Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00023001%3A_____%2F23%3A00084081" target="_blank" >RIV/00023001:_____/23:00084081 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/23:10472832 RIV/00216208:11110/23:10472832 RIV/00027073:_____/23:N0000034

Výsledek na webu

<a href="https://academic.oup.com/biomethods/article/8/1/bpad011/7230015?login=true" target="_blank" >https://academic.oup.com/biomethods/article/8/1/bpad011/7230015?login=true</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/biomethods/bpad011" target="_blank" >10.1093/biomethods/bpad011</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction

Popis výsledku v původním jazyce

Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite&apos;s proteins but absent in the host&apos;s proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P &lt; 0.0001, Cohen&apos;s d &gt; 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results.

Název v anglickém jazyce

Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction

Popis výsledku anglicky

Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite&apos;s proteins but absent in the host&apos;s proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P &lt; 0.0001, Cohen&apos;s d &gt; 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

<a href="/cs/project/GA22-20785S" target="_blank" >GA22-20785S: Efekt infekce toxoplasmou a cytomegalovirem na kognitivní výkon – longitudinální, průřezová a retrospektivní studie</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Biology methods &amp; protocols

ISSN

2396-8923

e-ISSN

2396-8923

Svazek periodika

8

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

"art. no. bpad011"

Kód UT WoS článku

001032675500001

EID výsledku v databázi Scopus

2-s2.0-85168001957