Application of Whole-Genome Regulatory Networks in Studying Drug Action

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 3231

Special Issue Editor

Mayo Clinic Cancer Center, Mayo Clinic, Rochester, NY, USA
Interests: systems biology; systems pharmacology; network biology; disease network; gene regulatory network;

Special Issue Information

Dear Colleagues,

We would like to invite you to participate in this Special Issue, “Application of Whole-Genome Regulatory Networks in Studying Drug Action”.

The burgeoning of next-generation sequencing, systems biology and artificial intelligence in the past few years had provided an unprecedentedly detailed understanding of how gene regulatory networks under specific disease contexts at the genomic scale can affect the action and efficacy of drugs. Such genetic complexity is beyond the conventional drug discovery approach of solely maximizing the binding specificity of drugs to their respective targets but requires broader considerations to include the activities of regulatory networks within disease cells to enhance drug actions. State-of-the-art computational tool development including artificial intelligence and novel systems biology perspectives are needed to revolutionize “next-generation” drug discovery pipelines. The advancement of approaches to prioritize drugs and their respective targets under specific gene regulatory contexts can facilitate the translation of individualized and precision medicine.

The purpose of this Special Issue is to host research, perspectives, and review papers to further advance our understanding to better maximize drug efficacies and minimize side effects by incorporating new knowledge regarding how disease genes and the activity of drug targets are regulated genome-wide. New results, confirmatory results, and contradictory results will also be considered for publication.

Dr. Hu Li
Guest Editor

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Keywords

  • systems biology
  • systems pharmacology
  • network biology
  • disease network
  • gene regulatory network
  • reverse engineering
  • machine learning
  • artificial intelligence
  • precision medicine
  • individualized medicine
  • drug discovery

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Published Papers (1 paper)

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Research

14 pages, 2686 KiB  
Article
NR2F2 Regulates Cell Proliferation and Immunomodulation in Whartons’ Jelly Stem Cells
by Li Ma, Min Huang, Xiaohua Liao, Xiyu Cai and Qiang Wu
Genes 2022, 13(8), 1458; https://doi.org/10.3390/genes13081458 - 16 Aug 2022
Cited by 4 | Viewed by 2841
Abstract
(1) Background: Wharton’s Jelly stem cells (WJ-MSCs) are multipotent mesenchymal stem cells that can proliferate rapidly and have low immunogenicity. Therefore, WJ-MSCs have gained considerable attention in the fields of immunomodulation and disease treatment and have entered clinical trials for the treatment of [...] Read more.
(1) Background: Wharton’s Jelly stem cells (WJ-MSCs) are multipotent mesenchymal stem cells that can proliferate rapidly and have low immunogenicity. Therefore, WJ-MSCs have gained considerable attention in the fields of immunomodulation and disease treatment and have entered clinical trials for the treatment of various diseases. Therefore, it is crucial to study the underlying mechanisms of WJ-MSCs proliferation, immune regulation, and disease treatment. Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) is a transcription factor that is involved in the regulation of many different genes. However, it remains unknown how NR2F2 regulates stem cell identity in WJ-MSCs. (2) Methods: We used RNAi technology to knock down NR2F2 in WJ-MSCs, and studied the regulatory role of NR2F2 in WJ-MSCs by MTT, flow cytometry, RNA-seq, and other methods. We also utilized a co-culture system in which NR2F2-depleted WJ-MSCs with MH7A and HCT116/HepG2 were used to investigate the role of NR2F2 in immunomodulation and the inhibition of cancer cell growth. (3) Results: NR2F2 knockdown resulted in decreased expressions of Cyclin D1 and CDK4, slower cell proliferation, and increased expressions of IL6 and IL8. Furthermore, Cyclin D1, CDK4, and inflammatory factors were increased in human rheumatoid fibroblast-like synoviocyte line MH7A if co-cultured with NR2F2 depleted WJ-MSCs. In addition, we observed increased p53, decreased BCL-2, and increased cell apoptosis in liver cancer cell line HepG2 if co-cultured with NR2F2-depleted WJ-MSCs. (4) Conclusions: NR2F2 not only plays an important role in the cell cycle and immune regulation of WJ-MSCs but also has potential effects on the WJ-MSCs treatment of related diseases. Full article
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