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Dysregulated Genes, Biological pathways, and Gastrocnemius Muscle Fiber Types Associated With Progression of Peripheral Artery Disease: A preliminary analysis

ABSTRACT: Dysregulated Genes, Biological pathways, and Gastrocnemius Muscle Fiber Types Associated With Progression of Peripheral Artery Disease: A preliminary analysis

PROVIDER: PRJNA753866 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15418943.fastq.gz	Fastqsanger.gz
	SRR15418944_1.fastq.gz	Fastqsanger.gz
	SRR15418944_2.fastq.gz	Fastqsanger.gz
	SRR15418945_1.fastq.gz	Fastqsanger.gz
	SRR15418945_2.fastq.gz	Fastqsanger.gz

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Dysregulated Genes, MicroRNAs, Biological Pathways, and Gastrocnemius Muscle Fiber Types Associated With Progression of Peripheral Artery Disease: A Preliminary Analysis.

Project description:Background Peripheral artery disease (PAD) is associated with gastrocnemius muscle abnormalities. However, the biological pathways associated with gastrocnemius muscle dysfunction and their associations with progression of PAD are largely unknown. This study characterized differential gene and microRNA (miRNA) expression in gastrocnemius biopsies from people without PAD compared with those with PAD. Participants with PAD included those with and without PAD progression. Methods and Results mRNA and miRNA sequencing were performed to identify differentially expressed genes, differentially expressed miRNAs, mRNA-miRNA interactions, and associated biological pathways for 3 sets of comparisons: (1) PAD progression (n=7) versus non-PAD (n=7); (2) PAD no progression (n=6) versus non-PAD; and (3) PAD progression versus PAD no progression. Immunohistochemistry was performed to determine gastrocnemius muscle fiber types and muscle fiber size. Differentially expressed genes and differentially expressed miRNAs were more abundant in the comparison of PAD progression versus non-PAD compared with PAD with versus without progression. Among the top significant cellular pathways in subjects with PAD progression were muscle contraction or development, transforming growth factor-beta, growth/differentiation factor, and activin signaling, inflammation, cellular senescence, and notch signaling. Subjects with PAD progression had increased frequency of smaller Type 2a gastrocnemius muscle fibers in exploratory analyses. Conclusions Humans with PAD progression exhibited greater differences in the number of gene and miRNA expression, biological pathways, and Type 2a muscle fiber size compared with those without PAD. Fewer differences were observed between people with PAD without progression and control patients without PAD. Further study is needed to confirm whether the identified transcripts may serve as potential biomarkers for diagnosis and progression of PAD.

| S-EPMC9673627 | biostudies-literature

Dysregulated Genes, Biological pathways, and Gastrocnemius Muscle Fiber Types Associated With Progression of Peripheral Artery Disease: A preliminary analysis

Project description:We report the differentially expressed genes among people with PAD Progression, PAD no progression compared to non-PAD.

2023-03-14 | GSE181930 | GEO

Single Nuclei RNA Sequencing of the Gastrocnemius Muscle Reveals Unique Transcriptomic Signatures of Peripheral Artery Disease

Project description:This study examines the transcriptional profile at the single-nuclei resolution human gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 non-PAD controls. In all libraries, muscle specimens were pooled prior to nuclei isolations were performed.

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Single Nuclei RNA Sequencing of the Gastrocnemius Muscle Reveals Unique Transcriptomic Signatures of Peripheral Artery Disease

Project description:Single Nuclei RNA Sequencing of the Gastrocnemius Muscle Reveals Unique Transcriptomic Signatures of Peripheral Artery Disease

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Multiomic Analysis of Calf Muscle in Peripheral Artery Disease and Chronic Kidney Disease

Project description:This study examines the transcriptional profile at the single-nuclei resolution human gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 patients with both PAD and Chronic Kidney Disease (CKD). In all libraries, muscle specimens were pooled prior to nuclei isolations were performed.

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Dysregulated Microbial Fermentation of Soluble Fiber Induces Cholestatic Liver Cancer

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Gene expression profiling of gastrocnemius of mini muscle mice

Project description:Few studies have investigated heterogeneity of selection response in replicate lines subjected to equivalent selection. We developed 4 replicate lines of mice based on high levels of voluntary wheel running (high runner or HR lines) while also maintaining 4 non-selected control lines. This led to the unexpected discovery of the HR mini-muscle (HRmini) phenotype, recognized by a 50% reduction in hindlimb muscle mass, which became fixed in 1 of the 4 HR selected lines. Here, we report genome-wide expression profiling describing transcriptome differences between HRnormal and HRmini medial gastrocnemius. This work provides a resource for understanding differences in muscle phenotypes in populations exhibiting high running capacity. Male mice were used from an animal model of 4 closed lines selectively bred for high voluntary wheel-running behaviour (HR) and 4 control lines bred without intentional selection, described in Swallow et al. Animals used in the current work were sampled from generation 37 at a mean age of 84 days (range = 79-86). For microarray analysis, we used gastrocnemius muscles (including both lateral and medial portions) from HRmini line #3 and HRnormal line #8 (n = 6, in each group). To obtain sufficient RNA, gastrocnemius samples of HRmini were pooled from left and right limbs from each animal, whereas HRnormal gastrocnemius was sampled from either left or right limb only.

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Matrisome age-related changes in the mouse gastrocnemius muscle

Project description:In recent years, thanks to the great development of mass spectrometry (MS)-based high-throughput proteomic techniques, a large-scale protein characterization is less challenging. Proteomic approaches have been successfully applied to SM in different experimental models [21–24]; however, to date, there is little information on ECM proteins and how they change during ageing. The identification and quantification of ECM components and their interactions are es-sential steps to understand the role of the matrisome in sarcopenia. In this context, we combined a proteomic approach (i.e., LC-MS/MS and bioinformatic analyses) with mor-phological and morphometrical evaluations at fluorescence and transmission electron microscopy of the gastrocnemius muscle in adult and old mice. This age range has been selected since it has been observed that most of changes in muscle protein expression take place after middle age. The gastrocnemius muscle was selected for analysis since it is prevalently composed of fast-twitch fibre, which are especially affected by atrophy during aging. Our findings highlighted several modifications of ECM protein composition and organization in old mice, which likely play a role in the alteration of muscle properties during aging.

2022-02-17 | PXD027895 | Pride

microRNA counts from gastrocnemius medialis (ENCSR505IZZ)

Project description:microRNA counts from gastrocnemius medialis (ENCSR505IZZ)

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