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By Richard Owen
It’s well known that pharma clinical trials are extremely expensive to run, typically costing over £10,000 per patient . A routine aspect is the collection of blood samples and analysis of the DNA, RNA and proteins within them. The information is used not only to measure the outcome of the trial, but to collect additional information on how the disease develops, and hopefully, to find new biomarkers that can monitor how the therapy interacts with, the disease processes.
Often methods used to prepare blood samples focus on harvesting one specific biological entity and consequently destroy other components. For example, current methods for collecting DNA will also destroy free proteins, other methods filter out and discard all cellular entities when harvesting cell-free DNA, or else they will discard all other biological components when isolating exosomes . This is wasteful as each blood sample could potentially contain extremely useful clinical information about the disease’s processes and the impact of the therapy, including genomic DNA and mRNA from leukocytes, circulating cell-free DNA, microRNA from exosomes, mRNA/genomic DNA from circulating tumour cells and proteins in plasma.
This is because usually preparation methods collect only one biological component from blood at a time. They are based on methods developed in the 1980’s using phenol and chloroform by Birnboim  and then improved upon in the 1990’s by Boom using silica and chaotropes . These were significant advances in their time but were focused on the rapid purification of a single entity from (most commonly) bacterial growth media with minimal interest in what other components were being destroyed by the process. Since then there has been little change and sample preparation is often seen as much less sexy than the many new and exciting technologies that can be used to analyse the resultant purified nucleic acids. However, sample preparation is critical to analysing nucleic acids and is absolutely key to the quality of the final result. Innovation in this area has the potential to be a real game changer.
When using the current destructive methods, to analyse the multiple components in blood you must take more samples from each patient or split each sample into separate sub samples. Patients don’t like giving blood and you can’t collect too great a volume at each blood draw as this depletes their oxygen-carrying capacity and ill oncology patients need their blood! Splitting each sample will not only limit the amount of nucleic acid that can be extracted but also adds significant statistical “noise” as samples begin to show increased variation once they are split into multiple containers, making the vital task of discovering statistical significance in the data much more difficult.
An innovative solution to this challenge would be to utilise microfluidic sample purification methods to harvest all the different components in a blood sample simultaneously without additional stress to the patient and without adding statistical noise. Such a multi-parameter separator would function in an analogous way to how oil is fractionated into many different usable outputs – each one is utilised, and the wastage is minimal. There are many different microfluidic approaches that could be used to achieve this such as standing surface acoustic waves (SAW), pinched flow fractionation, deterministic lateral displacement, optical force switching, inertial microfluidics etc. These technologies require serial and parallel linkage to achieve full utilisation of all the components and could result in 6 different populations of nucleic acid: genomic mRNA + DNA, circulating cell-free DNA, exosome microRNA, mRNA + DNA from circulating tumour cells and plasma proteins.
The potential benefits of these systems are significant as each sample could deliver so much more information for each clinical trial. This information could lead to a deeper understanding of the clinical mechanism of a new therapy being tested, provide additional proof of the clinical benefit and possibly discover new biomarkers that can be used to monitor the impact of a drug in much greater detail. Also, the method could decrease the problem caused in the analysis of both exosomes and CTCs of a large variety of different sample preparation methods, each of which generates slightly different results – this is seen as a key barrier to progress in both fields [5, 6]. When viewed as a cost per additional datapoint delivered and compared to the original cost of the trial, the proposed “fractionator” would deliver significant value. It would create more clinical data with increased statistical significance and also standardisation that could potentially enable the widespread investigation of new biological entities.
1 – Biopharmaceutical Industry-Sponsored Clinical trials Growing State Economics – April 2019
(The Pharmaceutical Research and Manufacturers of America) (https://www.phrma.org/Resources/State-Map/Clinical-Trials)
2 – Raymond et al. PLoS ONE 12(4): e0176241
3 – Birnboim et al. Nucleic Acids Research, 1979, 7: 6, 1513-1523
4 – Boom et al. J Clin Microbiol, 1990 Mar, 494-503
5 – Lane et al. Clin Transl Med. 2018 May 31;7(1):14
6 – van der Toom et al. Oncotarget. 2016 Sep 20;7(38):62754-62766
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