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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 DOI: 10.1152/physrev.00025.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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2
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Zajac M, Mukherjee S, Anees P, Oettinger D, Henn K, Srikumar J, Zou J, Saminathan A, Krishnan Y. A mechanism of lysosomal calcium entry. SCIENCE ADVANCES 2024; 10:eadk2317. [PMID: 38354239 PMCID: PMC10866540 DOI: 10.1126/sciadv.adk2317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024]
Abstract
Lysosomal calcium (Ca2+) release is critical to cell signaling and is mediated by well-known lysosomal Ca2+ channels. Yet, how lysosomes refill their Ca2+ remains hitherto undescribed. Here, from an RNA interference screen in Caenorhabditis elegans, we identify an evolutionarily conserved gene, lci-1, that facilitates lysosomal Ca2+ entry in C. elegans and mammalian cells. We found that its human homolog TMEM165, previously designated as a Ca2+/H+ exchanger, imports Ca2+ pH dependently into lysosomes. Using two-ion mapping and electrophysiology, we show that TMEM165, hereafter referred to as human LCI, acts as a proton-activated, lysosomal Ca2+ importer. Defects in lysosomal Ca2+ channels cause several neurodegenerative diseases, and knowledge of lysosomal Ca2+ importers may provide previously unidentified avenues to explore the physiology of Ca2+ channels.
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Affiliation(s)
- Matthew Zajac
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Sourajit Mukherjee
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Daphne Oettinger
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Katharine Henn
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Jainaha Srikumar
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Junyi Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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3
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Kulkarni M, Hardwick JM. Programmed Cell Death in Unicellular Versus Multicellular Organisms. Annu Rev Genet 2023; 57:435-459. [PMID: 37722687 DOI: 10.1146/annurev-genet-033123-095833] [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: 09/20/2023]
Abstract
Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms, allaying earlier doubts that self-inflicted cell death pathways exist in microorganisms. Approximately 20 mammalian death pathways have been partially characterized over the last 35 years. By contrast, more than 100 death mechanisms have been identified in bacteria and a few fungi in recent years. However, cell death is nearly unstudied in most human pathogenic microbes that cause major public health burdens. Here, we consider how the current understanding of programmed cell death arose through animal studies and how recently uncovered microbial cell death mechanisms in fungi and bacteria resemble and differ from mechanisms of mammalian cell death.
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Affiliation(s)
- Madhura Kulkarni
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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4
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Dhaouadi N, Vitto VAM, Pinton P, Galluzzi L, Marchi S. Ca 2+ signaling and cell death. Cell Calcium 2023; 113:102759. [PMID: 37210868 DOI: 10.1016/j.ceca.2023.102759] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/23/2023]
Abstract
Multiple forms of regulated cell death (RCD) have been characterized, each of which originates from the activation of a dedicated molecular machinery. RCD can occur in purely physiological settings or upon failing cellular adaptation to stress. Ca2+ions have been shown to physically interact with - and hence regulate - various components of the RCD machinery. Moreover, intracellular Ca2+ accumulation can promote organellar dysfunction to degree that can be overtly cytotoxic or sensitize cells to RCD elicited by other stressors. Here, we provide an overview of the main links between Ca2+and different forms of RCD, including apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, lysosome-dependent cell death, and parthanatos.
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Affiliation(s)
- Nada Dhaouadi
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy; GVM Care & Research, Maria Cecilia Hospital, Cotignola, Italy
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
| | - Saverio Marchi
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy.
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5
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Milani M, Pihán P, Hetz C. Calcium signaling in lysosome-dependent cell death. Cell Calcium 2023; 113:102751. [PMID: 37178674 DOI: 10.1016/j.ceca.2023.102751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Calcium is a crucial messenger of intracellular and extracellular signals, regulating a great variety of cellular processes such as cell death, proliferation, and metabolism. Inside the cell, calcium signaling is one of the main interorganelle communication mediators, with central functional roles at the endoplasmic reticulum (ER), mitochondria, Golgi complex, and lysosomes. Lysosomal function is highly dependent on lumenal calcium and most of the lysosomal membrane-localised ion channels regulate several lysosomal functions and properties such as lumenal pH. One of these functions configures a specific type of cell death involving lysosomes, named lysosome-dependent cell death (LDCD), which contributes to maintenance of tissue homeostasis, development and pathology when deregulated. Here, we cover the fundamental aspects of LDCD with a special focus on recent advances in calcium signaling in LDCD.
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Affiliation(s)
- Mateus Milani
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Philippe Pihán
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, United States of America.
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6
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Lan YJ, Cheng CC, Chu SC, Chiang YW. A gating mechanism of the BsYetJ calcium channel revealed in an endoplasmic reticulum lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184153. [PMID: 36948481 DOI: 10.1016/j.bbamem.2023.184153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
The transmembrane BAX inhibitor-1-containing motif 6 (TMBIM6) is suggested to modulate apoptosis by regulating calcium homeostasis in the endoplasmic reticulum (ER). However, the precise molecular mechanism underlying this calcium regulation remains poorly understood. To shed light on this issue, we investigated all negatively charged residues in BsYetJ, a bacterial homolog of TMBIM6, using mutagenesis and fluorescence-based functional assays. We reconstituted BsYetJ in membrane vesicles with a lipid composition similar to that of the ER. Our results show that the charged residues E49 and R205 work together as a major gate, regulating calcium conductance in these ER-like lipid vesicles. However, these residues become largely inactive when reconstituted in other lipid environments. In addition, we found that D195 acts as a minor filter compared to the E49-R205 dyad. Our study uncovers a previously unknown function of BsYetJ/TMBIM6 in the calcium-dependent inactivation of BsYetJ, providing a framework for the development of a lipid-dependent mechanistic model of BsYetJ that will facilitate our understanding of calcium-dependent apoptosis.
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Affiliation(s)
- Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Chu-Chun Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Shu-Chi Chu
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.
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7
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Lomphithak T, Fadeel B. Die hard: cell death mechanisms and their implications in nanotoxicology. Toxicol Sci 2023; 192:kfad008. [PMID: 36752525 PMCID: PMC10109533 DOI: 10.1093/toxsci/kfad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Cell death is a fundamental biological process, and its fine-tuned regulation is required for life. However, the complexity of regulated cell death is often reduced to a matter of live-dead discrimination. Here, we provide a perspective on programmed or regulated cell death, focusing on apoptosis, pyroptosis, necroptosis, and ferroptosis (the latter three cell death modalities are examples of regulated necrosis). We also touch on other, recently described manifestations of (pathological) cell death including cuproptosis. Furthermore, we address how engineered nanomaterials impact on regulated cell death. We posit that an improved understanding of nanomaterial-induced perturbations of cell death may allow for a better prediction of the consequences of human exposure and could also yield novel approaches by which to mitigate these effects. Finally, we provide examples of the harnessing of nanomaterials to achieve cancer cell killing through the induction of regulated cell death.
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Affiliation(s)
- Thanpisit Lomphithak
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
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8
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Zajac M, Modi S, Krishnan Y. The evolution of organellar calcium mapping technologies. Cell Calcium 2022; 108:102658. [PMID: 36274564 PMCID: PMC10224794 DOI: 10.1016/j.ceca.2022.102658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 01/25/2023]
Abstract
Intracellular Ca2+ fluxes are dynamically controlled by the co-involvement of multiple organellar pools of stored Ca2+. Endolysosomes are emerging as physiologically critical, yet underexplored, sources and sinks of intracellular Ca2+. Delineating the role of organelles in Ca2+ signaling has relied on chemical fluorescent probes and electrophysiological strategies. However, the acidic endolysosomal environment presents unique issues, which preclude the use of traditional chemical reporter strategies to map lumenal Ca2+. Here, we broadly address the current state of knowledge about organellar Ca2+ pools. We then outline the application of traditional probes, and their sensing paradigms. We then discuss how a new generation of probes overcomes the limitations of traditional Ca2+probes, emphasizing their ability to offer critical insights into endolysosomal Ca2+, and its feedback with other organellar pools.
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Affiliation(s)
- Matthew Zajac
- Department of Chemistry, The University of Chicago, Chicago, Illinois, 60637, USA; Neuroscience Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Souvik Modi
- Esya Labs, Translation and Innovation Hub, Imperial College White City Campus, 84 Wood Lane, London, W12 0BZ, UK
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois, 60637, USA; Neuroscience Institute, The University of Chicago, Chicago, IL, 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, 60637, USA.
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9
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Milani M, Pihán P, Hetz C. Mitochondria-associated niches in health and disease. J Cell Sci 2022; 135:285141. [DOI: 10.1242/jcs.259634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
ABSTRACT
The appreciation of the importance of interorganelle contacts has steadily increased over the past decades. Advances in imaging, molecular biology and bioinformatic techniques allowed the discovery of new mechanisms involved in the interaction and communication between organelles, providing novel insights into the inner works of a cell. In this Review, with the mitochondria under the spotlight, we discuss the most recent findings on the mechanisms mediating the communication between organelles, focusing on Ca2+ signaling, lipid exchange, cell death and stress responses. Notably, we introduce a new integrative perspective to signaling networks that is regulated by interorganelle interactions – the mitochondria-associated niches – focusing on the link between the molecular determinants of contact sites and their functional outputs, rather than simply physical and structural communication. In addition, we highlight the neuropathological and metabolic implications of alterations in mitochondria-associated niches and outline how this concept might improve our understanding of multi-organelle interactions.
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Affiliation(s)
- Mateus Milani
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile 1 , Santiago 8380000 , Chile
- FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO) 2 , Santiago 7750000 , Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile 3 , Santiago 8380000 , Chile
| | - Philippe Pihán
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile 1 , Santiago 8380000 , Chile
- FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO) 2 , Santiago 7750000 , Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile 3 , Santiago 8380000 , Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile 1 , Santiago 8380000 , Chile
- FONDAP Center for Geroscience, Brain Health, and Metabolism (GERO) 2 , Santiago 7750000 , Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile 3 , Santiago 8380000 , Chile
- Buck Institute for Research on Aging 4 , Novato, CA 94945 , USA
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10
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Zhang L, Dietsche F, Seitaj B, Rojas-Charry L, Latchman N, Tomar D, Wüst RC, Nickel A, Frauenknecht KB, Schoser B, Schumann S, Schmeisser MJ, Vom Berg J, Buch T, Finger S, Wenzel P, Maack C, Elrod JW, Parys JB, Bultynck G, Methner A. TMBIM5 loss of function alters mitochondrial matrix ion homeostasis and causes a skeletal myopathy. Life Sci Alliance 2022; 5:5/10/e202201478. [PMID: 35715207 PMCID: PMC9206080 DOI: 10.26508/lsa.202201478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 01/13/2023] Open
Abstract
TMBIM5 deficiency reduces mitochondrial K+/H+ exchange. Mutation of the channel pore in mice destabilizes the protein and results in increased embryonic lethality and a skeletal myopathy. Ion fluxes across the inner mitochondrial membrane control mitochondrial volume, energy production, and apoptosis. TMBIM5, a highly conserved protein with homology to putative pH-dependent ion channels, is involved in the maintenance of mitochondrial cristae architecture, ATP production, and apoptosis. Here, we demonstrate that overexpressed TMBIM5 can mediate mitochondrial calcium uptake. Under steady-state conditions, loss of TMBIM5 results in increased potassium and reduced proton levels in the mitochondrial matrix caused by attenuated exchange of these ions. To identify the in vivo consequences of TMBIM5 dysfunction, we generated mice carrying a mutation in the channel pore. These mutant mice display increased embryonic or perinatal lethality and a skeletal myopathy which strongly correlates with tissue-specific disruption of cristae architecture, early opening of the mitochondrial permeability transition pore, reduced calcium uptake capability, and mitochondrial swelling. Our results demonstrate that TMBIM5 is an essential and important part of the mitochondrial ion transport system machinery with particular importance for embryonic development and muscle function.
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Affiliation(s)
- Li Zhang
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | - Bruno Seitaj
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of Molecular and Cellular Signaling, Leuven, Belgium
| | - Liliana Rojas-Charry
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nadina Latchman
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Dhanendra Tomar
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Rob Ci Wüst
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alexander Nickel
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Katrin Bm Frauenknecht
- Institute of Neuropathology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Munich, Germany
| | - Sven Schumann
- Institute of Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michael J Schmeisser
- Institute of Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Johannes Vom Berg
- Institute of Laboratory Animal Science, University of Zurich, Zürich, Switzerland
| | - Thorsten Buch
- Institute of Laboratory Animal Science, University of Zurich, Zürich, Switzerland
| | - Stefanie Finger
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Philip Wenzel
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Department of Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Christoph Maack
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - John W Elrod
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Jan B Parys
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of Molecular and Cellular Signaling, Leuven, Belgium
| | - Geert Bultynck
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of Molecular and Cellular Signaling, Leuven, Belgium
| | - Axel Methner
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
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11
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Cai J, Ye Z, Hu Y, Wang Y, Ye L, Gao L, sun Q, Tong S, Sun Z, Yang J, Chen Q. FAIM2 is a potential pan-cancer biomarker for prognosis and immune infiltration. Front Oncol 2022; 12:998336. [PMID: 36185230 PMCID: PMC9516132 DOI: 10.3389/fonc.2022.998336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Fas apoptosis inhibitory molecule 2 (FAIM2) is an important member of the transmembrane BAX inhibitor motif containing (TMBIM) family. However, the role of FAIM2 in tumor prognosis and immune infiltration has rarely been studied. Here, we conducted a pan-cancer analysis to explore the role of FAIM2 in various tumors and further verified the results in glioma through molecular biology experiment. FAIM2 expression and clinical stages in tumor samples and para-cancerous samples were analyzed by TIMER2 database, GEPIA database, and the TISIDB database. The role of FAIM2 on prognosis was analyzed via GEPIA2. We utilized the ESTIMATE algorithm to evaluate the ImmuneScore and StromalScore of various tumors. In addition, we explored the correlation between FAIM2 expression and tumor immune cell infiltration by the TIMER2 database. The immune checkpoint genes, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), and DNA methylation related to FAIM2 were analyzed based on the TCGA database. The correlation between FAIM2 expression with Copy number variations (CNV) and methylation is explored by GSCA database. Protein-Protein Interaction (PPI) analysis was obtained from the STRING database and the CellMiner database was used to explore the association between FAIM2 expression and drug response. FAIM2 co-expression genes were studied by the LinkedOmics database. Immunohistochemistry, Western Blotting Analysis, Cell Viability Assay, Colony Formation Assay, and Edu staining assay were used in the molecular biology experiments section. The FAIM2 expression was down-regulated in most tumors and highly expressed FAIM2 was associated with a better prognosis in several cancers. FAIM2 plays an essential role in the tumor microenvironment and is closely associated with immune Infiltration in various tumors. The expression of FAIM2 was closely correlated to TMB, MSI, MMR, CNV, and DNA methylation. Furthermore, FAIM2 related genes in the PPI network and its co-expression genes in glioma are involved in a large number of immune-related pathways. Molecular biology experiments verified a cancer suppressor role for FAIM2 in glioma. FAIM2 may serve as a potential pan-cancer biomarker for prognosis and immune infiltration, especially in glioma. Moreover, this study might provide a potential target for tumor immunotherapy.
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Affiliation(s)
- Jiayang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuanyuan Hu
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yixuan Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liguo Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ji'an Yang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Qianxue Chen, ; Ji'an Yang,
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Qianxue Chen, ; Ji'an Yang,
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