was performed during the implantation window (LH + 7). The development of pinopodes in the endometrial biopsy samples from all groups was evaluated using scanning electron microscopy (SEM). Quantitative reverse transcription-polymerase chain reaction and western blotting were used to investigate the expression levels of miR-30d-5p, SOCS1, and the LIF pathway. Results The presence of developed pinopodes decreased in patients with RIF on LH + 7. The expression level of miR-30d-5p decreased in the endometria during the implantation window of patients with RIF, whereas the mRNA and protein levels of SOCS1 were significantly higher in the RIF group than in the control group. Furthermore, a negative correlation was observed between the expression of miR-30d-5p and SOCS1 (r2 = 0.8362). In addition, a significant decrease in LIF and p-STAT3 expression was observed during the implantation window in patients with RIF. Conclusions MiR-30d-5p and SOCS1 may be potential biomarkers for endometrial receptivity. Changes in pinopode development and abnormal expression of miR-30d-5p, SOCS1 and LIF pathway in the endometrium could be the reasons for implantation failure.

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Faculty Opinions recommendation of An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1066817.519755 ◽

2007 ◽

Author(s):

Vitaly Citovsky

Keyword(s):

Gene Expression ◽

Genome Wide ◽

A Genome

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A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model

Neurochemical Research ◽

10.1007/s11064-021-03241-0 ◽

2021 ◽

Vol 46 (5) ◽

pp. 1101-1111

Author(s):

Jun Li ◽

Hongyu Zhao ◽

Yongqiang Xing ◽

Tongling Zhao ◽

Lu Cai ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Mouse Model ◽

Hypoxic Preconditioning ◽

Whole Body ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome ◽

Alternative Splicing Events

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Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape

Translational Psychiatry ◽

10.1038/s41398-021-01270-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Divya Mehta ◽

Karen Grewen ◽

Brenda Pearson ◽

Shivangi Wani ◽

Leanne Wallace ◽

...

Keyword(s):

Gene Expression ◽

Depressive Symptoms ◽

Postpartum Depression ◽

Expression Profiles ◽

Depression Scale ◽

Well Being ◽

Health Concern ◽

Genome Wide ◽

A Genome ◽

Genome Wide Gene Expression

AbstractMaternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29–53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4–2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.

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Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution

Microorganisms ◽

10.3390/microorganisms9020240 ◽

2021 ◽

Vol 9 (2) ◽

pp. 240

Author(s):

Bruno Cavadas ◽

Marina Leite ◽

Nicole Pedro ◽

Ana C. Magalhães ◽

Joana Melo ◽

...

Keyword(s):

Gene Expression ◽

Helicobacter Pylori ◽

Host Response ◽

Homo Sapiens ◽

European Ancestry ◽

Genome Wide ◽

Expression Host ◽

H Pylori ◽

Human Ancestry

The continuous characterization of genome-wide diversity in population and case–cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the long-standing associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.

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A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity

Scientific Reports ◽

10.1038/s41598-021-81226-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Laura Bernhardt ◽

Marcus Dittrich ◽

Rabih El-Merahbi ◽

Antoine-Emmanuel Saliba ◽

Tobias Müller ◽

...

Keyword(s):

Gene Expression ◽

Negative Impact ◽

Preimplantation Embryos ◽

High Fat ◽

Cell Stage ◽

Genetic Transmission ◽

Diet Induced Obesity ◽

Genome Wide ◽

A Genome ◽

Paternal Obesity

AbstractPaternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.

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Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer’s disease

Acta Neuropathologica Communications ◽

10.1186/s40478-021-01199-2 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Joseph S. Reddy ◽

Mariet Allen ◽

Charlotte C. G. Ho ◽

Stephanie R. Oatman ◽

Özkan İş ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Genome Wide Association Study ◽

Transcriptome Profiling ◽

Brain Regions ◽

Common Finding ◽

Amyloid Angiopathy ◽

Genome Wide ◽

A Genome ◽

Male Sex

AbstractCerebral amyloid angiopathy (CAA) contributes to accelerated cognitive decline in Alzheimer’s disease (AD) dementia and is a common finding at autopsy. The APOEε4 allele and male sex have previously been reported to associate with increased CAA in AD. To inform biomarker and therapeutic target discovery, we aimed to identify additional genetic risk factors and biological pathways involved in this vascular component of AD etiology. We present a genome-wide association study of CAA pathology in AD cases and report sex- and APOE-stratified assessment of this phenotype. Genome-wide genotypes were collected from 853 neuropathology-confirmed AD cases scored for CAA across five brain regions, and imputed to the Haplotype Reference Consortium panel. Key variables and genome-wide genotypes were tested for association with CAA in all individuals and in sex and APOEε4 stratified subsets. Pathway enrichment was run for each of the genetic analyses. Implicated loci were further investigated for functional consequences using brain transcriptome data from 1,186 samples representing seven brain regions profiled as part of the AMP-AD consortium. We confirmed association of male sex, AD neuropathology and APOEε4 with increased CAA, and identified a novel locus, LINC-PINT, associated with lower CAA amongst APOEε4-negative individuals (rs10234094-C, beta = −3.70 [95% CI −0.49—−0.24]; p = 1.63E-08). Transcriptome profiling revealed higher LINC-PINT expression levels in AD cases, and association of rs10234094-C with altered LINC-PINT splicing. Pathway analysis indicates variation in genes involved in neuronal health and function are linked to CAA in AD patients. Further studies in additional and diverse cohorts are needed to assess broader translation of our findings.

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