Ανάλυση δεδομένων μικροσυστοιχιών για την επίδραση ακτινοβολιών υψηλού LET με εφαρμογές στη θεραπεία του καρκίνου ή το διάστημα.

Εισαγωγή Η χρήση ιοντίζουσας ακτινοβολίας (IR) υψηλής γραμμικής μεταφοράς ενέργειας (LET), προοδευτικά ενσωματώνεται στην ακτινοθεραπεία (RT) λόγω της στοχευμένης εναπόθεσης ενέργειας και της υψηλής σχετικής βιολογικής αποτελεσματικότητας (RBE), η οποία έχει συσχετιστεί και με την επαγωγή σύνθετων βλαβών DNA. Αυτά τα πλεονεκτήματα της σωματιδιακής ακτινοβολίας καθίστανται παράλληλα παράγοντας κινδύνου για τους αστροναύτες, εξαιτίας της αναπόφευκτης έκθεσης στην κοσμική ακτινοβολία. Κάνοντας λόγο λοιπόν για υγιείς ιστούς και οργανισμούς, η απόκριση σε βλάβες DNA (DDR) ως αποτέλεσμα της επαγωγής σύνθετων βλαβών DNA, οι οποίες προκύπτουν από τέτοιους τύπους ακτινοβολίας, μπορεί να συμβάλει στις διάφορες χρόνιες και όψιμες επιδράσεις της IR. Η μέθοδος προσέγγισης που προτείνουμε προς μελέτη των πιθανών υποβοσκόντων πολύπλοκων μηχανισμών, είναι η μελέτη των μεταβολών στην έκφραση γονιδίων ύστερα από έκθεση σε IR υψηλού LET, μέσω βιοπληροφορικής. Μέθοδος Επιλέχθηκαν ανθρώπινα δείγματα ακτινοβολημένα με υψηλής LET IR και μη-ακτινοβολημένα (δείγματα ελέγχου) στα οποία καθορίστηκε η γονιδιακή έκφραση μέσω τεχνολογίας μικροσυστοιχιών cDNA. Χρησιμοποιήθηκαν μη επεξεργασμένα δεδομένα από κατατεθειμένες μελέτες στα δημόσια αποθετήρια του GEO και ArrayExpress. Η προ-επεξεργασία και η ανάλυση διαφορικής έκφρασης πραγματοποιήθηκε σε γλώσσα προγραμματισμού R. Τα διαφορικώς εκφρασμένα γονίδια που προέκυψαν, υποβλήθηκαν σε ανάλυση λειτουργικού εμπλουτισμού ώστε να ταυτοποιηθούν όροι γονιδιακής οντολογίας (GO) και βιολογικών μονοπατιών που σχετίζονται με τις επιδράσεις της υψηλής LET IR, καθώς και για σχετιζόμενες παθήσεις με τα εργαλεία WebGestalt και Enrichr, αντίστοιχα. Εκτελέστηκε βιβλιογραφική αναζήτηση βασιζόμενη στο GO και στην κατασκευή δικτύων πρωτεϊνικών αλληλεπιδράσεων (PPI networks) με το εργαλείο STRING, ώστε να αναδειχθούν γονίδια ενδιαφέροντος σχετιζόμενα με την DDR. Τέλος, διευρύναμε την μελέτη, προς αναζήτηση συγγενών παθήσεων που έχουν συνδεθεί με έκθεση σε βαρέα ιόντα (HZE), συνδυάζοντας συσχετίσεις γονιδίων-ασθενειών από το DisGeNET και δίκτυα ασθενειών από το DISNOR. Αποτελέσματα-Συζήτηση Τα ευρήματά μας υποδεικνύουν την επαγωγή μιας διαφορικής βιολογικής απόκρισης σε ακτινοβολία υψηλής LET (σε σχέση με χαμηλού LET όπως ακτίνων Χ), κυρίως μέσω ενισχυμένης φλεγμονώδους απόκρισης που συμπεριλαμβάνει μηχανισμούς που σχετίζονται με το επίκτητο ανοσοποιητικό σύστημα. Η ενεργοποίηση της σηματοδότησης JAK-STAT υποστηρίζει περαιτέρω αυτή την υπόθεση. Επιπλέον, οι αποπτωτικοί μηχανισμοί φαίνεται να αναστέλλονται, όπως υποστηρίζεται και από την διέγερση της εστιακής προσκόλλησης (focal adhesion), γεγονός που μπορεί να οδηγήσει στην επαγωγή κυτταρικής γήρανσης. Επεκτείνοντας την μελέτη αυτή προς αναζήτηση πιθανών συγγενών παθήσεων της έκθεσης σε HZE, η ανάλυση λειτουργικού εμπλουτισμού ανέδειξε τη συμμετοχή μηχανισμών που συσχετίζονται με νευροεκφυλιστικές παθήσεις, μέσω των μονοπατιών σηματοδότησης Wnt και ασβεστίου, καθώς και του σχηματισμού αμυλοειδών ινιδίων. Η ενεργοποίηση του μονοπατιού σηματοδότησης NOTCH, η οποία υποστηρίζεται και από την υπερ-έκφραση του SIRT1 σε επίπεδο βιολογίας συστημάτων, είναι ενδεικτική της σύνδεσης με καρδιαγγειακές παθήσεις. Τέλος, μέσω της απορρύθμισης στην έκφραση του PLA2G4A, εξάγεται η σύνδεση με φλεγμονώδεις μεταβολικές ασθένειες.Introduction The use of high Linear Energy Transfer (LET) Ionizing Radiation (IR) is progressively being incorporated in Radiation Therapy (RT) due to its precise dose localization and high relative biological effectiveness, also associated with the induction of highly complex DNA damage. At the same time, these benefits of particle radiation become a high risk in the case of inevitable, cosmic radiation exposure for astronauts. Nonetheless, DNA Damage Response (DDR) activated via complex DNA damage on healthy tissue, occurring from such types of radiation, may be instrumental in the induction of various chronic and late effects. A method of approach for better understanding the possible complicated underlying response mechanisms, is studying alterations in gene expression after exposure to high-LET IR with the use of bioinformatics. Methods To this end, human samples irradiated with high LET IR and non-irradiated (control) were selected and gene expression was determined using cDNA microarray data analysis. Raw data from various studies were downloaded from GEO and ArrayExpress public databases. Pre-processing and differential expression analysis was performed using R programming language. Differentially expressed genes were subjected to functional enrichment analysis to identify Gene Ontology (GO) terms and biological pathways related to high LET IR effects as well as associated diseases, using WebGestalt and Enrichr, respectively. A bibliographical research was performed using GO and Protein to Protein Interaction (PPI) network construction via STRING, to select a group of genes of interest, regarding DDR. Finally, we expanded our study in search of possible comorbidities for heavy ion (HZE) exposure, combining gene-disease associations from DisGeNET platform and disease networks from DISNOR. Results-Discussion Our findings suggest the induction of a differential biological response for high-LET radiations, in comparison to low-LET IR, mainly through an enhanced inflammatory response, including several mechanisms associated with the adaptive immune system. Activation of JAK-STAT signaling pathway further upholds this premise. In addition, apoptotic mechanisms seem to be inhibited, further supported by stimulation of focal adhesion, which may imply the induction of cellular senescence. By expanding our study in search of possible comorbidities for HZE particle exposure, functional enrichment analysis suggests the involvement of mechanisms, tightly correlated with neurodegenerative disorders through Wnt and Calcium signaling pathways as well as amyloid fibrils formation. NOTCH signaling pathway activation, also supported by the up-regulation of SIRT1 at a systems biology level, is indicative of a connection to cardiovascular disease. Finally, through dysregulation in the expression of PLA2G4A, inflammatory metabolic diseases are suggested

Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue

Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue

GENE EXPRESSION COLLECTIVE DATA ANALYSIS FOR STUDYING THE EFFECTS OF HIGH-LET IONIZING RADIATION: A BIOINFORMATICS APPROACH

The use of high linear energy (LET) ionizing radiation (IR) is progressively being incorporated in radiation therapy (RT) due to its precise dose localization and high relative biological effectiveness. At the same time, these benefits of particle radiation become a high risk for astronauts in the case of inevitable long-term cosmic radiation exposure. Nonetheless, DNA Damage Response (DDR) activated via complex DNA damage on healthy tissue, occurring from such types of radiation, may be instrumental in the induction of various chronic and late effects. A method of approach in understanding the possible underlying mechanisms, is studying alterations in gene expression. To this end we identified Differentially Expressed Genes (DEGs) in IR-exposed healthy human tissue, utilizing microarray data available in public repositories. DEG analysis was conducted using R programming language. Consequently, through functional enrichment and biological network analysis, we identified biological pathways and processes implicated in DDR. By comparing low and high-LET radiation effects, our primary results indicate the induction of a differential biological response for high-LET, like an enhanced inflammatory response.In addition, patterns of DNA repair are substantially distinct compared to low-LET. Finally, we expanded our study in search of possible comorbidities for HZE particle exposure. Pathway enrichment analysis suggests the involvement of mechanisms, tightly correlated with neurodegenerative disorders like amyloid fibrils formation. Regarding blood tissue, platelet activation signaling was found, upholding the connection to cardiovascular disease. This holistic bioinformatics approach revealed cellular trends towards inflammation and degeneration which might be central to the development of late effects of high-LET radiation exposure. It can contribute to the identification of molecular targets for effective countermeasures

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression

The use of high linear energy transfer (LET) ionizing radiation (IR) is progressively being incorporated in radiation therapy due to its precise dose localization and high relative biological effectiveness. At the same time, these benefits of particle radiation become a high risk for astronauts in the case of inevitable cosmic radiation exposure. Nonetheless, DNA Damage Response (DDR) activated via complex DNA damage in healthy tissue, occurring from such types of radiation, may be instrumental in the induction of various chronic and late effects. An approach to elucidating the possible underlying mechanisms is studying alterations in gene expression. To this end, we identified differentially expressed genes (DEGs) in high Z and high energy (HZE) particle-, γ-ray- and X-rayexposed healthy human tissues, utilizing microarray data available in public repositories. Differential gene expression analysis (DGEA) was conducted using the R programming language. Consequently, four separate meta-analyses were conducted, after DEG lists were grouped depending on radiation type, radiation dose and time of collection post-irradiation. To highlight the biological background of each meta-analysis group, functional enrichment analysis and biological network construction were conducted. For HZE particle exposure at 8–24 h post-irradiation, the most interesting finding is the variety of DNA repair mechanisms that were downregulated, a fact that is probably correlated with complex DNA damage formation. Simultaneously, after X-ray exposure during the same hours after irradiation, DNA repair mechanisms continue to take place. Finally, in a further comparison of lowand high-LET radiation effects, the most prominent result is that autophagy mechanisms seem to persist and that adaptive immune induction seems to be present. Such bioinformatics approaches may aid in obtaining an overview of the cellular response to high-LET particles. Understanding these response mechanisms can consequently aid in the development of countermeasures for future space missions and ameliorate heavy ion treatments

Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

Abstract We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue