We evaluated 18 methods capable of identifying initial contact (IC) and terminal contact (TC) gait events during human running using data from a single wearable sensor on the shank or sacrum. We ...adapted or created code to automatically execute each method, then applied it to identify gait events from 74 runners across different foot strike angles, surfaces, and speeds. To quantify error, estimated gait events were compared to ground truth events from a time-synchronized force plate. Based on our findings, to identify gait events with a wearable on the shank, we recommend the Purcell or Fadillioglu method for IC (biases +17.4 and -24.3 ms; LOAs -96.8 to +131.6 and -137.0 to +88.4 ms) and the Purcell method for TC (bias +3.5 ms; LOAs -143.9 to +150.9 ms). To identify gait events with a wearable on the sacrum, we recommend the Auvinet or Reenalda method for IC (biases -30.4 and +29.0 ms; LOAs -149.2 to +88.5 and -83.3 to +141.3 ms) and the Auvinet method for TC (bias -2.8 ms; LOAs -152.7 to +147.2 ms). Finally, to identify the foot in contact with the ground when using a wearable on the sacrum, we recommend the Lee method (81.9% accuracy).
Gene replacement therapies utilizing adeno-associated viral (AAV) vectors hold great promise for treating Duchenne muscular dystrophy (DMD). A related approach uses AAV vectors to edit specific ...regions of the DMD gene using CRISPR/Cas9. Here we develop multiple approaches for editing the mutation in dystrophic mdx
mice using single and dual AAV vector delivery of a muscle-specific Cas9 cassette together with single-guide RNA cassettes and, in one approach, a dystrophin homology region to fully correct the mutation. Muscle-restricted Cas9 expression enables direct editing of the mutation, multi-exon deletion or complete gene correction via homologous recombination in myogenic cells. Treated muscles express dystrophin in up to 70% of the myogenic area and increased force generation following intramuscular delivery. Furthermore, systemic administration of the vectors results in widespread expression of dystrophin in both skeletal and cardiac muscles. Our results demonstrate that AAV-mediated muscle-specific gene editing has significant potential for therapy of neuromuscular disorders.
For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that ...embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs). Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the ...NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
Epigenetic mechanisms have been proposed to play crucial roles in mammalian development, but their precise functions are only partially understood. To investigate epigenetic regulation of embryonic ...development, we differentiated human embryonic stem cells into mesendoderm, neural progenitor cells, trophoblast-like cells, and mesenchymal stem cells and systematically characterized DNA methylation, chromatin modifications, and the transcriptome in each lineage. We found that promoters that are active in early developmental stages tend to be CG rich and mainly engage H3K27me3 upon silencing in nonexpressing lineages. By contrast, promoters for genes expressed preferentially at later stages are often CG poor and primarily employ DNA methylation upon repression. Interestingly, the early developmental regulatory genes are often located in large genomic domains that are generally devoid of DNA methylation in most lineages, which we termed DNA methylation valleys (DMVs). Our results suggest that distinct epigenetic mechanisms regulate early and late stages of ES cell differentiation.
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•Epigenome was mapped in depth for hESCs and four hESC-derived cell types•Lineage-restricted genes and regulatory sequences were identified in these cell types•Distinct mechanisms regulate lineage-restricted genes at early and late stages•Developmental genes tend to reside in large genomic domains devoid of DNA methylation
DNA methylation, histone modifications, and the transcriptome have been mapped in human ES cells and four lineages. The results suggest that early and late stages of ES cell differentiation are regulated by distinct epigenetic mechanisms.
Twenty-seven methods of estimating vertical ground reaction force first peak, loading rate, second peak, average, and/or time series from a single wearable accelerometer worn on the shank or ...approximate center of mass during running were compared. Force estimation errors were quantified for 74 participants across different running surfaces, speeds, and foot strike angles and biases, repeatability coefficients, and limits of agreement were modeled with linear mixed effects to quantify the accuracy, reliability, and precision. Several methods accurately and reliably estimated the first peak and loading rate, however, none could do so precisely (the limits of agreement exceeded ±65% of target values). Thus, we do not recommend first peak or loading rate estimation from accelerometers with the methods currently available. In contrast, the second peak, average, and time series could all be estimated accurately, reliably, and precisely with several different methods. Of these, we recommend the ‘Pogson’ methods due to their accuracy, reliability, and precision as well as their stability across surfaces, speeds, and foot strike angles.
Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, ...conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs ...(lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms. We highlight the use of genome-wide chromatin conformation capture (Hi-C) coupled with oligonucleotide capture technology (capture Hi-C) to map interactions between gene promoters and distal regulatory elements such as enhancers that are enriched for disease variants from genome-wide association studies (GWASs). We discuss how aberrations in architectural units are associated with various pathological outcomes, and explore how recent advances in genome and epigenome editing show great promise for a systematic understanding of complex genetic disorders. Our growing understanding of 3D genome architecture-coupled with the ability to engineer changes in it-may create novel therapeutic opportunities.
The primary goal of this study was to examine changes in peak insole force and cumulative weighted peak force (CWPF)/km with increased step rate in collegiate runners. The secondary goal was to ...determine whether sacral acceleration correlates with insole force when increasing step rate.
Twelve collegiate distance runners ran 1000 m outdoors at 3.83 m·s -1 at preferred and 10% increased step rates while insole force and sacral acceleration were recorded. Cumulative weighted peak force/km was calculated from insole force based on cumulative damage models. The effects of step rate on peak insole force and CWPF·km -1 were tested using paired t tests or Wilcoxon tests. Correlation coefficients between peak axial (approximately vertical) sacral acceleration times body mass and peak insole force were calculated on cohort and individual levels.
Peak insole force and CWPF·km -1 decreased ( P < 0.001) with increased step rate. Peak axial sacral acceleration did not correlate with peak insole force on the cohort level ( r = 0.35, P = 0.109) but did within individuals (mean, r = 0.69-0.78; P < 0.05).
Increasing step rate may reduce peak vGRF and CWPF·km -1 in collegiate runners. Therefore, clinicians should consider step rate interventions to reduce peak and cumulative vGRF in this population. Individual-specific calibrations may be required to assess changes in peak vGRF in response to increasing step rate using wearable accelerometers.
While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes ...in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.
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