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Comprehensive Evaluation of Coextraction Workflows for Enhanced Multiomics Integration in Complex Biological Samples
Xianfeng Shao1,2, Bingqian Chu1,2, Xiaoxiao Duan1,2
1State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, National Clinical Research Center for Blood Diseases, PUMC Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
A new coextraction method for mouse brain tissue improves RNA yield and enhances multiomics data integration. This strategy offers better RNA-protein correlations and deeper insights into neural pathways for complex biological system studies.
Area of Science:
- Neuroscience
- Molecular Biology
- Biochemistry
Background:
- Conventional multiomics analysis faces challenges due to tissue spatial heterogeneity and technical biases from stepwise extraction.
- These limitations can compromise cross-omics comparability and hinder comprehensive understanding of biological systems.
Purpose of the Study:
- To evaluate a coextraction strategy for simultaneous multiomics profiling of mouse brain tissue.
- To assess the impact of coextraction on RNA yield, proteomic coverage, phosphoproteomic depth, and RNA-protein correlations.
Main Methods:
- A coextraction method was developed and applied to mouse brain tissue for multiomics profiling.
- RNA yield, sequence coverage, and reproducibility were compared to traditional methods.
- Proteomic and phosphoproteomic analyses were performed, and RNA-protein correlations were calculated.
Main Results:
- Coextraction increased RNA yield by 32.55% per milligram of tissue, with high reproducibility (r > 0.98).
- Approximately 7100 proteins were identified, comparable to conventional methods, with consistent neural functional protein categories.
- Phosphoproteomic analysis identified 4347 additional high-confidence phosphosites, enhancing regulatory pathway resolution.
- Integrated analysis revealed improved RNA-protein correlations (median r from 0.25 to 0.56) and strengthened neural pathway enrichment.
Conclusions:
- The coextraction strategy offers a practical workflow for enhanced multiomics integration in brain tissue.
- This method overcomes limitations of conventional techniques, providing deeper insights into complex molecular regulation in neural systems.
- The improved data quality facilitates studies on synaptic transmission and nervous system development.