RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy

Marta Ribeiro; Marta Furtado; Sandra Martins; Teresa Carvalho; Maria Carmo-Fonseca

doi:10.3390/ijms21041329

RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy

International Journal of Molecular Sciences ◽

10.3390/ijms21041329 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1329

Author(s):

Marta Ribeiro ◽

Marta Furtado ◽

Sandra Martins ◽

Teresa Carvalho ◽

Maria Carmo-Fonseca

Keyword(s):

Hypertrophic Cardiomyopathy ◽

Rna Splicing ◽

Clinical Utility ◽

Clinical Diagnostics ◽

Rna Analysis ◽

Uncertain Significance ◽

Associated Proteins ◽

High Throughput Dna Sequencing ◽

Splicing Defects ◽

Diagnostic Outcomes

Hypertrophic cardiomyopathy (HCM), the most common inherited heart disease, is predominantly caused by mutations in genes that encode sarcomere-associated proteins. Effective gene-based diagnosis is critical for the accurate clinical management of patients and their family members. However, the introduction of high-throughput DNA sequencing approaches for clinical diagnostics has vastly expanded the number of variants of uncertain significance, leading to many inconclusive results that limit the clinical utility of genetic testing. More recently, developments in RNA analysis have been improving diagnostic outcomes by identifying new variants that interfere with splicing. This review summarizes recent discoveries of RNA mis-splicing in HCM and provides an overview of research that aims to apply the concept of RNA therapeutics to HCM.

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Clinical Utility of a Phenotype-Enhanced MYH7 -Specific Variant Classification Framework in Hypertrophic Cardiomyopathy Genetic Testing

Circulation Genomic and Precision Medicine ◽

10.1161/circgen.120.003039 ◽

2020 ◽

Vol 13 (5) ◽

pp. 453-459

Author(s):

Connor L. Mattivi ◽

J. Martijn Bos ◽

Richard D. Bagnall ◽

Natalie Nowak ◽

John R. Giudicessi ◽

...

Keyword(s):

Genetic Testing ◽

Hypertrophic Cardiomyopathy ◽

Mayo Clinic ◽

Clinical Utility ◽

Similar Distribution ◽

Variant Classification ◽

Classification Framework ◽

Uncertain Significance ◽

Genetics And Genomics ◽

Independent Cohort

Background: Missense variants in the MYH7 -encoded MYH7 (beta myosin heavy chain 7) represent a leading cause of hypertrophic cardiomyopathy (HCM). MYH7 -specific American College of Medical Genetics and Genomics (ACMG) variant classification guidelines were released recently but have yet to be assessed independently. We set out to assess the performance of the MYH7 -specific ACMG guidelines and determine if the addition of phenotype-enhanced criteria (PE-ACMG) using the HCM Genotype Predictor Score can further reduce the burden of variants of uncertain significance (VUS). Methods: Re-assessment was performed on 70 MYH7 -variants in 121 unique patients from Mayo Clinic, and an independent cohort of 54 variants in 70 patients from Royal Prince Alfred Hospital (Australia). Qualifying variants were re-adjudicated using both standard ACMG and MYH7 -ACMG guidelines, and HCM Genotype Predictor Score was used to provide a validated measure of strength of clinical phenotype to be incorporated into the MYH7 -ACMG framework. Results: Among Mayo Clinic identified variants, 11/70 (16%) were classified as pathogenic (P), 10/70 (14%) as likely pathogenic, and 49/70 (70%) as a VUS. A similar distribution was seen in the Australian patients (12/54 [22%] P, 12/54 [22%] likely pathogenic, and 30/54 [56%] VUS; P =not significant). Application of the MYH7 -ACMG resulted in a nonsignificant reduction of the VUS burden in both cohorts from 49/70 to 39/70 (56%; P =0.1; Mayo Clinic) and from 30/54 to 20/54 (37%; P =0.1; Australia). Using the combined PE-MYH7-ACMG framework, the VUS decreased significantly from 49 to 27 ( P <0.001, Mayo Clinic) and from 30 to 16 ( P <0.001; Australia). Conclusions: Use of the MYH7 -specific guidelines alone failed to significantly decrease VUS burden in 2 independent cohorts. However, a significant reduction in VUS burden was observed after the addition of phenotypic criteria. Using a patient’s strength of sarcomeric HCM phenotype for variant adjudication can increase significantly the clinical utility of genetic testing for patients with HCM.

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Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis

Familial Cancer ◽

10.1007/s10689-020-00224-y ◽

2021 ◽

Author(s):

Paola Nix ◽

Erin Mundt ◽

Bradford Coffee ◽

Elizabeth Goossen ◽

Bryan M. Warf ◽

...

Keyword(s):

Rna Splicing ◽

Case Series ◽

Cancer History ◽

Rna Analysis ◽

Pathogenic Variants ◽

Conflicting Evidence ◽

Increased Risk ◽

Splicing Variants ◽

Uncertain Significance ◽

In Silico Models

AbstractA substantial proportion of pathogenic variants associated with an increased risk of hereditary cancer are sequence variants affecting RNA splicing. The classification of these variants can be complex when both non-functional and functional transcripts are produced from the variant allele. We present four BRCA2 splice site variants with complex variant interpretations (BRCA2 c.68-3T>G, c.68-2A>G, c.425G>T, c.8331+2T>C). Evidence supporting a pathogenic classification is available for each variant, including in silico models, absence in population databases, and published functional data. However, comprehensive RNA analysis showed that some functional transcript may be produced by each variant. BRCA2 c.68-3T>G results in a partial splice defect. For BRCA2 c.68-2A>G and c.425G>T, aberrant splicing was shown to produce a potentially functional, in-frame transcript. BRCA2 c.8331+2T>C may utilize a functional GC donor in place of the wild-type GT donor. The severity of cancer history for carriers of these variants was also assessed using a history weighting algorithm and was not consistent with pathogenic controls (carriers of known pathogenic variants in BRCA2). Due to the conflicting evidence, our laboratory classifies these BRCA2 variants as variants of uncertain significance. This highlights the importance of evaluating new and existing evidence to ensure accurate variant classification and appropriate patient care.

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Protein haploinsufficiency drivers identify MYBPC3 mutations that cause hypertrophic cardiomyopathy

10.1101/2020.05.04.20087726 ◽

2020 ◽

Cited By ~ 2

Author(s):

Carmen Suay-Corredera ◽

Maria Rosaria Pricolo ◽

Elías Herrero-Galán ◽

Diana Velázquez-Carreras ◽

David Sánchez-Ortiz ◽

...

Keyword(s):

Hypertrophic Cardiomyopathy ◽

Protein Stability ◽

Rna Splicing ◽

Specific Gene ◽

Gene Encoding ◽

Pathogenic Variants ◽

Myosin Binding Protein ◽

Disease Mutations ◽

Uncertain Significance ◽

Molecular Phenotypes

ABSTRACTHypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease. Mutations in MYBPC3, the gene encoding cardiac myosin-binding protein C (cMyBP-C), are a leading cause of HCM. However, it remains challenging to define whether specific gene variants found in patients are pathogenic or not, limiting the reach of cardiovascular genetics in the management of HCM. Here, we have examined cMyBP-C haploinsufficiency drivers in 68 clinically annotated non-truncating variants of MYBPC3. We find that 45% of the pathogenic variants show alterations in RNA splicing or protein stability, which can be linked to pathogenicity with 100% and 94% specificity, respectively. Relevant for variant annotation, we uncover that 9% of non-truncating variants of MYBPC3 currently classified as of uncertain significance induce one of these molecular phenotypes. We propose that alteration of RNA splicing or protein stability caused by MYBPC3 variants provide strong evidence of their pathogenicity, leading to improved clinical management of HCM patients and their families.

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Tracking the Antibody Immunome in Sporadic Colorectal Cancer by Using Antigen Self-Assembled Protein Arrays

Cancers ◽

10.3390/cancers13112718 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2718

Author(s):

María González-González ◽

José María Sayagués ◽

Luis Muñoz-Bellvís ◽

Carlos Eduardo Pedreira ◽

Marcello L. R. de Campos ◽

...

Keyword(s):

Colorectal Cancer ◽

Clinical Utility ◽

Genetic Alterations ◽

Western World ◽

Sporadic Colorectal Cancer ◽

Protein Arrays ◽

Humoral Immune ◽

Cellular Processes ◽

Healthy Donors ◽

Associated Proteins

Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.

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The yeast nuclear geneMRF1encodes a mitochondrial peptide chain release factor and cures several mitochondrial RNA splicing defects

Nucleic Acids Research ◽

10.1093/nar/20.23.6339 ◽

1992 ◽

Vol 20 (23) ◽

pp. 6339-6346 ◽

Cited By ~ 30

Author(s):

Herman J. Pel ◽

Corien Maat ◽

Martijn Rep ◽

Leslie A. Grivell

Keyword(s):

Rna Splicing ◽

Peptide Chain ◽

Mitochondrial Rna ◽

Release Factor ◽

Splicing Defects

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Hypertrophic cardiomyopathy: genetics

ESC CardioMed ◽

10.1093/med/9780198784906.003.0350 ◽

2018 ◽

pp. 1443-1450

Author(s):

Mohammed Majid Akhtar ◽

Luis Rocha Lopes

Keyword(s):

Genetic Testing ◽

Hypertrophic Cardiomyopathy ◽

Mapk Pathway ◽

Glycogen Storage ◽

Cellular Level ◽

Causative Mutation ◽

Clinical Role ◽

Genes Encoding ◽

Associated Proteins

Hypertrophic cardiomyopathy is most commonly transmitted as an autosomal dominant trait, caused by mutations in genes encoding cardiac sarcomere and associated proteins. Knowledge of the genetic pathophysiology of the disease has advanced significantly since the initial identification of a point mutation in the beta-myosin heavy chain (MYH7) gene in 1990. Other genetic causes of the disease include mutations in genes coding for proteins implicated in calcium handling or which form part of the cytoskeleton. The recent emergence of next-generation sequencing allows quicker and less expensive identification of causative mutations. However, a causative mutation is not identified in up to 50% of probands. At present, the primary clinical role of genetic testing in hypertrophic cardiomyopathy is in the context of familial screening, allowing the identification of those at risk of developing the condition. Genetic testing can also be used to exclude genocopies, particularly in the presence of certain diagnostic ‘red flag’ features, where lysosomal, glycogen storage, neuromuscular or Ras-MAPK pathway disorders may be suspected. The role of individual mutations in predicting prognosis is limited at present. However, the higher incidence of sudden cardiac death in the presence of a family history of such, suggests that genetics play a significant role in determining outcome. With an increased understanding of the impact of these mutations on a cellular level and on longer-term clinical outcomes, the aim in future for gene and mutation specific prognosis or potential disease-modifying therapy is closer.

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Genotype-Related Clinical Characteristics and Myocardial Fibrosis and Their Association with Prognosis in Hypertrophic Cardiomyopathy

Journal of Clinical Medicine ◽

10.3390/jcm9061671 ◽

2020 ◽

Vol 9 (6) ◽

pp. 1671 ◽

Cited By ~ 1

Author(s):

Hyung Yoon Kim ◽

Jong Eun Park ◽

Sang-Chol Lee ◽

Eun-Seok Jeon ◽

Young Keun On ◽

...

Keyword(s):

Hypertrophic Cardiomyopathy ◽

Myocardial Fibrosis ◽

Genetic Variants ◽

Asian Patients ◽

Pathogenic Variants ◽

Clinical Events ◽

Cerebrovascular Events ◽

Genotypic Analysis ◽

Uncertain Significance

Background: The spectrum of genetic variants and their clinical significance of Hypertrophic cardiomyopathy (HCM) have been poorly studied in Asian patients. The objectives of this study were to assess the spectrum of genetic variants and genotype–phenotype relationships within a Korean HCM population. Methods: Eighty-nine consecutive unrelated HCM patients were included. All patients underwent genotypic analysis for 23 HCM-associated genes. Clinical parameters including echocardiographic and cardiac magnetic resonance (CMR) parameters were evaluated. A composite of major adverse cardiac and cerebrovascular events was assessed. Results: Genetic variants were detected in 55 of 89 subjects. Pathogenic variants or likely pathogenic variants were identified in 27 of HCM patients in MYBPC3, TNNI3, MYH7, and MYL7. Variants of uncertain significance were identified in 28 patients. There were significant differences in the presence of non-sustained ventricular tachycardia (p = 0.030) and myocardial fibrosis on CMR (p = 0.029) in the detected compared to the not-detected groups. Event-free survival was superior in the not-detected group (p = 0.006). Conclusion: Genetic variants in patients with HCM are relatively common and are associated with adverse clinical events and myocardial fibrosis on CMR. Genotypic analysis may add important information to clinical variables in the assessment of long-term risk for HCM patients.

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Correction: Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance

Genetics in Medicine ◽

10.1038/s41436-020-0789-2 ◽

2020 ◽

Vol 22 (6) ◽

pp. 1129-1129

Author(s):

Htoo A. Wai ◽

◽

Jenny Lord ◽

Matthew Lyon ◽

Adam Gunning ◽

...

Keyword(s):

Variants Of Uncertain Significance ◽

Rna Analysis ◽

Clinical Diagnostic ◽

Uncertain Significance

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A Common Human β Globin Splicing Mutation Modeled in Mice

Blood ◽

10.1182/blood.v91.6.2152 ◽

1998 ◽

Vol 91 (6) ◽

pp. 2152-2156 ◽

Cited By ~ 52

Author(s):

Jada Lewis ◽

Baoli Yang ◽

Ronald Kim ◽

Halina Sierakowska ◽

Ryszard Kole ◽

...

Keyword(s):

Animal Model ◽

Rna Splicing ◽

Southern China ◽

Embryonic Stem ◽

Mutant Gene ◽

Single Copy ◽

Globin Genes ◽

Globin Chains ◽

Splicing Defects ◽

Aberrant Rna

Abstract The βIVS-2-654 C→T mutation accounts for approximately 20% of β thalassemia mutations in southern China; it causes aberrant RNA splicing and leads to β0 thalassemia. To provide an animal model for testing therapies for correcting splicing defects, we have used the “plug and socket” method of gene targeting in murine embryonic stem cells to replace the two (cis) murine adult β globin genes with a single copy of the human βIVS-2-654 gene. No homozygous mice survive postnatally. Heterozygous mice carrying this mutant gene produce reduced amounts of the mouse β globin chains and no human β globin, and have a moderate form of β thalassemia. The heterozygotes show the same aberrant splicing as their human counterparts and provide an animal model for testing therapies to correct splicing defects at either the RNA or DNA level.

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