RESEARCH ACTIVITY OF LUNG AND UPPER RESPIRATORY TRACT TUMORS PROGRAM
Work Plan. The scientific main goals of our proposal are to understand the biological intricacies of the disease in order to develop diagnostic, prognostic or predictive markers and more successful therapies. W e are also determined to optimize preventive strategies in lung cancer. To achieve these goals we have developed a work plan which includes 6 work packages (WPs).
The main goal of WP1 is the identification and functional characterization of the genetic and epigenetic events driving lung and head and neck carcinogenesis and metastasis. Specifically we will pursue the following objectives:
Tasks 1.1 Identification of genetic and epigenetic alterations. Sequencing of exomes and transcriptomes of tumorgrafts and lung tumors from mice models (Illumina's technology-HiScanSQ) (MS-C); methylomes analysis of tumorgrafts, lung primaries and cancer cell lines using the infinium methylation 450K beadchip arrays.(Ilumina) (M. Esteller); aberrant splice isoforms (splicing microarrays) using lung primary tumors (L. Montuenga).
Task 1.2 Validation, determination of frequencies and histomolecular/clinical classification of gene alterations. Material: panel of lung primary tumors from the different collections (M. Sanchez-Cespedes, C. Suarez, R. Rosell) and lung cancer cell lines (M. Sanchez-Cespedes). Given the etiological and histopathogical similarity between lung squamous cell carcinomas (SCCs) and HNSCC, the alterations found to be frequent in lung SCCs will also be tested in primary HNSCCs (M. Sanchez-Cespedes, C. Suarez). Sanger sequencing, methylation specific PCR, Taqman.
Task 1.3 Functional analysis, biological pathways and feedback mechanisms. Material: mice models and cancer cell lines models. Restoring tumor suppressors or depleting the mRNA levels in oncogenes found altered. Generation of cancer cell lines models using constructs for stable transfections and, if necessary, stably inducible transfections using tet-off strategies.
Deliverables: Novel genes altered in lung cancer. Histomolecular and prognosis/metastatic markers. Markers for implementing therapeutics, and foretelling cancer outcome and responses.
Task leader: Montserrat Sanchez-Cespedes. Lung and upper respiratory tract tumors program groups involved: R. Rosell, L. Montuenga, J.M. Paramio, C. Suarez & M. Esteller
The overall goal of W P2 will be the identification and validation of clinically useful biomarkers in the context of early stage lung cancer. The molecular characterization of early tumors is challenging due to the small frequency and scarcity of the available material. There are three main specific objectives in this workpackage.
Tasks 2.1 Molecular and genetic profiling of early stage tumors for biomarker's discovery, with a special interest in the differences between histological subtypes.
Characterization of DNA methylation signatures to identify epigenetic markers (M. Esteller) Characterization of splicing alterations by the use of high throughput technologies.(L. Montuenga). Characterization of miRNA expression. (C. Camps). Identification and characterization of cells involved in tumor initiation (C. Suarez). The information generated in the different tasks will be integrated in order to identify biological pathways and signatures associated with early tumors. A refinement of the genetic and molecular alterations will also be done with information from alterations previously identified by members of the program (M. Sanchez-Cespedes) and information generated on WP1.
Tasks 2.2. Development of biomarkers based on molecular alterations of early tumors
Prognostic biomarkers in primary tumors. Evaluation by ICC in FFPE tissues or by PCR in frozen specimens of makers with prognostic potential. Biomarkers in blood. Serum or plasma-based markers would be monitored. For this and the previous task, the re-biopsy program in W P5 will be exploited. (R.Rosell). Cancer risk molecular markers in premalignant lesions in head and neck primary tumors for their implementation into clinical practice (C. Suarez).
Tasks 2.3 Assessment of the clinical utility of the candidates by multiinstitutional validation of the biomarkers in large statistically powered studies.
This aim will take advance of the high quality bio-repositories from early stage lung cancer patients available within the program. The most common genetic alterations found in NSCLC are also characterized in many of these series. (L. Montuenga, M. Sánchez-Céspedes, C. Camps, L. Paz-Ares, C. Suarez). Validation of diagnostic biomarkers in biological fluids. Validation of prognostic markers to identify patients at need of receiving adjuvant therapy after radical treatment with surgery. Prospective studies: Groups in the program may develop well managed prospective studies to fully validate the clinical utility of a marker. (L. Paz-Ares).
Deliverables: Histology-specific molecular alterations or pathways in early stage lung cancer. Assessment of the clinical diagnostic usefulness of candidates for diagnosis, prognosis or therapeutic intervention. Markers valuable clinically for risk assessment or early detection of aggressive tumors in the context of screening programs.
Task leader: L. Montuenga. Lung and upper respiratory tract tumors program groups involved: R. Rosell, M. Sanchez-Cespedes, C. Camps, L. Paz-Ares, J.M. Paramio, M. Esteller & E. Diaz-Rubio.
This work package is transversal to the Program, being feed by other W Ps' discoveries, and hopefully feeding the WP4. Therefore, the main aim is the identification of new therapeutic targets suitable to be transferred to chemical engineering to generate new drugs and late preclinical testing. To that end we will rely technically on the discoveries made by molecular profiling, deep sequencing and phenotypic genetic screenings.
Tasks 3.1 In coordination with other WPs (ie WP1, WP2 and W P5) we will proceed to the identification of new putative therapeutic targets based on the molecular profiling and deep sequencing. We will explore the feasibility of using individual targets vs whole pathway as targets, designing discriminatory experiments of validation.
Tasks 3.2 Identification of new targets by phenotypic genetic screenings. As in Task 3.1, from the total of causal alterations identified, we will explore the feasibility of using individual targets vs. whole pathway.
Tasks 3.3 In cell validation. Exploring the role of the target in the maintenance of tumoral phenotype or survival of lung tumor cells. Explore the effect of genetic inhibition of the target (ie. siRNA) in combination with current use antitumor drugs for lung cancer. If pertinent, analyze the effect of compound-driven inhibition of the target in lung cancer cells.
Tasks 3.4 In vivo validation. Exploring the role of inhibition of the target (genetical or compound-driven if possible) in xenograft. Relying in the tumor graft lines generated in WP1, test the role of the target inhibition by compounds in tumor growth. Also by using the genetically modified mouse models generated by partner JP.
Tasks 3.5 Ascribing the target to a subset of tumors. We will explore if the target is validated in all lung cancer subtypes (NSCLC-AdCvs SCC- or SCLC) or only in one of them by exploring different cell lines and xenograft models. W e will also explore if the targets show associated biomarkers for patient selection by exploring molecular profiling associated tothe target in a collaborative manner with WP4.
Deliverables: List of putative targets and pathways a) validated in cells, b) validated in human tumors and c) validated in vivo. Identifying the group of patients the new therapeutic strategy (specific target inhibition).
Task leader: Amancio Carnero. Lung and upper respiratory tract tumors program groups involved: M. Sanchez-Cespedes, L. Montuenga & J.C. Lacal.
The main goal of this W P is the evaluation of novel treatment strategies(targeted agents, gene therapy, immune-therapy, new combinations...) in late preclinical models and early clinical studies (phase I trials, pharmacokinetic and pharmacodynamic evaluations, biological target modulation studies) and changing treatment paradigm phase III trials. Therefore we will like to propose the following specific aims:
Tasks 4.1 Evaluation of new therapies in preclinical models. Apart from our ortothopic direct tumor explants, models will be generated in collaboration with WP1 and WP3, and specifically we'll try to validate the new therapies in genetically modified mouse models recapitulating human lung cancer events (J.M Paramio). Evaluation of targeted agents either chemical compounds or gene therapy based. Evaluation of immune therapy and cellular therapeutic strategies to strengthen the immune system against cancer with dendritic cell vaccination in combination with immunomodulatory agents. The partner group of F.Prosper / I. Melero's has developed technical strategies to preclinically approach this aspect. Evaluation of toxicity and efficacy of new combinations in late preclinical models.
Tasks 4.2 Evaluation of new strategies in early phase clinical trials. Implementing pharmacokinetic and pharmacodynamic evaluations as well as biological target modulation studies. These new studies will be implemented in parallel to efficacy studies in phases I-II. Biological endpoints in these studies will be attempted in order to characterize biomarkers predictive of outcome and understand the pharmacodynamic changes induced (gen profiling, signalling, etc). (A.Carnero, R.Rosell, M. Sánchez-Cespedes, M. Esteller).
Tasks 4.3 Changing treatment paradigm phase III trials. Design, conduction and development of phase III trials. A number of other clinical groups will synergize our efforts including (R. Rosell, EA, C. Camps, E. Diaz-Rubio, I. Melero, M. Sánchez-Cespedes) Our alliances with our clinical platforms (SLCG, CAIBER, EORTC, ETOP), Dutch and Italian Lung Cancer Groups may be of Prime importance.
Deliverables: Late Preclinical evaluation of novel therapies: Go or no go decision for phase I trials. Phase I trials with new molecules and new combinations: Recommended dose and schedule for future trials. Proof of concept phase II trials: Show efficacy on a disease context or subgroup of tumors. Changing paradigm phase III trials. Development and/or validation of Markers associated with phase I-III trials.
Task leader: L. Paz-Ares. Lung and upper respiratory tract tumors program groups involved: R. Rosell, C. Camps, J.M. Paramio, F. Prosper (I. Melero), J Albanell ( Arriola) & E. Diaz-Rubio.
The main goal of this work package is to find novel mechanisms of sensitivity/resistance to anticancer treatment, specifically in patients with advanced disease and in the adjuvant setting. Our objectives will focus on customizing chemotherapy in upfront treatment and overcoming resistance, both intrinsic and acquired (progressive disease), based on the molecular findings. This work package offers a unique opportunity to create different levels of synergism: a ) pre-clinical (lung cancer cell lines and mice xenografts/tumorgrafts models) and clinical expertise; b) the capacity to retrospectively but also prospectively analyze patient samples with very high quality associated clinical data; c) the capabilities to provide an exceptional contribution in the identification and validation of new molecular targets; d) the implementation of a successful program for the design, synthesis and validation of new anticancer drugs. Additionally, in this work package there are two reference laboratories for molecular assessment of biomarkers in exploratory and clinical trials in metastatic lung cancer, sponsored by the SLCG.
Tasks 5.1 Predictive markers and molecular mechanisms for sensitivity and resistance to conventional chemotherapy and targeted therapies in metastatic disease.
Tasks 5.2 Test the potential role/impact on patient outcome (resistance/sensitivity to therapy) of the different driver mutations identified and functionally characterized in this programme.
Tasks 5.3 Differential molecular and (epi)genetic profiling of the different histological types of metastatic lung carcinoma.
Tasks 5.4 Rebiopsy program: molecular and (epi)genetic profiling of acquired resistance (follow-up and relapse). Molecular and genetic analyses of clonal evolution.
Tasks 5.5 Quantification of Circulating Tumor Cells (CTC) in order to identify their role as prognostic and predictive factors.
Deliverables: Analysis of multiple biomarkers in patient samples at the laboratory level Genetic markers for individualized therapy in upfront treatment; Genetic markers for individualized therapy at the time of treatment failure/time of relapse; Genetic and molecular profiles of sensitivity/resistance to anticancer treatment (chemotherapy and targeted therapies);- Histological-based signatures; Drug development.
Task leader: R. Rosell. Lung and upper respiratory tract tumors program groups involved:, M. Sánchez-Cespedes, C. Camps, L. Paz-Ares, J.C. Lacal, C. Suarez, E. Diaz-Rubio & J Albanell (Arriola).
The overall goal of this W P is to address some of the many research questions still open in relation to CT-based screening of lung cancer. Three of the groups in our programme are focused on several important aspects related to screening. J.M. Borras will provide large experience in assessment of cancer screening. The group lead by J. Zulueta provides ample experience in lung cancer screening using LDCT, both clinically and from a research point of view. Members of this group have collaborated in this project since 2000, thus providing the needed experience to coordinate a research program on lung cancer screening within RTICC. During the last ten years other groups of the programme (L. Montuenga) have actively collaborated with J. Zulueta collecting biological samples from high risk individual enrolled in the program and tumor samples from screen-detected tumors. Biological profiling (phenotypic, genetic and epigenetic alterations) can be performed in the tumors resected within the trial, to determine whether their malignant molecular features are informative of their aggressiveness, prognosis and/or response to anti cancer drugs. Plasma samples from controls and lung cancer patients can also be used for the validation of biomarkers useful to select patients suitable for CT screening, reducing the cost of the screening program, or to discriminate which of the nodules found by imaging may lead to more aggressive tumors and would need more active follow up. W P5 of the Epidemiology programme will focus on a feasibility study of screening of lung cancer. In WP6 of the Lung cancer programme we will address other important objectives.
Tasks 6.1 New tools for risk stratification in the context of lung cancer screening. Analysis of emphysema and COPD. Validation of biomarkers that may select individuals who are at higher risk of developing lung cancer
Tasks 6.2 Molecular profiling of CT-detected nodules and biomarkers in screen positive individuals. In coordination with WP2, identification of new biomarkers that may help to distinguish those nodules with potentially higher aggressiveness. Analysis of prognostic markers in the blood of screen positive individuals.
Task leader: J. Zulueta. Lung and upper respiratory tract tumors program groups involved:, L. Montuenga & J.M. Borrás.