Metabolomic Fingerprints in Large Population Cohorts : Impact of Preanalytical Heterogeneity

Non peer reviewe

Impact of the pre-examination phase on multicenter metabolomic studies

The development of metabolomics in clinical applications has been limited by the lack of validation in large multicenter studies. Large population cohorts and their biobanks are a valuable resource for acquiring insights into molecular disease mechanisms. Nevertheless, most of their collections are not tailored for metabolomics and have been created without specific attention to the pre-analytical requirements for high-quality metabolome assessment. Thus, comparing samples obtained by different pre-analytical procedures remains a major challenge. Here, H-1 NMR-based analyses are used to demonstrate how human serum and plasma samples collected with different operating procedures within several large European cohort studies from the Biobanking and Biomolecular Resources Infrastructure - Large Prospective Cohorts (BBMRI-LPC) consortium can be easily revealed by supervised multivariate statistical analyses at the initial stages of the process, to avoid biases in the downstream analysis. The inter-biobank differences are discussed in terms of deviations from the validated CEN/TS 16945:2016 / ISO 23118:2021 norms. It clearly emerges that biobanks must adhere to the evidence-based guidelines in order to support wider-scale application of metabolomics in biomedicine, and that NMR spectroscopy is informative in comparing the quality of different sample sources in multi cohort/center studies.Peer reviewe

Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter-and intra-assay as well as intra-and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity

Steatosis and gut microbiota dysbiosis induced by high-fat diet are reversed by 1-week chow diet administration

Many studies have recently shown that diet and its impact on gut microbiota are closelyrelated to obesity and metabolic diseases including nonalcoholic fatty liver disease. Gutmicrobiota may be an important intermediate link, causing gastrointestinal and metabolicdiseases under the influence of changes in diet and genetic predisposition. The aim of thisstudy was to assess the reversibility of liver phenotype in parallel with exploring theresilience of the mice gut microbiota by switching high-fat diet (HFD) to chow diet (CD). Micewere fed an HF for 8 weeks. A part of the mice was euthanized, whereas the rest were thenfed a CD. These mice were euthanized after 3 and 7 days of feeding with CD, respectively.Gut microbiota composition, serum parameters, and liver morphology were assessed. Eightweeks of HFD treatment induced marked liver steatosis in mice with a perturbedmicrobiome. Interestingly, only 7 days of CD was enough to recover the liver to a normalstatus, whereas the microbiome was accordingly reshaped to a close to initial pattern. Theabundance of some of the bacteria includingPrevotella,Parabacteroides,Lactobacillus, andAllobaculumwas reversible upon diet change from HFD to CD. This suggests thatmicrobiome modifications contribute to the metabolic effects of HFD feeding and thatrestoration of a normal microbiota may lead to improvement of the liver phenotype. Inconclusion, we found that steatosis and gut microbiota dysbiosis induced by 8 weeks ofhigh-fat diet can be reversed by 1 week of chow diet administration, and we identified gutbacteria associated with the metabolic phenotyp

The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit?

Recently, CEN/TS 17626:2021, the European pre-analytical standard for human specimens intended for microbiome DNA analysis, was published. Although this standard relates to diagnostic procedures for microbiome analysis and is relevant for in vitro diagnostic (IVD) manufacturers and diagnostic laboratories, it also has implications for research and development (R&D). We present here why standards are needed in biomedical research, what pre-analytical standards can accomplish, and which elements of the pre-analytical workflow they cover. The benefits of standardization for the generation of FAIR (findable, accessible, interoperable, reusable) data and to support innovation are briefly discussed