1
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Banuelos A, Baez M, Zhang A, Yılmaz L, Kasberg W, Volk R, Georgeos N, Koren-Sedova E, Le U, Burden AT, Marjon KD, Lippincott-Schwartz J, Zaro BW, Weissman IL. Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal. Proc Natl Acad Sci U S A 2025; 122:e2426644122. [PMID: 40397678 DOI: 10.1073/pnas.2426644122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Accepted: 04/16/2025] [Indexed: 05/23/2025] Open
Abstract
Calreticulin (CALR) is primarily an endoplasmic reticulum chaperone protein that also plays a key role in facilitating programmed cell removal (PrCR) by acting as an "eat-me" signal for macrophages, directing their recognition and engulfment of dying, diseased, or unwanted cells. Recent findings have demonstrated that macrophages can transfer their own CALR onto exposed asialoglycans on target cells, marking them for PrCR. Despite the critical role CALR plays in this process, the molecular mechanisms behind its secretion by macrophages and the formation of binding sites on target cells remain unclear. Our findings show that CALR undergoes C-terminal cleavage upon secretion, producing a truncated form that functions as the active eat-me signal detectable on target cells. We identify cathepsins as potential proteases involved in this cleavage process. Furthermore, we demonstrate that macrophages release neuraminidases, which modify the surface of target cells and facilitate CALR binding. These insights reveal a coordinated mechanism through which lipopolysaccharide (LPS)-activated macrophages regulate CALR cleavage and neuraminidase activity to mark target cells for PrCR. How they recognize the cells to be targeted remains unknown.
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Affiliation(s)
- Allison Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Michelle Baez
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Leyla Yılmaz
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Regan Volk
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Nardin Georgeos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Elle Koren-Sedova
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Uyen Le
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Andrew T Burden
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Kristopher D Marjon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Balyn W Zaro
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Pathology, Stanford University, Stanford, CA 94305
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2
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Shivers JL, Nguyen M, Dinner AR, Vlahovska PM, Vaikuntanathan S. Renormalized mechanics and stochastic thermodynamics of growing model protocells. ARXIV 2025:arXiv:2503.24120v1. [PMID: 40236840 PMCID: PMC11998854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Uncovering the rules governing the nonequilibrium dynamics of the membranes that define biological cells is of central importance to understanding the physics of living systems. We theoretically and computationally investigate the behavior of model protocells-flexible quasispherical vesicles-that exchange membrane constituents, internal volume, and heat with an external reservoir. The excess chemical potential and osmotic pressure difference imposed by the reservoir act as generalized thermodynamic driving forces that modulate vesicle morphology. We identify an associated nonequilibrium morphological transition between a weakly driven regime, in which growing vesicles remain quasispherical, and a strongly driven regime, in which vesicles accommodate rapid membrane uptake by developing surface wrinkles. This transition emerges due to the renormalization of membrane mechanical properties by nonequilibrium driving. Further, using insights from stochastic thermodynamics we propose a minimal vesicle growth-shape law that remains robust even in strongly driven, far-from-equilibrium regimes.
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Affiliation(s)
- Jordan L Shivers
- The James Franck Institute, University of Chicago, Chicago, Illinois USA
- Department of Chemistry, University of Chicago, Chicago, Illinois USA
| | - Michael Nguyen
- The James Franck Institute, University of Chicago, Chicago, Illinois USA
- Department of Chemistry, University of Chicago, Chicago, Illinois USA
| | - Aaron R Dinner
- The James Franck Institute, University of Chicago, Chicago, Illinois USA
- Department of Chemistry, University of Chicago, Chicago, Illinois USA
| | - Petia M Vlahovska
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois USA
| | - Suriyanarayanan Vaikuntanathan
- The James Franck Institute, University of Chicago, Chicago, Illinois USA
- Department of Chemistry, University of Chicago, Chicago, Illinois USA
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3
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Hein MY, Peng D, Todorova V, McCarthy F, Kim K, Liu C, Savy L, Januel C, Baltazar-Nunez R, Sekhar M, Vaid S, Bax S, Vangipuram M, Burgess J, Njoya L, Wang E, Ivanov IE, Byrum JR, Pradeep S, Gonzalez CG, Aniseia Y, Creery JS, McMorrow AH, Sunshine S, Yeung-Levy S, DeFelice BC, Mehta SB, Itzhak DN, Elias JE, Leonetti MD. Global organelle profiling reveals subcellular localization and remodeling at proteome scale. Cell 2025; 188:1137-1155.e20. [PMID: 39742809 DOI: 10.1016/j.cell.2024.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 10/05/2024] [Accepted: 11/19/2024] [Indexed: 01/04/2025]
Abstract
Defining the subcellular distribution of all human proteins and their remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immunocapture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membraneless compartments. A graph-based analysis assigns the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following HCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides key insights for elucidating cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org.
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Affiliation(s)
| | - Duo Peng
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Kibeom Kim
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Chad Liu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | | | | | - Sophie Bax
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - James Burgess
- Institute for Computational & Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Leila Njoya
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Eileen Wang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Serena Yeung-Levy
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
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4
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Tago T, Ogawa T, Goto Y, Toyooka K, Tojima T, Nakano A, Satoh T, Satoh AK. RudLOV is an optically synchronized cargo transport method revealing unexpected effects of dynasore. EMBO Rep 2025; 26:613-634. [PMID: 39658747 PMCID: PMC11811055 DOI: 10.1038/s44319-024-00342-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 09/24/2024] [Accepted: 11/13/2024] [Indexed: 12/12/2024] Open
Abstract
Live imaging of secretory cargoes is a powerful method for understanding the mechanisms of membrane trafficking. Inducing the synchronous release of cargoes from an organelle is key for enhancing microscopic observation. We developed an optical cargo-releasing method, 'retention using dark state of LOV2' (RudLOV), which enables precise spatial, temporal, and quantity control during cargo release. A limited amount of cargo-release using RudLOV is able to visualize cargo cisternal-movement and cargo-specific exit sites on the Golgi/trans-Golgi network. Moreover, by controlling the timing of cargo-release using RudLOV, we reveal the canonical and non-canonical effects of the well-known dynamin inhibitor dynasore, which inhibits early- but not late-Golgi transport and exits from the trans-Golgi network where dynamin-2 is active. Accumulation of COPI vesicles at the cis-side of the Golgi stacks in dynasore-treated cells suggests that dynasore targets COPI-uncoating/tethering/fusion machinery in the early-Golgi cisternae or endoplasmic reticulum but not in the late-Golgi cisternae. These results provide insight into the cisternal maturation of Golgi stacks.
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Affiliation(s)
- Tatsuya Tago
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Takumi Ogawa
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Yumi Goto
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Takuro Tojima
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takunori Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan.
| | - Akiko K Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan.
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5
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Van Theemsche KM, Frans L, Van de Sande DV, Martinez-Morales E, Snyders DJ, Labro AJ. Evaluating the proarrhythmic risk of delayed-action compounds in serum free cell culture conditions; serum-starvation accelerates/amplifies the effect of probucol on the KCNQ1 + KCNE1 channel. J Pharmacol Toxicol Methods 2024; 130:107566. [PMID: 39357805 DOI: 10.1016/j.vascn.2024.107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 09/26/2024] [Accepted: 09/28/2024] [Indexed: 10/04/2024]
Abstract
In vitro testing procedures for evaluating acute effects of compound on ion channels, utilizing heterologous expression systems (HES), are well-established, while slowly manifesting delayed effects remain challenging to detect. For this, immortalized HES are exposed to the compounds for a longer time, in general 24 h. As these cells proliferate every 12-20 h, we evaluated if the proliferation status, and by extension cell metabolism, influences the delayed compound response. The intervention of halting cell proliferation by excluding serum from the culturing medium was evaluated on CHO cells, stably expressing the KCNQ1 + KCNE1 channel complex that mediates the slow delayed rectifier potassium current (Iks). No abnormal changes in KCNQ1 + KCNE1 current were observed upon serum-starvation, except for a negative shift in the voltage dependence of channel activation (GV-curve) after 72 h. The delayed effect of probucol, a compound reported to interfere with Iks expression, was evaluated after 24 and 72 h of incubation. In serum-free conditions the inhibitory effect of probucol was increased fourfold after 24 h, compared to serum supplemented conditions. After 72 h, the current inhibition was similar between both culture conditions. Besides decreasing current expression, probucol shifted the GV-curve more positive combined with a shallower voltage response, changes that were more pronounced in serum-depleted conditions. The results indicated that serum-starvation had no substantial effect on the KCNQ1 + KCNE1 current in the tested CHO cells, but it amplified or accelerated the response to probucol, suggesting that halting cell proliferation is a method for enhancing the detection of delayed compound effects in HES.
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Affiliation(s)
- Kenny M Van Theemsche
- Department of Basic and Applied Medical Sciences, Faculty of Medicine, Ghent University, 9000 Ghent, Belgium; Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Lisse Frans
- Department of Basic and Applied Medical Sciences, Faculty of Medicine, Ghent University, 9000 Ghent, Belgium
| | - Dieter V Van de Sande
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Evelyn Martinez-Morales
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Dirk J Snyders
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Alain J Labro
- Department of Basic and Applied Medical Sciences, Faculty of Medicine, Ghent University, 9000 Ghent, Belgium.
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6
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Hodgson JJ, Chen RY, Blissard GW, Buchon N. Viral and cellular determinants of polarized trafficking of viral envelope proteins from insect-specific and insect-vectored viruses in insect midgut and salivary gland cells. J Virol 2024; 98:e0054024. [PMID: 39162433 PMCID: PMC11406959 DOI: 10.1128/jvi.00540-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Systemic viral infection of insects typically begins with the primary infection of midgut epithelial cells (enterocytes) and subsequent transit of the progeny virus in an apical-to-basal orientation into the hemocoel. For insect-vectored viruses, an oppositely oriented process (basal-to-apical transit) occurs upon secondary infection of salivary glands and is necessary for virus transmission to non-insect hosts. To examine this inversely oriented virus transit in these polarized tissues, we assessed the intracellular trafficking of two model viral envelope proteins (baculovirus GP64 and vesicular stomatitis virus G) in the midgut and salivary gland cells of the model insect, Drosophila melanogaster. Using fly lines that inducibly express either GP64 or VSV G, we found that each protein, expressed alone, was trafficked basally in midgut enterocytes. In salivary gland cells, VSV G was trafficked apically in most but not all cells, whereas GP64 was consistently trafficked basally. We demonstrated that a YxxØ motif present in both proteins was critical for basal trafficking in midgut enterocytes but dispensable for trafficking in salivary gland cells. Using RNAi, we found that clathrin adaptor protein complexes AP-1 and AP-3, as well as seven Rab GTPases, were involved in polarized VSV G trafficking in midgut enterocytes. Our results indicate that these viral envelope proteins encode the requisite information and require no other viral factors for appropriately polarized trafficking. In addition, they exploit tissue-specific differences in protein trafficking pathways to facilitate virus egress in the appropriate orientation for establishing systemic infections and vectoring infection to other hosts. IMPORTANCE Viruses that use insects as hosts must navigate specific routes through different insect tissues to complete their life cycles. The routes may differ substantially depending on the life cycle of the virus. Both insect pathogenic viruses and insect-vectored viruses must navigate through the polarized cells of the midgut epithelium to establish a systemic infection. In addition, insect-vectored viruses must also navigate through the polarized salivary gland epithelium for transmission. Thus, insect-vectored viruses appear to traffic in opposite directions in these two tissues. In this study, we asked whether two viral envelope proteins (VSV G and baculovirus GP64) alone encode the signals necessary for the polarized trafficking associated with their respective life cycles. Using Drosophila as a model to examine tissue-specific polarized trafficking of these viral envelope proteins, we identified one of the virus-encoded signals and several host proteins associated with regulating the polarized trafficking in the midgut epithelium.
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Affiliation(s)
- Jeffrey J. Hodgson
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
- Boyce Thompson Institute at Cornell University, Ithaca, New York, USA
| | - Robin Y. Chen
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
| | - Gary W. Blissard
- Boyce Thompson Institute at Cornell University, Ithaca, New York, USA
| | - Nicolas Buchon
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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7
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Xu Y, Wang B, Bush I, Saunders HAJ, Wildonger J, Han C. In vivo optogenetic manipulations of endogenous proteins reveal spatiotemporal roles of microtubule and kinesin in dendrite patterning. SCIENCE ADVANCES 2024; 10:eadp0138. [PMID: 39213355 PMCID: PMC11364106 DOI: 10.1126/sciadv.adp0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
During animal development, the spatiotemporal properties of molecular events largely determine the biological outcomes. Conventional gene analysis methods lack the spatiotemporal resolution for precise dissection of developmental mechanisms. Although optogenetic tools exist for manipulating designer proteins in cultured cells, few have been successfully applied to endogenous proteins in live animals. Here, we report OptoTrap, a light-inducible clustering system for manipulating endogenous proteins of diverse sizes, subcellular locations, and functions in Drosophila. This system turns on fast, is reversible in minutes or hours, and contains variants optimized for neurons and epithelial cells. By using OptoTrap to disrupt microtubules and inhibit kinesin-1 in neurons, we show that microtubules support the growth of highly dynamic dendrites and that kinesin-1 is required for patterning of low- and high-order dendritic branches in differential spatiotemporal domains. OptoTrap allows for precise manipulation of endogenous proteins in a spatiotemporal manner and thus holds promise for studying developmental mechanisms in a wide range of cell types and developmental stages.
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Affiliation(s)
- Yineng Xu
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Inle Bush
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Harriet AJ Saunders
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI 53706, USA
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI 53706, USA
- Pediatrics Department and Biological Sciences Division, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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8
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Taylor CA, Maor-Nof M, Metzl-Raz E, Hidalgo A, Yee C, Gitler AD, Shen K. Histone deacetylase inhibition expands cellular proteostasis repertoires to enhance neuronal stress resilience. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.608176. [PMID: 39229034 PMCID: PMC11370365 DOI: 10.1101/2024.08.21.608176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Neurons are long-lived, terminally differentiated cells with limited regenerative capacity. Cellular stressors such as endoplasmic reticulum (ER) protein folding stress and membrane trafficking stress accumulate as neurons age and accompany age-dependent neurodegeneration. Current strategies to improve neuronal resilience are focused on using factors to reprogram neurons or targeting specific proteostasis pathways. We discovered a different approach. In an unbiased screen for modifiers of neuronal membrane trafficking defects, we unexpectedly identified a role for histone deacetylases (HDACs) in limiting cellular flexibility in choosing cellular pathways to respond to diverse types of stress. Genetic or pharmacological inactivation of HDACs resulted in improved neuronal health in response to ER protein folding stress and endosomal membrane trafficking stress in C. elegans and mammalian neurons. Surprisingly, HDAC inhibition enabled neurons to activate latent proteostasis pathways tailored to the nature of the individual stress, instead of generalized transcriptional upregulation. These findings shape our understanding of neuronal stress responses and suggest new therapeutic strategies to enhance neuronal resilience.
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Affiliation(s)
- Caitlin A. Taylor
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Maya Maor-Nof
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Eyal Metzl-Raz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron Hidalgo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, 94158, USA
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
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9
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Zenere G, Wu C, Midkiff CC, Johnson NM, Grice CP, Wimley WC, Kaur A, Braun SE. Extracellular domain, hinge, and transmembrane determinants affecting surface CD4 expression of a novel anti-HIV chimeric antigen receptor (CAR) construct. PLoS One 2024; 19:e0293990. [PMID: 39133676 PMCID: PMC11318886 DOI: 10.1371/journal.pone.0293990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 07/03/2024] [Indexed: 08/15/2024] Open
Abstract
Chimeric antigen receptor (CAR)-T cells have demonstrated clinical potential, but current receptors still need improvements to be successful against chronic HIV infection. In this study, we address some requirements of CAR motifs for strong surface expression of a novel anti-HIV CAR by evaluating important elements in the extracellular, hinge, and transmembrane (TM) domains. When combining a truncated CD4 extracellular domain and CD8α hinge/TM, the novel CAR did not express extracellularly but was detectable intracellularly. By shortening the CD8α hinge, CD4-CAR surface expression was partially recovered and addition of the LYC motif at the end of the CD8α TM fully recovered both intracellular and extracellular CAR expression. Mutation of LYC to TTA or TTC showed severe abrogation of CAR expression by flow cytometry and confocal microscopy. Additionally, we determined that CD4-CAR surface expression could be maximized by the removal of FQKAS motif at the junction of the extracellular domain and the hinge region. CD4-CAR surface expression also resulted in cytotoxic CAR T cell killing of HIV Env+ target cells. In this study, we identified elements that are crucial for optimal CAR surface expression, highlighting the need for structural analysis studies to establish fundamental guidelines of CAR designs.
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Affiliation(s)
- Giorgio Zenere
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Chengxiang Wu
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
| | - Cecily C. Midkiff
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
| | - Nathan M. Johnson
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Christopher P. Grice
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - William C. Wimley
- Department of BioChemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Stephen E. Braun
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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10
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. eLife 2024; 12:RP89306. [PMID: 38837189 PMCID: PMC11152573 DOI: 10.7554/elife.89306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting the Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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Affiliation(s)
- Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | | | | | - Rossana Ippolito
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Carolyn R Shurer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
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11
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Ding Z, Han L, Zhang Q, Hu J, Li L, Qian X. Membrane Trafficking-Related Genes Predict Tumor Immune Microenvironment and Prognosis in Colorectal Cancer. Biochem Genet 2024; 62:1413-1427. [PMID: 37615899 DOI: 10.1007/s10528-023-10498-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with varying clinical outcomes. The identification of distinct subgroups of CRC patients based on molecular profiling can aid in better understanding the disease and improving patient outcomes. This study aimed to investigate the potential of membrane trafficking-related genes (MTRGs) in sub-grouping colorectal cancer patients based on their overall survival and immune microenvironments. Consensus clustering analysis identified two distinct clusters with different expression profiles of membrane trafficking-related genes. The patients in cluster 1 had a significantly better overall survival than those in cluster 2. Furthermore, the immune microenvironments in the two clusters were also found to be significantly different, with cluster 1 having a higher immune score and more immune cells present. Functional analysis of differentially expressed genes between the two clusters revealed that MTRGs were involved in immune response and metabolic processes, and a risk signature model based on MTRGs was established to predict the prognosis of CRC patients. These findings suggest that MTRGs play a crucial role in the immune microenvironment and overall survival of CRC patients and may provide a potential target for personalized therapy.
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Affiliation(s)
- Zhou Ding
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Lu Han
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Qun Zhang
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Jing Hu
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Li Li
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Xiaoping Qian
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, China.
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China.
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12
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Sasaki S, Schlarmann P, Hanaoka K, Nishii H, Moriya H, Muñiz M, Funato K. Protein sorting upon exit from the endoplasmic reticulum dominates Golgi biogenesis in budding yeast. FEBS Lett 2024; 598:548-555. [PMID: 38395606 DOI: 10.1002/1873-3468.14830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
Cells sense and control the number and quality of their organelles, but the underlying mechanisms of this regulation are not understood. Our recent research in the yeast Saccharomyces cerevisiae has shown that long acyl chain ceramides in the endoplasmic reticulum (ER) membrane and the lipid moiety of glycosylphosphatidylinositol (GPI) anchor determine the sorting of GPI-anchored proteins in the ER. Here, we show that a mutant strain, which produces shorter ceramides than the wild-type strain, displays a different count of Golgi cisternae. Moreover, deletions of proteins that remodel the lipid portion of GPI anchors resulted in an abnormal number of Golgi cisternae. Thus, our study reveals that protein sorting in the ER plays a critical role in maintaining Golgi biogenesis.
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Affiliation(s)
- Saku Sasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Philipp Schlarmann
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuki Hanaoka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hinako Nishii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hisao Moriya
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Japan
| | - Manuel Muñiz
- Department of Cell Biology, Faculty of Biology, University of Seville, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Spain
| | - Kouichi Funato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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13
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Zhang J, Wang Y. Emerging roles of O-GlcNAcylation in protein trafficking and secretion. J Biol Chem 2024; 300:105677. [PMID: 38272225 PMCID: PMC10907171 DOI: 10.1016/j.jbc.2024.105677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
The emerging roles of O-GlcNAcylation, a distinctive post-translational modification, are increasingly recognized for their involvement in the intricate processes of protein trafficking and secretion. This modification exerts its influence on both conventional and unconventional secretory pathways. Under healthy and stress conditions, such as during diseases, it orchestrates the transport of proteins within cells, ensuring timely delivery to their intended destinations. O-GlcNAcylation occurs on key factors, like coat protein complexes (COPI and COPII), clathrin, SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors), and GRASP55 (Golgi reassembly stacking protein of 55 kDa) that control vesicle budding and fusion in anterograde and retrograde trafficking and unconventional secretion. The understanding of O-GlcNAcylation offers valuable insights into its critical functions in cellular physiology and the progression of diseases, including neurodegeneration, cancer, and metabolic disorders. In this review, we summarize and discuss the latest findings elucidating the involvement of O-GlcNAc in protein trafficking and its significance in various human disorders.
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Affiliation(s)
- Jianchao Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA; Department of Neurology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
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14
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.18.537395. [PMID: 37131599 PMCID: PMC10153169 DOI: 10.1101/2023.04.18.537395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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15
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Ragagnin AMG, Sundaramoorthy V, Farzana F, Gautam S, Saravanabavan S, Takalloo Z, Mehta P, Do-Ha D, Parakh S, Shadfar S, Hunter J, Vidal M, Jagaraj CJ, Brocardo M, Konopka A, Yang S, Rayner SL, Williams KL, Blair IP, Chung RS, Lee A, Ooi L, Atkin JD. ALS/FTD-associated mutation in cyclin F inhibits ER-Golgi trafficking, inducing ER stress, ERAD and Golgi fragmentation. Sci Rep 2023; 13:20467. [PMID: 37993492 PMCID: PMC10665471 DOI: 10.1038/s41598-023-46802-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severely debilitating neurodegenerative condition that is part of the same disease spectrum as frontotemporal dementia (FTD). Mutations in the CCNF gene, encoding cyclin F, are present in both sporadic and familial ALS and FTD. However, the pathophysiological mechanisms underlying neurodegeneration remain unclear. Proper functioning of the endoplasmic reticulum (ER) and Golgi apparatus compartments is essential for normal physiological activities and to maintain cellular viability. Here, we demonstrate that ALS/FTD-associated variant cyclin FS621G inhibits secretory protein transport from the ER to Golgi apparatus, by a mechanism involving dysregulation of COPII vesicles at ER exit sites. Consistent with this finding, cyclin FS621G also induces fragmentation of the Golgi apparatus and activates ER stress, ER-associated degradation, and apoptosis. Induction of Golgi fragmentation and ER stress were confirmed with a second ALS/FTD variant cyclin FS195R, and in cortical primary neurons. Hence, this study provides novel insights into pathogenic mechanisms associated with ALS/FTD-variant cyclin F, involving perturbations to both secretory protein trafficking and ER-Golgi homeostasis.
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Affiliation(s)
- Audrey M G Ragagnin
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Vinod Sundaramoorthy
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shashi Gautam
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Zeinab Takalloo
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Prachi Mehta
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Dzung Do-Ha
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Sonam Parakh
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie Hunter
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Marta Vidal
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Cyril J Jagaraj
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mariana Brocardo
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Anna Konopka
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shu Yang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Kelly L Williams
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian P Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Roger S Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Julie D Atkin
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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16
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Zenere G, Wu C, Midkiff CC, Johnson NM, Grice CP, Wimley WC, Kaur A, Braun SE. Extracellular domain, hinge, and transmembrane determinants affecting surface CD4 expression of a novel anti-HIV chimeric antigen receptor (CAR) construct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563930. [PMID: 37961145 PMCID: PMC10634810 DOI: 10.1101/2023.10.25.563930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Chimeric antigen receptor (CAR)-T cells have demonstrated clinical potential, but current receptors still need improvements to be successful against chronic HIV infection. In this study, we address some requirements of CAR motifs for strong surface expression of a novel anti-HIV CAR by evaluating important elements in the extracellular, hinge, and transmembrane (TM) domains. When combining a truncated CD4 extracellular domain and CD8α hinge/TM, the novel CAR did not express extracellularly but was detectable intracellularly. By shortening the CD8α hinge, CD4-CAR surface expression was partially recovered and addition of the LYC motif at the end of the CD8α TM fully recovered both intracellular and extracellular CAR expression. Mutation of LYC to TTA or TTC showed severe abrogation of CAR expression by flow cytometry and confocal microscopy. Additionally, we determined that CD4-CAR surface expression could be maximized by the removal of FQKAS motif at the junction of the extracellular domain and the hinge region. CD4-CAR surface expression also resulted in cytotoxic CAR T cell killing of HIV Env+ target cells. In this study, we identified elements that are crucial for optimal CAR surface expression, highlighting the need for structural analysis studies to establish fundamental guidelines of CAR designs.
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Affiliation(s)
- Giorgio Zenere
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Chengxiang Wu
- Tulane National Primate Research Center, Covington, LA 70433
| | | | - Nathan M. Johnson
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Christopher P. Grice
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
| | - William C. Wimley
- Department of BioChemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Amitinder Kaur
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Stephen E. Braun
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
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17
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Ma X, Zhao C, Xu Y, Zhang H. Roles of host SUMOylation in bacterial pathogenesis. Infect Immun 2023; 91:e0028323. [PMID: 37725062 PMCID: PMC10580907 DOI: 10.1128/iai.00283-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Bacteria frequently interfere with the post-translational modifications of host cells to facilitate their survival and growth after invasion. SUMOylation, a reversible post-translational modification process, plays an important role in biological life activities. In addition to being critical to host cell metabolism and survival, SUMOylation also regulates gene expression and cell signal transmission. Moreover, SUMOylation in eukaryotic cells can be used by a variety of bacterial pathogens to advance bacterial invasion. In this minireview, we focused on the role and mechanism of host SUMOylation in the pathogenesis of six important clinical bacterial pathogens (Listeria monocytogenes, Shigella flexneri, Salmonella Typhimurium, Klebsiella pneumoniae, Staphylococcus aureus, and Escherichia coli). Taken together, this review provided new insights for understanding the unique pathogen-host interaction based on host SUMOylation and provided a novel perspective on the development of new strategies to combat bacterial infections in the future.
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Affiliation(s)
- Xin Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chenhao Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuyao Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Clinical Laboratory, Zhangjiagang Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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18
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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19
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Xu Y, Wang B, Bush I, Saunders HAJ, Wildonger J, Han C. Light-induced trapping of endogenous proteins reveals spatiotemporal roles of microtubule and kinesin-1 in dendrite patterning of Drosophila sensory neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560303. [PMID: 37873262 PMCID: PMC10592855 DOI: 10.1101/2023.09.30.560303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Animal development involves numerous molecular events, whose spatiotemporal properties largely determine the biological outcomes. Conventional methods for studying gene function lack the necessary spatiotemporal resolution for precise dissection of developmental mechanisms. Optogenetic approaches are powerful alternatives, but most existing tools rely on exogenous designer proteins that produce narrow outputs and cannot be applied to diverse or endogenous proteins. To address this limitation, we developed OptoTrap, a light-inducible protein trapping system that allows manipulation of endogenous proteins tagged with GFP or split GFP. This system turns on fast and is reversible in minutes or hours. We generated OptoTrap variants optimized for neurons and epithelial cells and demonstrate effective trapping of endogenous proteins of diverse sizes, subcellular locations, and functions. Furthermore, OptoTrap allowed us to instantly disrupt microtubules and inhibit the kinesin-1 motor in specific dendritic branches of Drosophila sensory neurons. Using OptoTrap, we obtained direct evidence that microtubules support the growth of highly dynamic dendrites. Similarly, targeted manipulation of Kinesin heavy chain revealed differential spatiotemporal requirements of kinesin-1 in the patterning of low- and high-order dendritic branches, suggesting that different cargos are needed for the growth of these branches. OptoTrap allows for precise manipulation of endogenous proteins in a spatiotemporal manner and thus holds great promise for studying developmental mechanisms in a wide range of cell types and developmental stages.
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Affiliation(s)
- Yineng Xu
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Inle Bush
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Harriet AJ Saunders
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI 53706, USA
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI 53706, USA
- Pediatrics Department and Biological Sciences Division, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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20
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Maguvu TE, Travadon R, Cantu D, Trouillas FP. Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California. Sci Rep 2023; 13:14873. [PMID: 37684350 PMCID: PMC10491840 DOI: 10.1038/s41598-023-41746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Ceratocystis canker caused by Ceratocystis destructans is a severe disease of almond, reducing the longevity and productivity of infected trees. Once the disease has established in an individual tree, there is no cure, and management efforts are often limited to removing the infected area of cankers. In this study, we present the genome assemblies of five C. destructans isolates isolated from symptomatic almond trees. The genomes were assembled into a genome size of 27.2 ± 0.9 Mbp with an average of 6924 ± 135 protein-coding genes and an average GC content of 48.8 ± 0.02%. We concentrated our efforts on identifying putative virulence factors of canker pathogens. Analysis of the secreted carbohydrate-active enzymes showed that the genomes harbored 83.4 ± 1.8 secreted CAZymes. The secreted CAZymes covered all the known categories of CAZymes. AntiSMASH revealed that the genomes had at least 7 biosynthetic gene clusters, with one of the non-ribosomal peptide synthases encoding dimethylcoprogen, a conserved virulence determinant of plant pathogenic ascomycetes. From the predicted proteome, we also annotated cytochrome P450 monooxygenases, and transporters, these are well-established virulence determinants of canker pathogens. Moreover, we managed to identify 57.4 ± 2.1 putative effector proteins. Gene Ontology (GO) annotation was applied to compare gene content with two closely related species C. fimbriata, and C. albifundus. This study provides the first genome assemblies for C. destructans, expanding genomic resources for an important almond canker pathogen. The acquired knowledge provides a foundation for further advanced studies, such as molecular interactions with the host, which is critical for breeding for resistance.
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Affiliation(s)
- Tawanda E Maguvu
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
- Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Florent P Trouillas
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
- Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA.
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21
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Meng X, Wijaya CS, Shao Q, Xu S. Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair. J Cell Biol 2023; 222:214098. [PMID: 37158801 PMCID: PMC10176212 DOI: 10.1083/jcb.202303017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
The maintenance of plasma membrane integrity and a capacity for efficiently repairing damaged membranes are essential for cell survival. Large-scale wounding depletes various membrane components at the wound sites, including phosphatidylinositols, yet little is known about how phosphatidylinositols are generated after depletion. Here, working with our in vivo C. elegans epidermal cell wounding model, we discovered phosphatidylinositol 4-phosphate (PtdIns4P) accumulation and local phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] generation at the wound site. We found that PtdIns(4,5)P2 generation depends on the delivery of PtdIns4P, PI4K, and PI4P 5-kinase PPK-1. In addition, we show that wounding triggers enrichment of the Golgi membrane to the wound site, and that is required for membrane repair. Moreover, genetic and pharmacological inhibitor experiments support that the Golgi membrane provides the PtdIns4P for PtdIns(4,5)P2 generation at the wounds. Our findings demonstrate how the Golgi apparatus facilitates membrane repair in response to wounding and offers a valuable perspective on cellular survival mechanisms upon mechanical stress in a physiological context.
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Affiliation(s)
- Xinan Meng
- International Biomedicine-X Research Center of the Second Affiliated Hospital, Zhejiang University School of Medicine and the Zhejiang University-University of Edinburgh Institute , Haining Zhejiang, China
| | - Chandra Sugiarto Wijaya
- Department of Burn and Wound Repair of the Second Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine , Hangzhou Zhejiang, China
| | - Qingfang Shao
- International Biomedicine-X Research Center of the Second Affiliated Hospital, Zhejiang University School of Medicine and the Zhejiang University-University of Edinburgh Institute , Haining Zhejiang, China
| | - Suhong Xu
- International Biomedicine-X Research Center of the Second Affiliated Hospital, Zhejiang University School of Medicine and the Zhejiang University-University of Edinburgh Institute , Haining Zhejiang, China
- Department of Burn and Wound Repair of the Second Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine , Hangzhou Zhejiang, China
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22
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Neuhaus JM, Pimpl P, Zhao Q, Wang H. Editorial: Regulation of plant organelle biogenesis and trafficking. FRONTIERS IN PLANT SCIENCE 2023; 14:1211807. [PMID: 37304708 PMCID: PMC10250707 DOI: 10.3389/fpls.2023.1211807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023]
Affiliation(s)
- Jean-Marc Neuhaus
- Laboratory of Cell and Molecular Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Peter Pimpl
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qiong Zhao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, China
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23
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Tamura T, Hamachi I. Quantitative Analysis of the Endoplasmic Reticulum-Associated Proteins Using ER-Localizable Reactive Molecules. Methods Mol Biol 2023; 2603:139-150. [PMID: 36370276 DOI: 10.1007/978-1-0716-2863-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle responsible for many cellular functions, including protein synthesis and folding, lipid synthesis, membrane trafficking, and storage of Ca2+. Therefore, global profiling of ER-associated proteins should be invaluable for understanding these biological processes. However, the difficulty of isolating the intact ER hampered proteome-wide analysis of ER proteins. This chapter describes a chemoproteomic approach for ER proteome analysis using ER-localizable reactive molecules (ERMs), which need neither ER fractionation nor genetic transformation. ERMs spontaneously accumulate in the ER of live cells, and the resultant high concentration of ERMs facilitates spatially limited chemical modification of ER-localized proteins with a detection/purification tag via simple intermolecular reactions. This enables the tag-mediated enrichment and quantitative analysis of the ER-associated proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with SILAC technology.
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Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, Japan.
- ERATO (Exploratory Research for Advanced Technology, JST), Chiyodaku, Tokyo, Japan.
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24
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Frye KB, Zhu X, Khodjakov A, Kaverina I. Unbiased Quantification of Golgi Scattering and Golgi-Centrosome Association. Methods Mol Biol 2023; 2557:529-541. [PMID: 36512235 PMCID: PMC9844073 DOI: 10.1007/978-1-0716-2639-9_31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The vertebrate Golgi complex is a large dynamic organelle which undergoes morphological changes and fragmentation both as a part of normal physiological dynamics and under disease conditions. The Golgi is known to have a functionally important relationship with the centrosome. The extent of the spatial association between these two organelles varies in a dynamic and regulated manner. It is essential to have a reliable unbiased approach to evaluate Golgi volume, Golgi extension/scattering in the 3D cell space, and spatial association of the Golgi with the centrosome. It is also important that each of these features is evaluated by a simple metric, one measurement per cell, so that the variability and deviations in the cell population can be easily assessed. Here, we present an approach to analyze confocal microscopy image stacks to easily measure Golgi volume, scattering, and association with the centrosome. The approach is based on a custom MATLAB script, provided here as a supplement, and also uses widely available software (ImageJ and/or Imaris). The output of the script is a table with the following parameters: Golgi volume in voxels, Golgi volume in μm3, "Golgi-Golgi" distance (averaged distance between all Golgi voxels), Golgi-centrosome distance (averaged distance between each Golgi voxel and the nearest mother centriole), and centrosome-centrosome distance (for cells with duplicated centrosome, the distance between the mother centrioles). The approach can also be applied to analyze distribution of any fluorescently- labeled structure within a cell and its association with the centrosome or any single point within the cell volume.
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Affiliation(s)
- Keyada B Frye
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Xiaodong Zhu
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Irina Kaverina
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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25
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Patel A, Rasheed A, Reilly I, Pareek Z, Hansen M, Haque Z, Simon-Fajardo D, Davies C, Tummala A, Reinhardt K, Bustabad A, Shaw M, Robins J, Vera Gomez K, Suphakorn T, Camacho Gemelgo M, Law A, Lin K, Hospedales E, Haley H, Perez Martinez JP, Khan S, DeCanio J, Padgett M, Abramov A, Nanjundan M. Modulation of Cytoskeleton, Protein Trafficking, and Signaling Pathways by Metabolites from Cucurbitaceae, Ericaceae, and Rosaceae Plant Families. Pharmaceuticals (Basel) 2022; 15:1380. [PMID: 36355554 PMCID: PMC9698530 DOI: 10.3390/ph15111380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 10/22/2023] Open
Abstract
One promising frontier within the field of Medical Botany is the study of the bioactivity of plant metabolites on human health. Although plant metabolites are metabolic byproducts that commonly regulate ecological interactions and biochemical processes in plant species, such metabolites also elicit profound effects on the cellular processes of human and other mammalian cells. In this regard, due to their potential as therapeutic agents for a variety of human diseases and induction of toxic cellular responses, further research advances are direly needed to fully understand the molecular mechanisms induced by these agents. Herein, we focus our investigation on metabolites from the Cucurbitaceae, Ericaceae, and Rosaceae plant families, for which several plant species are found within the state of Florida in Hillsborough County. Specifically, we compare the molecular mechanisms by which metabolites and/or plant extracts from these plant families modulate the cytoskeleton, protein trafficking, and cell signaling to mediate functional outcomes, as well as a discussion of current gaps in knowledge. Our efforts to lay the molecular groundwork in this broad manner hold promise in supporting future research efforts in pharmacology and drug discovery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meera Nanjundan
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
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26
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Chen Y, Fan J, Xiao D, Li X. The role of SCAMP5 in central nervous system diseases. Neurol Res 2022; 44:1024-1037. [PMID: 36217917 DOI: 10.1080/01616412.2022.2107754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/26/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Secretory carrier membrane proteins (SCAMPs) constitute a group of membrane transport proteins in plants, insects and mammals. The mammalian genome contains five types of SCAMP genes, namely, SCAMP1-SCAMP5. SCAMPs participate in the vesicle cycling fusion of vesicles and cell membranes and play roles in regulating exocytosis and endocytosis, activating synaptic function and transmitting nerve signals. Among these proteins, SCAMP5 is highly expressed in the brain and has direct or indirect effects on the function of the central nervous system. This paper may allow us to better understand the role of SCAMP5 in the central nervous system diseases. SCAMP5 regulates membrane transport, controls the exocytosis of SVs and is related to secretion carrier and membrane function. In addition, SCAMP5 plays a major role in the normal maintenance of the physiological functions of nerve cells. This article summarizes the effects of SCAMP5 on nerve cell exocytosis, endocytosis and synaptic function, as well as the relationship between SCAMP5 and various neurological diseases, to better understand the role of SCAMP5 in the pathogenesis of neurological diseases. METHODS Through PubMed, this paper examined and analyzed the role of SCAMP5 in the central nervous system, as well as the relationship between SCAMP5 and various neurological diseases using the key terms "secretory carrier membrane proteins"," SCAMP5"," exocytosis"," endocytosis", "synaptic function", "central nervous system diseases" up to 01 March 2022. RESULTS SCAMP5 regulates membrane transport, controls the exocytosis of SVs and is related to secretion carrier and membrane function. In addition, SCAMP5 plays a major role in the normal maintenance of the physiological functions of nerve cells. CONCLUSION This article summarizes the effects of SCAMP5 on nerve cell exocytosis, endocytosis and synaptic function, as well as the relationship between SCAMP5 and various neurological diseases, to better understand the role of SCAMP5 in the pathogenesis of neurological diseases.
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Affiliation(s)
- Ye Chen
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Jiali Fan
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
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27
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Burger GA, Nesenberend DN, Lems CM, Hille SC, Beltman JB. Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFN γ-induced PD-L1 expression promotes tumour progression. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220186. [PMID: 36397970 PMCID: PMC9626257 DOI: 10.1098/rsos.220186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Epithelial-mesenchymal transition (EMT) and immunoevasion through upregulation of programmed death-ligand 1 (PD-L1) are important drivers of cancer progression. While EMT has been proposed to facilitate PD-L1-mediated immunosuppression, molecular mechanisms of their interaction remain obscure. Here, we provide insight into these mechanisms by proposing a mathematical model that describes the crosstalk between EMT and interferon gamma (IFNγ)-induced PD-L1 expression. Our model shows that via interaction with microRNA-200 (miR-200), the multi-stability of the EMT regulatory circuit is mirrored in PD-L1 levels, which are further amplified by IFNγ stimulation. This IFNγ-mediated effect is most prominent for cells in a fully mesenchymal state and less strong for those in an epithelial or partially mesenchymal state. In addition, bidirectional crosstalk between miR-200 and PD-L1 implies that IFNγ stimulation allows cells to undergo EMT for lower amounts of inducing signal, and the presence of IFNγ accelerates EMT and decelerates mesenchymal-epithelial transition (MET). Overall, our model agrees with published findings and provides insight into possible mechanisms behind EMT-mediated immune evasion, and primary, adaptive, or acquired resistance to immunotherapy. Our model can be used as a starting point to explore additional crosstalk mechanisms, as an improved understanding of these mechanisms is indispensable for developing better diagnostic and therapeutic options for cancer patients.
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Affiliation(s)
- Gerhard A. Burger
- Division of Drug Discovery and Safety, Leiden University, Leiden, The Netherlands
| | - Daphne N. Nesenberend
- Division of Drug Discovery and Safety, Leiden University, Leiden, The Netherlands
- Mathematical Institute, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Carlijn M. Lems
- Division of Drug Discovery and Safety, Leiden University, Leiden, The Netherlands
| | - Sander C. Hille
- Mathematical Institute, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Joost B. Beltman
- Division of Drug Discovery and Safety, Leiden University, Leiden, The Netherlands
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28
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Lin BC, Higgins NR, Phung TH, Monteiro MJ. UBQLN proteins in health and disease with a focus on UBQLN2 in ALS/FTD. FEBS J 2022; 289:6132-6153. [PMID: 34273246 PMCID: PMC8761781 DOI: 10.1111/febs.16129] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023]
Abstract
Ubiquilin (UBQLN) proteins are a dynamic and versatile family of proteins found in all eukaryotes that function in the regulation of proteostasis. Besides their canonical function as shuttle factors in delivering misfolded proteins to the proteasome and autophagy systems for degradation, there is emerging evidence that UBQLN proteins play broader roles in proteostasis. New information suggests the proteins function as chaperones in protein folding, protecting proteins prior to membrane insertion, and as guardians for mitochondrial protein import. In this review, we describe the evidence for these different roles, highlighting how different domains of the proteins impart these functions. We also describe how changes in the structure and phase separation properties of UBQLNs may regulate their activity and function. Finally, we discuss the pathogenic mechanisms by which mutations in UBQLN2 cause amyotrophic lateral sclerosis and frontotemporal dementia. We describe the animal model systems made for different UBQLN2 mutations and how lessons learnt from these systems provide fundamental insight into the molecular mechanisms by which UBQLN2 mutations drive disease pathogenesis through disturbances in proteostasis.
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Affiliation(s)
- Brian C. Lin
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicole R. Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Trong H. Phung
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mervyn J. Monteiro
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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29
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Bar-Peled L, Kory N. Principles and functions of metabolic compartmentalization. Nat Metab 2022; 4:1232-1244. [PMID: 36266543 PMCID: PMC10155461 DOI: 10.1038/s42255-022-00645-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/24/2022] [Indexed: 01/20/2023]
Abstract
Metabolism has historically been studied at the levels of whole cells, whole tissues and whole organisms. As a result, our understanding of how compartmentalization-the spatial and temporal separation of pathways and components-shapes organismal metabolism remains limited. At its essence, metabolic compartmentalization fulfils three important functions or 'pillars': establishing unique chemical environments, providing protection from reactive metabolites and enabling the regulation of metabolic pathways. However, how these pillars are established, regulated and maintained at both the cellular and systemic levels remains unclear. Here we discuss how the three pillars are established, maintained and regulated within the cell and discuss the consequences of dysregulation of metabolic compartmentalization in human disease. Organelles are increasingly emerging as 'command-and-control centres' and the increased understanding of metabolic compartmentalization is revealing new aspects of metabolic homeostasis, with this knowledge being translated into therapies for the treatment of cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Nora Kory
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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30
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Malis Y, Hirschberg K, Kaether C. Hanging the coat on a collar: Same function but different localization and mechanism for COPII. Bioessays 2022; 44:e2200064. [DOI: 10.1002/bies.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yehonathan Malis
- Department of Pathology, Sackler School of Medicine Tel‐Aviv University Tel Aviv Israel
| | - Koret Hirschberg
- Department of Pathology, Sackler School of Medicine Tel‐Aviv University Tel Aviv Israel
| | - Christoph Kaether
- Leibniz Institute for Age Research – Fritz Lipmann Institute Jena Germany
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31
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Cao Q, Zhang W, Liu X, Li Y. AtFTCD-L, a trans-Golgi network localized protein, modulates root growth of Arabidopsis in high-concentration agar culture medium. PLANTA 2022; 256:3. [PMID: 35637390 DOI: 10.1007/s00425-022-03911-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
AtFTCD-L protein is localized on the TGN vesicles in Arabidopsis root cap cells. AtFTCD-L mutation resulted in slow root growth of Arabidopsis in high-concentration agar culture medium. Arabidopsis formiminotransferase cyclodeaminase-like protein (AtFTCD-L) in Arabidopsis is homologous to the formiminotransferase cyclodeaminase (FTCD) protein in animal cells. However, the localization and function of AtFTCD-L remain unknown in Arabidopsis. In this study, we generated and analyzed a deletion mutant of AtFTCD-L with a T-DNA insertion. We found that the growth of Arabidopsis roots with the T-DNA insertion mutation in AtFTCD-L was slower than that of wild-type roots when grown in high-concentration 1/2 MS agar culture medium. AtFTCD-L-GFP could restore the ftcd-l mutant phenotype. In addition, the AtFTCD-L protein was localized on the trans-Golgi network (TGN) vesicles in Arabidopsis root cap cells. Fluorescence recovery after photobleaching (FRAP) experiment using Arabidopsis pollen-specific receptor-like kinase-GFP (AtPRK1-GFP) stably transformed plants showed that the deficiency of AtFTCD-L protein in Arabidopsis led to slower secretion in the root cap peripheral cells. The AtFTCD-L protein deficiency also resulted in a significantly reduced monosaccharides content in the culture medium. Based on the above results, we speculate that the AtFTCD-L protein may be involved in sorting and/or transportation of TGN vesicles in root cap peripheral cells, thereby regulating the extracellular secretion of mucilage components in the root cap.
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Affiliation(s)
- Qijiang Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- College of Life Sciences and Engineering, Shenyang University, Liaoning, 110044, China
| | - Wei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xinyan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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32
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UBR4/POE facilitates secretory trafficking to maintain circadian clock synchrony. Nat Commun 2022; 13:1594. [PMID: 35332162 PMCID: PMC8948264 DOI: 10.1038/s41467-022-29244-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
Ubiquitin ligases control the degradation of core clock proteins to govern the speed and resetting properties of the circadian pacemaker. However, few studies have addressed their potential to regulate other cellular events within clock neurons beyond clock protein turnover. Here, we report that the ubiquitin ligase, UBR4/POE, strengthens the central pacemaker by facilitating neuropeptide trafficking in clock neurons and promoting network synchrony. Ubr4-deficient mice are resistant to jetlag, whereas poe knockdown flies are prone to arrhythmicity, behaviors reflective of the reduced axonal trafficking of circadian neuropeptides. At the cellular level, Ubr4 ablation impairs the export of secreted proteins from the Golgi apparatus by reducing the expression of Coronin 7, which is required for budding of Golgi-derived transport vesicles. In summary, UBR4/POE fulfills a conserved and unexpected role in the vesicular trafficking of neuropeptides, a function that has important implications for circadian clock synchrony and circuit-level signal processing. Although ubiquitin ligases are known to control clock protein degradation, their other roles in clock neurons are unclear. Here the authors report that UBR4 promotes export of neuropeptides from the Golgi for axonal trafficking, which is important for circadian clock synchrony in mice and flies.
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33
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Glasgow KW, Dillard M, Hertenstein E, Justin A, George R, Brady AB. Going Nuclear with Amino Acids and Proteins - Basic Biochemistry and Molecular Biology Primer for the Technologist. J Nucl Med Technol 2022; 50:186-194. [PMID: 35197272 DOI: 10.2967/jnmt.122.263847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
In recent years, there has been an influx of new tracers into the field of nuclear medicine and molecular imaging. Most of these tracers that have been FDA approved for clinical imaging exploit various mechanisms of protein biochemistry and molecular biology to bring about their actions, such as amino acid metabolism, protein folding, receptor-ligand interactions, and surface transport mechanisms. In this review, we attempt to paint a clear picture of the basic biochemistry and molecular biology of protein structure, translation, transcription, post-translational modifications, and protein targeting, in the context of the various radiopharmaceuticals currently used clinically, all in an easy-to-understand language for entry level technologists in the field. Tracer characteristics, including indications, dosage, injection-to-imaging time, and the logic behind the normal and pathophysiologic biodistribution of these newer molecular tracers, are also discussed.
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Affiliation(s)
| | - Mike Dillard
- Nuclear Medicine, PET/CT, Therapeutics, Inland Imaging, LLC, United States
| | - Eric Hertenstein
- Nuclear Medicine Institute and Master of Science in Radiologic Sciences Graduate Program, University of Findlay, United States
| | - Allen Justin
- Western Sierra Collegiate Academy, United States
| | - Remo George
- Nuclear Medicine and Molecular Imaging Sciences Program, University of Alabama at Birmingham, United States
| | - Amy Byrd Brady
- Nuclear Medicine and Molecular Imaging Sciences Program, University of Alabama at Birmingham, United States
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34
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Gorrell L, Omari S, Makareeva E, Leikin S. Noncanonical ER-Golgi trafficking and autophagy of endogenous procollagen in osteoblasts. Cell Mol Life Sci 2021; 78:8283-8300. [PMID: 34779895 DOI: 10.1007/s00018-021-04017-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 10/01/2021] [Accepted: 10/27/2021] [Indexed: 01/05/2023]
Abstract
Secretion and quality control of large extracellular matrix proteins remain poorly understood and debated, particularly transport intermediates delivering folded proteins from the ER to Golgi and misfolded ones to lysosomes. Discrepancies between different studies are related to utilization of exogenous cargo, off-target effects of experimental conditions and cell manipulation, and identification of transport intermediates without tracing their origin and destination. To address these issues, here we imaged secretory and degradative trafficking of type I procollagen in live MC3T3 osteoblasts by replacing a region encoding N-propeptide in endogenous Col1a2 gDNA with GFP cDNA. We selected clones that produced the resulting fluorescent procollagen yet had normal expression of key osteoblast and ER/cell stress genes, normal procollagen folding, and normal deposition and mineralization of extracellular matrix. Live-cell imaging of these clones revealed ARF1-dependent transport intermediates, which had no COPII coat and delivered procollagen from ER exit sites (ERESs) to Golgi without stopping at ER-Golgi intermediate compartment (ERGIC). It also confirmed ERES microautophagy, i.e., lysosomes engulfing ERESs containing misfolded procollagen. Beyond validating these trafficking models for endogenous procollagen, we uncovered a probable cause of noncanonical cell stress response to procollagen misfolding. Recognized and retained only at ERESs, misfolded procollagen does not directly activate the canonical UPR, yet it disrupts the ER lumen by blocking normal secretory export from the ER.
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Affiliation(s)
- Laura Gorrell
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD, 20892, USA.,Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Shakib Omari
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD, 20892, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Elena Makareeva
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sergey Leikin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD, 20892, USA.
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35
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Yu X, Li W, Young KH, Li Y. Posttranslational Modifications in PD-L1 Turnover and Function: From Cradle to Grave. Biomedicines 2021; 9:1702. [PMID: 34829931 PMCID: PMC8615371 DOI: 10.3390/biomedicines9111702] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022] Open
Abstract
Programmed death-ligand 1 (PD-L1) is one of the most classic immune checkpoint molecules. Cancer cells express PD-L1 to inhibit the activity of effector T cells' cytotoxicity through programmed death 1 (PD-1) engagement in exposure to inflammatory cytokines. PD-L1 expression levels on cancer cells might affect the clinical response to anti-PD-1/PD-L1 therapies. Hence, understanding molecular mechanisms for regulating PD-L1 expression is essential for improving the clinical response rate and efficacy of PD-1/PD-L1 blockade. Posttranslational modifications (PTMs), including phosphorylation, glycosylation, ubiquitination, and acetylation, regulate PD-L1 stability, cellular translocation, and interaction with its receptor. A coordinated positive and negative regulation via PTMs is required to ensure the balance and function of the PD-L1 protein. In this review, we primarily focus on the roles of PTMs in PD-L1 expression, trafficking, and antitumor immune response. We also discuss the implication of PTMs in anti-PD-1/PD-L1 therapies.
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Affiliation(s)
- Xinfang Yu
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; (X.Y.); (W.L.)
| | - Wei Li
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; (X.Y.); (W.L.)
| | - Ken H. Young
- Hematopathology Division, Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Yong Li
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; (X.Y.); (W.L.)
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36
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Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5. Nat Commun 2021; 12:6227. [PMID: 34711829 PMCID: PMC8553859 DOI: 10.1038/s41467-021-26534-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
The SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the STX5 mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identify a human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients show defective glycosylation, altered Golgi morphology as measured by electron microscopy, mislocalization of glycosyltransferases, and compromised ER-Golgi trafficking. Measurements of cognate binding SNAREs, based on biotin-synchronizable forms of Stx5 (the RUSH system) and Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. Alternative starting codons of Stx5 are thus linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.
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37
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Zepeda O J, Bishop LDC, Dutta C, Sarkar-Banerjee S, Leung WW, Landes CF. Untying the Gordian KNOT: Unbiased Single Particle Tracking Using Point Clouds and Adaptive Motion Analysis. J Phys Chem A 2021; 125:8723-8733. [PMID: 34559965 DOI: 10.1021/acs.jpca.1c06100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Achieving mechanistic understanding of transport in complex environments such as inside cells or at polymer interfaces is challenging. We need better ways to image transport in 3-D and better single particle tracking algorithms to determine transport that are not systemically biased toward any classical motion model. Here we present an unbiased single particle tracking algorithm: Knowing Nothing Outside Tracking (KNOT). KNOT uses point clouds provided by iterative deconvolution to educate individual particle localizations and link particle positions between frames to achieve 2-D and 3-D tracking. Information from prior point clouds fuels an independent adaptive motion model for each particle to avoid global models that could introduce biases. KNOT competes with or surpasses other 2-D methods from the 2012 particle tracking challenge while accurately tracking adsorption dynamics of proteins on polymer surfaces and early endosome transport in live cells in 3-D. We apply KNOT to study 3-D endosome transport to reveal new physical insight into locally directed and diffusive transport in live cells. Our analysis demonstrates better accuracy in classifying local motion and its direction compared to previous methods, revealing intricate intracellular transport heterogeneities.
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Affiliation(s)
- Jorge Zepeda O
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Chayan Dutta
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | | | - Wesley W Leung
- Applied Physics Graduate Program, Smalley-Curl Institute, Rice University, Houston, Texas 77005, United States
| | - Christy F Landes
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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38
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Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021; 86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
Abstract
Nearly all proteins are synthesized in the cytosol. The majority of this proteome must be trafficked elsewhere, such as to membranes, to subcellular compartments, or outside of the cell. Proper trafficking of nascent protein is necessary for protein folding, maturation, quality control and cellular and organismal health. To better understand cellular biology, molecular and chemical technologies to properly characterize protein trafficking (and mistrafficking) have been developed and applied. Herein, we take a biochemical perspective to review technologies that enable spatial and temporal measurement of protein distribution, focusing on both the most widely adopted methodologies and exciting emerging approaches.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
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39
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Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells. Nat Commun 2021; 12:5729. [PMID: 34593818 PMCID: PMC8484582 DOI: 10.1038/s41467-021-25890-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022] Open
Abstract
Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Designer cell-surface assemblies could control these cellular functions. Such assemblies could be constructed from synthetic components ex vivo, making it possible to form such structures using modern nanoscale self-assembly and fabrication techniques, and then oriented on the cell surface. Here we integrate synthetic devices, micron-scale DNA nanotubes, with mammalian cells by anchoring them by their ends to specific cell surface receptors. These filaments can measure shear stresses between 0-2 dyn/cm2, a regime important for cell signaling. Nanotubes can also grow while anchored to cells, thus acting as dynamic cell components. This approach to cell surface engineering, in which synthetic biomolecular assemblies are organized with existing cellular architecture, could make it possible to build new types of sensors, machines and scaffolds that can interface with, control and measure properties of cells. Mesoscale molecular assemblies on the cell surface integrate information and amplify signals. Here the authors integrate DNA nanotubes in a controlled manner with mammalian cells to act as sheer stress meters.
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40
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Parakh S, Perri ER, Vidal M, Sultana J, Shadfar S, Mehta P, Konopka A, Thomas CJ, Spencer DM, Atkin JD. Protein disulphide isomerase (PDI) is protective against amyotrophic lateral sclerosis (ALS)-related mutant Fused in Sarcoma (FUS) in in vitro models. Sci Rep 2021; 11:17557. [PMID: 34475430 PMCID: PMC8413276 DOI: 10.1038/s41598-021-96181-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/26/2021] [Indexed: 12/04/2022] Open
Abstract
Mutations in Fused in Sarcoma (FUS) are present in familial and sporadic cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). FUS is localised in the nucleus where it has important functions in DNA repair. However, in ALS/FTD, mutant FUS mislocalises from the nucleus to the cytoplasm where it forms inclusions, a key pathological hallmark of neurodegeneration. Mutant FUS also inhibits protein import into the nucleus, resulting in defects in nucleocytoplasmic transport. Fragmentation of the neuronal Golgi apparatus, induction of endoplasmic reticulum (ER) stress, and inhibition of ER-Golgi trafficking are also associated with mutant FUS misfolding in ALS. Protein disulphide isomerase (PDI) is an ER chaperone previously shown to be protective against misfolding associated with mutant superoxide dismutase 1 (SOD1) and TAR DNA-binding protein-43 (TDP-43) in cellular and zebrafish models. However, a protective role against mutant FUS in ALS has not been previously described. In this study, we demonstrate that PDI is protective against mutant FUS. In neuronal cell line and primary cultures, PDI restores defects in nuclear import, prevents the formation of mutant FUS inclusions, inhibits Golgi fragmentation, ER stress, ER-Golgi transport defects, and apoptosis. These findings imply that PDI is a new therapeutic target in FUS-associated ALS.
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Affiliation(s)
- S Parakh
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - E R Perri
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - M Vidal
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - J Sultana
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - S Shadfar
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - P Mehta
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - A Konopka
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - C J Thomas
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, 3086, Australia
| | - D M Spencer
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - J D Atkin
- Macquarie Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia. .,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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41
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Tang H, Cui M, Han M. Fatty acids impact sarcomere integrity through myristoylation and ER homeostasis. Cell Rep 2021; 36:109539. [PMID: 34407398 PMCID: PMC8404530 DOI: 10.1016/j.celrep.2021.109539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 06/04/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Decreased ability to maintain tissue integrity is critically involved in aging and degenerative diseases. Fatty acid (FA) metabolism has a profound impact on animal development and tissue maintenance, but our understanding of the underlying mechanisms is limited. We investigated whether and how FA abundance affects muscle integrity using Caenorhabditis elegans. We show that reducing the overall FA level by blocking FA biosynthesis or inhibiting protein myristoylation leads to disorganization of sarcomere structure and adult-onset paralysis. Further analysis indicates that myristoylation of two ARF guanosine triphosphatases (GTPases) critically mediates the effect of FA deficiency on sarcomere integrity through inducing endoplasmic reticulum (ER) stress and ER unfolded protein response (UPRER), which in turn leads to reduction of the level of sarcomere component PINCH and myosin disorganization. We thus present a mechanism that links FA signal, protein myristoylation, and ER homeostasis with muscle integrity, which provides valuable insights into the regulatory role of nutrients and ER homeostasis in muscle maintenance.
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Affiliation(s)
- Hongyun Tang
- Department of MCDB, University of Colorado Boulder, Boulder, CO 80309, USA; Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Mingxue Cui
- Department of MCDB, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Min Han
- Department of MCDB, University of Colorado Boulder, Boulder, CO 80309, USA.
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42
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Bourke AM, Schwartz SL, Bowen AB, Kleinjan MS, Winborn CS, Kareemo DJ, Gutnick A, Schwarz TL, Kennedy MJ. zapERtrap: A light-regulated ER release system reveals unexpected neuronal trafficking pathways. J Cell Biol 2021; 220:212461. [PMID: 34241635 PMCID: PMC8276314 DOI: 10.1083/jcb.202103186] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/31/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022] Open
Abstract
Here we introduce zapalog-mediated endoplasmic reticulum trap (zapERtrap), which allows one to use light to precisely trigger forward trafficking of diverse integral membrane proteins from internal secretory organelles to the cell surface with single cell and subcellular spatial resolution. To demonstrate its utility, we use zapERtrap in neurons to dissect where synaptic proteins emerge at the cell surface when processed through central (cell body) or remote (dendrites) secretory pathways. We reveal rapid and direct long-range trafficking of centrally processed proteins deep into the dendritic arbor to synaptic sites. Select proteins were also trafficked to the plasma membrane of the axon initial segment, revealing a novel surface trafficking hotspot. Proteins locally processed through dendritic secretory networks were widely dispersed before surface insertion, challenging assumptions for precise trafficking at remote sites. These experiments provide new insights into compartmentalized secretory trafficking and showcase the tunability and spatiotemporal control of zapERtrap, which will have broad applications for regulating cell signaling and function.
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Affiliation(s)
- Ashley M Bourke
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Samantha L Schwartz
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Aaron B Bowen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Mason S Kleinjan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Christina S Winborn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Dean J Kareemo
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
| | - Amos Gutnick
- Department of Neurobiology, Harvard Medical School, Boston, MA
| | - Thomas L Schwarz
- Department of Neurobiology, Harvard Medical School, Boston, MA.,F.M. Kirby Neurobiology Center, Children's Hospital, Boston, MA
| | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO
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43
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Wilson ZT, Jiang M, Geng J, Kaur S, Workman SW, Hao J, Bernas T, Tseng GN. Delayed KCNQ1/KCNE1 assembly on the cell surface helps I Ks fulfil its function as a repolarization reserve in the heart. J Physiol 2021; 599:3337-3361. [PMID: 33963564 DOI: 10.1113/jp281773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/04/2021] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS In adult ventricular myocytes, the slow delayed rectifier (IKs ) channels are distributed on the surface sarcolemma, not t-tubules. In adult ventricular myocytes, KCNQ1 and KCNE1 have distinct cell surface and cytoplasmic pools. KCNQ1 and KCNE1 traffic from the endoplasmic reticulum to the plasma membrane by separate routes, and assemble into IKs channels on the cell surface. Liquid chromatography/tandem mass spectrometry applied to affinity-purified KCNQ1 and KCNE1 interacting proteins reveals novel interactors involved in protein trafficking and assembly. Microtubule plus-end binding protein 1 (EB1) binds KCNQ1 preferentially in its dimer form, and promotes KCNQ1 to reach the cell surface. An LQT1-associated mutation, Y111C, reduces KCNQ1 binding to EB1 dimer. ABSTRACT Slow delayed rectifier (IKs ) channels consist of KCNQ1 and KCNE1. IKs functions as a 'repolarization reserve' in the heart by providing extra current for ventricular action potential shortening during β-adrenergic stimulation. There has been much debate about how KCNQ1 and KCNE1 traffic in cells, where they associate to form IKs channels, and the distribution pattern of IKs channels relative to β-adrenergic signalling complex. We used experimental strategies not previously applied to KCNQ1, KCNE1 or IKs , to provide new insights into these issues. 'Retention-using-selected-hook' experiments showed that newly translated KCNE1 constitutively trafficked through the conventional secretory path to the cell surface. KCNQ1 largely stayed in the endoplasmic reticulum, although dynamic KCNQ1 vesicles were observed in the submembrane region. Disulphide-bonded KCNQ1/KCNE1 constructs reported preferential association after they had reached cell surface. An in situ proximity ligation assay detected IKs channels in surface sarcolemma but not t-tubules of ventricular myocytes, similar to the reported location of adenylate cyclase 9/yotiao. Fluorescent protein-tagged KCNQ1 and KCNE1, in conjunction with antibodies targeting their extracellular epitopes, detected distinct cell surface and cytoplasmic pools of both proteins in myocytes. We conclude that, in cardiomyocytes, KCNQ1 and KCNE1 traffic by different routes to surface sarcolemma where they assemble into IKs channels. This mode of delayed channel assembly helps IKs fulfil its function of repolarization reserve. Proteomic experiments revealed a novel KCNQ1 interactor, microtubule plus-end binding protein 1 (EB1). EB1 dimer (active form) bound KCNQ1 and increased its surface level. An LQT1 mutation, Y111C, reduced KCNQ1 binding to EB1 dimer.
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Affiliation(s)
- Zachary T Wilson
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Min Jiang
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA, USA.,Institute of Medicinal biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Geng
- Institute of Medicinal biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sukhleen Kaur
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Samuel W Workman
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA, USA.,Present address: School of Medicine, Rutgers University, Piscataway, NJ, USA
| | - Jon Hao
- Poochon Scientific, Frederick, MD, USA
| | - Tytus Bernas
- Department of Anatomy & Neurobiology, Virginia Commonwealth University, Richmond, VA, USA
| | - Gea-Ny Tseng
- Department of Physiology & Biophysics, Virginia Commonwealth University, Richmond, VA, USA
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44
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Samimi H, Mehta I, Docking TR, Zainulabadeen A, Karsan A, Zare H. DNA methylation analysis improves the prognostication of acute myeloid leukemia. EJHAEM 2021; 2:211-218. [PMID: 34308417 PMCID: PMC8294109 DOI: 10.1002/jha2.187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Integration of orthogonal data could provide new opportunities to pinpoint the underlying molecular mechanisms of hematologic disorders. Using a novel gene network approach, we integrated DNA methylation data from The Cancer Genome Atlas (n = 194 cases) with the corresponding gene expression profile. Our integrated gene network analysis classified AML patients into low-, intermediate-, and high-risk groups. The identified high-risk group had significantly shorter overall survival compared to the low-risk group (p-value ≤10-11). Specifically, our approach identified a particular subgroup of nine high-risk AML cases that died within 2 years after diagnosis. These high-risk cases otherwise would be incorrectly classified as intermediate-risk solely based on cytogenetics, mutation profiles, and common molecular characteristics of AML. We confirmed the prognostic value of our integrative gene network approach using two independent datasets, as well as through comparison with European LeukemiaNet and LSC17 criteria. Our approach could be useful in the prognostication of a subset of borderline AML cases. These cases would not be classified into appropriate risk groups by other approaches that use gene expression, but not DNA methylation data. Our findings highlight the significance of epigenomic data, and they indicate integrating DNA methylation data with gene coexpression networks can have a synergistic effect.
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Affiliation(s)
- Hanie Samimi
- Department of Computer ScienceTexas State UniversitySan MarcosTexasUSA
| | - Isha Mehta
- Department of Cell Systems & AnatomyThe University of Texas Health Science CenterSan AntonioTexasUSA
| | - Thomas Roderick Docking
- Canada's Michael Smith Genome Sciences CentreBritish Columbia Cancer Research CentreVancouverBritish ColumbiaCanada
| | | | - Aly Karsan
- Canada's Michael Smith Genome Sciences CentreBritish Columbia Cancer Research CentreVancouverBritish ColumbiaCanada
| | - Habil Zare
- Department of Cell Systems & AnatomyThe University of Texas Health Science CenterSan AntonioTexasUSA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative DiseasesUniversity of Texas Health Sciences CenterSan AntonioTexasUSA
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45
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Zagirova D, Autenried R, Nelson ME, Rezvani K. Proteasome Complexes and Their Heterogeneity in Colorectal, Breast and Pancreatic Cancers. J Cancer 2021; 12:2472-2487. [PMID: 33854609 PMCID: PMC8040722 DOI: 10.7150/jca.52414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/09/2021] [Indexed: 11/26/2022] Open
Abstract
Targeting the ubiquitin-proteasome system (UPS) - in particular, the proteasome complex - has emerged as an attractive novel cancer therapy. While several proteasome inhibitors have been successfully approved by the Food and Drug Administration for the treatment of hematological malignancies, the clinical efficacy of these inhibitors is unexpectedly lower in the treatment of solid tumors due to the functional and structural heterogeneity of proteasomes in solid tumors. There are ongoing trials to examine the effectiveness of compound and novel proteasome inhibitors that can target solid tumors either alone or in combination with conventional chemotherapeutic agents. The modest therapeutic efficacy of proteasome inhibitors such as bortezomib in solid malignancies demands further research to clarify the exact effects of these proteasome inhibitors on different proteasomes present in cancer cells. The structural, cellular localization and functional analysis of the proteasome complexes in solid tumors originated from different tissues provides new insights into the diversity of proteasomes' responses to inhibitors. In this study, we used an optimized iodixanol gradient ultracentrifugation to purify a native form of proteasome complexes with their intact associated protein partners enriched within distinct cellular compartments. It is therefore possible to isolate proteasome subcomplexes with far greater resolution than sucrose or glycerol fractionations. We have identified differences in the catalytic activities, subcellular distribution, and inhibitor sensitivity of cytoplasmic proteasomes isolated from human colon, breast, and pancreatic cancer cell lines. Our developed techniques and generated results will serve as a valuable guideline for investigators developing a new generation of proteasome inhibitors as an effective targeted therapy for solid tumors.
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Affiliation(s)
- Diana Zagirova
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Rebecca Autenried
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Morgan E Nelson
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
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46
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Lita A, Pliss A, Kuzmin A, Yamasaki T, Zhang L, Dowdy T, Burks C, de Val N, Celiku O, Ruiz-Rodado V, Nicoli ER, Kruhlak M, Andresson T, Das S, Yang C, Schmitt R, Herold-Mende C, Gilbert MR, Prasad PN, Larion M. IDH1 mutations induce organelle defects via dysregulated phospholipids. Nat Commun 2021; 12:614. [PMID: 33504762 PMCID: PMC7840755 DOI: 10.1038/s41467-020-20752-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
Infiltrating gliomas are devastating and incurable tumors. Amongst all gliomas, those harboring a mutation in isocitrate dehydrogenase 1 mutation (IDH1mut) acquire a different tumor biology and clinical manifestation from those that are IDH1WT. Understanding the unique metabolic profile reprogrammed by IDH1 mutation has the potential to identify new molecular targets for glioma therapy. Herein, we uncover increased monounsaturated fatty acids (MUFA) and their phospholipids in endoplasmic reticulum (ER), generated by IDH1 mutation, that are responsible for Golgi and ER dilation. We demonstrate a direct link between the IDH1 mutation and this organelle morphology via D-2HG-induced stearyl-CoA desaturase (SCD) overexpression, the rate-limiting enzyme in MUFA biosynthesis. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, addition of oleic acid, which tilts the balance towards elevated levels of MUFA, produces IDH1mut-specific cellular apoptosis. Collectively, these results suggest that IDH1mut-induced SCD overexpression can rearrange the distribution of lipids in the organelles of glioma cells, providing new insight into the link between lipid metabolism and organelle morphology in these cells, with potential and unique therapeutic implications.
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Affiliation(s)
- Adrian Lita
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Andrey Kuzmin
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
- Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Tomohiro Yamasaki
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Lumin Zhang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Christina Burks
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Natalia de Val
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Orieta Celiku
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Victor Ruiz-Rodado
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Elena-Raluca Nicoli
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Schmitt
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
- Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA.
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Casler JC, Zajac AL, Valbuena FM, Sparvoli D, Jeyifous O, Turkewitz AP, Horne-Badovinac S, Green WN, Glick BS. ESCargo: a regulatable fluorescent secretory cargo for diverse model organisms. Mol Biol Cell 2020; 31:2892-2903. [PMID: 33112725 PMCID: PMC7927198 DOI: 10.1091/mbc.e20-09-0591] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Membrane traffic can be studied by imaging a cargo protein as it transits the secretory pathway. The best tools for this purpose initially block export of the secretory cargo from the endoplasmic reticulum (ER) and then release the block to generate a cargo wave. However, previously developed regulatable secretory cargoes are often tricky to use or specific for a single model organism. To overcome these hurdles for budding yeast, we recently optimized an artificial fluorescent secretory protein that exits the ER with the aid of the Erv29 cargo receptor, which is homologous to mammalian Surf4. The fluorescent secretory protein forms aggregates in the ER lumen and can be rapidly disaggregated by addition of a ligand to generate a nearly synchronized cargo wave. Here we term this regulatable secretory protein ESCargo (Erv29/Surf4-dependent secretory cargo) and demonstrate its utility not only in yeast cells, but also in cultured mammalian cells, Drosophila cells, and the ciliate Tetrahymena thermophila. Kinetic studies indicate that rapid export from the ER requires recognition by Erv29/Surf4. By choosing an appropriate ER signal sequence and expression vector, this simple technology can likely be used with many model organisms.
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Affiliation(s)
- Jason C. Casler
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Allison L. Zajac
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Fernando M. Valbuena
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Daniela Sparvoli
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Okunola Jeyifous
- Department of Neurobiology, University of Chicago, Chicago, IL 60637
- Marine Biological Laboratory, Woods Hole, MA 02543
| | - Aaron P. Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Sally Horne-Badovinac
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - William N. Green
- Department of Neurobiology, University of Chicago, Chicago, IL 60637
- Marine Biological Laboratory, Woods Hole, MA 02543
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
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Omari S, Makareeva E, Gorrell L, Jarnik M, Lippincott-Schwartz J, Leikin S. Mechanisms of procollagen and HSP47 sorting during ER-to-Golgi trafficking. Matrix Biol 2020; 93:79-94. [DOI: 10.1016/j.matbio.2020.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
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Gutierrez-Armijos R, Sussmann RAC, Silber AM, Cortez M, Hernandez A. Abnormal sterol-induced cell wall glucan deficiency in yeast is due to impaired glucan synthase transport to the plasma membrane. Biochem J 2020; 477:BCJ20200663. [PMID: 33094814 DOI: 10.1042/bcj20200663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 01/01/2023]
Abstract
Abnormal sterols disrupt cellular functions through yet unclear mechanisms. In Saccharomyces cerevisiae, accumulation of Δ8-sterols, the same type of sterols observed in patients of Conradi-Hünermann-Happle syndrome or in fungi after amine fungicide treatment, leads to cell wall weakness. We have studied the influence of Δ8-sterols on the activity of glucan synthase I, the protein synthetizing the main polymer in fungal cell walls, its regulation by the Cell Wall Integrity (CWI) pathway, and its transport from the endoplasmic reticulum to the plasma membrane. We ascertained that the catalytic characteristics were mostly unaffected by the presence of abnormal sterols but the enzyme was partially retained in the endoplasmic reticulum, leading to glucan deficit at the cell wall. Furthermore, we observed that glucan synthase I traveled through an unconventional exocytic route to the plasma membrane that is associated with low density intracellular membranes. Also, we found out that the CWI pathway remained inactive despite low glucan levels at the cell wall. Taken together, these data suggest that Δ8-sterols affect cell walls by inhibiting unconventional secretion of proteins leading to retention and degradation of glucan synthase I, while the compensatory CWI pathway is unable to activate. These results could be instrumental to understand defects of bone development in cholesterol biosynthesis disorders and fungicide mechanisms of action.
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50
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Lu L, Xu X, Du X, Zeng T, Yang T, Chen Y, Tao Z, Zhong S, Wen J, Zhou C. Transcriptome analyses to reveal the dynamic change mechanism of pigeon magnum during one egg-laying cycle. Mol Reprod Dev 2020; 87:1141-1151. [PMID: 33084116 DOI: 10.1002/mrd.23428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 09/12/2020] [Indexed: 12/14/2022]
Abstract
We analyzed the transcriptome of pigeon magnum in three stages (C1: pre-ovulation, C2: post-ovulation, C3: 5-6 days after ovulation) to elucidate the molecular and cellular events associated with morphological changes during the laying cycle. We observed that C1 was highly developed, apoptosis rate was highest in C2, and C3 attained the smallest size. Through RNA-sequencing, we obtained 54,764,938 (97.2%) high-quality clean reads that aligned to 20,767 genes. Gene expression profile analysis showed the greatest difference between C1 and C3; 3966 differentially expressed genes (DEGs) were identified, of which 2250 genes were upregulated and 1716 genes were downregulated in C1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that protein processing and transport activities were prominent in C1, and upregulated genes included those related to signal recognition particle (SRP), signal recognition particle receptor (SRPR), translocon, GRP78, RRBP1, TRAP, TRAM1, and OST. Egg white protein-related gene expression was highest, with OVALY being the most highly expressed. In C2, apoptosis-related gene expression was higher than in C1, and fatty acid metabolism was active, which may be correlated with magnum tissue regression. Collagen- and laminin-related gene expression was prominent in C1 and C3, indicating roles in egg white protein generation and magnum reconstruction. PR gene expression was highest and exhibited drastic change in the three groups, indicating that PR and its regulation may be involved in changes in magnum morphology and function. Through the identification and functional analysis of DEGs and other crucial genes, this may contribute to understand the egg white protein production, magnum tissue regression, and magnum regeneration mechanisms.
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Affiliation(s)
- Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Xiaoqin Xu
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Xue Du
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Tingbang Yang
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Yao Chen
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
| | - Zhengrong Tao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, China
| | - Shengliang Zhong
- PingYang XingLiang Pigeon Farming Co. Ltd., Wenzhou, Zhejiang, China
| | - Jihui Wen
- PingYang AoFeng Pigeon Farming Co. Ltd., Wenzhou, Zhejiang, China
| | - Caiquan Zhou
- Institute of Ecology, China West Normal University, Nanchong, Sichuan, China
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