No abstract

Background In the last twenty years, new methodologies have made possible the gathering of large amounts of data concerning the genetic information and metabolic functions associated to the human gut microbiome. In spite of that, processing all this data available might not be the simplest of tasks, which could result in an excess of information awaiting proper annotation. This assessment intended on evaluating how well respected databases could describe a mock human gut microbiome. Methods In this work, we critically evaluate the output of the cross–reference between the Uniprot Knowledge Base (Uniprot KB) and the Kyoto Encyclopedia of Genes and Genomes Orthologs (KEGG Orthologs) or the evolutionary genealogy of genes: Non-supervised Orthologous groups (EggNOG) databases regarding a list of species that were previously found in the human gut microbiome. Results From a list which contemplates 131 species and 52 genera, 53 species and 40 genera had corresponding entries for KEGG Database and 82 species and 47 genera had corresponding entries for EggNOG Database. Moreover, we present the KEGG Orthologs (KOs) and EggNOG Orthologs (NOGs) entries associated to the search as their distribution over species and genera and lists of functions that appeared in many species or genera, the “core” functions of the human gut microbiome. We also present the relative abundance of KOs and NOGs throughout phyla and genera. Lastly, we expose a variance found between searches with different arguments on the database entries. Inferring functionality based on cross-referencing UniProt and KEGG or EggNOG can be lackluster due to the low number of annotated species in Uniprot and due to the lower number of functions affiliated to the majority of these species. Additionally, the EggNOG database showed greater performance for a cross-search with Uniprot about a mock human gut microbiome. Notwithstanding, efforts targeting cultivation, single-cell sequencing or the reconstruction of high-quality metagenome-assembled genomes (MAG) and their annotation are needed to allow the use of these databases for inferring functionality in human gut microbiome studies.

Extracellular vesicles (EVs) are released especially by cancer cells. They modulate the tumor microenvironment by interacting with immune cells while carrying immunosuppressive or immunostimulatory molecules. In this review, we will explore some conflicting reports regarding the immunological outcomes of EVs in cancer progression, in which they might initiate an antitumor immune response or an immunosuppressive response. Concerning immunosuppression, the role of tumor-derived EVs’ in the adenosinergic system is underexplored. The enhancement of adenosine (ADO) levels in the tumor microenvironment impairs T-cell function and cytokine release. However, some tumor-derived EVs may deliver immunostimulatory factors, promoting immunogenic activity, even with ADO production. The modulatory role of ADO over the tumor progression represents a piece in an intricate microenvironment with anti and pro tumoral seesaw-like mechanisms.

Natural products are a valuable source of new molecules and are important for drug discovery. Many chemotherapeutics currently in clinical use were originated from natural sources and are effective cytotoxic agents. In this study, we investigated the cytotoxic and pro‐apoptotic effects of achyrobichalcone (ACB) and 3‐O‐methylquercetin (3OMQ), two novel compounds isolated from the Achyrocline satureioides plant. Because extracts from this plant have been shown to have anticancer activity in vitro, we evaluated ACB and 3OMQ using a human breast cancer cell line, MDA‐MB‐231, and a nontumorigenic human breast epithelial cell line, MCF‐12A. We found that ACB demonstrates cytotoxic effects on MDA‐MB‐231 cells, but not MCF‐12A cells. 3OMQ also demonstrated cytotoxic effects on MDA‐MB‐231 cells, but with lower selectivity compared to treated MCF‐12A cells. Cell death by both compounds was associated with caspase‐9 and caspase‐3/7 activation. Using high‐resolution respirometry, we found that ACB and 3OMQ were able to cause acute mitochondrial dysfunction in MDA‐MB‐231‐treated cells. These results suggest that apoptosis in MDA‐MB‐231 cells is induced through the activation of the mitochondrial‐dependent pathway. Collectively, these findings suggest that ACB is a strong candidate for further anticancer in vivo tests.

Caveolin‐1 (Cav‐1) is an integral membrane protein present in all organelles, responsible for regulating and integrating multiple signals as a platform. Mitochondria are extremely adaptable to external cues in chronic liver diseases, and expression of Cav‐1 may affect mitochondrial flexibility in hepatic stellate cells (HSCs) activation. We previously demonstrated that exogenous expression of Cav‐1 was sufficient to increase some classical markers of activation in HSCs. Here, we aimed to evaluate the influence of exogenous expression and knockdown of Cav‐1 on regulating the mitochondrial plasticity, metabolism, endoplasmic reticulum (ER)‐mitochondria distance, and lysosomal activity in HSCs. To characterize the mitochondrial, lysosomal morphology, and ER‐mitochondria distance, we perform transmission electron microscope analysis. We accessed mitochondria and lysosomal networks and functions through a confocal microscope and flow cytometry. The expression of mitochondrial machinery fusion/fission genes was examined by real‐time polymerase chain reaction. Total and mitochondrial cholesterol content was measured using Amplex Red. To define energy metabolism, we used the Oroboros system in the cells. We report that GRX cells with exogenous expression or knockdown of Cav‐1 changed mitochondrial morphometric parameters, OXPHOS metabolism, ER‐mitochondria distance, lysosomal activity, and may change the activation state of HSC. This study highlights that Cav‐1 may modulate mitochondrial function and structural reorganization in HSC activation, being a potential candidate marker for chronic liver diseases and a molecular target for therapeutic intervention.