Our main research area concerns thoracic malignancies such as non-small cell lung cancer (NSCLC) and malignant pleural mesothelioma (MPM), which are among the most lethal human cancer types, as they spread rapidly, are diagnosed late, and respond poorly to standard treatment. Thus, we aim at identifying new biomarkers for earlier diagnosis and more effective targeted treatments of these extremely aggressive cancers.
Targeted therapy with tyrosine-kinase inhibitors (TKIs) has significantly improved the prognosis of NSCLC, but only for subsets of patients with specific genetic NSCLC-drivers such as mutations of Epidermal Growth Factor Receptor (EGFR) or fusions of Anaplastic Lymphoma Kinase (ALK), which are found in approx. 10% and 4% of NSCLCs. Despite very frequent and often prolonged clinical response, these patients inevitably develop variable mechanisms of resistance to TKIs. Moreover, approx. 30% of patients do not respond at all because of yet poorly understood intrinsic resistance. Thus, we study the mechanisms of acquired and intrinsic TKI-resistance in NSCLC by comprehensive pathological/molecular profiling of patient specimens (tumor and liquid biopsies) at baseline and at disease progression, and by validation in preclinical models. Such approach may aid in designing combinatorial targeted strategies for better treatment of NSCLC patients.
MPM’s poor therapeutic response and high lethality are largely due to its insufficiently understood molecular pathogenesis, challenging diagnostics, and lack of effective predictive biomarkers and therapeutic targets. A conclusive MPM diagnosis is histological, however differentiation from other cancer types and from benign mesothelial proliferations can be difficult. Thus, we aim at characterizing more sensitive and specific diagnostic and predictive biomarkers for MPM that could open innovative therapeutic avenues for this extremely aggressive malignancy.
Predictive biomarkers for treatment of non-small cell lung cancer and resistance mechanisms
- Targeted therapy with TKIs or immunotherapy can increase survival of fractions of NSCLC patients with specific genetic NSCLC-drivers such as EGFR-mutations or ALK-fusions. Thus, chemotherapy is still widely utilized for NSCLC patients without these mutations. We have identified and characterized new biomarkers and molecular signatures for predicting chemotherapy response in both advanced and early stage NSCLC patients (Vilmar et al. ).
- We have investigated the intra-/inter-tumor heterogeneity and longitudinal variation of biomarkers for chemotherapy response (Jakobsen et al. Eur. J. Cancer 2013; Jakobsen et al. ).
- We have also implemented methods to investigate response and resistance to EGFR- and ALK-TKIs, identifying various mechanisms of acquired resistance such as secondary on-target mutations, activation of parallel/downstream by-pass pathways or phenotypic resistance mechanisms, which can change in different metastatic lesions (Rossing et al. ).
- Moreover, we have addressed the variability in extent and duration of response to clarify why certain NSCLC patients are inherently resistant to EGFR- or ALK-TKIs. We have observed that EGFR-mutations or ALK-fusions are not necessarily mutually exclusive with changes in other cancer-driver genes as anticipated, but co-mutations in multiple drivers and/or transformation to small-cell lung cancer can occur and represent mechanisms of intrinsic TKI-resistance present at baseline or very rapidly induced in surviving cells as adaptive tumor response (Jakobsen et al. ).
New diagnostic and predictive biomarkers for malignant pleural mesothelioma.
- Our group has several years of experience with MPM research, as Copenhagen University Hospital is the specialized referral center for diagnostics and treatment of MPM in Denmark and the Scandinavian center for radically intended surgery for MPM. In connection with that we have been collecting unique MPM biobank samples (MESOBANK) that are included in the Danish Cancer Biobank for research purposes and testing of new molecular markers.
- It is often difficult to distinguish MPM from nonmalignant mesothelial proliferations, as current markers still lack sensitivity and the main diagnostic criterion (deep invasion) is often not appreciable on pleural biopsies. We have tested several potential biomarkers for MPM, identifying some that could complement current diagnostic or predictive procedures (Zimling et al J. Thorac. ).
- We have also shown for the first time that MPM’s specific micro-RNA signatures, related miRNA-targets, and miRNA epigenetic changes, not only have biological and prognostic value, but can accurately distinguish MPM from nonmalignant mesothelial proliferations (Andersen et al. ). This has also allowed to study the expression and mutation status of components of the microRNA-biogenesis and the epigenetic regulation of biomarker-miRNAs in MPM (Andersen et al. Anticancer Res. 2015; Santoni-Rugiu et al. Curr. Biom. Findings 2016), and to characterize other potential markers for targeted therapy in MPM (Chapel et al. Lung Cancer 2019).
Mechanisms of intrinsic and acquired resistance to targeted therapies in non-small cell lung cancer
We keep pinpointing the main, often co-existing, molecular mechanisms of intrinsic resistance to different TKIs using pre-treatment tumor biopsies and liquid biopsies from cohorts of EGFR-mutated or ALK-rearranged NSCLCs treated with these drugs. Types of EGFR-mutations or type ALK-fusions and fusion-partners, as well as co-mutations in EGFR/ALK and other genes are correlated with the variable responses of these patients to TKIs. A schematic representation of mechanisms for intrinsic resistance to EGFR-TKIs investigated/identified in patient-derived material is shown.
We also analyze by NGS, IHC, FISH and microscopy, tumor tissue re-biopsies from progressing lesions and circulating free (cf)DNA/RNA from liquid biopsies obtained at progression on 1st/2nd line TKIs. The identified mutational/phenotypical status is compared with that from samples at baseline to possibly identify acquired molecular/phenotypical TKI-resistance mechanisms that may be targetable by new drugs or combination of drugs.
New diagnostic and predictive biomarkers in malignant pleural mesothelioma
We are interested in identifying genetic/epigenetic biomarkers for earlier diagnosis and more effective therapies of MPM. We use biopsies and operation specimens from MPM patients to investigate the MPM’s genome, methylome, in-situ transcriptomics and in-situ expression of multiple proteins to identify, characterize, and validate these biomarkers. Further characterization is undertaken in cell lines.
We have access to well preserved patient material (formalin-fixed paraffin-embedded or snap-frozen tissue specimens, cytological samples, and different types of liquid biopsies), histological procedures for whole tissue paraffinized sections, frozen sections, and tissue-microarrays. The material is analyzed by light-microscopy, digital microscopy, histochemistry, immunohistochemistry (IHC), fluorescence in-situ hybridization (FISH), qPCR, and high-throughput techniques, such as next generation sequencing (NGS) of DNA/RNA, DNA methylation (pyrosequencing of specific genes and whole-genome methylome), in-situ transcriptomics (Nanostring techniques), and multiplex IHC. Tumor tissue biopsies/re-biopsies and liquid biopsies are used in a complementary fashion: the analysis of cfDNA/RNA from liquid biopsies reduces the problem of missing relevant mutations due to clonal tumor heterogeneity, whereas tumor biopsies/re-biopsies may identify “non-shedding” subclones/mutations. Concordance of informative value of tissue- and liquid-biopsy taken at baseline and progression (“shedders” vs. “non-shedders”, clonality), clinical significance of resistance mechanisms/tumor heterogeneity, and usefulness for therapy are primary endpoints.
- Urbanska EM, Sørensen JB, Santoni-Rugiu E. Treatment Algorithm for Advanced ALK-Rearranged NSCLC. J Thorac Oncol. 2020 Sep;15(9):e156-e157. doi: 10.1016/j.jtho.2020.04.039. PMID: 32854917.
- Urbanska EM, Sørensen JB, Melchior LC, Costa JC, Santoni-Rugiu E. Changing ALK-TKI-Resistance Mechanisms in Rebiopsies of ALK-Rearranged NSCLC: ALK- and BRAF-Mutations Followed by Epithelial-Mesenchymal Transition. Int J Mol Sci. 2020 Apr 19;21(8):2847. doi: 10.3390/ijms21082847. PMID: 32325863.
- Santoni-Rugiu E, Melchior LC, Urbanska EM, Jakobsen JN, Stricker K, Grauslund M, Sørensen JB. Intrinsic resistance to EGFR-Tyrosine Kinase Inhibitors in EGFR-Mutant Non-Small Cell Lung Cancer: Differences and Similarities with Acquired Resistance. Cancers (Basel). 2019 Jul 1;11(7):923. doi: 10.3390/cancers11070923. PMID: 31266248.
- Santoni-Rugiu E. Clinical outcomes provide new insights into transformation to small-cell lung cancer of pulmonary EGFR-mutant adenocarcinoma. Precis. Cancer Med. 2:5, 2019 doi: 10.21037/pcm.2019.02.03
- Chapel DB, Churg A, Santoni-Rugiu E, Tsujimura T, Hiroshima K, Husain AN. Molecular pathways and diagnosis in malignant mesothelioma: A review of the 14th International Conference of the International Mesothelioma Interest Group. Lung Cancer. 2019 Jan;127:69-75. doi: 10.1016/j.lungcan.2018.11.032. Epub 2018 Nov 26. PMID: 30642555.
- Jakobsen JN, Santoni-Rugiu E, Grauslund M, Melchior L, Sørensen JB. Concomitant driver mutations in advanced EGFR-mutated non-small-cell lung cancer and their impact on erlotinib treatment. Oncotarget. 2018 May 25;9(40):26195-26208. doi: 10.18632/oncotarget.25490. eCollection 2018 May 25. PMID: 29899852.
In the media
Petersen PM, Kalhauge A, Brandt B, Santoni-Rugiu E, Daugaard G, Ravn J, Petersen RH.
Ugeskr Laeger. 2020 Jan 6;182(2):V08190462. PMID: 31928621
Event arranged by BestPractice Nordic in collaboration with Dansk Lunge Cancer Gruppe, Copenhagen, 29. October 2019, Rigshospitalet, Auditorium 93. Translationel research/biomarker v/Eric Santoni-Rugiu.
BEST PRACTICE Nordic Aps Onkologi MEDCASTs:
Juni 2020/Edyta Urbanska/Eric Santoni-Rugiu
Juni 2020/Eric Santoni-Rugiu/Edyta Urbanska
Seponering af behandling trods komplet respons ved ALK+ ikke-småcellet lungecancer med cerebrale metastaser
Juni 2020/Edyta Urbanska/Eric Santoni-Rugiu
Multi-institutional collaboration within the International Mesothelioma Interest Group to update the histopathological guidelines and classification of MPM as well as assess new therapy protocols for MPM (Chapel et al. Molecular Pathways and Diagnosis in Malignant Mesothelioma: A review of the 14th International Conference of the International Mesothelioma Interest Group. Lung Cancer 127:69-75, 2019. doi: 10.1016/j.lungcan.2018.11.032; Klebe et al. Controversies in Pathology - The concept of mesothelioma in situ, with particular consideration of cytology diagnosis. Pathology, In press).
Collaboration with Niels Behrendt and Lars H. Engelholm’s groups at BRIC/Finsen on the role of the endocytic collagen receptor uPARAP in human diseases (Jürgensen et al. Immune-regulation by fibroblasts in tissue injury depends on uPARAP-mediated uptake of collectins. J. Cell Biol. 218:333-9, 2019. doi: 10.1083/jcb.201802148). This translational collaboration is currently focusing on the potential role of uPARAP as potential diagnostic marker and therapeutic target in MPM.
Collaboration with Morten Frödin’s group at BRIC on onco-kinases in mouse models for human cancers (Engelholm LH et al: CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1-Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma. Gastroenterology 153(6):1662-73, 2017. doi: 10.1053/j.gastro.2017.09.008).
Collaborative research with Oncology Phase I Unit at Rigshospitalet under the Copenhagen Prospective Personalized Oncology clinical trial program initiated in 2013 (Tuxen et al. Copenhagen Prospective Personalized Oncology (CoPPO) - Clinical utility of using molecular profiling to select patients to phase 1 trial. Clin. Cancer Res. 25:1239-47, 2019. doi: 10.1158/1078-0432.CCR-18-1780; Ahlborn et al. Application of cell-free DNA for genomic tumor profiling – A feasibility study. Oncotarget 10:1388-98, 2019. doi: 10.18632/oncotarget.26642; Bertelsen B et al. High frequency of pathogenic germline variants within homologous recombination repair in patients with advanced cancer. npj Genomic Medicine, 4(13):1-10, 2019. doi.org/10.1038/s41525-019-0087-6; Ahlborn et al. Circulating tumor DNA as a marker of treatment response in BRAF V600E mutated non-melanoma solid tumors. Oncotarget 9:32570-9, 2018. doi: 10.18632/oncotarget.25948).