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Pak, T.

Publications and source records attributed to Pak, T..

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Missense variants in the myosin binding domains of MYBPC3 and MYBPHL impair sarcomere incorporation

Approximately 40% of genetic hypertrophic cardiomyopathy cases involve mutations in MYBPC3, which encodes cardiac myosin binding protein-C (cMyBP-C), a key regulator of sarcomere contractility. The atrial-specific paralog, myosin binding protein-H like (MyBP-HL), has been associated with dilated cardiomyopathy in humans and mice. Both proteins bind to the same binding sites in the thick filament C-zone. In the atria, cMyBP-C and MyBP-HL are found at [~]1:1 ratios, while ventricles only express cMyBP-C, which is found at twice the atrial level, indicating a stoichiometric relationship. In the atria, we hypothesize that missense variants in either gene may cause alterations in thick filament binding affinity and changes in the normal [~]1:1 ratio. Notably, MyBP-HL deletion in atrial myofibrils accelerates relaxation kinetics, suggesting that altered stoichiometry impacts biophysical parameters. We hypothesized that deletion, overexpression, or missense variants in either gene would alter the abundance of the other protein in atrial sarcomeres, affecting sarcomere localization and function. To test this, we engineered two constructs: a mini-C construct comprising thick filament-binding domains of cMyBP-C and a MyBP-HL construct. Selected MYBPC3 and MYBPHL missense variants were introduced and expressed in neonatal rat ventricular cardiomyocytes (NRVMs). Sarcomere localization was assessed by co-localization with endogenous cMyBP-C. MYBPC3 variants were selected across a range of pathogenicity, while MYBPHL variants were based on evolutionary conservation of residues. MYBPHL variants Gly275Ser, Arg285His, and Ala342Thr induced significant sarcomere mislocalization, and MYBPC3 variants Pro1181Ala and Asn1257Lys showed variable effects on sarcomere mislocalization. To assess stoichiometric effects, we developed a T2A/P2A polycistronic construct to co-express mini-C, Td-Tomato, and MyBP-HL. Immunoblotting and mass spectrometry confirmed consistent and reproducible expression. We identified several MYBPC3 and MYBPHL variants that reduced the affinity of their protein for myofilament incorporation. These results suggest that this 2A construct is a useful tool for measuring the effect of myosin binding protein missense variants on sarcomere affinity, with implications for assessing pathogenicity of these variants.

biochemistry↗

Epigenomic landscape of the human pathogen Clostridium difficile

Clostridioides difficile is a leading cause of health care-associated infections. Although significant progress has been made in the understanding of its genome, the epigenome of C. difficile and its functional impact has not been systematically explored. Here, we performed the first comprehensive DNA methylome analysis of C. difficile using 36 human isolates and observed great epigenomic diversity. We discovered an orphan DNA methyltransferase with a well-defined specificity whose corresponding gene is highly conserved across our dataset and in all ~300 global C. difficile genomes examined. Inactivation of the methyltransferase gene negatively impacted sporulation, a key step in C. difficile disease transmission, consistently supported by multi-omics data, genetic experiments, and a mouse colonization model. Further experimental and transcriptomic analysis also suggested that epigenetic regulation is associated with cell length, biofilm formation, and host colonization. These findings open up a new epigenetic dimension to characterize medically relevant biological processes in this critical pathogen. This work also provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomics studies.

genomics↗