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Integrated Multi-omics Profiling of Mouse Brain Tissue Using the AllPrep Methods versus Traditional Extraction Methods

ABSTRACT: In the exploration of complex biological systems, integrated multi-omics analysis has emerged as a pivotal strategy for deciphering molecular interaction networks. However, traditional stepwise extraction methods are prone to technical biases introduced by tissue spatial heterogeneity and repeated processing, limiting the accuracy and comparability of results. Although existing co-extraction techniques enable efficient and sequential isolation of nucleic acids (DNA/RNA) and proteins from the same sample, a significant methodological gap remains in systematically evaluating their performance in integrated multi-omics studies. Addressing this critical issue, this study thoroughly investigated the performance of a co-extraction strategy (AllPrep) in multi-omics research using spatially heterogeneous mouse brain tissues.

ORGANISM(S): Mus Musculus

SUBMITTER: Hong Wang

PROVIDER: PXD068105 | iProX | Fri Sep 05 00:00:00 BST 2025

REPOSITORIES: iProX

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Project description:Here we describe our unprecedented approach in proposing parsley (PAR) as a nutraceutical intervention in inflammatory bowel disease (IBD) using a mouse model of dextran sodium sulphate (DSS)-induced colitis, following a multi-integrated-omics analysis. PAR supplementation (n=7) significantly improved colon shortening and increased the disease activity index compared to the DSS group (n=7). The colonic transcriptome revealed the down-regulation of inflammatory cytokines, and the hepatic transcriptome and metabolome revealed the up-regulation of fatty acid synthesis genes, thereby improving body weight loss. Down-regulated cancer markers were observed in the hepatic transcriptome and proteome. A global plasma metabolite analysis indicated shifts in the citric cycle and urea cycle, implicating improved impaired glycolysis and oxidative stress. Our integration of three omics analyses highlighted the involvement of the methionine-recycling pathway and PARM-bM-^@M-^Ys role in decreasing the risk of IBD. This pioneering use of multi-integrated-omics in the evaluation of nutrientsM-bM-^@M-^Y effects on physiology is expected to be widely useful and informative, shaping the future of nutritional research. Here we describe our unprecedented approach in proposing parsley (PAR) as a nutraceutical intervention in inflammatory bowel disease (IBD) using a mouse model of dextran sodium sulphate (DSS)-induced colitis, following a multi-integrated-omics analysis. PAR supplementation (n=7) significantly improved colon shortening and increased the disease activity index compared to the DSS group (n=7). The colonic transcriptome revealed the down-regulation of inflammatory cytokines, and the hepatic transcriptome and metabolome revealed the up-regulation of fatty acid synthesis genes, thereby improving body weight loss. Down-regulated cancer markers were observed in the hepatic transcriptome and proteome. A global plasma metabolite analysis indicated shifts in the citric cycle and urea cycle, implicating improved impaired glycolysis and oxidative stress. Our integration of three omics analyses highlighted the involvement of the methionine-recycling pathway and PARM-bM-^@M-^Ys role in decreasing the risk of IBD. This pioneering use of multi-integrated-omics in the evaluation of nutrientsM-bM-^@M-^Y effects on physiology is expected to be widely useful and informative, shaping the future of nutritional research. Total hepatic and colonic RNA from each respective group were pooled (n=7). The microarray analysis was carried as out as described by Jia et al. 8 Mouse Genome 430 2.0 Array GeneChips (Affymetrix, Santa Clara, CA) containing over 30,000 gene probe sets were used for genome-wide expression profiling.

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Integrated Multi-omics Profiling of Mouse Brain Tissue Using the AllPrep Methods versus Traditional Extraction Methods

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