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Smirnova AM, Hronová V, Mohammad MP, Herrmannová A, Gunišová S, Petráčková D, Halada P, Coufal Š, Świrski M, Rendleman J, Jendruchová K, Hatzoglou M, Beznosková P, Vogel C, Valášek LS. Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control. Cell Rep 2024; 43:113976. [PMID: 38507410 PMCID: PMC11058473 DOI: 10.1016/j.celrep.2024.113976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/15/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Activating transcription factor 4 (ATF4) is a master transcriptional regulator of the integrated stress response, leading cells toward adaptation or death. ATF4's induction under stress was thought to be due to delayed translation reinitiation, where the reinitiation-permissive upstream open reading frame 1 (uORF1) plays a key role. Accumulating evidence challenging this mechanism as the sole source of ATF4 translation control prompted us to investigate additional regulatory routes. We identified a highly conserved stem-loop in the uORF2/ATF4 overlap, immediately preceded by a near-cognate CUG, which introduces another layer of regulation in the form of ribosome queuing. These elements explain how the inhibitory uORF2 can be translated under stress, confirming prior observations but contradicting the original regulatory model. We also identified two highly conserved, potentially modified adenines performing antagonistic roles. Finally, we demonstrated that the canonical ATF4 translation start site is substantially leaky scanned. Thus, ATF4's translational control is more complex than originally described, underpinning its key role in diverse biological processes.
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Affiliation(s)
- Anna M Smirnova
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Denisa Petráčková
- Laboratory of Post-transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Petr Halada
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Štěpán Coufal
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Kristína Jendruchová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Christine Vogel
- Department of Biology, New York University, New York, NY, USA.
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
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Neurauter CG, Pannone M, Sousa MMLD, Wang W, Kuśnierczyk A, Luna L, Sætrom P, Scheffler K, Bjørås M. Enhanced glutathione levels confer resistance to apoptotic and ferroptotic programmed cell death in NEIL DNA glycosylase deficient HAP1 cells. Free Radic Biol Med 2024; 213:470-487. [PMID: 38301978 DOI: 10.1016/j.freeradbiomed.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/12/2024] [Accepted: 01/21/2024] [Indexed: 02/03/2024]
Abstract
The NTHL1 and NEIL1-3 DNA glycosylases are major enzymes in the removal of oxidative DNA base lesions, via the base excision repair (BER) pathway. It is expected that lack of these DNA glycosylases activities would render cells vulnerable to oxidative stress, promoting cell death. Intriguingly, we found that single, double, triple, and quadruple DNA glycosylase knockout HAP1 cells are, however, more resistant to oxidative stress caused by genotoxic agents than wild type cells. Furthermore, glutathione depletion in NEIL deficient cells further enhances resistance to cell death induced via apoptosis and ferroptosis. Finally, we observed higher basal level of glutathione and differential expression of NRF2-regulated genes associated with glutathione homeostasis in the NEIL triple KO cells. We propose that lack of NEIL DNA glycosylases causes aberrant transcription and subsequent errors in protein synthesis. This leads to increased endoplasmic reticulum stress and proteotoxic stress. To counteract the elevated intracellular stress, an adaptive response mediated by increased glutathione basal levels, rises in these cells. This study reveals an unforeseen role of NEIL glycosylases in regulation of resistance to oxidative stress, suggesting that modulation of NEIL glycosylase activities is a potential approach to improve the efficacy of e.g. anti-inflammatory therapies.
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Affiliation(s)
- Christine Gran Neurauter
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Marco Pannone
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Mirta Mittelstedt Leal de Sousa
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway.
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Katja Scheffler
- Department of Neurology, St.Olavs University Hospital, Trondheim, 7006, Norway; Department of Neuromedicine and Movement Science (INB), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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Smirnova AM, Hronova V, Mohammad MP, Herrmannova A, Gunisova S, Petrackova D, Halada P, Coufal S, Swirski M, Rendelman J, Jendruchova K, Hatzoglou M, Beznoskova P, Vogel C, Valasek LS. Stem-loop induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control. bioRxiv 2024:2023.07.12.548609. [PMID: 37502919 PMCID: PMC10369994 DOI: 10.1101/2023.07.12.548609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
ATF4 is a master transcriptional regulator of the integrated stress response leading cells towards adaptation or death. ATF4's induction under stress was thought to be mostly due to delayed translation reinitiation, where the reinitiation-permissive uORF1 plays a key role. Accumulating evidence challenging this mechanism as the sole source of ATF4 translation control prompted us to investigate additional regulatory routes. We identified a highly conserved stem-loop in the uORF2/ATF4 overlap, immediately preceded by a near-cognate CUG, which introduces another layer of regulation in the form of ribosome queuing. These elements explain how the inhibitory uORF2 can be translated under stress, confirming prior observations, but contradicting the original regulatory model. We also identified two highly conserved, potentially modified adenines performing antagonistic roles. Finally, we demonstrate that the canonical ATF4 translation start site is substantially leaky-scanned. Thus, ATF4's translational control is more complex than originally described underpinning its key role in diverse biological processes.
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5
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Owings KG, Chow CY. A Drosophila screen identifies a role for histone methylation in ER stress preconditioning. G3 (Bethesda) 2024; 14:jkad265. [PMID: 38098286 PMCID: PMC11021027 DOI: 10.1093/g3journal/jkad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023]
Abstract
Stress preconditioning occurs when transient, sublethal stress events impact an organism's ability to counter future stresses. Although preconditioning effects are often noted in the literature, very little is known about the underlying mechanisms. To model preconditioning, we exposed a panel of genetically diverse Drosophila melanogaster to a sublethal heat shock and measured how well the flies survived subsequent exposure to endoplasmic reticulum (ER) stress. The impact of preconditioning varied with genetic background, ranging from dying half as fast to 4 and a half times faster with preconditioning compared to no preconditioning. Subsequent association and transcriptional analyses revealed that histone methylation, and transcriptional regulation are both candidate preconditioning modifier pathways. Strikingly, almost all subunits (7/8) in the Set1/COMPASS complex were identified as candidate modifiers of preconditioning. Functional analysis of Set1 knockdown flies demonstrated that loss of Set1 led to the transcriptional dysregulation of canonical ER stress genes during preconditioning. Based on these analyses, we propose a preconditioning model in which Set1 helps to establish an interim transcriptional "memory" of previous stress events, resulting in a preconditioned response to subsequent stress.
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Affiliation(s)
- Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
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He F, Yu X, Zhang J, Cui J, Tang L, Zou S, Pu J, Ran P. Biomass-related PM 2.5 induced inflammatory microenvironment via IL-17F/IL-17RC axis. Environ Pollut 2024; 342:123048. [PMID: 38036089 DOI: 10.1016/j.envpol.2023.123048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023]
Abstract
Biomass exposure is a significant environmental risk factor for COPD, but the underlying mechanisms have not yet been fully elucidated. Inflammatory microenvironment has been shown to drive the development of many chronic diseases. Pollution exposure can cause increased levels of inflammatory factors in the lungs, leading to an inflammatory microenvironment which is prevalent in COPD. Our findings revealed that IL-17F was elevated in COPD, while exposure to biomass led to increased expression of IL-17F in both alveolar epithelial and macrophage cells in mice. Blocking IL-17F could alleviate the lung inflammation induced by seven days of biomass exposure in mice. We employed a transwell co-culture system to simulate the microenvironment and investigate the interactions between MLE-12 and MH-S cells. We demonstrated that anti-IL-17F antibody attenuated the inflammatory responses induced by BRPM2.5 in MLE-12 and MH-S co-cultured with BRPM2.5-MLE-12, which reduced inflammatory changes in microenvironment. We found that IL-17RC, an important receptor for IL-17F, played a key role in the interactions. Knockout of IL-17RC in MH-S resulted in inhibited IL-17F signaling and attenuated inflammatory response after MH-S co-culture with BRPM2.5-MLE-12. Our investigation suggests that BRPM2.5 induces lung epithelial-macrophage interactions via IL-17F/IL-17RC axis regulating the inflammatory response. These results may provide a novel strategy for effective prevention and treatment of biomass-related COPD.
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Affiliation(s)
- Fang He
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China; State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Xiaoyuan Yu
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Jiahuan Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Jieda Cui
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510000, China; Guangzhou National Laboratory, No.9 XingDaoHuanBei Road, Guangzhou International BioIsland, Guangzhou, Guangdong, 510000, China
| | - Lei Tang
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Siqi Zou
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Jinding Pu
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Pixin Ran
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510000, China; Guangzhou National Laboratory, No.9 XingDaoHuanBei Road, Guangzhou International BioIsland, Guangzhou, Guangdong, 510000, China.
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7
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Anisimova AS, Karagöz GE. Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells. RNA 2023; 29:1818-1836. [PMID: 37582618 PMCID: PMC10578486 DOI: 10.1261/rna.079714.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
The conserved family of RNA-binding proteins (RBPs), IGF2BPs, plays an essential role in posttranscriptional regulation controlling mRNA stability, localization, and translation. Mammalian cells express three isoforms of IGF2BPs: IGF2BP1-3. IGF2BP3 is highly overexpressed in cancer cells, and its expression correlates with a poor prognosis in various tumors. Therefore, revealing its target RNAs with high specificity in healthy tissues and in cancer cells is of crucial importance. Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) identifies the binding sites of RBPs on their target RNAs at nucleotide resolution in a transcriptome-wide manner. Here, we optimized the PAR-CLIP protocol to study RNA targets of endogenous IGF2BP3 in a human colorectal carcinoma cell line. To this end, we first established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes. Second, we modified the protocol to use highly sensitive infrared (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method "IR-PAR-CLIP." Third, we compared RNase cleavage conditions and found that sequence preferences of the RNases impact the number of the identified IGF2BP3 targets and introduce a systematic bias in the identified RNA motifs. Fourth, we adapted the single adapter circular ligation approach to increase the efficiency in library preparation. The optimized IR-PAR-CLIP protocol revealed novel RNA targets of IGF2BP3 in a human colorectal carcinoma cell line. We anticipate that our IR-PAR-CLIP approach provides a framework for studies of other RBPs.
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Affiliation(s)
- Aleksandra S Anisimova
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, 1030 Vienna, Austria
| | - G Elif Karagöz
- Max Perutz Labs, Vienna BioCenter Campus (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, 1030 Vienna, Austria
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Papaspyropoulos A, Hazapis O, Altulea A, Polyzou A, Verginis P, Evangelou K, Fousteri M, Papantonis A, Demaria M, Gorgoulis V. Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence. Aging Cell 2023; 22:e13893. [PMID: 37547972 PMCID: PMC10497830 DOI: 10.1111/acel.13893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/04/2023] [Indexed: 08/08/2023] Open
Abstract
Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). These senescence subtypes are heterogeneous and often develop subset-specific phenotypes. Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery between senescence subsets.
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Affiliation(s)
- Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
| | - Orsalia Hazapis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Abdullah Altulea
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | | | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Maria Fousteri
- Institute for Fundamental Biomedical ResearchBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
| | - Marco Demaria
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Vassilis Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
- Clinical Molecular PathologyMedical School, University of DundeeDundeeUK
- Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
- Center for New Biotechnologies and Precision MedicineMedical School, National and Kapodistrian University of AthensAthensGreece
- Faculty of Health and Medical SciencesUniversity of SurreySurreyUK
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Zdrazilova L, Rakosnikova T, Himmelreich N, Ondruskova N, Pasak M, Vanisova M, Volfova N, Honzik T, Thiel C, Hansikova H. Metabolic adaptation of human skin fibroblasts to ER stress caused by glycosylation defect in PMM2-CDG. Mol Genet Metab 2023; 139:107629. [PMID: 37392701 DOI: 10.1016/j.ymgme.2023.107629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/16/2023] [Accepted: 06/18/2023] [Indexed: 07/03/2023]
Abstract
PMM2-CDG is the most prevalent type of congenital disorders of glycosylation (CDG). It is caused by pathogenic variants in the gene encoding phosphomannomutase 2 (PMM2), which converts mannose-6-phosphate to mannose-1-phosphate and thus activates this saccharide for further glycosylation processes. Defective glycosylation can lead to an abnormal accumulation of unfolded proteins in endoplasmic reticulum (ER) and cause its stress. The ER is a key compartment for glycosylation, and its connection and communication with mitochondria has been described extensively in literature. Their crosstalk is important for cell proliferation, calcium homeostasis, apoptosis, mitochondrial fission regulation, bioenergetics, autophagy, lipid metabolism, inflammasome formation and unfolded protein response. Therefore, in the present study we posed a question, whether defective glycosylation leads to bioenergetic disruption. Our data reveal possible chronic stress in ER and activated unfolded protein response via PERK pathway in PMM2-CDG fibroblasts. Presumably, it leads to bioenergetic reorganization and increased assembly of respiratory chain complexes into supercomplexes together with suppressed glycolysis in PMM2-CDG patient cells. These changes cause alterations in Krebs cycle, which is tightly connected to electron transport system in mitochondria. In summary, we present data showing metabolic adaptation of cells to glycosylation defect caused by various pathogenic variants in PMM2.
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Affiliation(s)
- L Zdrazilova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - T Rakosnikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - N Himmelreich
- Centre for Child and Adolescent Medicine Heidelberg, Department 1, Heidelberg, Germany
| | - N Ondruskova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - M Pasak
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - M Vanisova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - N Volfova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - T Honzik
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - C Thiel
- Centre for Child and Adolescent Medicine Heidelberg, Department 1, Heidelberg, Germany
| | - H Hansikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
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10
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Harris TJ, Liao Y, Shi W, Evangelista M, Pal B, Puthalakath H, Aston R, Mollard R, Mariadason JM, Lee EF, Fairlie WD. Induction of endoplasmic reticulum stress is associated with the anti-tumor activity of monepantel across cancer types. Cancer Med 2023. [PMID: 37148543 DOI: 10.1002/cam4.6021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Monepantel is an anti-helminthic drug that also has anti-cancer properties. Despite several studies over the years, the molecular target of monepantel in mammalian cells is still unknown, and its mechanism-of-action is not fully understood, though effects on cell cycle, mTOR signalling and autophagy have been implicated. METHODS Viability assays were performed on >20 solid cancer cell cells, and apoptosis assays were performed on a subset of these, including 3D cultures. Genetic deletion of BAX/BAK and ATG were used to establish roles of apoptosis and autophagy in killing activity. RNA-sequencing was performed on four cell lines after monepantel treatment, and differentially regulated genes were confirmed by Western blotting. RESULTS We showed that monepantel has anti-proliferative activity on a broad range of cancer cell lines. In some, this was associated with induction of apoptosis which was confirmed using a BAX/BAK-deficient cell line. However, proliferation is still inhibited in these cells following monepantel treatment, indicating cell-cycle disruption as the major anti-cancer effect. Previous studies have also indicated autophagic cell death occurs following monepantel treatment. We showed autophagy induction in multiple cell lines; however, deletion of a key autophagy regulator ATG7 had minimal impact on monepantel's anti-proliferative activity, suggesting autophagy is associated with, but not required for its anti-tumour effects. Transcriptomic analysis of four cell lines treated with monepantel revealed downregulation of many genes involved in the cell cycle, and upregulation of genes linked to ATF4-mediated ER stress responses, especially those involved in amino-acid metabolism and protein synthesis. CONCLUSIONS As these outcomes are all associated with mTOR signalling, cell cycle and autophagy, we now provide a likely triggering mechanism for the anti-cancer activity of monepantel.
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Affiliation(s)
- Tiffany J Harris
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Marco Evangelista
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Hamsa Puthalakath
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | | | - Richard Mollard
- PharmAust Ltd, Claremont, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Erinna F Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Walter D Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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11
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Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Life Sci Alliance 2022; 6:6/1/e202201514. [PMID: 36283702 PMCID: PMC9595208 DOI: 10.26508/lsa.202201514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
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Affiliation(s)
- Barbara Uszczynska-Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sreedevi Sugunan
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Monika Kwiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Centre of New Technologies, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Sokol
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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12
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Almeida LM, Pinho BR, Duchen MR, Oliveira JMA. The PERKs of mitochondria protection during stress: insights for PERK modulation in neurodegenerative and metabolic diseases. Biol Rev Camb Philos Soc 2022; 97:1737-1748. [PMID: 35475315 DOI: 10.1111/brv.12860] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 02/06/2023]
Abstract
Protein kinase RNA-like ER kinase (PERK) is an endoplasmic reticulum (ER) stress sensor that responds to the accumulation of misfolded proteins. Once activated, PERK initiates signalling pathways that halt general protein production, increase the efficiency of ER quality control, and maintain redox homeostasis. PERK activation also protects mitochondrial homeostasis during stress. The location of PERK at the contact sites between the ER and the mitochondria creates a PERK-mitochondria axis that allows PERK to detect stress in both organelles, adapt their functions and prevent apoptosis. During ER stress, PERK activation triggers mitochondrial hyperfusion, preventing premature apoptotic fragmentation of the mitochondria. PERK activation also increases the formation of mitochondrial cristae and the assembly of respiratory supercomplexes, enhancing cellular ATP-generating capacity. PERK strengthens mitochondrial quality control during stress by promoting the expression of mitochondrial chaperones and proteases and by increasing mitochondrial biogenesis and mitophagy, resulting in renewal of the mitochondrial network. But how does PERK mediate all these changes in mitochondrial homeostasis? In addition to the classic PERK-eukaryotic translation initiation factor 2α (eIF2α)-activating transcription factor 4 (ATF4) pathway, PERK can activate other protective pathways - PERK-O-linked N-acetyl-glucosamine transferase (OGT), PERK-transcription factor EB (TFEB), and PERK-nuclear factor erythroid 2-related factor 2 (NRF2) - contributing to broader regulation of mitochondrial dynamics, metabolism, and quality control. The pharmacological activation of PERK is protective in models of neurodegenerative and metabolic diseases, such as Huntington's disease, progressive supranuclear palsy and obesity, while the inhibition of PERK was protective in models of Parkinson's and prion diseases and diabetes. In this review, we address the molecular mechanisms by which PERK regulates mitochondrial dynamics, metabolism and quality control, and discuss the therapeutic potential of targeting PERK in neurodegenerative and metabolic diseases.
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Affiliation(s)
- Liliana M Almeida
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal
| | - Brígida R Pinho
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal
| | - Michael R Duchen
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, U.K.,Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, London, WC1E 6BT, U.K
| | - Jorge M A Oliveira
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, Department of Drug Sciences, Pharmacology Lab, University of Porto, 4050-313, Porto, Portugal.,Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, London, WC1E 6BT, U.K
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13
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Latorre P, Böttcher R, Nadal-Ribelles M, Li CH, Solé C, Martínez-Cebrián G, Boutros PC, Posas F, de Nadal E. Data-driven identification of inherent features of eukaryotic stress-responsive genes. NAR Genom Bioinform 2022; 4:lqac018. [PMID: 35265837 PMCID: PMC8900196 DOI: 10.1093/nargab/lqac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/20/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Living organisms are continuously challenged by changes in their environment that can propagate to stresses at the cellular level, such as rapid changes in osmolarity or oxygen tension. To survive these sudden changes, cells have developed stress-responsive mechanisms that tune cellular processes. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here, we generated a comprehensive catalog of osmostress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83%) were distinct in osmostress-responsive genes. We then identified 13 non-redundant minimal osmostress gene traits and used statistical modeling to rank the most stress-predictive features. Intriguingly, the most relevant features of osmostress-responsive genes are the number of transcription factors targeting them and gene conservation. Using data on HeLa samples, we showed that the same features that define yeast osmostress-responsive genes can predict osmostress-responsive genes in humans, but with changes in the rank-ordering of feature-importance. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.
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Affiliation(s)
- Pablo Latorre
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - René Böttcher
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mariona Nadal-Ribelles
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Constance H Li
- Departments of Human Genetics and Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Carme Solé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gerard Martínez-Cebrián
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Paul C Boutros
- Departments of Human Genetics and Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Francesc Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eulàlia de Nadal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
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14
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Jackson CA, Vogel C. New horizons in the stormy sea of multimodal single-cell data integration. Mol Cell 2022; 82:248-259. [PMID: 35063095 PMCID: PMC8830781 DOI: 10.1016/j.molcel.2021.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
While measurements of RNA expression have dominated the world of single-cell analyses, new single-cell techniques increasingly allow collection of different data modalities, measuring different molecules, structural connections, and intermolecular interactions. Integrating the resulting multimodal single-cell datasets is a new bioinformatics challenge. Equally important, it is a new experimental design challenge for the bench scientist, who is not only choosing from a myriad of techniques for each data modality but also faces new challenges in experimental design. The ultimate goal is to design, execute, and analyze multimodal single-cell experiments that are more than just descriptive but enable the learning of new causal and mechanistic biology. This objective requires strict consideration of the goals behind the analysis, which might range from mapping the heterogeneity of a cellular population to assembling system-wide causal networks that can further our understanding of cellular functions and eventually lead to models of tissues and organs. We review steps and challenges toward this goal. Single-cell transcriptomics is now a mature technology, and methods to measure proteins, lipids, small-molecule metabolites, and other molecular phenotypes at the single-cell level are rapidly developing. Integrating these single-cell readouts so that each cell has measurements of multiple types of data, e.g., transcriptomes, proteomes, and metabolomes, is expected to allow identification of highly specific cellular subpopulations and to provide the basis for inferring causal biological mechanisms.
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Affiliation(s)
- Christopher A Jackson
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
| | - Christine Vogel
- New York University, Department of Biology, Center for Genomics and Systems Biology, New York NY, USA
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15
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Ward CP, Peng L, Yuen S, Chang M, Karapetyan R, Nyangau E, Mohammed H, Palacios H, Ziari N, Joe LK, Frakes AE, Dandan M, Dillin A, Hellerstein MK. ER Unfolded Protein Response in Liver In Vivo Is Characterized by Reduced, Not Increased, De Novo Lipogenesis and Cholesterol Synthesis Rates with Uptake of Fatty Acids from Adipose Tissue: Integrated Gene Expression, Translation Rates and Metabolic Fluxes. Int J Mol Sci 2022; 23:ijms23031073. [PMID: 35162995 PMCID: PMC8835023 DOI: 10.3390/ijms23031073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
The unfolded protein response in the endoplasmic reticulum (UPRER) is involved in a number of metabolic diseases. Here, we characterize UPRER-induced metabolic changes in mouse livers in vivo through metabolic labeling and mass spectrometric analysis of lipid and proteome-wide fluxes. We induced UPRER by tunicamycin administration and measured synthesis rates of proteins, fatty acids and cholesterol, as well as RNA-seq. Contrary to reports in isolated cells, hepatic de novo lipogenesis and cholesterogenesis were markedly reduced, as were mRNA levels and synthesis rates of lipogenic proteins. H&E staining showed enrichment with lipid droplets while electron microscopy revealed ER morphological changes. Interestingly, the pre-labeling of adipose tissue prior to UPRER induction resulted in the redistribution of labeled fatty acids from adipose tissue to the liver, with replacement by unlabeled glycerol in the liver acylglycerides, indicating that the liver uptake was of free fatty acids, not whole glycerolipids. The redistribution of adipose fatty acids to the liver was not explicable by altered plasma insulin, increased fatty acid levels (lipolysis) or by reduced food intake. Synthesis of most liver proteins was suppressed under UPRER conditions, with the exception of BiP, other chaperones, protein disulfide isomerases, and proteins of ribosomal biogenesis. Protein synthesis rates generally, but not always, paralleled changes in mRNA. In summary, this combined approach, linking static changes with fluxes, revealed an integrated reduction of lipid and cholesterol synthesis pathways, from gene expression to translation and metabolic flux rates, under UPRER conditions. The reduced lipogenesis does not parallel human fatty liver disease. This approach provides powerful tools to characterize metabolic processes underlying hepatic UPRER in vivo.
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Affiliation(s)
- Catherine P. Ward
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Lucy Peng
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Samuel Yuen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Michael Chang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Rozalina Karapetyan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Edna Nyangau
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Hussein Mohammed
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Hector Palacios
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Naveed Ziari
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Larry K. Joe
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 92093, USA; (L.K.J.); (A.E.F.); (A.D.)
| | - Ashley E. Frakes
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 92093, USA; (L.K.J.); (A.E.F.); (A.D.)
| | - Mohamad Dandan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
| | - Andrew Dillin
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 92093, USA; (L.K.J.); (A.E.F.); (A.D.)
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 92093, USA; (C.P.W.); (L.P.); (S.Y.); (M.C.); (R.K.); (E.N.); (H.M.); (H.P.); (N.Z.); (M.D.)
- Correspondence:
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16
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Liou YH, Personnaz J, Jacobi D, Knudsen NH, Chalom MM, Starost KA, Nnah IC, Lee CH. Hepatic Fis1 regulates mitochondrial integrated stress response and improves metabolic homeostasis. JCI Insight 2022; 7:150041. [PMID: 35015731 PMCID: PMC8876406 DOI: 10.1172/jci.insight.150041] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022] Open
Abstract
Mitophagy and mitochondrial integrated stress response (ISR) are 2 primary protective mechanisms to maintain functional mitochondria. Whether these 2 processes are coordinately regulated remains unclear. Here we show that mitochondrial fission 1 protein (Fis1), which is required for completion of mitophagy, serves as a signaling hub linking mitophagy and ISR. In mouse hepatocytes, high fat diet (HFD) feeding induces unresolved oxidative stress, defective mitophagy and enhanced type I interferon (IFN-I) response implicated in promoting metabolic inflammation. Adenoviral-mediated acute hepatic Fis1 overexpression is sufficient to reduce oxidative damage and improve glucose homeostasis in HFD-fed mice. RNA-Seq analysis reveals that Fis1 triggers a retrograde mitochondria-to-nucleus communication upregulating ISR genes encoding anti-oxidant defense, redox homeostasis, and proteostasis pathways. Fis1-mediated ISR also suppresses expression of IFN-I–stimulated genes through activating transcription factor 5 (Atf5), which inhibits the transactivation activity of interferon regulatory factor 3 (Irf3) known to control IFN-I production. Metabolite analysis demonstrates that Fis1 activation leads to accumulation of fumarate, a TCA cycle intermediate capable of increasing Atf5 activity. Consequently, hepatic Atf5 overexpression or monomethyl fumarate (MMF) treatment improves glucose homeostasis in HFD-fed mice. Collectively, these results support the potential use of small molecules targeting the Fis1-Atf5 axis, such as MMF, to treat metabolic diseases.
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Affiliation(s)
- Yae-Huei Liou
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Jean Personnaz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - David Jacobi
- Inserm UMR 1087, l'institut du thorax, Nantes, France
| | - Nelson H Knudsen
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States of America
| | - Mayer M Chalom
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Kyle A Starost
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Israel C Nnah
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Chih-Hao Lee
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, United States of America
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17
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Ramdas Nair A, Lakhiani P, Zhang C, Macchi F, Sadler KC. A permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver. Genomics 2021; 114:107-124. [PMID: 34863900 DOI: 10.1016/j.ygeno.2021.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 12/01/2022]
Abstract
Restoring homeostasis following proteostatic stress hinges on a stress-specific transcriptional signature. How these signatures are regulated is unknown. We use functional genomics to uncover how activating transcription factor 6 (ATF6), a central factor in the unfolded protein response, regulates its target genes in response to toxicant induced and physiological stress in the liver. We identified 652 conserved putative ATF6 targets (CPATs), which functioned in metabolism, development and proteostasis. Strikingly, Atf6 activation in the zebrafish liver by transgenic nAtf6 overexpression, ethanol and arsenic exposure resulted in a distinct CPAT signature for each; with only 34 CPATs differentially expressed in all conditions. In contrast, during liver regeneration in mice resulted in a dynamic differential expression pattern of 53% of CPATs. These CPATs were distinguished by residing in open chromatin, H3K4me3 occupancy and the absence of H3K27me3 on their promoters. This suggests that a permissive epigenetic landscape allows stress-specific Atf6 target gene expression.
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Affiliation(s)
- Anjana Ramdas Nair
- Program in Biology, New York University Abu Dhabi, PO Box. 129188, Abu Dhabi, United Arab Emirates
| | - Priyanka Lakhiani
- Program in Biology, New York University Abu Dhabi, PO Box. 129188, Abu Dhabi, United Arab Emirates
| | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, PO Box. 129188, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, PO Box. 129188, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, PO Box. 129188, Abu Dhabi, United Arab Emirates.
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18
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Abstract
Pancreatic β cells dedicate much of their protein translation capacity to producing insulin to maintain glucose homeostasis. In response to increased secretory demand, β cells can compensate by increasing insulin production capability even in the face of protracted peripheral insulin resistance. The ability to amplify insulin secretion in response to hyperglycemia is a critical facet of β-cell function, and the exact mechanisms by which this occurs have been studied for decades. To adapt to the constant and fast-changing demands for insulin production, β cells use the unfolded protein response of the endoplasmic reticulum. Failure of these compensatory mechanisms contributes to both type 1 and 2 diabetes. Additionally, studies in which β cells are "rested" by reducing endogenous insulin demand have shown promise as a therapeutic strategy that could be applied more broadly. Here, we review recent findings in β cells pertaining to the metabolic amplifying pathway, the unfolded protein response, and potential advances in therapeutics based on β-cell rest.
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Affiliation(s)
- Michael A Kalwat
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Donalyn Scheuner
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | | | - Decio L Eizirik
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Melanie H Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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19
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Child JR, Chen Q, Reid DW, Jagannathan S, Nicchitta CV. Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules. RNA 2021; 27:1241-1256. [PMID: 34244458 PMCID: PMC8456999 DOI: 10.1261/rna.078858.121] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation of translation initiation. In general, SG recruitment is limited to a subpopulation of a given mRNA species and RNA-seq analyses of purified SGs revealed that signal sequence-encoding (i.e., endoplasmic reticulum [ER]-targeted) transcripts are significantly underrepresented, consistent with prior reports that ER localization can protect mRNAs from SG recruitment. Using translational profiling, cell fractionation, and single molecule mRNA imaging, we examined SG biogenesis following activation of the unfolded protein response (UPR) by 1,4-dithiothreitol (DTT) and report that gene-specific subsets of cytosolic and ER-targeted mRNAs can be recruited into SGs. Furthermore, we demonstrate that SGs form in close proximity to or directly associated with the ER membrane. ER-associated SG assembly was also observed during arsenite stress, suggesting broad roles for the ER in SG biogenesis. Recruitment of a given mRNA into SGs required stress-induced translational repression, though translational inhibition was not solely predictive of an mRNA's propensity for SG recruitment. SG formation was prevented by the transcriptional inhibitors actinomycin D or triptolide, suggesting a functional link between gene transcriptional state and SG biogenesis. Collectively these data demonstrate that ER-targeted and cytosolic mRNAs can be recruited into ER-associated SGs and this recruitment is sensitive to transcriptional inhibition. We propose that newly transcribed mRNAs exported under conditions of suppressed translation initiation are primary SG substrates, with the ER serving as the central subcellular site of SG formation.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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20
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Abstract
Large-scale mapping of protein structures and their different states is crucial for gaining a mechanistic understanding of proteome function and regulation. In this issue of Cell, Cappelletti et al. achieve such a feat and identify hundreds of protein structural changes in response to outside stressors, providing a rich "structuromics" resource characterizing cellular adaptation.
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Affiliation(s)
- Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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21
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Delgado-Benito V, Berruezo-Llacuna M, Altwasser R, Winkler W, Sundaravinayagam D, Balasubramanian S, Caganova M, Graf R, Rahjouei A, Henke MT, Driesner M, Keller L, Prigione A, Janz M, Akalin A, Di Virgilio M. PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification. J Exp Med 2021; 217:151913. [PMID: 32609329 PMCID: PMC7537392 DOI: 10.1084/jem.20200137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The establishment of protective humoral immunity is dependent on the ability of mature B cells to undergo antibody gene diversification while adjusting to the physiological stressors induced by activation with the antigen. Mature B cells diversify their antibody genes by class switch recombination (CSR) and somatic hypermutation (SHM), which are both dependent on efficient induction of activation-induced cytidine deaminase (AID). Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation and ensures efficient antibody diversification by promoting their survival and optimal function.
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Berruezo-Llacuna
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robert Altwasser
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Wiebke Winkler
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marieta Caganova
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Robin Graf
- Laboratory of Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ali Rahjouei
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marie-Thérèse Henke
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Madlen Driesner
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lisa Keller
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Alessandro Prigione
- Laboratory of Mitochondria and Cell Fate Reprogramming, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Janz
- Laboratory of Biology of Malignant Lymphomas, Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité, University Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Technology Platform, Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
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22
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Filippova N, Yang X, Ananthan S, Calano J, Pathak V, Bratton L, Vekariya RH, Zhang S, Ofori E, Hayward EN, Namkoong D, Crossman DK, Crowley MR, King PH, Mobley J, Nabors LB. Targeting the HuR Oncogenic Role with a New Class of Cytoplasmic Dimerization Inhibitors. Cancer Res 2021; 81:2220-2233. [PMID: 33602784 DOI: 10.1158/0008-5472.can-20-2858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/29/2020] [Accepted: 02/10/2021] [Indexed: 11/16/2022]
Abstract
The development of novel therapeutics that exploit alterations in the activation state of key cellular signaling pathways due to mutations in upstream regulators has generated the field of personalized medicine. These first-generation efforts have focused on actionable mutations identified by deep sequencing of large numbers of tumor samples. We propose that a second-generation opportunity exists by exploiting key downstream "nodes of control" that contribute to oncogenesis and are inappropriately activated due to loss of upstream regulation and microenvironmental influences. The RNA-binding protein HuR represents such a node. Because HuR functionality in cancer cells is dependent on HuR dimerization and its nuclear/cytoplasmic shuttling, we developed a new class of molecules targeting HuR protein dimerization. A structure-activity relationship algorithm enabled development of inhibitors of HuR multimer formation that were soluble, had micromolar activity, and penetrated the blood-brain barrier. These inhibitors were evaluated for activity validation and specificity in a robust cell-based assay of HuR dimerization. SRI-42127, a molecule that met these criteria, inhibited HuR multimer formation across primary patient-derived glioblastoma xenolines (PDGx), leading to arrest of proliferation, induction of apoptosis, and inhibition of colony formation. SRI-42127 had favorable attributes with central nervous system penetration and inhibited tumor growth in mouse models. RNA and protein analysis of SRI-42127-treated PDGx xenolines across glioblastoma molecular subtypes confirmed attenuation of targets upregulated by HuR. These results highlight how focusing on key attributes of HuR that contribute to cancer progression, namely cytoplasmic localization and multimerization, has led to the development of a novel, highly effective inhibitor. SIGNIFICANCE: These findings utilize a cell-based mechanism of action assay with a structure-activity relationship compound development pathway to discover inhibitors that target HuR dimerization, a mechanism required for cancer promotion.
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Affiliation(s)
- Natalia Filippova
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiuhua Yang
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Subramaniam Ananthan
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Jennifer Calano
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Vibha Pathak
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Larry Bratton
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Rakesh H Vekariya
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Sixue Zhang
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Edward Ofori
- Drug Discovery Division, Chemistry Department, Southern Research Institute, Birmingham, Alabama
| | - Emily N Hayward
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - David Namkoong
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - David K Crossman
- Department of Genetics, UAB Genomics Core, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michael R Crowley
- Department of Genetics, UAB Genomics Core, University of Alabama at Birmingham, Birmingham, Alabama
| | - Peter H King
- Department of Neurology, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - James Mobley
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, O'Neal Comprehensive Cancer Center MS/Proteomics Shared Facility, University of Alabama at Birmingham, Birmingham, Alabama
| | - Louis B Nabors
- Division of Neuro-oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama.
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23
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Kumar V, Maity S. ER Stress-Sensor Proteins and ER-Mitochondrial Crosstalk-Signaling Beyond (ER) Stress Response. Biomolecules 2021; 11:173. [PMID: 33525374 PMCID: PMC7911976 DOI: 10.3390/biom11020173] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Recent studies undoubtedly show the importance of inter organellar connections to maintain cellular homeostasis. In normal physiological conditions or in the presence of cellular and environmental stress, each organelle responds alone or in coordination to maintain cellular function. The Endoplasmic reticulum (ER) and mitochondria are two important organelles with very specialized structural and functional properties. These two organelles are physically connected through very specialized proteins in the region called the mitochondria-associated ER membrane (MAM). The molecular foundation of this relationship is complex and involves not only ion homeostasis through the shuttling of calcium but also many structural and apoptotic proteins. IRE1alpha and PERK are known for their canonical function as an ER stress sensor controlling unfolded protein response during ER stress. The presence of these transmembrane proteins at the MAM indicates its potential involvement in other biological functions beyond ER stress signaling. Many recent studies have now focused on the non-canonical function of these sensors. In this review, we will focus on ER mitochondrial interdependence with special emphasis on the non-canonical role of ER stress sensors beyond ER stress.
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24
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Hrstka SCL, Ankam S, Agac B, Klein JP, Moore RA, Narapureddy B, Schneider I, Hrstka RF, Dasari S, Staff NP. Proteomic analysis of human iPSC-derived sensory neurons implicates cell stress and microtubule dynamics dysfunction in bortezomib-induced peripheral neurotoxicity. Exp Neurol 2021; 335:113520. [PMID: 33129842 PMCID: PMC7750199 DOI: 10.1016/j.expneurol.2020.113520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/26/2022]
Abstract
The neurotoxic effects of the chemotherapeutic agent bortezomib on dorsal root ganglia sensory neurons are well documented, yet the mechanistic underpinnings that govern these cellular processes remain incompletely understood. In this study, system-wide proteomic changes were identified in human induced pluripotent stem cell-derived sensory neurons (iSNs) exposed to a clinically relevant dose of bortezomib. Label-free mass spectrometry facilitated the identification of approximately 2800 iSN proteins that exhibited differential levels in the setting of bortezomib. A significant proportion of these proteins affect the cellular processes of microtubule dynamics, cytoskeletal and cytoplasmic organization, and molecular transport, and pathway analysis revealed an enrichment of proteins in signaling pathways attributable to the unfolded protein response and the integrated stress response. Alterations in microtubule-associated proteins suggest a multifaceted relationship exists between bortezomib-induced proteotoxicity and microtubule cytoskeletal architecture, and MAP2 was prioritized as a topmost influential candidate. We observed a significant reduction in the overall levels of MAP2c in somata without discernable changes in neurites. As MAP2 is known to affect cellular processes including axonogenesis, neurite extension and branching, and neurite morphology, its altered levels are suggestive of a prominent role in bortezomib-induced neurotoxicity.
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Affiliation(s)
- Sybil C L Hrstka
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Soneela Ankam
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Busranur Agac
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Jon P Klein
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Raymond A Moore
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States of America
| | - Bhavya Narapureddy
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Isabella Schneider
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Ronald F Hrstka
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States of America
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America.
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25
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Monticolo F, Palomba E, Chiusano ML. Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses. Int J Mol Sci 2020; 21:ijms21249560. [PMID: 33334055 PMCID: PMC7765469 DOI: 10.3390/ijms21249560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
The main hallmarks of cancer diseases are the evasion of programmed cell death, uncontrolled cell division, and the ability to invade adjacent tissues. The explosion of omics technologies offers challenging opportunities to identify molecular agents and processes that may play relevant roles in cancer. They can support comparative investigations, in one or multiple experiments, exploiting evidence from one or multiple species. Here, we analyzed gene expression data from induction of programmed cell death and stress response in Homo sapiens and compared the results with Saccharomyces cerevisiae gene expression during the response to cell death. The aim was to identify conserved candidate genes associated with Homo sapiens cell death, favored by crosslinks based on orthology relationships between the two species. We identified differentially-expressed genes, pathways that are significantly dysregulated across treatments, and characterized genes among those involved in induced cell death. We investigated on co-expression patterns and identified novel genes that were not expected to be associated with death pathways, that have a conserved pattern of expression between the two species. Finally, we analyzed the resulting list by HumanNet and identified new genes predicted to be involved in cancer. The data integration and the comparative approach between distantly-related reference species that were here exploited pave the way to novel discoveries in cancer therapy and also contribute to detect conserved genes potentially involved in programmed cell death.
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Affiliation(s)
- Francesco Monticolo
- Department of Agricultural Sciences, Università Degli Studi di Napoli Federico II, 80055 Naples, Italy;
| | - Emanuela Palomba
- Department of RIMAR, Stazione Zoologica “Anton Dohrn”, 80122 Naples, Italy;
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, Università Degli Studi di Napoli Federico II, 80055 Naples, Italy;
- Department of RIMAR, Stazione Zoologica “Anton Dohrn”, 80122 Naples, Italy;
- Correspondence:
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26
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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27
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Dostal V, Wood SD, Thomas CT, Han Y, Lau E, Lam MPY. Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart. Sci Rep 2020; 10:18440. [PMID: 33116222 PMCID: PMC7595225 DOI: 10.1038/s41598-020-75505-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
The heart is sensitive to oxidative damage but a global view on how the cardiac proteome responds to oxidative stressors has yet to fully emerge. Using quantitative tandem mass spectrometry, we assessed the effects of acute exposure of the oxidative stress inducer paraquat on protein expression in mouse hearts. We observed widespread protein expression changes in the paraquat-exposed heart especially in organelle-containing subcellular fractions. During cardiac response to acute oxidative stress, proteome changes are consistent with a rapid reduction of mitochondrial metabolism, coupled with activation of multiple antioxidant proteins, reduction of protein synthesis and remediation of proteostasis. In addition to differential expression, we saw evidence of spatial reorganizations of the cardiac proteome including the translocation of hexokinase 2 to more soluble fractions. Treatment with the antioxidants Tempol and MitoTEMPO reversed many proteomic signatures of paraquat but this reversal was incomplete. We also identified a number of proteins with unknown function in the heart to be triggered by paraquat, suggesting they may have functions in oxidative stress response. Surprisingly, protein expression changes in the heart correlate poorly with those in the lung, consistent with differential sensitivity or stress response in these two organs. The results and data set here could provide insights into oxidative stress responses in the heart and avail the search for new therapeutic targets.
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Affiliation(s)
- Vishantie Dostal
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Silas D Wood
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Cody T Thomas
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Yu Han
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Maggie P Y Lam
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .,Department of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .,Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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28
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Hu XQ, Song R, Romero M, Dasgupta C, Min J, Hatcher D, Xiao D, Blood A, Wilson SM, Zhang L. Gestational Hypoxia Inhibits Pregnancy-Induced Upregulation of Ca 2+ Sparks and Spontaneous Transient Outward Currents in Uterine Arteries Via Heightened Endoplasmic Reticulum/Oxidative Stress. Hypertension 2020; 76:930-942. [PMID: 32683903 PMCID: PMC7429261 DOI: 10.1161/hypertensionaha.120.15235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hypoxia during pregnancy profoundly affects uterine vascular adaptation and increases the risk of pregnancy complications, including preeclampsia and fetal intrauterine growth restriction. We recently demonstrated that increases in Ca2+ sparks and spontaneous transient outward currents (STOCs) played an essential role in pregnancy-induced uterine vascular adaptation. In the present study, we hypothesize that gestational hypoxia suppresses Ca2+ sparks/STOCs coupling leading to increased uterine vascular tone via enhanced endoplasmic reticulum (ER)/oxidative stress. Uterine arteries were obtained from nonpregnant and near-term pregnant sheep residing in low altitude or acclimatizing to high-altitude (3801 m) hypoxia for ≈110 days. High-altitude hypoxia suppressed pregnancy-induced upregulation of RyR1 and RyR2 (ryanodine receptor 1 and 2) protein abundance, Ca2+ sparks, and STOCs in uterine arteries. Inhibition of Ca2+ sparks/STOCs with the RyR inhibitor ryanodine significantly increased pressure-dependent myogenic tone in uterine arteries from low-altitude normoxic pregnant animals but not those from high-altitude hypoxic pregnant animals. Gestational hypoxia significantly increased ER/oxidative stress in uterine arteries. Of importance, the hypoxia-mediated suppression of Ca2+ sparks/STOCs and increase in myogenic tone in uterine arteries of pregnant animals were reversed by inhibiting ER/oxidative stress. Of great interest, the impaired sex hormonal regulation of STOCs in high-altitude animals was annulled by scavenging reactive oxygen species but not by inhibiting ER stress. Together, the findings reveal the differential mechanisms of ER and oxidative stresses in suppressing Ca2+ sparks/STOCs and increasing myogenic tone of uterine arteries in hypoxia during gestation, providing new insights into the understanding of pregnancy complications associated with hypoxia.
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Affiliation(s)
- Xiang-Qun Hu
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Rui Song
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Monica Romero
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Chiranjib Dasgupta
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Joseph Min
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Daisy Hatcher
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Daliao Xiao
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Arlin Blood
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Sean M Wilson
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
| | - Lubo Zhang
- From the Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, CA
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29
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Ho JJD, Balukoff NC, Theodoridis PR, Wang M, Krieger JR, Schatz JH, Lee S. A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism. Nat Commun 2020; 11:2677. [PMID: 32472050 PMCID: PMC7260222 DOI: 10.1038/s41467-020-16504-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/30/2020] [Indexed: 01/30/2023] Open
Abstract
Protein expression evolves under greater evolutionary constraint than mRNA levels, and translation efficiency represents a primary determinant of protein levels during stimuli adaptation. This raises the question as to the translatome remodelers that titrate protein output from mRNA populations. Here, we uncover a network of RNA-binding proteins (RBPs) that enhances the translation efficiency of glycolytic proteins in cells responding to oxygen deprivation. A system-wide proteomic survey of translational engagement identifies a family of oxygen-regulated RBPs that functions as a switch of glycolytic intensity. Tandem mass tag-pulse SILAC (TMT-pSILAC) and RNA sequencing reveals that each RBP controls a unique but overlapping portfolio of hypoxic responsive proteins. These RBPs collaborate with the hypoxic protein synthesis apparatus, operating as a translation efficiency checkpoint that integrates upstream mRNA signals to activate anaerobic metabolism. This system allows anoxia-resistant animals and mammalian cells to initiate anaerobic glycolysis and survive hypoxia. We suggest that an oxygen-sensitive RBP cluster controls anaerobic metabolism to confer hypoxia tolerance. mRNA translation efficiency is regulated in response to stimuli. Here the authors employ mass spectrometry analysis of ribosome fractions and show that under hypoxia, oxygen-sensitive RNA binding proteins enhance the translation efficiency of glycolysis pathway transcripts.
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Affiliation(s)
- J J David Ho
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nathan C Balukoff
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Phaedra R Theodoridis
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Miling Wang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jonathan R Krieger
- The SickKids Proteomics, Analytics, Robotics & Chemical Biology Centre (SPARC Biocentre), The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Bioinformatics Solutions Inc., Waterloo, ON, N2L 6J2, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA. .,Department of Urology, Miller School of Medicine, University of Miami, Miami, 33136, USA.
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30
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Hijazi I, Knupp J, Chang A. Retrograde signaling mediates an adaptive survival response to endoplasmic reticulum stress in Saccharomyces cerevisiae. J Cell Sci 2020; 133:jcs.241539. [PMID: 32005698 DOI: 10.1242/jcs.241539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
One major cause of endoplasmic reticulum (ER) stress is homeostatic imbalance between biosynthetic protein folding and protein folding capacity. Cells utilize mechanisms such as the unfolded protein response (UPR) to cope with ER stress. Nevertheless, when ER stress is prolonged or severe, cell death may occur, accompanied by production of mitochondrial reactive oxygen species (ROS). Using a yeast model (Saccharomyces cerevisiae), we describe an innate, adaptive response to ER stress to increase select mitochondrial proteins, O2 consumption and cell survival. The mitochondrial response allows cells to resist additional ER stress. The ER stress-induced mitochondrial response is mediated by activation of retrograde (RTG) signaling to enhance anapleurotic reactions of the tricarboxylic acid cycle. Mitochondrial response to ER stress is accompanied by inactivation of the conserved TORC1 pathway, and activation of Snf1/AMPK, the conserved energy sensor and regulator of metabolism. Our results provide new insight into the role of respiration in cell survival in the face of ER stress, and should help in developing therapeutic strategies to limit cell death in disorders linked to ER stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Imadeddin Hijazi
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Jeffrey Knupp
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Amy Chang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
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31
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Pizzinga M, Harvey RF, Garland GD, Mordue R, Dezi V, Ramakrishna M, Sfakianos A, Monti M, Mulroney TE, Poyry T, Willis AE. The cell stress response: extreme times call for post‐transcriptional measures. WIREs RNA 2019; 11:e1578. [DOI: 10.1002/wrna.1578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/09/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Ryan Mordue
- MRC Toxicology Unit University of Cambridge Leicester UK
| | - Veronica Dezi
- MRC Toxicology Unit University of Cambridge Leicester UK
| | | | | | - Mie Monti
- MRC Toxicology Unit University of Cambridge Leicester UK
| | | | - Tuija Poyry
- MRC Toxicology Unit University of Cambridge Leicester UK
| | - Anne E. Willis
- MRC Toxicology Unit University of Cambridge Leicester UK
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32
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Abstract
Since its discovery more than 25 years ago, great progress has been made in our understanding of the unfolded protein response (UPR), a homeostatic mechanism that adjusts endoplasmic reticulum (ER) function to satisfy the physiological demands of the cell. However, if ER homeostasis is unattainable, the UPR switches to drive cell death to remove defective cells in an effort to protect the health of the organism. This functional dichotomy places the UPR at the crossroads of the adaptation versus apoptosis decision. Here, we focus on new developments in UPR signaling mechanisms, in the interconnectivity among the signaling pathways that make up the UPR in higher eukaryotes, and in the coordination between the UPR and other fundamental cellular processes.
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Affiliation(s)
- G Elif Karagöz
- Max Perutz Labs Vienna, Medical University of Vienna, Vienna, Austria
| | - Tomás Aragón
- Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, Pamplona, Spain
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, Santa Barbara, CA, USA
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33
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Takesue Y, Wei FY, Fukuda H, Tanoue Y, Yamamoto T, Chujo T, Shinojima N, Yano S, Morioka M, Mukasa A, Kuratsu J, Tomizawa K. Regulation of growth hormone biosynthesis by Cdk5 regulatory subunit associated protein 1-like 1 (CDKAL1) in pituitary adenomas. Endocr J 2019; 66:807-816. [PMID: 31189758 DOI: 10.1507/endocrj.ej18-0536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CDK5 regulatory subunit associated protein 1-like 1 (CDKAL1) is a tRNA-modifying enzyme that catalyzes 2-methylthiolation (ms2) and has been implicated in the development of type 2 diabetes (T2D). CDKAL1-mediated ms2 is important for efficient protein translation and regulates insulin biosynthesis in pancreatic cells. Interestingly, an association between T2D and release of growth hormone (GH) has been reported in humans. However, it is unknown whether CDKAL1 is important for hormone production in the pituitary gland. The present study investigated the role of CDKAL1 in GH-producing pituitary adenomas (GHPAs). CDKAL1 activity was suppressed in GHPAs, as evidenced by a decrease in ms2, compared with non-functioning pituitary adenomas (NFPAs), which do not produce specific hormones. Downregulation of Cdkal1 using small interfering and short hairpin RNAs increased the biosynthesis and secretion of GH in rat GH3 cells. Depletion of Cdkal1 increased the cytosolic calcium level via downregulation of DnaJ heat shock protein family (Hsp40) member C10 (Dnajc10), which is an endoplasmic reticulum protein related to calcium homeostasis. This stimulated transcription of GH via upregulation of Pit-1. Moreover, CDKAL1 activity was highly sensitive to proteostatic stress and was upregulated by suppression of this stress. Taken together, these results suggest that dysregulation of CDKAL1 is involved in the pathogenesis of GHPAs, and that modulation of the proteostatic stress response might control CDKAL1 activity and facilitate treatment of GHPAs.
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Affiliation(s)
- Yoshihiro Takesue
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyuki Fukuda
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuki Tanoue
- International Research Center for Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shigetoshi Yano
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Fukuoka Neurosurgical Hospital, Fukuoka 811-1313, Japan
| | - Motohiro Morioka
- Department of Neurosurgery, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Junichi Kuratsu
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Neurosurgery, Sakurajuji Hospital, Kumamoto 861-4173, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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34
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Vitrinel B, Koh HWL, Mujgan Kar F, Maity S, Rendleman J, Choi H, Vogel C. Exploiting Interdata Relationships in Next-generation Proteomics Analysis. Mol Cell Proteomics 2019; 18:S5-S14. [PMID: 31126983 PMCID: PMC6692783 DOI: 10.1074/mcp.mr118.001246] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/01/2019] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry based proteomics and other technologies have matured to enable routine quantitative, system-wide analysis of concentrations, modifications, and interactions of proteins, mRNAs, and other molecules. These studies have allowed us to move toward a new field concerned with mining information from the combination of these orthogonal data sets, perhaps called "integromics." We highlight examples of recent studies and tools that aim at relating proteomic information to mRNAs, genetic associations, and changes in small molecules and lipids. We argue that productive data integration differs from parallel acquisition and interpretation and should move toward quantitative modeling of the relationships between the data. These relationships might be expressed by temporal information retrieved from time series experiments, rate equations to model synthesis and degradation, or networks of causal, evolutionary, physical, and other interactions. We outline steps and considerations toward such integromic studies to exploit the synergy between data sets.
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Affiliation(s)
- Burcu Vitrinel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Hiromi W L Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Funda Mujgan Kar
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.
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35
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Gonen N, Meller A, Sabath N, Shalgi R. Amino Acid Biosynthesis Regulation during Endoplasmic Reticulum Stress Is Coupled to Protein Expression Demands. iScience 2019; 19:204-213. [PMID: 31377665 PMCID: PMC6698312 DOI: 10.1016/j.isci.2019.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) stress response, also known as the unfolded protein response (UPR), is a complex cellular response to ER protein misfolding that involves transcriptional regulatory branches and a PERK-mediated translational regulatory branch. Here we revealed that amino acid biosynthesis regulation is coupled to protein synthesis demands during ER stress. Specifically, we demonstrated that the UPR leads to PERK-dependent induction in the biosynthesis of specific amino acids, and to upregulation of their corresponding tRNA synthetases. Furthermore, we found that sequences of UPR-upregulated proteins are significantly enriched with these UPR-induced amino acids. Interestingly, whereas the UPR leads to repression of ER target proteins, we showed that secreted proteins tended to escape this repression and were highly enriched for the UPR-induced amino acids. Our results unravel coordination between amino acid supply, namely, biosynthesis and tRNA loading, and demand from UPR-induced proteins under ER stress, thus revealing an additional regulatory layer of protein synthesis. Coordination of amino acid supply and protein synthesis demand during ER stress Specific amino acid biosynthesis and cognate tRNA synthetases induction by the UPR UPR-induced amino acids support amino acid demand of UPR-upregulated proteins UPR-induced amino acids are highly enriched within secreted proteins
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Affiliation(s)
- Nir Gonen
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Anatoly Meller
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Niv Sabath
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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36
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Piazzi M, Bavelloni A, Gallo A, Faenza I, Blalock WL. Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster. Int J Mol Sci 2019; 20:ijms20112718. [PMID: 31163577 PMCID: PMC6600399 DOI: 10.3390/ijms20112718] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/27/2022] Open
Abstract
Energetically speaking, ribosome biogenesis is by far the most costly process of the cell and, therefore, must be highly regulated in order to avoid unnecessary energy expenditure. Not only must ribosomal RNA (rRNA) synthesis, ribosomal protein (RP) transcription, translation, and nuclear import, as well as ribosome assembly, be tightly controlled, these events must be coordinated with other cellular events, such as cell division and differentiation. In addition, ribosome biogenesis must respond rapidly to environmental cues mediated by internal and cell surface receptors, or stress (oxidative stress, DNA damage, amino acid depletion, etc.). This review examines some of the well-studied pathways known to control ribosome biogenesis (PI3K-AKT-mTOR, RB-p53, MYC) and how they may interact with some of the less well studied pathways (eIF2α kinase and RNA editing/splicing) in higher eukaryotes to regulate ribosome biogenesis, assembly, and protein translation in a dynamic manner.
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Affiliation(s)
- Manuela Piazzi
- Istituto di Genetica Molecolare-Luigi Luca Cavalli Sforza, UOS Bologna, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy.
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy.
| | | | - Angela Gallo
- RNA Editing Laboratory, Dipartimento di Oncoematologia, IRCCS, Ospedale Pediatrica Bambino Gesù, 00146 Rome, Italy.
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40126 Bologna, Italy.
| | - William L Blalock
- Istituto di Genetica Molecolare-Luigi Luca Cavalli Sforza, UOS Bologna, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy.
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy.
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37
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Tegeder I. Nitric oxide mediated redox regulation of protein homeostasis. Cell Signal 2019; 53:348-56. [PMID: 30408515 DOI: 10.1016/j.cellsig.2018.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
Abstract
Nitric oxide is a versatile diffusible signaling molecule, whose biosynthesis by three NO synthases (NOS) is tightly regulated at transcriptional and posttranslational levels, availability of co-factors, and calcium binding. Above normal levels of NO have beneficial protective effects for example in the cardiovascular system, but also contribute to the pathophysiology in the context of inflammatory diseases, and to aging and neurodegeneration in the nervous system. The effect specificity relies on the functional and spatial specificity of the NOS isoenzymes, and on the duality of two major signaling mechanisms (i) activation of soluble guanylycylase (sGC)-dependent cGMP production and (ii) direct S-nitrosylation of redox sensitive cysteines of susceptible proteins. The present review summarizes the functional implications of S-nitrosylation in the context of proteostasis, and focuses on two NO target proteins, heat shock cognate of 70 kDa (Hsc70/HSPA8) and the ubiquitin 2 ligase (UBE2D), because both are modified on functionally critical cysteines and are key regulators of chaperone mediated and assisted autophagy and proteasomal protein degradation. SNO modifications of these candidates are associated with protein accumulations and adoption of a senescent phenotype of neuronal cells suggesting that S-nitrosylations of protein homeostatic machineries contribute to aging phenomena.
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