Gemcitabine is a drug of choice in the treatment of human pancreatic cancer. chemo-resistance to this drug is common and has been attributed to a variety of distinct mechanisms, involving > 100 genes. A recently developed small-molecule G-quadruplex ligand, the trisubstituted naphthalene diimide compound CM03, has previously been shown to have equivalent potency to gemcitabine in the pancreatic cancer cell line MIA PaCa-2. We report here on cell lines of increased resistance to gemcitabine that have been generated from this line, with the most resistant having 1,000fold reduced sensitivity to gemcitabine. These resistant lines retain nM sensitivity to CM03. The molecular basis for the retention of potency by this G-quadruplex ligand has been examined using whole transcriptome data analysis with RnA-seq. this has revealed that the pattern of pathways down regulated by CM03 in the parental MIA PaCa-2 cell line is largely unaffected in the gemcitabineresistant line. the analysis has also shown that the expression patterns of numerous genes involved in gemcitabine sensitivity are down regulated in the resistant line upon CM03 treatment. These results are supportive of the concept that G-quadruplex small molecules such as CM03 have potential for clinical use in the treatment of gemcitabine-resistant human pancreatic cancer. Pancreatic cancer is among the 12 most common cancers in the UK and the USA, with 9,921 new cases in the UK in 2015 1 and 57,600 estimated new cases in the USA in 2020 2. 458,918 new cases were reported worldwide in 2018 3. Pancreatic ductal adenocarcinoma (PDAC: ca 85% of cases), is the most common form, and is also one of the most intractable of cancers to treatment. It has a bleak prognosis that has barely changed in over 20 years, with < 5% of patients surviving for five years 4-7 .The standard chemotherapy for PDAC has been the nucleoside analogue gemcitabine (Fig. 1a), which produces a modest improvement in mean survival of, typically, 2-3 months 8-10. Initial responses are almost invariably followed by the rapid onset of chemo-resistance 11-14. This has been attributed to, for example, changes in nucleoside transporter expression 15 , or in gemcitabine metabolising enzymes such as cytidine deaminase 16,17. The complexity of the underlying mechanisms of gemcitabine resistance in PDAC is increasingly apparent and over 100 genes and multiple pathways may be involved 18-24. We have recently reported that several small-molecule naphthalene diimide derivatives 25,26 , notably the trisubstituted compound CM03 27 , are potent inhibitors of cancer cell growth, with CM03 (Fig. 1b) having a GI 50 value of ca 11 nM in the PDAC cell lines PANC-1 and MIA PaCa-2. RNA-seq methodology has shown that CM03 targets a number of genes involved with PDAC initiation and progression in these cell lines, and also has significant anti-cancer activity in in vivo xenograft and genetic models for the disease. The mode of action of CM03 involves the stabilisation of genomic quadruplex DNA structures 28 and as a consequenc...