Bioinformatics of Potential Biomarkers in Patients with Repeated Implantation Failure

AbstractObjectiveThis study applied the public genetic databases high-throughput gene expression omnibus (GEO) database to compare the difference of gene screening between the repeated implantation failure (RIF) patients and women with normal endometrium. This study aims to provide additional information for the diagnosis and treatment in RIF patients through the gene set enrichment analysis and the construction of protein–protein interactions (PPIs) network.MethodThe human endometrial microarray data of RIF and normal control group were obtained from the GEO database provided by the National Center for Biotechnology Information (NCBI). The analysis and the review of differential gene screening, gene ontology (GO) pathway analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and PPIs network construction were carried out.Result273 genes with differential expression, 87 up-regulated and 186 down-regulated genes, were obtained through differential gene analysis. 50 genes with the most significant differential expression fold change were screened for subsequent analysis. KEGG results indicated that the top three related pathways were cancer pathway, MAPK signaling pathway, and homologous recombination pathway when the relevant pathways were sequenced according to the correlation size. GO analysis showed that differentially expressed genes were involved in protein phosphorylation, complement activation, and other biological processes. PPIs analysis demonstrated that targeted genes show high correlation to the endometrial receptivity, including PAEP, CXCL14, HOXB3, CD55, and VEGFA, all were down-regulated in RIF endometrial tissues compared to the control group, and these genes also influenced and regulated each other.ConclusionThrough public databases and bioinformatics, several factors in endometrial receptivity that affect RIF directly and indirectly were found. In particular, the immune and angiogenesis factors stood out the most. The different genes which regulate the immune response and angiogenesis response may become new targeted treatment for RIF.

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The Role of Transcriptomic Biomarkers of Endometrial Receptivity in Personalized Embryo Transfer for Patients with Repeated Implantation Failure

10.21203/rs.3.rs-126797/v1 ◽

2020 ◽

Author(s):

Aihua He ◽

Yangyun Zou ◽

Cheng Wan ◽

Jing Zhao ◽

Qiong Zhang ◽

...

Keyword(s):

Embryo Transfer ◽

Controlled Trial ◽

Embryo Implantation ◽

Endometrial Receptivity ◽

Training Dataset ◽

Control Group ◽

Second Phase ◽

Implantation Failure ◽

Repeated Implantation Failure ◽

Experimental Group

Abstract Background: Window of implantation (WOI) displacement was known as one of endometrial origin leading to embryo implantation failure, especially for repeated implantation failure (RIF). A accurately prediction tool of endometrial receptivity (ER) is extraordinary needed to precisely guide the successful embryo implantation. We aimed to establish an RNA-seq based endometrial receptivity test tool (rsERT) using transcriptomic biomarkers, and to evaluate the benefit of personalized embryo transfer (pET) guided by this tool in patients with repeated implantation failure (RIF).Methods: Two-phase strategy including tool establishment with retrospective data and benefit evaluation with prospective, nonrandomized controlled trial. In the first phase, the rsERT was established by sequencing and analyzing the RNA of endometrial tissues from 50 infertile patients with normal window of implantation (WOI) timing. In the second phase, 142 patients with RIF were recruited and grouped by patient self-selection (experimental group, n=56; control group, n=86). pET guided by rsERT in the experimental group, and conventional ET in the control group. Results: The rsERT, comprising 175 biomarker genes, showed an average accuracy of 98.4% by using 10-fold cross-validation. IPR of experimental group (50.0%) was significantly improved compared to that (23.7%) of control group (RR, 2.107; 95% CI, 1.159 to 3.830; P = 0.017) when transferring day 3 embryos. Although not statistically different, IPR of experimental group (63.6%) was still 20 percentage points higher than that (40.7%) of control group (RR, 1.562; 95% CI, 0.898 to 2.718; P = 0.111) when transferring blastocyst. Regression analysis can precisely predict the optimal WOI time by using all samples as training dataset (R2= 0.92).Conclusions: The rsERT was developed to accurately predict WOI period and significantly improve pregnancy outcomes of patients with RIF, indicating the clinical potential of rsERT-guided pET. Optimization of the model made it possible to predict the optimal WOI by one-point sampling.Trial registration: Chinese Clinical Trial Registry: ChiCTR-DDD-17013375. Registered 14 November 2017, http://www.chictr.org.cn/index.aspx

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The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

Journal of Translational Medicine ◽

10.1186/s12967-021-02837-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Aihua He ◽

Yangyun Zou ◽

Cheng Wan ◽

Jing Zhao ◽

Qiong Zhang ◽

...

Keyword(s):

Embryo Transfer ◽

Controlled Trial ◽

Embryo Implantation ◽

Endometrial Receptivity ◽

Control Group ◽

Second Phase ◽

Implantation Failure ◽

Clinical Trial Registry ◽

Repeated Implantation Failure ◽

Experimental Group

Abstract Background Window of implantation (WOI) displacement is one of the endometrial origins of embryo implantation failure, especially repeated implantation failure (RIF). An accurate prediction tool for endometrial receptivity (ER) is extraordinarily needed to precisely guide successful embryo implantation. We aimed to establish an RNA-Seq-based endometrial receptivity test (rsERT) tool using transcriptomic biomarkers and to evaluate the benefit of personalized embryo transfer (pET) guided by this tool in patients with RIF. Methods This was a two-phase strategy comprising tool establishment with retrospective data and benefit evaluation with a prospective, nonrandomized controlled trial. In the first phase, rsERT was established by sequencing and analyzing the RNA of endometrial tissues from 50 IVF patients with normal WOI timing. In the second phase, 142 patients with RIF were recruited and grouped by patient self-selection (experimental group, n = 56; control group, n = 86). pET guided by rsERT was performed in the experimental group and conventional ET in the control group. Results The rsERT, comprising 175 biomarker genes, showed an average accuracy of 98.4% by using tenfold cross-validation. The intrauterine pregnancy rate (IPR) of the experimental group (50.0%) was significantly improved compared to that (23.7%) of the control group (RR, 2.107; 95% CI 1.159 to 3.830; P = 0.017) when transferring day-3 embryos. Although not significantly different, the IPR of the experimental group (63.6%) was still 20 percentage points higher than that (40.7%) of the control group (RR, 1.562; 95% CI 0.898 to 2.718; P = 0.111) when transferring blastocysts. Conclusions The rsERT was developed to accurately predict the WOI period and significantly improve the pregnancy outcomes of patients with RIF, indicating the clinical potential of rsERT-guided pET. Trial registration Chinese Clinical Trial Registry: ChiCTR-DDD-17013375. Registered 14 November 2017, http://www.chictr.org.cn/index.aspx

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Differential expression of innate/adaptive immunity genes induced by endometrial scratching as a hopeful approach for implantation boosting in unexplained, repeated implantation failure: An RCT

Journal of Reproductive Immunology ◽

10.1016/j.jri.2021.103426 ◽

2021 ◽

pp. 103426

Author(s):

Samaneh Aghajanpour ◽

Elham Hosseini ◽

Elham Amirchaghmaghi ◽

Zahra Zandieh ◽

Fatemehsadat Amjadi ◽

...

Keyword(s):

Differential Expression ◽

Adaptive Immunity ◽

Implantation Failure ◽

Repeated Implantation Failure ◽

Endometrial Scratching ◽

Immunity Genes

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Abstract 545: Differential mRNA Expression is Influenced by Apolipoprotein A-I in Order to Promote Foam Cell Regression

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.36.suppl_1.545 ◽

2016 ◽

Vol 36 (suppl_1) ◽

Author(s):

Elisa C Maruko ◽

Hao Xu ◽

Sushma Kaul ◽

Brian J Capaldo ◽

Nathalie Pamir ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression ◽

Expression Analysis ◽

Immune Cell ◽

Foam Cell ◽

Differential Expression Analysis ◽

Ldl Receptor ◽

Gene Set Enrichment Analysis ◽

Control Group ◽

Apolipoprotein A

Atherosclerosis is a disease of both lipids and inflammatory immune cells. More specifically, elevated plasma levels of low-density lipoproteins (LDL) leads to migration of circulating monocytes into the artery wall. Lipid loaded monocyte cells subsequently proliferate in the arterial walls becoming macrophage foam cells; a hallmark of atherosclerotic lesions. A proposed mechanism of the protective effects of high-density lipoprotein (HDL) is apolipoprotein A-I (apo A-I) acting as a mediator of cholesterol efflux and subsequent foam cell regression. To better understand the biological changes stimulated by apo A-I treatment, differential expression analysis of microarray data was performed on spleen cells from apo A-I treated mice. LDL receptor null (LDLr -/- ) and LDL receptor and apo A-I null (LDLr -/- , apoA-I -/- ) mice were fed a western diet consisting of 0.2% cholesterol and 42% of calories as fat for 12 weeks. After 6 weeks of diet, a subset of mice for each genotype was subcutaneously injected with 200 micrograms of apo A-I 3 times a week for the remaining 6 weeks. The control group mice were subcutaneously injected with 200 micrograms of saline or BSA. Spleen cell RNA was isolated, purified, and analyzed for differential expression analysis using Illumina BeadArray Microarray Technology Analysis. Individual gene expression analysis for LDLr -/- , apoA-I -/- apo A-I treated mice showed 281 significantly differentially expressed genes compared to BSA treated mice. LDLr -/- A-I treated mice had 1502. Of the significant genes, 189 intersected across both genotypes. LDLr -/- , apoA-I -/- A-I mice showed 73 up-regulated and 116 down-regulated genes. Similarly, LDLr -/- A-I mice had 71 up-regulated and 118 down-regulated. One-directional Gene Set Enrichment Analysis (GSEA) of LDLr -/- , apoA-I -/- A-I mice revealed 49 significant pathways while a total of 63 were found for LDLr -/- . Of these pathways, 21 were up-regulated and 13 were down-regulated in both genotypes. Eight of the top 10 most significant up-regulated pathways in both genotypes were immune cell related. Their functions involve receptor, adhesion, and chemokine signaling. Overall, preliminary analysis suggests A-I treatment induces similar gene expression changes across different genotypes.

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The endometrial receptivity array for diagnosis and personalized embryo transfer as a treatment for patients with repeated implantation failure

Fertility and Sterility ◽

10.1016/j.fertnstert.2013.05.004 ◽

2013 ◽

Vol 100 (3) ◽

pp. 818-824 ◽

Cited By ~ 185

Author(s):

Maria Ruiz-Alonso ◽

David Blesa ◽

Patricia Díaz-Gimeno ◽

Eva Gómez ◽

Manuel Fernández-Sánchez ◽

...

Keyword(s):

Embryo Transfer ◽

Endometrial Receptivity ◽

Implantation Failure ◽

Repeated Implantation Failure

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Increased expression of HMGB1 in the implantation phase endometrium is related to recurrent implantation failure

10.21203/rs.3.rs-695265/v1 ◽

2021 ◽

Author(s):

Mi Han ◽

Yi Cao ◽

Wenjie Zhou ◽

Mingjuan Zhou ◽

Xiaowei Zhou ◽

...

Keyword(s):

Epithelial Cells ◽

Underlying Mechanism ◽

Endometrial Receptivity ◽

In Vitro Assays ◽

Control Group ◽

Implantation Failure ◽

Recurrent Implantation Failure ◽

Tubal Infertility ◽

Endometrial Stromal Cells

Abstract Impaired endometrial receptivity is the main cause of recurrent implantation failure (RIF), however, its underlying mechanism is unclear. In this study, we found that HMGB1 expression was significantly decreased in the implantation phase endometrium in the control group (patients with tubal infertility who successfully achieved conception after the first embryo transfer) (P = 0.006). However, the expression levels of HMGB1 mRNA and protein were significantly upregulated during the implantation phase in endometrial tissues obtained from patients with RIF compared to those in the control group (P = 0.001), consistent with the results of genome-wide expression profiling. Moreover, in vitro assays showed that increased expression of HMGB1 in human endometrial epithelial cells cause marked deficiency in supporting blastocysts and human embryonic JAR cell adhesion, mimicking the process of embryo adhesion. However, overexpression of HMGB1 had no effect on cell proliferation and in-vitro decidualization in a human endometrial stromal cell line (T-HESCs) and in primary human endometrial stromal cells (HESCs). These findings indicate that increased HMGB1 levels suppressed the adhesion capability of epithelial cells, contributing to impaired endometrial receptivity in patients with recurrent implantation failure. This characteristic can be used as a target for detecting and treating recurrent implantation failure in clinical practice.

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The SF3b Splicing Complex Regulates DNA Damage Response in Acute Lymphoblastic Leukemia

Blood ◽

10.1182/blood-2019-124787 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 1237-1237 ◽

Cited By ~ 1

Author(s):

Shalini Sankar ◽

Miriam Guillen Navarro ◽

Frida Ponthan ◽

Simon Bomken ◽

Sirintra Nakjang ◽

...

Keyword(s):

Gene Expression ◽

Dna Damage ◽

Differential Expression ◽

Differential Gene Expression ◽

Research Funding ◽

Gene Set Enrichment Analysis ◽

Rna Seq ◽

Self Renewal ◽

Strand Breaks ◽

Differential Gene

To identify potential regulators of propagation and self-renewal of Acute Lymphoblastic Leukaemia (ALL), we performed an explorative genome-wide RNAi screen followed by CRISPR ex vivo and in vivo validation screens in the t(4;11)-positive ALL cell line SEM. These screens identified the splicing factor PHF5A as a crucial component of the leukemic program. PHF5A is a subunit of the SF3b protein complex, which directs alternative splicing by binding to the branchpoint of pre-mRNA. Mutations in members of this complex including SF3B1 have been implicated in several haematological malignancies. Functional perturbation experiments demonstrated that PHF5A depletion impairs proliferation, viability and clonogenicity in a range of ALL and AML cell lines strongly suggesting that PHF5A is required for leukemic propagation and self-renewal. To identify genetic programs affected by PHF5A inhibition, we performed RNA-seq followed by analysis of differential gene expression and splicing events. We identified 473 genes with differential expression upon PHF5A knockdown. In addition, we performed in-depth analysis of splicing patterns by examining both differential exon/intron usage and exon junction formation. These analyses demonstrated that loss of PHF5A affects splicing of more than 2500 genes with exon skipping and intron retention being the most frequent splicing events. In order to identify processes and pathways affected by PHF5A, we performed gene set enrichment analysis (GSEA) on both differential expression and splicing. While gene sets associated with RNA processing including splicing, turnover and translation were enriched in both data sets, the differential gene expression signature was also linked to DNA repair processes including base excision, mismatch and homologous recombination repair. In line with these findings, knockdown of either PHF5A or its partner protein SF3B1 induced DNA strand breaks as indicated by comet assay and increased y-H2AX levels. Furthermore, both PHF5A and SF3B1 depletion sensitized ALL cells towards the DNA crosslinking agent mitomycin C. Closer inspection of RNA-seq datasets revealed reduced FANCD2 expression and skipping of exon 22 associated with impaired mono-ubiquitination of the FANCD2 protein as a consequence of PHF5A and SF3B1 knockdown. Furthermore, expression of RAD51, a key component of double strand break repair, also decreased upon PHF5A and SF3B1 knockdown. Notably, in vitro pharmacological inhibition of SF3b complex activity using H3B-8800 (or Pladienolide B) showed a very similar effect on FANCD2 expression, and ubiquitination as well as decrease of RAD51 and an increase in y-H2AX levels on a dose and time-dependent manner. This strongly suggests a mechanistic link between impaired RNA splicing and the repair of DNA double-strand breaks. These combined data show that leukemic cells are highly dependent on a functional SF3b splicing complex. Interference with its function results in DNA damage and also sensitizes towards DNA damaging agents pointing towards a possible benefit of the combined application of inhibitors targeting the SF3b complex with more conventional chemotherapy. Disclosures Ponthan: Epistem Ltd: Employment. Zwaan:Sanofi: Consultancy; Incyte: Consultancy; BMS: Research Funding; Roche: Consultancy; Janssen: Consultancy; Daiichi Sankyo: Consultancy; Servier: Consultancy; Jazz Pharmaceuticals: Other: Travel support; Pfizer: Research Funding; Celgene: Consultancy, Research Funding. Vormoor:Abbvie (uncompensated): Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Roche/Genentech: Consultancy, Honoraria, Research Funding; AstraZeneca: Research Funding.

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Modern methods of influence at endometrial receptivity in patients with recurrent implantation failure (review)

GYNECOLOGY ◽

10.26442/2079-5696_2018.3.66-70 ◽

2018 ◽

Vol 20 (3) ◽

pp. 66-70

Author(s):

M I Polovneva ◽

I E Korneeva ◽

O V Bourmenskaya

Keyword(s):

Mononuclear Cells ◽

Platelet Rich Plasma ◽

Test System ◽

Endometrial Receptivity ◽

Implantation Failure ◽

Recurrent Implantation Failure ◽

Peripheral Blood Mononuclear ◽

Repeated Implantation Failure ◽

Endometrial Scratching ◽

Modern Methods

Objective. To carry out an analysis of the data available in scientific literature on modern methods of influence at endometrial receptivity in patients with recurrent implantation failure. Materials and methods. The review includes the data of foreign and Russia papers published on PubMed during the last 7-10 years. Results. There are studies described the role of endometrial scratching, infusion granulocyte colony stimulating factor, autologous peripheral blood mononuclear cells, autologous platelet-rich plasma, the endometrial receptivity array in treatment for patients with repeated implantation failure. Conclusion. Several adjuvant therapies and diagnostic tests have been used along with IVF to increase the pregnancy rates for women with repeated implantation failure. Perhaps a new test-system to find personal predictors of endometrial receptivity can tern up a positive effect at patients with RIF.

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Non-invasive intra-uterine administration of Botulinum Toxin A enhances endometrial angiogenesis and improves the rates of embryo implantation

10.21203/rs.3.rs-47485/v1 ◽

2020 ◽

Author(s):

Hwa Seon Koo ◽

Min-Ji Yoon ◽

Seon-Hwa Hong ◽

Jungho Ahn ◽

Hwijae Cha ◽

...

Keyword(s):

Botulinum Toxin ◽

Botulinum Toxin A ◽

Embryo Implantation ◽

Endometrial Receptivity ◽

Marker Genes ◽

Implantation Failure ◽

Toxin A ◽

Major Barrier ◽

Repeated Implantation Failure ◽

Non Invasive

Abstract Background. Endometrial angiogenesis plays crucial roles in determining the endometrial receptivity. Defects in endometrial receptivity often cause repeated implantation failure, which is one of the major unmet needs for infertility and contributes a major barrier to the assisted reproductive technology. Despite the numerous extensive research work, there are currently no effective evidence-based treatments to prevent or cure this condition.Method. As a non-invasive treatment strategy, Botulinum toxin A (BoTA) was administered into one side of mouse uterine horns and saline was infused into the other side of horns for the control. Impact of BoTA was assessed in the endometrium at 3 or 8 days after infusion.Results. We demonstrated that BoTA administration enhances the capacity of endothelial cell tube formation and sprouting. The intrauterine BoTA administration significantly induced endometrial angiogenesis displaying increased numbers of vessel formation and expression levels of related-marker genes. Moreover, BoTA intrauterine application promoted the endometrial receptivity and the rates of embryo implantation were improved with BoTA treatment with no morphologically retarded embryos. Conclusion. Intrauterine BoTA treatment has a beneficial effect on vascular reconstruction of functional endometrium prior to embryo implantation by increasing endometrial blood flow near the uterine cavity suggesting BoTA treatment as a potential therapeutic strategy for patients who are suffering from repeated implantation failure with the problems with endometrial receptivity.

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