Directional next-generation RNA sequencing and examination of premature termination codon mutations in endoglin/hereditary haemorrhagic telangiectasia

Pathogenic Variant Frequencies in Hereditary Haemorrhagic Telangiectasia Support Clinical Evidence of Protection from Myocardial Infarction

Hereditary haemorrhagic telangiectasia (HHT) is a vascular dysplasia inherited as an autosomal dominant trait, due to a single heterozygous loss-of-function variant, usually in ACVRL1 (encoding activin receptor-like kinase 1 [ALK1]), ENG (encoding endoglin [CD105]), or SMAD4. In a consecutive single-centre series of 37 positive clinical genetic tests performed in 2021-2023, a skewed distribution pattern was noted, with 30 of 32 variants reported only once, but ACVRL1 c.1231C>T (p.Arg411Trp) identified as the disease-causal gene in five different HHT families. In the same centre's non-overlapping 1992-2020 series where 110/134 (82.1%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was identified in nine further families. In a 14-country, four-continent HHT Mutation Database where 181/250 (72.4%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was reported by 12 different laboratories, the adjacent ACVRL1 c.1232G>A (p.Arg411Gln) by 14, and ACVRL1 c.1120C>T (p.Arg374Trp) by 18. Unlike the majority of HHT-causal ACVRL1 variants, these encode ALK1 protein that reaches the endothelial cell surface but fails to signal. Six variants of this type were present in the three series and were reported 6.8-25.5 (mean 8.9) times more frequently than the other ACVRL1 missense variants (all p-values < 0.0039). Noting lower rates of myocardial infarction reported in HHT, we explore potential mechanisms, including a selective paradigm relevant to ALK1's role in the initiating event of atherosclerosis, where a plausible dominant negative effect of these specific variants can be proposed. In conclusion, there is an ~9-fold excess of kinase-inactive, cell surface-expressed ACVRL1/ALK1 pathogenic missense variants in HHT. The findings support further examination of differential clinical and cellular phenotypes by HHT causal gene molecular subtypes.

Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY, an analytic tool that integrates coordinates for regions with experimental evidence of functionality. Applied to WGS data from solved and unsolved hereditary hemorrhagic telangiectasia (HHT) recruits to the 100,000 Genomes Project, GROFFFY-based filtration reduced the mean number of variants/DNA from 4,867,167 to 21,486, without deleting disease-causal variants. In three unsolved cases (two related), GROFFFY identified ultra-rare deletions within the 3' untranslated region (UTR) of the tumor suppressor SMAD4, where germline loss-of-function alleles cause combined HHT and colonic polyposis (MIM: 175050). Sited >5.4 kb distal to coding DNA, the deletions did not modify or generate microRNA binding sites, but instead disrupted the sequence context of the final cleavage and polyadenylation site necessary for protein production: By iFoldRNA, an AAUAAA-adjacent 16-nucleotide deletion brought the cleavage site into inaccessible neighboring secondary structures, while a 4-nucleotide deletion unfolded the downstream RNA polymerase II roadblock. SMAD4 RNA expression differed to control-derived RNA from resting and cycloheximide-stressed peripheral blood mononuclear cells. Patterns predicted the mutational site for an unrelated HHT/polyposis-affected individual, where a complex insertion was subsequently identified. In conclusion, we describe a functional rare variant type that impacts regulatory systems based on RNA polyadenylation. Extension of coding sequence-focused gene panels is required to capture these variants.

Mutational and phenotypic characterization of hereditary hemorrhagic telangiectasia

Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular dysplasia. Care delivery for HHT patients is impeded by the need for laborious, repeated phenotyping and gaps in knowledge regarding the relationships between causal DNA variants in ENG, ACVRL1, SMAD4 and GDF2, and clinical manifestations. To address this, we analyzed DNA samples from 183 previously uncharacterized, unrelated HHT and suspected HHT cases using the ThromboGenomics high-throughput sequencing platform. We identified 127 rare variants across 168 heterozygous genotypes. Applying modified American College of Medical Genetics and Genomics Guidelines, 106 variants were classified as pathogenic/likely pathogenic and 21 as nonpathogenic (variant of uncertain significance/benign). Unlike the protein products of ACVRL1 and SMAD4, the extracellular ENG amino acids are not strongly conserved. Our inferences of the functional consequences of causal variants in ENG were therefore informed by the crystal structure of endoglin. We then compared the accuracy of predictions of the causal gene blinded to the genetic data using 2 approaches: subjective clinical predictions and statistical predictions based on 8 Human Phenotype Ontology terms. Both approaches had some predictive power, but they were insufficiently accurate to be used clinically, without genetic testing. The distributions of red cell indices differed by causal gene but not sufficiently for clinical use in isolation from genetic data. We conclude that parallel sequencing of the 4 known HHT genes, multidisciplinary team review of variant calls in the context of detailed clinical information, and statistical and structural modeling improve the prognostication and treatment of HHT.

Bevacizumab as Treatment for Epistaxis in Hereditary Hemorrhagic Telangiectasia: A Literature Review

Background:

Severe, recurring epistaxis is the most common symptom of hereditary hemorrhagic telangiectasias (HHT). Current treatment modalities range from noninvasive treatments that frequently fail to achieve even short-term control to surgeries and systemic therapies that carry significant risk of complications. Recently, bevacizumab, a VEGF inhibitor, has been proposed as an alternative option to alleviate epistaxis symptoms in HHT.

Objective:

To review the current literature regarding the use of bevacizumab for the treatment of epistaxis in patients with HHT and provide guidance on its usage for this indication.

Methods:

A narrative literature review was performed to analyze various methods and dosages of bevacizumab administration for the treatment of HHT-related epistaxis, along with a review of current treatment modalities and their drawbacks.

Results:

The current standard of care for HHT-related epistaxis consists of treatments that are largely ineffective or invasive with significant potential complications. Submucosal bevacizumab has demonstrated efficacy in reducing frequency, duration, and severity of epistaxis in those with HHT.

Conclusion:

Given the inadequacies and potential drawbacks of current treatments for epistaxis in HHT, there is a need for new therapeutic options. Submucosal bevacizumab has been effective with a limited risk profile in a number of studies and should now be considered as a treatment option for refractory epistaxis. Controlled studies are recommended to quantify optimal dosing, treatment schedule, and specific subpopulations that will respond best to this treatment.

Hemoglobin Is a Vital Determinant of Arterial Oxygen Content in Hypoxemic Patients with Pulmonary Arteriovenous Malformations

RATIONALE

Pa_O2 and Sa_O2 are commonly measured in respiratory practice, but arterial oxygen content (Ca_O2) refers to the volume of oxygen delivered to the tissues per unit blood volume. Ca_O2 is calculated from Sa_O2 and the hemoglobin concentration in blood, recognizing that each gram of hemoglobin can transport approximately 1.34 ml of oxygen when fully saturated.

OBJECTIVES

To prospectively evaluate serial changes in Ca_O2 in humans, incorporating and excluding dynamic changes to oxygenation and hemoglobin parameters that may occur during life.

METHODS

A cohort of 497 consecutive patients at risk of both hypoxemia and anemia were recruited. The patients had radiologically proven pulmonary arteriovenous malformations (PAVMs), which result in hypoxemia due to right-to-left shunting, and concurrent hereditary hemorrhagic telangiectasia, which placed them at risk of iron deficiency anemia due to recurrent hemorrhagic iron losses. Presentation Sa_O2 (breathing room air, by pulse oximetry), hemoglobin, red cell and iron indices were measured, and Ca_O2 calculated as Sa_O2 × hemoglobin × 1.34 ml/g. Serial measurements were evaluated in 100 cases spanning up to 32.1 (median, 10.5) years.

RESULTS

Presentation Ca_O2 ranged from 7.6 to 27.5 (median, 17.6) ml/dl. Ca_O2 did not change appreciably across the Sa_O2 quartiles. In contrast, hemoglobin ranged from 5.9 to 21.8 g/dl (median, 14.1 g/dl), with a linear increase in Ca_O2 across hemoglobin quartiles. After PAVM embolization and an immediate increase in Sa_O2, hemoglobin fell and Ca_O2 was unchanged 1.6-12 (median, 4) months later. When hemoglobin fell because of iron deficiency, there was no change in Sa_O2. Similarly, when hemoglobin rose after iron treatment, there was no change in Sa_O2, and the expected Ca_O2 increment was observed. These relationships were not evident during pregnancy when hemoglobin fell, and PAVMs usually deteriorated: in pregnancy Sa_O2 commonly increased, and serial Ca_O2 values (incorporating hemodilution/anemia) more accurately reflected deteriorating PAVM status. An apparent fall in Ca_O2 with age in females was attributable to the development of iron deficiency. There was an unexplained increase in Ca_O2 with age in follow-up of males after embolization.

CONCLUSIONS

Hemoglobin/Ca_O2 should be further incorporated into oxygenation considerations. More attention should be given to modest changes in hemoglobin that substantially modify Ca_O2.

Cerebral hemorrhage in monozygotic twins with hereditary hemorrhagic telangiectasia: case report and hemorrhagic risk evaluation

The authors present a case of monozygotic twins with hereditary hemorrhagic telangiectasia (HHT) who experienced cerebral arteriovenous malformation (AVM) hemorrhage at a very young age. The clinical variables influencing HHT-related AVM rupture are discussed, and questions surrounding the timing of screening and intervention are explored. This is only the second known case of monozygotic HHT twins published in the medical literature, and the youngest pair of first-degree relatives to experience AVM-related cerebral hemorrhage. Evidence guiding the screening and management of familial HHT is lacking, and cases such as this underscore the need for objective and validated protocols.

Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes

BACKGROUND

Spontaneous reports from patients able to report vascular sequelae in real time, and recognition that serum non transferrin bound iron may reach or exceed 10μmol/L in the blood stream after iron tablets or infusions, led us to hypothesize that conventional iron treatments may provoke acute vascular injury. This prompted us to examine whether a phenotype could be observed in normal human endothelial cells treated with low dose iron.

METHODOLOGY

Confluent primary human endothelial cells (EC) were treated with filter-sterilized iron (II) citrate or fresh media for RNA sequencing and validation studies. RNA transcript profiles were evaluated using directional RNA sequencing with no pre-specification of target sequences. Alignments were counted for exons and junctions of the gene strand only, blinded to treatment types.

PRINCIPAL FINDINGS

Rapid changes in RNA transcript profiles were observed in endothelial cells treated with 10μmol/L iron (II) citrate, compared to media-treated cells. Clustering for Gene Ontology (GO) performed on all differentially expressed genes revealed significant differences in biological process terms between iron and media-treated EC, whereas 10 sets of an equivalent number of randomly selected genes from the respective EC gene datasets showed no significant differences in any GO terms. After 1 hour, differentially expressed genes clustered to vesicle mediated transport, protein catabolism, and cell cycle (Benjamini p = 0.0016, 0.0024 and 0.0032 respectively), and by 6 hours, to cellular response to DNA damage stimulus most significantly through DNA repair genes FANCG, BLM, and H2AFX. Comet assays demonstrated that 10μM iron treatment elicited DNA damage within 1 hour. This was accompanied by a brisk DNA damage response pulse, as ascertained by the development of DNA damage response (DDR) foci, and p53 stabilization.

SIGNIFICANCE

These data suggest that low dose iron treatments are sufficient to modify the vascular endothelium, and induce a DNA damage response.

Specific cancer rates may differ in patients with hereditary haemorrhagic telangiectasia compared to controls

Background

Hereditary haemorrhagic telangiectasia (HHT) is inherited as an autosomal dominant trait, affects ~1 in 5,000, and causes multi-systemic vascular lesions and life-limiting complications. Life expectancy is surprisingly good, particularly for patients over 60ys. We hypothesised that individuals with HHT may be protected against life-limiting cancers.

Methods

To compare specific cancer rates in HHT patients and controls, we developed a questionnaire capturing data on multiple relatives per respondent, powered to detect differences in the four most common solid non skin cancers (breast, colorectal, lung and prostate), each associated with significant mortality. Blinded to cancer responses, reports of HHT-specific features allowed assignment of participants and relatives as HHT-subjects, unknowns, or controls. Logistic and quadratic regressions were used to compare rates of specific cancer types between HHT subjects and controls.

Results

1,307 participants completed the questionnaire including 1,007 HHT-subjects and 142 controls. The rigorous HHT diagnostic algorithm meant that 158 (12%) completed datasets were not assignable either to HHT or control status. For cancers predominantly recognised as primary cancers, the rates in the controls generally matched age-standardised rates for the general population. HHT subjects recruited through the survey had similar demographics to controls, although the HHT group reported a significantly greater smoking habit. Combining data of participants and uniquely-reported relatives resulted in an HHT-arm of 2,161 (58% female), and control-arm of 2,817 (52% female), with median ages of 66ys [IQR 53–77] and 77ys [IQR 65–82] respectively. In both crude and age-adjusted regression, lung cancers were significantly less frequent in the HHT arm than controls (age-adjusted odds ratio 0.48 [0.30, 0.70], p = 0.0012). Breast cancer prevalence was higher in HHT than controls (age-adjusted OR 1.52 [1.07, 2.14], p = 0.018). Overall, prostate and colorectal cancer rates were equivalent, but the pattern of colorectal cancer was modified, with a higher prevalence in younger HHT patients than controls.

Conclusions

These preliminary survey data suggest clinically significant differences in the rates of lung, breast and colorectal cancer in HHT patients compared to controls. For rare diseases in which longitudinal studies take decades to recruit equivalent datasets, this type of methodology provides a good first-step method for data collection.