1
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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2
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Morizet J, Chow D, Wijesinghe P, Schartner E, Dwapanyin G, Dubost N, Bruce GD, Anckaert E, Dunning K, Dholakia K. UVA Hyperspectral Light-Sheet Microscopy for Volumetric Metabolic Imaging: Application to Preimplantation Embryo Development. ACS PHOTONICS 2023; 10:4177-4187. [PMID: 38145166 PMCID: PMC10739996 DOI: 10.1021/acsphotonics.3c00900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/26/2023]
Abstract
Cellular metabolism is a key regulator of energetics, cell growth, regeneration, and homeostasis. Spatially mapping the heterogeneity of cellular metabolic activity is of great importance for unraveling the overall cell and tissue health. In this regard, imaging the endogenous metabolic cofactors, nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD), with subcellular resolution and in a noninvasive manner would be useful to determine tissue and cell viability in a clinical environment, but practical use is limited by current imaging techniques. In this paper, we demonstrate the use of phasor-based hyperspectral light-sheet (HS-LS) microscopy using a single UVA excitation wavelength as a route to mapping metabolism in three dimensions. We show that excitation solely at a UVA wavelength of 375 nm can simultaneously excite NAD(P)H and FAD autofluorescence, while their relative contributions can be readily quantified using a hardware-based spectral phasor analysis. We demonstrate the potential of our HS-LS system by capturing dynamic changes in metabolic activity during preimplantation embryo development. To validate our approach, we delineate metabolic changes during preimplantation embryo development from volumetric maps of metabolic activity. Importantly, our approach overcomes the need for multiple excitation wavelengths, two-photon imaging, or significant postprocessing of data, paving the way toward clinical translation, such as in situ, noninvasive assessment of embryo viability.
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Affiliation(s)
- Josephine Morizet
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
| | - Darren Chow
- Robinson
Research Institute, School of Biomedicine, The University of Adelaide, Adelaide 5501, Australia
- Australian
Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide 5505, Australia
- Institute
for Photonics and Advanced Sensing, The
University of Adelaide, Adelaide 5505, Australia
| | - Philip Wijesinghe
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
| | - Erik Schartner
- Robinson
Research Institute, School of Biomedicine, The University of Adelaide, Adelaide 5501, Australia
- Institute
for Photonics and Advanced Sensing, The
University of Adelaide, Adelaide 5505, Australia
- Centre
of Light for Life, The University of Adelaide, Adelaide 5005, Australia
| | - George Dwapanyin
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
| | - Nicolas Dubost
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
| | - Graham D. Bruce
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
| | - Ellen Anckaert
- Faculty of
Medicine and Pharmacy, Vrije Universiteit
Brussel, Brussels 1070, Belgium
| | - Kylie Dunning
- Robinson
Research Institute, School of Biomedicine, The University of Adelaide, Adelaide 5501, Australia
- Australian
Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide 5505, Australia
- Institute
for Photonics and Advanced Sensing, The
University of Adelaide, Adelaide 5505, Australia
| | - Kishan Dholakia
- SUPA,
School of Physics and Astronomy, University
of St Andrews, North Haugh, St Andrews Fife KY16, U.K.
- Centre
of Light for Life, The University of Adelaide, Adelaide 5005, Australia
- School
of Biological Sciences, The University of
Adelaide, Adelaide 5005, Australia
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4
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Barroso M, Monaghan MG, Niesner R, Dmitriev RI. Probing organoid metabolism using fluorescence lifetime imaging microscopy (FLIM): The next frontier of drug discovery and disease understanding. Adv Drug Deliv Rev 2023; 201:115081. [PMID: 37647987 PMCID: PMC10543546 DOI: 10.1016/j.addr.2023.115081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/20/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
Organoid models have been used to address important questions in developmental and cancer biology, tissue repair, advanced modelling of disease and therapies, among other bioengineering applications. Such 3D microenvironmental models can investigate the regulation of cell metabolism, and provide key insights into the mechanisms at the basis of cell growth, differentiation, communication, interactions with the environment and cell death. Their accessibility and complexity, based on 3D spatial and temporal heterogeneity, make organoids suitable for the application of novel, dynamic imaging microscopy methods, such as fluorescence lifetime imaging microscopy (FLIM) and related decay time-assessing readouts. Several biomarkers and assays have been proposed to study cell metabolism by FLIM in various organoid models. Herein, we present an expert-opinion discussion on the principles of FLIM and PLIM, instrumentation and data collection and analysis protocols, and general and emerging biosensor-based approaches, to highlight the pioneering work being performed in this field.
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Affiliation(s)
- Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Michael G Monaghan
- Department of Mechanical, Manufacturing and Biomedical Engineering, Trinity College Dublin, Dublin 02, Ireland
| | - Raluca Niesner
- Dynamic and Functional In Vivo Imaging, Freie Universität Berlin and Biophysical Analytics, German Rheumatism Research Center, Berlin, Germany
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium; Ghent Light Microscopy Core, Ghent University, 9000 Ghent, Belgium.
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5
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Vera-Siguenza E, Escribano-Gonzalez C, Serrano-Gonzalo I, Eskla KL, Spill F, Tennant D. Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model. PLoS Comput Biol 2023; 19:e1011374. [PMID: 37713666 PMCID: PMC10503963 DOI: 10.1371/journal.pcbi.1011374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 07/19/2023] [Indexed: 09/17/2023] Open
Abstract
It is increasingly apparent that cancer cells, in addition to remodelling their metabolism to survive and proliferate, adapt and manipulate the metabolism of other cells. This property may be a telling sign that pre-clinical tumour metabolism studies exclusively utilising in-vitro mono-culture models could prove to be limited for uncovering novel metabolic targets able to translate into clinical therapies. Although this is increasingly recognised, and work towards addressing the issue is becoming routinary much remains poorly understood. For instance, knowledge regarding the biochemical mechanisms through which cancer cells manipulate non-cancerous cell metabolism, and the subsequent impact on their survival and proliferation remains limited. Additionally, the variations in these processes across different cancer types and progression stages, and their implications for therapy, also remain largely unexplored. This study employs an interdisciplinary approach that leverages the predictive power of mathematical modelling to enrich experimental findings. We develop a functional multicellular in-silico model that facilitates the qualitative and quantitative analysis of the metabolic network spawned by an in-vitro co-culture model of bone marrow mesenchymal stem- and myeloma cell lines. To procure this model, we devised a bespoke human genome constraint-based reconstruction workflow that combines aspects from the legacy mCADRE & Metabotools algorithms, the novel redHuman algorithm, along with 13C-metabolic flux analysis. Our workflow transforms the latest human metabolic network matrix (Recon3D) into two cell-specific models coupled with a metabolic network spanning a shared growth medium. When cross-validating our in-silico model against the in-vitro model, we found that the in-silico model successfully reproduces vital metabolic behaviours of its in-vitro counterpart; results include cell growth predictions, respiration rates, as well as support for observations which suggest cross-shuttling of redox-active metabolites between cells.
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Affiliation(s)
- Elias Vera-Siguenza
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Watson School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Cristina Escribano-Gonzalez
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Irene Serrano-Gonzalo
- Instituto de Investigación Sanitaria Aragón, Fundación Española para el Estudio y Terapéutica de la enfermedad de Gaucher y otras Lisosomales, Zaragoza, España
| | - Kattri-Liis Eskla
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Fabian Spill
- Watson School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Daniel Tennant
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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6
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Debruyne AC, Okkelman IA, Dmitriev RI. Balance between the cell viability and death in 3D. Semin Cell Dev Biol 2023; 144:55-66. [PMID: 36117019 DOI: 10.1016/j.semcdb.2022.09.005] [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: 04/19/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022]
Abstract
Cell death is a phenomenon, frequently perceived as an absolute event for cell, tissue and the organ. However, the rising popularity and complexity of such 3D multicellular 'tissue building blocks' as heterocellular spheroids, organoids, and 'assembloids' prompts to revise the definition and quantification of cell viability and death. It raises several questions on the overall viability of all the cells within 3D volume and on choosing the appropriate, continuous, and non-destructive viability assay enabling for a single-cell analysis. In this review, we look at cell viability and cell death modalities with attention to the intrinsic features of such 3D models as spheroids, organoids, and bioprints. Furthermore, we look at emerging and promising methodologies, which can help define and understand the balance between cell viability and death in dynamic and complex 3D environments. We conclude that the recent innovations in biofabrication, biosensor probe development, and fluorescence microscopy can help answer these questions.
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Affiliation(s)
- Angela C Debruyne
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Irina A Okkelman
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium.
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7
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Conte F, Noga MJ, van Scherpenzeel M, Veizaj R, Scharn R, Sam JE, Palumbo C, van den Brandt FCA, Freund C, Soares E, Zhou H, Lefeber DJ. Isotopic Tracing of Nucleotide Sugar Metabolism in Human Pluripotent Stem Cells. Cells 2023; 12:1765. [PMID: 37443799 PMCID: PMC10340731 DOI: 10.3390/cells12131765] [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: 02/17/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Metabolism not only produces energy necessary for the cell but is also a key regulator of several cellular functions, including pluripotency and self-renewal. Nucleotide sugars (NSs) are activated sugars that link glucose metabolism with cellular functions via protein N-glycosylation and O-GlcNAcylation. Thus, understanding how different metabolic pathways converge in the synthesis of NSs is critical to explore new opportunities for metabolic interference and modulation of stem cell functions. Tracer-based metabolomics is suited for this challenge, however chemically-defined, customizable media for stem cell culture in which nutrients can be replaced with isotopically labeled analogs are scarcely available. Here, we established a customizable flux-conditioned E8 (FC-E8) medium that enables stem cell culture with stable isotopes for metabolic tracing, and a dedicated liquid chromatography mass-spectrometry (LC-MS/MS) method targeting metabolic pathways converging in NS biosynthesis. By 13C6-glucose feeding, we successfully traced the time-course of carbon incorporation into NSs directly via glucose, and indirectly via other pathways, such as glycolysis and pentose phosphate pathways, in induced pluripotent stem cells (hiPSCs) and embryonic stem cells. Then, we applied these tools to investigate the NS biosynthesis in hiPSC lines from a patient affected by deficiency of phosphoglucomutase 1 (PGM1), an enzyme regulating the synthesis of the two most abundant NSs, UDP-glucose and UDP-galactose.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marek J. Noga
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Raisa Veizaj
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rik Scharn
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Juda-El Sam
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chiara Palumbo
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | | | - Eduardo Soares
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huiqing Zhou
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J. Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- GlycoMScan B.V., 5349 AB Oss, The Netherlands
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8
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Wang Y, Yin N, Yang R, Faiola F. Pollution effects on retinal health: A review on current methodologies and findings. Toxicol Ind Health 2023; 39:336-344. [PMID: 37160417 DOI: 10.1177/07482337231174072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In our daily life, we are exposed to numerous industrial chemicals that may be harmful to the retina, which is a delicate and sensitive part of our eyes. This could lead to irreversible changes and cause retinal diseases or blindness. Current retinal environmental health studies primarily utilize animal models, isolated mammalian retinas, animal- or human-derived retinal cells, and retinal organoids, to address both pre- and postnatal exposure. However, as there is limited toxicological information available for specific populations, human induced pluripotent stem cell (hiPSC)-induced models could be effective tools to supplement such data. In order to obtain more comprehensive and reliable toxicological information, we need more appropriate models, novel evaluation methods, and computational technologies to develop portable equipment. This review mainly focused on current toxicology models with particular emphasis on retinal organoids, and it looks forward to future models, analytical methods, and equipment that can efficiently and accurately evaluate retinal toxicity.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Nuoya Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Renjun Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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9
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Abstract
Tumours exhibit notable metabolic alterations compared with their corresponding normal tissue counterparts. These metabolic alterations can support anabolic growth, enable survival in hostile environments and regulate gene expression programmes that promote malignant progression. Whether these metabolic changes are selected for during malignant transformation or can themselves be drivers of tumour initiation is unclear. However, intriguingly, many of the major bottlenecks for tumour initiation - control of cell fate, survival and proliferation - are all amenable to metabolic regulation. In this article, we review evidence demonstrating a critical role for metabolic pathways in processes that support the earliest stages of tumour development. We discuss how cell-intrinsic factors, such as the cell of origin or transforming oncogene, and cell-extrinsic factors, such as local nutrient availability, promote or restrain tumour initiation. Deeper insight into how metabolic pathways control tumour initiation will improve our ability to design metabolic interventions to limit tumour incidence.
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Affiliation(s)
- Julia S Brunner
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Okkelman IA, Dmitriev RI. Fluorescence Intensity and Fluorescence Lifetime Imaging Microscopies (FLIM) of Cell Differentiation in the Small Intestinal Organoids Using Cholera Toxin. Methods Mol Biol 2023; 2650:171-195. [PMID: 37310632 DOI: 10.1007/978-1-0716-3076-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Live cell microscopies of in vitro, ex vivo, and in vivo experimental intestinal models enable visualizing cell proliferation, differentiation, and functional cellular status in response to intrinsic and extrinsic (e.g., in the presence of microbiota) factors. While the use of transgenic animal models expressing biosensor fluorescent proteins can be laborious and not compatible with clinical samples and patient-derived organoids, the use of fluorescent dye tracers is an attractive alternative. In this protocol, we describe how the differentiation-dependent intestinal cell membrane composition can be labeled using fluorescent cholera toxin subunit B (CTX) derivatives. By using the culture of mouse adult stem cell-derived small intestinal organoids, we show that CTX can bind specific plasma membrane domains in differentiation-dependent manner. Green (Alexa Fluor 488) and red (Alexa Fluor 555) fluorescent CTX derivatives also display additional contrast in a fluorescence lifetime domain, when probed by the fluorescence lifetime imaging microscopy (FLIM), and can be used together with other fluorescent dyes and cell tracers. Importantly, CTX staining remains confined to specific regions in the organoids after fixation, which enables using it in both live cell and fixed tissue immunofluorescence microscopies.
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Affiliation(s)
- Irina A Okkelman
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medical and Health Sciences, Ghent University, Ghent, Belgium
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medical and Health Sciences, Ghent University, Ghent, Belgium.
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11
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Zhu P, Hamlish NX, Thakkar AV, Steffeck AWT, Rendleman EJ, Khan NH, Waldeck NJ, DeVilbiss AW, Martin-Sandoval MS, Mathews TP, Chandel NS, Peek CB. BMAL1 drives muscle repair through control of hypoxic NAD + regeneration in satellite cells. Genes Dev 2022; 36:149-166. [PMID: 35115380 PMCID: PMC8887128 DOI: 10.1101/gad.349066.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/05/2022] [Indexed: 01/07/2023]
Abstract
The process of tissue regeneration occurs in a developmentally timed manner, yet the role of circadian timing is not understood. Here, we identify a role for the adult muscle stem cell (MuSC)-autonomous clock in the control of muscle regeneration following acute ischemic injury. We observed greater muscle repair capacity following injury during the active/wake period as compared with the inactive/rest period in mice, and loss of Bmal1 within MuSCs leads to impaired muscle regeneration. We demonstrate that Bmal1 loss in MuSCs leads to reduced activated MuSC number at day 3 postinjury, indicating a failure to properly expand the myogenic precursor pool. In cultured primary myoblasts, we observed that loss of Bmal1 impairs cell proliferation in hypoxia (a condition that occurs in the first 1-3 d following tissue injury in vivo), as well as subsequent myofiber differentiation. Loss of Bmal1 in both cultured myoblasts and in vivo activated MuSCs leads to reduced glycolysis and premature activation of prodifferentiation gene transcription and epigenetic remodeling. Finally, hypoxic cell proliferation and myofiber formation in Bmal1-deficient myoblasts are restored by increasing cytosolic NAD+ Together, we identify the MuSC clock as a pivotal regulator of oxygen-dependent myoblast cell fate and muscle repair through the control of the NAD+-driven response to injury.
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Affiliation(s)
- Pei Zhu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Noah X Hamlish
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Abhishek Vijay Thakkar
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Adam W T Steffeck
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Nabiha H Khan
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Nathan J Waldeck
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Andrew W DeVilbiss
- Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Misty S Martin-Sandoval
- Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Thomas P Mathews
- Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Navdeep S Chandel
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Clara B Peek
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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Gebert N, Rahman S, Lewis CA, Ori A, Cheng CW. Identifying Cell-Type-Specific Metabolic Signatures Using Transcriptome and Proteome Analyses. Curr Protoc 2021; 1:e245. [PMID: 34516047 PMCID: PMC8722675 DOI: 10.1002/cpz1.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Studies in various tissues have revealed a central role of metabolic pathways in regulating adult stem cell function in tissue regeneration and tumor initiation. The unique metabolic dependences or preferences of adult stem cells, therefore, are emerging as a new category of therapeutic target. Recently, advanced methods including high-resolution metabolomics, proteomics, and transcriptomics have been developed to address the growing interest in stem cell metabolism. A practical framework integrating the omics analyses is needed to systematically perform metabolic characterization in a cell-type-specific manner. Here, we leverage recent advances in transcriptomics and proteomics research to identify cell-type-specific metabolic features by reconstructing cell identity using genes and the encoded enzymes involved in major metabolic pathways. We provide protocols for cell isolation, transcriptome and proteome analyses, and metabolite profiling and measurement. The workflow for mapping cell-type-specific metabolic signatures presented here, although initially developed for intestinal crypt cells, can be easily implemented for cell populations in other tissues, and is highly compatible with most public datasets. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Intestinal crypt isolation and cell population purification Basic Protocol 2: Transcriptome analyses for cell-type-specific metabolic gene expression Basic Protocol 3: Proteome analyses for cell-type-specific metabolic enzyme levels Basic Protocol 4: Metabolite profiling and measurement.
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Affiliation(s)
- Nadja Gebert
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Berlin-Buch, Germany
| | - Shahadat Rahman
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
| | - Caroline A. Lewis
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Alessandro Ori
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Chia-Wei Cheng
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
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Cable J, Pourquié O, Wellen KE, Finley LWS, Aulehla A, Gould AP, Teleman A, Tu WB, Garrett WS, Miguel-Aliaga I, Perrimon N, Hooper LV, Walhout AJM, Wei W, Alexandrov T, Erez A, Ralser M, Rabinowitz JD, Hemalatha A, Gutiérrez-Pérez P, Chandel NS, Rutter J, Locasale JW, Landoni JC, Christofk H. Metabolic decisions in development and disease-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:55-73. [PMID: 34414571 DOI: 10.1111/nyas.14678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022]
Abstract
There is an increasing appreciation for the role of metabolism in cell signaling and cell decision making. Precise metabolic control is essential in development, as evident by the disorders caused by mutations in metabolic enzymes. The metabolic profile of cells is often cell-type specific, changing as cells differentiate or during tumorigenesis. Recent evidence has shown that changes in metabolism are not merely a consequence of changes in cell state but that metabolites can serve to promote and/or inhibit these changes. Metabolites can link metabolic pathways with cell signaling pathways via several mechanisms, for example, by serving as substrates for protein post-translational modifications, by affecting enzyme activity via allosteric mechanisms, or by altering epigenetic markers. Unraveling the complex interactions governing metabolism, gene expression, and protein activity that ultimately govern a cell's fate will require new tools and interactions across disciplines. On March 24 and 25, 2021, experts in cell metabolism, developmental biology, and human disease met virtually for the Keystone eSymposium, "Metabolic Decisions in Development and Disease." The discussions explored how metabolites impact cellular and developmental decisions in a diverse range of model systems used to investigate normal development, developmental disorders, dietary effects, and cancer-mediated changes in metabolism.
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Affiliation(s)
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Stem Cell Institute, Boston, Massachusetts
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lydia W S Finley
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Aurelio Teleman
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - William B Tu
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Wendy Sarah Garrett
- Harvard T. H. Chan School of Public Health and Dana-Farber Cancer, Boston, Massachusetts
| | - Irene Miguel-Aliaga
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Howard Hughes Institute, Boston, Massachusetts
| | - Lora V Hooper
- Department of Immunology and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - A J Marian Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, California.,Department of Biology and Stanford ChEM-H, Stanford University, Stanford, California
| | - Theodore Alexandrov
- Structural and Computational Biology Unit and Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Anupama Hemalatha
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Navdeep S Chandel
- Department of Medicine, Robert H. Lurie Cancer Center, Chicago, Illinois.,Department of Biochemistry and Molecular Genetics, Robert H. Lurie Cancer Center Metabolomics Core, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jared Rutter
- Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Juan C Landoni
- Research Program in Stem Cells and Metabolism, University of Helsinki, Helsinki, Finland
| | - Heather Christofk
- Departments of Biological Chemistry and Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
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