Targeting succinate metabolism to lower brain injury during mechanical thrombectomy in ischemic stroke

The notebook contains: Metabolomics data of patients/mice from the brain tissue at different timepoints after ischemia (0min, 5min, 15min, 30min, 60min, 120min) that were analysed by liquid chromatography-mass spectrometry (LC-MS).

Reproducibility

Code for the R analysis can be reproduced by following the script in MetabolomicsAnalysis.Rmd. This includes the data normalisation, differential metabolite analysis and all subsequent plots.

Metabolic signatures used for pathway analysis where manually assigned based on our a priori knowledge.

Data

The Metabolomics data of will be deposited with the manuscript. LC-MS data aquistion has been performed by the Frezza Laboratory, CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Germany. Input data will be available upon publication in the folder "Input":

• 20211210_Amin_mousebrain_HAP02.csv (Metabolomics results mouse)
• 20211212_Amin_humanbrain_HAP01.csv (Metabolomics results patients)
• MetabolicPathways.csv (Metabolite names and associated pathways)

First we performed data filtering and normalisation (80%-filtering rule, missing value imputation, total/ion count normalisation) and outlier detection based on quality control (muma analysis, for details see html and folder "Muma"). The results will be saved in the folder "Output/DataTables"upon publication:

• Human_TIC-normalised.csv
• Mouse_TIC-normalised.csv

Using the normalised data, we removed the outliers and

1. calculated the mean of the analytical replicates. The results will be saved in the folder "Output/DataTables"upon publication:

• Human_TIC-normalised_Means.csv
• Mouse_TIC-normalised_Means.csv

2. Performed differential metabolite analysis comparing 0min versus Xmin using the mean data. Here we performed the t-Test and p-value adjustment using Benjamini Hochberg. The results will be saved in the folder "Output/DataTables"upon publication:

• Human_TotalPools_DMA_5minv0min.csv

• Human_TotalPools_DMA_15minv0min.csv

• Human_TotalPools_DMA_60minv0min.csv

• Human_TotalPools_DMA_120minv0min.csv

• Mouse_TotalPools_DMA_5minv0min.csv

• Mouse_TotalPools_DMA_15minv0min.csv

• Mouse_TotalPools_DMA_60minv0min.csv

• Mouse_TotalPools_DMA_120minv0min.csv

Figures

Generated figures can be found in the html files or in the folder "Output/Figures".