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Published on: May 31, 2024
Identification of novel anti-angiogenic factors by in silico functional gene screening method
Seok-Ki Lee1, Yong S Choi, Jaehyuk Cha
1Angiogenesis Research Laboratory, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, San 56-1, Shinlim-Dong, Kwanak-Gu, Seoul 151-742, South Korea.
Abstract:
Angiogenesis, the formation of new blood vessels out of pre-existing capillaries, occurs in a variety of pathophysiological conditions, and is regulated by a balance of angiogenic activators and inhibitors. To identify novel angiogenic factors, we developed a gene screening method by combining the prediction analysis of transcription factor (TF) binding site and the chromosomal localization analysis. First, we analyzed the promoter sequences from known angiogenesis-related factors using the MATINSPECTOR program in TRANSFAC database. Interestingly, we found that the binding site of LMO2 complex is highly conserved in the promoter regions of these factors. Second, we analyzed chromosome loci based on the hypothesis that angiogenesis-related factors might be co-localized in a specific chromosomal band. We found that angiogenesis-related factors are localized in specific 14 chromosomal bands including 5q31 and 19q13 using AngioDB and LocusLink database mining. From these two approaches, we identified 32 novel candidates that have the LMO2 complex binding site in their promoter and are located on one of 14 chromosomal bands. Among them, human recombinant troponin T and spectrin markedly inhibited the neovascularization in vivo and in vitro. Collectively, we suggest that the combination of the prediction analysis of TF binding site and the chromosomal localization analysis might be a useful strategy for gene screening of angiogenesis.
Insights
Researchers identified novel angiogenesis factors using a combined gene screening method. This approach identified troponin T and spectrin as inhibitors of new blood vessel formation.
Area of Science:
- Molecular Biology
- Genetics
- Biomedical Research
Background:
- Angiogenesis, the formation of new blood vessels, is crucial in various pathophysiological conditions.
- It is regulated by a delicate balance of angiogenic activators and inhibitors.
- Identifying novel angiogenic factors is essential for therapeutic development.
Purpose of the Study:
- To develop a novel gene screening method for identifying new angiogenesis-related factors.
- To combine transcription factor (TF) binding site prediction with chromosomal localization analysis.
- To discover novel candidates involved in angiogenesis regulation.
Main Methods:
- Analysis of promoter sequences of known angiogenesis-related factors for conserved TF binding sites (LMO2 complex) using MATINSPECTOR in TRANSFAC.
- Chromosomal localization analysis of angiogenesis-related factors using AngioDB and LocusLink to identify co-localized bands (e.g., 5q31, 19q13).
- Integration of TF binding site prediction and chromosomal localization to identify novel candidate genes.
Main Results:
- The LMO2 complex binding site was found to be highly conserved in the promoter regions of known angiogenesis-related factors.
- Angiogenesis-related factors were identified in specific chromosomal bands, including 5q31 and 19q13.
- 32 novel candidate genes were identified, possessing the LMO2 binding site and located on specific chromosomal bands.
- Human recombinant troponin T and spectrin significantly inhibited neovascularization both in vitro and in vivo.
Conclusions:
- The combined strategy of TF binding site prediction and chromosomal localization analysis is an effective approach for screening novel angiogenesis-related genes.
- Troponin T and spectrin emerge as promising candidates for further investigation in the context of angiogenesis inhibition.
- This methodology provides a powerful tool for discovering new factors involved in angiogenesis and related diseases.
