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Montenarh M, Götz C. Protein Kinase CK2α', More than a Backup of CK2α. Cells 2023; 12:2834. [PMID: 38132153 PMCID: PMC10741536 DOI: 10.3390/cells12242834] [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: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The serine/threonine protein kinase CK2 is implicated in the regulation of fundamental processes in eukaryotic cells. CK2 consists of two catalytic α or α' isoforms and two regulatory CK2β subunits. These three proteins exist in a free form, bound to other cellular proteins, as tetrameric holoenzymes composed of CK2α2/β2, CK2αα'/β2, or CK2α'2/β2 as well as in higher molecular forms of the tetramers. The catalytic domains of CK2α and CK2α' share a 90% identity. As CK2α contains a unique C-terminal sequence. Both proteins function as protein kinases. These properties raised the question of whether both isoforms are just backups of each other or whether they are regulated differently and may then function in an isoform-specific manner. The present review provides observations that the regulation of both CK2α isoforms is partly different concerning the subcellular localization, post-translational modifications, and aggregation. Up to now, there are only a few isoform-specific cellular binding partners. The expression of both CK2α isoforms seems to vary in different cell lines, in tissues, in the cell cycle, and with differentiation. There are different reports about the expression and the functions of the CK2α isoforms in tumor cells and tissues. In many cases, a cell-type-specific expression and function is known, which raises the question about cell-specific regulators of both isoforms. Another future challenge is the identification or design of CK2α'-specific inhibitors.
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Affiliation(s)
- Mathias Montenarh
- Medical Biochemistry and Molecular Biology, Saarland University, Building 44, 66421 Homburg, Germany;
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202
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Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fábián Z, Gambus A, Mailand N, Duxin JP, Nielsen ML. Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nat Commun 2023; 14:8293. [PMID: 38097601 PMCID: PMC10721886 DOI: 10.1038/s41467-023-43873-0] [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: 05/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFβ-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFβ-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.
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Affiliation(s)
- Camilla S Colding-Christensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Javier Arroyo-Gomez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Connor Arkinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- California Institute for Quantitative Biosciences and Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Niels Mailand
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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203
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Manousakis E, Miralles CM, Esquerda MG, Wright RHG. CDKN1A/p21 in Breast Cancer: Part of the Problem, or Part of the Solution? Int J Mol Sci 2023; 24:17488. [PMID: 38139316 PMCID: PMC10743848 DOI: 10.3390/ijms242417488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cyclin-dependent kinase inhibitor 1A (Cip1/Waf1/CDKN1A/p21) is a well-established protein, primarily recognised for its pivotal role in the cell cycle, where it induces cell cycle arrest by inhibiting the activity of cyclin-dependent kinases (CDKs). Over the years, extensive research has shed light on various additional mechanisms involving CDKN1A/p21, implicating it in processes such as apoptosis, DNA damage response (DDR), and the regulation of stem cell fate. Interestingly, p21 can function either as an oncogene or as a tumour suppressor in these contexts. Complicating matters further, the expression of CDKN1A/p21 is elevated in certain tumour types while downregulated in others. In this comprehensive review, we provide an overview of the multifaceted functions of CDKN1A/p21, present clinical data pertaining to cancer patients, and delve into potential strategies for targeting CDKN1A/p21 as a therapeutic approach to cancer. Manipulating CDKN1A/p21 shows great promise for therapy given its involvement in multiple cancer hallmarks, such as sustained cell proliferation, the renewal of cancer stem cells (CSCs), epithelial-mesenchymal transition (EMT), cell migration, and resistance to chemotherapy. Given the dual role of CDKN1A/p21 in these processes, a more in-depth understanding of its specific mechanisms of action and its regulatory network is imperative to establishing successful therapeutic interventions.
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Affiliation(s)
| | | | | | - Roni H. G. Wright
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Barcelona, Spain
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204
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Jiang B, Yang J, He R, Wang D, Huang Y, Zhao G, Ning M, Zeng T, Li G. Integrated multi-omics analysis for lung adenocarcinoma in Xuanwei, China. Aging (Albany NY) 2023; 15:14263-14291. [PMID: 38095636 PMCID: PMC10756121 DOI: 10.18632/aging.205300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Xuanwei lung cancer (XWLC) is well-known for its high incidence and mortality. However, the molecular mechanism is still unclear. METHODS We performed a comprehensive transcriptomic, proteomic, and phosphoproteomic characterization of tumors and matched normal adjacent tissues from three XWLC patients with lung adenocarcinoma (LUAD). RESULTS Integrated transcriptome and proteome analysis revealed dysregulated molecules and pathways in tumors and identified enhanced metabolic-disease coupling. Non-coding RNAs were widely involved in post-transcriptional regulatory mechanisms to coordinate the progress of LUAD and partially explained the molecular differences between RNA and protein expression patterns. Phosphoproteome provided evidence support for new phosphate sites, reporting the potential roles of core kinase family members and key kinase pathways involved in metabolism, immunity, and homeostasis. In addition, by comparing with the previous LUAD researches, we emphasized the higher degree of oxidative phosphorylation in Xuanwei LUAD and pointed that VIPR1 deficiency aggravated metabolic dysfunction. CONCLUSION Our integrated multi-omics analysis provided a powerful resource for a systematic understanding of the molecular structure of XWLC and proposed therapeutic opportunities based on redox metabolism.
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Affiliation(s)
- Boyi Jiang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Jiapeng Yang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Rui He
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Dong Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Yunchao Huang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangqiang Zhao
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Mingjie Ning
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Teng Zeng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangjian Li
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
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205
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Cordeiro-Spinetti E, Rothbart SB. Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights. Biochem J 2023; 480:1969-1986. [PMID: 38054592 DOI: 10.1042/bcj20230223] [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: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Lysine methylation signaling is well studied for its key roles in the regulation of transcription states through modifications on histone proteins. While histone lysine methylation has been extensively studied, recent discoveries of lysine methylation on thousands of non-histone proteins has broadened our appreciation for this small chemical modification in the regulation of protein function. In this review, we highlight the significance of histone and non-histone lysine methylation signaling in skeletal muscle biology, spanning development, maintenance, regeneration, and disease progression. Furthermore, we discuss potential future implications for its roles in skeletal muscle biology as well as clinical applications for the treatment of skeletal muscle-related diseases.
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Affiliation(s)
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, U.S.A
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206
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Abbaali I, Truong D, Day SD, Mushayeed F, Ganesh B, Haro-Ramirez N, Isles J, Nag H, Pham C, Shah P, Tomar I, Manel-Romero C, Morrissette NS. The tubulin database: Linking mutations, modifications, ligands and local interactions. PLoS One 2023; 18:e0295279. [PMID: 38064432 PMCID: PMC10707541 DOI: 10.1371/journal.pone.0295279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Microtubules are polymeric filaments, constructed of α-β tubulin heterodimers that underlie critical subcellular structures in eukaryotic organisms. Four homologous proteins (γ-, δ-, ε- and ζ-tubulin) additionally contribute to specialized microtubule functions. Although there is an immense volume of publicly available data pertaining to tubulins, it is difficult to assimilate all potentially relevant information across diverse organisms, isotypes, and categories of data. We previously assembled an extensive web-based catalogue of published missense mutations to tubulins with >1,500 entries that each document a specific substitution to a discrete tubulin, the species where the mutation was described and the associated phenotype with hyperlinks to the amino acid sequence and citation(s) for research. This report describes a significant update and expansion of our online resource (TubulinDB.bio.uci.edu) to nearly 18,000 entries. It now encompasses a cross-referenced catalog of post-translational modifications (PTMs) to tubulin drawn from public datasets, primary literature, and predictive algorithms. In addition, tubulin protein structures were used to define local interactions with bound ligands (GTP, GDP and diverse microtubule-targeting agents) and amino acids at the intradimer interface, within the microtubule lattice and with associated proteins. To effectively cross-reference these datasets, we established a universal tubulin numbering system to map entries into a common framework that accommodates specific insertions and deletions to tubulins. Indexing and cross-referencing permitted us to discern previously unappreciated patterns. We describe previously unlinked observations of loss of PTM sites in the context of cancer cells and tubulinopathies. Similarly, we expanded the set of clinical substitutions that may compromise MAP or microtubule-motor interactions by collecting tubulin missense mutations that alter amino acids at the interface with dynein and doublecortin. By expanding the database as a curated resource, we hope to relate model organism data to clinical findings of pathogenic tubulin variants. Ultimately, we aim to aid researchers in hypothesis generation and design of studies to dissect tubulin function.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Shania Deon Day
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Faliha Mushayeed
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Bhargavi Ganesh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Nancy Haro-Ramirez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Juliet Isles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Hindol Nag
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Catherine Pham
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Priya Shah
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Ishaan Tomar
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Carolina Manel-Romero
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Naomi S. Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
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207
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Zhao S, Cordes J, Caban KM, Götz MJ, Mackens-Kiani T, Veltri AJ, Sinha NK, Weickert P, Kaya S, Hewitt G, Nedialkova DD, Fröhlich T, Beckmann R, Buskirk AR, Green R, Stingele J. RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks. Mol Cell 2023; 83:4290-4303.e9. [PMID: 37951216 PMCID: PMC10783637 DOI: 10.1016/j.molcel.2023.10.012] [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: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are abundant endogenous metabolites that challenge homeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA damage requires repair to prevent cancer and premature aging, but it is unknown whether cells also possess mechanisms that resolve aldehyde-induced RNA lesions. Here, we establish photoactivatable ribonucleoside-enhanced crosslinking (PAR-CL) as a model system to study RNA crosslinking damage in the absence of confounding DNA damage in human cells. We find that such RNA damage causes translation stress by stalling elongating ribosomes, which leads to collisions with trailing ribosomes and activation of multiple stress response pathways. Moreover, we discovered a translation-coupled quality control mechanism that resolves covalent RNA-protein crosslinks. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their modification with atypical K6- and K48-linked ubiquitin chains. Ubiquitylation requires the E3 ligase RNF14 and leads to proteasomal degradation of the protein adduct. Our findings identify RNA lesion-induced translational stress as a central component of crosslinking damage.
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Affiliation(s)
- Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karolina M Caban
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timur Mackens-Kiani
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anthony J Veltri
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Selay Kaya
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Graeme Hewitt
- King's College London School of Cancer & Pharmaceutical Sciences, London, UK
| | - Danny D Nedialkova
- Max Planck Institute of Biochemistry, Martinsried, Germany; Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Thomas Fröhlich
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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208
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Pascual‐Reguant L, Serra‐Camprubí Q, Datta D, Cianferoni D, Kourtis S, Gañez‐Zapater A, Cannatá C, Espinar L, Querol J, García‐López L, Musa‐Afaneh S, Guirola M, Gkanogiannis A, Miró Canturri A, Guzman M, Rodríguez O, Herencia‐Ropero A, Arribas J, Serra V, Serrano L, Tian TV, Peiró S, Sdelci S. Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. EMBO Mol Med 2023; 15:e18459. [PMID: 37937685 PMCID: PMC10701626 DOI: 10.15252/emmm.202318459] [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: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Triple-negative breast cancer (TNBC) often develops resistance to single-agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B-MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co-inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4-MED1 colocalization, and the transcription of cell cycle genes, thus suppressing TNBC cell proliferation. Targeting the interaction between BRD4S and LOXL2 could be a starting point for the development of new anticancer strategies for the treatment of TNBC.
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Affiliation(s)
- Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Debayan Datta
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez‐Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Cannatá
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Lorena Espinar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Laura García‐López
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sara Musa‐Afaneh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Guirola
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Anestis Gkanogiannis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andrea Miró Canturri
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Marta Guzman
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Olga Rodríguez
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Joaquin Arribas
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de CáncerMonforte de LemosMadridSpain
- Department of Biochemistry and Molecular BiologyUniversitat Autónoma de BarcelonaBellaterraSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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209
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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210
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Pinheiro‐de‐Sousa I, Fonseca‐Alaniz MH, Giudice G, Valadão IC, Modestia SM, Mattioli SV, Junior RR, Zalmas L, Fang Y, Petsalaki E, Krieger JE. Integrated systems biology approach identifies gene targets for endothelial dysfunction. Mol Syst Biol 2023; 19:e11462. [PMID: 38031960 PMCID: PMC10698507 DOI: 10.15252/msb.202211462] [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: 11/18/2022] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Endothelial dysfunction (ED) is critical in the development and progression of cardiovascular (CV) disorders, yet effective therapeutic targets for ED remain elusive due to limited understanding of its underlying molecular mechanisms. To address this gap, we employed a systems biology approach to identify potential targets for ED. Our study combined multi omics data integration, with siRNA screening, high content imaging and network analysis to prioritise key ED genes and identify a pro- and anti-ED network. We found 26 genes that, upon silencing, exacerbated the ED phenotypes tested, and network propagation identified a pro-ED network enriched in functions associated with inflammatory responses. Conversely, 31 genes ameliorated ED phenotypes, pointing to potential ED targets, and the respective anti-ED network was enriched in hypoxia, angiogenesis and cancer-related processes. An independent screen with 17 drugs found general agreement with the trends from our siRNA screen and further highlighted DUSP1, IL6 and CCL2 as potential candidates for targeting ED. Overall, our results demonstrate the potential of integrated system biology approaches in discovering disease-specific candidate drug targets for endothelial dysfunction.
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Affiliation(s)
- Iguaracy Pinheiro‐de‐Sousa
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - Miriam Helena Fonseca‐Alaniz
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
| | - Girolamo Giudice
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - Iuri Cordeiro Valadão
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
| | - Silvestre Massimo Modestia
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
| | - Sarah Viana Mattioli
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
- Department of Biophysics and PharmacologyInstitute of Biosciences of Botucatu, Universidade Estadual PaulistaBotucatuBrazil
| | - Ricardo Rosa Junior
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
| | - Lykourgos‐Panagiotis Zalmas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUK
- Open Targets, Wellcome Genome CampusCambridgeUK
| | - Yun Fang
- Department of MedicineUniversity of ChicagoChicagoILUSA
| | - Evangelia Petsalaki
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - José Eduardo Krieger
- Laboratory of Genetics and Molecular CardiologyHeart Institute (InCor)/University of São Paulo Medical SchoolSão PauloBrazil
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211
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Zhang AMY, Xia YH, Lin JSH, Chu KH, Wang WCK, Ruiter TJJ, Yang JCC, Chen N, Chhuor J, Patil S, Cen HH, Rideout EJ, Richard VR, Schaeffer DF, Zahedi RP, Borchers CH, Johnson JD, Kopp JL. Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation. Cell Metab 2023; 35:2119-2135.e5. [PMID: 37913768 DOI: 10.1016/j.cmet.2023.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
The rising pancreatic cancer incidence due to obesity and type 2 diabetes is closely tied to hyperinsulinemia, an independent cancer risk factor. Previous studies demonstrated reducing insulin production suppressed pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in Kras-mutant mice. However, the pathophysiological and molecular mechanisms remained unknown, and in particular it was unclear whether hyperinsulinemia affected PanIN precursor cells directly or indirectly. Here, we demonstrate that insulin receptors (Insr) in KrasG12D-expressing pancreatic acinar cells are dispensable for glucose homeostasis but necessary for hyperinsulinemia-driven PanIN formation in the context of diet-induced hyperinsulinemia and obesity. Mechanistically, this was attributed to amplified digestive enzyme protein translation, triggering of local inflammation, and PanIN metaplasia in vivo. In vitro, insulin dose-dependently increased acinar-to-ductal metaplasia formation in a trypsin- and Insr-dependent manner. Collectively, our data shed light on the mechanisms connecting obesity-driven hyperinsulinemia and pancreatic cancer development.
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Affiliation(s)
- Anni M Y Zhang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi Han Xia
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey S H Lin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ken H Chu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wei Chuan K Wang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Titine J J Ruiter
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jenny C C Yang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nan Chen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Justin Chhuor
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Shilpa Patil
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Rene P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3A 1R9, Canada; Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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212
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Diawara M, Martin LJ. Regulatory mechanisms of SoxD transcription factors and their influences on male fertility. Reprod Biol 2023; 23:100823. [PMID: 37979495 DOI: 10.1016/j.repbio.2023.100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Members of the SRY-related box (SOX) subfamily D (SoxD) of transcription factors are well conserved among vertebrate species and play important roles in different stages of male reproductive development. In mammals, the SoxD subfamily contains three members: SOX5, SOX6 and SOX13. Here, we describe their implications in testicular development and spermatogenesis, contributing to fertility. We also cover the mechanisms of action of SoxD transcription factors in gene regulation throughout male development. The specificity of activation of target genes by SoxD members depends, in part, on their post-translational modifications and interactions with other partners. Sperm production in adult males requires the coordination in the regulation of gene expression by different members of the SoxD subfamily of transcription factors in the testis. Specifically, the regulation of genes promoting adequate spermatogenesis by SoxD members is discussed in comparison between species.
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Affiliation(s)
- Mariama Diawara
- Biology Department, Université de Moncton, Moncton, New Brunswick E1A 3E9, Canada
| | - Luc J Martin
- Biology Department, Université de Moncton, Moncton, New Brunswick E1A 3E9, Canada.
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213
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Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
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Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
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214
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Petrova B, Maynard AG, Wang P, Kanarek N. Regulatory mechanisms of one-carbon metabolism enzymes. J Biol Chem 2023; 299:105457. [PMID: 37949226 PMCID: PMC10758965 DOI: 10.1016/j.jbc.2023.105457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
One-carbon metabolism is a central metabolic pathway critical for the biosynthesis of several amino acids, methyl group donors, and nucleotides. The pathway mostly relies on the transfer of a carbon unit from the amino acid serine, through the cofactor folate (in its several forms), and to the ultimate carbon acceptors that include nucleotides and methyl groups used for methylation of proteins, RNA, and DNA. Nucleotides are required for DNA replication, DNA repair, gene expression, and protein translation, through ribosomal RNA. Therefore, the one-carbon metabolism pathway is essential for cell growth and function in all cells, but is specifically important for rapidly proliferating cells. The regulation of one-carbon metabolism is a critical aspect of the normal and pathological function of the pathway, such as in cancer, where hijacking these regulatory mechanisms feeds an increased need for nucleotides. One-carbon metabolism is regulated at several levels: via gene expression, posttranslational modification, subcellular compartmentalization, allosteric inhibition, and feedback regulation. In this review, we aim to inform the readers of relevant one-carbon metabolism regulation mechanisms and to bring forward the need to further study this aspect of one-carbon metabolism. The review aims to integrate two major aspects of cancer metabolism-signaling downstream of nutrient sensing and one-carbon metabolism, because while each of these is critical for the proliferation of cancerous cells, their integration is critical for comprehensive understating of cellular metabolism in transformed cells and can lead to clinically relevant insights.
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Affiliation(s)
- Boryana Petrova
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Adam G Maynard
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA; Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Peng Wang
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Naama Kanarek
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
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215
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Kast DJ, Jansen S. Purification of modified mammalian actin isoforms for in vitro reconstitution assays. Eur J Cell Biol 2023; 102:151363. [PMID: 37778219 PMCID: PMC10872616 DOI: 10.1016/j.ejcb.2023.151363] [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: 06/19/2023] [Revised: 08/19/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
In vitro reconstitution assays using purified actin have greatly improved our understanding of cytoskeletal dynamics and their regulation by actin-binding proteins. However, early purification methods consisted of harsh conditions to obtain pure actin and often did not include correct maturation and obligate modification of the isolated actin monomers. Novel insights into the folding requirements and N-terminal processing of actin as well as a better understanding of the interaction of actin with monomer sequestering proteins such as DNaseI, profilin and gelsolin, led to the development of more gentle approaches to obtain pure recombinant actin isoforms with known obligate modifications. This review summarizes the approaches that can be employed to isolate natively folded endogenous and recombinant actin from tissues and cells. We further emphasize the use and limitations of each method and describe how these methods can be implemented to study actin PTMs, disease-related actin mutations and novel actin-like proteins.
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Affiliation(s)
- David J Kast
- Department of Cell Biology and Physiology, Washington University in St. Louis, Saint Louis, MO, 63110, United States.
| | - Silvia Jansen
- Department of Cell Biology and Physiology, Washington University in St. Louis, Saint Louis, MO, 63110, United States.
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216
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Cao J, Ji L, Zhan Y, Shao X, Xu P, Wu B, Chen P, Cheng L, Zhuang X, Ou Y, Hua F, Sun L, Li F, Chen H, Zhou Z, Cheng Y. MST4 kinase regulates immune thrombocytopenia by phosphorylating STAT1-mediated M1 polarization of macrophages. Cell Mol Immunol 2023; 20:1413-1427. [PMID: 37833401 PMCID: PMC10687271 DOI: 10.1038/s41423-023-01089-8] [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: 04/05/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Primary immune thrombocytopenia (ITP) is an autoimmune hemorrhagic disorder in which macrophages play a critical role. Mammalian sterile-20-like kinase 4 (MST4), a member of the germinal-center kinase STE20 family, has been demonstrated to be a regulator of inflammation. Whether MST4 participates in the macrophage-dependent inflammation of ITP remains elusive. The expression and function of MST4 in macrophages of ITP patients and THP-1 cells, and of a macrophage-specific Mst4-/- (Mst4ΔM/ΔM) ITP mouse model were determined. Macrophage phagocytic assays, RNA sequencing (RNA-seq) analysis, immunofluorescence analysis, coimmunoprecipitation (co-IP), mass spectrometry (MS), bioinformatics analysis, and phosphoproteomics analysis were performed to reveal the underlying mechanisms. The expression levels of the MST4 gene were elevated in the expanded M1-like macrophages of ITP patients, and this elevated expression of MST4 was restored to basal levels in patients with remission after high-dose dexamethasone treatment. The expression of the MST4 gene was significantly elevated in THP-1-derived M1 macrophages. Silencing of MST4 decreased the expression of M1 macrophage markers and cytokines, and impaired phagocytosis, which could be increased by overexpression of MST4. In a passive ITP mouse model, macrophage-specific depletion of Mst4 reduced the numbers of M1 macrophages in the spleen and peritoneal lavage fluid, attenuated the expression of M1 cytokines, and promoted the predominance of FcγRIIb in splenic macrophages, which resulted in amelioration of thrombocytopenia. Downregulation of MST4 directly inhibited STAT1 phosphorylation, which is essential for M1 polarization of macrophages. Our study elucidates a critical role for MST4 kinase in the pathology of ITP and identifies MST4 kinase as a potential therapeutic target for refractory ITP.
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Affiliation(s)
- Jingjing Cao
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lili Ji
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yanxia Zhan
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xia Shao
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Pengcheng Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Boting Wu
- Department of Transfusion Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pu Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Luya Cheng
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xibing Zhuang
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yang Ou
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Fanli Hua
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, 201700, China
| | - Lihua Sun
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, 201700, China
| | - Feng Li
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, 201700, China
| | - Hao Chen
- Department of Thoracic Surgery, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China.
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Yunfeng Cheng
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, 201700, China.
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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217
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Marzi SJ, Schilder BM, Nott A, Frigerio CS, Willaime-Morawek S, Bucholc M, Hanger DP, James C, Lewis PA, Lourida I, Noble W, Rodriguez-Algarra F, Sharif JA, Tsalenchuk M, Winchester LM, Yaman Ü, Yao Z, Ranson JM, Llewellyn DJ. Artificial intelligence for neurodegenerative experimental models. Alzheimers Dement 2023; 19:5970-5987. [PMID: 37768001 DOI: 10.1002/alz.13479] [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: 04/17/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Experimental models are essential tools in neurodegenerative disease research. However, the translation of insights and drugs discovered in model systems has proven immensely challenging, marred by high failure rates in human clinical trials. METHODS Here we review the application of artificial intelligence (AI) and machine learning (ML) in experimental medicine for dementia research. RESULTS Considering the specific challenges of reproducibility and translation between other species or model systems and human biology in preclinical dementia research, we highlight best practices and resources that can be leveraged to quantify and evaluate translatability. We then evaluate how AI and ML approaches could be applied to enhance both cross-model reproducibility and translation to human biology, while sustaining biological interpretability. DISCUSSION AI and ML approaches in experimental medicine remain in their infancy. However, they have great potential to strengthen preclinical research and translation if based upon adequate, robust, and reproducible experimental data. HIGHLIGHTS There are increasing applications of AI in experimental medicine. We identified issues in reproducibility, cross-species translation, and data curation in the field. Our review highlights data resources and AI approaches as solutions. Multi-omics analysis with AI offers exciting future possibilities in drug discovery.
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Affiliation(s)
- Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Brian M Schilder
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Alexi Nott
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | | | - Magda Bucholc
- School of Computing, Engineering & Intelligent Systems, Ulster University, Derry, UK
| | - Diane P Hanger
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Patrick A Lewis
- Royal Veterinary College, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Wendy Noble
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | - Jalil-Ahmad Sharif
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Ümran Yaman
- UK Dementia Research Institute at UCL, London, UK
| | | | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- Alan Turing Institute, London, UK
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218
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Kumar R, Malik MZ, Thanaraj TA, Bagabir SA, Haque S, Tambuwala M, Haider S. A computational biology approach to identify potential protein biomarkers and drug targets for sporadic amyotrophic lateral sclerosis. Cell Signal 2023; 112:110915. [PMID: 37838312 DOI: 10.1016/j.cellsig.2023.110915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by the loss of upper and lower motor neurons. The sporadic ALS (sALS) is a multigenic disorder and the complex mechanisms underlying its onset are still not fully delineated. Despite the recent scientific advancements, certain aspects of ALS pathogenic targets need to be yet clarified. The aim of the presented study is to identify potential genetic biomarkers and drug targets for sALS, by analysing gene expression profiles, presented in the publicly available GSE68605 dataset, of motor neurons cells obtained from sALS patients. We used different computational approaches including differential expression analysis, protein network mapping, candidate protein biomarker (CPB) identification, elucidation of the role of functional modules, and molecular docking analysis. The resultant top ten up- and downregulated genes were further used to construct protein-protein interaction network (PPIN). The PPIN analysis resulted in identifying four CPBs (namely RIOK2, AKT1, CTNNB1, and TNF) that commonly overlapped with one another in network parameters (degree, bottleneck and maximum neighbourhood component). The RIOK2 protein emerged as a potential mediator of top five functional modules that are associated with RNA binding, lipoprotein particle receptor binding in pre-ribosome, and interferon, cytokine-mediated signaling pathway. Furthermore, molecular docking analysis revealed that cyclosporine exhibited the highest binding affinity (-8.6 kJ/mol) with RIOK2, and surpassed the FDA-approved ALS drugs, such as riluzole and edaravone. This suggested that cyclosporine may serve as a promising candidate for targeting RIOK2 downregulation observed in sALS patients. In order to validate our computational results, it is suggested that in vitro and in vivo studies may be conducted in future to provide a more detailed understanding of ALS diagnosis, prognosis, and therapeutic intervention.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Sec-62, Uttar Pradesh, India.
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, P.O. Box 1180, Kuwait city 15462, Kuwait.
| | - Thangavel Alphonse Thanaraj
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, P.O. Box 1180, Kuwait city 15462, Kuwait.
| | - Sali Abubaker Bagabir
- Genetics Unit, Department of Medical Laboratory Technology Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Murtaza Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Shazia Haider
- Department of Biosciences, Jamia Millia University, New Delhi 110025, India.
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219
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Cheng N, Trejo J. An siRNA library screen identifies CYLD and USP34 as deubiquitinases that regulate GPCR-p38 MAPK signaling and distinct inflammatory responses. J Biol Chem 2023; 299:105370. [PMID: 37865315 PMCID: PMC10694601 DOI: 10.1016/j.jbc.2023.105370] [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: 05/04/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are highly druggable and implicated in numerous diseases, including vascular inflammation. GPCR signals are transduced from the plasma membrane as well as from endosomes and controlled by posttranslational modifications. The thrombin-activated GPCR protease-activated receptor-1 is modified by ubiquitin. Ubiquitination of protease-activated receptor-1 drives recruitment of transforming growth factor-β-activated kinase-1-binding protein 2 (TAB2) and coassociation of TAB1 on endosomes, which triggers p38 mitogen-activated protein kinase-dependent inflammatory responses in endothelial cells. Other endothelial GPCRs also induce p38 activation via a noncanonical TAB1-TAB2-dependent pathway. However, the regulatory processes that control GPCR ubiquitin-driven p38 inflammatory signaling remains poorly understood. We discovered mechanisms that turn on GPCR ubiquitin-dependent p38 signaling, however, the mechanisms that turn off the pathway are not known. We hypothesize that deubiquitination is an important step in regulating ubiquitin-driven p38 signaling. To identify specific deubiquitinating enzymes (DUBs) that control GPCR-p38 mitogen-activated protein kinase signaling, we conducted a siRNA library screen targeting 96 DUBs in endothelial cells and HeLa cells. We identified nine DUBs and validated the function two DUBs including cylindromatosis and ubiquitin-specific protease-34 that specifically regulate thrombin-induced p38 phosphorylation. Depletion of cylindromatosis expression by siRNA enhanced thrombin-stimulated p38 signaling, endothelial barrier permeability, and increased interleukin-6 cytokine expression. Conversely, siRNA knockdown of ubiquitin-specific protease-34 expression decreased thrombin-promoted interleukin-6 expression and had no effect on thrombin-induced endothelial barrier permeability. These studies suggest that specific DUBs distinctly regulate GPCR-induced p38-mediated inflammatory responses.
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Affiliation(s)
- Norton Cheng
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California, USA.
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Esmaili F, Pourmirzaei M, Ramazi S, Shojaeilangari S, Yavari E. A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1266-1285. [PMID: 37863385 PMCID: PMC11082408 DOI: 10.1016/j.gpb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/16/2023] [Accepted: 03/23/2023] [Indexed: 10/22/2023]
Abstract
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.
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Affiliation(s)
- Farzaneh Esmaili
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Mahdi Pourmirzaei
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology (IROST), Tehran 33535-111, Iran
| | - Elham Yavari
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
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221
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Bayer FP, Gander M, Kuster B, The M. CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves. Nat Commun 2023; 14:7902. [PMID: 38036588 PMCID: PMC10689459 DOI: 10.1038/s41467-023-43696-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.
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Affiliation(s)
- Florian P Bayer
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Manuel Gander
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336, Munich, Germany
| | - Matthew The
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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Xu X, Li Y, Chen T, Hou C, Yang L, Zhu P, Zhang Y, Li T. VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis. Brief Bioinform 2023; 25:bbad480. [PMID: 38156562 PMCID: PMC10782907 DOI: 10.1093/bib/bbad480] [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: 04/11/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/30/2023] Open
Abstract
Disrupted protein phosphorylation due to genetic variation is a widespread phenomenon that triggers oncogenic transformation of healthy cells. However, few relevant phosphorylation disruption events have been verified due to limited biological experimental methods. Because of the lack of reliable benchmark datasets, current bioinformatics methods primarily use sequence-based traits to study variant impact on phosphorylation (VIP). Here, we increased the number of experimentally supported VIP events from less than 30 to 740 by manually curating and reanalyzing multi-omics data from 916 patients provided by the Clinical Proteomic Tumor Analysis Consortium. To predict VIP events in cancer cells, we developed VIPpred, a machine learning method characterized by multidimensional features that exhibits robust performance across different cancer types. Our method provided a pan-cancer landscape of VIP events, which are enriched in cancer-related pathways and cancer driver genes. We found that variant-induced increases in phosphorylation events tend to inhibit the protein degradation of oncogenes and promote tumor suppressor protein degradation. Our work provides new insights into phosphorylation-related cancer biology as well as novel avenues for precision therapy.
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Affiliation(s)
- Xiaofeng Xu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Li
- Department of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Taoyu Chen
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chao Hou
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Peiyu Zhu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yi Zhang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
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Tessier TM, King CR, Mymryk JS. Exploiting the endogenous yeast nuclear proteome to identify short linear motifs in vivo. CELL REPORTS METHODS 2023; 3:100637. [PMID: 37949066 PMCID: PMC10694487 DOI: 10.1016/j.crmeth.2023.100637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
Peptide-domain interactions mediated by short linear motifs (SLiMs) play crucial roles in cellular biology. The simplicity of SLiMs poses challenges in their computational identification. Existing high-throughput methods for discovering SLiMs lack cellular context as they are typically performed in vitro. We developed a functional selection method using yeast to identify peptides that interact with the endogenous yeast nuclear proteome. Remarkably, peptides selected for in yeast also mediated nuclear import in human cells. Notably, the identified peptides did not resemble classical nuclear localization sequences. This platform has the potential to identify and investigate motifs that interact with the nuclear proteome of yeast and human and to aid in the identification and understanding of alternative protein nuclear import mechanisms.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Cason R King
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Otolaryngology, Western University, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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Liu L, Lei I, Tian S, Gao W, Guo Y, Li Z, Sabry Z, Tang P, Chen YE, Wang Z. 14-3-3 binding motif phosphorylation disrupts Hdac4 organized condensates to stimulate cardiac reprogramming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567913. [PMID: 38045244 PMCID: PMC10690191 DOI: 10.1101/2023.11.20.567913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Cell fate conversion is associated with extensive epigenetic and post translational modifications (PTMs) and architectural changes of sub-organelles and organelles, yet how these events are interconnected remains unknown. We report here the identification of a phosphorylation code in 14-3-3 binding motifs (PC14-3-3) that greatly stimulates induced cardiomyocyte (iCM) formation from fibroblasts. PC14-3-3 was identified in pivotal functional proteins for iCM reprogramming, including transcription factors and epigenetic factors. Akt1 kinase and PP2A phosphatase were a key writer and eraser of the PC14-3-3 code, respectively. PC14-3-3 activation induces iCM formation with the presence of only Tbx5. In contrast, PC14-3-3 inhibition by mutagenesis or inhibitor-mediated code removal abolished reprogramming. We discovered that key PC14-3-3 embedded factors, such as Hdac4, Mef2c, Nrip1, and Foxo1, formed Hdac4 organized inhibitory nuclear condensates. Notably, PC14-3-3 activation disrupted Hdac4 condensates to promote cardiac gene expression. Our study suggests that sub-organelle dynamics regulated by a post-translational modification code could be a general mechanism for stimulating cell reprogramming and organ regeneration. Highlights A PC14-3-3 (phosphorylation code in 14-3-3 binding motifs) is identified in pivotal functional proteins, such as HDAC4 and Mef2c, that stimulates iCM formation.Akt1 kinase and PP2A phosphatase are a key writer and a key eraser of the PC14-3-3 code, respectively, and PC14-3-3 code activation can replace Mef2c and Gata4 in cardiac reprogramming.PC14-3-3 activation disrupts Hdac4 organized condensates which results in releasing multiple 14-3-3 motif embedded proteins from the condensates to stimulate cardiac reprogramming.Sub-organelle dynamics and function regulated by a post-translational modification code could be a general mechanism in stimulating cell reprogramming and organ regeneration. Graphic abstract
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González Dalmasy JM, Fitzsimmons CM, Frye WJ, Perciaccante AJ, Jewell CP, Jenkins LM, Batista PJ, Robey RW, Gottesman MM. The thiol methyltransferase activity of TMT1A (METTL7A) is conserved across species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567538. [PMID: 38076968 PMCID: PMC10705543 DOI: 10.1101/2023.11.17.567538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Although few resistance mechanisms for histone deacetylase inhibitors (HDACis) have been described, we recently demonstrated that TMT1A (formerly METTL7A) and TMT1B (formerly METTL7B) can mediate resistance to HDACis with a thiol as the zinc-binding group by methylating and inactivating the drug. TMT1A and TMT1B are poorly characterized, and their normal physiological role has yet to be determined. As animal model systems are often used to determine the physiological function of proteins, we investigated whether the ability of these methyltransferases to methylate thiol-based HDACis is conserved across different species. We found that TMT1A was conserved across rats, mice, chickens, and zebrafish, displaying 85.7%, 84.8%, 60.7% and 51.0% amino acid sequence identity, respectively, with human TMT1A. Because TMT1B was not found in the chicken or zebrafish, we focused our studies on the TMT1A homologs. HEK-293 cells were transfected to express mouse, rat, chicken, or zebrafish homologs of TMT1A and all conferred resistance to the thiol-based HDACIs NCH-51, KD-5170 and romidepsin compared to empty vector-transfected cells. Additionally, all homologs blunted the downstream effects of HDACi treatment such as increased p21 expression, increased acetylated histone H3, and cell cycle arrest. Increased levels of dimethylated romidepsin were also found in the culture medium of cells transfected to express any of the TMT1A homologs after a 24 h incubation with romidepsin compared to empty-vector transfected cells. Our results indicate that the ability of TMT1A to methylate molecules is conserved across species. Animal models may therefore be useful in elucidating the role of these enzymes in humans.
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Affiliation(s)
- José M. González Dalmasy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Christina M. Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - William J.E. Frye
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Andrew J. Perciaccante
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Connor P. Jewell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Lisa M. Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Pedro J. Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Robert W. Robey
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
| | - Michael M. Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health. Bethesda, MD
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226
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Kennedy PH, Deh Sheikh AA, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer C, Alarcón S, Newby G, Myers SA. Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566649. [PMID: 38014346 PMCID: PMC10680671 DOI: 10.1101/2023.11.11.566649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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227
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Banerjee S, Smith IM, Hengen AC, Stroka KM. Methods for studying mammalian aquaporin biology. Biol Methods Protoc 2023; 8:bpad031. [PMID: 38046463 PMCID: PMC10689382 DOI: 10.1093/biomethods/bpad031] [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: 09/06/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.
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Affiliation(s)
- Shohini Banerjee
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Ian M Smith
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Autumn C Hengen
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Kimberly M Stroka
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore MD 21201, United States
- Biophysics Program, University of Maryland, MD 20742, United States
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland, Baltimore MD 21201, United States
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228
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Kordala AJ, Stoodley J, Ahlskog N, Hanifi M, Garcia Guerra A, Bhomra A, Lim WF, Murray LM, Talbot K, Hammond SM, Wood MJA, Rinaldi C. PRMT inhibitor promotes SMN2 exon 7 inclusion and synergizes with nusinersen to rescue SMA mice. EMBO Mol Med 2023; 15:e17683. [PMID: 37724723 PMCID: PMC10630883 DOI: 10.15252/emmm.202317683] [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: 03/07/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of infant mortality. The advent of approved treatments for this devastating condition has significantly changed SMA patients' life expectancy and quality of life. Nevertheless, these are not without limitations, and research efforts are underway to develop new approaches for improved and long-lasting benefits for patients. Protein arginine methyltransferases (PRMTs) are emerging as druggable epigenetic targets, with several small-molecule PRMT inhibitors already in clinical trials. From a screen of epigenetic molecules, we have identified MS023, a potent and selective type I PRMT inhibitor able to promote SMN2 exon 7 inclusion in preclinical SMA models. Treatment of SMA mice with MS023 results in amelioration of the disease phenotype, with strong synergistic amplification of the positive effect when delivered in combination with the antisense oligonucleotide nusinersen. Moreover, transcriptomic analysis revealed that MS023 treatment has minimal off-target effects, and the added benefit is mainly due to targeting neuroinflammation. Our study warrants further clinical investigation of PRMT inhibition both as a stand-alone and add-on therapy for SMA.
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Affiliation(s)
- Anna J Kordala
- Department of Physiology Anatomy and GeneticsUniversity of OxfordOxfordUK
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Jessica Stoodley
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Nina Ahlskog
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | | | - Antonio Garcia Guerra
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Amarjit Bhomra
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Wooi Fang Lim
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
| | - Lyndsay M Murray
- Centre for Discovery Brain Sciences, College of Medicine and Veterinary MedicineUniversity of EdinburghEdinburghUK
- Euan McDonald Centre for Motor Neuron Disease ResearchUniversity of EdinburghEdinburghUK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, John Radcliffe HospitalUniversity of OxfordOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | | | - Matthew JA Wood
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
- MDUK Oxford Neuromuscular CentreOxfordUK
| | - Carlo Rinaldi
- Department of PaediatricsUniversity of OxfordOxfordUK
- Institute of Developmental and Regenerative Medicine (IDRM)OxfordUK
- MDUK Oxford Neuromuscular CentreOxfordUK
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Molzahn C, Kuechler ER, Zemlyankina I, Nierves L, Ali T, Cole G, Wang J, Albu RF, Zhu M, Cashman NR, Gilch S, Karsan A, Lange PF, Gsponer J, Mayor T. Shift of the insoluble content of the proteome in the aging mouse brain. Proc Natl Acad Sci U S A 2023; 120:e2310057120. [PMID: 37906643 PMCID: PMC10636323 DOI: 10.1073/pnas.2310057120] [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: 06/16/2023] [Accepted: 09/24/2023] [Indexed: 11/02/2023] Open
Abstract
During aging, the cellular response to unfolded proteins is believed to decline, resulting in diminished proteostasis. In model organisms, such as Caenorhabditis elegans, proteostatic decline with age has been linked to proteome solubility shifts and the onset of protein aggregation. However, this correlation has not been extensively characterized in aging mammals. To uncover age-dependent changes in the insoluble portion of a mammalian proteome, we analyzed the detergent-insoluble fraction of mouse brain tissue by mass spectrometry. We identified a group of 171 proteins, including the small heat shock protein α-crystallin, that become enriched in the detergent-insoluble fraction obtained from old mice. To enhance our ability to detect features associated with proteins in that fraction, we complemented our data with a meta-analysis of studies reporting the detergent-insoluble proteins in various mouse models of aging and neurodegeneration. Strikingly, insoluble proteins from young and old mice are distinct in several features in our study and across the collected literature data. In younger mice, proteins are more likely to be disordered, part of membraneless organelles, and involved in RNA binding. These traits become less prominent with age, as an increased number of structured proteins enter the pellet fraction. This analysis suggests that age-related changes to proteome organization lead a group of proteins with specific features to become detergent-insoluble. Importantly, these features are not consistent with those associated with proteins driving membraneless organelle formation. We see no evidence in our system of a general increase of condensate proteins in the detergent-insoluble fraction with age.
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Affiliation(s)
- Cristen Molzahn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Edward Leong Center for Healthy Aging, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Erich R. Kuechler
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Irina Zemlyankina
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Michael Cuccione Childhood Cancer Research Program, British Columbia Children's Hospital Research Institute, Vancouver, BCV5Z 4H4, Canada
| | - Tahir Ali
- Faculty of Veterinary Medicine and Hotchkiss Brain Institute, University of Calgary, Calgary, ABT2N 4Z6, Canada
| | - Grace Cole
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- British Columbia Cancer Research Institute, Vancouver, BCV5Z 1L3, Canada
| | - Jing Wang
- Division of Neurology and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Razvan F. Albu
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Mang Zhu
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Neil R. Cashman
- Division of Neurology and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Sabine Gilch
- Faculty of Veterinary Medicine and Hotchkiss Brain Institute, University of Calgary, Calgary, ABT2N 4Z6, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- British Columbia Cancer Research Institute, Vancouver, BCV5Z 1L3, Canada
| | - Philipp F. Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Michael Cuccione Childhood Cancer Research Program, British Columbia Children's Hospital Research Institute, Vancouver, BCV5Z 4H4, Canada
- British Columbia Cancer Research Institute, Vancouver, BCV5Z 1L3, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Edward Leong Center for Healthy Aging, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
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Platz KR, Rudisel EJ, Paluch KV, Laurin TR, Dittenhafer-Reed KE. Assessing the Role of Post-Translational Modifications of Mitochondrial RNA Polymerase. Int J Mol Sci 2023; 24:16050. [PMID: 38003238 PMCID: PMC10671485 DOI: 10.3390/ijms242216050] [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: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The mitochondrial proteome is subject to abundant post-translational modifications, including lysine acetylation and phosphorylation of serine, threonine, and tyrosine. The biological function of the majority of these protein modifications is unknown. Proteins required for the transcription and translation of mitochondrial DNA (mtDNA) are subject to modification. This suggests that reversible post-translational modifications may serve as a regulatory mechanism for mitochondrial gene transcription, akin to mechanisms controlling nuclear gene expression. We set out to determine whether acetylation or phosphorylation controls the function of mitochondrial RNA polymerase (POLRMT). Mass spectrometry was used to identify post-translational modifications on POLRMT. We analyzed three POLRMT modification sites (lysine 402, threonine 315, threonine 993) found in distinct structural regions. Amino acid point mutants that mimic the modified and unmodified forms of POLRMT were employed to measure the effect of acetylation or phosphorylation on the promoter binding ability of POLRMT in vitro. We found a slight decrease in binding affinity for the phosphomimic at threonine 315. We did not identify large changes in viability, mtDNA content, or mitochondrial transcript level upon overexpression of POLRMT modification mimics in HeLa cells. Our results suggest minimal biological impact of the POLRMT post-translational modifications studied in our system.
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HAPİL ZEVKLİLER FZ, ÇOPUROĞLU FE, ERTOSUN MG, MERT U, ÖZEŞ D, ÖZEŞ ON. TNFR1 signaling is positively regulated by Jak-2 and c-Src via tyrosine phosphorylation. Turk J Biol 2023; 48:1-12. [PMID: 38665776 PMCID: PMC11042867 DOI: 10.55730/1300-0152.2677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/27/2024] [Accepted: 11/06/2023] [Indexed: 04/28/2024] Open
Abstract
Background/aim Tumor necrosis factor alpha (TNFα, a.k.a. TNF) is a pleiotropic cytokine that exerts most of its effects through type 1 TNF receptor (TNFR1). Following TNF binding, TNFR1 recruits TRADD (tumor necrosis factor receptor type 1-associated DEATH domain). This interaction triggers formation of signalosome complexes which have been claimed to induce apoptosis (via downstream caspase activations), inflammation (via NF-kappaB) and stress pathways (JNK & p38). However, the mechanism underlying TNF-induced ERK and AKT activation is not completely revealed. TNFR1 is known to constitutively bind c-Src and JAK2, and these enzymes were previously demonstrated to modulate TNF signaling. Therefore, we hypothesized that TNFR1 could be tyrosine phosphorylated by JAK2 and/or c-Src and TNF-induced ERK and Akt activation may be mediated by this phosphorylation. Materials and methods Site-directed mutagenesis (SDM) was performed to substitute the two putative Tyrosine phosphorylation sites on TNFR1 (Y360 and Y401) with alanine (A) or with aspartic acid (D), to inhibit or mimic constitutive phosphorylation, respectively. In 293T cells transfected with mutated or wild type TNFR1, ERK and Akt activations were determined by western blot. TNFR1 interaction with c-Src, JAK2, p85 and Grb2 was examined by co-IP. NF-kB activation was measured by luciferase assay, while proliferation was measured by MTT and apoptosis was evaluated by colorimetric caspase 8/3 assays. For determination of necrosis rates, cellular DNA fragmentation ELISA was performed. Results In this report, we show that TNFR1 is phosphorylated by JAK2 tyrosine kinase at Y401 and by c-Src at Y360 and Y401. Phosphorylation of Y360 and Y401 augments the interaction of Grb2 and PI3Kp85 with TNFR1. We also demonstrate that phosphomimetic mutations of Y360D and Y401D enhance ERK and Akt activation. Conclusion TNFR1 is tyrosine phosphorylated by both c-Src and JAK2, triggering a "noncanonical" pathway, that activates ERK and Akt.
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Affiliation(s)
| | - Fatma Ece ÇOPUROĞLU
- Department of Medical Biology and Genetics, Akdeniz University, Antalya,
Turkiye
| | | | - Ufuk MERT
- Atatürk Health Care Vocational School, Ege University, İzmir,
Turkiye
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232
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Miao T, Bai H. Identification of Acetylation Sites of Fatty Acid Synthase (FASN) by Mass Spectrometry and FASN Activity Assay. Bio Protoc 2023; 13:e4873. [PMID: 37969759 PMCID: PMC10632157 DOI: 10.21769/bioprotoc.4873] [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: 07/10/2023] [Revised: 08/28/2023] [Accepted: 09/24/2023] [Indexed: 11/17/2023] Open
Abstract
Lysine acetylation is a conserved post-translational modification and a key regulatory mechanism for various cellular processes, including metabolic control, epigenetic regulation, and cellular signaling transduction. Recent advances in mass spectrometry (MS) enable the extensive identification of acetylated lysine residues of histone and non-histone proteins. However, protein enrichment before MS analysis may be necessary to improve the detection of low-abundant proteins or proteins that exhibit low acetylation levels. Fatty acid synthase (FASN), an essential enzyme catalyzing the de novo synthesis of fatty acids, has been found to be acetylated in various species, from fruit flies to humans. Here, we describe a step-by-step process of antibody-based protein enrichment and sample preparation for acetylation identification of endogenous FASN protein by MS-based proteomics analysis. Meanwhile, we provide a protocol for nicotinamide adenine dinucleotide phosphate (NADPH) absorbance assay for FASN activity measurement, which is one of the primary functional readouts of de novo lipogenesis. Key features • A comprehensive protocol for protein immunoprecipitation and sample preparation for acetylation site identification by mass spectrometry. • Step-by-step procedures for measurement of FASN activity of fruit fly larvae using an absorbance assay.
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Affiliation(s)
- Ting Miao
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
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233
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Dilliott AA, Kwon S, Rouleau GA, Iqbal S, Farhan SMK. Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes. Brain 2023; 146:4608-4621. [PMID: 37394881 PMCID: PMC10629772 DOI: 10.1093/brain/awad224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/28/2023] [Accepted: 06/11/2023] [Indexed: 07/04/2023] Open
Abstract
Within recent years, there has been a growing number of genes associated with amyotrophic lateral sclerosis (ALS), resulting in an increasing number of novel variants, particularly missense variants, many of which are of unknown clinical significance. Here, we leverage the sequencing efforts of the ALS Knowledge Portal (3864 individuals with ALS and 7839 controls) and Project MinE ALS Sequencing Consortium (4366 individuals with ALS and 1832 controls) to perform proteomic and transcriptomic characterization of missense variants in 24 ALS-associated genes. The two sequencing datasets were interrogated for missense variants in the 24 genes, and variants were annotated with gnomAD minor allele frequencies, ClinVar pathogenicity classifications, protein sequence features including Uniprot functional site annotations, and PhosphoSitePlus post-translational modification site annotations, structural features from AlphaFold predicted monomeric 3D structures, and transcriptomic expression levels from Genotype-Tissue Expression. We then applied missense variant enrichment and gene-burden testing following binning of variation based on the selected proteomic and transcriptomic features to identify those most relevant to pathogenicity in ALS-associated genes. Using predicted human protein structures from AlphaFold, we determined that missense variants carried by individuals with ALS were significantly enriched in β-sheets and α-helices, as well as in core, buried or moderately buried regions. At the same time, we identified that hydrophobic amino acid residues, compositionally biased protein regions and regions of interest are predominantly enriched in missense variants carried by individuals with ALS. Assessment of expression level based on transcriptomics also revealed enrichment of variants of high and medium expression across all tissues and within the brain. We further explored enriched features of interest using burden analyses and identified individual genes were indeed driving certain enrichment signals. A case study is presented for SOD1 to demonstrate proof-of-concept of how enriched features may aid in defining variant pathogenicity. Our results present proteomic and transcriptomic features that are important indicators of missense variant pathogenicity in ALS and are distinct from features associated with neurodevelopmental disorders.
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Affiliation(s)
- Allison A Dilliott
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Seulki Kwon
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sumaiya Iqbal
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 0G4, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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234
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Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernadó P, Banères JL, Sibille N. Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction. Structure 2023; 31:1394-1406.e7. [PMID: 37669668 DOI: 10.1016/j.str.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
Arrestin-dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR's C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three rhodopsin-like GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR), and the β2-adernergic receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motifs (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transitions appear to favor arrestin-2 binding. Hence, our results suggest a model in which the phosphorylation-dependent structuration of the GPCR C-terminal regions would modulate arrestin binding and therefore signaling outcomes in arrestin-dependent pathways.
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Affiliation(s)
- Myriam Guillien
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Glaécia A N Pereira
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélien Thureau
- HélioBio Section, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91190 Gif-sur-Yvette, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France.
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235
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Blankenship CM, Xie J, Benz C, Wang A, Ivarsson Y, Jiang J. Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase. Nat Chem Biol 2023; 19:1423-1431. [PMID: 37653170 PMCID: PMC10723112 DOI: 10.1038/s41589-023-01422-2] [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: 01/30/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023]
Abstract
The modification of intracellular proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) moieties is a highly dynamic process that spatiotemporally regulates nearly every important cellular program. Despite its significance, little is known about the substrate recognition and regulation modes of O-GlcNAc transferase (OGT), the primary enzyme responsible for O-GlcNAc addition. In this study, we identified the intervening domain (Int-D), a poorly understood protein fold found only in metazoan OGTs, as a specific regulator of OGT protein-protein interactions and substrate modification. Using proteomic peptide phage display (ProP-PD) coupled with structural, biochemical and cellular characterizations, we discovered a strongly enriched peptide motif, employed by the Int-D to facilitate specific O-GlcNAcylation. We further show that disruption of Int-D binding dysregulates important cellular programs, including response to nutrient deprivation and glucose metabolism. These findings illustrate a mode of OGT substrate recognition and offer key insights into the biological roles of this unique domain.
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Affiliation(s)
- Connor M Blankenship
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Jinshan Xie
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Ao Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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236
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Wamsley NT, Wilkerson EM, Guan L, LaPak KM, Schrank TP, Holmes BJ, Sprung RW, Gilmore PE, Gerndt SP, Jackson RS, Paniello RC, Pipkorn P, Puram SV, Rich JT, Townsend RR, Zevallos JP, Zolkind P, Le QT, Goldfarb D, Major MB. Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC. Mol Cell Proteomics 2023; 22:100647. [PMID: 37716475 PMCID: PMC10587640 DOI: 10.1016/j.mcpro.2023.100647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023] Open
Abstract
The NFE2L2 (NRF2) oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion, and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry-based targeted proteomics assay based on internal standard-triggered parallel reaction monitoring to quantify 69 NRF2 pathway components and targets, as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved an existing internal standard-triggered parallel reaction monitoring acquisition algorithm, called SureQuant, to increase throughput, sensitivity, and precision. Testing the optimized platform on 27 lung and upper aerodigestive cancer cell models revealed 35 NRF2 responsive proteins. In formalin-fixed paraffin-embedded HNSCCs, NRF2 signaling intensity positively correlated with NRF2-activating mutations and with SOX2 protein expression. Protein markers of T-cell infiltration correlated positively with one another and with human papilloma virus infection status. CDKN2A (p16) protein expression positively correlated with the human papilloma virus oncogenic E7 protein and confirmed the presence of translationally active virus. This work establishes a clinically actionable HNSCC protein biomarker assay capable of quantifying over 600 peptides from frozen or formalin-fixed paraffin-embedded archived tissues in under 90 min.
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Affiliation(s)
- Nathan T Wamsley
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Emily M Wilkerson
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Li Guan
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
| | - Kyle M LaPak
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Travis P Schrank
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brittany J Holmes
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Robert W Sprung
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Petra Erdmann Gilmore
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sophie P Gerndt
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ryan S Jackson
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Randal C Paniello
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Patrik Pipkorn
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sidharth V Puram
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jason T Rich
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Reid R Townsend
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - José P Zevallos
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Paul Zolkind
- Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA; Institute for Informatics, Washington University in St Louis, St Louis, Missouri, USA.
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA; Department of Otolaryngology/Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA.
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237
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Massacci G, Perfetto L, Sacco F. The Cyclin-dependent kinase 1: more than a cell cycle regulator. Br J Cancer 2023; 129:1707-1716. [PMID: 37898722 PMCID: PMC10667339 DOI: 10.1038/s41416-023-02468-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
The Cyclin-dependent kinase 1, as a serine/threonine protein kinase, is more than a cell cycle regulator as it was originally identified. During the last decade, it has been shown to carry out versatile functions during the last decade. From cell cycle control to gene expression regulation and apoptosis, CDK1 is intimately involved in many cellular events that are vital for cell survival. Here, we provide a comprehensive catalogue of the CDK1 upstream regulators and substrates, describing how this kinase is implicated in the control of key 'cell cycle-unrelated' biological processes. Finally, we describe how deregulation of CDK1 expression and activation has been closely associated with cancer progression and drug resistance.
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Affiliation(s)
- Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Livia Perfetto
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
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238
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Pollin G, De Assuncao T, Doria Jorge S, Chi YI, Charlesworth M, Madden B, Iovanna J, Zimmermann M, Urrutia R, Lomberk G. Writers and readers of H3K9me2 form distinct protein networks during the cell cycle that include candidates for H3K9 mimicry. Biosci Rep 2023; 43:BSR20231093. [PMID: 37782747 PMCID: PMC10611923 DOI: 10.1042/bsr20231093] [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: 06/13/2023] [Revised: 09/15/2023] [Accepted: 10/02/2023] [Indexed: 10/04/2023] Open
Abstract
Histone H3 lysine 9 methylation (H3K9me), which is written by the Euchromatic Histone Lysine Methyltransferases EHMT1 and EHMT2 and read by the heterochromatin protein 1 (HP1) chromobox (CBX) protein family, is dysregulated in many types of cancers. Approaches to inhibit regulators of this pathway are currently being evaluated for therapeutic purposes. Thus, knowledge of the complexes supporting the function of these writers and readers during the process of cell proliferation is critical for our understanding of their role in carcinogenesis. Here, we immunopurified each of these proteins and used mass spectrometry to define their associated non-histone proteins, individually and at two different phases of the cell cycle, namely G1/S and G2/M. Our findings identify novel binding proteins for these writers and readers, as well as corroborate known interactors, to show the formation of distinct protein complex networks in a cell cycle phase-specific manner. Furthermore, there is an organizational switch between cell cycle phases for interactions among specific writer-reader pairs. Through a multi-tiered bioinformatics-based approach, we reveal that many interacting proteins exhibit histone mimicry, based on an H3K9-like linear motif. Gene ontology analyses, pathway enrichment, and network reconstruction inferred that these comprehensive EHMT and CBX-associated interacting protein networks participate in various functions, including transcription, DNA repair, splicing, and membrane disassembly. Combined, our data reveals novel complexes that provide insight into key functions of cell cycle-associated epigenomic processes that are highly relevant for better understanding these chromatin-modifying proteins during cell cycle and carcinogenesis.
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Affiliation(s)
- Gareth Pollin
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI Center, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | - Thiago M. De Assuncao
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI Center, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | - Salomao Doria Jorge
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | - Young-In Chi
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI Center, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | | | - Benjamin Madden
- Medical Genome Facility, Proteomics Core, Mayo Clinic, Rochester, MN, U.S.A
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Michael T. Zimmermann
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | - Raul Urrutia
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI Center, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, U.S.A
| | - Gwen Lomberk
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI Center, Medical College of Wisconsin, Milwaukee, WI, U.S.A
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, U.S.A
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239
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Liu S, Wu R, Chen L, Deng K, Ou X, Lu X, Li M, Liu C, Chen S, Fu Y, Xu A. CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation. Cell Rep 2023; 42:113197. [PMID: 37777964 DOI: 10.1016/j.celrep.2023.113197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
Cancer cells usually exhibit shortened 3' untranslated regions (UTRs) due to alternative polyadenylation (APA) to promote cell proliferation and migration. Upregulated CPSF6 leads to a systematic prolongation of 3' UTRs, but CPSF6 expression in tumors is typically higher than that in healthy tissues. This contradictory observation suggests that it is necessary to investigate the underlying mechanism by which CPSF6 regulates APA switching in cancer. Here, we find that CPSF6 can undergo liquid-liquid phase separation (LLPS), and elevated LLPS is associated with the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs CPSF6 LLPS by phosphorylating its arginine/serine-like domain. The reduction of CPSF6 LLPS can lead to a shortened 3' UTR of cell-cycle-related genes and accelerate cell proliferation. These results suggest that CPSF6 LLPS, rather than its expression level, may be responsible for APA regulation in cancer cells.
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Affiliation(s)
- Susu Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Runze Wu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Liutao Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Ke Deng
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Ou
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xin Lu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Mengxia Li
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Chao Liu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Shangwu Chen
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yonggui Fu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China.
| | - Anlong Xu
- State Key Laboratory for Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, P.R. China.
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240
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Harris MT, Marr MT. The intrinsically disordered region of eIF5B stimulates IRES usage and nucleates biological granule formation. Cell Rep 2023; 42:113283. [PMID: 37862172 PMCID: PMC10680144 DOI: 10.1016/j.celrep.2023.113283] [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: 08/27/2022] [Revised: 03/22/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Cells activate stress response pathways to survive adverse conditions. Such responses involve the inhibition of global cap-dependent translation. This inhibition is a block that essential transcripts must escape via alternative methods of translation initiation, e.g., an internal ribosome entry site (IRES). IRESs have distinct structures and generally require a limited repertoire of translation factors. Cellular IRESs have been identified in many critical cellular stress response transcripts. We previously identified cellular IRESs in the murine insulin receptor (Insr) and insulin-like growth factor 1 receptor (Igf1r) transcripts and demonstrated their resistance to eukaryotic initiation factor 4F (eIF4F) inhibition. Here, we find that eIF5B preferentially promotes Insr, Igf1r, and hepatitis C virus IRES activity through a non-canonical mechanism that requires its highly charged and disordered N terminus. We find that the N-terminal region of eIF5B can drive cytoplasmic granule formation. This eIF5B granule is triggered by cellular stress and is sufficient to specifically promote IRES activity.
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Affiliation(s)
- Meghan T Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA
| | - Michael T Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA.
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241
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Santos BF, Grenho I, Martel PJ, Ferreira BI, Link W. FOXO family isoforms. Cell Death Dis 2023; 14:702. [PMID: 37891184 PMCID: PMC10611805 DOI: 10.1038/s41419-023-06177-1] [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: 01/16/2023] [Revised: 06/30/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
FOXO family of proteins are transcription factors involved in many physiological and pathological processes including cellular homeostasis, stem cell maintenance, cancer, metabolic, and cardiovascular diseases. Genetic evidence has been accumulating to suggest a prominent role of FOXOs in lifespan regulation in animal systems from hydra, C elegans, Drosophila, and mice. Together with the observation that FOXO3 is the second most replicated gene associated with extreme human longevity suggests that pharmacological targeting of FOXO proteins can be a promising approach to treat cancer and other age-related diseases and extend life and health span. However, due to the broad range of cellular functions of the FOXO family members FOXO1, 3, 4, and 6, isoform-specific targeting of FOXOs might lead to greater benefits and cause fewer side effects. Therefore, a deeper understanding of the common and specific features of these proteins as well as their redundant and specific functions in our cells represents the basis of specific targeting strategies. In this review, we provide an overview of the evolution, structure, function, and disease-relevance of each of the FOXO family members.
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Affiliation(s)
- Bruno F Santos
- Algarve Biomedical Center Research Institute-ABC-RI, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center (ABC), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Centro Hospitalar Universitário do Algarve (CHUA). Rua Leão Penedo, 8000-386, Faro, Portugal
| | - Inês Grenho
- Algarve Biomedical Center Research Institute-ABC-RI, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center (ABC), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Paulo J Martel
- Center for Health Technology and Services Research (CINTESIS)@RISE, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Bibiana I Ferreira
- Algarve Biomedical Center Research Institute-ABC-RI, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- Algarve Biomedical Center (ABC), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Wolfgang Link
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM). Arturo Duperier 4, 28029, Madrid, Spain.
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242
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Chang YW, Chen YC, Chen CC. Identification of Novel Targeting Sites of Calcineurin and CaMKII in Human Ca V3.2 T-Type Calcium Channel. Biomedicines 2023; 11:2891. [PMID: 38001892 PMCID: PMC10669385 DOI: 10.3390/biomedicines11112891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The Cav3.2 T-type calcium channel is implicated in various pathological conditions, including cardiac hypertrophy, epilepsy, autism, and chronic pain. Phosphorylation of Cav3.2 by multiple kinases plays a pivotal role in regulating its calcium channel function. The calcium/calmodulin-dependent serine/threonine phosphatase, calcineurin, interacts physically with Cav3.2 and modulates its activity. However, it remains unclear whether calcineurin dephosphorylates Cav3.2, the specific spatial regions on Cav3.2 involved, and the extent of the quantitative impact. In this study, we elucidated the serine/threonine residues on Cav3.2 targeted by calcineurin using quantitative mass spectrometry. We identified six serine residues in the N-terminus, II-III loop, and C-terminus of Cav3.2 that were dephosphorylated by calcineurin. Notably, a higher level of dephosphorylation was observed in the Cav3.2 C-terminus, where calcineurin binds to this channel. Additionally, a previously known CaMKII-phosphorylated site, S1198, was found to be dephosphorylated by calcineurin. Furthermore, we also discovered that a novel CaMKII-phosphorylated site, S2137, underwent dephosphorylation by calcineurin. In CAD cells, a mouse central nervous system cell line, membrane depolarization led to an increase in the phosphorylation of endogenous Cav3.2 at S2137. Mutation of S2137 affected the calcium channel function of Cav3.2. Our findings advance the understanding of Cav3.2 regulation not only through kinase phosphorylation but also via calcineurin phosphatase dephosphorylation.
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Affiliation(s)
- Yu-Wang Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;
| | | | - Chien-Chang Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;
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243
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Zheng K, Chen S, Ren Z, Wang Y. Protein arginine methylation in viral infection and antiviral immunity. Int J Biol Sci 2023; 19:5292-5318. [PMID: 37928266 PMCID: PMC10620831 DOI: 10.7150/ijbs.89498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Protein arginine methyltransferase (PRMT)-mediated arginine methylation is an important post-transcriptional modification that regulates various cellular processes including epigenetic gene regulation, genome stability maintenance, RNA metabolism, and stress-responsive signal transduction. The varying substrates and biological functions of arginine methylation in cancer and neurological diseases have been extensively discussed, providing a rationale for targeting PRMTs in clinical applications. An increasing number of studies have demonstrated an interplay between arginine methylation and viral infections. PRMTs have been found to methylate and regulate several host cell proteins and different functional types of viral proteins, such as viral capsids, mRNA exporters, transcription factors, and latency regulators. This modulation affects their activity, subcellular localization, protein-nucleic acid and protein-protein interactions, ultimately impacting their roles in various virus-associated processes. In this review, we discuss the classification, structure, and regulation of PRMTs and their pleiotropic biological functions through the methylation of histones and non-histones. Additionally, we summarize the broad spectrum of PRMT substrates and explore their intricate effects on various viral infection processes and antiviral innate immunity. Thus, comprehending the regulation of arginine methylation provides a critical foundation for understanding the pathogenesis of viral diseases and uncovering opportunities for antiviral therapy.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Siyu Chen
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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244
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Brunner A, Li Q, Fisicaro S, Kourtesakis A, Viiliäinen J, Johansson HJ, Pandey V, Mayank AK, Lehtiö J, Wohlschlegel JA, Spruck C, Rantala JK, Orre LM, Sangfelt O. FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Mol Cell 2023; 83:3720-3739.e8. [PMID: 37591242 PMCID: PMC10592106 DOI: 10.1016/j.molcel.2023.07.026] [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: 06/16/2022] [Revised: 05/14/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023]
Abstract
Fanconi anemia (FA) signaling, a key genomic maintenance pathway, is activated in response to replication stress. Here, we report that phosphorylation of the pivotal pathway protein FANCD2 by CHK1 triggers its FBXL12-dependent proteasomal degradation, facilitating FANCD2 clearance at stalled replication forks. This promotes efficient DNA replication under conditions of CYCLIN E- and drug-induced replication stress. Reconstituting FANCD2-deficient fibroblasts with phosphodegron mutants failed to re-establish fork progression. In the absence of FBXL12, FANCD2 becomes trapped on chromatin, leading to replication stress and excessive DNA damage. In human cancers, FBXL12, CYCLIN E, and FA signaling are positively correlated, and FBXL12 upregulation is linked to reduced survival in patients with high CYCLIN E-expressing breast tumors. Finally, depletion of FBXL12 exacerbated oncogene-induced replication stress and sensitized cancer cells to drug-induced replication stress by WEE1 inhibition. Collectively, our results indicate that FBXL12 constitutes a vulnerability and a potential therapeutic target in CYCLIN E-overexpressing cancers.
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Affiliation(s)
- Andrä Brunner
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden.
| | - Qiuzhen Li
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Samuele Fisicaro
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Alexandros Kourtesakis
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Johanna Viiliäinen
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Henrik J Johansson
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - Vijaya Pandey
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Adarsh K Mayank
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Charles Spruck
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla 92037, CA, USA
| | - Juha K Rantala
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, South Yorkshire, UK; Misvik Biology, Turku 20520, Finland
| | - Lukas M Orre
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden.
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245
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Alteen MG, Meek RW, Kolappan S, Busmann JA, Cao J, O’Gara Z, Chou Y, Derda R, Davies GJ, Vocadlo DJ. Phage display uncovers a sequence motif that drives polypeptide binding to a conserved regulatory exosite of O-GlcNAc transferase. Proc Natl Acad Sci U S A 2023; 120:e2303690120. [PMID: 37819980 PMCID: PMC10589721 DOI: 10.1073/pnas.2303690120] [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: 03/05/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
The modification of nucleocytoplasmic proteins by O-linked N-acetylglucosamine (O-GlcNAc) is an important regulator of cell physiology. O-GlcNAc is installed on over a thousand proteins by just one enzyme, O-GlcNAc transferase (OGT). How OGT is regulated is therefore a topic of interest. To gain insight into these questions, we used OGT to perform phage display selection from an unbiased library of ~109 peptides of 15 amino acids in length. Following rounds of selection and deep mutational panning, we identified a high-fidelity peptide consensus sequence, [Y/F]-x-P-x-Y-x-[I/M/F], that drives peptide binding to OGT. Peptides containing this sequence bind to OGT in the high nanomolar to low micromolar range and inhibit OGT in a noncompetitive manner with low micromolar potencies. X-ray structural analyses of OGT in complex with a peptide containing this motif surprisingly revealed binding to an exosite proximal to the active site of OGT. This structure defines the detailed molecular basis driving peptide binding and explains the need for specific residues within the sequence motif. Analysis of the human proteome revealed this motif within 52 nuclear and cytoplasmic proteins. Collectively, these data suggest a mode of regulation of OGT by which polypeptides can bind to this exosite to cause allosteric inhibition of OGT through steric occlusion of its active site. We expect that these insights will drive improved understanding of the regulation of OGT within cells and enable the development of new chemical tools to exert fine control over OGT activity.
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Affiliation(s)
- Matthew G. Alteen
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Richard W. Meek
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Subramania Kolappan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Jil A. Busmann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Jessica Cao
- 48 Hour Discovery, Nanotechnology Research Centre, Edmonton, ABT6G 2M9, Canada
| | - Zoe O’Gara
- 48 Hour Discovery, Nanotechnology Research Centre, Edmonton, ABT6G 2M9, Canada
| | - Ying Chou
- 48 Hour Discovery, Nanotechnology Research Centre, Edmonton, ABT6G 2M9, Canada
| | - Ratmir Derda
- 48 Hour Discovery, Nanotechnology Research Centre, Edmonton, ABT6G 2M9, Canada
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
| | - David J. Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
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246
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Klement K, Brückner M, Bernkopf DB. Phosphorylation of axin within biomolecular condensates counteracts its tankyrase-mediated degradation. J Cell Sci 2023; 136:jcs261214. [PMID: 37721093 PMCID: PMC10652037 DOI: 10.1242/jcs.261214] [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: 03/31/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023] Open
Abstract
Axin (also known as AXIN1) is a central negative regulator of the proto-oncogenic Wnt/β-catenin signaling pathway, as axin condensates provide a scaffold for the assembly of a multiprotein complex degrading β-catenin. Axin, in turn, is degraded through tankyrase. Consequently, tankyrase small-molecule inhibitors block Wnt signaling by stabilizing axin, revealing potential for cancer therapy. Here, we discovered that axin is phosphorylated by casein kinase 1 alpha 1 (CSNK1A1, also known as CK1α) at an N-terminal casein kinase 1 consensus motif, and that this phosphorylation is antagonized by the catalytic subunit alpha of protein phosphatase 1 (PPP1CA, hereafter referred to as PP1). Axin condensates promoted phosphorylation by enriching CK1α over PP1. Importantly, the phosphorylation took place within the tankyrase-binding site, electrostatically and/or sterically hindering axin-tankyrase interaction, and counteracting tankyrase-mediated degradation of axin. Thus, the presented data propose a novel mechanism regulating axin stability, with implications for Wnt signaling, cancer therapy and self-organization of biomolecular condensates.
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Affiliation(s)
- Katharina Klement
- Experimental Medicine II, Nikolaus-Fiebiger-Center, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Martina Brückner
- Experimental Medicine II, Nikolaus-Fiebiger-Center, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Dominic B. Bernkopf
- Experimental Medicine II, Nikolaus-Fiebiger-Center, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
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247
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Li J, Krause GJ, Gui Q, Kaushik S, Rona G, Zhang Q, Liang FX, Dhabaria A, Anerillas C, Martindale JL, Vasilyev N, Askenazi M, Ueberheide B, Nudler E, Gorospe M, Cuervo AM, Pagano M. A noncanonical function of SKP1 regulates the switch between autophagy and unconventional secretion. SCIENCE ADVANCES 2023; 9:eadh1134. [PMID: 37831778 PMCID: PMC10575587 DOI: 10.1126/sciadv.adh1134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Intracellular degradation of proteins and organelles by the autophagy-lysosome system is essential for cellular quality control and energy homeostasis. Besides degradation, endolysosomal organelles can fuse with the plasma membrane and contribute to unconventional secretion. Here, we identify a function for mammalian SKP1 in endolysosomes that is independent of its established role as an essential component of the family of SCF/CRL1 ubiquitin ligases. We found that, under nutrient-poor conditions, SKP1 is phosphorylated on Thr131, allowing its interaction with V1 subunits of the vacuolar ATPase (V-ATPase). This event, in turn, promotes V-ATPase assembly to acidify late endosomes and enhance endolysosomal degradation. Under nutrient-rich conditions, SUMOylation of phosphorylated SKP1 allows its binding to and dephosphorylation by the PPM1B phosphatase. Dephosphorylated SKP1 interacts with SEC22B to promote unconventional secretion of the content of less acidified hybrid endosomal/autophagic compartments. Collectively, our study implicates SKP1 phosphorylation as a switch between autophagy and unconventional secretion in a manner dependent on cellular nutrient status.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gregory J. Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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248
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Iyer SR, Nusser K, Jones K, Shinde P, Keddy C, Beach CZ, Aguero E, Force J, Shinde U, Davare MA. Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors. EMBO Mol Med 2023; 15:e17367. [PMID: 37587872 PMCID: PMC10565643 DOI: 10.15252/emmm.202217367] [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: 12/27/2022] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/18/2023] Open
Abstract
ROS1 is the largest receptor tyrosine kinase in the human genome. Rearrangements of the ROS1 gene result in oncogenic ROS1 kinase fusion proteins that are currently the only validated biomarkers for targeted therapy with ROS1 TKIs in patients. While numerous somatic missense mutations in ROS1 exist in the cancer genome, their impact on catalytic activity and pathogenic potential is unknown. We interrogated the AACR Genie database and identified 34 missense mutations in the ROS1 tyrosine kinase domain for further analysis. Our experiments revealed that these mutations have varying effects on ROS1 kinase function, ranging from complete loss to significantly increased catalytic activity. Notably, Asn and Gly substitutions at Asp2113 in the ROS1 kinase domain were found to be TKI-sensitive oncogenic variants in cell-based model systems. In vivo experiments showed that ROS1 D2113N induced tumor formation that was sensitive to crizotinib and lorlatinib, FDA-approved ROS1-TKIs. Collectively, these findings highlight the tumorigenic potential of specific point mutations within the ROS1 kinase domain and their potential as therapeutic targets with FDA-approved ROS1-TKIs.
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Affiliation(s)
- Sudarshan R Iyer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Kevin Nusser
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Kristen Jones
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Pushkar Shinde
- Department of Chemical PhysiologyOregon Health and Sciences UniversityORPortlandUSA
| | - Clare Keddy
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Catherine Z Beach
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Erin Aguero
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Jeremy Force
- Department of Medicine, Division of Medical Oncology, Duke Cancer InstituteDuke UniversityNCDurhamUSA
| | - Ujwal Shinde
- Department of Chemical PhysiologyOregon Health and Sciences UniversityORPortlandUSA
| | - Monika A Davare
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
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249
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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250
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Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andrés-Sanchez N, Paloni M, Bernadó P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M. A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation. Nat Commun 2023; 14:6316. [PMID: 37813838 PMCID: PMC10562473 DOI: 10.1038/s41467-023-42049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.
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Affiliation(s)
- Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Geronimo Dubra
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | | | - Aurélie Fournet
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Emile Alghoul
- IGH, CNRS, University of Montpellier, Montpellier, France
| | - Dhanvantri Chahar
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Nuria Andrés-Sanchez
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Matteo Paloni
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Pau Bernadó
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | | | | | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | - Nathalie Sibille
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center, Utrecht, 3584 CT, Netherlands
| | - Liliana Krasinska
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Daniel Fisher
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France.
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France.
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands.
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