Title: Translational proteomics to understand and overcome drug resistance to targeted anticancer drugs in KRAS and PIK3CA driven cancers
Funder: Department of Health and Social Care

Abstract: Translational proteomics to understand and overcome drug resistance to targeted anticancer drugs in KRAS and PIK3CA driven cancersBackground Cancer results in over 160,000 deaths per year and accounts for more than 25% of all deaths in the UK. Recent advances in molecularly targeted agents, in large part kinase inhibitors, have resulted in significant benefit in defined clinical contexts; however, large areas of unmet medical need remain. There are no targeted anticancer drugs used specifically in common cancers with known oncogenic mutations; for example, non-small-cell lung cancer (NSCLC), colorectal cancer (CRC), pancreatic ductal adenocarcinoma (PDAC) and breast cancers which harbour KRAS or PIK3CA mutations and these cancers have de-novo resistance to many targeted drugs. In addition, cancers that do respond eventually develop resistance, a phenomenon called acquired resistance. It is becoming evident that there is a varied clinical response when targeted anticancer agents are used to treat tumours driven by common oncogenes, depending on the tissue of origin of the cancer. Thus, understanding drug resistance and finding strategies to overcome this is an area of urgent unmet need. Overall objectivesTo use primary tumour samples derived from patients, combined with the application of emerging technology, to understand the mechanisms of drug resistance caused by re-wiring of signalling and dynamic changes in protein levels within cancer cells. This information will be used to guide rational combinations strategies of targeted anticancer drugs.To understand the contribution of tissue context in drug resistance to targeted anticancer drugs, which is critical in the development of anticancer drugs and in the design of future clinical trials. Methods The project will optimize existing tissue digestion protocols to extract cancer cells from tumours. Barcoded antibody technology on the NanoString platform has recently been commercialised and the project will use the technology to develop an assay allowing the measurement of 100 phosphoprotein/proteins exposed to 25 drugs from a single biopsy or surgical specimen. The information related to quantifying re-wiring of signalling within cancer cells will be analysed as part of existing collaborations with bioinformaticians at The Institute of Cancer Research to understand mechanisms of resistance and propose rational combinations of anticancer drugs to overcome this resistance. Differences in rewiring of KRAS mutant CRC, PDAC and NSCLC cells and PIK3CA mutant breast, NSCLC and CRC cells when exposed to a range of 25 targeted anticancer agents will be studied and any correlation to differences in sensitivity to targeted anticancer drugs will be established. KRAS mutant CRC, PDAC and NSCLC will be co-cultured with and without cancer associated fibroblasts to study the influence of stroma on re-wiring of signal transduction in response to anticancer drugs. Information from these experiments will be used to design clinical trials of rational combinations of anticancer drugs in specific tumour types.Impact on patients and the NHS This proposal will lead to improved understanding of the mechanisms of resistance of common KRAS-driven cancers. Importantly, the work will help devise rational combination therapies that can be tested in hypothesis-testing clinical trials within a period of 3 - 5 years. The information related to context specificity of drug resistance in different tumour types e.g. NSCLC, PDAC and CRC will further help to tailor clinical trials of combinations in these tumour types. The outcomes of these clinical trials conducted within the Experimental Cancer Medicine Centre (ECMC) at The Institute of Cancer Research and The Royal Marsden, and The National Institute of Health Research (NIHR) will improve the outcomes of patients with common mutant KRAS- and PIK3CA-driven cancers, which are areas of high unmet need.

Lay abstract: Translational proteomics to understand and overcome drug resistance to targeted anticancer drugs in KRAS and PIK3CA driven cancersIntroduction Anticancer drug development in the last two decades has focused on making drugs that either target specific proteins within a tumour or increase the efficiency of the immune system to attack tumours. Drugs targeting specific proteins in cancer cells are collectively called targeted anticancer drugs. These targeted anticancer drugs have had some success in treating patients with cancer. There are, however, limitations to the use of these targeted agents for the treatment of cancers. Firstly, there are some cancers which have genetic abnormalities that don't have drugs targeting them; examples of these mutated or abnormal genes are KRAS and PIK3CA. These cancers don't respond to currently licensed targeted anticancer drugs when they are treated with these drugs for the first time. This is called innate resistance. Secondly, in cancers where targeted drugs do work, the cancer starts to re-grow within 1-2 years and this is called acquired drug resistance. Thirdly, in some instances drugs will work in a one cancer with an abnormal gene but not another. For example, drugs called BRAF inhibitors shrink skin cancers with an abnormal BRAF gene but not a colon or bowel cancer with the same abnormal gene. This is called context specificity of drug resistance. Abnormal genes like KRAS and PIK3CA are present in a variety of common cancers like lung, bowel, pancreatic and breast cancers and finding new treatment strategies for these cancers is an area of unmet need.Overall objectives 1) To use cancer cells derived from patients undergoing surgery or a biopsy and study changes that occur within the cancer cells when they are exposed to anticancer drugs in a laboratory. This information will then be studied and analyzed by computer programmes which will suggest combinations of drugs that can be used together to prevent or overcome drug resistance. 2) To study context specificity of drug resistance. Lung, bowel and pancreatic cancer cells with the same abnormal KRAS gene will be exposed to different anticancer drugs in a laboratory and differences in the way proteins change inside these cells will be studied. These changes in proteins within cancer cells will explain why some cancers like lung cancer, colon cancer and pancreatic cancers respond differently to the same anticancer drug even though they have the same abnormal gene in all of them. The effect of non-cancer cells within these organs like lung, bowel and pancreas on this resistance will also be studied. In addition to cancers with the abnormal KRAS gene, cancers with the abnormal PIK3CA gene will also be studied.Methods Changes of proteins within a cancer cell when it is exposed to anticancer cells will be studied using new technology which attaches barcodes to different proteins. The barcode is then read in a machine to tell a computer how much protein is present in the cell in the same way as a barcode reader in a supermarket till tells a computer how many items have been scanned. The tumours will also be tested for abnormalities of a group of genes other than KRAS and PIK3CA which may influence resistance to anticancer drugs. The combined information will be fed into computer programmes to suggest combinations that will be effective to treat cancer. Impact This project will help to understand why cancers with the abnormal KRAS or PIK3CA genes are resistant to anticancer drugs. The project will help to select combinations of anticancer drugs that are most likely to work in cancers with these abnormal genes. The results from these studies will be used to design clinical trials of combinations of anticancer drugs which will be run across multiple NHS hospitals across the country. Patient and public involvement This project has been reviewed by patients and The Patient and Carer Research Review Panel at the Institute of Cancer Research and The Royal Marsden. Further, the panel will review clinical trial protocols and information sheets given out to patients in clinical trials that result from this work.Dissemination of results All patient data is strictly anonymized. The early results of these trials are presented at national and international conferences. Once completed, the results will be published in institutional websites and free for access scientific journals. Results from conferences and publications are also disseminated using social media outlets, such as Twitter.

Research activity codes: 6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS