Drug Repurposing Analyses in Polycystic Kidney Disease

Authors

• Elizabeth J. Wilk, Timothy C. Howton, Jennifer L. Fisher, Vishal H. Oza, Ryan T. Brownlee, Brittany N. Lasseigne

Overview

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by renal cyst expansion and is primarily caused by variants in the PKD1 or PKD2 gene that encode the transmembrane proteins Polycystin-1 (PC1) and Polycystin-2 (PC2), respectively.1 The current only FDA approved drug for ADPKD is Tolvaptan, a vasopressin receptor 2 antagonist that cannot be used as long-term treatment due to liver toxicity side effects.2 Molecular signature reversion is a method of drug repurposing that could lead to new treatment options for ADPKD patients significantly sooner than traditional drug discovery. As gene expression profiles from ADPKD patients and preclinical models have significantly altered transcriptomic signatures, this approach presents an opportunity to compare ADPKD disease signatures to drug response signatures from cell lines treated with drugs and identify candidates that may reverse ADPKD-associated cellular phenotypes, ultimately slowing or reducing kidney cyst growth. In these analyses, we evaluated transcriptomic signatures to determine drug repurposing candidates for ADPKD using publicly available Pkd2 mouse data by detecting inversely related gene expression signatures from the Library of Integrated Network-Based Cellular Signatures (LINCS)3 database. We filtered for drugs that were already FDA-approved by comparing to the active ingredients downloaded from the Drugs@FDA4 database. Drug candidates were further prioritized based on their known mechanism of action (MOA), FDA status, and targets from the Drug Repurposing Hub5 and by functional enrichment analysis.

Data Sets

• Pre-Cystic P70: GSE149739
• Cystic P21: GSE134719
• Cystic P28: GSE69556

code/.

Differential Expression Analysis.

DESeq2 analyses and visualizations for 3 publicly available Pkd2-KO mouse kidney RNA-seq data sets. Input for each data set was STAR-salmon gene counts from nf-core's RNA-seq pipeline (version 3.6).

• deseq2_analyses.Rmd

FEA and Data Set Comparisons.

Data set comparisons and functional enrichment analyses with gprofiler2

• compare_datasets.Rmd

Signature Reversion and Drug Annotations.

Analyses using signatureSearch for signature reversion and the Drug Repurposing Hub

• sigsearch_analyses.Rmd

Drug Target Analyses.

Drug target comparison (from drug candidates found from pre-cystic p70 signature reversion in sigsearch_analyses.Rmd) to differentially expressed genes in each dataset and drug set enrichment analyses.

• drugtarget_analyses.Rmd

Functions.

All custom functions used for the analyses in this repo.

• functions.R

data/.

• Metadata for each dataset (*_metadata.txt)
• Processed STAR-salmon count data (*_salmonmerged_gene_counts.rds)
• Ensembl human and mouse gene conversion annotation (annot_ens_humanmouse.csv)
• Background gene list (for FEA) (background_genelist_genestoLINCSgenes.csv)
• FDA drug data downloaded from Drugs@FDA (accessed August 2022)(fda_data/*)
• Merged tables from FDA drug data for analyses (FDA_approved_unique_ingredients.csv, FDA_products_status_220816.csv)
• Drug data incuding clinical trial status, MOA, original indication, etc. (Repurposing_Hub_export.txt)
• Document with table of upregulated and downregulated acute kidney injury genes6 (aki_overlappeddegs.doc)

res/.

• deseq2_outputs
• sigsearch_outputs
• FEA
• biorender (repo workflow image)

Acknowledgements

• Michal Mrug
• Brad Yoder
• Kasi McPherson
• Hanna Cleary

License

MIT

Versions

Dependencies

##  signatureSearchData      EnhancedVolcano                 here 
##             "1.10.0"             "1.14.0"              "1.0.1" 
##              viridis          viridisLite              biomaRt 
##              "0.6.2"              "0.4.0"             "2.52.0" 
##                rhdf5        ExperimentHub        AnnotationHub 
##             "2.40.0"              "2.4.0"              "3.4.0" 
##        BiocFileCache               dbplyr      signatureSearch 
##              "2.4.0"              "2.2.1"             "1.10.0" 
##                 Rcpp              ggrepel              ggplot2 
##              "1.0.9"              "0.9.1"              "3.3.6" 
##                dplyr             pheatmap               apeglm 
##              "1.0.9"             "1.0.12"             "1.18.0" 
##              stringr               DESeq2 SummarizedExperiment 
##              "1.4.0"             "1.36.0"             "1.26.1" 
##              Biobase       MatrixGenerics          matrixStats 
##             "2.56.0"              "1.8.1"             "0.62.0" 
##        GenomicRanges         GenomeInfoDb              IRanges 
##             "1.48.0"             "1.32.2"             "2.30.0" 
##            S4Vectors         BiocGenerics 
##             "0.34.0"             "0.42.0"

Platform

x86_64-apple-darwin17.0 
R version 4.1.1 (2021-08-10)