Trisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors

Our preprint is available on bioRxiv here.

Authors:

Rani K. Powers^1,2,3, Rachel Culp-Hill⁴, Michael P. Ludwig^1,3, Keith P. Smith¹, Katherine A. Waugh¹, Ross Minter¹, Kathryn D. Tuttle¹, Hannah C. Lewis¹, Angela L. Rachubinski^1,5, Ross E. Granrath¹, Maria Carmona^6,7, Rebecca B. Wilkerson⁴, Darcy E. Kahn¹, Molishree Joshi⁸, Alberto Lleo⁶, Rafael Blesa⁶, Juan Fortea^6,7, Angelo D’Alessandro^1,4, James C. Costello^2,3, Kelly D. Sullivan^1,3,5,8*, & Joaquin M. Espinosa^1,3,8,9*

Affiliations:

¹ Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

² Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

³ Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

⁴ Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

⁵ Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

⁶ Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autonoma de Barcelona, CIBERNED, Barcelona, Spain

⁷ Down Medical Center, Catalan Down Syndrome Foundation, Barcelona, Spain

⁸ Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

⁹ Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA

* Corresponding Authors:

Kelly D. Sullivan: [email protected]

Joaquin M. Espinosa: [email protected]

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Included in this repository

To ensure reproducibility, all data for this project can be found in the Data/ directory and the R code to generate all figures and supplementary data from the manuscript can be found in the R/ directory.

Data

• Human_plasma_metabolomics_eset.rds - Cohort 1 and Cohort 2 participant characteristics and raw, LC-MS plasma metabolomics intensity values (relative abundance) formatted as an R eset
• human_MSD_data.rds - Mesoscale discovery assay data from Cohort 2 human plasma samples
• mouse_metabolomics_data.rds - Targeted metabolomics data on plasma from WT and T21 (Dp10, Dp16 and Dp17 strains) mice

Code

To reproduce the figures from our paper, make sure you have all dependencies installed then run each of the numbered R scripts in order. These scripts will output plots and/or tables to an appropriate subdirectory named for each figure (e.g. Results/Figure_1). General descriptions of each script are below, and additional information can be found at the beginning of the scripts themselves.

Dependencies:

• plyr (>= 1.8.4), tidyr (>= 0.8.0), dplyr (>= 0.7.4)
• affy (>= 1.54.0), Biobase (>= 2.36.2), preprocessCore (>= 1.38.1)
• impute (>= 1.50.1), limma (>= 3.32.10), glmnet (>= 2.0-13)
• RColorBrewer (>= 1.1-2), beeswarm (>= 0.2.3)
• ROCR (>= 1.0-7), pROC (>= 1.10.0), classInt (>= 0.2-3)

R Scripts:

• 00-model_fitting.R - Pre-processes human metabolomics data and fits linear model with batch, age and sex covariates. Saves plots and supplementary data.
• 01-differential_abundance.R - Performs differential abundance analysis on human plasma samples from D21 and T21 individuals. Saves plots and supplementary data.
• 02-boxplots_t21_vs_d21 - Saves boxplots for kynurenine, quinolinic acid, KYN/TRP, and QA/PA ratios in the Results/Figure_1/ folder. Additional boxplots for Supp Figure 1 are saved in the Results/Supplementary_Figures/ folder.
• 03-cytokine_correlations.R - Correlates Cohort 2 human plasma metabolomics data with MSD cytokine measurements. Saves heatmaps and scatterplots in the Results/Figure_2/ folder. Outputs supplementary data to Results/Supplementary_Files/.
• 04-fibroblast_timecourse.R - Pre-processes and plots timecourse data from the flux metabolomics experiment on human fibroblasts. Saves plots for Figure 3 in the Results/Figure_3 directory.
• 05-mouse_kynurenine.R - Plots basal kynurenine levels in WT, Dp10, Dp16 and Dp17 mouse strains and calculates statistical significance. Saves plots in the Results/Figure_4/ folder.