Caractérisation du microDNome et sa modulation par le traitement anti-cancer

Récemment, une nouvelle classe d'ADN circulaire extrachromosomique (eccDNA) appelée microADN a été identifiée dans des tissus humains et murins. Ces microADNs ont une longueur de 100 à 400 pb, sont dérivés de régions génomiques non répétitives uniques et présentent un enrichissement au niveau des régions géniques et riches en GC. Bien qu'il ait été proposé qu'ils puissent provenir du métabolisme de l'ARN ou des défauts de réplication, leurs mécanismes de production et leur éventuelle fonctionnalité restent à déterminer. Grâce à l'analyse des microADNs extraits d'une série de 10 lignées cellulaires lymphoblastoïdes humaines (LCL), nous avons confirmé la distribution nonaléatoire des microADNs vers les régions actives du génome. Les microADNs identifiés présentaient des loci d'origine redondants et une périodicité de taille de 190 pb pouvant correspondre à la fragmentation de l'ADN lors de l'apoptose caspase-dépendante. L'apoptose induite de ces LCLs par des drogues chimiothérapeutiques (méthotrexate ou L-asparaginase) a entrainé la modulation de la diversité et de la taille des microADNs, suggérant qu'une partie de ces entités pourrait être des produits résiduels de la mort cellulaire apoptotique. Ainsi, bien que compatible avec l'observation initiale suggérant que les microADNs proviennent d'un processus physiologique normal, ces résultats impliquent une source de production alternative ou complémentaire.Recently, a new class of extrachromosomal circular DNA (eccDNA) called microDNA was identified in mouse and human tissues. These microDNAs are 100 to 400 bp long, derive from unique nonrepetitive genomic regions and show an enrichment in GC rich and genic sequences. While it has been proposed that they could arise from RNA metabolism or replication defects, their production mechanisms and eventual functionality remain unclear. Through the analysis of microDNAs extracted from a series of 10 human lymphoblastoid cell lines (LCLs), we confirmed the non-random distribution of microDNA towards active regions of the genome. Identified microDNAs showed redundant loci of origin and a size periodicity of 190 bp that matched caspase-dependant DNA fragmentation of apoptotic cells. Strikingly, the chemotherapeutic drug-induced apoptosis (using methotrexate or Lasparaginase) of these LCLs modulated both diversity and size of microDNAs further suggesting that a part of microDNAs could represent circularized by-products of the programmed cell death. Thus, while compatible with the original observation that microDNAs originated from a normal physiological process, these results imply an alternative or complementary source of production

Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results

Metabolite genome-wide association studies (mGWAS) have advanced our understanding of the genetic control of metabolite levels. However, interpreting these associations remains challenging due to a lack of tools to annotate gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we introduce the shortest reactional distance (SRD) metric, drawing from the comprehensive KEGG database, to enhance the biological interpretation of mGWAS results. We applied this approach to three independent mGWAS, including a case study on sickle cell disease patients. Our analysis reveals an enrichment of small SRD values in reported mGWAS pairs, with SRD values significantly correlating with mGWAS p values, even beyond the standard conservative thresholds. We demonstrate the utility of SRD annotation in identifying potential false negatives and inaccuracies within current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs, suitable to integrate statistical evidence to biological networks

Ancient Human Parasites in Ethnic Chinese Populations

Whilst archaeological evidence for many aspects of life in ancient China is well studied, there has been much less interest in ancient infectious diseases, such as intestinal parasites in past Chinese populations. Here, we bring together evidence from mummies, ancient latrines, and pelvic soil from burials, dating from the Neolithic Period to the Qing Dynasty, in order to better understand the health of the past inhabitants of China and the diseases endemic in the region. Seven species of intestinal parasite have been identified, namely roundworm, whipworm, Chinese liver fluke, oriental schistosome, pinworm, Taenia sp. tapeworm, and the intestinal fluke Fasciolopsis buski. It was found that in the past, roundworm, whipworm, and Chinese liver fluke appear to have been much more common than the other species. While roundworm and whipworm remained common into the late 20th century, Chinese liver fluke seems to have undergone a marked decline in its prevalence over time. The iconic transport route known as the Silk Road has been shown to have acted as a vector for the transmission of ancient diseases, highlighted by the discovery of Chinese liver fluke in a 2,000 year-old relay station in northwest China, 1,500 km outside its endemic range

Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines

Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified.They are on average 100 to 400 bp long and are derived from unique non-repetitive genomicregions with high gene density. MicroDNAs are thought to arise from DNA breaks associatedwith RNA metabolism or replication slippage. Given the paucity of information on thisentirely novel phenomenon, we aimed to get an additional insight into microDNA features byperforming the microDNA analysis in 20 independent human lymphoblastoid cell lines(LCLs) prior and after treatment with chemotherapeutic drugs. The results showed non-randomgenesis of microDNA clusters from the active regions of the genome. The size periodicityof 190 bp was observed, which matches DNA fragmentation typical for apoptotic cells.The chemotherapeutic drug-induced apoptosis of LCLs increased both number and size ofclusters further suggesting that part of microDNAs could result from the programmed celldeath. Interestingly, proportion of identified microDNA sequences has common loci of originwhen compared between cell line experiments. While compatible with the original observationthat microDNAs originate from a normal physiological process, obtained results implycomplementary source of its production. Furthermore, non-random genesis of microDNAsdepicted by redundancy between samples makes these entities possible candidates fornew biomarker generation. [...

Differential modulation of polyunsaturated fatty acids in patients with myocardial infarction treated with ticagrelor or clopidogrel

Untargeted metabolomics is used to refine the development of biomarkers for the diagnosis of cardiovascu-lar disease. Myocardial infarction (MI) has major individual and societal consequences for patients, whoremain at high risk of secondary events, despite advances in pharmacological therapy. To monitor their dif-ferential response to treatment, we performed untargeted plasma metabolomics on 175 patients from theplatelet inhibition and patient outcomes (PLATO) trial treated with ticagrelor and clopidogrel, two commonP2Y12inhibitors. We identified a signature that discriminates patients, which involves polyunsaturated fattyacids (PUFAs) and particularly the omega-3 fatty acids docosahexaenoate and eicosapentaenoate. Theknown cardiovascular benefits of PUFAs could contribute to the efficacy of ticagrelor. Our work, beyondpointing out the high relevance of untargeted metabolomics in evaluating response to treatment, establishesPUFA metabolism as a pathway of clinical interest in the recovery path from MI

Some microDNAs are shared between and within drug groups.

<p>Number of genes where from microDNA derived shared between drug groups (Sensitive: S; Resistant: R; Treated: T; Non-Treated: NT) (<b>A</b>) Observed numbers per drug <b>Top</b>: MTX <b>Bottom</b>: ASP (<b>B</b>) Observed <i>vs</i>. expected numbers of microDNA-derived genes per group. Expected numbers were computed by generating 1000 random new microDNAs with lengths corresponding to those we identified. <b>Top</b>: MTX <b>Bottom</b>: ASP. p<0.01 (estimated by chi-square) for the difference between observed and expected numbers in all cases except MTX R_NT group.</p

MicroDNA length and periodicity.

<p>Size distribution in base pairs (bp) of all identified microDNAs (<b>A</b>) regardless of drug used for treatment. Vertical lines depict the 190 bp periodicity. (<b>B</b>) per drug (ASP: Asparaginase, MTX: Methotrexate) and per sensitivity status (resistant: R, sensitive: S, treated: T, non-treated: NT).</p

Percentage of shared entities between samples.

<p><b>Left</b>: Gene intersects, microDNA derivied for the same gene, shared between ≥ 2 samples. <b>Right</b>: Cluster intersects, microDNA derived from the same genomic position shared between ≥ 2 samples with > = 1 bp overlap. The number/total and (%) of intersects per drug group are indicated. Difference between groups was assessed using a two-tailed Chi-square test.</p

MicroDNA are significantly enriched in coding and active genomic regions.

<p>Fold enrichment is calculated as the ratio of the observed by expected number. Expected numbers were computed by generating 1000 random new positions with lengths corresponding to those of identified microDNAs and outputting the median. The dotted line shows a hypothetical situation where expected number would be equal to the observed number. <b>Top</b>: Methotrexate (MTX). <b>Bottom</b>: Asparaginase (ASP). Statistical significance was assessed using Fisher's Exact test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184365#pone.0184365.s009" target="_blank">S3 Table</a>).</p