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Diaz-Gimeno P, Sebastian-Leon P, Spath K, Marti-Garcia D, Sanchez-Reyes JM, Vidal MDC, Devesa-Peiro A, Sanchez-Ribas I, Martinez-Martinez A, Pellicer N, Wells D, Pellicer A. Predicting risk of endometrial failure: a biomarker signature that identifies a novel disruption independent of endometrial timing in patients undergoing hormonal replacement cycles. Fertil Steril 2024; 122:352-364. [PMID: 38518993 DOI: 10.1016/j.fertnstert.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
OBJECTIVE To propose a new gene expression signature that identifies endometrial disruptions independent of endometrial luteal phase timing and predicts if patients are at risk of endometrial failure. DESIGN Multicentric, prospective study. SETTING Reproductive medicine research department in a public hospital affiliated with private fertility clinics and a reproductive genetics laboratory. PATIENTS Caucasian women (n = 281; 39.4 ± 4.8 years old with a body mass index of 22.9 ± 3.5 kg/m2) undergoing hormone replacement therapy between July 2018 and July 2021. Endometrial samples from 217 patients met RNA quality criteria for signature discovery and analysis. INTERVENTION(S) Endometrial biopsies collected in the mid-secretory phase. MAIN OUTCOME MEASURE(S) Endometrial luteal phase timing-corrected expression of 404 genes and reproductive outcomes of the first single embryo transfer (SET) after biopsy collection to identify prognostic biomarkers of endometrial failure. RESULTS Removal of endometrial timing variation from gene expression data allowed patients to be stratified into poor (n = 137) or good (n = 49) endometrial prognosis groups on the basis of their clinical and transcriptomic profiles. Significant differences were found between endometrial prognosis groups in terms of reproductive rates: pregnancy (44.6% vs. 79.6%), live birth (25.6% vs. 77.6%), clinical miscarriage (22.2% vs. 2.6%), and biochemical miscarriage (20.4% vs. 0%). The relative risk of endometrial failure for patients predicted as a poor endometrial prognosis was 3.3 times higher than those with a good prognosis. The differences in gene expression between both profiles were proposed as a biomarker, coined the endometrial failure risk (EFR) signature. Poor prognosis profiles were characterized by 59 upregulated and 63 downregulated genes mainly involved in regulation (17.0%), metabolism (8.4%), immune response, and inflammation (7.8%). This EFR signature had a median accuracy of 0.92 (min = 0.88, max = 0.94), median sensitivity of 0.96 (min = 0.91, max = 0.98), and median specificity of 0.84 (min = 0.77, max = 0.88), positioning itself as a promising biomarker for endometrial evaluation. CONCLUSION(S) The EFR signature revealed a novel endometrial disruption, independent of endometrial luteal phase timing, present in 73.7% of patients. This EFR signature stratified patients into 2 significantly distinct and clinically relevant prognosis profiles providing opportunities for personalized therapy. Nevertheless, further validations are needed before implementing this gene signature as an artificial intelligence (AI)-based tool to reduce the risk of patients experiencing endometrial failure.
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Affiliation(s)
- Patricia Diaz-Gimeno
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.
| | - Patricia Sebastian-Leon
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | | | - Diana Marti-Garcia
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Josefa Maria Sanchez-Reyes
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - Maria Del Carmen Vidal
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Reproductive Medicine Center, IVI RMA Valencia, Valencia, Spain
| | - Almudena Devesa-Peiro
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - Immaculada Sanchez-Ribas
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Reproductive Medicine Center, IVI RMA Barcelona, Barcelona, Spain
| | - Asunta Martinez-Martinez
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Nuria Pellicer
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; Reproductive Medicine Center, IVI RMA Valencia, Valencia, Spain
| | - Dagan Wells
- JUNO Genetics, Winchester House, Oxford, United Kingdom; Nuffield Department of Women's & Reproductive Health, University of Oxford, Women's Centre John Radcliffe Hospital, Oxford, United Kingdom
| | - Antonio Pellicer
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain; JUNO Genetics, Winchester House, Oxford, United Kingdom; Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain; Reproductive Medicine Center, IVI RMA Rome, Largo Il de brando Pizzetti, Roma, Italy
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Parraga-Leo A, Sebastian-Leon P, Devesa-Peiro A, Marti-Garcia D, Pellicer N, Remohi J, Dominguez F, Diaz-Gimeno P. Deciphering a shared transcriptomic regulation and the relative contribution of each regulator type through endometrial gene expression signatures. Reprod Biol Endocrinol 2023; 21:84. [PMID: 37700285 PMCID: PMC10496172 DOI: 10.1186/s12958-023-01131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGORUND While various endometrial biomarkers have been characterized at the transcriptomic and functional level, there is generally a poor overlap among studies, making it unclear to what extent their upstream regulators (e.g., ovarian hormones, transcription factors (TFs) and microRNAs (miRNAs)) realistically contribute to menstrual cycle progression and function. Unmasking the intricacies of the molecular interactions in the endometrium from a novel systemic point of view will help gain a more accurate perspective of endometrial regulation and a better explanation the molecular etiology of endometrial-factor infertility. METHODS An in-silico analysis was carried out to identify which regulators consistently target the gene biomarkers proposed in studies related to endometrial progression and implantation failure (19 gene lists/signatures were included). The roles of these regulators, and of genes related to progesterone and estrogens, were then analysed in transcriptomic datasets compiled from samples collected throughout the menstrual cycle (n = 129), and the expression of selected TFs were prospectively validated in an independent cohort of healthy participants (n = 19). RESULTS A total of 3,608 distinct genes from the 19 gene lists were associated with endometrial progression and implantation failure. The lists' regulation was significantly favoured by TFs (89% (17/19) of gene lists) and progesterone (47% (8 /19) of gene lists), rather than miRNAs (5% (1/19) of gene lists) or estrogen (0% (0/19) of gene lists), respectively (FDR < 0.05). Exceptionally, two gene lists that were previously associated with implantation failure and unexplained infertility were less hormone-dependent, but primarily regulated by estrogen. Although endometrial progression genes were mainly targeted by hormones rather than non-hormonal contributors (odds ratio = 91.94, FDR < 0.05), we identified 311 TFs and 595 miRNAs not previously associated with ovarian hormones. We highlight CTCF, GATA6, hsa-miR-15a-5p, hsa-miR-218-5p, hsa-miR-107, hsa-miR-103a-3p, and hsa-miR-128-3p, as overlapping novel master regulators of endometrial function. The gene expression changes of selected regulators throughout the menstrual cycle (FDR < 0.05), dually validated in-silico and through endometrial biopsies, corroborated their potential regulatory roles in the endometrium. CONCLUSIONS This study revealed novel hormonal and non-hormonal regulators and their relative contributions to endometrial progression and pathology, providing new leads for the potential causes of endometrial-factor infertility.
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Affiliation(s)
- Antonio Parraga-Leo
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Av. Blasco Ibáñez 15, 46010, Valencia, Valencia, Spain
| | - Patricia Sebastian-Leon
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
| | - Almudena Devesa-Peiro
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Av. Blasco Ibáñez 15, 46010, Valencia, Valencia, Spain
| | - Diana Marti-Garcia
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Av. Blasco Ibáñez 15, 46010, Valencia, Valencia, Spain
| | - Nuria Pellicer
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
- IVIRMA Global Research Alliance, IVIRMA Valencia, Plaza de La Policia Local 3, 46015, Valencia, Spain
| | - Jose Remohi
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Av. Blasco Ibáñez 15, 46010, Valencia, Valencia, Spain
- IVIRMA Global Research Alliance, IVIRMA Valencia, Plaza de La Policia Local 3, 46015, Valencia, Spain
| | - Francisco Dominguez
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain
| | - Patricia Diaz-Gimeno
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Av. Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Valencia, Spain.
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Aplin JD, Stevens A. Use of 'omics for endometrial timing: the cycle moves on. Hum Reprod 2022; 37:644-650. [PMID: 35147196 PMCID: PMC8971645 DOI: 10.1093/humrep/deac022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
For some years, the prospect of precise and personalized timing of the endometrial cycle for optimal embryo replacement has been held out as a potential solution to low implantation rates. It is envisaged that a receptive state can be defined and reached at a predictable time, and embryo replacement performed in synchrony. In the last century, morphological changes characteristic of the mid secretory phase were defined in precisely timed cycles in women of proven fertility, but when deviations from this standardized schedule occur, their significance for implantation has remained uncertain. ‘Omics technologies have been widely advocated for staging the endometrial cycle and defining a set of biochemical requirements for implantation, but after two decades of research, improvements to pregnancy rates have not followed, and there is a striking lack of agreement regarding the molecular characterization of the receptive state. Some of the rationale underlying these problems is now emerging with the application of higher-level computational and biological methodology. Here, we consider the challenges of defining an endometrial phenotype that can support implantation and continuing pregnancy. Receptivity may be an emergent trait depending on contributions from multiple proteins that have low pathway connectivity. We recommend that authors choose language which rigorously avoids the implication that protocols for molecular staging of the mid secretory phase inherently identify a state of receptivity to the implanting blastocyst.
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Affiliation(s)
- John D Aplin
- Maternal and Fetal Health Centre, Manchester Academic Health Sciences Centre, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Adam Stevens
- Maternal and Fetal Health Centre, Manchester Academic Health Sciences Centre, University of Manchester, St Mary's Hospital, Manchester, UK
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Zeng H, Fu Y, Shen L, Quan S. Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure. Front Endocrinol (Lausanne) 2022; 13:785462. [PMID: 35197930 PMCID: PMC8859149 DOI: 10.3389/fendo.2022.785462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/10/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Recurrent implantation failure (RIF) is an intricate complication following IVF-ET, which refers to the situation that good-quality embryos repeatedly fail to implant following two or more IVF cycles. Intrinsic molecular mechanisms underlying RIF have not yet been fully elucidated. With enormous improvement in high-throughput technologies, researchers screened biomarkers for RIF using microarray. However, the findings of published studies are inconsistent. An integrated study on the endometrial molecular determinants of implantation will help to improve pregnancy outcomes. OBJECTIVE To identify robust differentially expressed genes (DEGs) and hub genes in endometrium associated with RIF, and to investigate the diagnostic role of hub genes in RIF. METHODS Raw data from five GEO microarrays regarding RIF were analyzed. Integrated genetic expression analyses were performed using the Robust Rank Aggregation method to identify robust DEGs. Enrichment analysis and protein-protein interaction (PPI) analysis were further performed with the robust DEGs. Cytohubba was used to screen hub genes based on the PPI network. GSE111974 was used to validate the expression and diagnostic role of hub genes in RIF. RESULTS 1532 Robust DEGs were identified by integrating four GEO datasets. Enrichment analysis showed that the robust DEGs were mainly enriched in processes associated with extracellular matrix remodeling, adhesion, coagulation, and immunity. A total of 18 hub genes (HMGCS1, SQLE, ESR1, LAMC1, HOXB4, PIP5K1B, GNG11, GPX3, PAX2, TF, ALDH6A1, IDH1, SALL1, EYA1, TAGLN, TPD52L1, ST6GALNAC1, NNMT) were identified. 10 of the 18 hub genes were significantly differentially expressed in RIF patients as validated by GSE111974. The 10 hub genes (SQLE, LAMC1, HOXB4, PIP5K1B, PAX2, ALDH6A1, SALL1, EYA1, TAGLN, ST6GALNAC1) were effective in predicting RIF with an accuracy rate of 85%, specificity rate of 100%, and sensitivity rate of 88.9%. CONCLUSIONS Our integrated analysis identified novel robust DEGs and hub genes in RIF. The hub genes were effective in predicting RIF and will contribute to the understanding of comprehensive molecular mechanisms in RIF pathogenesis.
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Affiliation(s)
- Hong Zeng
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Foshan, China
- Department of Gynecology and Obstetrics, NanFang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Fu
- Department of Gynecology and Obstetrics, NanFang Hospital, Southern Medical University, Guangzhou, China
| | - Lang Shen
- Department of Gynecology and Obstetrics, NanFang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Lang Shen, ; Song Quan,
| | - Song Quan
- Department of Gynecology and Obstetrics, NanFang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Lang Shen, ; Song Quan,
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