Meta-analysis of cardiomyopathy-associated variants in troponin genes identifies loci and intragenic hot spots that are associated with worse clinical outcomes

https://doi.org/10.1016/j.yjmcc.2020.04.005Get rights and content

Highlights

  • It is unclear how certain variants are well tolerated and others pathogenic.

  • TNNC1-positive probands carried the poorest prognosis compared to TNNT2 and TNNI3-positive probands.

  • Signal-to-noise mapping of TNN revealed locations in TNNT2 and TNNI3 associated with pathogenicity and poor prognosis.

  • De novo variants, homozygosity, compound heterozygotes, and double heterozygotes have poorer prognosis.

Abstract

Introduction

Troponin (TNN)-encoded cardiac troponins (Tn) are critical for sensing calcium and triggering myofilament contraction. TNN variants are associated with development of cardiomyopathy; however, recent advances in genetic analysis have identified rare population variants. It is unclear how certain variants are associated with disease while others are tolerated.

Objective

To compare probands with TNNT2, TNNI3, and TNNC1 variants and utilize high-resolution variant comparison mapping of pathologic and rare population variants to identify loci associated with disease pathogenesis.

Methods

Cardiomyopathy-associated TNN variants were identified in the literature and topology mapping conducted. Clinical features were compiled and compared. Rare population variants were obtained from the gnomAD database. Signal-to-noise (S:N) normalized pathologic variant frequency against population variant frequency. Abstract review of clinical phenotypes was applied to “significant” hot spots.

Results

Probands were compiled (N = 70 studies, 224 probands) as were rare variants (N = 125,748 exomes; 15,708 genomes, MAF <0.001). TNNC1-positive probands demonstrated the youngest age of presentation (20.0 years; P = .016 vs TNNT2; P = .004 vs TNNI3) and the highest death, transplant, or ventricular fibrillation events (P = .093 vs TNNT2; P = .024 vs TNNI3; Kaplan Meir: P = .025). S:N analysis yielded hot spots of diagnostic significance within the tropomyosin-binding domains, α-helix 1, and the N-Terminus in TNNT2 with increased sudden cardiac death and ventricular fibrillation (P = .004). The inhibitory region and C-terminal region in TNNI3 exhibited increased restrictive cardiomyopathy (P =.008). HCM and RCM models tended to have increased calcium sensitivity and DCM decreased sensitivity (P < .001). DCM and HCM studies typically showed no differences in Hill coefficient which was decreased in RCM models (P < .001). CM models typically demonstrated no changes to Fmax (P = .239).

Conclusion

TNNC1-positive probands had younger ages of diagnosis and poorer clinical outcomes. Mapping of TNN variants identified locations in TNNT2 and TNNI3 associated with heightened pathogenicity, RCM diagnosis, and increased risk of sudden death.

Introduction

Cardiomyopathies are a heterogeneous group of primary diseases of the heart muscle, that can predispose to heart failure and cardiovascular death, with risk of sudden cardiac death (SCD) at first presentation [1]. Although many classifications exist, the American Heart Association classifies primary cardiomyopathies by genetic, mixed genetic, and non-genetic variants. Structural genetic primary cardiomyopathies include hypertrophic cardiomyopathy (HCM), left ventricular non-compaction cardiomyopathy (LVNC), and arrhythmogenic right ventricular cardiomyopathy (ARVC). Mixed structural cardiomyopathies, or those with both genetic and non-genetic etiologies, include dilated cardiomyopathy (DCM) and restrictive cardiomyopathy (RCM) [2].

The etiology of the majority of cardiomyopathies, independent of the clinical presentation, is believed to be genetic. Genetic variants resulting in molecular defects in the components of the contractile myofilaments represent a major cause of cardiomyopathies [3,4]. The cardiac troponin molecular complex (Tn) is essential for the regulation of striated muscle contraction and is located along the sarcomere thin filament [5,6]. Disruption of any of these processes likely leads to cardiac dysfunction and cardiomyopathy.

While variants in TNN-encoding genes are clear causes of cardiomyopathy, there is marked clinical heterogeneity. Genotype-phenotype correlations to explain this heterogeneity have been limited by small numbers of probands and a lack of comprehensive knowledge of population variants. Recent genetic studies have identified previously reported pathologic variants in large population studies as well as rare variants of unknown disease risk [7,8]. It is unclear how certain TNN variants are associated with disease while others are physiologically tolerated. To address this, we set out to 1) create a compendium of cardiomyopathy (CM)-associated variants and population-associated variants, and 2) identify prognostic characteristics associated with genotype.

Section snippets

Nomenclature

Nomenclature in this study is detailed in Supplemental Materials.

Compendium of cardiomyopathy-associated TNN variants

To compile pathologic TNN variants, PubMed and the Human Gene Mutation database were queried through June 2018 for studies identifying patients with cardiomyopathy and confirmed TNN variants [9]. Inclusion criteria for the studies included 1) study of individuals with primary cardiomyopathic disease, 2) comprehensive genetic analysis of the coding exons of TNNT2, TNNI3, or TNNC1, 3) availability of individual variants and their

Creation of troponin variant database and meta-analysis

To identify all pathologic variants and rare population variants, we created a compendium of cardiomyopathy-associated variants and gnomAD-based population variants (Fig. 1A). A comprehensive review of the literature identified 224 probands hosting variants in TNN from 70 studies. A total of 55 distinct variants were identified in TNNT2, 53 in TNNI3, and 16 in TNNC1 (Supplemental Table 1). Individual proband data for TNNT2, TNNI3, and TNNC1 are detailed in Supplemental Tables 2, 3, and 4,

Variant investigation in cardiomyopathy

In light of the rapid progression of precision or personalized medicine, efforts to utilize an individual's specific genetic abnormality to predict outcomes and guide therapy are underway. Thus, understanding both the functional and prognostic implications of rare variation is critical to the development of personalized medicine [20]. Recent studies have highlighted that specific genetic variation that is associated with the development of cardiomyopathy, in particular HCM, may guide rational

Limitations

Studies compiled were variable in data collection and were performed retrospectively. Comprehensive clinical data were not always available for probands and patients may have been lost to follow-up. Given that TNN variants are rare, we were likely underpowered to detect the prognostic impact of TNNC1 variants. Further, when calculating variant frequencies based on cardiomyopathy subtype, it is possible that minor cardiomyopathy variant frequencies are inflated due to limited patients screened

Clinical perspectives

In light of population-based data showing variants, it has become unclear how certain variants are well tolerated and others pathogenic. S:N analysis is a viable tool to better analyze variant hot spots, while integrating rare population variants. S:N analysis can be used to identify pathologic hot spots in other genes that demonstrate rare variants found in ostensibly healthy individuals.

Grant support

JRP is supported by the NIH Grant R01-HL128683. MSP is supported by AHA SDG #16SDG29120002. UF CTSI is supported by the NIH UL1TR001427. APL is supported by the Pediatric and Congenital Electrophysiology Society Paul C. Gillette Award, pilot grant funding from the Baylor College of Medicine Department of Pediatrics and Duke University School of Medicine.

Declaration of Competing Interest

No conflicts of interest to declare.

References (61)

  • T. Palm et al.

    Disease-causing mutations in cardiac troponin T: identification of a critical tropomyosin-binding region

    Biophys. J.

    (2001)
  • N. Bohlooli Ghashghaee et al.

    Role of the C-terminus mobile domain of cardiac troponin I in the regulation of thin filament activation in skinned papillary muscle strips

    Arch. Biochem. Biophys.

    (2018)
  • N.L. Meyer et al.

    Role of cardiac troponin I carboxy terminal mobile domain and linker sequence in regulating cardiac contraction

    Arch. Biochem. Biophys.

    (2016)
  • J.E. Gilda et al.

    The functional significance of the last 5 residues of the C-terminus of cardiac troponin I

    Arch. Biochem. Biophys.

    (2016)
  • MdA Marques et al.

    Allosteric transmission along a loosely structured backbone allows a cardiac troponin C mutant to function with only one Ca(2+) ion

    J. Biol. Chem.

    (2017)
  • L. Smith et al.

    The effects of deletion of the amino-terminal helix on troponin C function and stability

    J. Biol. Chem.

    (1994)
  • L. Smith et al.

    Mutations in the N- and D-helices of the N-domain of troponin C affect the C-domain and regulatory function

    Biophys. J.

    (1999)
  • M. Chandra et al.

    The effects of N helix deletion and mutant F29W on the Ca2+ binding and functional properties of chicken skeletal muscle troponin

    J. Biol. Chem.

    (1994)
  • J.R. Pinto et al.

    A functional and structural study of troponin C mutations related to hypertrophic cardiomyopathy

    J. Biol. Chem.

    (2009)
  • R. Wexler et al.

    Cardiomyopathy: an overview

    Am. Fam. Physician

    (2009)
  • B.J. Maron et al.

    Contemporary definitions and classification of the cardiomyopathies

    Circulation.

    (2006)
  • M.S. Parvatiyar et al.

    Cardiac troponin mutations and restrictive cardiomyopathy

    J. Biomed. Biotechnol.

    (2010)
  • A.M. Gordon et al.

    Regulation of contraction in striated muscle

    Physiol. Rev.

    (2000)
  • A.M. de Mayra et al.

    The missing links within troponin

    Arch. Biochem. Biophys.

    (2018)
  • J.R. Golbus et al.

    Population-based variation in cardiomyopathy genes

    Circ. Cardiovasc. Genet.

    (2012)
  • C. Andreasen et al.

    New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants

    Eur. J. Human Genet.

    (2013)
  • P.D. Stenson et al.

    Human gene mutation database (HGMD): 2003 update

    Hum. Mutat.

    (2003)
  • M.J. Landrum et al.

    ClinVar: improving access to variant interpretations and supporting evidence

    Nucleic Acids Res.

    (2018)
  • D.R. Zerbino et al.

    Ensembl 2018

    Nucleic Acids Res.

    (2018)
  • M. Lek et al.

    Analysis of protein-coding genetic variation in 60,706 humans

    Nature.

    (2016)
  • Cited by (0)

    View full text