The first genome-wide association study identifying new susceptibility loci for obstetric antiphospholipid syndrome

Recurrent pregnancy loss: risk factors and predictive modeling approaches

PURPOSE

This review aims to identify and analyze the risk factors associated with recurrent pregnancy loss (RPL) and to evaluate the effectiveness of various predictive models in estimating the risk of RPL. The review also explores recent advancements in machine learning algorithms that can enhance the accuracy of these predictive models. The ultimate goal is to provide a comprehensive understanding of how these tools can aid in the personalized management of women experiencing RPL.

MATERIALS AND METHODS

The review synthesizes current literature on RPL, focusing on various risk factors such as chromosomal abnormalities, autoimmune conditions, hormonal imbalances, and structural uterine anomalies. It also analyzes different predictive models for RPL risk assessment, including genetic screening tools, risk scoring systems that integrate multiple clinical parameters, and machine learning algorithms capable of processing complex datasets. The effectiveness and limitations of these models are critically evaluated to provide insights into their clinical application.

RESULTS

Key risk factors for RPL were identified, including chromosomal abnormalities (e.g. translocations and aneuploidies), autoimmune conditions (e.g. antiphospholipid syndrome), hormonal imbalances (e.g. thyroid dysfunction and luteal phase defects), and structural uterine anomalies (e.g. septate or fibroid-affected uteri). Predictive models such as genetic screening tools and risk scoring systems were shown to be effective in estimating RPL risk. Recent advancements in machine learning algorithms demonstrate potential for enhancing predictive accuracy by analyzing complex datasets, which may lead to improved personalized management strategies.

CONCLUSIONS

The integration of risk factors and predictive modeling offers a promising approach to improving outcomes for women affected by RPL. A comprehensive understanding of these factors and models can aid clinicians and researchers in refining risk assessment and developing targeted interventions. The review underscores the need for further research into specific pathways involved in RPL and the potential of novel treatments aimed at mitigating risk.

Genetic and genomic associations in antiphospholipid syndrome: A systematic review

BACKGROUND

Numerous genes have been associated with APS in the literature. In recent years, microRNA (miRNA) and long non-coding RNA (lncRNA) have also been shown to modulate the expression of APS-related genes.

OBJECTIVE

We performed a systematic review to identify all studies reporting on genetic mechanisms that have been shown to be associated with APS.

METHODS

An extensive literature search was performed in the PubMed, Cochrane and Web of Science databases gathering all available articles through February 2024. We only selected case-control studies that met inclusion criteria and that focused on genetic contributors and modifiers related to primary APS.

RESULTS

Sixty studies were selected for data extraction. Selected studies were grouped into 8 broad categories for review and analysis: (1) gene expression studies; (2) thrombophilia genotypes; (3) single nucleotide polymorphisms (SNPs); (4) interferon-inducible genes; (5) microRNA studies; (6) long non-coding RNA (lncRNA) studies; (7) DNA methylation studies; and (8) differential gene expression studies. Several genes have been identified as associated with APS by more than one approach, including TF, complement associated genes, and interferon-inducible genes. It has been demonstrated that miRNA and lncRNA may alter the expression of important genes in patients with APS.

CONCLUSION

This systematic review has helped highlight important genes implicated in APS. Most importantly, pathways such as thrombosis/hemostasis, complement and interferon appear to be involved. Further studies are needed to help uncover important genes that could serve as biomarkers.

Autoimmune diseases and cardiovascular risk: Mendelian randomization analysis for the impact of 19 autoimmune diseases on 14 cardiovascular conditions

Backgroud

Autoimmune diseases (AIDs) have been associated with various cardiovascular diseases (CVDs) in observational data. However, the causality of these associations remains uncertain. Therefore, a systematic assessment of the impact of AIDS on cardiovascular risk is required.

Results

We assessed the impact of 19 common AIDs on 14 CVDs using bidirectional Mendelian randomization (MR). Celiac disease (odds ratio [OR] = 2.949, 95 % confidence interval [CI]: 1.111-7.827, P = 0.030) and type 1 diabetes mellitus (T1DM) (OR = 1.044, 95 % CI: 1.021-1.068, P = 1.82e-4) were associated with an increased risk of peripheral arterial disease (PAD). Additionally, celiac disease was linked to an increased risk of arrhythmia (OR = 1.008, 95 % CI: 1.002-1.013, P = 0.004), multiple sclerosis to venous thromboembolism (OR = 1.001, 95 % CI: 1.000-1.001, P = 0.010), and psoriasis to heart failure (OR = 1.048, 95 % CI: 1.021-1.077, P = 0.001). Sensitivity analyses were conducted to enhance the robustness of these findings. Predominantly, immune response and inflammation-related pathways were enriched in the aforementioned associations. Mediation analysis identified human leukocyte antigen-DR positive myeloid dendritic cells as partially mediating the effect of T1DM on PAD, with a mediated proportion of 16.61 % (P = 0.028). Potential therapeutic agents, such as tumor necrosis factor-alpha inhibitors and interferon, may have efficacy in treating AID-related CVDs.

Conclusions

This study presents genetic evidence of certain AIDs impacting specific CVDs and identifies potential mediators and drugs.

Genetic causes of sporadic and recurrent miscarriage

Approximately 80% of miscarriages happen within the first 12 weeks of gestation. More than half of early losses result from genetic defects, usually presenting as abnormal chromosome numbers or gene rearrangements in the embryo. However, the impact of genetics on pregnancy loss goes well beyond embryonic aneuploidy. For example, the use of big data has recently led to the discovery of specific gene mutations that may be implicated in sporadic and recurrent miscarriages. Further, emerging data suggest that genetic factors play a role in conditions for which there is a causative association with recurrent pregnancy loss. Here, we summarize the evidence on the genetics of miscarriage and provide an overview of the diagnosis and prevention of genetic causes associated with sporadic and recurrent pregnancy loss.

The association of APOH and NCF1 polymorphisms on susceptibility to recurrent pregnancy loss in women with antiphospholipid syndrome

BACKGROUND

Recurrent pregnancy loss (RPL) is the main manifestation of pathological pregnancy in antiphospholipid syndrome (APS) women. The immune state plays a significant role in the occurrence/development of APS and RPL susceptibility, but there is little research on genetic factors.

METHOD

Previous studies have described the important role of APOH and NCF1 in APS and pregnancy. To explore the association of APOH and NCF1 gene variants with RPL susceptibility in APS patients, we collected and analyzed 871 controls, 182 APS and RPL, and 231 RPL patients. Four single nucleotide polymorphisms (SNPs) (rs1801690, rs52797880, and rs8178847 of APOH and rs201802880 of NCF1) were selected and genotyped.

RESULTS

We found rs1801690 (p = 0.001, p = 0.003), rs52797880 (p = 8.73e-04, p = 0.001), and rs8178847 (p = 0.001, p = 0.001) of APOH and rs201802880 (p = 3.77e-26, p = 1.31e-26) of NCF1 showed significant differences between APS and RPL patients and controls in allelic and genotype frequencies respectively. Moreover, rs1801690, rs52797880, and rs8178847 showed strong linkage disequilibrium. Especially, our results revealed a complete linkage disequilibrium (D' = 1) between rs52797880 and rs8178847. Furthermore, higher serum TP (total protein) level was described in APOH rs1801690 CG/GG (p = 0.007), rs52797880 AG/GG (p = 0.033), and rs8178847 CT/TT (p = 0.033), while the higher frequency of positive serum ACA-IgM was found in NCF1 rs201802880 GA (p = 0.017) in APS and RPL patients.

CONCLUSION

Rs1801690, rs52797880, and rs8178847 of APOH and rs201802880 of NCF1 were associated with RPL susceptibility in APS patients.

High-throughput sequencing technology facilitates the discovery of novel biomarkers for antiphospholipid syndrome

Antiphospholipid syndrome (APS) is characterized by arterial and venous thrombosis and/or morbid pregnancy, accompanied by persistent antiphospholipid antibody (aPL) positivity. However, due to the complex pathogenesis of APS and the large individual differences in the expression of aPL profiles of patients, the problem of APS diagnosis, prognosis judgment, and risk assessment may not be solved only from the antibody level. It is necessary to use new technologies and multiple dimensions to explore novel APS biomarkers. The application of next-generation sequencing (NGS) technology in diseases with a high incidence of somatic mutations, such as genetic diseases and tumors, has been very mature. Thus, we try to know the research and application progress of APS by NGS technology from genome, transcriptome, epigenome and other aspects. This review will describe the related research of NGS technology in APS and provide more reference for the deep understanding of APS-related screening markers and disease pathogenesis.

Assessment-based management of placenta-mediated pregnancy complications: Pragmatism until a precision medicine approach evolves

The management of pregnant women with thrombophilia and a history of gestational vascular complications remains debatable. Treatment of the latter is often based on clinical outcome rather than disease mechanism. While the use of venous thromboembolism prophylaxis in pregnancy is recommended for those at increased risk, the ability of anticoagulant and/or antiplatelet agents to lower the risk of placenta-mediated complications in this clinical setting remains controversial. The available guidelines are inconsistent in some situations, which reflects the limited evidence base. This review critically discusses risk assessment models (RAMs) and management strategies of women with thrombophilia and pregnancy complications, using clinical vignettes. RAMs, taking into account obstetric and thrombotic history as well as thrombophilia status, could drive a precision medicine approach, based on disease mechanism, and guide individual therapeutic interventions in high-risk clinical settings.

Intergenerational trends in reproduction: Infertility and pregnancy loss

This review article summarises the evidence for intergenerational trends observed to date within infertility and pregnancy loss. There appears to be evidence of intergenerational trends between mothers and daughters for the age at menopause, endometriosis, polycystic ovarian syndrome (PCOS), male factor infertility and miscarriage. At present, there is no evidence for a predisposition to stillbirth between mothers and daughters. One study found an association with familial predisposition for ectopic pregnancy. Very few studies have considered the potential for paternal transmission of risk of infertility or pregnancy loss. The majority of studies to date have significant limitations because of their observational design, risk of recall bias and risk of confounding. Therefore, high-quality well-designed research, with multi-centre collaboration and utilisation of registry-based data sources and individual patient data, is needed to understand whether infertility and pregnancy loss may have heritable factors. Epidemiological findings need to be followed up and investigated with translational research to determine the possible causalities as well as any implications for clinical practice.

Predictors Associated with Adverse Pregnancy Outcomes in a Cohort of Women with Systematic Lupus Erythematosus from Romania-An Observational Study (Stage 2)

Background: Pregnancy in women with systemic lupus erythematosus (SLE) is accompanied by adverse pregnancy outcomes (APOs). We aimed to investigate the association between clinical, sonographic, and laboratory parameters and APOs (preeclampsia, intrauterine growth restriction, premature birth, and maternal mortality). Methods: This observational retrospective study included all pregnancies in women with SLE who attended two tertiary maternity hospitals from Romania between January 2013 and December 2020. Clinical, sonographic, and laboratory variables were examined. Bivariate associations of APO status and each predictor variable were evaluated, and significant predictors were further included in a classification model based on discriminant analysis. Results: Predictors of APOs included BMI > 25 kg/m2, personal history of lupus nephritis or chronic hypertension, proteinuria, low C3, SLE Disease Activity Index 2000 (SLEDAI-2k score ≥ 4 and physician’s global-assessment (PGA) score ≥ 1 throughout pregnancy, increased mean uterine arteries pulsatility index in the first and second trimesters, cerebroplacental ratio < 1 in the second and third trimesters, and small fetal abdominal circumference in the third trimester. Glucocorticoids, methyldopa, and aspirin use appeared to be protective against APOs. Conclusions: This study provides a comprehensive analysis of the most important predictors for APOs in pregnant patients with SLE, which could constitute a basis for further research.

Genome-wide association study in patients with pulmonary Mycobacterium avium complex disease

RATIONALE

Nontuberculous mycobacteria (NTM) are environmental mycobacteria that can cause a chronic progressive lung disease. Although epidemiological data indicate potential genetic predisposition, its nature remains unclear.

OBJECTIVES

We aimed to identify host susceptibility loci for Mycobacterium avium complex (MAC), the most common NTM pathogen.

METHODS

This genome-wide association study (GWAS) was conducted in Japanese patients with pulmonary MAC and healthy controls, followed by genotyping of candidate single-nucleotide polymorphisms (SNPs) in another Japanese cohort. For verification by Korean and European ancestry, we performed SNP genotyping.

RESULTS

The GWAS discovery set included 475 pulmonary MAC cases and 417 controls. Both GWAS and replication analysis of 591 pulmonary MAC cases and 718 controls revealed the strongest association with chromosome 16p21, particularly with rs109592 (p=1.64×10^-13, OR 0.54), which is in an intronic region of the calcineurin-like EF-hand protein 2 (CHP2). Expression quantitative trait loci analysis demonstrated an association with lung CHP2 expression. CHP2 was expressed in the lung tissue in pulmonary MAC disease. This SNP was associated with the nodular bronchiectasis subtype. Additionally, this SNP was significantly associated with the disease in patients of Korean (p=2.18×10^-12, OR 0.54) and European (p=5.12×10^-03, OR 0.63) ancestry.

CONCLUSIONS

We identified rs109592 in the CHP2 locus as a susceptibility marker for pulmonary MAC disease.

Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids

Inference of causality between gene expression and complex traits using Mendelian randomization (MR) is confounded by pleiotropy and linkage disequilibrium (LD) of gene-expression quantitative trait loci (eQTL). Here, we propose an MR method, MR-link, that accounts for unobserved pleiotropy and LD by leveraging information from individual-level data, even when only one eQTL variant is present. In simulations, MR-link shows false-positive rates close to expectation (median 0.05) and high power (up to 0.89), outperforming all other tested MR methods and coloc. Application of MR-link to low-density lipoprotein cholesterol (LDL-C) measurements in 12,449 individuals with expression and protein QTL summary statistics from blood and liver identifies 25 genes causally linked to LDL-C. These include the known SORT1 and ApoE genes as well as PVRL2, located in the APOE locus, for which a causal role in liver was not known. Our results showcase the strength of MR-link for transcriptome-wide causal inferences.

Mendelian randomization is a useful tool to infer causal relationships between traits, but can be confounded by the presence of pleiotropy. Here, the authors have developed MR-link, a Mendelian randomization method which accounts for unobserved pleiotropy and linkage disequilibrium between instrumental variables.

Risk of pre-eclampsia in patients with a maternal genetic predisposition to common medical conditions: a case-control study

OBJECTIVE

To assess whether women with a genetic predisposition to medical conditions known to increase pre-eclampsia risk have an increased risk of pre-eclampsia in pregnancy.

DESIGN

Case-control study.

SETTING AND POPULATION

Pre-eclampsia cases (n = 498) and controls (n = 1864) in women of European ancestry from five US sites genotyped on a cardiovascular gene-centric array.

METHODS

Significant single-nucleotide polymorphisms (SNPs) from 21 traits in seven disease categories (cardiovascular, inflammatory/autoimmune, insulin resistance, liver, obesity, renal and thrombophilia) with published genome-wide association studies (GWAS) were used to create a genetic instrument for each trait. Multivariable logistic regression was used to test the association of each continuous scaled genetic instrument with pre-eclampsia. Odds of pre-eclampsia were compared across quartiles of the genetic instrument and evaluated for significance.

MAIN OUTCOME MEASURES

Genetic predisposition to medical conditions and relationship with pre-eclampsia.

RESULTS

An increasing burden of risk alleles for elevated diastolic blood pressure (DBP) and increased body mass index (BMI) were associated with an increased risk of pre-eclampsia (DBP, overall OR 1.11, 95% CI 1.01-1.21, P = 0.025; BMI, OR 1.10, 95% CI 1.00-1.20, P = 0.042), whereas alleles associated with elevated alkaline phosphatase (ALP) were protective (OR 0.89, 95% CI 0.82-0.97, P = 0.008), driven primarily by pleiotropic effects of variants in the FADS gene region. The effect of DBP genetic loci was even greater in early-onset pre-eclampsia cases (at <34 weeks of gestation, OR 1.30, 95% CI 1.08-1.56, P = 0.005). For other traits, there was no evidence of an association.

CONCLUSIONS

These results suggest that the underlying genetic architecture of pre-eclampsia may be shared with other disorders, specifically hypertension and obesity.

TWEETABLE ABSTRACT

A genetic predisposition to increased diastolic blood pressure and obesity increases the risk of pre-eclampsia.

Levothyroxine and subclinical hypothyroidism in patients with recurrent pregnancy loss

PROBLEM

The association between subclinical hypothyroidism (SCH) and recurrent pregnancy loss (RPL) remains unclear. We evaluated whether SCH affects subsequent live births and whether levothyroxine is effective in improving the live birth rate in patients with RPL.

METHOD OF STUDY

This observational cohort study included 1418 pregnancies of 1014 patients with a history of 2 or more pregnancy losses, who were euthyroid or had hypothyroidism, and had at least one subsequent pregnancy outcome. Some patients with SCH, as defined as a TSH >2.5 mIU/L, were treated with levothyroxine, and these comprised the levothyroxine group. The prevalence of SCH, subsequent live birth rates per patient and per pregnancy were compared among patients with SCH treated with and without levothyroxine and patients with euthyroid.

RESULTS

The prevalence of SCH was 14.4%. Subsequent live birth rates were 75.0% for the levothyroxine group, 68.6% for the untreated SCH group, and 70.1% for the euthyroid group. After excluding miscarriages with abnormal karyotypes, live birth rates were 89.2%, 90.0%, and 91.1%. The adjusted odds ratio (95%CI) was 0.95 (0.23-3.83) after controlling covariables when comparing SCH patients with and without treatment. The live birth rates per pregnancy were 93.1%, 85.7%, and 90.9%, respectively. The adjusted OR was 0.95 (0.23-3.83).

CONCLUSION

Levothyroxine has no effect on improving the live birth rate in patients with RPL associated with SCH. Treatment in patients with RPL and SCH raised TSH levels (2.5-10mIU/L) might not be beneficial in improving the live birth rate.

Genetics of Antiphospholipid Syndrome

PURPOSE OF REVIEW

Antiphospholipid syndrome (APS) is a rare heterogenous disorder associated with the presence of antiphospholipid antibodies and can present in a wide variety of clinical manifestations including thrombosis and pregnancy complications. Although the etiology of APS remains poorly understood, there is strong support for considering APS as a complex genetic disease in which multiple genetic risk factors, in conjunction with environmental factors, affect its onset, progression, and severity. Here, we provide a comprehensive review of the current knowledge of the genetic basis of APS, which remains in its infancy.

RECENT FINDINGS

Most genetic studies to date in APS were performed in small cohorts of patients. As a result, only few genetic associations reported are convincing. Several reports suggested genetic associations with HLA class II alleles in APS, and only two genetic loci outside of the HLA region (STAT4 and C1D) reached the threshold for genome-wide level of significance (P < 5 × 10^-8). In this review, we also shed light on the genetic differences among the diverse clinical subsets of APS and briefly discuss the role that DNA methylation changes might play in the pathophysiology of this disease. The genetic basis of APS remains poorly characterized. Larger collaborative multicenter studies using well-characterized patients are needed to comprehensively understand the role of genetic susceptibility in APS.

Moving towards a molecular taxonomy of autoimmune rheumatic diseases

Autoimmune rheumatic diseases pose many problems that have, in general, already been solved in the field of cancer. The heterogeneity of each disease, the clinical similarities and differences between different autoimmune rheumatic diseases and the large number of patients that remain without a diagnosis underline the need to reclassify these diseases via new approaches. Knowledge about the molecular basis of systemic autoimmune diseases, along with the availability of bioinformatics tools capable of handling and integrating large volumes of various types of molecular data at once, offer the possibility of reclassifying these diseases. A new taxonomy could lead to the discovery of new biomarkers for patient stratification and prognosis. Most importantly, this taxonomy might enable important changes in clinical trial design to reach the expected outcomes or the design of molecularly targeted therapies. In this Review, we discuss the basis for a new molecular taxonomy for autoimmune rheumatic diseases. We highlight the evidence surrounding the idea that these diseases share molecular features related to their pathogenesis and development and discuss previous attempts to classify these diseases. We evaluate the tools available to analyse and combine different types of molecular data. Finally, we introduce PRECISESADS, a project aimed at reclassifying the systemic autoimmune diseases.

Pregnancy Immunogenetics and Genomics: Implications for Pregnancy-Related Complications and Autoimmune Disease

Pregnancy presents a singular physiological scenario during which the maternal immune system must accommodate the semiallogeneic fetus. Fluctuations between pro- and anti-inflammatory states are required throughout gestation to facilitate uterine tissue remodeling, fetal growth and development, and finally birth. Tolerance for the fetus must be established and maintained without fundamentally compromising the maternal immune system function, so that both the mother and fetus are protected from foreign insults. Here, we review our current understanding of how genetic variation at both maternal and fetal loci affects implantation and placenta formation, thereby determining the likelihood of a successful pregnancy outcome or the development of pregnancy-related complications. We also consider the impact of pregnancy on both the maternal and fetal systemic immune systems and the related implications for modulating ongoing autoimmune diseases and triggering their development.

Primary antiphospholipid syndrome and antiphospholipid syndrome associated to systemic lupus: Are they different entities?

Primary antiphospholipid syndrome (PAPS) and antiphospholipid syndrome associated to lupus (SAPS) have several overlapping characteristics. As systemic manifestations are also reported in patients with PAPS, and as a subgroup of PAPS patients could evaluate to a SAPS, the differentiation between the two types of APS could be performed based on the clinical experience of the medical teams and is related to a variety of clinical, biological, histological and genetic features. Several data are available in the literature with respect to the identification of distinctive features between these two entities. However, there are some limitation in the interpretation of results issued from studies performed prior to updated Sydney criteria. Based on recent data, a certain number of features more frequent in one type of APS as compared to the other could be distinguished. The major differentiation between these two entities is genetical. New genetic data allowing the identification of specific subgroups of APS are ongoing.

First Bosnian Study of the Relationship between APOE rs7412 and rs429358 Variants and Pregnancy Loss

Due to inconsistent results of APOE variants in the survival of pregnancy we investigated the potential relationship of APOE rs7412 and rs429358 with pregnancy loss (PL) in Bosnian women. We enrolled 154 women with PL. The minimum week of miscarriage was 6, while the maximum was 28. As a control group, an equal number of mothers with at least one live-born child was included. All women were recruited from the Institution of Health Protection of Women and Motherhood in Sarajevo, Bosnia and Herzegovina. Genotyping was performed by real- time PCR at the Department of General Pharmacology and Pharmacoeconomics, Pomeranian Medical University. The prevalence of genotypes E2/E3, E2/E4, E3/E3, E3/E4, E4/E4 in the group with and without PL were: 14.3 %, 1.3 %, 70.8 %, 12.3 %, 1.3 %, and 13.6 %, 1.3 %, 70.1 %, 14.3 %, 0.7 %, respectively. The frequency of the E4/E4 genotype in women with 1-2 and 3-4 PL compared to women without PL did not differ significantly between those three groups (P value = 0.0712). The frequencies of alleles ԑ2, ԑ3, ԑ4 in the group with and without PL were: 6.8 %, 85.1 %, 8.1 % and 7.5 %, 84.1 %, 8.4 %, respectively, and did not differ significantly. We conclude that our study does not confirm rs7412 and rs429358 as a potential risk factor for PL in the studied group. To elucidate the relationship between PL and variants of the APOE gene, studies with a larger sample size and placental histomorphology and genetic diagnosis are required.