A widespread role for SLC transmembrane transporters in resistance to cytotoxic drugs

Abstract

The activity and potency of a drug is inherently affected by the metabolic state of its target cell.Solute Carriers (SLCs) represent the largest family of transmembrane transporters in humans and constitute major determinants of cellular metabolism. Several SLCs have been shown to be required for the uptake of individual chemical compounds into cellular systems, but systematic surveys of transporter-drug relationships in human cells are currently lacking. We performed a series of genetic screens in the haploid human cell line HAP1 using a set of 60 cytotoxic compounds representative of the chemical space populated by approved drugs. By using a SLC-focused CRISPR/Cas9 lentiviral library, we identified transporters whose absence induced resistance to the drugs tested. Among the hundreds of drug-SLC relationships identified, we confirmed the role of the folate transporter SLC19A1 on the activity of antifolates and of SLC29A1 on several nucleoside analogs. Among the newly discovered dependencies, we identified the transporters SLC11A2/SLC16A1 for artemisinin derivatives and SLC35A2/SLC38A5 for cisplatin. The functional dependence on SLCs observed for a significant proportion of the compounds screened suggested a widespread role for SLCs in the uptake and cellular activity of cytotoxic drugs and provided an experimentally validated set of SLC-drug associations for a number of clinically relevant compounds.

A systematic genetic interaction map of human solute carriers assigns a role to SLC25A51/MCART1 in mitochondrial NAD uptake

“…1a, Extended Data Fig. 1a) with a CRISPR/Cas9 library targeting 390 human SLC genes as well as a set of 20 genes previously shown to be important for optimal HAP1 growth 14,15 (Fig. 1b).…”

“…Cellular fitness was employed as a readout as it integrates cellular physiology, is functionally informative and is readily measurable 5 . Genetic interactions were tested in full media as it allowed us to directly correlate our results with other extensive datasets available for this cellular system [13][14][15] . To determine the ability of our approach to identify functionally relevant interactions, we initially screened two nonessential metabolic genes (CPS1, DBT) with well-characterized biological functions 16,17 .…”

“…The yeast NAD+ transporters ndt1/yil006w and ndt2/yel006w were obtained from Horizon Discovery (catalog IDs YSC3867-202327426 and YSC3867-202326304, respectively). cDNAs were cloned into a modified pCW57.1 lentiviral vector (Addgene #41393) generated within the ReSOLUTE consortium and carrying a Strep-HA tag and blasticidin resistance.Genetic screeningGenetic screening was performed by transducing wild type or knockout cell lines with the SLC CRISPR/Cas9 library15 at an MOI of 0.2-0.3 and 2000x coverage, in triplicate, followed by selection with puromycin (1µg/ml) for 7 days. Samples were collected at 2, 9 and 16 days postinfection, the genomic DNA extracted with QIAGEN DNA Easy kit.…”

“…Samples were collected at 2, 9 and 16 days postinfection, the genomic DNA extracted with QIAGEN DNA Easy kit. Amplification was performed by PCR using Q5 polymerase (NEB) for 26-28 cycles using primers carrying dual indexes as previously described15 . Samples were normalized based on band intensity and multiplexed together to achieve a coverage of approximately 2000x by NGS on an Illumina 3000/4000 platform (BSF facility, CeMM/MUW).Sample sequencing and genetic interaction analysisReads were demultiplexed and mapped to the sgRNAs present in the library using a custom procedure implemented in Python (crispyCount).…”

A Membrane Transporter Determines the Spectrum of Activity of a Potent DNA-Targeted Hybrid Anticancer Agent

“…48 These findings corroborate the critical role solute carrier (SLC) transporters may play in mediating delivery of pharmacologically relevant levels of drug to diseased tissue. 49 Finally, we provide proof-of-concept data to demonstrate that colorectal cancer cells treated with epigenetic drugs can be sensitized to compound 1 and that the enhanced cytotoxicity is caused by hMATE1-mediated drug accumulation. A growing body of clinical evidence supports the utility of coadministering cytotoxic drugs with epigenetic drugs (see also clinicaltrials.gov).…”