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MicroRNAs (miRNAs) have been implicated in childhood acute lymphoblastic leukemia (ALL) pathogenesis. We performed a systematic review and meta-analysis of miRNA single-nucleotide polymorphisms (SNPs) in childhood ALL compared with healthy children, which revealed (i) that the CC genotype of rs4938723 in pri-miR-34b/c and the TT genotype of rs543412 in miR-100 confer protection against ALL occurrence in children; (ii) no significant association between rs2910164 genotypes in miR-146a and childhood ALL; and (iii) SNPs in DROSHA, miR-449b, miR-938, miR-3117 and miR-3689d-2 genes seem to be associated with susceptibility to B-ALL in childhood. A review of published literature on differential expression of miRNAs in children with ALL compared with controls revealed a significant upregulation of the miR-128 family, miR-130b, miR-155, miR-181 family, miR-210, miR-222, miR-363 and miR-708, along with significant downregulation of miR-143 and miR-148a, seem to have a definite role in childhood ALL development. MicroRNA signatures among childhood ALL subtypes, along with differential miRNA expression patterns between B-ALL and T-ALL cases, were scrutinized. With respect to T-ALL pediatric cases, we reanalyzed RNA-seq datasets with a robust and sensitive pipeline and confirmed the significant differential expression of hsa-miR-16-5p, hsa-miR-19b-3p, hsa-miR-92a-2-5p, hsa-miR-128-3p (ranked first), hsa-miR-130b-3p and -5p, hsa-miR-181a-5p, -2-3p and -3p, hsa-miR-181b-5p and -3p, hsa-miR-145-5p and hsa-miR-574-3p, as described in the literature, along with novel identified miRNAs.

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Genome assemblers are computational tools for de novo genome assembly, based on a plenitude of primary sequencing data. The quality of genome assemblies is estimated by their contiguity and the occurrences of misassemblies (duplications, deletions, translocations or inversions). The rapid development of sequencing technologies has enabled the rise of novel de novo genome assembly strategies. The ultimate goal of such strategies is to utilise the features of each sequencing platform in order to address the existing weaknesses of each sequencing type and compose a complete and correct genome map. In the present study, the hybrid strategy, which is based on Illumina short paired-end reads and Nanopore long reads, was benchmarked using MaSuRCA and Wengan assemblers. Moreover, the long-read assembly strategy, which is based on Nanopore reads, was benchmarked using Canu or PacBio HiFi reads were benchmarked using Hifiasm and HiCanu. The assemblies were performed on a computational cluster with limited computational resources. Their outputs were evaluated in terms of accuracy and computational performance. PacBio HiFi assembly strategy outperforms the other ones, while Hi-C scaffolding, which is based on chromatin 3D structure, is required in order to increase continuity, accuracy and completeness when large and complex genomes, such as the human one, are assembled. The use of Hi-C data is also necessary while using the hybrid assembly strategy. The results revealed that HiFi sequencing enabled the rise of novel algorithms which require less genome coverage than that of the other strategies making the assembly a less computationally demanding task. Taken together, these developments may lead to the democratisation of genome assembly projects which are now approachable by smaller labs with limited technical and financial resources.

SummaryThe precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Genome assemblers are computational tools for de novo genome assembly, based on a plenitude of primary sequencing data. The quality of genome assemblies is estimated by their contiguity and the occurrences of misassemblies (duplications, deletions, translocations or inversions). The rapid development of sequencing technologies has enabled the rise of novel de novo genome assembly strategies. The ultimate goal of such strategies is to utilise the features of each sequencing platform in order to address the existing weaknesses of each sequencing type and compose a complete and correct genome map. In the present study, the hybrid strategy, which is based on Illumina short paired-end reads and Nanopore long reads, was benchmarked using MaSuRCA and Wengan assemblers. Moreover, the long-read assembly strategy, which is based on Nanopore reads, was benchmarked using Canu or PacBio HiFi reads were benchmarked using Hifiasm and HiCanu. The assemblies were performed on a computational cluster with limited computational resources. Their outputs were evaluated in terms of accuracy and computational performance. PacBio HiFi assembly strategy outperforms the other ones, while Hi-C scaffolding, which is based on chromatin 3D structure, is required in order to increase continuity, accuracy and completeness when large and complex genomes, such as the human one, are assembled. The use of Hi-C data is also necessary while using the hybrid assembly strategy. The results revealed that HiFi sequencing enabled the rise of novel algorithms which require less genome coverage than that of the other strategies making the assembly a less computationally demanding task. Taken together, these developments may lead to the democratisation of genome assembly projects which are now approachable by smaller labs with limited technical and financial resources.

The use of high-dose Ionizing Radiation (IR) is currently one of the most common modalities in treatment of many types of cancer. The objective of this work was to investigate the effects of high-dose ionizing radiation on healthy human tissue, utilizing quantitative analysis of gene expression. To this end, publicly available transcriptomics datasets from human samples irradiated with a high dose of radiation and non-irradiated (control) ones were selected, and gene expression was determined using RNA-Seq data analysis. Raw data from these studies were subjected to quality control and trimming. Mapping of RNA-Seq reads was performed by the partial selective alignment method, and differential gene expression analysis was conducted. Subsequently, a meta-analysis was performed to select differentially expressed genes across datasets. Based on the differentially expressed genes discovered by meta-analysis, we constructed a protein-to-protein interaction network, and we identified biological pathways and processes related to high-dose IR effects. Our findings suggest that cell cycle arrest is activated, supported by our top down-regulated genes associated with cell cycle activation. DNA repair genes are down-regulated in their majority. However, several genes implicated in the nucleotide excision repair pathway are upregulated. Nevertheless, apoptotic mechanisms seem to be activated probably due to severe high-dose-induced complex DNA damage. The significant upregulation of CDKN1A, as a downstream gene of TP53, further validates programmed cell death. Finally, down-regulation of TIMELESS, signifies a correlation between IR response and circadian rhythm. Nonetheless, high-dose IR exposure effects regarding normal tissue (radiation toxicity) and its possible long-term outcomes should be studied to a greater extend.

Next-generation sequencing has prompted the development of numerous -omics applications. Along with experimental procedures, various computational pipelines became available to address the inherent complexities concerning the volume and quality of data. These pipelines are effective and routinely applied; however, interpreting their outcomes into actionable evidence is still poorly addressed. In this context, this work proposes a method for translating patient genomic profiles to drug response aberrations by integrating pharmacogenomic data into sequencing data analysis pipelines.

Στην παρούσα διατριβή διερευνήθηκε, για πρώτη φορά, η πιθανήαυτορυθμιστική δράση της ισταμίνης και η συμμετοχή των υποδοχέων της σταμεγάλα αγγεία επίμυων, υπό φυσιολογικές συνθήκες και στη συστηματικήφλεγμονή. Η επιλογή των σπλαχνικών αγγείων της κοιλιακής αορτής και τηςκάτω κοίλης φλέβας έγινε, αφενός λόγω του κομβικού τους ρόλου στοαγγειακό και κυκλοφορικό σύστημα, και κατ΄επέκταση στην παθοφυσιολογίατου οργανισμού, αφετέρου λόγω προηγούμενων ευρημάτων που υποδήλωναντην αυτορυθμιστική δράση της ισταμίνης στην περιφέρεια. Για το σκοπό αυτόχορηγήθηκαν συστηματικά ανταγωνιστές των υποδοχέων της ισταμίνης σεφυσιολογικούς επίμυες και σε επίμυες με πειραματική αρθρίτιδα καιπροσδιορίστηκαν τα επίπεδα ισταμίνης στα αγγεία, καθώς και η βέλτιστηδοσολογία των ανταγωνιστών σύμφωνα με τη σχέση δόσης-αποτελέσματος. Ηεπιλογή των ουσιών έγινε με βάση τις φαρμακολογικές τους ιδιότητες.Χρησιμοποιήθηκαν η διμεθινδένη, ανταγωνιστής των Η1 υποδοχέων, κυρίωςως μάρτυρας, αφού ο ρόλος των Η1 υποδοχέων στα αγγεία και τη φλεγμονήείναι αποδεκτός, αν και όχι πλήρως μελετημένος, και οι ουσίες GSK334429και JNJ7777120, οι οποίες αναπτύχθηκαν πρόσφατα ως εκλεκτικοίανταγωνιστές/ανάστροφοι αγωνιστές των Η3 και Η4 υποδοχέων αντίστοιχα.Μετά από στατιστική επεξεργασία και αξιολόγηση, τα αποτελέσματα έδειξαντην αυτορυθμιστική δράση της ισταμίνης στα περιφερικά αγγεία φυσιολογικώνεπίμυων, στην οποία συμμετέχουν οι Η3 και Η4 υποδοχείς. Η δράση αυτήδιαφοροποιήθηκε στην πειραματική αρθρίτιδα, όπου οι Η1 και Η3 υποδοχείςρύθμισαν αντίστοιχα τα επίπεδα ισταμίνης στις φλέβες και στις αρτηρίες τωνεπίμυων. Στη συνέχεια, επειδή το ενδοθήλιο ρυθμίζει τον αγγειακό τόνο καιτην απελευθέρωση ισταμίνης και άλλων αγγειοδραστικών ουσιών,πραγματοποιήθηκαν προκαταρκτικές μελέτες μετά από ex vivo αφαίρεση τουενδοθηλίου στα αγγεία των επίμυων. Τα ευρήματα παρείχαν ενδείξεις για τηνεμπλοκή του ενδοθηλίου στην αυτορυθμιστική δράση της ισταμίνης σταπεριφερικά αγγεία των επίμυων. Συμπερασματικά, τα αποτελέσματα τηςδιατριβής αποκάλυψαν νέους ρόλους της ισταμίνης στα περιφερικά αγγεία μετην πιθανή συμμετοχή του αγγειακού ενδοθηλίου. Συγκεκριμένα, τα ευρήματαέδειξαν ότι τα επίπεδα της ισταμίνης στα φυσιολογικά σπλαχνικά αγγείαρυθμίζονται μέσω των Η3 και Η4 υποδοχέων, ενώ κατά τη συστηματικήφλεγμονή, η ρύθμιση διαφοροποιείται και εξαρτάται από τους Η1 και Η3υποδοχείς στις φλέβες και στις αρτηρίες αντίστοιχα. Λαμβάνοντας υπόψη τησυμμετοχή των Η1 υποδοχέων στη φλεγμονή, το νευρορυθμιστικό ρόλο τωνΗ3 υποδοχέων και τις ανοσορυθμιστικές ιδιότητες των Η4 υποδοχέων, τααποτελέσματα αναμένεται να συμβάλουν στην περεταίρω αξιολόγηση τηςαλληλεπίδρασης των υποδοχέων της ισταμίνης στις ομοιοστατικές λειτουργίεςτων αγγείων και στην αγγειακή συμμετοχή στη συστηματική φλεγμονή.Απώτερος σκοπός είναι η φαρμακολογική αξιολόγηση νέωναποτελεσματικότερων θεραπευτικών προσεγγίσεων στη φλεγμονή τωναγγείων.