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1.
BMC Genomics ; 25(1): 378, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38632523

RESUMO

OBJECTIVE: This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS: Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS: All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION: SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Pandemias , Genômica , China , Aminoácidos , Nucleotídeos
2.
J Med Virol ; 96(8): e29846, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39138641

RESUMO

Seasonal H3N2 influenza virus, known for its rapid evolution, poses a serious threat to human health. This study focuses on analyzing the influenza virus trends in Jining City (2018-2023) and understanding the evolving nature of H3N2 strains. Data on influenza-like cases were gathered from Jining City's sentinel hospitals: Jining First People's Hospital and Rencheng Maternal and Child Health Hospital, using the Chinese Influenza Surveillance Information System. Over the period from 2018 to 2023, 7844 throat swab specimens were assessed using real-time fluorescence quantitative PCR for influenza virus nucleic acid detection. For cases positive for seasonal H3N2 influenza virus, virus isolation was followed by whole genome sequencing. Evolutionary trees were built for the eight gene segments, and protein variation analysis was performed. From 2018 to 2023, influenza-like cases in Jining City represented 6.99% (237 299/3 397 247) of outpatient visits, peaking in December and January. Influenza virus was detected in 15.67% (1229/7844) of cases, primarily from December to February. Notably, no cases were found in the 2020-2021 season. Full genome sequencing was conducted on 70 seasonal H3N2 strains, revealing distinct evolutionary branches across seasons. Significant antigenic site variations in the HA protein were noted. No resistance mutations to inhibitors were found, but some strains exhibited mutations in PA, NS1, PA-X, and PB1-F2. Influenza trends in Jining City saw significant shifts in the 2020-2021 and 2022-2023 seasons. Seasonal H3N2 exhibited rapid evolution. Sustained vigilance is imperative for vaccine updates and antiviral selection.


Assuntos
Genoma Viral , Vírus da Influenza A Subtipo H3N2 , Influenza Humana , Filogenia , Estações do Ano , Sequenciamento Completo do Genoma , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/isolamento & purificação , Humanos , Influenza Humana/epidemiologia , Influenza Humana/virologia , China/epidemiologia , Epidemias , Evolução Molecular
3.
Cancer Cell Int ; 24(1): 58, 2024 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-38321460

RESUMO

Tongue squamous cell carcinoma (TSCC) is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. We aim to identify and verify potential biomarkers for TSCC using bioinformatics analysis. To begin with, we examined clinical and RNA expression information of individuals with TSCC from the Gene Expression Omnibus (GEO) database. Differential expression analysis and functional analysis were conducted. Multiple machine-learning strategies were next employed to screen and determine the hub gene, and receiver operating characteristic (ROC) analysis was used to assess diagnostic value. Semaphorin3C (SEMA3C) was identified as a critical biomarker, presenting high diagnostic accuracy for TSCC. In the validation cohorts, SEMA3C exhibited high expression levels in TSCC. The high expression of SEMA3C was a poor prognostic factor in TSCC by the Kaplan-Meier curve. Based on the Gene Ontology (GO) analysis, SEMA3C was mapped in terms related to cell adhesion, positive regulation of JAK-STAT, positive regulation of stem cell maintenance, and positive regulation of NF-κB activity. Single-cell RNA sequencing (ScRNA-seq) analysis showed cells expressing SEMA3C were predominantly tumor cells. Then, we further verified that SEMA3C had high expression in TSCC clinical samples. In addition, the knockdown of SEMA3C suppressed the proliferation, migration, and invasion of TSCC cells in vitro. This study is the first to report the involvement of SEMA3C in TSCC, suggesting that upregulated SEMA3C could be a novel and critical potential biomarker for future predictive diagnostics, prevention, prognostic assessment, and personalized medical services in TSCC.

4.
Eur J Med Res ; 29(1): 428, 2024 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-39169439

RESUMO

OBJECTIVE: In this study, we employed a bioinformatics approach to identify diagnostic biomarkers for tongue squamous cell carcinoma (TSCC) and investigate the infiltration of immune cells in TSCC, as well as the relationship between biomarkers and immune cells. METHODS: We obtained the TSCC expression dataset from a database and conducted differential gene expression analysis between TSCC and adjacent normal tissues using R software. Enrichment analysis of the differentially expressed genes (DEGs) was performed using the DAVID website. Protein interaction networks for the DEGs were constructed, and hub genes were identified using tools such as STRING and Cytoscape. Survival analysis was conducted to identify diagnostic biomarkers and the infiltration of immune cells in TSCC was analyzed using the inverse convolution algorithm with Cibersort software. Finally, the expression of the discovered molecules was verified through clinical pathological sections. RESULTS: We identified 24 DEGs in TSCC, primarily associated with signal transduction, substance metabolism, innate immune response, and other related signaling pathways. Among the 24 hub genes screened through the construction of a protein-protein interaction (PPI) network, seven (MMP13, POSTN, MMP9, MMP10, MMP3, SPP1, MMP1) exhibited prognostic value. Survival analysis indicated that SPP1 demonstrated diagnostic potential. The expression level of the SPP1 gene showed a correlation with TSCC as well as several immune cell types, including macrophage M0, M1, M2, CD8+ T cell, activated NK cell, and monocyte (p < 0.05). Histological results confirmed higher expression of SPP1 in TSCC tissues compared to adjacent non-cancerous tissues, particularly in CD68-expressing macrophages. CONCLUSION: Our findings suggest that SPP1 serves as a diagnostic biomarker for TSCC and is involved in immune cell infiltration within TSCC tissues. The correlation between SPP1 and macrophages may offer new insights for targeted therapeutic research on TSCC.


Assuntos
Biomarcadores Tumorais , Carcinoma de Células Escamosas , Biologia Computacional , Mapas de Interação de Proteínas , Neoplasias da Língua , Humanos , Neoplasias da Língua/genética , Neoplasias da Língua/imunologia , Neoplasias da Língua/patologia , Neoplasias da Língua/metabolismo , Biologia Computacional/métodos , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Mapas de Interação de Proteínas/genética , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/imunologia , Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/patologia , Regulação Neoplásica da Expressão Gênica , Prognóstico , Osteopontina/genética , Osteopontina/metabolismo , Perfilação da Expressão Gênica/métodos , Redes Reguladoras de Genes
5.
Heliyon ; 10(7): e28325, 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38571655

RESUMO

Background: Periodontal disease and coronary heart disease are both prevalent diseases worldwide and cause patients physical and mental suffering and a global burden. Recent studies have suggested a link between periodontal disease and coronary heart disease, but there is less research in this field from the perspective of bibliometrics. Objective: This study aimed to quantitatively analyze the literature on periodontal disease and coronary heart disease to summarize intellectual bases, research hotspots, and emerging trends and pave the way for future research. Methods: The Science Citation Index Expanded database was used to retrieve study records on periodontal disease and coronary heart disease from 1993 to 2022. After manual screening, the data were used for cooperative network analysis (including countries/regions, institutions and authors), keyword analysis, and reference co-citation analysis by CiteSpace software. Microsoft Excel 2019 was applied for curve fitting of annual trend in publications and citations. Results: A total of 580 studies were included in the analysis. The number of publications and citations in this field has shown an upward trend over the past 30 years. There was less direct collaboration among authors and institutions in this field but closer collaboration between countries. The United States was the country with the most published articles in this field (169/580, 29.14%). Based on the results of keyword analysis and literature co-citation analysis, C-reactive protein, oral flora, atherosclerosis, infection, and inflammation were previous research hotspots, while global burden and cardiovascular outcomes were considered emerging trends in this field. Conclusion: Studies on periodontal disease and coronary heart disease, which have attracted the attention of an increasing number of researchers, have been successfully analyzed using bibliometrics and visualization techniques. This paper will help scholars better understand the dynamic evolution of periodontal disease and coronary heart disease and point out the direction for future research. Clinical significance: This paper presents an overview between periodontal disease and coronary heart disease. Further exploration of the two diseases themselves and the potential causal relationship between the two is necessary and relevant, which may impact basic research, diagnosis, and treatment related to both diseases. This will aid the work of researchers and specialist doctors, and ultimately benefit patients with both diseases.

6.
Front Microbiol ; 14: 1196451, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37426015

RESUMO

Background: The influenza virus poses a significant threat to global public health due to its high mutation rate. Continuous surveillance, development of new vaccines, and public health measures are crucial in managing and mitigating the impact of influenza outbreaks. Methods: Nasal swabs were collected from individuals with influenza-like symptoms in Jining City during 2021-2022. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses, followed by isolation using MDCK cells. Additionally, nucleic acid detection was performed to identify influenza A H1N1, seasonal H3N2, B/Victoria, and B/Yamagata strains. Whole-genome sequencing was conducted on 24 influenza virus strains, and subsequent analyses included characterization, phylogenetic construction, mutation analysis, and assessment of nucleotide diversity. Results: A total of 1,543 throat swab samples were collected. The study revealed the dominance of the B/Victoria influenza virus in Jining during 2021-2022. Whole-genome sequencing showed co-prevalence of B/Victoria influenza viruses in the branches of Victoria clade 1A.3a.1 and Victoria clade 1A.3a.2, with a higher incidence observed in winter and spring. Comparative analysis demonstrated lower similarity in the HA, MP, and PB2 gene segments of the 24 sequenced influenza virus strains compared to the Northern Hemisphere vaccine strain B/Washington/02/2019. Mutations were identified in all antigenic epitopes of the HA protein at R133G, N150K, and N197D, and the 17-sequence antigenic epitopes exhibited more than 4 amino acid variation sites, resulting in antigenic drift. Moreover, one sequence had a D197N mutation in the NA protein, while seven sequences had a K338R mutation in the PA protein. Conclusion: This study highlights the predominant presence of B/Victoria influenza strain in Jining from 2021 to 2022. The analysis also identified amino acid site variations in the antigenic epitopes, contributing to antigenic drift.

7.
J Tissue Eng ; 11: 2041731420930379, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32566118

RESUMO

Mesenchymal stem cells sheets have been verified as a promising non-scaffold strategy for bone regeneration. Alveolar bone marrow mesenchymal stem cells, derived from neural crest, have the character of easily obtained and strong multi-differential potential. However, the bone regenerative features of alveolar bone marrow mesenchymal stem cells sheets in the craniofacial region remain unclear. The purpose of the present study was to compare the osteogenic differentiation and bone defect repairment characteristics of bone marrow mesenchymal stem cells sheets derived from alveolar bone (alveolar bone marrow mesenchymal stem cells) and iliac bone (Lon-bone marrow mesenchymal stem cells) in vitro and in vivo. Histology character, osteogenic differentiation, and osteogenic gene expression of human alveolar bone marrow mesenchymal stem cells and Lon-bone marrow mesenchymal stem cells were compared in vitro. The cell sheets were implanted in rabbit calvarial defects to evaluate tissue regeneration characteristics. Integrated bioinformatics analysis was used to reveal the specific gene and pathways expression profile of alveolar bone marrow mesenchymal stem cells. Our results showed that alveolar bone marrow mesenchymal stem cells had higher osteogenic differentiation than Lon-bone marrow mesenchymal stem cells. Although no obvious differences were found in the histological structure, fibronectin and integrin ß1 expression between them, alveolar-bone marrow mesenchymal stem cells sheet exhibited higher mineral deposition and expression levels of osteogenic marker genes. After being transplanted in the rabbit calvarial defects area, the results showed that greater bone volume and trabecular thickness regeneration were found in bone marrow mesenchymal stem cells sheet group compared to Lon-bone marrow mesenchymal stem cells group at both 4 weeks and 8 weeks. Finally, datasets of bone marrow mesenchymal stem cells versus Lon-bone marrow mesenchymal stem cells, and periodontal ligament mesenchymal stem cells (another neural crest derived mesenchymal stem cells) versus umbilical cord mesenchymal stem cells were analyzed. Total 71 differential genes were identified by overlap between the 2 datasets. Homeobox genes, such as LHX8, MKX, PAX9, MSX, and HOX, were identified as the most significantly changed and would be potential specific genes in neural crest mesenchymal stem cells. In conclusion, the Al-bone marrow mesenchymal stem cells sheet-based tissue regeneration appears to be a promising strategy for craniofacial defect repair in future clinical applications.

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