Functional genomic identification of predictive biomarkers of everolimus sensitivity and of new molecular targets in ren

Lead Research Organisation: Imperial Cancer Research Fund
Department Name: Cancer Research UK

Abstract

Everolimus is an effective new drug for the treatment of kidney cancer, however not all patients respond to everolimus and even those who respond develop resistance after 6-9 months of treatment. We will use a technique called ‘functional genomics‘ to de-activate each of the 21.000 human genes individually in kidney cancer cells grown in the laboratory, to identify genes that can lead to everolimus resistance. Resistance genes will be further studies to understand how resistance develops and how it can be prevented or treated. We will also analyse kidney cancer samples from patients treated with everolimus to determine whether the identified resistance genes are commonly altered in resistant cancers. This should lead to the development of a test that can determine whether a patient with kidney cancer is likely to respond to everolimus before treatment is actually started. Such a test would spare patients with resistant disease the side effects of the treatment and improve their quality of life. Everolimus is not approved for the use in the NHS because of the high costs. A test that allows targeting the drug to patients with sensitive disease would reduce overall costs and hopefully make it available to NHS patients.

Technical Summary

Background:

The mTOR (mammalian Target Of Rapamycin) inhibitor everolimus is active in renal cell carcinoma (RCC) but intrinsic and acquired drug resistance limits efficacy. Everolimus has direct cytostatic effects on RCC cells and anti-angiogenic activity through the suppression of hypoxia inducible factor 1 (HIF1 ) and its target VEGF in von-Hippel-Lindau (VHL)-gene deficient RCCs, and by inhibiting mTOR in endothelial cells. Mechanisms of everolimus resistance are poorly understood and there are no reliable predictive biomarkers of response.

Aims:

Whole genome siRNA screens will be applied to RCC cell lines to identify genes that mediate resistance to the cytostatic effect of everolimus, the hypoxic environment generated by its anti-angiogenic activity, and to the suppression of the HIF1 -VEGF pathway by mTOR inhibition. These results and their integration with transcriptomic and genomic profiles of pre- and post-treatment tumour samples from a clinical trial of everolimus in patients with RCC will identify:

1. Clinically relevant resistance mechanisms
2. Predictors of everolimus sensitivity and resistance
3. Therapeutic targets leading to synthetic lethality in VHL deficient RCC cell lines

Design and methodology:

A siRNA screen has already been performed in a VHL deficient RCC cell line and identified novel mediators of everolimus resistance and sensitivity. Further immunostaining of this screen for carbonic anhydrase IX as a marker for HIF1 activity will identify genes that contribute to in vivo resistance by rescuing HIF1 activity and -target gene expression in the presence of everolimus. A second siRNA screen will be performed to reveal how RCC cells can develop resistance to hypoxic conditions. Resistance mechanisms will be further characterized in vitro and by systems biology approaches. Screening results will be compared with mRNA expression, copy number variation and whole genome exon capture sequencing datasets obtained from pre- and post- treatment RCC tumour samples to identify which genes are relevant to resistance in patients. Candidate predictive biomarkers will be assessed in a validation cohort. Genes causing synthetic lethality in the VHL-null background when repressed will be identified in isogenic VHL-wt and VHL-null cell lines.

Scientific and clinical opportunities:
This approach should lead to the identification of a predictive biomarker of everolimus response in RCC. It should simultaneously define molecular mechanisms of resistance and potential targets to facilitate the development of new therapeutic strategies. These strategies could reduce the health economic burden associated with therapeutic resistance and improve outcomes in RCC by targeting treatment to patients with molecularly pre-defined drug sensitive disease.

Publications

10 25 50
 
Description CRUK BIDD Genomics Initiatics
Amount £100,000 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2011 
End 10/2012
 
Description European Research Council Consolidator Grant
Amount € 2,000,000 (EUR)
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 03/2019 
End 02/2024
 
Description Prostate Cancer UK Starter Grant
Amount £50,000 (GBP)
Funding ID PA12-15 
Organisation Prostate Cancer UK 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2012 
End 08/2013
 
Title Kidney cancer multi region exome sequencing dataset 
Description The first multi-region exome sequencing dataset from 10 clear cell renal cell carcinomas was generated through my MRC award and deposited in the EPG public archive. This dataset has been used by multiple researchers subsequently to investigate the impact of intratumour heterogeneity on disease biology and precision cancer medidine 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact Our publication in Nature Genetics 2014 and European Urology in 2014. In addition, the dataset has been used by multiple other groups and publications have arisen from this. It is also hosted on the cBIO cancer genomics portal at the Memorial Sloan Kettering Cancer Centre 
URL https://www.ebi.ac.uk/ega/studies/EGAS00001000667
 
Description Circulating Tumour DNA analysis in Prostate Cancer 
Organisation Queen Mary University of London
Department Barts Cancer Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution I designed the genetic tests which will be applied to patients specimens to trace genetic changes in prostate cancer in patients undergoing treatment. I also provided feasibility data from my renal cancer work.
Collaborator Contribution All partners are clinicians who will contribute to sample and data collection and pathology reporting.
Impact This project has started this year and first results are expected next year.
Start Year 2012
 
Description Intra-Tumour Heterogeneity in Prostate Cancer 
Organisation University College London Hospital
Department Department of Urology
Country United Kingdom 
Sector Academic/University 
PI Contribution We have designed the genetic analyses necessary to perform this research project and will do the sequencing and data analysis similar to our recent work in renal cancer.
Collaborator Contribution The urology team at UCL is responsible for samples collection and contributed significantly to the clinical questions we are trying to answer.
Impact Publication submitted
Start Year 2012
 
Description PREDICT Consortium 
Organisation Gustave-Roussy Institute
Department Gustave-Roussy Institute of Oncology
Country France 
Sector Multiple 
PI Contribution Our lab performs molecular analysis of tumour specimens and generates correlating functional in vitro data to identify mechanisms of drug resistance
Collaborator Contribution Provision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertise
Impact Detailed description of intratumour heterogeneity in kidney cancer The work had profound impact on precision cancer medicine as our description of intratumour heteroegenity and cancer evolution has wide implications on biomarker development and drug development. The work led to large clinical trials including the CRUK TRACERx trial (CI: Swanton)
Start Year 2011
 
Description PREDICT Consortium 
Organisation Netherlands Cancer Institute (NKI)
Country Netherlands 
Sector Academic/University 
PI Contribution Our lab performs molecular analysis of tumour specimens and generates correlating functional in vitro data to identify mechanisms of drug resistance
Collaborator Contribution Provision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertise
Impact Detailed description of intratumour heterogeneity in kidney cancer The work had profound impact on precision cancer medicine as our description of intratumour heteroegenity and cancer evolution has wide implications on biomarker development and drug development. The work led to large clinical trials including the CRUK TRACERx trial (CI: Swanton)
Start Year 2011
 
Description PREDICT Consortium 
Organisation Royal Marsden NHS Foundation Trust
Department Department of Medicine
Country United Kingdom 
Sector Hospitals 
PI Contribution Our lab performs molecular analysis of tumour specimens and generates correlating functional in vitro data to identify mechanisms of drug resistance
Collaborator Contribution Provision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertise
Impact Detailed description of intratumour heterogeneity in kidney cancer The work had profound impact on precision cancer medicine as our description of intratumour heteroegenity and cancer evolution has wide implications on biomarker development and drug development. The work led to large clinical trials including the CRUK TRACERx trial (CI: Swanton)
Start Year 2011
 
Description PREDICT Consortium 
Organisation St Bartholomew's Hospital
Department Medical Oncology Department St Barts
Country United Kingdom 
Sector Hospitals 
PI Contribution Our lab performs molecular analysis of tumour specimens and generates correlating functional in vitro data to identify mechanisms of drug resistance
Collaborator Contribution Provision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertiseProvision of clinical samples and expertise
Impact Detailed description of intratumour heterogeneity in kidney cancer The work had profound impact on precision cancer medicine as our description of intratumour heteroegenity and cancer evolution has wide implications on biomarker development and drug development. The work led to large clinical trials including the CRUK TRACERx trial (CI: Swanton)
Start Year 2011
 
Title Contribution to the development of the TRACERx lung cancer trial protocol 
Description The discovery and description of intra-tumour heterogeneity (Gerlinger et al, NEJM 2012) has led to teh development of the TRACERx lung cancer trial (PI Charles Swanton). I have contributed to the trial design development and the development of the genomic analysis strategy for trial specimens from the TRACERx trial which wil linvestigate the clonal evolution of lung cancer during treatment and intratumour heterogeneity and clonal structures of tumours as a novel potential biomarker 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2014
Development Status Under active development/distribution
Clinical Trial? Yes
Impact Tracerx trial multicentre opened in 2014 after receiving funding from CRUK and UCL and has generated several publications 
 
Description Lab Tours for CRUK fundraisers and donors 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Primary Audience Public/other audiences
Results and Impact Groups of 2-10 people visit our lab approximately every other month for a guided lab tour.

High interest in our work
Year(s) Of Engagement Activity 2010,2011