4 research outputs found
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
OXALATE OXIDASE FROM HORDEUM VULGARE:DOWNSTREAM PROCESSING WITH AFFINI TY CHROMATOGRAPHY MOLECULAR STUDY,AND APPLICATION TO THE DETEDRMINA- TION OF OXALIC ACID
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