1
|
Schwab B, Yin J. Computational multigene interactions in virus growth and infection spread. Virus Evol 2023; 10:vead082. [PMID: 38361828 PMCID: PMC10868543 DOI: 10.1093/ve/vead082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 02/17/2024] Open
Abstract
Viruses persist in nature owing to their extreme genetic heterogeneity and large population sizes, which enable them to evade host immune defenses, escape antiviral drugs, and adapt to new hosts. The persistence of viruses is challenging to study because mutations affect multiple virus genes, interactions among genes in their impacts on virus growth are seldom known, and measures of viral fitness are yet to be standardized. To address these challenges, we employed a data-driven computational model of cell infection by a virus. The infection model accounted for the kinetics of viral gene expression, functional gene-gene interactions, genome replication, and allocation of host cellular resources to produce progeny of vesicular stomatitis virus, a prototype RNA virus. We used this model to computationally probe how interactions among genes carrying up to eleven deleterious mutations affect different measures of virus fitness: single-cycle growth yields and multicycle rates of infection spread. Individual mutations were implemented by perturbing biophysical parameters associated with individual gene functions of the wild-type model. Our analysis revealed synergistic epistasis among deleterious mutations in their effects on virus yield; so adverse effects of single deleterious mutations were amplified by interaction. For the same mutations, multicycle infection spread indicated weak or negligible epistasis, where single mutations act alone in their effects on infection spread. These results were robust to simulation in high- and low-host resource environments. Our work highlights how different types and magnitudes of epistasis can arise for genetically identical virus variants, depending on the fitness measure. More broadly, gene-gene interactions can differently affect how viruses grow and spread.
Collapse
Affiliation(s)
- Bradley Schwab
- Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
| | - John Yin
- Wisconsin Institute for Discovery, Chemical and Biological Engineering, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA
| |
Collapse
|
2
|
Wang Y, Zhao Y, Li Y, Zhang K, Fan Y, Li B, Su W, Li S. piggyBac-mediated genomic integration of linear dsDNA-based library for deep mutational scanning in mammalian cells. Cell Mol Life Sci 2023; 80:321. [PMID: 37815732 PMCID: PMC11071730 DOI: 10.1007/s00018-023-04976-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Deep mutational scanning (DMS) makes it possible to perform massively parallel quantification of the relationship between genetic variants and phenotypes of interest. However, the difficulties in introducing large variant libraries into mammalian cells greatly hinder DMS under physiological states. Here, we developed two novel strategies for DMS library construction in mammalian cells, namely 'piggyBac-in vitro ligation' and 'piggyBac-in vitro ligation-PCR'. For the first strategy, we took the 'in vitro ligation' approach to prepare high-diversity linear dsDNAs, and integrate them into the mammalian genome with a piggyBac transposon system. For the second strategy, we further added a PCR step using the in vitro ligation dsDNAs as templates, for the construction of high-content genome-integrated libraries via large-scale transfection. Both strategies could successfully establish genome-integrated EGFP-chromophore-randomized libraries in HEK293T cells and enrich the green fluorescence-chromophore amino-acid sequences. And we further identified a novel transcriptional activator peptide with the 'piggyBac-in vitro ligation-PCR' strategy. Our novel strategies greatly facilitate the construction of large variant DMS library in mammalian cells, and may have great application potential in the future.
Collapse
Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yan Fan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Bo Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| |
Collapse
|