Biology subjects

Huffman, K. M.

Publications and source records attributed to Huffman, K. M..

6 recordsLinked to original sources

bioRxiv2026

Regulation of Small RNAs by Exercise and Their Role in Insulin Sensitivity

We investigated effects of three aerobic exercise interventions, varying in amount and intensity with durations of 8-9-months on small RNA (smRNA) expression and regulatory pathways in skeletal muscle and plasma from 120 participants. Using untargeted smRNA sequencing focused on miRNAs and piRNAs, adjusting for demographics and bodyweight, we identified 124 muscle smRNAs altered by exercise amount and 15 by intensity, and 47 plasma smRNAs altered by intensity and one by amount. These smRNAs were enriched in metabolic, transcriptional, translational, and cell cycle pathways. Exercise-induced changes in several smRNAs-six from muscle and five from plasma-and exercise-induced reduction in body weight, aligned with improvement in insulin sensitivity (p<0.05). These findings demonstrate tissue-specific regulation of smRNAs by exercise and identify potential candidates for exercise mimetics to modulate muscle insulin sensitivity.

physiology↗

bioRxiv2026

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to systematically characterize the molecular basis of the health benefits of exercise. Here, we present the integrative, multi-omics response of human skeletal muscle to acute endurance (EE) and resistance (RE) exercise. Distinct temporal responses were observed, with changes in ATAC-seq, phosphoproteome, and metabolome occurring before changes in the transcriptome and proteome. These distinct temporal multi-omic dynamics were used to identify transcriptional regulatory hubs converging around MEF2A and NFIC regulation of autophagy, angiogenesis and metabolism. Further, early RE-specific phosphoproteome signatures counteracted epigenetic modifications and downregulated transcripts involved in protein turnover. Additional findings include suppression of HIPK2/3 kinase signatures linked to the acute exercise regulation of sarcomeric proteins TTN, NEB, ANKRD2 and LMOD2. Our data demonstrate distinct temporal regulation across the multi-omic landscape of human skeletal muscle, with EE and RE eliciting common and unique molecular signatures.

systems biology↗

bioRxiv2026

Biological Mechanisms of Strength Preservation During Calorie Restriction-Induced Weight Loss Among Young- to Middle-Aged Adults without Obesity

PurposeWeight loss is often pursued to improve cardiometabolic health and quality of life. However, rapid weight loss can lead to reductions in lean soft tissue mass and strength to compromise body composition and functional ability. Thus, identifying molecular predictors of muscular strength preservation during weight loss is critical to mitigating these effects. MethodsWe conducted a secondary analysis of the CALERIETM (Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy) trial, a two-year randomized controlled study of caloric restriction (CR) or ad-libitum intake in healthy adults without obesity. Among 198 participants, changes in whole-body mass and knee extensor strength were assessed over the first 12 months of the study which was primarily characterized by weight loss. Transcriptomic profiling was conducted in a subset of 42 participants who provided skeletal muscle samples. Linear regression was used to model the relationship between strength change and gene expression change, while controlling for changes in whole-body mass. Gene set enrichment analysis (GSEA) was performed using Hallmark pathways. Individual-level pathway analysis was performed via gene set variation analysis (GSVA). ResultsWe identified 96 out of 198 individuals (48.5%) who maintained or improved strength relative to body mass during weight loss (i.e. individuals with residuals > 0). Transcriptomics analysis on a subset of 42 individuals revealed 151 genes significantly associated with change in strength after accounting for change in whole-body mass (p < 0.01). Hub genes were identified as HSP90AA1 ({beta} = 34.45, SE = 7.32, p <0.001), EIF3A ({beta} = 36.14, SE = 10.27, p < 0.001), EIF5B ({beta} = 49.94, SE = 11.28, p < 0.001), and H3C1 ({beta} = -15.87, SE = 4.85, p < 0.001). GSEA revealed significant involvement of pathways related to cellular proliferation, immune regulation, protein secretion, and checkpoint control processes. GSVA identified a similar set of pathways. ConclusionsThese findings highlight molecular pathways supporting strength retention during CR-induced weight loss. Heat-shock protein, HSP90AA1, warrants further investigation as a candidate target for preserving muscle strength during interventions aimed at weight reduction.

molecular biology↗

bioRxiv2024

Comparison of Infinium MethylationEPIC v2.0 to v1.0 for human population epigenetics: considerations for addressing EPIC version differences in DNA methylation-based tools

The recently launched Illumina Infinium MethylationEPIC v2.0 (EPICv2), successor of MethylationEPIC v1.0 (EPICv1), retains a majority of probes in EPICv1, while expanding coverage of regulatory elements. The concordance between the two EPIC versions in DNA methylation-based tools has not yet been investigated. To address this, DNA methylation was profiled on both versions using matched blood samples across four cohorts spanning early to late adulthood. High concordance between versions at the array level but variable agreement at the individual probe level was noted. A significant contribution of EPIC version to DNA methylation variation was observed, though it was to a smaller extent compared to sample relatedness and cell type composition. Modest but significant differences in DNA methylation-based estimates between versions were observed, irrespective of the data preprocessing method used. Adjustments for EPIC version or calculation of estimates separately for each version largely mitigated these version-specific discordances. This work emphasizes the importance of accounting for EPIC version differences in research scenarios, especially in meta-analyses and longitudinal studies that require data harmonization across versions. Summary blurbOur work illustrates the importance of accounting for EPIC version in DNA methylation-based tools, specifically in research scenarios when samples profiled across different versions are harmonized.

genomics↗

bioRxiv2024

The CALERIE™ Genomic Data Resource

Caloric restriction (CR) slows biological aging and prolongs healthy lifespan in model organisms. Findings from CALERIE-2 - the first ever randomized, controlled trial of long-term CR in healthy, non-obese humans - broadly supports a similar pattern of effects in humans. To expand our understanding of the molecular pathways and biological processes underpinning CR effects in humans, we generated a series of genomic datasets from stored biospecimens collected from n=218 participants during the trial. These data constitute the first publicly-accessible genomic data resource for a randomized controlled trial of an intervention targeting the biology of aging. Datasets include whole-genome SNP genotypes, and three-timepoint-longitudinal DNA methylation, mRNA, and small RNA datasets generated from blood, skeletal muscle, and adipose tissue samples (total sample n=2327). The CALERIE Genomic Data Resource described in this article is available from the Aging Research Biobank. This multi-tissue, multi-omic, longitudinal data resource has great potential to advance translational geroscience.

genomics↗

bioRxiv2022

Epigenome-wide association study analysis of calorie restriction in humans, CALERIE™ Trial analysis

BACKGROUNDCalorie restriction (CR) increases healthy lifespan and is accompanied by slowing or reversal of aging-associated DNA methylation (DNAm) changes in animal models. In the Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIE) human trial we evaluated associations of CR and changes in whole-blood DNAm. METHODSCALERIE randomized 220 healthy, non-obese adults in a 2:1 allocation to two years of CR or ad libitum (AL) diet. The average CR in the treatment group through 24-months of follow-up was 12%. Whole blood (baseline, 12 and 24 month) DNAm profiles were measured. Epigenome-wide association study (EWAS) analysis tested CR-induced changes from baseline to 12- and 24-months in the n=197 participants with available DNAm data. RESULTSNo CpG-site-specific changes with CR reached epigenome-wide significance (FDR<0.05). Secondary analyses of CpG sites identified in published EWAS suggest, we found that CR induced DNAm changes opposite those associated with body mass index (BMI) and smoking (p<0.003 at 12- and 24-month follow-ups). In contrast, CR altered DNAm at chronological-age associated CpG sites in the direction of older age (p<0.003 at 12- and 24-month follow-ups). CONCLUSIONAlthough individual CpG site DNAm changes in response to CR were not identified, analyses of sets CpGs identified in prior EWAS revealed CR-induced changes to blood DNAm. Altered CpG sets were enriched for insulin-production, glucose-tolerance, inflammation, and DNA-binding and -regulation pathways, several of which are known to be modified by CR. DNAm changes may contribute to CR effects on aging.

genomics↗