Μεταγονιδιωματική ανάλυση σε ιστούς ασθενών με μεταστατικό καρκίνο

Η διερεύνηση του ρόλου του ανθρώπινου μικροβιώματος αποτελεί τα τελευταία χρόνια ένα αναπόσπαστο κομμάτι της έρευνας στα πεδία της Βιολογίας και της Ιατρικής. Το μικροβιακό σύστημα που εντοπίζεται στον άνθρωπο, και ειδικά αυτό του πεπτικού σωλήνα, αποτελεί μεγάλο μέρος του ανοσοποιητικού συστήματος και την σύνδεσης αυτού με αρκετά ανθρώπινα όργανα. Το μικροβίωμα ενεργεί συνεργατικά με το ανθρώπινο σύστημα, επιτυγχάνοντας κατά αυτόν τον τρόπο ισορροπία, καθώς οι μικροοργανισμοί βοηθούν στην παραγωγή απαραίτητων, για εκείνο, θρεπτικών συστατικών και όχι μόνο. Σε περιπτώσεις διατάραξης αυτής της ισορροπίας, έρευνες έχουν δείξει πως οι μικροοργανισμοί είναι ικανοί να προκαλέσουν ή να εμπλακούν σε διάφορες ασθένειες, συμπεριλαμβανομένου του καρκίνου. Σκοπός της παρούσας διπλωματικής εργασίας είναι η διερεύνηση του μικροβιώματος σε ιστούς ασθενών με μεταστατικό καρκίνο, χρησιμοποιώντας δεδομένα από πειράματα RNA-Seq. Η διαφοροποιημένη έκφραση μικροοργανισμών στις διαφορετικές καταστάσεις (adjacent tissue, primary tissue, metastatic tissue) υπονοούν την πιθανή συσχέτισή τους με λειτουργίες της ασθένειας του καρκίνου. Τα δεδομένα που χρησιμοποιήθηκαν προέρχονται από τη βάση δεδομένων NCBI GEO. Οι αλγόριθμοι μεταγονιδιωματικής που χρησιμοποιήθηκαν ήταν το HISAT2 και ο AGAMEMNON. Η εκτέλεση τους επέτρεψε τον εντοπισμό μικροβιακών αλληλουχιών αρκετές από τις οποίες έχουν συσχετιστεί, στη βιβλιογραφία, με τη δημιουργία τοξικού περιβάλλοντος το οποίο ευνοεί τη δημιουργία φλεγμονής και κατά συνέπεια την ογκογένεση. Η μετάσταση του καρκίνου αποτελεί μια διαδικασία αυξημένης πολυπλοκότητας, ενώ η βιβλιογραφία που αναφέρεται στις συσχετίσεις μικροοργανισμών με αυτήν είναι περιορισμένη. Αρκετοί μικροοργανισμοί που έχει δειχθεί πως κατέχουν προστατευτικό ρόλο ενάντια στον καρκίνο, βρέθηκαν στην παρούσα μελέτη να είναι μειωμένοι ή και απόντες στις καρκινικές καταστάσεις.In recent years, the research on the role of the human microbiome consists an essential part of investigation in the fields of Biology and Medicine. The microbial system that can be found in humans, and especially that of the digestive tract, makes up a notable part of the immune system and its connections to other human organs. The microbiome acts synergistically with the human system to achieve balance, since microorganisms assist in the production of necessary nutrients and more. In cases where this balance fails to be achieved, studies have found that microorganisms can cause or be involved in several diseases, including cancer. The aim of this thesis is to investigate the microbiome in tissues of patients with metastatic cancer, using data from RNA-seq experiments. The differential expression of microorganisms in different tissue states (adjacent tissue, primary tissue, metastatic tissue) imply their possible association in pathways related to cancer. The data used were taken from NCBI GEO database. The algorithms used to carry out the metagenome analysis included HISAT2 and AGAMEMNON. Their execution allowed the detection of microbial sequences several of which have been associated, in related literature, with the creation of toxic environments that favor inflammation and, therefore, cancer. Cancer metastasis is a process of increased complexity, while the literature on the association of microorganisms with it is currently limited. Several microorganisms that have been observed to possess a protective role against cancer have been found in this study to be downregulated or absent in cancerous conditions

PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value

Simple Summary Only recently have the important biomarker capacities of microRNAs (miRNAs) in blood samples during disease been revealed. miRNAs are abundantly detected in circulation, and are less prone to degradation than longer RNA. Details regarding potential discriminatory miRNAs against numerous pathologic conditions are dispersed across articles, while existing resources that catalogue miRNA abundance in blood samples are not tailored to biomarker research. This study presents the meticulous manual curation of more than 200 articles that specifically interrogate the biomarker potential of miRNAs in whole blood, serum, or plasma. This annotation effort resulted in the creation of plasmiR, a database that systematically provides experimental evidence for the diagnostic and prognostic potential of circulating miRNAs against human diseases. plasmiR features 1021 entries, accompanied by rich study-specific meta-information, and an intuitive interface that enables the formation of complex queries and visualizations. Only recently, microRNAs (miRNAs) were found to exist in traceable and distinctive amounts in the human circulatory system, bringing forth the intriguing possibility of using them as minimally invasive biomarkers. miRNAs are short non-coding RNAs that act as potent post-transcriptional regulators of gene expression. Extensive studies in cancer and other disease landscapes investigate the protective/pathogenic functions of dysregulated miRNAs, as well as their biomarker potential. A specialized resource amassing experimentally verified, circulating miRNA biomarkers does not exist. We queried the existing literature to identify articles assessing diagnostic/prognostic roles of miRNAs in blood, serum, or plasma samples. Articles were scrutinized in order to exclude instances lacking sufficient experimental documentation or employing no biomarker assessment methods. We incorporated information from more than 200 biomedical articles, annotating crucial meta-information including cohort sizes, inclusion-exclusion criteria, disease/healthy confirmation methods and quantification details. miRNAs and diseases were systematically characterized using reference resources. Our circulating miRNA biomarker collection is provided as an online database, plasmiR. It consists of 1021 entries regarding 251 miRNAs and 112 diseases. More than half of plasmiR’s entries refer to cancerous and neoplastic conditions, 183 of them (32%) describing prognostic associations. plasmiR facilitates smart queries, emphasizing visualization and exploratory modes for all researchers

TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs

TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.e-ce.uth.gr/tarbasev9), it pushes the envelope by introducing virally-encoded miRNAs, interactions leading to target-directed miRNA degradation (TDMD) events and the largest collection of miRNA-gene interactions to date in a plethora of experimental settings, tissues and cell-types. It catalogues similar to 6 million entries, comprising similar to 2 million unique miRNA-gene pairs, supported by 37 experimental (high- and low-yield) protocols in 172 tissues and cell-types. Interactions are annotated with rich metadata including information on genes/transcripts, miRNAs, samples, experimental contexts and publications, while millions of miRNA-binding locations are also provided at cell-type resolution. A completely re-designed interface with state-of-the-art web technologies, incorporates more features, and allows flexible and ingenious use. The new interface provides the capability to design sophisticated queries with numerous filtering criteria including cell lines, experimental conditions, cell types, experimental methods, species and/or tissues of interest. Additionally, a plethora of fine-tuning capacities have been integrated to the platform, offering the refinement of the returned interactions based on miRNA confidence and expression levels, while boundless local retrieval of the offered interactions and metadata is enabled. Graphical Abstrac