Center for Molecular Medicine Cologne

Martin Sos - A 11

Genomic and molecular characterization of the evolutionary process of drug resistance in EGFR-mutant lung cancer

Despite major improvements in targeted therapies in the last years, lung cancer still remains one of the deadliest cancers worldwide. Targeted drugs that inhibit mutant EGFR in lung adenocarcinoma has dramatically prolonged the overall survival of these patients. However, the development of resistance remains inevitable. In this project, we aim for understanding the molecular drivers that shape the evolutionary process of resistance in EGFR-mutant lung tumors.

Introduction

Lung cancer is the leading cause of cancer death in men and women in developed countries. Over the last decade novel techniques like next-generation sequencing and high-throughput analyses have enabled us and other groups to systematically classify lung tumors on a genomic level and to develop novel, targeted therapies for genetically defined subgroups of lung cancer patients. This type of a precision medicine approach is based on the observation that mutant oncogenes such as mutant EGFR or rearranged RET can drive growth of individual tumors and may serve as Achilles heels for an effective therapy. 

However, the targeted treatment of oncogenically driven tumors inevitably leads to the selection of resistant clones and the recurrence of disease. This is not too surprising considering the genomic complexity of cancer and the dynamic evolution of unique cell clones that contribute to the heterogeneity of individual tumors. In our project, we aimed at characterizing the genomic and molecular dynamics of clonal evolution in EGFR-driven lung tumors and their implication for therapeutic responses to targeted drugs. For this purpose, we combined systematic in vitro modelling of tumor resistance development and the analysis of patient cohorts with several complementary genomic and transcriptomic approaches. 

Furthermore, we embarked on the characterization of therapeutic response to RET targeted agents in RET rearranged lung cancer models. Here, we were able to identify structural elements that are responsible for drug efficacy but also molecular drivers that limit the overall response to targeted agents (Plenker et al., Science Transl Med 2017). 

This approach provides important insights into the molecular processes that drive resistance to targeted inhibition of oncogenic signalling and may help to further improve the treatment options for lung cancer patients.

Aim 1: Systematic characterization of the genomic and transcriptomic architecture of EGFR-mutant tumors

During our work with patient samples from a study investigating the effectiveness of third-generation EGFR inhibitors, we have shown the potential to elucidate the diversity of occurring resistance patterns (Ortiz-Cuaran et al., 2016).

Within this project part, we systematically extend this approach to samples obtained before and after treatment with different EGFR inhibitors. 

One of the currently investigated routes is the characterization of a novel resistance mutation within EGFR that arises as a subclone in EGFR TKI treated patients (Fig. 2). This novel mechanism shifts the sensitivity from the class of third-generation EGFR inhibitors to second-generation EGFR inhibitors (Fassunke et al., Nat Comm 2018). This data is closely related to our results obtained in RET-driven tumors in which we identified novel determinants of drug resistance (Plenker et al., Science Trans Med 2017).

Furthermore, we were able to expand our genomic and transcriptomic analyses of defined resistance clones that arise during therapy with EGFR inhibitors to further define the re-wiring of transcriptional networks and signalling pathways in oncogenically driven tumors (Müller et al., submitted).

Aim 2: Functionally linking the subclonal evolution of EGFR-driven lung tumors with their vulnerability to targeted drugs

We and others have shown that the spectrum of resistance mechanisms after treatment with third-generation inhibitors significantly differs from that of first-generation inhibitors. Furthermore, it is known that cell lines driven by the same genetic aberration in EGFR and challenged by the same inhibitor can give rise to distinct resistance mechanisms. 

In this project part, we use cellular models as well as patient-derived cell lines to assess the impact of the subclonal architecture (analyzed in Aim 1) on response to targeted drugs in EGFR-mutant lung cancer. One interesting finding that needs to be further explored is the frequent activation of EMT and stem cell signalling across different cellular models. These signatures were present in vitro as well as in in vivo models suggesting that this is a conserved response, independent of the culture conditions. Further delineation of these findings might be helpful to identify novel vulnerabilities that arise during the process of drug resistance in lung cancer patients.

Perspectives 

Our project will strongly foster the basic understanding of tumor evolution, but will also offer insights that may rapidly be translated into clinical applications, such as improved therapies for patients with oncogenically driven lung cancer.

Selected publications

1. Fassunke J, Müller F, Keul M, Michels S, Dammert MA, Schmitt A, Plenker D, Lategahn J, Heydt C, Brägelmann J, Tumbrink HL, Alber Y, Klein S, Heimsoeth A, Dahmen I, Fischer RN, Scheffler M, Ihle MA, Priesner V, Scheel AH, Wagener S, Kron A, Frank K, Garbert K, Persigehl T, Püsken M, Haneder S, Schaaf B, Rodermann E, Engel-Riedel W, Felip E, Smit EF, Merkelbach-Bruse S, Reinhardt HC, Kast SM, Wolf J, Rauh D, Büttner R, Sos ML (2018). Overcoming EGFR(G724S)-mediated osimertinib resistance through unique binding characteristics of second-generation EGFR inhibitors. Nat Commun. 9(1), 4655.

2. Plenker D, Riedel M, Brägelmann J, Dammert MA, Chauhan R, Knowles PP, Lorenz C, Keul M, Bührmann M, Pagel O, Tischler V, Scheel AH, Schütte D, Song Y, Stark J, Mrugalla F, Alber Y, Richters A, Engel J, Leenders F, Heuckmann JM, Wolf J, Diebold J, Pall G, Peifer M, Aerts M, Gevaert K, Zahedi RP, Buettner R, Shokat KM, McDonald NQ, Kast SM, Gautschi O, Thomas RK, Sos ML (2017). Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors. Sci Transl Med. 9(394).

3. Ortiz-Cuaran S, Scheffler M, Plenker D, Dahmen L, Scheel AH, Fernandez-Cuesta  L, Meder L, Lovly CM, Persigehl T, Merkelbach-Bruse S, Bos M, Michels S, Fischer  R, Albus K, König K, Schildhaus HU, Fassunke J, Ihle MA, Pasternack H, Heydt C, Becker C, Altmüller J, Ji H, Müller C, Florin A, Heuckmann JM, Nuernberg P, Ansén S, Heukamp LC, Berg J, Pao W, Peifer M, Buettner R, Wolf J, Thomas RK, Sos ML (2016). Heterogeneous Mechanisms of Primary and Acquired Resistance to Third Generation EGFR Inhibitors. Clin Cancer Res. 22(19), 4837-4847.

Dammert, M.A., Bragelmann, J., Olsen, R.R., Bohm, S., Monhasery, N., Whitney, C.P., Chalishazar, M.D., Tumbrink, H.L., Guthrie, M.R., Klein, S., Ireland, A.S., Ryan, J., Schmitt, A., Marx, A., Ozretic, L., Castiglione, R., Lorenz, C., Jachimowicz, R.D., Wolf, E., Thomas, R.K., Poirier, J.T., Buttner, R., Sen, T., Byers, L.A., Reinhardt, H.C., Letai, A., Oliver, T.G., and Sos, M.L. (2019). MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer. Nat Commun 10, 3485.

Fassunke J, Muller F, Keul M, Michels S, Dammert MA, Schmitt A, Plenker D, Lategahn J, Heydt C, Bragelmann J, Tumbrink HL, Alber Y, Klein S, Heimsoeth A, Dahmen I, Fischer RN, Scheffler M, Ihle MA, Priesner V, Scheel AH, Wagener S, Kron A, Frank K, Garbert K, Persigehl T, Pusken M, Haneder S, Schaaf B, Rodermann E, Engel-Riedel W, Felip E, Smit EF, Merkelbach-Bruse S, Reinhardt HC, Kast SM, Wolf J, Rauh D, Buttner R, and Sos ML (2018). Overcoming EGFR(G724S)-mediated osimertinib resistance through unique binding characteristics of second-generation EGFR inhibitors. Nat Commun 9, 4655.

Plenker D, Bertrand M, de Langen AJ, Riedel R, Lorenz C, Scheel AH, Muller J, Bragelmann J, Dassler-Plenker J, Kobe C, Persigehl T, Kluge A, Wurdinger T, Schellen P, Hartmann G, Zacherle T, Menon R, Thunnissen E, Buttner R, Griesinger F, Wolf J, Heukamp L, Sos ML, and Heuckmann JM (2018). Structural Alterations of MET Trigger Response to MET Kinase Inhibition in Lung Adenocarcinoma Patients. Clin Cancer Res 24, 1337-1343.

Scheffler M, Ihle MA, Hein R, Merkelbach-Bruse S, Scheel AH, Siemanowski J, Bragelmann J, Kron A, Abedpour N, Ueckeroth F, Schuller M, Koleczko S, Michels S, Fassunke J, Pasternack H, Heydt C, Serke M, Fischer R, Schulte W, Gerigk U, Nogova L, Ko YD, Abdulla DSY, Riedel R, Kambartel KO, Lorenz J, Sauerland I, Randerath W, Kaminsky B, Hagmeyer L, Grohe C, Eisert A, Frank R, Gogl L, Schaepers C, Holzem A, Hellmich M, Thomas RK, Peifer M, Sos ML, Buttner R, and Wolf J (2018). K-ras mutation subtypes in NSCLC and associated co-occuring mutations in other oncogenic pathways. J Thorac Oncol 10.1016/j.jtho.2018.12.013.

Bragelmann J, Bohm S, Guthrie MR, Mollaoglu G, Oliver TG, and Sos ML (2017a). Family matters: How MYC family oncogenes impact small cell lung cancer. Cell Cycle 16, 1489-98.

Bragelmann J, Dammert MA, Dietlein F, Heuckmann JM, Choidas A, Bohm S, Richters A, Basu D, Tischler V, Lorenz C, Habenberger P, Fang Z, Ortiz-Cuaran S, Leenders F, Eickhoff J, Koch U, Getlik M, Termathe M, Sallouh M, Greff Z, Varga Z, Balke-Want H, French CA, Peifer M, Reinhardt HC, Orfi L, Keri G, Ansen S, Heukamp LC, Buttner R, Rauh D, Klebl BM, Thomas RK, and Sos ML (2017b). Systematic Kinase Inhibitor Profiling Identifies CDK9 as a Synthetic Lethal Target in NUT Midline Carcinoma. Cell Rep 20, 2833-45.

Buttner R, Wolf J, Thomas RK, and Sos ML (2017). Resistance Mechanisms to AZD9291 and Rociletinib-Response. Clin Cancer Res 23, 3967-8.

Malchers F, Ercanoglu M, Schutte D, Castiglione R, Tischler V, Michels S, Dahmen I, Bragelmann J, Menon R, Heuckmann JM, George J, Ansen S, Sos ML, Soltermann A, Peifer M, Wolf J, Buttner R, and Thomas RK (2017). Mechanisms of Primary Drug Resistance in FGFR1-Amplified Lung Cancer. Clin Cancer Res 23, 5527-36.

Mollaoglu G, Guthrie MR, Bohm S, Bragelmann J, Can I, Ballieu PM, Marx A, George J, Heinen C, Chalishazar MD, Cheng H, Ireland AS, Denning KE, Mukhopadhyay A, Vahrenkamp JM, Berrett KC, Mosbruger TL, Wang J, Kohan JL, Salama ME, Witt BL, Peifer M, Thomas RK, Gertz J, Johnson JE, Gazdar AF, Wechsler-Reya RJ, Sos ML, and Oliver TG (2017). MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. Cancer Cell 31, 270-85.

Prof. Dr. Martin Sos CMMC Cologne
Prof. Dr. Martin Sos

Institute for Pathology / Dept. of Translational Genomics

Principal Investigator A 11

+49 221 478 96175

+49 221 478 32400

Institute for Pathology / Dept. of Translational Genomics

Weyertal 115b

50931 Cologne

CMMC Profile Page

Curriculum Vitae (CV)

Publications - Martin Sos

Link to PubMed

Group Members

Katia Garbert (Project Coordination)
Johannes Brägelmann (Postdoc, EKFS Fellow)
Armin Khonsari (Postdoc)
Stefanie Lennartz (technician)
Marcel Dammert (PhD student)
Alena Heimsoeth (PhD student)
Jenny Ostendorp (PhD student)
Hannah Tumbrink (PhD student)
Carina Lorenz (MD student)
David Ast (MD student)
Fatma Parmaksiz (BSc student)

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