Global gene expression profiling in human lung cells exposed to cobalt.

International audienceBACKGROUND: It has been estimated that more than 1 million workers in the United States are exposed to cobalt. Occupational exposure to 59 Co occurs mainly via inhalation and leads to various lung diseases. Cobalt is classified by the IARC as a possible human carcinogen (group 2B). Although there is evidence for in vivo and in vitro toxicity, the mechanisms of cobalt-induced lung toxicity are not fully known. The purpose of this work was to identify potential signatures of acute cobalt exposure using a toxicogenomic approach. Data analysis focused on some cellular processes and protein targets that are thought to be relevant for carcinogenesis, transport and biomarker research. RESULTS: A time course transcriptome analysis was performed on A549 human pulmonary cells, leading to the identification of 85 genes which are repressed or induced in response to soluble 59 Co. A group of 29 of these genes, representing the main biological functions, was assessed by quantitative RT-PCR. The expression profiles of six of them were then tested by quantitative RT-PCR in a time-dependent manner and three modulations were confirmed by Western blotting. The 85 modulated genes include potential cobalt carriers (FBXL2, ZNT1, SLC12A5), tumor suppressors or transcription factors (MAZ, DLG1, MYC, AXL) and genes linked to the stress response (UBC, HSPCB, BNIP3L). We also identified nine genes coding for secreted proteins as candidates for biomarker research. Of those, TIMP2 was found to be down-regulated and this modulation was confirmed, in a dose-dependent manner, at protein level in the supernatant of exposed cells. CONCLUSION: Most of these genes have never been described as related to cobalt stress and provide original hypotheses for further study of the effects of this metal ion on human lung epithelial cells. A putative biomarker of cobalt toxicity was identified

Development of qPCR assays targeting biothreat agents

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Recombinase Polymerase Amplification combines with Lateral Flow Strip for detection of Biothreats agents

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Functional characterization of sonic hedgehog mutations associated with holoprosencephaly.

Mutations of the developmental gene Sonic hedgehog (SHH) and alterations of SHH signaling have been associated with holoprosencephaly (HPE), a rare disorder characterized by a large spectrum of brain and craniofacial anomalies. Based on the crystal structure of mouse N-terminal and Drosophila C-terminal hedgehog proteins, we have developed three-dimensional models of the corresponding human proteins (SHH-N, SHH-C) that have allowed us to identify within these two domains crucial regions associated with HPE missense mutations. We have further characterized the functional consequences linked to 11 of these mutations. In transfected HEK293 cells, the production of the active SHH-N fragment was dramatically impaired for eight mutants (W117R, W117G, H140P, T150R, C183F, L271P, I354T, A383T). The supernatants from these cell cultures showed no significant SHH-signaling activity in a reporter cell-based assay. Two mutants (G31R, D222N) were associated with a lower production of SHH-N and signaling activity. Finally, one mutant harboring the A226T mutation displays an activity comparable with the wild-type protein. This work demonstrates that most of the HPE-associated SHH mutations analyzed have a deleterious effect on the availability of SHH-N and its biological activity. However, because of the lack of correlation between genotype and phenotype for SHH-associated mutations, our study suggests that other factors intervene in the development of the spectrum of HPE anomalies

Global gene expression profiling in human lung cells exposed to cobalt-4

<p><b>Copyright information:</b></p><p>Taken from "Global gene expression profiling in human lung cells exposed to cobalt"</p><p>http://www.biomedcentral.com/1471-2164/8/147</p><p>BMC Genomics 2007;8():147-147.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904204.</p><p></p>lt. Cell viability was determined by ATP Celltiter-Glow Luminescence Cell Viability Assay (Promega). Measurements were made on the Lumistar Galaxy (BMG) luminometer. The viability (V) was determined as the ATP ratio of treated cells versus control cells in %. The results are presented as mean ± SD (n = 4 to 8)

Global gene expression profiling in human lung cells exposed to cobalt-2

<p><b>Copyright information:</b></p><p>Taken from "Global gene expression profiling in human lung cells exposed to cobalt"</p><p>http://www.biomedcentral.com/1471-2164/8/147</p><p>BMC Genomics 2007;8():147-147.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904204.</p><p></p>e to 2 mM cobalt for 24 h. Treated (Co+) and control (Co-) extracts were probed with anti-ubiquitin, anti-DLG1, or anti-HSP90 antibodies. An anti-actin antibody was used as a control

Global gene expression profiling in human lung cells exposed to cobalt-1

<p><b>Copyright information:</b></p><p>Taken from "Global gene expression profiling in human lung cells exposed to cobalt"</p><p>http://www.biomedcentral.com/1471-2164/8/147</p><p>BMC Genomics 2007;8():147-147.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904204.</p><p></p>ed by qRT-PCR in sextuplets for each time point. Mean results are given in Log2 ratios ± SD. *: significant modulation calculated by pairwise testing with p < 0.0

Taxonomical and functional changes in COVID ‐19 faecal microbiome could be related to SARS‐CoV‐2 faecal load

International audienceSince the beginning of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the gastrointestinal (GI) tract has emerged as an important organ influencing the propensity to and potentially the severity of the related COVID-19 disease. However, the contribution of the SARS-CoV-2 intestinal infection on COVID-19 pathogenesis remains to be clarified. In this exploratory study, we highlighted a possible link between alterations in the composition of the gut microbiota and the levels of SARS-CoV-2 RNA in the gastrointestinal tract, which could be more important than the presence of SARS-CoV-2 in the respiratory tract, COVID-19 severity and GI symptoms. As established by metaproteomics, altered molecular functions in the microbiota profiles of high SARS-CoV-2 RNA level faeces highlight mechanisms such as inflammation-induced enterocyte damage, increased intestinal permeability and activation of immune response that may contribute to vicious cycles. Uncovering the role of this gut microbiota dysbiosis could drive the investigation of alternative therapeutic strategies to favour the clearance of the virus and potentially mitigate the effect of the SARS-CoV-2 infection

Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing

International audienceCOVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an unprecedented investigation to characterize its molecular structure and intimate functioning. While markers for its detection have been proposed and several diagnostic methodologies developed, its propensity to evolve and evade diagnostic tools and the immune response is of great concern. The recent spread of new variants with increased infectivity requires even more attention. Here, we document how shotgun proteomics can be useful for rapidly monitoring the evolution of the SARS-CoV-2 virus. We evaluated the heterogeneity of purified SARS-CoV-2 virus obtained after culturing in the Vero E6 cell line. We found that cell culture induces significant changes that are translated at the protein level, such changes being detectable by tandem mass spectrometry. Production of viral particles requires careful quality control which can be easily performed by shotgun proteomics. Although considered relatively stable so far, the SARS-CoV-2 genome turns out to be prone to frequent variations. Therefore, the sequencing of SARS-CoV-2 variants from patients reporting only the consensus genome after its amplification would deserve more attention and could benefit from more in-depth analysis of low level but crystal-clear signals, as well as complementary and rapid analysis by shotgun proteomics