1
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Xie J, Ruan S, Tu M, Yuan Z, Hu J, Li H, Li S. Clustering single-cell RNA sequencing data via iterative smoothing and self-supervised discriminative embedding. Oncogene 2024:10.1038/s41388-024-03074-5. [PMID: 38834657 DOI: 10.1038/s41388-024-03074-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
Single-cell transcriptome sequencing (scRNA-seq) is a high-throughput technique used to study gene expression at the single-cell level. Clustering analysis is a commonly used method in scRNA-seq data analysis, helping researchers identify cell types and uncover interactions between cells. However, the choice of a robust similarity metric in the clustering procedure is still an open challenge due to the complex underlying structures of the data and the inherent noise in data acquisition. Here, we propose a deep clustering method for scRNA-seq data called scRISE (scRNA-seq Iterative Smoothing and self-supervised discriminative Embedding model) to resolve this challenge. The model consists of two main modules: an iterative smoothing module based on graph autoencoders designed to denoise the data and refine the pairwise similarity in turn to gradually incorporate cell structural features and enrich the data information; and a self-supervised discriminative embedding module with adaptive similarity threshold for partitioning samples into correct clusters. Our approach has shown improved quality of data representation and clustering on seventeen scRNA-seq datasets against a number of state-of-the-art deep learning clustering methods. Furthermore, utilizing the scRISE method in biological analysis against the HNSCC dataset has unveiled 62 informative genes, highlighting their potential roles as therapeutic targets and biomarkers.
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Affiliation(s)
- Jinxin Xie
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Shanshan Ruan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Mingyan Tu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianguo Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai, 200062, China.
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2
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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [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: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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3
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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [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: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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4
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Miller WE, O'Connor CM. CMV-encoded GPCRs in infection, disease, and pathogenesis. Adv Virus Res 2024; 118:1-75. [PMID: 38461029 DOI: 10.1016/bs.aivir.2024.01.001] [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] [Indexed: 03/11/2024]
Abstract
G protein coupled receptors (GPCRs) are seven-transmembrane domain proteins that modulate cellular processes in response to external stimuli. These receptors represent the largest family of membrane proteins, and in mammals, their signaling regulates important physiological functions, such as vision, taste, and olfaction. Many organisms, including yeast, slime molds, and viruses encode GPCRs. Cytomegaloviruses (CMVs) are large, betaherpesviruses, that encode viral GPCRs (vGPCRs). Human CMV (HCMV) encodes four vGPCRs, including UL33, UL78, US27, and US28. Each of these vGPCRs, as well as their rodent and primate orthologues, have been investigated for their contributions to viral infection and disease. Herein, we discuss how the CMV vGPCRs function during lytic and latent infection, as well as our understanding of how they impact viral pathogenesis.
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Affiliation(s)
- William E Miller
- Department of Molecular and Cellular Bioscience, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christine M O'Connor
- Infection Biology, Sheikha Fatima bint Mubarak Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
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5
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Chen M, Zhu JY, Mu WJ, Luo HY, Li Y, Li S, Yan LJ, Li RY, Guo L. Cdo1-Camkk2-AMPK axis confers the protective effects of exercise against NAFLD in mice. Nat Commun 2023; 14:8391. [PMID: 38110408 PMCID: PMC10728194 DOI: 10.1038/s41467-023-44242-7] [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: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
Exercise is an effective non-pharmacological strategy for ameliorating nonalcoholic fatty liver disease (NAFLD), but the underlying mechanism needs further investigation. Cysteine dioxygenase type 1 (Cdo1) is a key enzyme for cysteine catabolism that is enriched in liver, whose role in NAFLD remains poorly understood. Here, we show that exercise induces the expression of hepatic Cdo1 via the cAMP/PKA/CREB signaling pathway. Hepatocyte-specific knockout of Cdo1 (Cdo1LKO) decreases basal metabolic rate of the mice and impairs the effect of exercise against NAFLD, whereas hepatocyte-specific overexpression of Cdo1 (Cdo1LTG) increases basal metabolic rate of the mice and synergizes with exercise to ameliorate NAFLD. Mechanistically, Cdo1 tethers Camkk2 to AMPK by interacting with both of them, thereby activating AMPK signaling. This promotes fatty acid oxidation and mitochondrial biogenesis in hepatocytes to attenuate hepatosteatosis. Therefore, by promoting hepatic Camkk2-AMPK signaling pathway, Cdo1 acts as an important downstream effector of exercise to combat against NAFLD.
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Affiliation(s)
- Min Chen
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Jie-Ying Zhu
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Wang-Jing Mu
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Hong-Yang Luo
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Yang Li
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Shan Li
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Lin-Jing Yan
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Ruo-Ying Li
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China
| | - Liang Guo
- School of Exercise and Health and Collaborative Innovation Center for Sports and Public Health, Shanghai University of Sport, Shanghai, 200438, China.
- Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, 200438, China.
- Key Laboratory of Exercise and Health Sciences of the Ministry of Education, Shanghai University of Sport, Shanghai, 200438, China.
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6
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DiRusso CJ, DeMaria AM, Wong J, Wang W, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A conserved core region of the scaffold NEMO is essential for signal-induced conformational change and liquid-liquid phase separation. J Biol Chem 2023; 299:105396. [PMID: 37890781 PMCID: PMC10694592 DOI: 10.1016/j.jbc.2023.105396] [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: 05/23/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between the N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | - Anthony M DeMaria
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Judy Wong
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Wei Wang
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jack J Jordanides
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA.
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7
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Jiang X, Xu Z, Jiang S, Wang H, Xiao M, Shi Y, Wang K. PDZ and LIM Domain-Encoding Genes: Their Role in Cancer Development. Cancers (Basel) 2023; 15:5042. [PMID: 37894409 PMCID: PMC10605254 DOI: 10.3390/cancers15205042] [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: 09/10/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
PDZ-LIM family proteins (PDLIMs) are a kind of scaffolding proteins that contain PDZ and LIM interaction domains. As protein-protein interacting molecules, PDZ and LIM domains function as scaffolds to bind to a variety of proteins. The PDLIMs are composed of evolutionarily conserved proteins found throughout different species. They can participate in cell signal transduction by mediating the interaction of signal molecules. They are involved in many important physiological processes, such as cell differentiation, proliferation, migration, and the maintenance of cellular structural integrity. Studies have shown that dysregulation of the PDLIMs leads to tumor formation and development. In this paper, we review and integrate the current knowledge on PDLIMs. The structure and function of the PDZ and LIM structural domains and the role of the PDLIMs in tumor development are described.
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Affiliation(s)
| | | | | | | | | | - Yueli Shi
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China; (X.J.); (Z.X.); (S.J.); (H.W.); (M.X.)
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China; (X.J.); (Z.X.); (S.J.); (H.W.); (M.X.)
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8
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Lambert KA, Clements CM, Mukherjee N, Pacheco TR, Shellman SX, Henen MA, Vögeli B, Goldstein NB, Birlea S, Hintzsche J, Tan AC, Zhao R, Norris DA, Robinson WA, Wang Y, VanTreeck JG, Shellman YG. SASH1 interacts with TNKS2 and promotes human melanocyte stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559624. [PMID: 37808724 PMCID: PMC10557680 DOI: 10.1101/2023.09.26.559624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Both aging spots (hyperpigmentation) and hair graying (lack of pigmentation) are associated with aging, two seemingly opposite pigmentation phenotypes. It is not clear how they are mechanistically connected. This study investigated the underlying mechanism in a family with an inherited pigmentation disorder. Clinical examinations identified accelerated hair graying and skin dyspigmentation (intermixed hyper and hypopigmentation) in the family members carrying the SASH1 S519N variant. Cell assays indicated that SASH1 promoted stem-like characteristics in human melanocytes, and SASH1 S519N was defective in this function. Multiple assays showed that SASH1 binds to tankyrase 2 (TNKS2), which is required for SASH1's promotion of stem-like function. Further, the SASH1 S519N variant is in a bona fide Tankyrase-binding motif, and SASH1 S519N alters the binding kinetics and affinity. Results here indicate SASH1 as a novel protein regulating the appropriate balance between melanocyte stem cells (McSC) and mature melanocytes (MCs), with S519N variant causing defects. We propose that dysfunction of McSC maintenance connects multiple aging-associated pigmentation phenotypes in the general population.
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9
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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10
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DiRusso CJ, DeMaria AM, Wong J, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A Conserved Core Region of the Scaffold NEMO is Essential for Signal-induced Conformational Change and Liquid-liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542299. [PMID: 37292615 PMCID: PMC10245932 DOI: 10.1101/2023.05.25.542299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO, due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | | | - Judy Wong
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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11
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Samulevich ML, Shamilov R, Aneskievich BJ. Thermostable Proteins from HaCaT Keratinocytes Identify a Wide Breadth of Intrinsically Disordered Proteins and Candidates for Liquid-Liquid Phase Separation. Int J Mol Sci 2022; 23:ijms232214323. [PMID: 36430801 PMCID: PMC9692912 DOI: 10.3390/ijms232214323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) move through an ensemble of conformations which allows multitudinous roles within a cell. Keratinocytes, the predominant cell type in mammalian epidermis, have had only a few individual proteins assessed for intrinsic disorder and its possible contribution to liquid-liquid phase separation (LLPS), especially in regard to what functions or structures these proteins provide. We took a holistic approach to keratinocyte IDPs starting with enrichment via the isolation of thermostable proteins. The keratinocyte protein involucrin, known for its resistance to heat denaturation, served as a marker. It and other thermostable proteins were identified by liquid chromatography tandem mass spectrometry and subjected to extensive bioinformatic analysis covering gene ontology, intrinsic disorder, and potential for LLPS. Numerous proteins unique to keratinocytes and other proteins with shared expression in multiple cell types were identified to have IDP traits (e.g., compositional bias, nucleic acid binding, and repeat motifs). Among keratinocyte-specific proteins, many that co-assemble with involucrin into the cell-specific structure known as the cornified envelope scored highly for intrinsic disorder and potential for LLPS. This suggests intrinsic disorder and LLPS are previously unrecognized traits for assembly of the cornified envelope, echoing the contribution of intrinsic disorder and LLPS to more widely encountered features such as stress granules and PML bodies.
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Affiliation(s)
- Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269-3092, USA
- Correspondence: ; Tel.: +1-860-486-3053; Fax: +1-860-486-5792
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