Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.

Exosomes are lipid membrane-enclosed vesicles released by all cell types that act at the paracrine or endocrine level to favor cell differentiation, tissue homeostasis, organ remodeling and immune regulation. Their biosynthesis begins with a cell membrane invagination which generates an early endosome that matures to a late endosome. By inward budding of the late endosome membrane, a multivesicular body (MVB) with intraluminal vesicles (ILVs) is generated. The fusion of MVBs with the plasma membrane releases ILVs into the extracellular space as exosomes, ranging in size from 30 to 100 nm in diameter. The bilipid exosome membrane is rich in cholesterol, ceramides and phosphatidylserine and can be loaded with DNA, RNA, microRNAs, proteins and lipids. It has been demonstrated that exosome secretion is a common mechanism used by the tumor to generate an immunosuppressive microenvironment that favors cancer development and progression, allowing tumor escape from immune control. Due to their ability to transport proteins, lipids and nucleic acids from the cell that gave rise to them, exosomes can be used as a source of biomarkers with great potential for clinical applications in diagnostic, prognostic or therapeutic areas. This article will review the latest research findings on exosomes and their contribution to cancer development.

Background: Microsatellite instability (MSI) is a hallmark of DNA mismatch repair (MMR) deficiency that leads to genomic instability and increased cancer risk. The tumor microenvironment (TME) significantly influences MSI‐driven tumorigenesis, and emerging evidence points to a critical role of the microbiome in shaping this complex interplay.Methods: This review comprehensively examines the existing literature on the intricate relationship between MSI, microbiome, and cancer development, with a particular focus on the impact of microbial dysbiosis on the TME.Results: MSI‐high tumors exhibited increased immune cell infiltration owing to the generation of neoantigens. However, immune evasion mechanisms such as PD‐1/CTLA‐4 upregulation limit the efficacy of immune checkpoint inhibitors (ICIs) in a subset of patients. Pathobionts, such as Fusobacterium nucleatum and Bacteroides fragilis, contribute to MSI through the production of genotoxins, further promoting inflammation and oxidative stress within the TME.Conclusions: The microbiome profoundly affects MSI‐driven tumorigenesis. Modulation of the gut microbiota through interventions such as fecal microbiota transplantation, probiotics, and dietary changes holds promise for improving ICI response rates. Further research into cancer pharmacomicrobiomics, investigating the interplay between microbial metabolites and anticancer therapies, is crucial for developing personalized treatment strategies.

Primary breast angiosarcoma, with de novo appearance and not associated with exposure to radiation or lymphedema, is a rare pathology representing less than 0.05% of the neoplasms related to this organ. The pathology is characterized by its aggressiveness, poor prognosis, and difficulties in its differential diagnosis. This article reports the case of a 55-year-old white woman with no family history of cancer, with a rapidly growing mass in the left mammary gland that ulcerates and bleeds. It is confirmed as primary breast angiosarcoma by immunostaining in the tumor tissue for CD31, CD34, and FLI-1. In addition, a sample of neoplastic and healthy tissues is collected from the patient for RNA sequencing; the results are contrasted with a tissue sample from a patient with Luminal A subtype of breast cancer, as well as data from other cases of angiosarcoma available in public databases. These findings revealed a genetic profile associated with the immune and inflammatory response in the patient’s sample when compared to available angiosarcoma data; these molecular patterns are consistent with other recent studies. Due to the rarity of the disease, the studies carried out on each patient contribute to the expanding knowledge of the etiology and molecular pathways that are still partially known and continue to be the subject of research. Aside from a comparative transcriptome study, this article aims to provide an update on the state of knowledge about this disease.

Background: Gastric cancer is a heterogeneous pathology that represents the fifth most frequent malignancy in the world, with more than 750,000 deaths by 2020. With significant repercussions in public health, this pathology lacks biomarkers for early diagnosis, with endoscopy biopsy being the golden test for its detection. In the exploration of new strategies to control gastric cancer in recent years, liquid biopsy appears as a potential source of biomarkers using non-invasive procedures. Methods: Here we present the characterization of miRNAs contained in plasma-derived exosomes from patients with gastric cancer. Extracellular vesicles (EVs) were isolated using size-exclusion chromatography (SEC) and their characterization was performed by electron microscopy, protein expression, and nanoparticle analysis techniques. Total RNA from isolated exosomes was obtained for small RNA-seq analysis. Results: Transcriptomic miRNA data were used to identify differentially expressed miRNAs between patients with benign and malignant gastric diseases, which resulted in a molecular signature of nine miRNAs, that were used in a regression model to classify individuals as either having benign or malignant disease. Further, we compared benign-malignant patients at different stages of gastric cancer, and we detected 15 differentially expressed miRNAs. Among these 15 miRNAs, miR-92a-3p, miR451a, and miR126-3p were identified as winners due to their clinical and regulatory relevance. Results: Our results offer relevant information of a Colombian case study allowing us to propose three transcriptomic gastric cancer biomarkers in liquid biopsy. Graphical Summary: EVs are structures surrounded by a lipid bilayer that facilitate intercellular communication by transporting biomolecules commonly referred to as part of liquid biopsy. In this study, we examine the miRNAs contents of plasma isolated EVs from patients with both benign gastric diseases and gastric cancer to identify potential biomarkers for gastric cancer.

Exosomes carry molecules of great biological and clinical interest, such as miRNAs. The contents of exosomes vary between healthy controls and cancer patients. Therefore, miRNAs and other molecules transported in exosomes are considered a potential source of diagnostic and prognostic biomarkers in cancer. Many miRNAs have been detected in recent years. Consequently, a substantial amount of miRNA-related data comparing patients and healthy individuals is available, which contributes to a better understanding of the initiation, development, malignancy, and metastasis of cancer using non-invasive sampling procedures. However, a re-analysis of available ncRNA data is rare. This study used available data about miRNAs in exosomes comparing healthy individuals and cancer patients to identify possible global changes related to the presence of cancer. A robust transcriptomic analysis identified two common miRNAs (miR-495-3p and miR-543) deregulated in five cancer datasets. They had already been implicated in different cancers but not reported in exosomes circulating in blood. The study also examined their target genes and the implications of these genes for functional processes.