High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs

Akhtari, Farida S.; Green, Adrian; Small, George W.; Havener, Tammy M.; House, John S.; Roell, Kyle; Reif, David M.; McLeod, Howard L.; Wiltshire, Timothy J; Motsinger‐Reif, Alison A.

doi:10.1371/journal.pgen.1009732

Cited by 10 publications

(15 citation statements)

References 77 publications

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“…Zero-passage organoids can test mechanisms of action by combining genetic and small-molecule perturbations. As an illustration, we pursued one gene widely implicated in resistance to anti-cancer therapies: the NAD(P)H quinone dehydrogenase 1, NQO1 [53, 54]. As part of the phase II antioxidant response, NQO1 is heterogeneously upregulated in luminal breast cancers [52, 55].…”

Section: Resultsmentioning

confidence: 99%

Patient-derived response estimates from zero-passage organoids of luminal breast cancer

Przanowska,

Labban,

Przanowski

et al. 2024

Preprint

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Background Primary luminal breast cancer cells lose their identity rapidly in standard tissue culture, which is problematic for testing hormone interventions and molecular pathways specific to the luminal subtype. Breast cancer organoids are thought to retain tumor characteristics better, but long-term viability of luminal-subtype cases is a persistent challenge. Our goal was to adapt short-term organoids of luminal breast cancer for parallel testing of genetic and pharmacologic perturbations. Methods We freshly isolated patient-derived cells from luminal tumor scrapes, miniaturized the organoid format into 5 microliter replicates for increased throughput, and set an endpoint of 14 days to minimize drift. Therapeutic hormone targeting was mimicked in these zero-passage organoids by withdrawing beta-estradiol and adding 4-hydroxytamoxifen. We also examined sulforaphane as an electrophilic stress and commercial neutraceutical with reported anti-cancer properties. Downstream mechanisms were tested genetically by lentiviral transduction of two complementary sgRNAs and Cas9 stabilization for the first week of organoid culture. Transcriptional changes were measured by RT-qPCR or RNA sequencing, and organoid phenotypes were quantified by serial brightfield imaging, digital image segmentation, and regression modeling of cellular doubling times. Results We achieved >50% success in initiating luminal breast cancer organoids from tumor scrapes and maintaining them to the 14-day zero-passage endpoint. Success was mostly independent of clinical parameters, supporting general applicability of the approach. Abundance of ESR1 and PGR in zero-passage organoids consistently remained within the range of patient variability at the endpoint. However, responsiveness to hormone withdrawal and blockade was highly variable among luminal breast cancer cases tested. Combining sulforaphane with knockout of NQO1 (a phase II antioxidant response gene and downstream effector of sulforaphane) also yielded a breadth of organoid growth phenotypes, including growth inhibition with sulforaphane, growth promotion with NQO1 knockout, and growth antagonism when combined. Conclusions Zero-passage organoids are a rapid and scalable way to interrogate properties of luminal breast cancer cells from patient-derived material. This includes testing drug mechanisms of action in different clinical cohorts. A future goal is to relate inter-patient variability of zero-passage organoids to long-term outcomes.

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Section: Resultsmentioning

confidence: 99%

Patient-derived response estimates from zero-passage organoids of luminal breast cancer

Przanowska,

Labban,

Przanowski

et al. 2024

Preprint

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“…The results of a high-throughput dose-response screen of 44 anticancer drugs conducted on the 1000 Genome collection of LCLs by Akhtari et al showed one significant SNP association with OXAL response, as indicated on the Manhattan plot ( Figure 1 a) [ 13 ]. This association was centered on chromosome 10, and the locus zoom plot of the region’s genes ( Figure 1 b) showed that the SNP rs11006706 ( p -value = 1.22 × 10 −9 ) exceeded genome-wide significance ( p < 10 × 10 −8 ).…”

Section: Resultsmentioning

confidence: 99%

“…The OXAL viability data was available for all LCLs (n = 680) from a high-throughput anticancer agent screen developed by Akhtari et al [ 13 ]. Background fluorescence control, 10% dimethyl sulfoxide (DMSO), and a drug vehicle control were included on every plate.…”

Section: Methodsmentioning

confidence: 99%

“…High throughput drug screens utilizing cell line models assessed the sensitivity and resistance of different compounds and identified both germline and somatic variants that influence drug response to improve our understanding of cancer biology and novel therapeutic strategies [ 13 , 14 , 15 , 16 ]. The 1000 Genomes Project’s collection of immortalized B lymphocytes (LCLs) and the use of cancer cell lines provide resources for studying the impact of human genetics on drug response and disease, allowing for large-scale gene expression and genome-wide association studies across diverse, multinational populations.…”

Section: Introductionmentioning

confidence: 99%

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MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients

et al. 2023

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Oxaliplatin (OXAL) is a commonly used chemotherapy for treating colorectal cancer (CRC). A recent genome wide association study (GWAS) showed that a genetic variant (rs11006706) in the lncRNA gene MKX-AS1 and partnered sense gene MKX could impact the response of genetically varied cell lines to OXAL treatment. This study found that the expression levels of MKX-AS1 and MKX in lymphocytes (LCLs) and CRC cell lines differed between the rs11006706 genotypes, indicating that this gene pair could play a role in OXAL response. Further analysis of patient survival data from the Cancer Genome Atlas (TCGA) and other sources showed that patients with high MKX-AS1 expression status had significantly worse overall survival (HR = 3.2; 95%CI = (1.17–9); p = 0.024) compared to cases with low MKX-AS1 expression status. Alternatively, high MKX expression status had significantly better overall survival (HR = 0.22; 95%CI = (0.07–0.7); p = 0.01) compared to cases with low MKX expression status. These results suggest an association between MKX-AS1 and MKX expression status that could be useful as a prognostic marker of response to OXAL and potential patient outcomes in CRC.

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“…In vitro models of human gliomas have the potential to improve our understanding of glioma biology and novel therapeutic strategies [ 20 ]. High throughput drug screens utilizing cell line models have assessed the sensitivity and resistance of different compounds and identified both germline and somatic variants that influence drug response [ 21 , 22 , 23 ]. The 1000 Genomes Project collection is a valuable resource for studying the impact of diverse global human genetics on drug response and disease.…”

Section: Introductionmentioning

confidence: 99%

RYK Gene Expression Associated with Drug Response Variation of Temozolomide and Clinical Outcomes in Glioma Patients

et al. 2023

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Temozolomide (TMZ) chemotherapy is an important tool in the treatment of glioma brain tumors. However, variable patient response and chemo-resistance remain exceptionally challenging. Our previous genome-wide association study (GWAS) identified a suggestively significant association of SNP rs4470517 in the RYK (receptor-like kinase) gene with TMZ drug response. Functional validation of RYK using lymphocytes and glioma cell lines resulted in gene expression analysis indicating differences in expression status between genotypes of the cell lines and TMZ dose response. We conducted univariate and multivariate Cox regression analyses using publicly available TCGA and GEO datasets to investigate the impact of RYK gene expression status on glioma patient overall (OS) and progression-free survival (PFS). Our results indicated that in IDH mutant gliomas, RYK expression and tumor grade were significant predictors of survival. In IDH wildtype glioblastomas (GBM), MGMT status was the only significant predictor. Despite this result, we revealed a potential benefit of RYK expression in IDH wildtype GBM patients. We found that a combination of RYK expression and MGMT status could serve as an additional biomarker for improved survival. Overall, our findings suggest that RYK expression may serve as an important prognostic or predictor of TMZ response and survival for glioma patients.

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High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs

Cited by 10 publications

References 77 publications

Patient-derived response estimates from zero-passage organoids of luminal breast cancer

Patient-derived response estimates from zero-passage organoids of luminal breast cancer

MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients

RYK Gene Expression Associated with Drug Response Variation of Temozolomide and Clinical Outcomes in Glioma Patients

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