Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anti-cancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug-gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct anti-tumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the S. cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug-gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug-gene interaction specific to cytarabine was less enriched in Gene Ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-GO-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast-human homologs with correlated differential gene expression and drug-efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
List of abbreviations and glossary of terms
- AraC
- cytarabine; cytosine arabinoside
- CPPs
- Cell proliferation parameters: parameters of the logistic growth equation used to fit cell proliferation data obtained by Q-HTCP. The CPPs used to assess gene interaction in this study were K (carrying capacity) and L (time required to reach half of carrying capacity) [7-9,38].
- DAmP
- Decreased Abundance of mRNA Production: refers to a method of making YKD alleles, where the 3’ UTR of essential genes is disrupted, reducing mRNA stability and gene dosage [291].
- dCK
- deoxycytidine kinase
- dCMP
- deoxycytidine monophosphate
- DE
- Deletion enhancer: gene loss of function (knockout or knockdown) that results in enhancement / increase of drug sensitivity [9].
- dFdC
- 2’,2’-difluoro 2’-deoxycytidine, gemcitabine
- dNTP
- deoxyribonucleotide triphosphate
- DS
- Deletion suppressor: gene loss of function (knockout or knockdown) that results in suppression / reduction of drug sensitivity [9].
- ESCRT
- endosomal sorting complex required for transport
- GARP complex
- Golgi-associated retrograde protein complex.
- gCSI
- The Genentech Cell Line Screening Initiative: One of two pharmacogenomics datasets used in this study (https://pharmacodb.pmgenomics.ca/datasets/4).
- GDSC1000
- Genomics of Drug Sensitivity in Cancer: One of two pharmacogenomics datasets used in this study (https://pharmacodb.pmgenomics.ca/datasets/5)
- GO
- Gene ontology
- GTF
- Gene ontology term finder: an algorithm to assess GO term enrichment amongst a list of genes; applied to REMc (clustering) results [41].
- GTA
- Gene ontology term averaging: an assessment of GO term function obtained by averaging the gene interaction values for all genes of a GO term
- GTA value
- Gene ontology term average value
- gtaSD
- standard deviation of GTA value
- GTA score
- (GTA value - gtaSD)
- HaL
- hematopoietic & lymphoid tissue
- HDAC
- Histone deacetylase complex
- HLD
- Human-like media with dextrose [8]: the yeast media used in this study.
- INT
- Interaction score
- NDK
- nucleoside diphosphate kinase
- OES
- Overexpression sensitivity: refers to association of increased gene expression with drug sensitivity in pharmacogenomics data [33].
- PharmacoDB
- The resource used for cancer pharmacogenomics analysis [33].
- PPOD
- Princeton protein orthology database
- Q-HTCP
- Quantitative high throughput cell array phenotyping: a method of imaging, image analysis, and growth curve fitting to obtain cell proliferation parameters [7,38].
- Ref
- Reference: the genetic background from which the YKO/KD library was derived
- REMc
- Recursive expectation maximization clustering: a probabilistic clustering algorithm that determines a discrete number of clusters from a data matrix [40].
- RNR
- ribonucleotide reductase
- SD
- Standard deviation
- SGA
- Synthetic genetic array
- SGD
- Saccharomyces genome database
- UES
- Underexpression sensitivity: refers to association of reduced gene expression with drug sensitivity in pharmacogenomics data [33].
- YKO
- Yeast knockout
- YKD
- Yeast knockdown: DAmP alleles
- YKO/KD
- Yeast knockout or knockdown
