P-409 The endometrial transcriptome of infertile women with and without recurrent implantation failure

Study question

Does the endometrial transcriptome profile differ between infertile women with or without a recurrent implantation failure (RIF)?

Summary answer

Although two different clusters emerged from the endometrial transcriptome data, these were not associated with clinical phenotype (RIF vs non-RIF).

What is known already

Despite the transfer of morphologically ‘good-quality’ embryos in IVF/ICSI, implantation failure often occurs, which may be explained by impaired endometrial receptivity. In order to guide prognosis and use effective therapeutic interventions, identifying a gene expression profile predictive of endometrial receptivity as well as implantation failure, would be of great value. Additionally, transcriptome analysis may also shed light on alterations in biological processes responsible for the implantation failure. Thousands of potential biomarkers for endometrial receptivity have already been identified by transcriptomic approach, however due to differences in study methodology, there is little overlap of markers between studies.

Study design, size, duration

Endometrial tissue was obtained from a cohort of 141 infertile women undergoing endometrial scratching within a randomised controlled trial (RCT) (SCRaTCH trial, NL5193/NTR5342). Briefly, women aged 18-44 years with failed implantation after one full IVF/ICSI cycle and planning a subsequent IVF/ICSI cycle, were eligible. Participants were followed-up until 12 months after randomisation, with the primary outcome being live birth, defined as the delivery of at least one live foetus after 24 weeks of gestation.

Participants/materials, setting, methods

Endometrial tissue was obtained with an endometrial biopsy catheter in the midluteal phase of a natural cycle preceding subsequent IVF/ICSI. Biopsies were snap-frozen and stored at -80 °C until use. After thawing, total RNA isolation, library preparation and paired-end RNA-sequencing were performed. Raw data was preprocessed and mapped to GRCh38. Reads (counts per million) were normalised using library size. Differential gene expression (DGE) analysis was conducted using the EdgeR package with significance threshold FDR <0.05.

Main results and the role of chance

Out of 141 endometrium samples, 107 were included in the RNA-sequencing based on RNA quality. For DGE analysis, data of two groups were compared: the ‘fertile’ group, women with a live birth after ≤3 good quality embryo(s) transfers (n = 23), and the RIF group, women with no live birth after ≥3 good quality embryo(s) transfers (n = 23). Two clusters were visible in the principle component analysis (PCA) plot showing transcriptome data of the fertile and RIF samples (cluster 1, n = 29; cluster 2, n = 10), which was not explained by clinical phenotype, as both clusters contained samples of both the fertile and RIF group. DGE analysis between the fertile and RIF group resulted in respectively 3 significantly upregulated and 0 significantly downregulated genes, whereas DGE analysis between the two clusters resulted in 2,235 significantly upregulated and 2,162 significantly downregulated genes. Enrichment analysis of differentially expressed genes between both clusters demonstrated upregulation of enriched terms mainly annotated to cell migration and downregulation of enriched terms mainly annotated to lipid and mitochondrial metabolism.

Limitations, reasons for caution

A strength of the study is the large number of samples included. Bulk RNA-sequencing was conducted and there was a variation in LH-based timing of the biopsies (5-8 days after LH surge) for which adjustments of the transcriptome data for tissue cellular composition and menstrual cycle were performed.

Wider implications of the findings

Future studies investigating underlying biological mechanisms in the endometrium in (in)fertility by a (multi-)omics analysis approach with standardised methodology are required to obtain consistencies in relevant biomarkers/pathways, and in due course create possibilities to improve and personalise care for infertile couples.

Trial registration number

NL5193/NTR5342

Endometriosis and irritable bowel syndrome: similarities and differences in the spectrum of comorbidities

STUDY QUESTION

Do the spectrum and prevalence of comorbidities of endometriosis and irritable bowel syndrome (IBS) overlap?

SUMMARY ANSWER

Despite several overlapping symptoms, the most significantly associated comorbidities of endometriosis and IBS are different and are rather related to the organ systems primarily involved in the index diagnosis.

WHAT IS KNOWN ALREADY

Endometriosis and IBS both have several similar unspecific symptoms, such as recurrent abdominal pain, cramping and anxiety, and both diseases affect young women and are associated with a number of comorbidities causing a poor quality of life. However, a detailed study, revealing the full spectrum of endometriosis and IBS comorbidities in the same study population, is lacking.

STUDY DESIGN, SIZE, DURATION

This article presents a retrospective in silico analysis of the data from a large nationwide biobank-based cohort consisting of 121 773 women. After excluding all first- and second-degree relatives, the data of up to 65 421 women were analyzed.

PARTICIPANTS/MATERIALS, SETTING, METHODS

International Classification of Disease-10 diagnosis main codes associated with endometriosis (N80) and IBS (K58) diagnoses were identified from the Estonian Biobank dataset by linking with the Estonian Health Insurance Fund and other relevant registries. The associations between N80 and K58 and other diagnosis codes were tested using logistic regression, adjusting for age at recruitment and 10 genetic principal components to account for potential population stratification. Bonferroni correction was applied to account for multiple testing.

MAIN RESULTS AND THE ROLE OF CHANCE

Both women with endometriosis and IBS suffered from more conditions compared to the control group, with 226 and 428 diagnosis codes statistically significantly more frequent in women with respective diagnosis compared to controls. Women suffering from both conditions had 275 significantly associated comorbidities. A remarkable proportion of women with IBS or endometriosis suffered also from endometriosis (9.0%) or IBS (13.6%), respectively. In endometriosis, the most prevalent diagnoses were related to diseases of the genitourinary system (33 N-category codes) and in women with IBS, the most associated diagnoses were related to digestive disorders and gastrointestinal tract (52 codes from K-category). Among the most significant diagnoses in endometriosis were uterine leiomyomas (D25), menstrual disorders (N92) and infertility (N97) (P < 1 × 10-315 for all), and in IBS, lactose intolerance (E73), gastritis and duodenitis (K29) and functional dyspepsia (K30) were in the top list of most significant comorbidities (P < 1 × 10-315 for all).

LIMITATIONS, REASONS FOR CAUTION

The information about the severity stages of endometriosis and subtypes of IBS was not available for analysis. The findings may not be fully extrapolated to all female populations, because all participants were from one geographic area and had good access to health services.

WIDER IMPLICATIONS OF THE FINDINGS

These findings support previous studies that have found a high prevalence of pre-selected comorbidities in women with endometriosis and IBS. However, taking into account the differences in the full spectrum of comorbidities of endometriosis and IBS may aid in diagnosing these disorders. Women and healthcare providers need to be aware that women with endometriosis are at high risks of complications during pregnancy and should be carefully monitored.

STUDY FUNDING/COMPETING INTEREST(S)

This research was funded by the Estonian Research Council (grant PRG1076), Horizon 2020 innovation grant (ERIN, grant no. EU952516), Enterprise Estonia (grant no. EU48695), MSCA-RISE-2020 project TRENDO (grant no. 101008193) and by the European Union through the European Regional Development Fund (Projects no. 2014-2020.4.01.15-0012 and no. 2014-2020.4.01.16-0125). The authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

P–374 Investigating causality of risk factors for miscarriage – a Mendelian randomization analysis

Study question

Do modifiable risk factors such as smoking, alcohol or coffee consumption, and adiposity causally increase the risk of sporadic or recurrent miscarriage?

Summary answer

We found evidence for a causal relationship between smoking initiation and sporadic miscarriage, but not for any other risk factor tested.

What is known already

Miscarriage is estimated to end between 10–25% of clinically confirmed pregnancies, and many observational studies have suggested numerous lifestyle factors, such as coffee and alcohol consumption, smoking and increased adiposity, may increase miscarriage risk. However, results are not always consistent across studies, and definitive causal relationships between various risk factors and miscarriage have not yet been demonstrated. Mendelian randomization utilizes genetic variants significantly associated with heritable risk factors (i.e. at P-values &lt;5x10–8 in large genome-wide association studies) as instrumental variables to investigate causality of risk factors in population health outcomes.

Study design, size, duration

We conducted two-sample Mendelian randomization analyses to investigate causality of smoking (initiation and quantity), alcohol and coffee consumption (quantity), and adiposity (body mass index and waist-hip ratio) in sporadic and recurrent miscarriage. Data included in this study were taken from previously published summary genetic association statistics (betas, standard errors and P-values) from large-scale genome-wide association studies (GWAS) for each risk factor, and from our recently published GWAS of sporadic and recurrent miscarriage.

Participants/materials, setting, methods

Instrumental variables were constructed using 5–306 genetic variants significantly associated with the listed risk factors in published GWAS (minimum N = 178,000 individuals). Two instrumental variables were constructed per risk factor using data from different GWAS. Associations of the instrumental variables with miscarriage were investigated using summary association data from women of European ancestry included in our miscarriage GWAS, including 49,996 sporadic miscarriage cases and 174,109 female controls, and 750 recurrent miscarriage cases and 150,215 female controls.

Main results and the role of chance

We found a significant association between sporadic miscarriage and the instrumental variables for two smoking measures: smoking initiation (inverse variance weighted Odds Ratio = 1.17, 95% confidence intervals = 1.10–1.24, P = 2.7 x 10–07) and lifetime smoking (inverse variance weighted Odds Ratio = 1.22, 95% confidence intervals 1.11–1.35, P = 4.2x10–5). No other risk factors (smoking quantity, coffee or alcohol consumption, or BMI or waist-hip ratio) were associated with either sporadic or recurrent miscarriage. A priori power calculations considering the amount of phenotypic variance in each risk factor explained by the associated SNPs suggested our analysis to have at least 75% power to detect an association with Odds Ratio of 1.2 with sporadic miscarriage for analyses of body mass index, waist hip ratio and smoking initiation, quantity and the lifetime smoking measure, but that the alcohol and coffee consumption analyses were underpowered (4.9% and 48%, respectively). All analyses were underpowered for recurrent miscarriage given the small case sample size (N = 750).

Limitations, reasons for caution

While data utilised here come from large-scale GWAS including 1000s of individuals, genetic variants significantly associated with each risk factor currently explain small percentages (0.02–6%) of the variance in each trait. Larger GWAS for specific risk factors, and for sporadic and recurrent miscarriage, are required to clarify some published associations.

Wider implications of the findings: We find no evidence of a causal link between adiposity and miscarriage, indicating that observational findings of increased miscarriage risk with increasing body mass index require further explanation. Significant associations between measures of ever-smoking and sporadic miscarriage highlights that no amount of smoking is safe in regards to miscarriage risk.

Trial registration number

Not applicable

O-116 Genetic association analyses identify links between pelvic prolapse (PP) and connective tissue biology, cardiovascular and reproductive health

Study question

Can genome-wide association analysis unravel the biological underpinnings of PP and facilitate personalized risk assessment via genetic risk scores construction?

Summary answer

We unravel novel links with urogenital development and vascular health in PP and present polygenic risk score as a tool to stratify PP risk.

What is known already

Prolapse is characterized by a descent of the pelvic organs into the vaginal cavity. PP affects around 40% of women after menopause and is the main indication for major gynecological surgery, having an important health, social and economic burden. Although the etiology and biological mechanisms underlying PP remain poorly understood, prior studies suggest genetic factors might play a role. Recently, a genome-wide association study (GWAS) identified seven genome-wide significant loci, located in or near genes involved in connective tissue metabolism and estrogen exposure in the etiology of PP.

Study design, size, duration

We conducted a three-stage case-control genome-wide association study. Firstly, in the discovery phase, we meta-analyzed Icelandic, UK Biobank and the FinnGen R3 datasets, comprising a total of 20118 cases and 427426 controls of European ancestry. For replication we used an independent dataset from Estonian Biobank (7968 cases and 118895 controls). Finally, we conducted a joint meta-analysis, containing 28086 cases and 546321 controls, which is the largest GWAS of PP to date.

Participants/materials, setting, methods

We performed functional annotation on genetic variants unraveled by GWAS and integrated these with expression quantitative trait loci and chromatin interaction data. In addition, we looked at enrichment of association signal on gene-set, tissue and cell type level and analyzed associations with other phenotypes both on genetic and phenotypic level. Colocalisation analyses were conducted to help pinpoint causal genes. We further constructed polygenic risk scores to explore options for personalized risk assessment and prevention.

Main results and the role of chance

In the discovery phase, we identified 18 genetic loci and 20 genetic variants significantly associated with POP (p &lt; 5 × 10−8) and 75% of the variants show nominal significance association (p &lt; 0.05) in the replication. Notably, the joint meta-analyses detected 20 genetic loci significantly associated with POP, from which 13 loci were novel. Novel genetic variants are located in or near genes involved in gestational duration and preterm birth (rs2687728 p = 2.19x10-9, EEFSEC), cardiovascular health and pregnancy success (rs1247943 p = 5.83x10-18, KLF13), endometriosis (rs12325192 p = 3.72x10-18, CRISPLD2), urogenital tract development (rs7126322, p = 4.35x10-15, WT1 and rs42400, p = 4.8x10-10, ADAMTS16) and regulation of the oxytocin receptor (rs2267372, p = 4.49x10-13, MAFF). Further analyses demonstrated that POP GWAS signals colocalise with several eQTLS (including EEFSEC, MAFF, KLF13, etc.), providing further evidence for mapping associated genes. Tissue and cell enrichment analyses underlined the role of the urogenital system, muscle cells, myocytes and adipocytes (p &lt; 0.00001, FDR&lt;0.05). Furthermore, genetic correlation analyses supported a shared genetic background with gastrointestinal disorders, joint and musculoskeletal disorders and cardiovascular disease. Polygenic risk scores analyses included a total of 125551 people in the target dataset, with 5379 prevalent patients and 2517 incident patients. Analyzing the best GRS as a quintile showed association with incident disease (Harrell c-statistic= 0.603, SD = 0.006).

Limitations, reasons for caution

This GWAS meta-analyses focused on European ancestry populations, which challenges the generalizability of GWAS findings to non-European populations. Moreover, this study included women with PP from population-based biobanks identified using the ICD-10 code N81, which limits analyses considering different disease stages and severity.

Wider implications of the findings

Our study provides genetic evidence to improve the current understanding of PP pathogenesis and serves as basis for further functional studies. Moreover, we provide a genetic tool for personalized risk stratification, which could help prevent PP development and improve the quality of a vast quantity of women.

Trial registration number

not applicable

Insulin gene VNTR, CTLA-4 +49A/G and HLA-DQB1 alleles distinguish latent autoimmune diabetes in adults from type 1 diabetes and from type 2 diabetes group

Recent research has underlined the need to explore pathogenic, genetic and clinical spectrum of adult onset autoimmune diabetes, also known as latent autoimmune diabetes in adults (LADA). We aimed to investigate whether genetic factors that are associated with type 1 diabetes (T1D) susceptibility, namely HLA-DQB1 alleles, cytotoxic T-lymphocyte antigen 4 gene (CTLA-4) and insulin gene (INS) polymorphisms, are also associated with an atypical subset of patients diagnosed with type 2 diabetes (T2D). The case-control study included 70 T1D, 305 T2D and 252 nondiabetic controls. The T2D group was divided into atypical T2D (LADA, n = 61) or typical T2D (n = 244) subgroups based on the presence of at least one pancreas-specific antibody. Our data suggested that HLA-DQB1 alleles of all three risk classes, INS variable number of tandem repeat (VNTR) I/I and CTLA-4 +49 GG or AG genotypes, were independent risk factors for developing LADA and could be used as a diagnostic tool to discriminate between LADA and T2D. Additionally, there was an increased association between LADA and CTLA-4 diabetes-susceptibility genotypes and decreased association with INS VNTR and high-risk HLA-DQB1 alleles, compared with T1D. Our study suggested the need for further investigation into the genetic background and functional genomics of LADA in comparison with T1D and T2D.