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Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Cell Syst 2021; 12:1144-1159.e6. [PMID: 34529928 DOI: 10.1016/j.cels.2021.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have an identifiable paralog, exploiting synthetic lethality between paralogs may be a broadly applicable approach for targeting gene loss in cancer. However, only a biased subset of human paralog pairs has been tested for synthetic lethality to date. Here, by analyzing genome-wide CRISPR screens and molecular profiles of over 700 cancer cell lines, we identify features predictive of synthetic lethality between paralogs, including shared protein-protein interactions and evolutionary conservation. We develop a machine-learning classifier based on these features to predict which paralog pairs are most likely to be synthetic lethal and to explain why. We show that our classifier accurately predicts the results of combinatorial CRISPR screens in cancer cell lines and furthermore can distinguish pairs that are synthetic lethal in multiple cell lines from those that are cell-line specific. A record of this paper's transparent peer review process is included in the supplemental information.
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52
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Colardo M, Martella N, Pensabene D, Siteni S, Di Bartolomeo S, Pallottini V, Segatto M. Neurotrophins as Key Regulators of Cell Metabolism: Implications for Cholesterol Homeostasis. Int J Mol Sci 2021; 22:5692. [PMID: 34073639 PMCID: PMC8198482 DOI: 10.3390/ijms22115692] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Neurotrophins constitute a family of growth factors initially characterized as predominant mediators of nervous system development, neuronal survival, regeneration and plasticity. Their biological activity is promoted by the binding of two different types of receptors, leading to the generation of multiple and variegated signaling cascades in the target cells. Increasing evidence indicates that neurotrophins are also emerging as crucial regulators of metabolic processes in both neuronal and non-neuronal cells. In this context, it has been reported that neurotrophins affect redox balance, autophagy, glucose homeostasis and energy expenditure. Additionally, the trophic support provided by these secreted factors may involve the regulation of cholesterol metabolism. In this review, we examine the neurotrophins' signaling pathways and their effects on metabolism by critically discussing the most up-to-date information. In particular, we gather experimental evidence demonstrating the impact of these growth factors on cholesterol metabolism.
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Affiliation(s)
- Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (M.C.); (N.M.); (D.P.); (S.D.B.)
| | - Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (M.C.); (N.M.); (D.P.); (S.D.B.)
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (M.C.); (N.M.); (D.P.); (S.D.B.)
| | - Silvia Siteni
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Sabrina Di Bartolomeo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (M.C.); (N.M.); (D.P.); (S.D.B.)
| | - Valentina Pallottini
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy;
- Neuroendocrinology Metabolism and Neuropharmacology Unit, IRCSS Fondazione Santa Lucia, Via del Fosso Fiorano 64, 00143 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (M.C.); (N.M.); (D.P.); (S.D.B.)
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53
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Rahman M, Billmann M, Costanzo M, Aregger M, Tong AHY, Chan K, Ward HN, Brown KR, Andrews BJ, Boone C, Moffat J, Myers CL. A method for benchmarking genetic screens reveals a predominant mitochondrial bias. Mol Syst Biol 2021; 17:e10013. [PMID: 34018332 PMCID: PMC8138267 DOI: 10.15252/msb.202010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/29/2022] Open
Abstract
We present FLEX (Functional evaluation of experimental perturbations), a pipeline that leverages several functional annotation resources to establish reference standards for benchmarking human genome-wide CRISPR screen data and methods for analyzing them. FLEX provides a quantitative measurement of the functional information captured by a given gene-pair dataset and a means to explore the diversity of functions captured by the input dataset. We apply FLEX to analyze data from the diverse cell line screens generated by the DepMap project. We identify a predominant mitochondria-associated signal within co-essentiality networks derived from these data and explore the basis of this signal. Our analysis and time-resolved CRISPR screens in a single cell line suggest that the variable phenotypes associated with mitochondria genes across cells may reflect screen dynamics and protein stability effects rather than genetic dependencies. We characterize this functional bias and demonstrate its relevance for interpreting differential hits in any CRISPR screening context. More generally, we demonstrate the utility of the FLEX pipeline for performing robust comparative evaluations of CRISPR screens or methods for processing them.
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Affiliation(s)
- Mahfuzur Rahman
- Department of Computer Science and EngineeringUniversity of Minnesota – Twin CitiesMinneapolisMNUSA
| | - Maximilian Billmann
- Department of Computer Science and EngineeringUniversity of Minnesota – Twin CitiesMinneapolisMNUSA
| | | | | | - Amy H Y Tong
- Donnelly CentreUniversity of TorontoTorontoONCanada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate ProgramUniversity of Minnesota – Twin CitiesMinneapolisMNUSA
| | | | - Brenda J Andrews
- Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Charles Boone
- Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Jason Moffat
- Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Chad L Myers
- Department of Computer Science and EngineeringUniversity of Minnesota – Twin CitiesMinneapolisMNUSA
- Bioinformatics and Computational Biology Graduate ProgramUniversity of Minnesota – Twin CitiesMinneapolisMNUSA
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54
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Sekine Y, Houston R, Sekine S. Cellular metabolic stress responses via organelles. Exp Cell Res 2021; 400:112515. [PMID: 33582095 DOI: 10.1016/j.yexcr.2021.112515] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/08/2023]
Abstract
Metabolite fluctuations following nutrient metabolism or environmental stresses impact various intracellular signaling networks and stress responses to maintain cellular and organismal homeostasis. It has been shown that subcellular organelles, such as the endoplasmic reticulum, the Golgi apparatus, lysosomes and mitochondria serve as crucial hubs linking alterations in metabolite levels to cellular responses. This role is coordinated by molecular machineries that are associated with the lipid membranes of organelles, which sense the fluctuations in specific metabolites and activate the appropriate signaling and effector molecules. Moreover, recent studies have demonstrated that membraneless organelles, such as the nucleolus and stress granules, are involved in the metabolic stress response. Metabolite-induced post-translational modifications appear to play an important role in this process. Here, we review the molecular mechanisms of metabolite sensing and metabolite-mediated stress responses through membrane-bound and membraneless organelles in mammalian cells.
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Affiliation(s)
- Yusuke Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Ryan Houston
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shiori Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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55
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Li Z, Bin Luo, Yu L, Lan F, Wu Y. Intermolecular B-N coordination and multi-interaction synergism induced selective glycoprotein adsorption by phenylboronic acid-functionalized magnetic composites under acidic and neutral conditions. J Mater Chem B 2021; 9:453-463. [PMID: 33289778 DOI: 10.1039/d0tb01901a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abnormal protein glycosylation is associated with many diseases including cardiovascular disease, diabetes, and cancer. Therefore, selective capturing of glycoproteins under physiological or weak acid conditions (tumor microenvironment) is vital for disease diagnosis and further comprehensive analysis. Here, we propose a strategy of intermolecular B-N bond-based phenylboronic acid affinity to capture glycoproteins under neutral and slightly acidic conditions. Surprisingly, the captured glycoproteins were released in alkaline solution. This is contrary to the traditional phenylboric acid affinity, and we studied this from the perspective of materials, proteins, and incubation conditions. We identified the synergistic effect of intermolecular B-N bond-based phenylboronic acid affinity, electrostatic interaction, and polymer brush structure-based glycoprotein adsorption under slightly acidic conditions. The electrostatic repulsion between Fe3O4@SiO2@poly (2-aminoethyl methacrylate hydrochloride)-4-carboxyphenylboronic acid (Fe3O4@SiO2@PAMA-CPBA) nanoparticles and transferrin (TRF) was far greater than the specific binding between phenylboric acid of CPBA and glycosylation residues of TRF resulting in the release of the captured glycoproteins in alkaline solution. Fe3O4@SiO2@PAMA-CPBA nanoparticles exhibited different selectivity capabilities toward different glycoproteins in multiprotein solutions due to protein interactions. These results may pave a new way for the design of phenylboric acid-based materials towards glycoprotein adsorption in a physiological environment.
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Affiliation(s)
- Zhiyu Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Lingzhu Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
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Vos DY, van de Sluis B. Function of the endolysosomal network in cholesterol homeostasis and metabolic-associated fatty liver disease (MAFLD). Mol Metab 2021; 50:101146. [PMID: 33348067 PMCID: PMC8324686 DOI: 10.1016/j.molmet.2020.101146] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
Background Metabolic-associated fatty liver disease (MAFLD), also known as non-alcoholic fatty liver disease, has become the leading cause of chronic liver disease worldwide. In addition to hepatic accumulation of triglycerides, dysregulated cholesterol metabolism is an important contributor to the pathogenesis of MAFLD. Maintenance of cholesterol homeostasis is highly dependent on cellular cholesterol uptake and, subsequently, cholesterol transport to other membrane compartments, such as the endoplasmic reticulum (ER). Scope of review The endolysosomal network is key for regulating cellular homeostasis and adaptation, and emerging evidence has shown that the endolysosomal network is crucial to maintain metabolic homeostasis. In this review, we will summarize our current understanding of the role of the endolysosomal network in cholesterol homeostasis and its implications in MAFLD pathogenesis. Major conclusions Although multiple endolysosomal proteins have been identified in the regulation of cholesterol uptake, intracellular transport, and degradation, their physiological role is incompletely understood. Further research should elucidate their role in controlling metabolic homeostasis and development of fatty liver disease. The intracellular cholesterol transport is tightly regulated by the endocytic and lysosomal network. Dysfunction of the endolysosomal network affects hepatic lipid homeostasis. The endosomal sorting of lipoprotein receptors is precisely regulated and is not a bulk process.
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Affiliation(s)
- Dyonne Y Vos
- Department of Pediatrics, section Molecular Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bart van de Sluis
- Department of Pediatrics, section Molecular Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Xiao J, Xiong Y, Yang LT, Wang JQ, Zhou ZM, Dong LW, Shi XJ, Zhao X, Luo J, Song BL. POST1/C12ORF49 regulates the SREBP pathway by promoting site-1 protease maturation. Protein Cell 2020; 12:279-296. [PMID: 32666500 PMCID: PMC8019017 DOI: 10.1007/s13238-020-00753-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Sterol-regulatory element binding proteins (SREBPs) are the key transcriptional regulators of lipid metabolism. The activation of SREBP requires translocation of the SREBP precursor from the endoplasmic reticulum to the Golgi, where it is sequentially cleaved by site-1 protease (S1P) and site-2 protease and releases a nuclear form to modulate gene expression. To search for new genes regulating cholesterol metabolism, we perform a genome-wide CRISPR/Cas9 knockout screen and find that partner of site-1 protease (POST1), encoded by C12ORF49, is critically involved in the SREBP signaling. Ablation of POST1 decreases the generation of nuclear SREBP and reduces the expression of SREBP target genes. POST1 binds S1P, which is synthesized as an inactive protease (form A) and becomes fully mature via a two-step autocatalytic process involving forms B'/B and C'/C. POST1 promotes the generation of the functional S1P-C'/C from S1P-B'/B (canonical cleavage) and, notably, from S1P-A directly (non-canonical cleavage) as well. This POST1-mediated S1P activation is also essential for the cleavages of other S1P substrates including ATF6, CREB3 family members and the α/β-subunit precursor of N-acetylglucosamine-1-phosphotransferase. Together, we demonstrate that POST1 is a cofactor controlling S1P maturation and plays important roles in lipid homeostasis, unfolded protein response, lipoprotein metabolism and lysosome biogenesis.
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Affiliation(s)
- Jian Xiao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Yanni Xiong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Liu-Ting Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Ju-Qiong Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Zi-Mu Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Le-Wei Dong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Xiong-Jie Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Jie Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
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58
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Affiliation(s)
- Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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