Biology subjects

Rose, C.

Publications and source records attributed to Rose, C..

2 recordsLinked to original sources

bioRxiv2018

Transposable Element Expression In Tumors Is Associated With Immune Infiltration And Increased Antigenicity

Profound loss of DNA methylation is a well-recognized hallmark of cancer. Given its role in silencing transposable elements (TEs), we hypothesized that extensive TE expression occurs in tumors with highly demethylated DNA. We developed REdiscoverTE, a computational method for quantifying genome-wide TE expression in RNA sequencing data. Using The Cancer Genome Atlas database, we observed increased expression of over 400 TE subfamilies, of which 262 appeared to result from a proximal loss of DNA methylation. The most recurrent TEs were among the evolutionarily youngest in the genome, predominantly expressed from intergenic loci, and associated with antiviral or DNA damage responses. Treatment of glioblastoma cells with a demethylation agent resulted in both increased TE expression and de novo presentation of TE-derived peptides on MHC class I molecules. Therapeutic reactivation of tumor-specific TEs may synergize with immunotherapy by inducing both inflammation and the display of potentially immunogenic neoantigens.\n\nOne Sentence SummaryTransposable element expression in tumors is associated with increased immune response and provides tumor-associated antigens

cancer biology↗

bioRxiv2017

Bacterial Biofilm Formation On Soil Fungi: A Widespread Ability Under Controls

In natural environments, bacteria preferentially live in biofilms that they build on abiotic surfaces but also on living tissues. Although fungi form extensive networks of hyphae within soils and thus could provide immense surfaces for bacteria to build biofilms and to proliferate, the extent on such phenomenon and the consequences for the fitness of both microorganisms is poorly known in soils. Here, we analyzed the process of formation of biofilms by various bacteria on hyphae of soil fungi in an in vitro setting using confocal and electron microscopy. We showed that the ability to form biofilms on fungal hyphae is widely shared among soil bacteria. In contrast, some fungi, mainly belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also strongly modulated by the presence of tree roots and by the development of the ectomycorrhizal symbiosis, suggesting that biofilm formation does not occur randomly in soil but that it is highly regulated by several biotic factors. Finally, our study led to the unexpected finding that networks of filaments made of extracellular DNA were used to build the skeleton of biofilms by a large array of bacteria.

microbiology↗