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Biology subjects

Vischioni, C.

Publications and source records attributed to Vischioni, C..

2 recordsLinked to original sources

miRNAs Copy Number Variations repertoire as hallmark indicator of cancer species predisposition

Aging is one of the hallmarks of multiple human diseases, including cancer. However, the molecular mechanisms associated with high longevity and low cancer incidence percentages characterizing long-living organisms have not been fully understood yet. In this context, we hypothesized that variations in the number of copies (CNVs) of specific genes may protect some species from cancer onset. Based on the statistical comparison of gene copy numbers within the genomes of cancer -prone and -resistant organisms, we identified novel gene targets linked to the tumor predisposition of a species, such as CD52, SAT1 and SUMO protein family members. Furthermore, for the first time, we were able to discover that, considering the entire genome copy number landscape of a species, microRNAs (miRNAs) are among the most significant gene families enriched for cancer progression and predisposition. However, their roles in ageing and cancer resistance from a comparative perspective remains largely unknown. To this end, we identified through bioinformatics analysis, several alterations in miRNAs copy number patterns, represented by duplication of miR-221, miR-222, miR-21, miR-372, miR-30b, miR-30d and miR-31 among others. Therefore, our analysis provides the first evidence that an altered copy number miRNAs signature is able to statistically discriminate species more susceptible to cancer than those that are tumor resistant, helping researchers to discover new possible therapeutic targets involved in tumor predisposition.

genomics↗

GBRAP: a tool to retrieve, parse and analyze GenBank files of viral and bacterial species

SummaryGenBank files contain genomic data of sequenced living organisms. Here, we present GBRAP (GenBank Retrieving, Analyzing and Parsing software), a tool written in Python 3 that can be used to easily download, parse and analyze viral and bacterial GenBank files, even when contain more than one genomic sequence for each species. GBRAP can analyze more files simultaneously through single command-line parameters that give as output a single table showing the genomic characteristics of each organism. It is also able to calculate Shannon, LZSS (Lempel-Ziv-Storer-Szymanski) and topological entropy for both the entire genome and its constitutive elements such as genes, rRNAs, tRNAs, tmRNAs and ncRNAs together with Chargaffs second parity rule scores obtained using different mathematical methods. Moreover, GBRAP can calculate, the number, the length and the nucleotides abundance of genomic components for each DNA strand and for the overlapping regions among the two complementary helixes. To our knowledge, this is the only software capable of providing this type of genomic analyses all together in a single tool, that, therefore can be used by the scientists interested in both genomics and evolutionary research. Availability and implementationThe data underlying this article are available from the corresponding author on reasonable request.

bioinformatics↗