The Challenges - and our approaches
My career goal has been to understand the molecular basis of disease. I focus on the sequelae of DNA variation impacting on human health in the context of environmental and other genetic stressors, in order to rapidly deliver benefit to patients.
Delivering numeric confidence to guide personalised medicine is demanding in the setting of individually unique genomes each harbouring multiple rare, high-impact DNA variants absent from genome wide association studies, and barely represented in tissue banks from genomically- unselected donors. My group devises and validates methodologies that enhance opportunities to interrogate contributions of rare variants to health and disease.
Developing Reverse Translation, and why
In 1997, based on my 1993-1996 observations in 36 families (>300 individuals) with hereditary haemorrhagic telangiectasia (HHT) or adenosine deaminase deficiency, and earlier training in classical genetics, I developed an overarching model of human disease (left hand figure). This predicted that where genetic diseases bring an unspecified pathology closer towards a detectable threshold, monogenic diseases might serve as high-risk models for identification of environmental and other genetic factors contributing to pathological states. To test, while continuing to use traditional genetic approaches (right hand figure, blue arrows) to identify genes which when mutated, cause human disease, I supplemented by an approach I termed Reverse Translation (right hand figure, red arrows). This required set up of dual clinical and research programmes that have taken 22 years and >1500 patients to come to ‘academic’ fruition, meanwhile delivering clinical benefit for more than 15 years.
The principal target has been a multisystemic inherited condition, hereditary haemorrhagic telangiectasia (HHT), that results from causative, pathogenic, loss-of-function “mutations” in genes that encode transforming growth factor (TGF)-β/bone morphogenetic protein (BMP) superfamily members. HHT variants cause two main vascular malformation types: (i) arteriovenous malformations (AVMs) that develop in utero/childhood, remain in adult life, and cause complications (most commonly strokes due to pulmonary AVMs), and (ii) adult onset, dynamic, but numerically progressive, smaller telangiectasia that are responsible, via bleeding/anaemia, for most of the day-to-day burden of disease and healthcare [Shovlin 2020]. HHT is clinically and mechanistically distinct from other inherited and vascular malformation syndromes, and has been my major focus because:
- The clinically important complications (strokes through right-to-left paradoxical emboli; iron deficiency anaemia) are relevant to more than one-third of the human population, transcending the rare disease origin;
- I was puzzled by the extreme clinical variability within members of the same family (from non-penetrance i.e. no clinical sequelae, to very severe [Shovlin, 1994]) and hypothesised that their study would illuminate modifiable risks relevant to the general population [Shovlin, 1999, reprinted in Shovlin, 2010];
- The patients provide a source of blood-derived cells to examine a molecular process operational in patient cells (nonsense mediated decay, Shovlin 1997) but obscured by conventional recombinant technological approaches.
Molecular causes- spectra of consequences
- My early contributions to HHT genetics (Shovlin 1994, Shovlin 1997) highlighted intrafamilial phenotypic diversity but the potential paucity of symptoms and signs was overlooked until our latest paper (Anderson 2022) and data that changed the National Genomic Test Directory.
- Through the 100,000 Genomes Project we have (i) identified a new HHT disease gene (GDF2) (Balanchandar 2022); (ii) demonstrated that 10-15% mosaicism missed by Sanger is detectable by WGS (Clarke 2020), and (iii) Validated a novel filter developed by Sihao Xiao under my supervision, that reduces ~5 million variants per DNA to ~20,000 restricted to regions of functional significance (Xiao 2020), enabling machine learning to identify new HHT-associated loci.
- Through my novel precision phenotyping of patients, supplementing usual binary phenotypic discriminators with validated severity scales, we were able to (i) demonstrate that secondary phenotypes (bleeding/anaemia) are not related to HHT causal genes (Shovlin 2020; Joyce 2022); (ii) show platelet/coagulation gene deleterious variants to be commonly present, and less well tolerated in HHT than the general population (Joyce 2022) and (iii) develop a platform ‘towards personalised genomic interpretations’ (TPGI) (Joyce 2022) expected to be relevant to discrimination of phenotypes in other conditions.
Variability in same donor endothelial cells
Recognising that >60% of loss-of-function DNA variants lead to premature termination codons predicted to be degraded by nonsense mediated decay (NMD, Govani 2013), with evidence in HHT-derived EBV-transformed lymphoblastoid cells (Shovlin 1997), my group established blood outgrowth endothelial cells (BOECs) from pre-genotyped HHT patients. Our transcriptome data is currently available as a preprint (Bernabeu-Herrero 2021), with a Qeios review regarding the implication for the specific rare disease. The data also identified a second, more generic process that explained in part, the variability between replicate cultures from the same donor, and related to differing degrees of NMD efficiency which could be quantified at 78-92% per culture. This is being taken forward in 2022.
Iron treatment - a phenotypic modifier
Seven Shovlin 2016-2021 manuscripts demonstrate that iron treatments (prescribed >6 million times p.a. in England, and generators of reactive oxygen species (ROS)), can cause endothelial injury, and HHT bleeding and anaemia. Our 2020 RNASeq data of HHT-derived BOECs provided evidence for reciprocal changes in mRNAs and miRNAs to normal endothelial cells after 1hr 10μM iron (Mollet 2016; Bernabeu-Herrero 2021), and are being taken forward in 2022.
2020-2022 HHT Genomic Publications
- Shovlin et al Blood, Oct 2020
Mutational and phenotypic characterization of hereditary hemorrhagic telangiectasia
- Clarke et al J Med Genet, Dec 2020
Low grade mosaicism in hereditary haemorrhagic telangiectasia identified by bidirectional whole genome sequencing reads through the 100,000 Genomes Project clinical diagnostic pipeline
- Davieson et al Eur J Hum Genet, Oct 2021
DNA variant classification-reconsidering "allele rarity" and "phenotype" criteria in ACMG/AMP guidelines
- Anderson et al Thorax, Feb 2022
Pulmonary arteriovenous malformations may be the only clinical criterion present in genetically confirmed hereditary haemorrhagic telangiectasia
- Balanchander et al, Am J Med Genet Mar 2022
Identification and validation of a novel pathogenic variant in GDF2 (BMP9) responsible for hereditary hemorrhagic telangiectasia and pulmonary arteriovenous malformations
- Joyce et al Blood Advances, Mar 2022
Whole genome sequences discriminate hereditary hemorrhagic telangiectasia phenotypes by non-HHT deleterious DNA variants
2021-2022 HHT/PAVM Clinical Manuscripts
For hereditary haemorrhagic telangiectasia (HHT), the 2022 Frameworks manuscript from the European Reference Network for HHT (VASCERN HHT) summarises all of the 100% consensus statements generated 2016-2020 while chaired by Shovlin, and expands on key underlying circulatory physiology principles required to understand and appropriately manage HHT:
- Anaemia, bleeding and iron intake
- Pulmonary capillary bypass
- High cardiac output
Low systemic vascular resistance (AVMs), anaemia, hypoxaemia
For pulmonary arteriovenous malformations (PAVMs), the 2017 Clinical Statement from the British Thoracic Society, chaired by Shovlin, remains valid. We have generated further data and insights into the mechanisms of exercise capacity/dyspnoea, and ischaemic stroke (summarised in the 2021 Orphanet Statement).
2022 Research Presentations
 AoPGBI Association of Physicians
Dublin,10-11 March 2022
New paradigms for “truncated proteins” in medicine and biology: Failure to degrade associated with reduced expression of injury-responsive RNA transcripts
 Genomics England Research Summit
London, 4 May 2022
Deciphering the rare and impactful: Development and application of functional tools for rare variant interrogation in genomic medicine
 Royal Pharmaceutical Society Science and Research Summit
London, 24 June 2022
- see also Personalised Prescribing: Pharmacogenomics in the NHS: RCP/BPS Working Party Report
 Gordon Research Conference on Post Transcriptional Gene Regulation Maine, 10-15 July 2022 (poster)
Towards an understanding of generic consequences from inefficient nonsense mediated decay.
Achievement Award for Rare Pulmonary Disease Lecture, European Respiratory Society, Vienna, Austria, 2012
Presidential Lecture, American Society of Haematology, New Orleans, US, 1999
>65 invited international and national lectures, including, American Thoracic Society; International Society on Thrombosis and Haemostasis; Royal Colleges of Physicians (London and Edinburgh); Royal Society of Medicine; British Thoracic Society (including two scientific plenary lectures); and multiple academic institutions in, US, Canada, Japan, Argentina, Spain, Germany, Italy, Turkey and UK, from, 1993