1
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Horn PJ, Chapman KD. Imaging plant metabolism in situ. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1654-1670. [PMID: 37889862 PMCID: PMC10938046 DOI: 10.1093/jxb/erad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
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Affiliation(s)
- Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
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2
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Lork AA, Rabasco S, Ernst C, du Toit A, Rizzoli SO, Phan NTN. Subcellular protein turnover in human neural progenitor cells revealed by correlative electron microscopy and nanoscale secondary ion mass spectrometry imaging. Chem Sci 2024; 15:3311-3322. [PMID: 38425528 PMCID: PMC10901485 DOI: 10.1039/d3sc05629e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024] Open
Abstract
Protein turnover is a critical process for accurate cellular function, in which damaged proteins in the cells are gradually replaced with newly synthesized ones. Many previous studies on cellular protein turnover have used stable isotopic labelling by amino acids in cell culture (SILAC), followed by proteomic bulk analysis. However, this approach does not take into account the heterogeneity observed at the single-cell and subcellular levels. To address this, we investigated the protein turnover of neural progenitor cells at the subcellular resolution, using correlative TEM and NanoSIMS imaging, relying on a pulse-chase analysis of isotopically-labelled protein precusors. Cellular protein turnover was found significantly heterogenous across individual organelles, which indicates a possible relation between protein turnover and subcellular activity. In addition, different isotopically-labelled amino acids provided different turnover patterns, in spite of all being protein precursors, suggesting that they undergo distinct protein synthesis and metabolic pathways at the subcellular level.
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Affiliation(s)
- Alicia A Lork
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Carl Ernst
- Human Genetics, McGill University H4H1R3 Montreal Canada
| | - André du Toit
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Center for Biostructural Imaging of Neurodegeneration Göttingen Germany
| | - Nhu T N Phan
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
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3
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Yuan F, Li Y, Zhou X, Meng P, Zou P. Spatially resolved mapping of proteome turnover dynamics with subcellular precision. Nat Commun 2023; 14:7217. [PMID: 37940635 PMCID: PMC10632371 DOI: 10.1038/s41467-023-42861-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
Cellular activities are commonly associated with dynamic proteomic changes at the subcellular level. Although several techniques are available to quantify whole-cell protein turnover dynamics, such measurements often lack sufficient spatial resolution at the subcellular level. Herein, we report the development of prox-SILAC method that combines proximity-dependent protein labeling (APEX2/HRP) with metabolic incorporation of stable isotopes (pulse-SILAC) to map newly synthesized proteins with subcellular spatial resolution. We apply prox-SILAC to investigate proteome dynamics in the mitochondrial matrix and the endoplasmic reticulum (ER) lumen. Our analysis reveals a highly heterogeneous distribution in protein turnover dynamics within macromolecular machineries such as the mitochondrial ribosome and respiratory complexes I-V, thus shedding light on their mechanism of hierarchical assembly. Furthermore, we investigate the dynamic changes of ER proteome when cells are challenged with stress or undergoing stimulated differentiation, identifying subsets of proteins with unique patterns of turnover dynamics, which may play key regulatory roles in alleviating stress or promoting differentiation. We envision that prox-SILAC could be broadly applied to profile protein turnover at various subcellular compartments, under both physiological and pathological conditions.
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Affiliation(s)
- Feng Yuan
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Yi Li
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Peiyuan Meng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
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4
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Georgiev SV, Rizzoli SO. The long-loop recycling (LLR) of synaptic components as a question of economics. Mol Cell Neurosci 2023; 126:103862. [PMID: 37236414 DOI: 10.1016/j.mcn.2023.103862] [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: 02/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The pre- and post-synaptic compartments contain a variety of molecules that are known to recycle between the plasma membrane and intracellular organelles. The recycling steps have been amply described in functional terms, with, for example, synaptic vesicle recycling being essential for neurotransmitter release, and postsynaptic receptor recycling being a fundamental feature of synaptic plasticity. However, synaptic protein recycling may also serve a more prosaic role, simply ensuring the repeated use of specific components, thereby minimizing the energy expenditure on the synthesis of synaptic proteins. This type of process has been recently described for components of the extracellular matrix, which undergo long-loop recycling (LLR), to and from the cell body. Here we suggest that the energy-saving recycling of synaptic components may be more widespread than is generally acknowledged, potentially playing a role in both synaptic vesicle protein usage and postsynaptic receptor metabolism.
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Affiliation(s)
- Svilen Veselinov Georgiev
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Germany; International Max Planck Research School for Neuroscience, Göttingen, Germany.
| | - Silvio O Rizzoli
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, Germany; Biostructural Imaging of Neurodegeneration (BIN) Center, Göttingen, Germany; Excellence Cluster Multiscale Bioimaging, Göttingen, Germany.
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5
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Liu J, Hu W, Han Y, Nie H. Recent advances in mass spectrometry imaging of single cells. Anal Bioanal Chem 2023:10.1007/s00216-023-04774-9. [PMID: 37269305 DOI: 10.1007/s00216-023-04774-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
Mass spectrometry imaging (MSI) is a sensitive, specific, label-free imaging analysis technique that can simultaneously obtain the spatial distribution, relative content, and structural information of hundreds of biomolecules in cells and tissues, such as lipids, small drug molecules, peptides, proteins, and other compounds. The study of molecular mapping of single cells can reveal major scientific issues such as the activity pattern of living organisms, disease pathogenesis, drug-targeted therapy, and cellular heterogeneity. Applying MSI technology to the molecular mapping of single cells can provide new insights and ideas for the study of single-cell metabolomics. This review aims to provide an informative resource for those in the MSI community who are interested in single-cell imaging. Particularly, we discuss advances in imaging schemes and sample preparation, instrumentation improvements, data processing and analysis, and 3D MSI over the past few years that have allowed MSI to emerge as a powerful technique in the molecular imaging of single cells. Also, we highlight some of the most cutting-edge studies in single-cell MSI, demonstrating the future potential of single-cell MSI. Visualizing molecular distribution at the single-cell or even sub-cellular level can provide us with richer cell information, which strongly contributes to advancing research fields such as biomedicine, life sciences, pharmacodynamic testing, and metabolomics. At the end of the review, we summarize the current development of single-cell MSI technology and look into the future of this technology.
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Affiliation(s)
- Jikun Liu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Analytical Instrumental Center, Peking University, Beijing, 100871, China
| | - Wenya Hu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Analytical Instrumental Center, Peking University, Beijing, 100871, China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China.
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Analytical Instrumental Center, Peking University, Beijing, 100871, China.
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6
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Wertheim BM, Wang RS, Guillermier C, Hütter CV, Oldham WM, Menche J, Steinhauser ML, Maron BA. Proline and glucose metabolic reprogramming supports vascular endothelial and medial biomass in pulmonary arterial hypertension. JCI Insight 2023; 8:163932. [PMID: 36626231 PMCID: PMC9977503 DOI: 10.1172/jci.insight.163932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
In pulmonary arterial hypertension (PAH), inflammation promotes a fibroproliferative pulmonary vasculopathy. Reductionist studies emphasizing single biochemical reactions suggest a shift toward glycolytic metabolism in PAH; however, key questions remain regarding the metabolic profile of specific cell types within PAH vascular lesions in vivo. We used RNA-Seq to profile the transcriptome of pulmonary artery endothelial cells (PAECs) freshly isolated from an inflammatory vascular injury model of PAH ex vivo, and these data were integrated with information from human gene ontology pathways. Network medicine was then used to map all aa and glucose pathways to the consolidated human interactome, which includes data on 233,957 physical protein-protein interactions. Glucose and proline pathways were significantly close to the human PAH disease module, suggesting that these pathways are functionally relevant to PAH pathobiology. To test this observation in vivo, we used multi-isotope imaging mass spectrometry to map and quantify utilization of glucose and proline in the PAH pulmonary vasculature at subcellular resolution. Our findings suggest that elevated glucose and proline avidity underlie increased biomass in PAECs and the media of fibrosed PAH pulmonary arterioles. Overall, these data show that anabolic utilization of glucose and proline are fundamental to the vascular pathology of PAH.
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Affiliation(s)
| | - Rui-Sheng Wang
- Division of Cardiovascular Medicine, Department of Medicine.,Channing Division of Network Medicine, Department of Medicine; and
| | - Christelle Guillermier
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Center for NanoImaging, Cambridge, Massachusetts, USA
| | - Christiane Vr Hütter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - William M Oldham
- Division of Pulmonary and Critical Medicine, Department of Medicine
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria.,Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Matthew L Steinhauser
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Center for NanoImaging, Cambridge, Massachusetts, USA.,Division of Cardiovascular Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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7
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Fornasiero EF, Savas JN. Determining and interpreting protein lifetimes in mammalian tissues. Trends Biochem Sci 2023; 48:106-118. [PMID: 36163144 PMCID: PMC9868050 DOI: 10.1016/j.tibs.2022.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
The orchestration of protein production and degradation, and the regulation of protein lifetimes, play a central role in the majority of biological processes. Recent advances in proteomics have enabled the estimation of protein half-lives for thousands of proteins in vivo. What is the utility of these measurements, and how can they be leveraged to interpret the proteome changes occurring during development, aging, and disease? This opinion article summarizes leading technical approaches and highlights their strengths and weaknesses. We also disambiguate frequently used terminology, illustrate recent mechanistic insights, and provide guidance for interpreting and validating protein turnover measurements. Overall, protein lifetimes, coupled to estimates of protein levels, are essential for obtaining a deep understanding of mammalian biology and the basic processes defining life itself.
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Affiliation(s)
- Eugenio F Fornasiero
- Department of Neuro-Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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8
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Becquart C, Stulz R, Thomen A, Dost M, Najafinobar N, Dahlén A, Andersson S, Ewing AG, Kurczy ME. Intracellular Absolute Quantification of Oligonucleotide Therapeutics by NanoSIMS. Anal Chem 2022; 94:10549-10556. [PMID: 35830231 DOI: 10.1021/acs.analchem.2c02111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antisense oligonucleotide (ASO)-based therapeutics hold great potential for the treatment of a variety of diseases. Therefore, a better understanding of cellular delivery, uptake, and trafficking mechanisms of ASOs is highly important for early-stage drug discovery. In particular, understanding the biodistribution and quantifying the abundance of ASOs at the subcellular level are needed to fully characterize their activity. Here, we used a combination of electron microscopy and NanoSIMS to assess the subcellular concentrations of a 34S-labeled GalNAc-ASO and a naked ASO in the organelles of primary human hepatocytes. We first cross-validated the method by including a 127I-labeled ASO, finding that the absolute concentration of the lysosomal ASO using two independent labeling strategies gave matching results, demonstrating the strength of our approach. This work also describes the preparation of external standards for absolute quantification by NanoSIMS. For both the 34S and 127I approaches used for our quantification methodology, we established the limit of detection (5 and 2 μM, respectively) and the lower limit of quantification (14 and 5 μM, respectively).
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Affiliation(s)
- Cécile Becquart
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Rouven Stulz
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | | | - Maryam Dost
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Neda Najafinobar
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Michael E Kurczy
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
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9
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A Reliable Approach for Revealing Molecular Targets in Secondary Ion Mass Spectrometry. Int J Mol Sci 2022; 23:ijms23094615. [PMID: 35563005 PMCID: PMC9103194 DOI: 10.3390/ijms23094615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/10/2022] Open
Abstract
Nano secondary ion mass spectrometry (nanoSIMS) imaging is a rapidly growing field in biological sciences, which enables investigators to describe the chemical composition of cells and tissues with high resolution. One of the major challenges of nanoSIMS is to identify specific molecules or organelles, as these are not immediately recognizable in nanoSIMS and need to be revealed by SIMS-compatible probes. Few laboratories have generated such probes, and none are commercially available. To address this, we performed a systematic study of probes initially developed for electron microscopy. Relying on nanoscale SIMS, we found that antibodies coupled to 6 nm gold particles are surprisingly efficient in terms of labeling specificity while offering a reliable detection threshold. These tools enabled accurate visualization and sample analysis and were easily employed in correlating SIMS with other imaging approaches, such as fluorescence microscopy. We conclude that antibodies conjugated to moderately sized gold particles are promising tools for SIMS imaging.
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10
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Islimye E, Girard V, Gould AP. Functions of Stress-Induced Lipid Droplets in the Nervous System. Front Cell Dev Biol 2022; 10:863907. [PMID: 35493070 PMCID: PMC9047859 DOI: 10.3389/fcell.2022.863907] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
Lipid droplets are highly dynamic intracellular organelles that store neutral lipids such as cholesteryl esters and triacylglycerols. They have recently emerged as key stress response components in many different cell types. Lipid droplets in the nervous system are mostly observed in vivo in glia, ependymal cells and microglia. They tend to become more numerous in these cell types and can also form in neurons as a consequence of ageing or stresses involving redox imbalance and lipotoxicity. Abundant lipid droplets are also a characteristic feature of several neurodegenerative diseases. In this minireview, we take a cell-type perspective on recent advances in our understanding of lipid droplet metabolism in glia, neurons and neural stem cells during health and disease. We highlight that a given lipid droplet subfunction, such as triacylglycerol lipolysis, can be physiologically beneficial or harmful to the functions of the nervous system depending upon cellular context. The mechanistic understanding of context-dependent lipid droplet functions in the nervous system is progressing apace, aided by new technologies for probing the lipid droplet proteome and lipidome with single-cell type precision.
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11
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Monji A, Zhang Y, Kumar GN, Guillermier C, Kim S, Olenchock B, Steinhauser ML. A Cycle of Inflammatory Adipocyte Death and Regeneration in Murine Adipose Tissue. Diabetes 2022; 71:412-423. [PMID: 35040481 PMCID: PMC8893943 DOI: 10.2337/db20-1306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/19/2021] [Indexed: 11/13/2022]
Abstract
Adipose tissue (AT) expands by a combination of two fundamental cellular mechanisms: hypertrophic growth of existing adipocytes or through generation of new adipocytes, also known as hyperplastic growth. Multiple lines of evidence suggest a limited capacity for hyperplastic growth of AT in adulthood and that adipocyte number is relatively stable, even with fluctuations in AT mass. If the adipocyte number is stable in adulthood, despite well-documented birth and death of adipocytes, then this would suggest that birth may be coupled to death in a regenerative cycle. To test this hypothesis, we examined the dynamics of birth of new fat cells in relationship to adipocyte death by using high-fidelity stable isotope tracer methods in C57Bl6 mice. We discovered birth of new adipocytes at higher frequency in histological proximity to dead adipocytes. In diet-induced obesity, adipogenesis surged after an adipocyte death peak beyond 8 weeks of high-fat feeding. Through transcriptional analyses of AT and fractionated adipocytes, we found that the dominant cell death signals were inflammasome related. Proinflammatory signals were particularly evident in hypertrophied adipocytes or with deletion of a constitutive oxygen sensor and inhibitor of hypoxia-inducible factor, Egln1. We leveraged the potential role for the inflammasome in adipocyte death to test the adipocyte death-birth hypothesis, finding that caspase 1 loss of function attenuated adipocyte death and birth in murine visceral AT. These data collectively point to a regenerative cycle of adipocyte death and birth as a driver of adipogenesis in adult murine AT.
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Affiliation(s)
- Akio Monji
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yang Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - G.V. Naveen Kumar
- Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Christelle Guillermier
- Harvard Medical School, Boston, MA
- Center for NanoImaging, Division of Genetics, Brigham and Women’s Hospital, Boston, MA
| | - Soomin Kim
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Benjamin Olenchock
- Division of Cardiology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Matthew L. Steinhauser
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Center for NanoImaging, Division of Genetics, Brigham and Women’s Hospital, Boston, MA
- Division of Cardiology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Corresponding author: Matthew L. Steinhauser,
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12
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Mohan S, Sampognaro PJ, Argouarch AR, Maynard JC, Welch M, Patwardhan A, Courtney EC, Zhang J, Mason A, Li KH, Huang EJ, Seeley WW, Miller BL, Burlingame A, Jacobson MP, Kao AW. Processing of progranulin into granulins involves multiple lysosomal proteases and is affected in frontotemporal lobar degeneration. Mol Neurodegener 2021; 16:51. [PMID: 34344440 PMCID: PMC8330050 DOI: 10.1186/s13024-021-00472-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/13/2021] [Indexed: 11/24/2022] Open
Abstract
Background Progranulin loss-of-function mutations are linked to frontotemporal lobar degeneration with TDP-43 positive inclusions (FTLD-TDP-Pgrn). Progranulin (PGRN) is an intracellular and secreted pro-protein that is proteolytically cleaved into individual granulin peptides, which are increasingly thought to contribute to FTLD-TDP-Pgrn disease pathophysiology. Intracellular PGRN is processed into granulins in the endo-lysosomal compartments. Therefore, to better understand the conversion of intracellular PGRN into granulins, we systematically tested the ability of different classes of endo-lysosomal proteases to process PGRN at a range of pH setpoints. Results In vitro cleavage assays identified multiple enzymes that can process human PGRN into multi- and single-granulin fragments in a pH-dependent manner. We confirmed the role of cathepsin B and cathepsin L in PGRN processing and showed that these and several previously unidentified lysosomal proteases (cathepsins E, G, K, S and V) are able to process PGRN in distinctive, pH-dependent manners. In addition, we have demonstrated a new role for asparagine endopeptidase (AEP) in processing PGRN, with AEP having the unique ability to liberate granulin F from the pro-protein. Brain tissue from individuals with FTLD-TDP-Pgrn showed increased PGRN processing to granulin F and increased AEP activity in degenerating brain regions but not in regions unaffected by disease. Conclusions This study demonstrates that multiple lysosomal proteases may work in concert to liberate multi-granulin fragments and granulins. It also implicates both AEP and granulin F in the neurobiology of FTLD-TDP-Pgrn. Modulating progranulin cleavage and granulin production may represent therapeutic strategies for FTLD-Pgrn and other progranulin-related diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00472-1.
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Affiliation(s)
- Swetha Mohan
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Paul J Sampognaro
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Andrea R Argouarch
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Jason C Maynard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, USA
| | - Mackenzie Welch
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Anand Patwardhan
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Emma C Courtney
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Jiasheng Zhang
- Department of Pathology, University of California, San Francisco, California, 94143, USA
| | - Amanda Mason
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, USA
| | - Eric J Huang
- Department of Pathology, University of California, San Francisco, California, 94143, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Bruce L Miller
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, USA
| | - Mathew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, USA
| | - Aimee W Kao
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, California, 94143, USA.
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Yester JW, Liu H, Gyngard F, Ammanamanchi N, Little KC, Thomas D, Sullivan MLG, Lal S, Steinhauser ML, Kühn B. Use of stable isotope-tagged thymidine and multi-isotope imaging mass spectrometry (MIMS) for quantification of human cardiomyocyte division. Nat Protoc 2021; 16:1995-2022. [PMID: 33627842 PMCID: PMC8221415 DOI: 10.1038/s41596-020-00477-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
Quantification of cellular proliferation in humans is important for understanding biology and responses to injury and disease. However, existing methods require administration of tracers that cannot be ethically administered in humans. We present a protocol for the direct quantification of cellular proliferation in human hearts. The protocol involves administration of non-radioactive, non-toxic stable isotope 15Nitrogen-enriched thymidine (15N-thymidine), which is incorporated into DNA during S-phase, in infants with tetralogy of Fallot, a common form of congenital heart disease. Infants with tetralogy of Fallot undergo surgical repair, which requires the removal of pieces of myocardium that would otherwise be discarded. This protocol allows for the quantification of cardiomyocyte proliferation in this discarded tissue. We quantitatively analyzed the incorporation of 15N-thymidine with multi-isotope imaging spectrometry (MIMS) at a sub-nuclear resolution, which we combined with correlative confocal microscopy to quantify formation of binucleated cardiomyocytes and cardiomyocytes with polyploid nuclei. The entire protocol spans 3-8 months, which is dependent on the timing of surgical repair, and 3-4.5 researcher days. This protocol could be adapted to study cellular proliferation in a variety of human tissues.
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Affiliation(s)
- Jessie W Yester
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Honghai Liu
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Frank Gyngard
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Niyatie Ammanamanchi
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Kathryn C Little
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- UPMC Shadyside Hospital, Pittsburgh, PA, USA
| | - Dawn Thomas
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Mara L G Sullivan
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Department of Cell Biology, Pittsburgh, PA, USA
| | - Sean Lal
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Division of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew L Steinhauser
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA.
- UPMC Heart and Vascular Institute, UPMC Presbyterian, Pittsburgh, PA, USA.
- Aging Institute, University of Pittsburgh, Bridgeside Point 1, Pittsburgh, PA, USA.
| | - Bernhard Kühn
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA.
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Narendra DP, Steinhauser ML. Metabolic Analysis at the Nanoscale with Multi-Isotope Imaging Mass Spectrometry (MIMS). CURRENT PROTOCOLS IN CELL BIOLOGY 2020; 88:e111. [PMID: 32706155 PMCID: PMC7484994 DOI: 10.1002/cpcb.111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Incorporation of a stable-isotope metabolic tracer into cells or tissue can be followed at submicron resolution by multi-isotope imaging mass spectrometry (MIMS), a form of imaging secondary ion microscopy optimized for accurate isotope ratio measurement from microvolumes of sample (as small as ∼30 nm across). In a metabolic MIMS experiment, a cell or animal is metabolically labeled with a tracer containing a stable isotope. Relative accumulation of the heavy isotope in the fixed sample is then measured as an increase over its natural abundance by MIMS. MIMS has been used to measure protein turnover in single organelles, track cellular division in vivo, visualize sphingolipid rafts on the plasma membrane, and measure dopamine incorporation into dense-core vesicles, among other biological applications. In this article, we introduce metabolic analysis using NanoSIMS by focusing on two specific applications: quantifying protein turnover in single organelles of cultured cells and tracking cell replication in mouse tissues in vivo. These examples illustrate the versatility of metabolic analysis with MIMS. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Metabolic labeling for MIMS Basic Protocol 2: Embedding of samples for correlative transmission electron microscopy and MIMS with a genetically encoded reporter Alternate Protocol: Embedding of samples for correlative light microscopy and MIMS Support Protocol: Preparation of silicon wafers as sample supports for MIMS Basic Protocol 3: Analysis of MIMS data.
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Affiliation(s)
- Derek P Narendra
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Matthew L Steinhauser
- Department of Medicine, Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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15
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Zhang Y, Guillermier C, De Raedt T, Cox AG, Maertens O, Yimlamai D, Lun M, Whitney A, Maas RL, Goessling W, Cichowski K, Steinhauser ML. Imaging Mass Spectrometry Reveals Tumor Metabolic Heterogeneity. iScience 2020; 23:101355. [PMID: 32712466 PMCID: PMC7390776 DOI: 10.1016/j.isci.2020.101355] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/10/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
Malignant tumors exhibit high degrees of genomic heterogeneity at the cellular level, leading to the view that subpopulations of tumor cells drive growth and treatment resistance. To examine the degree to which tumors also exhibit metabolic heterogeneity at the level of individual cells, we employed multi-isotope imaging mass spectrometry (MIMS) to quantify utilization of stable isotopes of glucose and glutamine along with a label for cell division. Mouse models of melanoma and malignant peripheral nerve sheath tumors (MPNSTs) exhibited striking heterogeneity of substrate utilization, evident in both proliferating and non-proliferating cells. We identified a correlation between metabolic heterogeneity, proliferation, and therapeutic resistance. Heterogeneity in metabolic substrate usage as revealed by incorporation of glucose and glutamine tracers is thus a marker for tumor proliferation. Collectively, our data demonstrate that MIMS provides a powerful tool with which to dissect metabolic functions of individual cells within the native tumor environment.
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Affiliation(s)
- Yang Zhang
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christelle Guillermier
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Thomas De Raedt
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Andrew G Cox
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ophelia Maertens
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Dean Yimlamai
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Boston, MA, USA
| | - Mingyue Lun
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Adam Whitney
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Richard L Maas
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Wolfram Goessling
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Karen Cichowski
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Ludwig Center, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - Matthew L Steinhauser
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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16
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Telpoukhovskaia MA, Liu K, Sayed FA, Etchegaray JI, Xie M, Zhan L, Li Y, Zhou Y, Le D, Bahr BA, Bogyo M, Ding S, Gan L. Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. Sci Rep 2020; 10:13688. [PMID: 32792571 PMCID: PMC7426857 DOI: 10.1038/s41598-020-70534-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Patients with frontotemporal dementia (FTD) resulting from granulin (GRN) haploinsufficiency have reduced levels of progranulin and exhibit dysregulation in inflammatory and lysosomal networks. Microglia produce high levels of progranulin, and reduction of progranulin in microglia alone is sufficient to recapitulate inflammation, lysosomal dysfunction, and hyperproliferation in a cell-autonomous manner. Therefore, targeting microglial dysfunction caused by progranulin insufficiency represents a potential therapeutic strategy to manage neurodegeneration in FTD. Limitations of current progranulin-enhancing strategies necessitate the discovery of new targets. To identify compounds that can reverse microglial defects in Grn-deficient mouse microglia, we performed a compound screen coupled with high throughput sequencing to assess key transcriptional changes in inflammatory and lysosomal pathways. Positive hits from this initial screen were then further narrowed down based on their ability to rescue cathepsin activity, a critical biochemical readout of lysosomal capacity. The screen identified nor-binaltorphimine dihydrochloride (nor-BNI) and dibutyryl-cAMP, sodium salt (DB-cAMP) as two phenotypic modulators of progranulin deficiency. In addition, nor-BNI and DB-cAMP also rescued cell cycle abnormalities in progranulin-deficient cells. These data highlight the potential of a transcription-based platform for drug screening, and advance two novel lead compounds for FTD.
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Affiliation(s)
- Maria A Telpoukhovskaia
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Kai Liu
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Faten A Sayed
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA.,Neuroscience Graduate Program, University of California, San Francisco, CA, 94158, USA
| | | | - Min Xie
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Lihong Zhan
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Yaqiao Li
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Yungui Zhou
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - David Le
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Ben A Bahr
- Biotechnology Research and Training Center, University of North Carolina At Pembroke, Pembroke, NC, 28372, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Sheng Ding
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA. .,Department of Neurology, University of California, San Francisco, CA, 94158, USA. .,Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
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