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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. Life Sci Alliance 2024; 7:e202402641. [PMID: 39013578 PMCID: PMC11252446 DOI: 10.26508/lsa.202402641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
Cancer development and progression are generally associated with gene dysregulation, often resulting from changes in the transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network, as well as an extensive promoter clone resource for future studies. Highly connected TFs bind to promoters of genes associated with either good or poor cancer prognosis, suggesting that strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene-targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activators or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF ESR1 in DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study broadens our knowledge of the TFs involved in cancer gene regulation and provides a valuable resource for future studies and therapeutics.
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Affiliation(s)
- Yunwei Lu
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Anna Berenson
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Ryan Lane
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Isabelle Guelin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Zhaorong Li
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Yilin Chen
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Sakshi Shah
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Meimei Yin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | | | - Ana Fiszbein
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Juan Ignacio Fuxman Bass
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
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Rottenberg JT, Taslim TH, Soto-Ugaldi LF, Martinez-Cuesta L, Martinez-Calejman C, Fuxman Bass JI. Viral cis-regulatory elements as sensors of cellular states and environmental cues. Trends Genet 2024:S0168-9525(24)00108-2. [PMID: 38821843 DOI: 10.1016/j.tig.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
To withstand a hostile cellular environment and replicate, viruses must sense, interpret, and respond to many internal and external cues. Retroviruses and DNA viruses can intercept these cues impinging on host transcription factors via cis-regulatory elements (CREs) in viral genomes, allowing them to sense and coordinate context-specific responses to varied signals. Here, we explore the characteristics of viral CREs, the classes of signals and host transcription factors that regulate them, and how this informs outcomes of viral replication, immune evasion, and latency. We propose that viral CREs constitute central hubs for signal integration from multiple pathways and that sequence variation between viral isolates can rapidly rewire sensing mechanisms, contributing to the variability observed in patient outcomes.
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Affiliation(s)
| | - Tommy H Taslim
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Lucia Martinez-Cuesta
- Department of Biology, Boston University, Boston, MA, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA.
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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577099. [PMID: 38352498 PMCID: PMC10862707 DOI: 10.1101/2024.01.24.577099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Cancer development and progression are generally associated with dysregulation of gene expression, often resulting from changes in transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network as well as an extensive promoter clone resource for future studies. Most highly connected TFs do not show a preference for binding to promoters of genes associated with either good or poor cancer prognosis, suggesting that emerging strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activator or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF estrogen receptor ɑ (ESR1) on DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study not only broadens our knowledge of TFs involved in the cancer gene regulatory network but also provides a valuable resource for future studies, laying a foundation for potential therapeutic strategies targeting TFs in cancer.
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Affiliation(s)
- Yunwei Lu
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Anna Berenson
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
| | - Ryan Lane
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Isabelle Guelin
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Yilin Chen
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Sakshi Shah
- Biology Department, Boston University, Boston, MA, 02215, USA
| | - Meimei Yin
- Biology Department, Boston University, Boston, MA, 02215, USA
| | | | - Ana Fiszbein
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Juan Ignacio Fuxman Bass
- Biology Department, Boston University, Boston, MA, 02215, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, 02215, USA
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
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