Distinguishable topological properties of functional genome networks in HIV-1 reservoirs

Wisniewski, J.; Wiecek, K.; Ali, H.; Pyrc, K.; Kula-Pacurar, A.; Wagner, M.; CHEN, H.-C.

doi:10.1101/2024.02.05.578936

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bioRxiv · 10.1101/2024.02.05.578936

Distinguishable topological properties of functional genome networks in HIV-1 reservoirs

Wisniewski, J.·Wiecek, K.·Ali, H.·Pyrc, K.·Kula-Pacurar, A.·Wagner, M.·CHEN, H.-C.

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Abstract

HIV-1 reservoirs display heterogeneous nature, lodging both intact and defective proviruses. Recent evidence has shed light on their difference, particularly in the context of immune-mediated selection. To deepen our understanding of such heterogeneous HIV-1 reservoirs and their functional implications, we pioneered the integration of basic concepts of graph theory to characterize the composition of HIV-1 reservoirs. Our analysis revealed noticeable topological properties in networks, featuring immunologic signatures enriched by genes harboring intact and defective proviruses, when comparing antiretroviral therapy (ART)-treated HIV-1-infected individuals and elite controllers. The key variable, the rich factor, played a pivotal role in classifying distinct topological properties in networks. The host gene expression strengthened the accuracy of classification between elite controllers and ART-treated patients. Overall, our work provides a prime example of leveraging genomic approaches alongside mathematical tools to unravel the complexities of HIV-1 reservoirs.

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Wisniewski, J., Wiecek, K., Ali, H., Pyrc, K., Kula-Pacurar, A., Wagner, M., CHEN, H.-C.. 2024-02-08. Distinguishable topological properties of functional genome networks in HIV-1 reservoirs. https://doi.org/10.1101/2024.02.05.578936

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