Defining the clinical validity of genes reported to cause pulmonary arterial hypertension

PURPOSE

Pulmonary arterial hypertension (PAH) is a rare, progressive vasculopathy with significant cardiopulmonary morbidity and mortality. Genetic testing is currently recommended for adults diagnosed with heritable, idiopathic, anorexigen-, hereditary hemorrhagic telangiectasia-, and congenital heart disease-associated PAH, PAH with overt features of venous/capillary involvement, and all children diagnosed with PAH. Variants in at least 27 genes have putative evidence for PAH causality. Rigorous assessment of the evidence is needed to inform genetic testing.

METHODS

An international panel of experts in PAH applied a semi-quantitative scoring system developed by the NIH Clinical Genome Resource to classify the relative strength of evidence supporting PAH gene-disease relationships based on genetic and experimental evidence.

RESULTS

Twelve genes (BMPR2, ACVRL1, ATP13A3, CAV1, EIF2AK4, ENG, GDF2, KCNK3, KDR, SMAD9, SOX17, and TBX4) were classified as having definitive evidence and 3 genes (ABCC8, GGCX, and TET2) with moderate evidence. Six genes (AQP1, BMP10, FBLN2, KLF2, KLK1, and PDGFD) were classified as having limited evidence for causal effects of variants. TOPBP1 was classified as having no known PAH relationship. Five genes (BMPR1A, BMPR1B, NOTCH3, SMAD1, and SMAD4) were disputed because of a paucity of genetic evidence over time.

CONCLUSION

We recommend that genetic testing includes all genes with definitive evidence and that caution be taken in the interpretation of variants identified in genes with moderate or limited evidence. Genes with no known evidence for PAH or disputed genes should not be included in genetic testing.

The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder

De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.

Molecular Function and Contribution of TBX4 in Development and Disease

Over the past decade, recognition of the profound impact of the TBX4 (T-box 4) gene, which encodes a member of the evolutionarily conserved family of T-box-containing transcription factors, on respiratory diseases has emerged. The developmental importance of TBX4 is emphasized by the association of TBX4 variants with congenital disorders involving respiratory and skeletal structures; however, the exact role of TBX4 in human development remains incompletely understood. Here, we discuss the developmental, tissue-specific, and pathological TBX4 functions identified through human and animal studies and review the published TBX4 variants resulting in variable disease phenotypes. We also outline future research directions to fill the gaps in our understanding of TBX4 function and of how TBX4 disruption affects development.

First Genotype-Phenotype Study in TBX4 Syndrome: Gain-of-Function Mutations Causative for Lung Disease

Rationale: Despite the increased recognition of TBX4 (T-BOX transcription factor 4)-associated pulmonary arterial hypertension (PAH), genotype-phenotype associations are lacking and may provide important insights. Objectives: To compile and functionally characterize all TBX4 variants reported to date and undertake a comprehensive genotype-phenotype analysis. Methods: We assembled a multicenter cohort of 137 patients harboring monoallelic TBX4 variants and assessed the pathogenicity of missense variation (n = 42) using a novel luciferase reporter assay containing T-BOX binding motifs. We sought genotype-phenotype correlations and undertook a comparative analysis with patients with PAH with BMPR2 (Bone Morphogenetic Protein Receptor type 2) causal variants (n = 162) or no identified variants in PAH-associated genes (n = 741) genotyped via the National Institute for Health Research BioResource-Rare Diseases. Measurements and Main Results: Functional assessment of TBX4 missense variants led to the novel finding of gain-of-function effects associated with older age at diagnosis of lung disease compared with loss-of-function effects (P = 0.038). Variants located in the T-BOX and nuclear localization domains were associated with earlier presentation (P = 0.005) and increased incidence of interstitial lung disease (P = 0.003). Event-free survival (death or transplantation) was shorter in the T-BOX group (P = 0.022), although age had a significant effect in the hazard model (P = 0.0461). Carriers of TBX4 variants were diagnosed at a younger age (P < 0.001) and had worse baseline lung function (FEV1, FVC) (P = 0.009) than the BMPR2 and no identified causal variant groups. Conclusions: We demonstrated that TBX4 syndrome is not strictly the result of haploinsufficiency but can also be caused by gain of function. The pleiotropic effects of TBX4 in lung disease may be in part explained by the differential effect of pathogenic mutations located in critical protein domains.

P–261 The human embryo following biopsy on day5 vs day3: Implantation, cytoskeleton, ultrastructure and effects of endometrial damage/inflammation on receptivity as revealed by scanning electron microscopy

Study question

Are there any differences in implantation, cytoskeleton and ultrastructure of embryos biopsied on day5 vs day3 and how endometrial damage/inflammation may affect receptivity and implantation?

Summary answer

No differences are observed in implantation rates but vitrification following day5 biopsy led to more cytoskeletal/ultrastructural anomalies. Infections and epithelial damage severely affected endometrial receptivity.

What is known already

Successful implantation is dependent on the correct synchronization of the window of implantantation with the transfer of chromosomally/genetically normal embryos, in a well prepared receptive endometrium. This is the first study to examine the effects of day5 vs day3 embryo biopsy by comparing implantation/pregnancy rates and by analysing cytoskeleton using Confocal Laser Scanning Microscopy (CLSM), and ultrastructure by Transmission Electron Microscopy (TEM). In addition, Scanning Electron Microscopy (SEM) was used on endometrial biopsies to assess possible uterine pathologies/inflammation that may be responsible for the failed implantation after PGT-A/M and if subsequent treatment can increase implantation/pregnancy rates in succeeding PGT-A/M cycles.

Study design, size, duration

470 embryos were biopsied on day5 for PGT-A (n = 152–37 cycles) or on day3 for PGT-A (n = 162–29 cycles) and PGT-M (n = 156–22 cycles). Following transfer of normal embryos, spare embryos, rejected for transfer following day5 or day3 biopsy were processed for Cytoskeletal analysis (n = 30 fresh day3 biopsied, n = 30 day5 biopsied/vitrified) or TEM (n = 20 fresh day3 biopsied, n = 20 day5 biopsied/vitrified). Also, patients with a –ve hCG test, underwent endometrial biopsy to detect infection/inflammation and assess receptivity.

Participants/materials, setting, methods

Cytoskeletal analysis was performed by embryo immunostaining with α-tubulin, γ-tubulin, acetylated-tubulin antibodies and DAPI or/ PI to visualise DNA. TEM analysis was carried out following embryo fixation in gluteraldehyde, incubation in osmium, aqueous uranyl acetate, dehydration through ethanol series, and immersion in Epon. Endometrial biopsies were fixed in gluteraldehyde solution and processed for SEM using standard methods. The study was conducted in an academic hospital with an IVF/PGD laboratory and 3 private IVF Units.

Main results and the role of chance

162 embryos were biopsied on day 3 for PGT-A (29 cycles), 10 cycles had no normal embryos for transfer, 30 normal embryos were transferred in 19 cycles leading to 12/19 (63.2%) +vehCG/ET and 11/19 (57.9%) Ongoing pregnancy rate/ET. 156 embryos were biopsied on day 3 for PGT-M (22 cycles), 2 cycles had no normal embryos for transfer, 34 normal or carrier embryos were transferred in 20 cycles leading to 15/20 (75.0%) +vehCG/ET and 13/20 Ongoing pregnancy rate/ET (65.0%). 152 embryos were biopsied on day 5 for PGT-A (37 cycles), 8 cycles had no normal embryos for transfer, 34 normal embryos were transferred in 29 cycles leading to 18/29 (62.1%) +vehCG/ET and 16/29 (55.2%) Ongoing pregnancy rate /ET. Analysis of endometrial biopsies with SEM revealed bacterial infections, inflammation and epithelial damage. So far, 33.3% of patients who received intracavitary infusions-antibiotic treatment per os achieved a +vehCG/ET in their next PGT-A/M cycle. Cytoskeletal analysis showed that the majority of spindles examined in both day3 and day5 biopsied embryos were normal (85/114(74.6%) and 87/137(63.5). However vitrification following day5 biopsy led to more cytoskeletal/ultrastructural anomalies which included multipolar/abnormally shaped spindles, chromosome-bridging, chromosome-lagging and more vacuoles, lipofuscins. and distension of mitochondria.

Limitations, reasons for caution

Patients undergoing PGT-A have various aetiologies (heterogeneous group). The embryos used for cytoskeletal and ultrastructural analysis in this study were all diagnosed with either chromosomal abnormalities or single gene defects following PGT-A or PGT-M.

Wider implications of the findings: This is the first study to compare implantation/pregnancy rates, cytoskeleton and ultrastructure of day5 vs day3 biopsied embryos. The similarities observed in implantation/pregnancy rates, and the limited ultrastuctural and cytoskeletal anomalies identified confirm the procedures’ safety and indicate in certain cases endometrial factors/inflammation responsible for failed implantation following PGT-A/M.

Trial registration number

Not applicable

'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension

Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.

Identification of novel pathogenic variants and features in patients with pseudohypoparathyroidism and acrodysostosis, subtypes of the newly classified inactivating PTH/PTHrP signaling disorders

Albright hereditary osteodystrophy (AHO) is a complex disorder defined by the presence of a short adult stature relative to the height of an unaffected parent and brachydactyly type E, as well as a stocky build, round face, and ectopic calcifications. AHO and pseudohypoparathyroidism (PHP) have been used interchangeably in the past. The term PHP describes end-organ resistance to parathyroid hormone (PTH), occurring with or without the physical features of AHO. Conversely, pseudopseudohypoparathyroidism (PPHP) describes individuals with AHO features in the absence of PTH resistance. PHP and PPHP are etiologically linked and caused by genetic and/or epigenetic alterations in the guanine nucleotide-binding protein alpha-stimulating (G_s α) locus (GNAS) in chromosome 20q13. Another less-recognized group of skeletal dysplasias, termed acrodysostosis, partially overlap with skeletal, endocrine, and neurodevelopmental features of AHO/PHP and can be overlooked in clinical practice, causing confusion in the literature. Acrodysostosis is caused by defects in two genes, PRKAR1A and PDE4D, both encoding important components of the G_s α-cyclic adenosine monophosphate-protein kinase A signaling pathway. We describe the clinical course and genotype of two adult patients with overlapping AHO features who harbored novel pathogenic variants in GNAS (c.2273C > G, p.Pro758Arg, NM_080425.2) and PRKAR1A (c.803C > T, p.Ala268Val, NM_002734.4), respectively. We highlight the value of expert radiological opinion and molecular testing in establishing correct diagnoses and discuss phenotypic features of our patients, including the first description of subcutaneous ossification and spina bifida occulta in PRKAR1A-related acrodysostosis, in the context of the novel inactivating PTH/PTH related peptide signaling disorder classification system.

The use of panel testing in familial breast and ovarian cancer

Advances in sequencing technology have led to the introduction of panel testing in hereditary breast and ovarian cancer. While direct-to-consumer testing services have become widely available, the clinical validity of many of the genes on panel tests remains contentious and risk management guidelines are often lacking. This article gives an overview of advantages with panel testing as well as important challenges, including clinical translation of test results.

Tachycardia-induced cardiomyopathy in pregnancy

Heart failure in pregnancy is rare, but usually ascribed to peripartum cardiomyopathy in the absence of other possible diagnoses. However, heart failure can develop solely due to a tachycardia, so-called 'tachycardia-induced cardiomyopathy'. The incidence of tachycardia-induced cardiomyopathy in pregnancy is unknown, but it is a treatable and potentially reversible cause of heart failure. Clinically, tachycardia-induced cardiomyopathy during pregnancy might present in a similar manner, but its management has to be individualized according to the arrhythmic substrate and usually involve multidisciplinary input from specialists in obstetrics, cardiac electrophysiology and heart failure.