Dataset Information

Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas.

ABSTRACT: The causal relationship between HPV and cervical cancer in association with the high prevalence of high risk HPV genotypes led to the design of HPV vaccines based on the major capsid L1 protein. In recent years, capsid protein L2 has also become a focal point in the field of vaccine research. The present review focuses on the variability of HPV16 L1 and L2 genes, emphasizing the distribution of specific amino acid changes in the epitopes of capsid proteins. Moreover, a substantial bioinformatics analysis was conducted to describe the worldwide distribution of amino acid substitutions throughout HPV16 L1, L2 proteins. Five amino acid changes (T176N, N181T; EF loop), (T266A; FG loop), (T353P, T389S; HI loop) are frequently observed in the L1 hypervariable surface loops, while two amino acid substitutions (D43E, S122P) are adjacent to L2 specific epitopes. These changes have a high prevalence in certain geographic regions. The present review suggests that the extensive analysis of the amino acid substitutions in the HPV16 L1 immunodominant loops may provide insights concerning the ability of the virus in evading host immune response in certain populations. The genetic variability of the HPV16 L1 and L2 epitopes should be extensively analyzed in a given population.

SUBMITTER: Tsakogiannis D

PROVIDER: S-EPMC9867070 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas.

Tsakogiannis Dimitris D Nikolaidis Marios M Zagouri Flora F Zografos Eleni E Kottaridi Christine C Kyriakopoulou Zaharoula Z Tzioga Lamprini L Markoulatos Panayotis P Amoutzias Grigoris D GD Bletsa Garyfalia G

Viruses 20221231 1

The causal relationship between HPV and cervical cancer in association with the high prevalence of high risk HPV genotypes led to the design of HPV vaccines based on the major capsid L1 protein. In recent years, capsid protein L2 has also become a focal point in the field of vaccine research. The present review focuses on the variability of HPV16 L1 and L2 genes, emphasizing the distribution of specific amino acid changes in the epitopes of capsid proteins. Moreover, a substantial bioinformatics ...[more]

PMID: 36680181

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Project description:Multi-word expressions (MWEs) are fixed, conventional phrases often used by native speakers of a given language (L1). The type of MWEs investigated in this study were collocations. For bilinguals who have intensive contact with the second language (L2), collocational patterns can be transferred from the L2 to the L1 as a result of cross-linguistic influence (CLI). For example, bilingual migrants can accept collocations from their L2 translated to their L1 as correct. In this study, we asked whether such CLI is possible in native speakers living in the L1 environment and whether it depends on their L2 English proficiency. To this end, we created three lists of expressions in Polish: (1) well-formed Polish verb-noun collocations (e.g., ma sens - ∗has sense), (2) collocational calques from English (loan translations), where the English verb was replaced by a Polish translation equivalent (e.g., ∗ robi sens - makes sense), and, as a reference (3) absurd verb-noun expression, where the verb did not collocate with the noun (e.g., ∗ zjada sens - ∗eats sense). We embedded the three types of collocations in sentences and presented them to L1 Polish participants of varying L2 English proficiency in two experiments. We investigated whether L2 calques would (1) be explicitly judged as non-native in the L1; (2) whether they would evoke differential brain response than native L1 Polish equivalents in the event-related potentials (ERPs). We also explored whether the sensitivity to CLI in calques depended on participants' level of proficiency in L2 English. The results indicated that native speakers of Polish assessed the calques from English as less acceptable than the correct Polish collocations. Still, there was no difference in online processing of correct and calques collocations as measured by the ERPs. This suggests a dissociation between explicit offline judgments and indices of online language processing. Interestingly, English L2 proficiency did not modulate these effects. The results indicate that the influence of English on Polish is so pervasive that collocational calques from this language are likely to become accepted and used by Poles.

Project description:BackgroundProgrammed cell death ligand-1 (PD-L1) and ligand-2 (PD-L2) interaction with programmed cell death protein-1 (PD-1) represent an immune-inhibiting checkpoint mediating immune evasion and is, accordingly, an important target for blockade-based immunotherapy in cancer. In non-small-cell lung cancer (NSCLC), improved understanding of PD-1 checkpoint blockade-responsive biology and identification of biomarkers for prediction of a clinical response to immunotherapy is warranted. Thus, in the present study, we systematically described PD-L1 and PD-L2 expression correlated genes in NSCLC.MethodsWe performed comparative retrospective analyses to identify PD-L1 and PD-L2 mRNA expression correlated genes in NSCLC. For this, we examined available datasets from the cancer cell line encyclopedia (CCLE) project lung non-small-cell (Lung_NSC) and the cancer genome atlas (TCGA) projects lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC).ResultsAnalysis of the CCLE dataset Lung_NSC identified expression correlation between PD-L1 and PD-L2. Moreover, we identified expression correlation between 489 genes and PD-L1, 191 genes and PD-L2, and 111 genes for both. PD-L1 and PD-L2 also expression correlated in TCGA datasets LUAD and LUSC. In LUAD, we identified expression correlation between 257 genes and PD-L1, 914 genes and PD-L2, and 211 genes for both. In LUSC, we identified expression correlation between 26 genes and PD-L1, 326 genes and PD-L2, and 13 genes for both. Only a few genes expression correlated with PD-L1 and PD-L2 across the CCLE and TCGA datasets. Expression of Interferon signaling-involved genes converged in particular with the expression correlated genes for PD-L1 in Lung_NSC, for PD-L2 in LUSC, and for both PD-L1 and PD-L2 in LUAD. In LUSC, PD-L1, and to a lesser extent PD-L2, expression correlated with chromosome 9p24 localized genes, indicating a chromosome 9p24 topologically associated domain as an important driver of in particular LUSC PD-L1 expression. Expression correlation analyses of the PD-L1 and PD-L2 receptors programmed cell death protein-1 (PD-1), Cluster of differentiation 80 (CD80), and Repulsive guidance molecule B (RGMB) showed that PD-1 and CD80 expression correlated with both PD-L1 and PD-L2 in LUAD. CD80 expression correlated with PD-L2 in LUSC.ConclusionsWe present gene signatures associated with PD-L1 and PD-L2 mRNA expression in NSCLC which could possess importance in relation to understand PD-1 checkpoint blockade-responsive biology and development of gene signature based biomarkers for predicting clinical responses to immunotherapy.

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Dataset Information

Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas.

Publications

Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas.

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