Biomarkers in oncology can be used for early detection, more precise diagnosis, risk stratification, treatment selection, prediction of response, prognosis, and monitoring for recurrence.
Traditionally, tissue biopsies have been the source of genetic and epigenetic oncology biomarkers. The presence of a driver and/or actionable mutations can act as a prognostic factor or as a predictor of either response or non-response to therapy. Examples of biomarkers as predictors of response include HER2 expression and BRCA mutation in breast cancer, BRAF mutation in melanoma, EGFR mutations in non-small cell lung cancer (NSCLC), KRAS mutations in colorectal cancer, and the Philadelphia chromosomal translocation in chronic myelogenous leukemia.
It has recently become apparent that there is a significant amount of tumour spatial and temporal heterogeneity. Thus, a single biopsy is not necessarily representative of the whole tumour’s mutational burden raising concerns about basing a therapy on the sequencing data of a single biopsy. Moreover, most solid tumours have an intrinsic genetic instability and treatment courses can result in the selection of acquired resistance mutations. Since the acquired resistance mutation generally appears during the course of the therapy, it would not have been present at the initial biopsy. However, multiple sequential biopsies are not routinely undertaken due to their invasive nature. Consequently, there are limitations to the information one could gather from tumour biopsies.
There are several alternative sources of cancer biomarkers other than biopsies. These include serum, plasma, sputum, saliva, bronchoalveolar lavage (BAL), pleural effusion, volatile organic compounds (VOC), urine and cerebrospinal fluid. Of these, serum biomarkers are the most frequently used although sensitivity can be a concern.
A more recent approach aims to overcome the spatial and temporal heterogeneity limitations of biopsies as well the decreased sensitivity of serum biomarkers. Liquid biopsies encompass circulating tumour cells (CTCs), circulating tumour DNA (ctDNA/cfDNA), circulating miRNAs and exosomes. These are shed into the blood stream from the primary tumour and the metastases. Thus a non-invasive blood sample can provide information on prognostic and predictive biomarkers, as well as monitoring the cancer progression and the presence of acquired resistance mutations.
Synexa has a state-of-the-art facility for analysing liquid biopsies. Circulating tumour cells (CTCs) are captured using Parsortix technology that allows capture of all CTC subpopulations, including epithelial, mesenchymal, stem-cell-like and CTC clusters. By capturing CTCs based on their physical properties rather than their biological properties, we are not limiting ourselves to capturing epithelial cells but instead capture all CTCs that are likely to have important biological roles in drug resistance, self-renewal and seeding capabilities. Fluorescent microscopy provides information on the number of cells, which has been linked to prognosis, as well as the epithelial versus mesenchymal phenotype of the cells. We can also determine the presence of a particular antigen, such as a drug target, expressed on CTCs during the course of a clinical trial. Downstream applications include gene expression analysis of captured CTCs using the Nanostring pan-cancer panel of 770 genes or a customized panel of up to 800 genes. The Ion Torrent next-generation sequencing platform can identify the presence of up to 150 commonly occurring cancer mutations, whereas digital drop PCR can detect the presence of a particular mutation at a sensitivity of 0.02%.
Although there is a wide variation of cfDNA levels within a population due to the fact that healthy cells shed low levels of cfDNA, cancer patients have overall higher levels of cfDNA relative to healthy individuals and these levels vary according to tumour burden. cfDNA is a highly sensitive approach for monitoring patients’ progress and has been shown to detect tumour relapse up to 8 months prior to imaging in breast cancer. Moreover, the size of the cfDNA fragments has been correlated with how aggressive the tumour is. The benefits of cfDNA is the ease of isolation, whereas the drawback is that the analysis is limited to information derived from DNA. As with CTCs, next generation sequencing can identify commonly mutated cancer genes whilst digital drop PCR has the sensitivity to detect low levels of cfDNA mutations.
Putting a strong emphasis on oncology biomarkers allows the clinical trials to be set up in a manner that takes the science of the drug into consideration and enables the sponsors to gather significant and relevant data on the efficacy, mechanism of action and potential resistance mechanisms to the drug.