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Park J, Desai H, Liboy-Lugo JM, Gu S, Jowhar Z, Xu A, Floor SN. IGHMBP2 deletion suppresses translation and activates the integrated stress response. Life Sci Alliance 2024; 7:e202302554. [PMID: 38803225 PMCID: PMC11109757 DOI: 10.26508/lsa.202302554] [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: 12/22/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
IGHMBP2 is a nonessential, superfamily 1 DNA/RNA helicase that is mutated in patients with rare neuromuscular diseases SMARD1 and CMT2S. IGHMBP2 is implicated in translational and transcriptional regulation via biochemical association with ribosomal proteins, pre-rRNA processing factors, and tRNA-related species. To uncover the cellular consequences of perturbing IGHMBP2, we generated full and partial IGHMBP2 deletion K562 cell lines. Using polysome profiling and a nascent protein synthesis assay, we found that IGHMBP2 deletion modestly reduces global translation. We performed Ribo-seq and RNA-seq and identified diverse gene expression changes due to IGHMBP2 deletion, including ATF4 up-regulation. With recent studies showing the integrated stress response (ISR) can contribute to tRNA metabolism-linked neuropathies, we asked whether perturbing IGHMBP2 promotes ISR activation. We generated ATF4 reporter cell lines and found IGHMBP2 knockout cells demonstrate basal, chronic ISR activation. Our work expands upon the impact of IGHMBP2 in translation and elucidates molecular mechanisms that may link mutant IGHMBP2 to severe clinical phenotypes.
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Affiliation(s)
- Jesslyn Park
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- https://ror.org/043mz5j54 Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hetvee Desai
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - José M Liboy-Lugo
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- https://ror.org/043mz5j54 Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Sohyun Gu
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Ziad Jowhar
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- https://ror.org/043mz5j54 Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Xu
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- https://ror.org/043mz5j54 Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- https://ror.org/043mz5j54 Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- https://ror.org/043mz5j54 Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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Shao B, Yan J, Zhang J, Liu L, Chen Y, Buskirk AR. Riboformer: a deep learning framework for predicting context-dependent translation dynamics. Nat Commun 2024; 15:2011. [PMID: 38443396 PMCID: PMC10915169 DOI: 10.1038/s41467-024-46241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts in these data and identify sequence determinants of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. When trained on an unbiased dataset, Riboformer corrects experimental artifacts in previously unseen datasets, which reveals subtle differences in synonymous codon translation and uncovers a bottleneck in translation elongation. Further, we show that Riboformer can be combined with in silico mutagenesis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Lili Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ye Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Park JE, Desai H, Liboy-Lugo J, Gu S, Jowhar Z, Xu A, Floor SN. IGHMBP2 deletion suppresses translation and activates the integrated stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571166. [PMID: 38168189 PMCID: PMC10760061 DOI: 10.1101/2023.12.11.571166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
IGHMBP2 is a non-essential, superfamily 1 DNA/RNA helicase that is mutated in patients with rare neuromuscular diseases SMARD1 and CMT2S. IGHMBP2 is implicated in translational and transcriptional regulation via biochemical association with ribosomal proteins, pre-rRNA processing factors, and tRNA-related species. To uncover the cellular consequences of perturbing IGHMBP2, we generated full and partial IGHMBP2 deletion K562 cell lines. Using polysome profiling and a nascent protein synthesis assay, we found that IGHMBP2 deletion modestly reduces global translation. We performed Ribo-seq and RNA-seq and identified diverse gene expression changes due to IGHMBP2 deletion, including ATF4 upregulation. With recent studies showing the ISR can contribute to tRNA metabolism-linked neuropathies, we asked whether perturbing IGHMBP2 promotes ISR activation. We generated ATF4 reporter cell lines and found IGHMBP2 knockout cells demonstrate basal, chronic ISR activation. Our work expands upon the impact of IGHMBP2 in translation and elucidates molecular mechanisms that may link mutant IGHMBP2 to severe clinical phenotypes.
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Affiliation(s)
- Jesslyn E. Park
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Hetvee Desai
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
| | - José Liboy-Lugo
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Sohyun Gu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Ziad Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA, 94143
| | - Stephen N. Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, USA, 94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA, 94143
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Shao B, Yan J, Zhang J, Buskirk AR. Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538053. [PMID: 37163112 PMCID: PMC10168224 DOI: 10.1101/2023.04.24.538053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined with in silico mutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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