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Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer

Nature Medicine volume 23, pages 114–119 (2017)Cite this article

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Abstract

In most patients with small-cell lung cancer (SCLC)—a metastatic, aggressive disease—the condition is initially chemosensitive but then relapses with acquired chemoresistance. In a minority of patients, however, relapse occurs within 3 months of initial treatment; in these cases, disease is defined as chemorefractory. The molecular mechanisms that differentiate chemosensitive from chemorefractory disease are currently unknown. To identify genetic features that distinguish chemosensitive from chemorefractory disease, we examined copy-number aberrations (CNAs) in circulating tumor cells (CTCs) from pretreatment SCLC blood samples. After analysis of 88 CTCs isolated from 13 patients (training set), we generated a CNA-based classifier that we validated in 18 additional patients (testing set, 112 CTC samples) and in six SCLC patient-derived CTC explant tumors1. The classifier correctly assigned 83.3% of the cases as chemorefractory or chemosensitive. Furthermore, a significant difference was observed in progression-free survival (PFS) (Kaplan–Meier P value = 0.0166) between patients designated as chemorefractory or chemosensitive by using the baseline CNA classifier. Notably, CTC CNA profiles obtained at relapse from five patients with initially chemosensitive disease did not switch to a chemorefractory CNA profile, which suggests that the genetic basis for initial chemoresistance differs from that underlying acquired chemoresistance.

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Figure 1: Initial molecular analysis of CTCs from 13 patients with SCLC.
Figure 2: Development of a CTC CNA-based classifier linked to chemoresponse.
Figure 3: Comparison of the CTC CNA-based classifier with clinical outcome.
Figure 4: CTC CNA analysis of paired baseline and relapse samples.

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Acknowledgements

L.C. was funded via a Clinical Pharmacology Fellowship educational grant from CRUK and AstraZeneca (C147/A12328). We would like to acknowledge the help of the CRUK Molecular Biology Core Facilities and members of the CRUK Manchester Institute Clinical and Experimental Pharmacology Group for their support of this study. We also thank the patients and healthy volunteers who provided their blood samples. This work was supported by core funding to CRUK Manchester Institute (C5759/A12328), and via Manchester CRUK Centre Award (A12197) and a research grant from Menarini Biomarkers Singapore PTE Ltd. (funding for all assigned to C.D.)

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Author notes

  1. Louise Carter, Dominic G Rothwell and Barbara Mesquita: These authors contributed equally to this work.

Authors and Affiliations

  1. Clinical and Experimental Pharmacology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK

    Louise Carter, Dominic G Rothwell, Barbara Mesquita, Christopher Smowton, Fabiola Fernandez-Gutierrez, Deborah J Burt, Jenny Antonello, Christopher J Morrow, Cassandra L Hodgkinson, Karen Morris, Lynsey Priest, Mathew Carter, Caroline Dive & Ged Brady

  2. Computational Biology Support Group, CRUK Manchester Institute, University of Manchester, Manchester, UK

    Hui Sun Leong & Crispin Miller

  3. Faculty of Life Sciences, University of Manchester, Manchester, UK

    Yaoyong Li

  4. RNA Biology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK

    Crispin Miller

  5. AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, UK

    Andrew Hughes

  6. Institute of Cancer Sciences, University of Manchester, Manchester, UK

    Fiona Blackhall

  7. Cancer Research UK Lung Cancer Centre of Excellence, CRUK Manchester Institute, University of Manchester, Manchester, UK

    Fiona Blackhall & Caroline Dive

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  1. Louise Carter
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Contributions

G.B., F.B., A.H. and C.D. supervised and devised the study, interpreted data and co-wrote the manuscript. L.C., D.G.R. and B.M. interpreted data, co-wrote the manuscript and planned and ran the WGA and NGS experiments. C.S., H.S.L., F.F.-G., Y.L. and C.M. performed the bioinformatics analysis. D.J.B. and J.A. ran the DEPArray isolations and optimized the WGA pipeline. C.J.M. and C.L.H. generated the CDX models. K.M. managed the CellSearch CTC analysis. L.C., M.C., L.P. and F.B. oversaw the acquisition of ethical permission and patient consent and the collection of blood samples. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Caroline Dive or Ged Brady.

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Competing interests

A. Hughes was previously employed by AstraZeneca and holds shares in AstraZeneca. A. Hughes is currently employed by the University of Manchester.

Supplementary information

Supplementary Text, Figures and Tables

Supplementary Figures 1–6 and Supplementary Tables 1–5 (PDF 4531 kb)

Supplementary Table 6

Excel spread sheet of 2281 loci identified in 16 profiles of CTC CNA predictive signature. (XLSX 30 kb)

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Carter, L., Rothwell, D., Mesquita, B. et al. Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer. Nat Med 23, 114–119 (2017). https://doi.org/10.1038/nm.4239

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