The 10+1 Santorini Conference

The quest for missing heritability: role of rare variant and gene-environment interactions

Guillaume Pare, MD
McMaster University, Ontario, Canada

Biobank-scale genotyping has enabled the routine use of statistical genetics applications, such as Mendelian randomization, polygenic scores and heritability estimations. However, many questions remain less well explored, such as the contribution of gene-by-environment interactions (GxE) and the role of rare coding variants (RV) in complex traits. Leveraging the speed, versatility and robustness of large linear models, we sought to address these two questions. First, we introduce MonsterLM, a multiple linear regression method that does not rely on model specification and provides unbiased estimates of variance explained by GxE. Identification of GxE is crucial to understand the interplay of environmental effects on complex traits. However, current methods evaluating GxE on biobank-scale datasets have limitations. We demonstrate robustness of MonsterLM through comprehensive genome-wide simulations using real genetic data from 325K UK Biobank participants. We estimate GxE using waist-to-hip-ratio, smoking, and exercise as the environmental variables on 13 outcomes and find significant GxE for 8 environment-outcome pairs. The majority of GxE variance involves SNPs without strong marginal or interaction associations. Second, we developed a novel framework, the Rare variant heritability (RARity) estimator, to assess RV heritability (h2RV) without assuming a particular genetic architecture. We applied RARity to 31 complex traits in the UK Biobank (N=167K) and showed that gene-level RV aggregation suffers from 79% (95% CI: 68-93%) loss of h2RV. Using unaggregated variants, 27 traits had h2RV>5%, with height having the highest h2RV at 21.9% (95% CI: 19.0-24.8%). The total heritability, including common and rare variants, recovered pedigree-based estimates for 11 traits. We also used RARity to reveal 11 novel gene-phenotype relationships. Finally, we demonstrated that in silico pathogenicity prediction (variant-level) and gene-level annotations do not generally enrich for RVs that over-contribute to complex trait variance, and thus, novel methods are needed to predict RV functionality.

Cardiac inflammation: the relative contribution of autoimmunity and genes

Federica M Marelli-Berg1,
Silvia Fanti1*, Edward Stephenson1,2*, Etel Rocha-Vieira1,3, Alexandros Protonotarios2,4, Stavroula Kanoni1, Perry Elliott2,4, Saidi A Mohiddin1,2*,

1William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
2Barts Heart Centre, Barts Health NHS Trust, St Bartholomew’s Hospital, West Smithfield, London EC1A 7BE
3Federal University of Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
4Institute of Cardiovascular Science, University College London, 72 Huntley Street, London WC1E 6AG

Autoimmunity is increasingly recognized as a key contributing factor in heart muscle diseases. The functional features of cardiac autoimmunity in humans remain undefined, due to the challenge of studying immune responses in-situ. We have previously described a subset of cMet-expressing memory T-lymphocytes, which preferentially migrate to cardiac tissue in mice and humans.
In-depth phenotyping of peripheral blood T-cells, including cMet+ T-cells, was undertaken in groups of patients with inflammatory and non-inflammatory cardiomyopathies, patients with non-cardiac autoimmunity and healthy controls. Validation studies were carried out using human cardiac tissue and in an experimental model of cardiac inflammation.
We show that cMet+ T-cells are selectively increased in the circulation and in the heart of patients with inflammatory cardiomyopathies. cMet+ T-cells display distinct phenotype and function compared to cMet-negative T-cells, including preferential proliferation to cardiac myosin and co-production of multiple cytokines (IL-4, IL-17 and IL-22). Further, circulating cMet+ T-cell subpopulations in different heart muscle diseases identify distinct and overlapping mechanisms of heart inflammation including in genetic cardiomyopathies.
In experimental autoimmune myocarditis, rise of autoantigen-specific cMet+ T-cells in peripheral blood marks the loss of immune tolerance to the heart. Importantly, disease development can be halted by pharmacological cMet inhibition, indicating a causative role for cMet+ T-cells.

Trends in precision medicine, pharmacogenetics as adjuvant in establishing a correct immunosuppressive therapy of kidney transplant

Sergio Bernardini,
Dept. of Experimental Medicine, University of Tor Vergata, Rome, IT

Allogenic transplant of solid organ is now considered the election clinical procedure in patients with organ failure. Indeed, in the last decades important milestones have been reached especially in kidney transplant. Although the transplanted organ can compensate the function of original one, the main problem remains the immune response by the host organism that can lead to a possible rejection. The management of the immune response is at the basis for a long-life successful organ transplantation. To achieve this objective, drugs targeting the key immunological players of the immunological pathways, fundamental in graft rejection mechanisms have been developed. These can be now used in clinical management of transplanted patients. It is important to note that the wide inter and intra-patient variability of both the pharmacokinetics (PK) and pharmacodynamics (PD) represent the major clinical problem. Although the plasma concentrations of drugs are constantly monitored, variation of these parameters mainly due to the polymorphic status (genetic heterogeneity) of the genes involved in xenobiotic-metabolizing enzymes, transport proteins, and in some cases drug targets, can affects metabolite concentrations in each specific patient. This can induce an important toxicity or loss of efficacy. Numerous studies have been recently conducted to examine the relationship among genetic factors, drug pharmacokinetics, and therapy outcomes. Now several polymorphic genes, influencing drug’s efficacy have been catalogued, and they are now easily detected using Next generation sequencing (NGS) methods. Further research, and new investment in creating validated NGS commercial panel for the analysis of pharmacogenetics in renal transplant recipients will represent the future of precision medicine in the management of immunosuppressive therapy.

Interindividual variability and pharmacogenomics: possible ways forward

Munir Pirmohamed,
Department of Pharmacology and Therapeutics, The Wolfson Centre for Personalised Medicine, University of Liverpool, L69 3GL, UK

Interindividual variability in drug response (efficacy and/or safety) is the rule rather than the exception in clinical practice. This can be due to a number of clinical factors and genomic factors. While a genomic variant may play a major role in determining drug response, it is important not to forget about the clinical factors which also contribute. Our approach at present is unimodal (i.e. we look at one factor at a time), and we need to move to more multimodal approaches (combining genetic and clinical factors). This becomes even more important as our population grows older (with decreasing renal and hepatic function) and there is an increasing prevalence of multimorbidity and consequently polypharmacy. This puts them at higher risk of adverse drug reactions, drug interactions, and worse clinical outcomes. Tackling this will be a challenge, but genomics will add value to the usual approach of undertaking medicines reviews. In such populations, panel genotyping is likely to be the most pragmatic, and will enable us to move from reactive to pre-emptive genotyping approaches. This will be more convenient for the clinician and for the patient, as it fits in seamlessly with the current clinical pathways. The questions which need to be evaluated is when people should have panel genotyping undertaken, and which will be the most clinically-effective and cost-effective approach.