Primary analytical observation

MYH7 becomes most interpretable when variant consequence, sarcomere biology, ventricular cardiomyocyte state, and cardiac phenotype agree. Broad tissue expression alone is insufficient, and signals that depend on a single atlas or label resolution should not be promoted to mechanism claims.

Executive interpretation

At a high level, this study asks a simple question: when a rare MYH7 variant is biologically important, where should its effect become visible? A conventional tissue-level answer—“the heart”—is correct but not discriminating. The heart contains multiple cell classes, and cardiomyocytes themselves occupy developmental, metabolic, contractile, and stress-associated states that can make the same gene signal mean different things.

Our conclusion is that cellular context should be treated as an evidence gate. A candidate mechanism is strengthened when the implicated variant consequence is compatible with established MYH7 biology, the relevant phenotype is cardiac and structurally coherent, and the signal localizes to reproducible ventricular cardiomyocyte programs. It is weakened when enrichment is driven by ubiquitous expression, one annotation source, one donor, or one atlas taxonomy.

Biological and genetic context

MYH7 encodes beta-myosin heavy chain, a major component of the thick filament in cardiac sarcomeres. Pathogenic variation has established relationships with inherited cardiomyopathies, but the molecular direction and phenotypic expression are not interchangeable across variant classes. Missense variation affecting the motor or filament-forming regions cannot be interpreted as though it were generic loss of function, and a gene-level association cannot substitute for transcript, domain, inheritance, segregation, or variant-specific evidence.

This distinction matters computationally. Expression-based analyses often reward genes that are abundant, well annotated, and connected to many known pathways. MYH7 satisfies all three conditions. Without explicit null models, a strong score can therefore recapitulate prior knowledge rather than identify the cell state in which a proposed mechanism is most testable. We frame the analysis around localization and coherence, not rediscovery of cardiac expression.

  • Separate gene–disease validity from variant-level pathogenicity.
  • Retain transcript and protein-domain context rather than collapsing to one gene symbol.
  • Model hypertrophic, dilated, skeletal-muscle, and mixed phenotypic branches independently before testing convergence.

Evidence assembly and harmonization

The input layer combines public variant annotations, population-frequency evidence, gene- and transcript-level constraint, structured phenotypes, and cardiac single-cell or single-nucleus references. Every derived object retains its source release, genome build, transcript set, identifier mapping, exclusion rules, and download date. Conflicting consequences are preserved as disagreement rather than resolved silently.

Cardiac atlases are harmonized twice. First, original author labels are retained so the analysis respects the resolution supported by each study. Second, labels are mapped to a conservative shared hierarchy: non-myocyte compartment, cardiomyocyte lineage, chamber-enriched identity, maturation state, and stress or remodeling state. Results must be intelligible at both the source-label and shared-label levels. A conclusion that exists only after aggressive relabeling is considered taxonomy-dependent.

Cell-state model and statistical design

Cells are not treated as independent biological replicates. Where donor identifiers and counts are available, expression is aggregated within donor-by-state strata to create pseudobulk profiles, and donor is the unit of inference. This reduces pseudoreplication and prevents a large cell yield from one specimen from masquerading as biological certainty. Detection fraction, normalized abundance, rank-based specificity, and module coherence are reported separately because each answers a different question.

The primary state score is an evidence vector rather than a single opaque number. It contains transcript-compatible expression, state specificity, co-expression with sarcomere and proteostasis modules, phenotype concordance, and cross-reference transfer. Alternate weights can reorder candidates without changing the underlying evidence graph. This makes it possible to ask whether the conclusion survives a reasonable change in priorities rather than defending one preferred parameterization.

  • Donor-stratified pseudobulk summaries for inferential comparisons.
  • Matched null genes selected on expression level, transcript length, and constraint neighborhood.
  • Bootstrap intervals over donors and leave-one-reference-out replication over atlases.
  • Sensitivity to chamber labels, maturation resolution, and ontology propagation depth.

Controls and competing explanations

The main competing explanation is abundance: MYH7 may score highly because it is a dominant cardiac transcript, not because the tested cell state is mechanistically informative. We address this with expression-matched null genes and by requiring enrichment beyond a broad cardiomyocyte baseline. A second explanation is annotation circularity, in which known cardiomyopathy labels enter both the phenotype definition and the validation set. We therefore maintain phenotype-only, cell-state-only, and integrated analyses and inspect their agreement.

A third explanation is atlas-specific composition. Adult surgical tissue, developmental tissue, organoid references, and diseased myocardium sample different biology. We do not expect identical effect sizes across these resources. We require agreement in direction and biological neighborhood, while allowing the most specific label to differ. Failure to transfer is reported as a boundary of the hypothesis rather than erased by integration.

Technical findings

Across the analytical variants we consider credible, the informative signal is not “MYH7 is expressed in heart.” The stable observation is that MYH7-linked evidence remains coherent in ventricular cardiomyocyte programs characterized by organized contractile machinery, sarcomere maintenance, force generation, and maturation-associated metabolic support. Broad fibroblast, endothelial, immune, and undifferentiated progenitor compartments do not carry equivalent integrated support after expression matching.

The result is sensitive to mechanism specification. A missense-compatible contractile hypothesis remains interpretable when evaluated in mature sarcomere-bearing states, whereas a generic haploinsufficiency model is not supported simply by high cardiac expression. Phenotype terms that distinguish ventricular hypertrophy, chamber dilation, impaired systolic function, or skeletal-muscle involvement materially change which mechanistic branch is coherent. This is a desired behavior: the model should respond to biologically informative phenotype differences.

Consolidated findings

What the analysis establishes

Cell state adds discrimination

Ventricular cardiomyocyte maturation and contractile programs carry more mechanistic information than organ-level expression or cell-type detection alone.

Mechanism cannot be inferred from abundance

High MYH7 expression establishes relevance to contractile tissue but does not determine gain of function, dominant-negative behavior, reduced motor performance, or pathogenicity.

Replication is biological, not lexical

The most stable evidence transfers as a conserved sarcomere-centered neighborhood even when atlas-specific cell-state names differ.

Phenotype structure changes the branch

Hypertrophic, dilated, and skeletal-muscle features should be represented as partially shared but non-equivalent phenotype programs.

Research conclusion

Conclusion and experimental handoff

We conclude that an MYH7 variant hypothesis is ready for experimental prioritization only when it specifies the variant mechanism, the cardiomyocyte state, the phenotype branch, and a directional molecular readout. The most defensible context from this analysis is a mature or maturing ventricular cardiomyocyte system in which sarcomere organization, contractile kinetics, force production, and energetic adaptation can be measured together.

The direct next step is not another generic enrichment analysis. It is a variant-specific perturbation in an isogenic cardiomyocyte model or engineered cardiac tissue, with rescue or correction, matched differentiation state, and orthogonal readouts of myosin function and cellular mechanics. A result that fails to localize to the predicted state—or that persists identically in non-cardiac controls—would weaken the proposed context-specific mechanism.

Interpretive boundary

Limitations

  • Public atlases are observational and differ in donor composition, tissue acquisition, platform, and annotation depth.
  • Single-cell RNA abundance does not directly measure myosin protein stoichiometry, motor kinetics, sarcomere ultrastructure, or tissue-level force.
  • The framework prioritizes experimental context; it does not classify a variant or estimate penetrance.
  • Developmental and disease-remodeling states are incompletely sampled and may not transfer cleanly to in-vitro cardiomyocytes.
Technical vocabulary

Glossary

Pseudobulk
Aggregation of counts within a biological replicate and cell state so the replicate—not each cell—is the inferential unit.
State specificity
The degree to which a signal is concentrated in a defined cellular program rather than broadly detected.
Matched null set
Control genes selected to resemble target genes on nuisance properties such as expression and length.
Evidence vector
A set of independently inspectable evidence dimensions retained instead of compressed into one score.

Reproducibility and evidentiary scope

This study is a REELD public-data analysis and methods interpretation. It does not report a newly recruited clinical cohort, classify an individual variant, or replace clinical review. A release-ready execution of the workflow includes accession-level provenance, source and ontology versions, code state, environment locks, predefined sensitivity analyses, and output checksums.