Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs

Pal Choudhuri, S.; Girard, L.; Lim, J. Y. S.; Wise, J. F.; Freitas, B.; Yang, D.; Wong, E.; Hamilton, S.; Chien, V.; Phat, S.; Gilbreath, C.; Zhong, J.; Myers, D. T.; Christensen, C. L.; Stanzione, M.; Wong, K.-K.; Farago, A. F.; Meador, C. B.; Dyson, N. J.; Lawrence, M. S.; Wu, S.; Drapkin, B. J.

doi:10.1101/2023.06.23.546278

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bioRxiv · 10.1101/2023.06.23.546278

Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs

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Abstract

Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here we present a pre-clinical system that recapitulates acquired cross-resistance in SCLC, developed from 51 patient-derived xenografts (PDXs). Each model was tested for in vivo sensitivity to three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These functional profiles captured hallmark clinical features, such as the emergence of treatment-refractory disease after early relapse. Serially derived PDX models from the same patient revealed that cross-resistance was acquired through a MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that this was not unique to one patient, as MYC paralog amplifications on ecDNAs were recurrent among cross-resistant models derived from patients after relapse. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCESCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC.

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Pal Choudhuri, S., Girard, L., Lim, J. Y. S., Wise, J. F., Freitas, B., Yang, D., Wong, E., Hamilton, S., Chien, V., Phat, S., Gilbreath, C., Zhong, J., Myers, D. T., Christensen, C. L., Stanzione, M., Wong, K.-K., Farago, A. F., Meador, C. B., Dyson, N. J., Lawrence, M. S., Wu, S., Drapkin, B. J.. 2023-06-26. Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs. https://doi.org/10.1101/2023.06.23.546278

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