Biomarker panels for characterizing microbial community biofilm formation as composite molecular process.

Microbial consortia execute collaborative molecular processes with contributions from individual species, on such basis enabling optimized molecular function. Such collaboration and synergies benefit metabolic flux specifically in extreme environmental conditions as seen in acid mine drainage, with biofilms as relevant microenvironment. However, knowledge about community species composition is not sufficient for deducing presence and efficiency of composite molecular function. For this task molecular resolution of the consortium interactome is to be retrieved, with molecular biomarkers particularly suited for characterizing composite molecular processes involved in biofilm formation and maintenance. A microbial species set identified in 18 copper environmental sites provides a data matrix for deriving a cross-species molecular process model of biofilm formation composed of 191 protein coding genes contributed from 25 microbial species. Computing degree and stress centrality of biofilm molecular process nodes allows selection of network hubs and central connectors, with the top ranking molecular features proposed as biomarker candidates for characterizing biofilm homeostasis. Functional classes represented in the biomarker panel include quorum sensing, chemotaxis, motility and extracellular polysaccharide biosynthesis, complemented by chaperones. Abundance of biomarker candidates identified in experimental data sets monitoring different biofilm conditions provides evidence for the selected biomarkers as sensitive and specific molecular process proxies for capturing biofilm microenvironments. Topological criteria of process networks covering an aggregate function of interest support the selection of biomarker candidates independent of specific community species composition. Such panels promise efficient screening of environmental samples for presence of microbial community composite molecular function.

Vascular endothelial growth factor A as predictive marker for mTOR inhibition in relapsing high-grade serous ovarian cancer.

BACKGROUND: Development of resistance against first line drug therapy including cisplatin and paclitaxel in high-grade serous ovarian cancer (HGSOC) presents a major challenge. Identifying drug candidates breaking resistance, ideally combined with predictive biomarkers allowing precision use are needed for prolonging progression free survival of ovarian cancer patients. Modeling of molecular processes driving drug resistance in tumor tissue further combined with mechanism of action of drugs provides a strategy for identification of candidate drugs and associated predictive biomarkers. RESULTS: Consolidation of transcriptomics profiles and biomedical literature mining results provides 1242 proteins linked with ovarian cancer drug resistance. Integrating this set on a protein interaction network followed by graph segmentation results in a molecular process model representation of drug resistant HGSOC embedding 409 proteins in 24 molecular processes. Utilizing independent transcriptomics profiles with follow-up data on progression free survival allows deriving molecular biomarker-based classifiers for predicting recurrence under first line therapy. Biomarkers of specific relevance are identified in a molecular process encapsulating TGF-beta, mTOR, Jak-STAT and Neurotrophin signaling. Mechanism of action molecular model representations of cisplatin and paclitaxel embed the very same signaling components, and specifically proteins afflicted with the activation status of the mTOR pathway become evident, including VEGFA. Analyzing mechanism of action interference of the mTOR inhibitor sirolimus shows specific impact on the drug resistance signature imposed by cisplatin and paclitaxel, further holding evidence for a synthetic lethal interaction to paclitaxel mechanism of action involving cyclin D1. CONCLUSIONS: Stratifying drug resistant high grade serous ovarian cancer via VEGFA, and specifically treating with mTOR inhibitors in case of activation of the pathway may allow adding precision for overcoming resistance to first line therapy.

Interaction networks for identifying coupled molecular processes in microbial communities.

BACKGROUND: Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications including metal bioleaching and bioremediation processes. With significant advancements in metagenomics the composition of microbial communities became amenable for integrative analysis on the level of entangled molecular processes involving more than one species, in turn offering a data matrix for analyzing the molecular basis of cooperative phenomena. METHODS: We present an analysis framework aligned with a dynamical hierarchies concept for unraveling emergent properties in microbial communities, and exemplify this approach for a co-culture setting of At. ferrooxidans and At. thiooxidans. This minimum microbial community demonstrates a significant increase in bioleaching efficiency compared to the activity of individual species, involving mechanisms of the thiosulfate, the polysulfide and the iron oxidation pathway. RESULTS: Populating gene-centric data structures holding rich functional annotation and interaction information allows deriving network models at the functional level coupling energy production and transport processes of both microbial species. Applying a network segmentation approach on the interaction network of ortholog genes covering energy production and transport proposes a set of specific molecular processes of relevance in bioleaching. The resulting molecular process model essentially involves functionalities such as iron oxidation, nitrogen metabolism and proton transport, complemented by sulfur oxidation and nitrogen metabolism, as well as a set of ion transporter functionalities. At. ferrooxidans-specific genes embedded in the molecular model representation hold gene functions supportive for ammonia utilization as well as for biofilm formation, resembling key elements for effective chalcopyrite bioleaching as emergent property in the co-culture situation. CONCLUSIONS: Analyzing the entangled molecular processes of a microbial community on the level of segmented, gene-centric interaction networks allows identification of core molecular processes and functionalities adding to our mechanistic understanding of emergent properties of microbial consortia.