Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling

Abstract

ABSTRACTA majority of human genes produce non protein-coding RNA (ncRNA) and some have important roles in development and disease. Neither ncRNA nor multinucleated adult human skeletal muscle is ideally studied using sequencing technologies, so using a customised RNA profiling pipeline and quantitative network modelling we studies cell-type specific ncRNA responses during muscle growth at scale. We completed five human resistance-training studies (n=144 subjects) to stimulate growth, and found 61% of individuals successfully accrued muscle mass. One hundred and ten ncRNAs were modulatedin vivoand a network model of the muscle transcriptome (n=437) assigned these to functional pathways or single-cell types. We replicated the few known hypertrophy-related ncRNAs, includingCYTOR– which in humans was leukocyte-associatedin vivo(FDR = 4.9 x10-7). Numerous novel hypertrophy linked ncRNAs includedPPP1CB-DT(myofibril assembly genes, FDR = 8.15 x 10-8), andEEF1A1P24andTMSB4XP8(vascular remodelling and angiogenesis genes, FDR = 2.77 x 10-5). We discovered that hypertrophy linkedMYREMhas a specific myonuclear expression patternin vivousing spatial transcriptomic probes. Our multi-layered analyses established that single-cell type associations of ncRNA are identifiable from bulk muscle transcriptomic data, and that hypertrophy-linked ncRNA genes mediate their association with muscle growth via multiple cell types.One Sentence SummaryWe used an optimised transcriptomic strategy to identify a set of ncRNA genes regulated during skeletal muscle hypertrophy in one hundred and forty-four people, with network modelling and spatial imaging providing biological context.