Impact of platelet activation on the release of cell-free mitochondria and circulating mitochondrial DNA

BACKGROUND

Research on circulating mitochondrial DNA (cir-mtDNA) based diagnostic is insufficient, as to its function, origin, structural features, and particularly its standardization of isolation. To date, plasma preparation performed in previous studies do not take into consideration the potential bias resulting from the release of mitochondria by activated platelets.

METHODS

To tackle this, we compared the mtDNA amount determined by a standard plasma preparation method or a method optimally avoiding platelet activation. MtDNA extracted from the plasma of seven healthy individuals was quantified by Q-PCR in the course of the process of both methods submitted to filtration, freezing or differential centrifugation.

RESULTS

98.7 to 99.4% of plasma mtDNA corresponded to extracellular mitochondria, either free or into large extracellular vesicles. Without platelet activation, the proportion of both types of entities remained preponderant (76-80%), but the amount of detected mtDNA decreased 67-fold.

CONCLUSION

We show the high capacity of platelets to release free mitochondria in "in vitro" conditions. This represents a potent confounding factor when extracting mtDNA for cir-mtDNA investigation. Platelet activation during pre-analytical conditions should therefore be avoided when studying cir-mtDNA. Our findings lead to a profound revision of the assumptions previously made by most works in this field. Overall, our data suggest the need to characterize or isolate mtDNA associated various structural forms, as well as to standardize plasma preparation, to better circumscribe cir-mtDNA's diagnostic capacity.

Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR

The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.

Blood transfusion and the presence of biological structures in the circulation

Advances in knowledge continue to be made regarding biological structures which may be present in blood circulation, such as circulating cell-free DNA, extracellular vesicles, neutrophil extracellular traps (NETs), and activated platelet-derived or circulating cell-free mitochondria. These circulating elements may be of systemic significance, in particular with respect to immunomodulation and cell-to-cell communication. This fact highlights the need to take into consideration the delivery to the host of various biological structures and by-products by means of blood- or blood products transfusion; and to investigate their potential side effects. The significance of these structures and their reported potential effects are discussed in this review. However, to date, no evidence of deleterious effect following blood or blood products transfusion was reported.

Decoherence of V[Formula: see text] spin defects in monoisotopic hexagonal boron nitride

Spin defects in hexagonal boron nitride (hBN) are promising quantum systems for the design of flexible two-dimensional quantum sensing platforms. Here we rely on hBN crystals isotopically enriched with either 10B or 11B to investigate the isotope-dependent properties of a spin defect featuring a broadband photoluminescence signal in the near infrared. By analyzing the hyperfine structure of the spin defect while changing the boron isotope, we first confirm that it corresponds to the negatively charged boron-vacancy center ([Formula: see text]). We then show that its spin coherence properties are slightly improved in 10B-enriched samples. This is supported by numerical simulations employing cluster correlation expansion methods, which reveal the importance of the hyperfine Fermi contact term for calculating the coherence time of point defects in hBN. Using cross-relaxation spectroscopy, we finally identify dark electron spin impurities as an additional source of decoherence. This work provides new insights into the properties of [Formula: see text] spin defects, which are valuable for the future development of hBN-based quantum sensing foils.

Association of neutrophil extracellular traps with the production of circulating DNA in patients with colorectal cancer

We postulate that a significant part of circulating DNA (cirDNA) originates in the degradation of neutrophil extracellular traps (NETs). In this study, we examined the plasma level of two markers of NETs (myeloperoxidase (MPO) and neutrophil elastase (NE)), as well as cirDNA levels in 219 patients with a metastatic colorectal cancer (mCRC), and in 114 healthy individuals (HI). We found that in patients with mCRC the content of these analytes was (i) highly correlated, and (ii) all statistically different (p < 0.0001) than in HI (N = 114). These three NETs markers may readily distinguish between patients with mCRC from HI, (0.88, 0.86, 0.84, and 0.95 AUC values for NE, MPO, cirDNA, and NE + MPO + cirDNA, respectively). Concomitant analysis of anti-phospholipid (anti-cardiolipin), NE, MPO, and cirDNA plasma concentrations in patients with mCRC might have value for thrombosis prevention, and suggested that NETosis may be a critical factor in the immunological response/phenomena linked to tumor progression.

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NETs markers correlate with cirDNA amounts in patients with mCRC not in healthy subjects

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Quantifying NETs markers and cirDNA could distinguish mCRC from healthy subjects

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Analysis of NETs markers, cirDNA, and aPL may have value for thrombosis prevention

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A strong fraction of cirDNA concentration could be derived from NETs in patients with mCRC

Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics

To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes, and chromatin of higher molecular size (>1000 bp) can be estimated as 67.5% to 80%, 9.4% to 11.5%, and 8.5% to 21.0%, respectively. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97%–98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between metastatic colorectal cancer patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content.

Machine Learning-Assisted Evaluation of Circulating DNA Quantitative Analysis for Cancer Screening

While the utility of circulating cell-free DNA (cfDNA) in cancer screening and early detection have recently been investigated by testing genetic and epigenetic alterations, here, an original approach by examining cfDNA quantitative and structural features is developed. First, the potential of cfDNA quantitative and structural parameters is independently demonstrated in cell culture, murine, and human plasma models. Subsequently, these variables are evaluated in a large retrospective cohort of 289 healthy individuals and 983 patients with various cancer types; after age resampling, this evaluation is done independently and the variables are combined using a machine learning approach. Implementation of a decision tree prediction model for the detection and classification of healthy and cancer patients shows unprecedented performance for 0, I, and II colorectal cancer stages (specificity, 0.89 and sensitivity, 0.72). Consequently, the methodological proof of concept of using both quantitative and structural biomarkers, and classification with a machine learning method are highlighted, as an efficient strategy for cancer screening. It is foreseen that the classification rate may even be improved by the addition of such biomarkers to fragmentomics, methylation, or the detection of genetic alterations. The optimization of such a multianalyte strategy with this machine learning method is therefore warranted.

Recent advances in circulating nucleic acids in oncology

Circulating cell-free DNA (cfDNA) is one of the fastest growing and most exciting areas in oncology in recent years. Its potential clinical uses cover now each phase of cancer patient management care (predictive information, detection of the minimal residual disease, early detection of resistance, treatment monitoring, recurrence surveillance, and cancer early detection/screening). This review relates the recent advances in the application of circulating DNA or RNA in oncology building on unpublished or initial findings/work presented at the 10th international symposium on circulating nucleic acids in plasma and serum held in Montpellier from the 20th to the 22nd of September 2017. This year, presenters revealed their latest data and crucial observations notably in relation to (i) the circulating cell-free (cfDNA) structure and implications regarding their optimal detection; (ii) their role in the metastatic or immunological processes; (iii) evaluation of miRNA panels for cancer patient follow up; (iv) the detection of the minimal residual disease; (v) the evaluation of a screening tests for cancer using cfDNA analysis; and (vi) elements of preanalytical guidelines. This work reviews the recent progresses in the field brought to light in the meeting, as well as in the most important reports from the literature, past and present. It proposes a broader picture of the basic research and its potential, and of the implementation and current challenges in the use of circulating nucleic acids in oncology.

Blood contains circulating cell-free respiratory competent mitochondria

Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases.

Towards a screening test for cancer by circulating DNA analysis

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Background: Following works on the clinical potentials of circulating DNA (cfDNA), our group is now particularly focused on evaluating its potential for early detection of cancer. We recently developed a test (MNR: Multi Normalized Ratio), based on various cfDNA parameters determined by a specific q-PCR based method, targeting both nuclear and mitochondrial sequences. When applied to the supernatant of cell culture, the MNR had a discriminative potential of 100% between normal and cancer cell lines. Methods: We recently developed a screening test (MNR: Multi Normalized Ratio), based on various cfDNA parameters determined by a specific q-PCR based method, targeting both nuclear and mitochondrial sequences. When applied to the supernatant of cell culture, the MNR had a discriminative potential of 100% between normal and cancer cell lines. Results: We are currently carrying out an extensive evaluation of this test in plasma samples from diagnosed and healthy individuals. Preliminary results on the plasma of 289 healthy subjects and 1,200 patients with various types of cancer (colorectal, breast, lung, liver, pancreatic, ovarian) of all stages, revealed a high potential with an AUC of 0.82 (0.78-0.84, 95% confidence interval, CI) and 70% sens. with 78% spe.. In breast cancer (N = 169), an AUC of 0.82 (0.78-0.86, 95% CI) with 72% sens. and 80% spe. were observed. In all stages CRC patients (N = 887), the results showed an AUC of 0.81 (0.78-0.84, 95%, CI) and 68% sens. with 80% spe.; for CRC stages 0/I/II (N = 249), an AUC of 0.75 (0.71-0.80, 95% CI) and 60% sens. with 79% spe.; and for CRC stage IV (N = 101), a 0.86 AUC (0.82-0.91, 95% CI) with 81% sens. and 78% spe.. When combining the MNR test to a threshold value of the total concentration of cfDNA (AUC = 0.82 (0.79-0.84, 95% CI), 70% sens. and 80% spe. in all stage cancers (N = 1078)), in CRC stages 0/I/II (N = 249) vs Healthy Individuals (N = 289), we observed a 63% sens. with 84% spe. Conclusions: Furthermore we recently discovered that cfDNA fragmentation, as determined by Whole Genome Sequencing using either double or single strand library, is also a parameter enabling discrimination between healthy and cancer individuals. Data on a multi-parametric test combining total cfDNA quantification, MNR and fragmentation biomarkers with help of a ongoing decision tree algorithm in machine learning will be presented during the meeting. Our on-going data suggest that our strategy in targeting cfDNA quantitative/structural features might be powerful for cancer screening/early detection and appears as an alternative or a synergistic combination to searching mutations.

La biopsie liquide

La biopsie liquide est apparue comme une voie prometteuse pour le dépistage du cancer. En effet, plusieurs biomarqueurs comme les ADN circulants, les cellules tumorales circulantes, les micro-ARN circulants etc. se sont révélés prometteurs pour le théragnostic ou le suivi du patient. La détection précoce peut aider à réduire la mortalité associée au cancer et augmenter la survie globale des patients. La plupart des types de cancer manquent de biomarqueurs spécifiques et le développement de techniques de dépistage efficaces appliquées en clinique a été limité malgré des efforts intenses dans ce domaine. La nature non invasive de la biopsie liquide lui donne un avantage vis-à-vis d’autres méthodes, notamment pour le développement de tests de dépistage du cancer. Les différentes études fondées sur l’analyse de la biopsie liquide dans le but de développer des tests de dépistage et de détection précoce du cancer sont présentées dans cette revue. Bien qu’actuellement aucun test développé à partir de la biopsie liquide s’avère à la fois assez spécifique et sensible pour être utilisé comme test universel de dépistage, le potentiel de cette nouvelle approche apparaît de plus en plus crédible, eu égard aux récents développements de méthodes sophistiquées, notamment multiparamétriques.