Predicting tumour resistance to paclitaxel and carboplatin utilising genome-wide screening in haploid human embryonic stem cells

Abstract

Taxanes and platinum molecules, specifically paclitaxel and carboplatin, are widely used anticancer drugs that induce cell death and serve as first-line chemotherapy for various cancer types. Despite the efficient effect of both drugs on cancer cell proliferation, many tumours have innate resistance against paclitaxel and carboplatin, which leads to inefficient treatment and poor survival rates. Haploid human embryonic stem cells (hESCs) are a novel and robust platform for genetic screening. To gain a comprehensive view of genes that affect or regulate paclitaxel and carboplatin resistance, genome-wide loss-of-function screens in haploid hESCs were performed. Both paclitaxel and carboplatin screens have yielded selected plausible gene lists and pathways relevant to resistance prediction. The effects of mutations in selected genes on the resistance to the drugs were demonstrated. Based on the results, an algorithm that can predict resistance to paclitaxel or carboplatin was developed. Applying the algorithm to the DNA mutation profile of patients' tumours enabled the separation of sensitive versus resistant patients, thus, providing a prediction tool. As the anticancer drugs arsenal can offer alternatives in case of resistance to either paclitaxel or carboplatin, an early prediction can provide a significant advantage and should improve treatment. The algorithm assists this unmet need and helps predict whether a patient will respond to the treatment and may have an immediate clinically actionable application.

References

[1] Calvert AH. Introduction: a history of the progress of anticancer chemotherapy. Cancer Surv. 1989; 8(3): 493-509.

[2] DeVita VT, Chu E. A history of cancer chemotherapy. Cancer Res. 2008; 68(21): 8643-8653.

[3] Du Bois A, Neijt JP, Thigpen JT. First line chemotherapy with carboplatin plus paclitaxel in advanced ovarian cancer-a new standard of care? Ann Oncol. 1999; 10: S35-S41.

[4] Belani CP. Paclitaxel/carboplatin in the treatment of non-small-cell lung cancer. Oncology. 1998; 12(1 Suppl 2): 74-79.

[5] Neijt JP, Lund B. Paclitaxel with carboplatin for the treatment of ovarian cancer. Semin Oncol. 1996; 23(6 Suppl 15): 2-4.

[6] Pentheroudakis G, Razis E, Athanassiadis A, Pavlidis N, Fountzilas G. Paclitaxel-carboplatin combination chemotherapy in advanced breast cancer: accumulating evidence for synergy, efficacy, and safety. Med Oncol. 2006; 23: 147-160.

[7] Selvaggi G, Belani CP. Carboplatin and paclitaxel in non-small cell lung cancer: the role of amifostine. Semin Oncol. 1999; 26(2 Suppl 7): 51-60.

[8] Gornstein E, Schwarz TL. The paradox of paclitaxel neurotoxicity: mechanisms and unanswered questions. Neuropharmacology. 2014; 76: 175-183.

[9] Sazonova EV, Kopeina GS, Imyanitov EN, Zhivotovsky B. Platinum drugs and taxanes: can we overcome resistance? Cell Death Discov. 2021; 7(1): 155.

[10] Ben-Hamo R, Zilberberg A, Cohen H, et al. Resistance to paclitaxel is associated with a variant of the gene BCL2 in multiple tumor types. NPJ Precision Oncol. 2019; 3(1): 12.

[11] Shen Z, Chen M, Luo F, et al. Identification of key genes and pathways associated with paclitaxel resistance in esophageal squamous cell carcinoma based on bioinformatics analysis. Front Genet. 2021; 12: 671639.

[12] Xu JH, Hu SL, Shen GD, Shen G. Tumor suppressor genes and their underlying interactions in paclitaxel resistance in cancer therapy. Cancer Cell Int. 2016; 16: 1-10.

[13] Zhou J, Kang Y, Chen L, et al. The drug-resistance mechanisms of five platinum-based antitumor agents. Front Pharmacol. 2020; 11: 343.

[14] Cowley GS, Weir BA, Vazquez F, et al. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci Data. 2014; 1(1): 1-12.

[15] Hinterndorfer M, Zuber J. Functional-genetic approaches to understanding drug response and resistance. Curr Opin Genet Dev. 2019; 54: 41-47.

[16] Luo J. CRISPR/Cas9: from genome engineering to cancer drug discovery. Trends Cancer. 2016; 2(6): 313-324.

[17] Munoz DM, Cassiani PJ, Li L, et al. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discov. 2016; 6(8): 900-913.

[18] Lau MT, Ghazanfar S, Parkin A, et al. Systematic functional identification of cancer multi-drug resistance genes. Genome Biol. 2020; 21: 1-12.

[19] Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol. 2015; 33(6): 661-667.

[20] Garnett MJ, Edelman EJ, Heidorn SJ, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012; 483(7391): 570-575.

[21] Li H, Bartke R, Zhao L, et al. Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells. Nat Biomed Eng. 2024; 8(2): 165-176.

[22] Ben-David U, Benvenisty N. The tumorigenicity of human embryonic and induced pluripotent stem cells. Nat Rev Cancer. 2011; 11(4): 268-277.

[23] Bindhya S, Sidhanth C, Shabna A, Krishnapriya S, Garg M, Ganesan TS. Induced pluripotent stem cells: a new strategy to model human cancer. Int J Biochem Cell Biol. 2019; 107: 62-68.

[24] Werbowetski-Ogilvie TE, Bhatia M. Pluripotent human stem cell lines: what we can learn about cancer initiation. Trends Mol Med. 2008; 14(8): 323-332.

[25] Yilmaz A, Peretz M, Sagi I, Benvenisty N. Haploid human embryonic stem cells: half the genome, double the value. Cell Stem Cell. 2016; 19(5): 569-572.

[26] Elling U, Taubenschmid J, Wirnsberger G, et al. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell. 2011; 9(6): 563-574.

[27] Leeb M, Wutz A. Derivation of haploid embryonic stem cells from mouse embryos. Nature. 2011; 479(7371): 131-134.

[28] Li W, Li X, Li T, et al. Genetic modification and screening in rat using haploid embryonic stem cells. Cell Stem Cell. 2014; 14(3): 404-414.

[29] Yang H, Liu Z, Ma Y, et al. Generation of haploid embryonic stem cells from Macaca fascicularis monkey parthenotes. Cell Res. 2013; 23(10): 1187-1200.

[30] Sagi I, Chia G, Golan-Lev T, et al. Derivation and differentiation of haploid human embryonic stem cells. Nature. 2016; 532(7597): 107-111.

[31] Zhong C, Zhang M, Yin Q, et al. Generation of human haploid embryonic stem cells from parthenogenetic embryos obtained by microsurgical removal of male pronucleus. Cell Res. 2016; 26(6): 743-746.

[32] Yilmaz A, Peretz M, Aharony A, Sagi I, Benvenisty N. Defining essential genes for human pluripotent stem cells by CRISPR-Cas9 screening in haploid cells. Nat Cell Biol. 2018; 20(5): 610-619.

[33] Bar S, Vershkov D, Keshet G, et al. Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells. Nat Commun. 2021; 12(1): 6718.

[34] Li Y, Li W, Zhou Q. Haploid pluripotent stem cells: twofold benefits with half the effort in genetic screening and reproduction. Curr Opin Genet Dev. 2020; 64: 6-12.

[35] Segal E, Nissenbaum J, Peretz M, et al. Genome-wide screen for anticancer drug resistance in haploid human embryonic stem cells. Cell Prolif. 2023; 56(6):e13475.

[36] Vershkov D, Yilmaz A, Yanuka O, Nielsen AL, Benvenisty N. Genome-wide screening for genes involved in the epigenetic basis of fragile X syndrome. Stem Cell Rep. 2022; 17(5): 1048-1058.

[37] Yilmaz A, Braverman-Gross C, Bialer-Tsypin A, Peretz M, Benvenisty N. Mapping gene circuits essential for germ layer differentiation via loss-of-function screens in haploid human embryonic stem cells. Cell Stem Cell. 2020; 27(4): 679-691.

[38] Yilmaz A, Benvenisty N. Defining human pluripotency. Cell Stem Cell. 2019; 25(1): 9-22.

[39] Elling U, Wimmer RA, Leibbrandt A, et al. A reversible haploid mouse embryonic stem cell biobank resource for functional genomics. Nature. 2017; 550(7674): 114-118.

[40] Wang H, Zhang W, Yu J, et al. Genetic screening and multipotency in rhesus monkey haploid neural progenitor cells. Development. 2018; 145(11):160531.

[41] Xu M, Zhao Y, Zhang W, et al. Genome-scale screening in a rat haploid system identifies Thop1 as a modulator of pluripotency exit. Cell Prolif. 2022; 55(4):e13209.

[42] Zhang J, Zhao Y, Tian Y, et al. Genome-wide screening in the haploid system reveals Slc25a43 as a target gene of oxidative toxicity. Cell Death Dis. 2022; 13(3): 284.

[43] Zhang W, Sun S, Wang Q, et al. Haploid-genetic screening of trophectoderm specification identifies Dyrk1a as a repressor of totipotent-like status. Sci Adv. 2023; 9(51): 5683.

[44] Li W, Xu H, Xiao T, et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014; 15: 1-12.

[45] Housden BE, Muhar M, Gemberling M, et al. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet. 2017; 18(1): 24-40.

[46] Ortiz M, Wabel E, Mitchell K, Horibata S. Mechanisms of chemotherapy resistance in ovarian cancer. Cancer Drug Resist. 2022; 5(2): 304-316.

[47] Kastenhuber ER, Lowe SW. Putting p53 in context. Cell. 2017; 170(6): 1062-1078.

[48] Zbuk KM, Eng C. Cancer phenomics: RET and PTEN as illustrative models. Nature Reviews Cancer. 2007; 7: 35-45.

[49] Ben-David U, Amon A. Context is everything: aneuploidy in cancer. Nat Rev Genet. 2020; 21(1): 44-62.

[50] Isaka T, Nestor AL, Takada T, Allison DC. Chromosomal variations within aneuploid cancer lines. J Histochem Cytochem. 2003; 51(10): 1343-1353.

[51] Safier LZ, Zuccaro MV, Egli D. Efficient SNP editing in haploid human pluripotent stem cells. J Assist Reprod Genet. 2020; 37: 735-745.

[52] Brachova P, Mueting SR, Carlson MJ, et al. TP53 oncomorphic mutations predict resistance to platinum-and taxane-based standard chemotherapy in patients diagnosed with advanced serous ovarian carcinoma. Int J Oncol. 2014; 46(2): 607-618.

[53] Hientz K, Mohr A, Bhakta-Guha D, Efferth T. The role of p53 in cancer drug resistance and targeted chemotherapy. Oncotarget. 2017; 8(5): 8921-8946.

[54] Muller PA, Vousden KH. Mutant p53 in cancer: new functions and therapeutic opportunities. Cancer Cell. 2014; 25(3): 304-317.

[55] Shetzer Y, Solomon H, Koifman G, Molchadsky A, Horesh S, Rotter V. The paradigm of mutant p53-expressing cancer stem cells and drug resistance. Carcinogenesis. 2014; 35(6): 1196-1208.

[56] Shu C, Zheng X, Wuhafu A, et al. Acquisition of taxane resistance by p53 inactivation in ovarian cancer cells. Acta Pharmacol Sin. 2022; 43(9): 2419-2428.

[57] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012; 9: 357-359.

[58] Artegiani B, Hendriks D, Beumer J, et al. Fast and efficient generation of knock-in human organoids using homology-independent CRISPR-Cas9 precision genome editing. Nat Cell Biol. 2020; 22(3): 321-331.

RIGHTS & PERMISSIONS

2024 The Author(s). Cell Proliferation published by Beijing Institute for Stem Cell and Regenerative Medicine and John Wiley & Sons Ltd.