Comparison of Transcriptomic Signatures between Monkeypox-Infected Monkey and Human Cell Lines

Xuan, Do Thi Minh; Yeh, I‐Jeng; Wu, Chung-Che; Su, Chien Wei; Liu, Hsin-Liang; Chiao, Chung-Chieh; Ku, Su-Chi; Jiang, Junjian; Sun, Zhonghua; Ta, Hoang Dang Khoa; Anuraga, Gangga; Wang, Chih‐Yang; Yen, Meng‐Chi

doi:10.1155/2022/3883822

Cited by 30 publications

(25 citation statements)

References 78 publications

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“…They also compared the expression profile of MPXV to VACV and found that only the minority of transcripts are species-specific 15 . And though recent studies have re-evaluated these data using comparative pathway analyses, the detailed transcriptomic characteristics of MPXV-infected cells remains undescribed 16 . Thus, while micro-array-based techniques reveal useful insights, they are unable to resolve many aspects of the transcriptome, including the detection of the plethora of different transcript isoforms, which have been detected in closely related viruses, for example in VACV 17 .…”

Section: Background and Summarymentioning

confidence: 99%

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

Kakuk¹,

Dörmő²,

Csabai³

et al. 2022

Preprint

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The recent Monkeypox outbreak showed the importance of studying the basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. Our direct cDNA and native RNA sequencing data enable the in-depth characterization of the transcriptomic architecture and dynamics of the gene expressions of monkeypox virus; and also the deeper understanding of the changes it causes in the host cells on a transcriptome level.

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Section: Background and Summarymentioning

confidence: 99%

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

Kakuk¹,

Dörmő²,

Csabai³

et al. 2022

Preprint

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“…Next, we used the median expression of targeted genes and then performed a differential analysis with an algorithm in the "DESeq2" package in R/Bioconductor. After the differential analysis, results were utilized for the gene set enrichment analysis (GSEA) with the Hallmark database [71][72][73]. Then, we used the "fgsea" packages in R Studio software to evaluate enriched pathways in transcriptional data by the GSEA, and online platform (http://www.bioinformatics.com.cn/) and used "SRplot" for visualization (http://www.bioinformatics.com.cn/ srplot) [74,75].…”

Section: Functional Enrichment and Mirna-regulated Network Analysesmentioning

confidence: 99%

Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer

Liu

et al. 2022

Aging

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Breast cancer is one of the leading deaths in all kinds of malignancies; therefore, it is important for early detection. At the primary tumor site, tumor cells could take on mesenchymal properties, termed the epithelialto-mesenchymal transition (EMT). This process is partly regulated by members of the cadherin (CDH) family of genes, and it is an essential step in the formation of metastases. There has been a lot of study of the roles of some of the CDH family genes in cancer; however, a holistic approach examining the roles of distinct CDH family genes in the development of breast cancer remains largely unexplored. In the present study, we used a bioinformatics approach to examine expression profiles of CDH family genes using the Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, MetaCore, and Tumor IMmune Estimation Resource (TIMER) platforms. We revealed that CDH1/2/4/11/12/13 messenger (m)RNA levels are overexpressed in breast cancer cells compared to normal cells and were correlated with poor prognoses in breast cancer patients' distant metastasis-free survival. An enrichment analysis showed that high expressions of CDH1/2/4/11/12/13 were significantly correlated with cell adhesion, the extracellular matrix remodeling process, the EMT, WNT/beta-catenin, and interleukin-mediated immune responses. Collectively, CDH1/2/4/11/12/13 are thought to be potential biomarkers for breast cancer progression and metastasis. AGING Table 1. Basic characteristics of the CDH gene family.

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“…While millions of deaths were reported worldwide due to the SARS-CoV-2 pandemic [ 1 ], a new zoonotic disease, monkeypox (mPox), caused by the monkeypox virus (MPV), has become a severe public health concern. The monkeypox virus, closely related to the variola virus that causes smallpox, was initially identified in monkeys in 1958 [ 2 ] and in humans in a forested area of central Africa in 1970 [ 3 , 4 ]. While mPox is endemic in parts of west and central Africa, its recent occurrence in a number of nonendemic locations outside of Africa has caused public health officials to express grave concerns [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…While mPox is endemic in parts of west and central Africa, its recent occurrence in a number of nonendemic locations outside of Africa has caused public health officials to express grave concerns [ 5 ]. Since smallpox was eradicated due to widespread vaccination, there have been very few natural outbreaks of the Orthopoxvirus until recently [ 2 ]. However, after the confirmed outbreaks in over 70 countries where the virus has not been reported before, the World Health Organization on July 23 issued its highest level alert, designating mPox as a public health emergency of international concern.…”

Section: Introductionmentioning

confidence: 99%

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Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study

Mazumder

Hasan

Fatema

et al. 2023

Journal of Immunology Research

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Background. Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus’s cell surface binding protein through an in silico approach to combat monkeypox-associated diseases. Results. The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among the T cell epitopes, epitope “ILFLMSQRY” was found to be one of the most potential peptide vaccine candidates. The docking analysis revealed an excellent binding affinity of this epitope with the human receptor HLA-B ∗ 15:01 with a very low binding energy (-7.5 kcal/mol). Conclusion. The outcome of this research will aid the development of a T cell epitope-based peptide vaccine, and the discovered B and T cell epitopes will facilitate the creation of other epitope and multi-epitope-based vaccines in the future. This research will also serve as a basis for further in vitro and in vivo analysis to develop a vaccine that is effective against the monkeypox virus.

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Comparison of Transcriptomic Signatures between Monkeypox-Infected Monkey and Human Cell Lines

Cited by 30 publications

References 78 publications

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer

Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study

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