Publishable Summary - M48 - November 2016

Project context and objectives

Cervical cancer (CC) is the second most common malignancy in women worldwide. While epidemiologists at the recent IGCS meeting in Melbourne (November 2014) judged that Human Papilloma Virus (HPV) was eradicable if women were screened worldwide, the reality is that regular screening for all can presently not be reinforced in highly endemic areas (such as India, Africa and certain areas in South America) where 4/5th of the population at risk may not be aware of screening practices.


Although CC is a single diagnostic entity and infection of high-risk HPV is recognized as an important initiating event in tumourigenesis, CC exhibits differences in clinical behaviour. Stratification of CC into subclasses for progression and response to targeted treatment remains to be defined. At present, the dominant targets under scrutiny for innovative CC treatments are the following: EGFR/PI3K pathway, proliferation/DNA checkpoint and angiogenesis inhibition as well as anti-HPV vaccines. There have been recent publications (Ojesina, 2014; Wright, 2013) on high resolution genetic investigations in CC. So far, there has been no prospective assessment on patient outcome based on whole genome/exome sequencing or protein profiling of their tumours together with quality control evaluation of patient treatment. Early prospective data is available from a small phase 2 clinical trials by Institut Curie, the coordinators’ center, suggesting that EGFR inhibition at the membrane is ineffective in the presence of a downstream PI3K pathway activation (de la Rochefordière et al., 2015). 

 

▪ We are lacking prognostic and predictive biomarkers for CC treatment and there is a growing need for the development of biomarkers to follow up the course of the disease.

 

RAIDs is a multidisciplinary co-operation between academic clinical centers, SMEs and translational research platforms. It combines Next Generation Sequencing (NGS) and Reverse Phase Protein array (RPPA) in a large patient population prior to standard therapy. It includes:
▪ a cognitive cohort study (BioRAIDs) intended to define tumour stratification for targeted therapies,
▪ as well as precision medicine trials using an HPV directed vaccine in combination with checkpoint inhibition. 
In addition, high throughput screening techniques have been performed in CC cell lines, allowing to identify new drugs of relevance for advanced stage multi resistant CC. These molecules are to be validated in preclinical mouse models. Ongoing studies will assess in vitro efficacy of drug targeting according to molecular phenotypes.

 

The main objectives of RAIDs as stated in the DoW are:
▪ To identify prognostic and predictive biomarkers for standard and innovative therapies in cervical cancer patients using both high throughput genomic and proteomic approaches, the final aim being to improve treatment response for the individual patient;
▪ To define a set of stratification criteria for therapy in patients with cervical cancer based on the tumour’s molecular profile;
▪ To identify underlying mechanisms causing immune tolerance of this sexually transmitted viral disease in order to facilitate innovative clinical interventions by vaccination studies (together with micro-environment modulators and/or checkpoint inhibitors);
▪ To improve clinical outcome of patients with cervical cancer by conducting interventional precision medicine trials. 

      

    Work performed and main results achieved

    RAIDs started October 1st, 2012 and will end March 2017 following an 18 months extension’s approval from the European Commission. The consortium is composed of 9 research centers (Institut Curie, INSERM, KEM, IOV, TEO HEALTH, IMSP IO, IGR, NKI and HCTC), 2 universities (Erasmus and EMAUG) and 4 comapnies (AmBTU, Seqomics, Quanticsoft and Ayming) all from 7 European countries (France, Germany, the Netherlands, Serbia, Moldova, Romania and Hungary). 

     

    PROGRESS IN CLINICAL STUDIES

    A. BioRAIDs STUDY (Ngo et al., 2015 and Samuels et al., 2016a)
    Patient accrual was closed end of September 2016 with the inclusion of 419 patients. Half of all patients are from French centers; IOV - Serbia accrued 101 patients.

    The quality control for MRI imaging is ongoing at IOV in Serbia.

    Curation of the clinical data for the first 100 patients for whom exome sequencing was performed is finalized. Bioinformatics analyses are ongoing and will correlate tumour molecular profiles with clinical response.

     

    B. DNA VACCINE TRIAL
    The phase I DNA vaccine (HPV targeted therapy) trial sponsored by NKI in the Netherlands completed patient inclusions and immunological analysis finalized. The vaccine format is safe yet, only limited immune response is observed and no clinical response. A new phase I trial with a new more potent DNA vaccine is accepted by the competent authorities in The Netherlands. Patient inclusion is expected to start before the end of 2016.

     

    SCIENTIFIC WORK ACHIEVED

    • Sequencing on tumour samples is ongoing. The first 100 exome sequencing pairs of tumour and constitutive DNA samples are finalized. Exome sequencing on 20 cervical cell lines has been completed and analyzed. Major somatic alterations and DNA copy number alteration from exome sequencing profiles confirm PI3K pathway mutations to be a dominant feature in CC (in at least 1/3 of patients). Targeted sequencing is about to start for the remaining tumours. RAIDS and public datasets already allowed tumour stratification into 5 clusters. Two clusters regroup tumours with issues in DNA repair and mutations in genes involved in the mitochondrial respiratory chain. All cell lines are represented in these 2 clusters.
    • An efficient pipeline to isolate circulating (tumour) DNA from serum and plasma was developed at Erasmus Rotterdam together with methods for the detection of low-frequency mutations. The analyses of ct DNA from BioRAIDs patients is still ongoing.
    • RPPA analysis is finalized and first results are submitted to AACR at the time of reporting. Of particular interest, a biomarker profile for metabolic targeting could be detected. This will need confirmation in a separate population.
    • HPV integration sites and HPV viral gene detection in circulation are ongoing on HPV16 and HPV18 positive patients. We are awaiting statistical analysis for their impact on early detection of poorly responding/progressing tumours.
    • Pharmacological profiling of cell lines has already detected a group of drugs that synergize with the “standard treatment” of advanced cervical cancers. The validation of these data is ongoing and the reformulation/use of old drugs is continued to be investigated according to molecular profiles.
    • Preclinical mouse models for tumour micro-environmental studies have been developed and are published in journals with a high impact factor. Preclinical mouse data on combining vaccine and radiotherapy are published and report the efficacy of a novel dual targeting approach in a preclinically relevant animal model. A patent has been deposited.

     

    DISSEMINATION TO THE PUBLIC AND SCIENTIFIC COMMUNITIES
    Dissemination actions have led to a high visibility of the RAIDs project on a European and on an international level and to the wider understanding of the need and the opportunity for targeted approaches in the field of cervical cancer.

    Video clips explaining RAIDs have been produced (http://www.raids-fp7.eu/press/videos.html).

    A dropbox for patients (RAIDs drop box - http://www.raids-fp7.eu/a-question.html) allowing requests for information in the field of precision medicine has been inserted on the RAIDs website as well as in the cervical cancer factsheet of ESGO. The dropbox allows patients to ask questions in relation to standard treatment and to innovative protocols regarding precision medicine in their native language.

    Interaction with patients and patient advocacy groups is ongoing. A patients’ working group was organized at Institut Curie around precision medicine issues:
    http://curie.fr/actualites/echange-avec-patients-autour-projet-entreprise-2015-2020-007181
    https://www.facebook.com/InstitutCurie/

     

    Expected final results, potential impact and use

    RAIDs aims to define a set of stratification criteria based on molecular profiling. Its results will give insight into dominant genomic and protein signaling pathway alterations, enabling the identification of prognostic and predictive biomarkers for standard or targeted therapy in CC.

    The RAIDs consortium aims

    • to provide a safer and more efficient therapy for the individual patient;
    • to raise awareness in countries with lesser screening practices;
    • to improve the quality of life for women with cancer via:

      • a) the acquisition of defined molecular data for better treatment decisions,
      • b) targeted pilot trials directed at specific alterations as well as targeted vaccine trials directed against the HPV
      • c) the continuous evaluation of standards of care by comparing standards and outcome in all the RAIDs centers

    • to disseminate information on innovative practices in concertation with the help of other international structures, be the clinical trial orientated [EORTC (European Oranisation for Research and Treatment of Cancer) and ENGOT (European Network for Gyneacological Oncology Trials)] centers or international societies such as [ESGO (European Society for Gynaecological Oncology), ESMO (European Society for Medical Oncology) and IGCS (International Gynaecological Cancer Society)].

    • to provide information on predisposing conditions for immune rejection or tolerance of this virally transmitted disease rendering immune interventions more effective

    • to develop new tools and ideas on future treatments using drug combinations which may be exploited and create economic wealth.