Can liquid biopsies transform precision medicine?

Brett Swansiger, Chief Commercial Officer at ANGLE, discusses the importance of liquid biopsies in precision medicine trials for cancer.  

Challenges in the oncology clinical trials space

The oncology market is a key growth driver for the pharma industry, with global drug revenues expected to reach US$390 billion by 2027 and the annual number of new cancer cases set to grow from 18 to 27 million by 20401,2. With oncology accounting for a third of pharma’s product pipeline, significant challenges include fierce competition, high research and development costs over, 10-15 years for clinical development, and pressures to rapidly meet the demand for new treatments2-4. Furthermore, oncology clinical trials are frequently challenged by low enrolment rates, failure to achieve primary endpoints, study design complexity and limited funding5. As such there is a need to develop fast and accurate methods to assess drug safety and efficacy, facilitating early success or failure. 

The identification of molecular drivers of cancer and the development of drugs to target these biomarkers, has led to an evolution in clinical trial design. This, coupled with a growing understanding of the heterogeneity of cancer as the basis for treatment resistance, tumour evolution and therefore the main source of therapeutic failure,6 has highlighted the importance of developing personalised therapy. This has facilitated a shift towards biomarker-based studies and data-driven selection of patients based on the likelihood of response to a therapy.7  

This evolution in clinical trial design is being influenced by the emergence of fast and cost-effective liquid biopsy technologies, that provide a wealth of longitudinal information on disease status and heterogeneity, tumour evolution over time, response to therapy, development of resistance mechanisms and disease relapse.  

Utility of liquid biopsies

A liquid biopsy is a minimally invasive test performed on a body fluid, usually blood, that allows for the isolation and analysis of circulating tumour cells (CTCs), circulating tumour DNA (ctDNA) exosomes, nucleic acids or proteins derived from a patient’s tumour, and provides valuable information for the management of patient care (Figure 1). Liquid biopsies have specific advantages over the current gold standard for tumour characterisation, tissue biopsies: not only are they less invasive and less costly, they provide results faster, are more suitable for longitudinal disease monitoring and less likely to cause harmful side effects.8 Moreover, tissue biopsies are not always feasible once the tumour has been excised or has metastasised to two or more sites, and can fail to capture tumour heterogeneity. The liquid biopsy market is an area of rapid growth, providing a real-time assessment of the evolving landscape of cancer.9   

Liquid biopsies are established as valuable tools in drug discovery and clinical development as well as in patient care management. More specifically, liquid biopsies are used as stratification tools to identify patients most likely to benefit from a targeted treatment,8 and as an early efficacy-response biomarker for treatment response evaluation in clinical development.8 The use of liquid biopsies for longitudinal monitoring allows for serial assessment of disease status and early signs of drug treatment failure.8A number of large consortiums have been founded to analyse, implement and develop standards for liquid biopsy in clinical trials and drug development, including Friends of Cancer research ctMONiTR, the International Liquid Biopsy Standardization Alliance (ILSA), and the Blood profiling Atlas in Cancer (BloodPAC) Consortium. 

Figure 1: Utility of liquid biopsies across the patient care pathway

Liquid biopsy analytes

CTCs are live cancer cells released by the tumour into the bloodstream that are responsible for metastatic seeding. CTCs reflect high levels of tumour heterogeneity, represent clonal evolution, and are suitable for treatment selection, real-time longitudinal disease monitoring and in vitro/in vivo culture. Although they are extremely rare (one CTC in one billion healthy cells), techniques are available to isolate CTCs from blood for immunocytochemical and/or molecular analysis. ctDNA is fragmented DNA released from dead or dying cancer cells, through the process of apoptosis or necrosis. ctDNA is the most established liquid biopsy analyte in the clinical setting for targeted treatment selection and is suitable for early cancer detection, tumour localisation, and disease monitoring. ctDNA carries fragments of genomic information, whereas CTCs carry whole sequences, facilitating not only genomic, but transcriptomic and proteomic analysis.6 Genomic (DNA) analysis provides information on past mutations acquired during the evolutionary history of the tumour, whereas transcriptomic (RNA) analysis provides accurate phenotypic information of the tumour at the time of sampling10, thus CTCs provide prospective information on the evolving tumour or metastasis. As such CTCs and ctDNA can provide complementary information.  

The importance of transcriptomic analysis was demonstrated in a review of real-world clinical data sets, in which RNA-sequencing discovered more clinically actionable targets than DNA alone, resulting in a 24% increase in the number of patients who were suitable for matched therapies.11 Furthermore, in a comparative study of metastatic breast cancer patients where CTC mRNA and ctDNA expression profiles were quantified, CTC mRNA had the largest number and highest diversity of overexpression signals12. Moreover, it has been reported that CTCs have shown higher degrees of heterogeneity and clonal selection as compared to ctDNA.13 For example, research into non-small cell lung cancer patients has found differences in – and in some cases higher prevalence – of clinically actionable targets in CTC analysis as compared to ctDNA, such as BRAF, KRAS, PIK3CA and EGFR.14,15 Thus, recent research has highlighted the importance of multi-parametric liquid biopsies that can harness transcriptomic information from CTCs in addition to genomic information gained from analysis of ctDNA. 

The dual analysis of CTCs and ctDNA is emerging for personalised treatment planning. A study of 84 melanoma patients, reported that the combined analysis of CTCs and ctDNA predicted relapse earlier than conventional imaging and was more accurate than the current blood-based biomarker in the melanoma staging system.16 In the same study, mutations were detected on CTCs and ctDNA that were not present in the primary tumour, providing real-time information on tumour mutational status, heterogeneity and clonal evolution.16 Similar results have been reported in lung and breast cancer research, suggesting that CTCs and ctDNA have a higher similarity to the metastatic tumour than the primary tumour, indicating that the two analytes can provide information on the heterogeneity of metastasis13 

Clinical trials undertaking dual assessment of CTCs and ctDNA are underway in a number of cancer types to assess; patterns in diagnosis17, to monitor biomarker response to treatment18,19, and to test if dual analysis is more sensitive than standard parameters and imaging for disease monitoring20. These are just a few exemplars of how liquid biopsy is increasingly being leveraged to provide insight into drug development.  

Molecular advances

Rapid evolution and uptake of molecular analysis techniques is transforming oncology diagnostics. Advances in digital polymerase chain reaction (PCR) are facilitating low cost, rapid analysis of known sequences, from limited starting material to provide clinically actionable information.9 Next generation sequencing (NGS) is fuelling a revolution in liquid biopsy analysis, providing genomic and transcriptomic characterisation for personalised therapy selection.21  

In a recent publication, Silvestri et al., (2021) utilised NGS technology to study copy number alterations in single CTCs before, during and after neoadjuvant chemotherapy, and reported that CTC analysis after treatment shared more genomic alterations with the residual tumour, as compared to the primary tumour. Moreover, these alterations were associated with proliferation and metastasis and revealed druggable pathways such as EGFR and Ras signalling. Thus, NGS-based liquid biopsy characterisation identified treatment-induced clonal selection informing targeted treatment selection.22 Ring et al., (2022) performed RNA-sequencing analysis on metastatic tumour biopsies and CTCs from breast cancer patients, to find that overall expression of clinically actionable genes was concordant between the two samples and that CTCs revealed a higher expression of immune oncology targets.23 This shows the potential of CTC molecular analysis as a real-time tool for personalised treatment planning.23  

Data analysed from the National Survey of Precision Medicine in Cancer Treatment reported that 75.6% of oncologists surveyed use NGS testing in the clinic to guide treatment decisions. Moreover, NGS testing is being used in three main clinical circumstances, including: (i) the determination of patient eligibility for clinical trials, (ii) for guiding advanced refractory disease treatment when first line treatments have failed, and (iii) for off-label use of FDA-approved drugs.24 These molecular techniques applied to liquid biopsies provide highly sensitive, rapid, and affordable longitudinal monitoring of patients in oncology drug trials and the clinic.  

Concluding remarks

Liquid biopsies are of growing importance for the management of cancer and in drug development. This sampling technique has multifaceted utility in the patient care pathway and is less invasive, less costly, and is better suited for real-time longitudinal monitoring compared to the current gold standard, tissue biopsy. Liquid biopsies can be implemented in clinical studies as a fast and accurate method for patient cohort stratification, as an early efficacy-response biomarker, for assessment of clonal evolution and the emergence of treatment resistance. CTCs are emerging as a key component of liquid biopsies that can provide additional transcriptomic insight into clinically relevant biomarkers for a more holistic view of disease status. Furthermore, molecular analysis of liquid biopsies is advancing to provide a rapid and increasingly cost-effective method to evaluate clinically actionable information. 

Bibliography  

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