Liquid biopsies for omics-based analysis in sentinel mussels

Abstract

Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transcriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in mussels to assess the quality of aquatic ecosystems.

Skin and Blood Microbial Signatures of Sedentary and Migratory Trout (Salmo trutta) of Kerguelen Islands

“…This study and our previous work in bivalves indicate that FTA® card-based sampling is perfectly adapted for establishing skin and blood (or hemolymphatic) 16S rRNA microbiome signatures. The efficacy of FTA® cards as a stable means to preserve DNA samples, even at room temperature, has been well documented [39]. Such a minimally invasive and ethical (nonlethal) sampling procedure is particularly well adapted for longterm monitoring programs in remote areas and for limiting the impact of large cohort studies on a given population inhabiting, for example, natural reserves, such as the Kerguelen Islands, for endangered species, or for storage and transport for fieldwork in areas where proper conditions for RNA preservation are challenging to achieve [75].…”

“…Blood was immediately withdrawn from the caudal vein using sterile nonheparinized syringes and spotted on Whatman 903™ Flinders Technology Associates filter paper (FTA® Cards) (Sigma-Aldrich, Oakville, ON, Canada). To avoid cross-contamination between samples, all samples were allowed to air dry and kept individually in a plastic bag with a desiccant, as previously described [39]. Mucus samples were collected using a sterile scalpel blade and scraping along the fish's lateral line and immediately spotted to cover an entire disc of the FTA cards.…”

Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems

“…Analysis of ccfDNA from LB does not require tissular biopsy and specialized and occasionally costly equipment and logistics associated with eDNA or tissular biopsies. In fact, we have recently reported that ccfDNA from LB can be stored and analyzed on FTA support, bypassing the need for maintaining a cold chain, a major issue for studies in remote regions [ 76 ]. Extraction of ccfDNA from liquid biopsies is also simple and provides high-quality DNA for shotgun sequencing and PCR analysis.…”

Species and population specific gene expression in blood transcriptomes of marine turtles

“…Using blood for transcriptomics analyses from minimally invasive non-lethal sampling can substantially expand the species and life stages from which transcriptomic data can be gathered, which is particularly important for protected species like marine turtles. Additionally, because ample high-quality RNA can be extracted from a very small volume of blood samples in reptiles [ 14 ], transcriptomic data from blood can be gathered from individuals repeatedly as part of long-term monitoring of their health and used to answer a host of ecological and evolutionary questions. However, we recognize there are limitations in using blood for transcriptomic studies, as tissue-specific expression is common [ 48 , 49 ].…”

“…Characterizing transcriptomes from blood samples is appealing because blood circulates through the whole body and perfuses most organs and other tissues. Its utility as a liquid biopsy has been developed in human and wildlife medicine [ 12 – 14 ]. While blood does not capture the full array of physiological functions within an organism’s tissues, blood transcriptomes have been shown to contain two thirds of orthologous genes present in liver samples (an organ with high functional gene expression diversity frequently used in transcriptomics studies) in six species of reptiles [ 15 ], and contain 61% of protein coding genes in the genome of a species of bat [ 16 ].…”