Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks

Meng, Xiangmao; Li, Wenkai; Ju, Xu; Bedru, Hayat Dino; Wang, Wenkang; Wu, Fang‐Xiang; Li, Min

doi:10.1109/tnse.2022.3185717

Cited by 9 publications

(8 citation statements)

References 56 publications

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“…Such proteins, often referred to as hub proteins or genes, are typically central to the network and are deemed crucial molecular targets. This concept is supported by Meng et al (2022) [49], who emphasize…”

Section: Bioinformatics-based Investigation Of Protein-protein Intera...mentioning

confidence: 85%

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Wound healing potential of Cystoseira/mesenchymal stem cells in immunosuppressed rats supported by overwhelming immuno-inflammatory crosstalk

Zahran,

Mohyeldin,

Abd El-Mordy

et al. 2024

PLoS ONE

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Wound healing, one of the most intricate and dynamic processes of the body, maintains skin integrity following trauma. One of the main issues that still exists is impaired wound healing, particularly for immunosuppressed patients. Recently, natural products from marine environments have been employed in wound-repairing activities. This work investigates the mesenchymal stem cells in the combined capacity of the bone marrow (BMMSC) for wound healing and Cystoseira sp. Algae extract in immunosuppressed rats. High-resolution liquid chromatography / MS investigation of Cystoseira extract revealed the prevalence of fatty acids that have wound-soothing potential. From constructed PPI network for wound healing and further analysis through molecular docking and molecular dynamics (MD) simulation experiments suggested that cystalgerone metabolite may be responsible for the wound healing-promoting effect of Cystoseira extract. According to the CD marker characterization of the BMMSC, 98.21% of them expressed CD90, and 97.1% expressed CD105. Sixteen d after immunity suppression (by 40 mg/kg hydrocortisone daily), an incision was made in the dorsal skin of the rat. The treatments were applied for 16 d and samples were taken from the tested groups on the 8th, 14th, and 16th days. The BMMSCs / Cystoseira group showed significantly improved wound closure, thickness, density of new layers, and skin elasticity than the control group (p < 0.001). The BMMSCs / Cystoseira combination significantly reduced the oxidative indicators, pro-inflammatory cytokines, and immune markers, according to the RT-PCR gene expression study. In order to delve deeper into the complex interconnections among wound healing-related biological targets and pinpoint key factors in this complex process, we engaged in network pharmacology and computational research. Subsequently, we conducted a comprehensive computational analysis, including reverse docking, free energy (ΔG) computation, and molecular dynamics simulations, on the molecular structures of the annotated compounds. The purpose of this investigation was to identify potential new targets for these chemicals as well as any potential interactions they may have with different signaling pathways related to the wound healing process. Our research indicates that the primary compounds of Cystoseira holds potential wound healing therapeutic activity. Although more safety testing and clinical studies are required, the combination has great potential for regenerative medicine and could be a revolutionary advance in the healing of the wounds of immunosuppressed patients.

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Section: Bioinformatics-based Investigation Of Protein-protein Intera...mentioning

confidence: 85%

“…This concept is supported by Meng et al . (2022) [ 49 ], who emphasize the significance of these hub proteins in therapeutic strategies. In line with this perspective, our study concentrated on the upper 4% of these proteins, amounting to ten proteins ( Fig 8B ).…”

Section: Resultsmentioning

confidence: 99%

Wound healing potential of Cystoseira/mesenchymal stem cells in immunosuppressed rats supported by overwhelming immuno-inflammatory crosstalk

Zahran,

Mohyeldin,

Abd El-Mordy

et al. 2024

PLoS ONE

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“…Therapeutic strategies for cancer may have a better chance of success if they focus on proteins having a high level of interaction, as these are typically the most significant and pertinent molecular targets (i.e., hub proteins or genes) in a given network 77 . Therefore, we focused on the top 8% (38 proteins) of the most intensively molecular targets that interact (i.e., hub proteins) sorted according to their degree value (Fig.…”

Section: Ppi Network Of the Cancer Related Targets And Kegg-based Enr...mentioning

confidence: 99%

New cytotoxic dammarane type saponins from Ziziphus spina-christi

Elmaidomy,

El Zawily,

Salem

et al. 2023

Sci Rep

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Cancer is the world's second-leading cause of death. Drug development efforts frequently focus on medicinal plants since they are a valuable source of anticancer medications. A phytochemical investigation of the edible Ziziphus spina-christi (F. Rhamnaceae) leaf extract afforded two new dammarane type saponins identified as christinin E and F (1, 2), along with the known compound christinin A (3). Different cancer cell lines, such as lung cancer (A549), glioblastoma (U87), breast cancer (MDA-MB-231), and colorectal carcinoma (CT-26) cell lines, were used to investigate the extracted compounds' cytotoxic properties. Our findings showed significant effects on all the tested cell lines at varying concentrations (1, 5, 10, and 20 µg/mL). The three compounds exhibited potent activity at low concentrations (< 10 μg/mL), as evidenced by their low IC50 values. To further investigate the complex relationships between these identified cancer-relevant biological targets and to identify critical targets in the pathogenesis of the disease, we turned to network pharmacology and in silico-based investigations. Following this, in silico-based analysis (e.g., inverse docking, ΔG calculation, and molecular dynamics simulation) was performed on the structures of the isolated compounds to identify additional potential targets for these compounds and their likely interactions with various signalling pathways relevant to this disease. Based on our findings, Z. spina-christi's compounds showed promise as potential anti-cancer therapeutic leads in the future.

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“…In [3], Li et al constructed a temporal network using spatial information and gene expression data and then applied the clustering algorithm on the temporal network constructed to identify protein complexes. Similarly in [4], Meng et al constructed temporal-spatial dynamic PPI networks by integrating protein-protein interaction networks with gene expression data and subcellular localization information. They introduced the maximum degree centrality (MDC) method the constructed temporal network to evaluate the essentiality of hub proteins.…”

Section: Introductionmentioning

confidence: 99%

Identifying Stage-Specific Genes in Disease Progression using Transition Centrality on Disease Temporal Graphs

Sahu,

2023

Preprint

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The search for biomarkers of diseases has traditionally involved analyzing disease data as a whole. But this approach has largely ignored the significance of disease progression at different stages. Acknowledging the fact that different genes may be responsible for disease progression in different stages, we have developed a novel approach to analyse the temporal graphs that employs a modified version of betweenness centrality, known as ''transition centrality''. Applying this measure to the stage-wise data of three common diseases, namely Alzheimer's disease, Parkinson's disease, and Human breast cancer, we identified successfully a set of genes that may be key players in disease progression. The findings reveal that stage-specific genes can be identified using transition centrality as the specificity of these genes in a particular stage was validated through an extensive review of the relevant literature. Remarkably, this analysis yielded a number of promising disease-related genes for each of the diseases that have been studied, such as RARA and NOS1 in Alzheimer's disease, LRRK2 in Parkinson's disease, and BRCA1, ACTB, TYMS, and many others in human breast cancer. Our results demonstrate that the transition centrality analysis can be utilized to identify stage-specific genes of diseases.

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Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks

Cited by 9 publications

References 56 publications

Wound healing potential of Cystoseira/mesenchymal stem cells in immunosuppressed rats supported by overwhelming immuno-inflammatory crosstalk

Wound healing potential of Cystoseira/mesenchymal stem cells in immunosuppressed rats supported by overwhelming immuno-inflammatory crosstalk

New cytotoxic dammarane type saponins from Ziziphus spina-christi

Identifying Stage-Specific Genes in Disease Progression using Transition Centrality on Disease Temporal Graphs

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