New insights from transcriptome profiling of rat quadriceps muscle response to catgut embedding acupoint
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ABSTRACT:
PROVIDER: PRJNA909203 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22547374_1.fastq.gz | Fastqsanger.gz | |||
| SRR22547374_2.fastq.gz | Fastqsanger.gz | |||
| SRR22547375_1.fastq.gz | Fastqsanger.gz | |||
| SRR22547375_2.fastq.gz | Fastqsanger.gz | |||
| SRR22547376_1.fastq.gz | Fastqsanger.gz |
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Project description:purpose:The goals of this study is to investigate rat quadriceps muscle responses treated with different catgut embedding acupoint in various molecular pahtways by RNA-seq and real-time quantitative PCR methods and evaluaate protocols for optimal high-throughput data analysis. Methods:mRNA profiles of rat quadriceps muscle responses treated with catgut embedding acupoint 1 and 2 group,treadmill group and control were generated by sequencing, in sextuplicate, utilizing Illumina HiSeq 4000 platform. The raw RNA-seq data was filtered to remove adaptor contamination, low quality bases, and undetermined beses utilizing Cutadapt software. The filtered reads were aligned and mapped to the reference genome using Hisat 2.0. RT-qPCR validation was performed using SYBR green assays. Results:The transcription profiling results showed that there were 346 differentially expressed genes (DEGs) between the A and B groups. These included 221 up-regulated DEGs and 125 down-regulated DEGs. There were 363 DEGs between the B group and the C, which included 144 up-regulated DEGs and 219 down-regulated DEGs. There were 458 DEGs between the B group and D which included 248 up-regulated DEGs and 210 down-regulated DEGs. Through GO functional annotation, the DEGs were divided into three categories: cellular components, biological processes, and molecular functions. The above three functions were further divided into positive regulation of transcription by RNA polymerase II, and RNA polymerase II on transcription. Negative regulation, participation in nuclear synthesis, synthesis with cytoplasm, participation in extracellular exosome synthesis, participation in protein binding, and participation in metal ion binding, etc. After enrichment analysis, 16 metabolic pathways were found to be significantly enriched (p<0.05), which included chemical carcinogenesis, metabolism of cytochrome P450 to exogenous substances, circadian entrainment, circadian rhythm, protein digestion and absorption, PPAR Signaling pathways, drug metabolism - cytochrome P450, parathyroid hormone synthesis, secretion and action, steroid hormone biosynthesis, leishmaniasis, arachidonic acid metabolism, bile secretion, measles, linoleic acid metabolism, fat digestion and absorption, and fluid shear stress and atherosclerosis. By inspecting the bubble enrichment plot, we decided that the following would be important targets of our future studies: protein digestion and absorption; PPAR signaling pathway; synthesis, secretion and action of parathyroid hormone and other metabolic pathways.DEGs that enriche into pathways were verified by RT-qPCR. Conclusions: Our study provides new insights on the interaction between catgut embedding acupoint and rat quadriceps muscle responses.
2023-03-01 | GSE220191 | GEO
Project description:Embedding is the key step in single-cell Hi-C (scHi-C) analysis which relies on capturing biological meaningful heterogeneity at various levels of genome architecture. To understand the strength and limitations of existing tools in various applications, here we use ten scHi-C datasets to benchmark thirteen embedding tools including Va3DE, a new convolutional neural network model that can accommodate large cell numbers. We built a software framework to decouple the preprocessing options of existing tools and found that no single tool works best across all datasets under default settings. The difficulty levels and preferred resolutions are different between benchmark datasets, and the choice of data representation and preprocessing strongly impact the embedding performance. Embedding cells from early embryonic stages relies on long-range compartment-scale contacts, but resolving cell cycle phases and complex tissue requires short-range loop-scale contacts. Both random-walk and inverse document frequency (IDF) transformation prefers long-range “compartment-scale” over short-range “loop-scale” embedding, while deep-learning methods better overcome sparsity at both scales and are more versatile with different resolutions. Finally, “diagonal integration” with independent data modal is a promising approach to distinguish similar cell subpopulations. Our findings underscore the significance of appropriate priors for scHi-C embedding and offer new insights into genome architecture heterogeneity.
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Project description:Dinoponera quadriceps Transcriptome or Gene expression
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Project description:Pain is a primary indication for acupuncture, with ST36 shown to effectively treat various types and locations of pain. Acupoints serve as pivotal starting points for acupuncture's therapeutic effects. However, how acupuncture stimulation alters the microenvironment at the ST36 acupoint to treat different pain conditions remains unclear. We investigated the analgesic effects of ST36 acupuncture in mice with adjuvant arthritis, identifying fibroblast and macrophage clusters as the main responsive populations at ST36 through single-cell sequencing analysis. These populations expressed high levels of S100 calcium-binding protein a8 (S100a8), S100a9, and Toll-like receptor 4 (TLR4) on both cells and afferent fibers. Furthermore, acupuncture at ST36 activated A and C afferent nerves. Intriguingly, acupoint injection of an S100a8/S100a9-TLR4 inhibitor reversed the excitation of A and C afferent nerves and diminished the analgesic effect of acupuncture. These findings offer novel insights into the ST36 acupoint microenvironment modulated by acupuncture and underscore the critical role of S100a8/S100a9 in initiating acupuncture-induced analgesia at ST36. The study identifies S100a8/S100a9 as a potential regulatory target for modulating acupuncture effects at acupoints, providing a molecular framework for standardized acupuncture interventions and their clinical applications.
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Project description:The cellular and molecular dynamics at human acupuncture points remain largely unexplored. To address this, we developed a novel acupuncture-needle technique capable of collecting sufficient numbers of cells from acupuncture points during treatment. Using this approach in combination with single-nucleus RNA sequencing (snRNA-seq), we identified heterogeneous cell populations at the acupoint BL23. This study enabled characterization of the cellular and transcriptional changes occurring before and after acupuncture treatment in patients with lower back pain (lumbar sprain), offering new insights into the mechanisms underlying acupuncture-induced pain relief.
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Project description:Purpose: We used RNA sequencing to investigate the effect of needling treatments on GB20 acupoint in EAE model mice Methods: Retinal mRNA profiles of 13-week-old female sham control mice (SHAM), EAE model mice with MOG injection (MOG), EAE model mice with needling treatment at acupoint GB20 (GB20) and its control acupoint GV16 (GV16) were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed with DESeq2 R package to identify differently expressed genes with padj<0.05. Results: RNA-seq identified total 234 DEGs, with 100 genes upregulated and 134 genes downregulated, comparing MOG group with SHAM group.Further analysis revealed that, among the MOG injection induced 100 up-regulated DEGs, 24 DEGs were reversed and significantly down-regulated by GB20 treatment, while 14 were reversed and significantly down-regulated by GV16 treatment. However, 12 of the 14 reversed DEGs of GV16 treatment were already included in the 24 DEGs of GB20. The left 2 DEGs specific to GV16 treatment were Gfap (glial fibrillary acidic protein) and Fgf2 (fibroblast growth factor 2). As to the MOG injection induced 134 down-regulated DEGs, 12 DEGs were reversed and significantly up-regulated by GB20 treatment, while only 3 DEGs were reversed and significantly up-regulated by GV16 control treatment, and all the 3 DEGs were included in the 12 DEGs of GB20 treatment. Conclusions: Our research first reported that needling treatment on GB20 had regulation effects on retinal transcriptome of EAE model mice, indicating potential way of therapy for treatment of optic neuritis.
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Project description:Acupuncture treatment is based on acupoint stimulation; however, the biological basis is not understood. We stimulated one acupoint with catgut embedding (CEP) for 8 weeks and then used isobaric tags for relative and absolute quantitation to screen proteins with altered expression in adjacent acupoints of Sprague Dawley rats. The expression levels of 10 proteins, including kininogen (KNG), consistently changed >1.5-fold in all three acupoints in CEP versus sham CEP-treated rats. Eight-week, but not 3-day, CEP treatment enhanced KNG expression. The enhanced KNG expression among small vessels in the subcutaneous layer was revealed via immunofluorescence. Nitric oxide synthesis was enhanced similar to KNG. These findings uncover biological changes at acupoints and suggest the critical role of the KNG–nitric oxide signaling pathway in acupoint activation.
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