23
DOI: https://doi.org/10.1186/s43141-022-00413-5
English
eng
Chetta, Massimiliano
Contributor
<div id="abs0005" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0010" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0030" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;">In the last 2 years, we have been fighting against SARS-CoV-2 <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/viral-disease" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">viral infection</a><span style="margin: 0px; padding: 0px;">, which continues to claim victims all over the world. The entire scientific community has been mobilized in an attempt to stop and eradicate the infection. A well-known feature of <a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/virus-rna" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RNA viruses</a> is their high </span></span><a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/mutation-rate" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">mutational rate</a>, particularly in specific gene regions. The SARS-CoV-2 </span><a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/vitronectin" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">S protein</a><span style="margin: 0px; padding: 0px;"> is also affected by these changes, allowing viruses to adapt and spread more easily. The vaccines developed using mRNA coding <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/protein-s" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">protein S</a><span style="margin: 0px; padding: 0px;"> undoubtedly contributed to the “fight” against the COVID-19 pandemic even though the presence of new variants in the spike protein could result in protein <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/conformational-transition" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">conformational changes</a><span style="margin: 0px; padding: 0px;">, which could affect <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/vaccine-immunogenicity" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">vaccine immunogenicity</a> and thus vaccine effectiveness.</span></span></span></div></div><div id="abs0010" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0015" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Results</h3><div class="u-margin-s-bottom" id="sp0035" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;">The study presents the findings of an <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/in-silico" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">in silico</a> analysis using various bioinformatics tools finding </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/conserved-sequence" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">conserved sequences</a><span style="margin: 0px; padding: 0px;"> inside SARS-CoV-2 <a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/vitronectin" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">S protein</a> (encoding mRNA) same as in the vaccine </span></span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/rna-sequence" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RNA sequences</a><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> that could be targeted by specific host RNA-binding proteins (RBPs). According to the results an interesting scenario emerges involving host <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/rna-binding" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RBPs</a><span style="margin: 0px; padding: 0px;"> competition and subtraction. The presence of viral <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/rna" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RNA</a><span style="margin: 0px; padding: 0px;"> in cytoplasm could be a new tool in the virus’s armory, allowing it to improve its chances of survival by altering cell gene expression and thus interfering with host cell processes. In silico analysis was used also to evaluate the presence of similar human <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/microrna" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">miRNA</a> sequences within </span></span></span><a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/protein-motif" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RBPs motifs</a> that can modulate human RNA expression. Increased cytoplasmic availability of exogenous RNA fragments derived from RNA physiological degradation could potentially mimic the effect of host human miRNAs within the cell, causing modulation of the host cell network.</span></div></div><div id="abs0015" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0020" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Conclusions</h3><div class="u-margin-s-bottom" id="sp0040" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">Our in silico analysis could aid in shedding light on the potential effects of exogenous RNA (i.e. viruses and vaccines), thereby improving our understanding of the <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cell-cell-interaction" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">cellular interactions</a> between virus and host biomolecules. Finally, using the computational approach, it is possible to obtain a safety assessment of RNA-based vaccines as well as indications for use in specific clinical conditions.</div></div>
Elsevier
December 2022
pdf
Journal of Genetic Engineering and Biotechnology
An in silico pipeline approach uncovers a potentially intricate network involving spike SARS-CoV-2 RNA, RNA vaccines, host RNA-binding proteins (RBPs), and host miRNAs at the cellular level
mixed material
Elsevier