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Sánchez-Ramírez E, Ung TPL, Stringari C, Aguilar-Arnal L. Emerging Functional Connections Between Metabolism and Epigenetic Remodeling in Neural Differentiation. Mol Neurobiol 2024; 61:6688-6707. [PMID: 38340204 PMCID: PMC11339152 DOI: 10.1007/s12035-024-04006-w] [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: 09/13/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Stem cells possess extraordinary capacities for self-renewal and differentiation, making them highly valuable in regenerative medicine. Among these, neural stem cells (NSCs) play a fundamental role in neural development and repair processes. NSC characteristics and fate are intricately regulated by the microenvironment and intracellular signaling. Interestingly, metabolism plays a pivotal role in orchestrating the epigenome dynamics during neural differentiation, facilitating the transition from undifferentiated NSC to specialized neuronal and glial cell types. This intricate interplay between metabolism and the epigenome is essential for precisely regulating gene expression patterns and ensuring proper neural development. This review highlights the mechanisms behind metabolic regulation of NSC fate and their connections with epigenetic regulation to shape transcriptional programs of stemness and neural differentiation. A comprehensive understanding of these molecular gears appears fundamental for translational applications in regenerative medicine and personalized therapies for neurological conditions.
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Affiliation(s)
- Edgar Sánchez-Ramírez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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2
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Miller MJ, Akter D, Mahmud J, Chan GC. Human cytomegalovirus modulates mTORC1 to redirect mRNA translation within quiescently infected monocytes. J Virol 2024; 98:e0188823. [PMID: 38289104 PMCID: PMC10878035 DOI: 10.1128/jvi.01888-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/21/2024] Open
Abstract
Human cytomegalovirus (HCMV) utilizes peripheral blood monocytes as a means to systemically disseminate throughout the host. Following viral entry, HCMV stimulates non-canonical Akt signaling leading to the activation of mTORC1 and the subsequent translation of select antiapoptotic proteins within infected monocytes. However, the full extent to which the HCMV-initiated Akt/mTORC1 signaling axis reshapes the monocyte translatome is unclear. We found HCMV entry alone was able to stimulate widescale changes to mRNA translation levels and that inhibition of mTOR, a component of mTORC1, dramatically attenuated HCMV-induced protein synthesis. Although monocytes treated with normal myeloid growth factors also exhibited increased levels of translation, mTOR inhibition had no effect, suggesting HCMV activation of mTOR stimulates the acquisition of a unique translatome within infected monocytes. Indeed, polyribosomal profiling of HCMV-infected monocytes identified distinct prosurvival transcripts that were preferentially loaded with ribosomes when compared to growth factor-treated cells. Sirtuin 1 (SIRT1), a deacetylase that exerts prosurvival effects through regulation of the PI3K/Akt pathway, was found to be highly enriched following HCMV infection in an mTOR-dependent manner. Importantly, SIRT1 inhibition led to the death of HCMV-infected monocytes while having minimal effect on uninfected cells. SIRT1 also supported a positive feedback loop to sustain Akt/mTORC1 signaling following viral entry. Taken together, HCMV profoundly reshapes mRNA translation in an mTOR-dependent manner to enhance the synthesis of select factors necessary for the survival of infected monocytes.IMPORTANCEHuman cytomegalovirus (HCMV) infection is a significant cause of morbidity and mortality among the immunonaïve and immunocompromised. Peripheral blood monocytes are a major cell type responsible for disseminating the virus from the initial site of infection. In order for monocytes to mediate viral spread within the host, HCMV must subvert the naturally short lifespan of these cells. In this study, we performed polysomal profiling analysis, which demonstrated HCMV to globally redirect mRNA translation toward the synthesis of cellular prosurvival factors within infected monocytes. Specifically, HCMV entry into monocytes induced the translation of cellular SIRT1 to generate an antiapoptotic state. Defining the precise mechanisms through which HCMV stimulates survival will provide insight into novel anti-HCMV drugs able to target infected monocytes.
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Affiliation(s)
- Michael J. Miller
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Dilruba Akter
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jamil Mahmud
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Gary C. Chan
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
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Singh C, Jin B, Shrestha N, Markhard AL, Panda A, Calvo SE, Deik A, Pan X, Zuckerman AL, Ben Saad A, Corey KE, Sjoquist J, Osganian S, AminiTabrizi R, Rhee EP, Shah H, Goldberger O, Mullen AC, Cracan V, Clish CB, Mootha VK, Goodman RP. ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits. Cell Metab 2024; 36:144-158.e7. [PMID: 38101397 PMCID: PMC10842884 DOI: 10.1016/j.cmet.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Common genetic variants in glucokinase regulator (GCKR), which encodes GKRP, a regulator of hepatic glucokinase (GCK), influence multiple metabolic traits in genome-wide association studies (GWASs), making GCKR one of the most pleiotropic GWAS loci in the genome. It is unclear why. Prior work has demonstrated that GCKR influences the hepatic cytosolic NADH/NAD+ ratio, also referred to as reductive stress. Here, we demonstrate that reductive stress is sufficient to activate the transcription factor ChREBP and necessary for its activation by the GKRP-GCK interaction, glucose, and ethanol. We show that hepatic reductive stress induces GCKR GWAS traits such as increased hepatic fat, circulating FGF21, and circulating acylglycerol species, which are also influenced by ChREBP. We define the transcriptional signature of hepatic reductive stress and show its upregulation in fatty liver disease and downregulation after bariatric surgery in humans. These findings highlight how a GCKR-reductive stress-ChREBP axis influences multiple human metabolic traits.
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Affiliation(s)
- Charandeep Singh
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Byungchang Jin
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nirajan Shrestha
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew L Markhard
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Apekshya Panda
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xingxiu Pan
- The Scintillon Institute, San Diego, CA 92121, USA
| | - Austin L Zuckerman
- The Scintillon Institute, San Diego, CA 92121, USA; Program in Mathematics and Science Education, University of California, San Diego, La Jolla, CA 92093; Program in Mathematics and Science Education, San Diego State University, San Diego, CA 92120
| | - Amel Ben Saad
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathleen E Corey
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia Sjoquist
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephanie Osganian
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roya AminiTabrizi
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Eugene P Rhee
- Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Nephrology Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, the University of Chicago, Chicago, IL 60637, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alan C Mullen
- Division of Gastroenterology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentin Cracan
- The Scintillon Institute, San Diego, CA 92121, USA; Department of Chemistry, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Russell P Goodman
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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4
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Gu C, Zhou Q, Hu X, Ge X, Hou M, Wang W, Liu H, Shi Q, Xu Y, Zhu X, Yang H, Chen X, Liu T, He F. Melatonin rescues the mitochondrial function of bone marrow-derived mesenchymal stem cells and improves the repair of osteoporotic bone defect in ovariectomized rats. J Pineal Res 2024; 76:e12924. [PMID: 37941528 DOI: 10.1111/jpi.12924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Osteoporotic bone defects, a severe complication of osteoporosis, are distinguished by a delayed bone healing process and poor repair quality. While bone marrow-derived mesenchymal stem cells (BMMSCs) are the primary origin of bone-forming osteoblasts, their mitochondrial function is impaired, leading to inadequate bone regeneration in osteoporotic patients. Melatonin is well-known for its antioxidant properties and regulation on bone metabolism. The present study postulated that melatonin has the potential to enhance the repair of osteoporotic bone defects by restoring the mitochondrial function of BMMSCs. In vitro administration of melatonin at varying concentrations (0.01, 1, and 100 μM) demonstrated a significant dose-dependent improvement in the mitochondrial function of BMMSCs obtained from ovariectomized rats (OVX-BMMSCs), as indicated by an elevation in mitochondrial membrane potential, adenosine triphosphate synthesis and expression of mitochondrial respiratory chain factors. Melatonin reduced the level of mitochondrial superoxide by activating the silent information regulator type 1 (SIRT1) and its downstream antioxidant enzymes, particularly superoxide dismutase 2 (SOD2). The protective effects of melatonin were found to be nullified upon silencing of Sirt1 or Sod2, underscoring the crucial role of the SIRT1-SOD2 axis in the melatonin-induced enhancement of mitochondrial energy metabolism in OVX-BMMSCs. To achieve a sustained and localized release of melatonin, silk fibroin scaffolds loaded with melatonin (SF@MT) were fabricated. The study involved the surgical creation of bilateral femur defects in OVX rats, followed by the implantation of SF@MT scaffolds. The results indicated that the application of melatonin partially restored the mitochondrial energy metabolism and osteogenic differentiation of OVX-BMMSCs by reinstating mitochondrial redox homeostasis. These findings suggest that the localized administration of melatonin through bone implants holds potential as a therapeutic approach for addressing osteoporotic bone defects.
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Affiliation(s)
- Chao Gu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
- Department of Orthopaedics, Suzhou Dushu Lake Hospital, Suzhou, China
| | - Quan Zhou
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xiayu Hu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xiaoyang Ge
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Mingzhuang Hou
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Wenhao Wang
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Hao Liu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Qin Shi
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Yong Xu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xuesong Zhu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huilin Yang
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xi Chen
- Department of Pathology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Tao Liu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fan He
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Orthopaedic Institute, Suzhou Medical College of Soochow University, Soochow University, Suzhou, China
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Schuty B, Martínez S, Guerra A, Lecumberry F, Magliano J, Malacrida L. Quantitative melanoma diagnosis using spectral phasor analysis of hyperspectral imaging from label-free slices. Front Oncol 2023; 13:1296826. [PMID: 38162497 PMCID: PMC10756080 DOI: 10.3389/fonc.2023.1296826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Melanoma diagnosis traditionally relies on microscopic examination of hematoxylin and eosin (H&E) slides by dermatopathologists to search for specific architectural and cytological features. Unfortunately, no single molecular marker exists to reliably differentiate melanoma from benign lesions such as nevi. This study explored the potential of autofluorescent molecules within tissues to provide molecular fingerprints indicative of degenerated melanocytes in melanoma. Methods Using hyperspectral imaging (HSI) and spectral phasor analysis, we investigated autofluorescence patterns in melanoma compared to intradermal nevi. Using UV excitation and a commercial spectral confocal microscope, we acquired label-free HSI data from the whole-slice samples. Results Our findings revealed distinct spectral phasor distributions between melanoma and intradermal nevi, with melanoma displaying a broader phasor phase distribution, signifying a more heterogeneous autofluorescence pattern. Notably, longer wavelengths associated with larger phases correlated with regions identified as melanoma by expert dermatopathologists using H&E staining. Quantitative analysis of phase and modulation histograms within the phasor clusters of five melanomas (with Breslow thicknesses ranging from 0.5 mm to 6 mm) and five intradermal nevi consistently highlighted differences between the two groups. We further demonstrated the potential for the discrimination of several melanocytic lesions using center-of-mass comparisons of phase and modulation variables. Remarkably, modulation versus phase center of mass comparisons revealed strong statistical significance among the groups. Additionally, we identified the molecular endogenous markers responsible for tissue autofluorescence, including collagen, elastin, NADH, FAD, and melanin. In melanoma, autofluorescence is characterized by a higher phase contribution, indicating an increase in FAD and melanin in melanocyte nests. In contrast, NADH, elastin, and collagen dominate the autofluorescence of the nevus. Discussion This work underscores the potential of autofluorescence and HSI-phasor analysis as valuable tools for quantifying tissue molecular fingerprints, thereby supporting more effective and quantitative melanoma diagnosis.
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Affiliation(s)
- Bruno Schuty
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
| | - Sofía Martínez
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Analía Guerra
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico Lecumberry
- Instituto de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Julio Magliano
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Doan TP, Zhang M, Park EJ, Ponce-Zea JE, Mai VH, Cho HM, Pham HTT, Oh WK. Oxindole and Benzoxazinone Alkaloids from the Seeds of Persea americana (Avocado) and Their SIRT1 Stimulatory Activity. JOURNAL OF NATURAL PRODUCTS 2023; 86:2270-2282. [PMID: 37792632 DOI: 10.1021/acs.jnatprod.3c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Persea americana Mill. (Lauraceae), commonly known as avocado, is a well-known food because of its nutrition and health benefits. The seeds of avocado are major byproducts, and thus their phytochemicals and bioactivities have been of interest for study. The chemical components of avocado seeds were investigated by using UPLC-qTOF-MS/MS-based molecular networking, resulting in the isolation of seven new oxindole alkaloids (1-7) and two new benzoxazinone alkaloids (8 and 9). The chemical structures of the isolated compounds were identified by the analysis of NMR data in combination with computational approaches, including NMR and ECD calculations. Bioactivities of the isolated compounds toward silent information regulation 2 homologue-1 (SIRT1) in HEK293 cells were assessed. The results showed that compound 1 had the most potent effect on SIRT1 activation with an elevated NAD+/NADH ratio with potential for further investigation as an anti-aging agent.
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Affiliation(s)
- Thi-Phuong Doan
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Mi Zhang
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Jin Park
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jorge-Eduardo Ponce-Zea
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Van-Hieu Mai
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyo-Moon Cho
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Won-Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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7
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Riggins RB, Ranjit S. Targeting the NAD+ Salvage Pathway: Synergistic Therapeutic Strategy for ER+ Metastatic Breast Cancer. Endocrinology 2023; 164:bqad140. [PMID: 37738166 DOI: 10.1210/endocr/bqad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Affiliation(s)
- Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
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8
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García MJ, Kamaid A, Malacrida L. Label-free fluorescence microscopy: revisiting the opportunities with autofluorescent molecules and harmonic generations as biosensors and biomarkers for quantitative biology. Biophys Rev 2023; 15:709-719. [PMID: 37681086 PMCID: PMC10480099 DOI: 10.1007/s12551-023-01083-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, the utilization of advanced fluorescence microscopy technologies has presented numerous opportunities to study or re-investigate autofluorescent molecules and harmonic generation signals as molecular biomarkers and biosensors for in vivo cell and tissue studies. The label-free approaches benefit from the endogenous fluorescent molecules within the cell and take advantage of their spectroscopy properties to address biological questions. Harmonic generation can be used as a tool to identify the occurrence of fibrillar or lipid deposits in tissues, by using second and third-harmonic generation microscopy. Combining autofluorescence with novel techniques and tools such as fluorescence lifetime imaging microscopy (FLIM) and hyperspectral imaging (HSI) with model-free analysis of phasor plots has revolutionized the understanding of molecular processes such as cellular metabolism. These tools provide quantitative information that is often hidden under classical intensity-based microscopy. In this short review, we aim to illustrate how some of these technologies and techniques may enable investigation without the need to add a foreign fluorescence molecule that can modify or affect the results. We address some of the most important autofluorescence molecules and their spectroscopic properties to illustrate the potential of these combined tools. We discuss using them as biomarkers and biosensors and, under the lens of this new technology, identify some of the challenges and potentials for future advances in the field.
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Affiliation(s)
- María José García
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Andrés Kamaid
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
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9
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Escalante-Covarrubias Q, Mendoza-Viveros L, González-Suárez M, Sitten-Olea R, Velázquez-Villegas LA, Becerril-Pérez F, Pacheco-Bernal I, Carreño-Vázquez E, Mass-Sánchez P, Bustamante-Zepeda M, Orozco-Solís R, Aguilar-Arnal L. Time-of-day defines NAD + efficacy to treat diet-induced metabolic disease by synchronizing the hepatic clock in mice. Nat Commun 2023; 14:1685. [PMID: 36973248 PMCID: PMC10043291 DOI: 10.1038/s41467-023-37286-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The circadian clock is an endogenous time-tracking system that anticipates daily environmental changes. Misalignment of the clock can cause obesity, which is accompanied by reduced levels of the clock-controlled, rhythmic metabolite NAD+. Increasing NAD+ is becoming a therapy for metabolic dysfunction; however, the impact of daily NAD+ fluctuations remains unknown. Here, we demonstrate that time-of-day determines the efficacy of NAD+ treatment for diet-induced metabolic disease in mice. Increasing NAD+ prior to the active phase in obese male mice ameliorated metabolic markers including body weight, glucose and insulin tolerance, hepatic inflammation and nutrient sensing pathways. However, raising NAD+ immediately before the rest phase selectively compromised these responses. Remarkably, timed NAD+ adjusted circadian oscillations of the liver clock until completely inverting its oscillatory phase when increased just before the rest period, resulting in misaligned molecular and behavioral rhythms in male and female mice. Our findings unveil the time-of-day dependence of NAD+-based therapies and support a chronobiology-based approach.
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Affiliation(s)
- Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Román Sitten-Olea
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Laura A Velázquez-Villegas
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Erick Carreño-Vázquez
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Paola Mass-Sánchez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ricardo Orozco-Solís
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados, 14330, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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10
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Zhang K, Sowers ML, Cherryhomes EI, Singh VK, Mishra A, Restrepo BI, Khan A, Jagannath C. Sirtuin-dependent metabolic and epigenetic regulation of macrophages during tuberculosis. Front Immunol 2023; 14:1121495. [PMID: 36993975 PMCID: PMC10040548 DOI: 10.3389/fimmu.2023.1121495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/01/2023] [Indexed: 03/14/2023] Open
Abstract
Macrophages are the preeminent phagocytic cells which control multiple infections. Tuberculosis a leading cause of death in mankind and the causative organism Mycobacterium tuberculosis (MTB) infects and persists in macrophages. Macrophages use reactive oxygen and nitrogen species (ROS/RNS) and autophagy to kill and degrade microbes including MTB. Glucose metabolism regulates the macrophage-mediated antimicrobial mechanisms. Whereas glucose is essential for the growth of cells in immune cells, glucose metabolism and its downsteam metabolic pathways generate key mediators which are essential co-substrates for post-translational modifications of histone proteins, which in turn, epigenetically regulate gene expression. Herein, we describe the role of sirtuins which are NAD+-dependent histone histone/protein deacetylases during the epigenetic regulation of autophagy, the production of ROS/RNS, acetyl-CoA, NAD+, and S-adenosine methionine (SAM), and illustrate the cross-talk between immunometabolism and epigenetics on macrophage activation. We highlight sirtuins as emerging therapeutic targets for modifying immunometabolism to alter macrophage phenotype and antimicrobial function.
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Affiliation(s)
- Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ellie I. Cherryhomes
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Vipul K. Singh
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Blanca I. Restrepo
- University of Texas Health Houston, School of Public Health, Brownsville, TX, United States
| | - Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
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11
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Sánchez-Ramírez E, Ung TPL, Alarcón del Carmen A, del Toro-Ríos X, Fajardo-Orduña GR, Noriega LG, Cortés-Morales VA, Tovar AR, Montesinos JJ, Orozco-Solís R, Stringari C, Aguilar-Arnal L. Coordinated metabolic transitions and gene expression by NAD+ during adipogenesis. J Biophys Biochem Cytol 2022; 221:213521. [PMID: 36197339 PMCID: PMC9538974 DOI: 10.1083/jcb.202111137] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 12/17/2022] Open
Abstract
Adipocytes are the main cell type in adipose tissue, which is a critical regulator of metabolism, highly specialized in storing energy as fat. Adipocytes differentiate from multipotent mesenchymal stromal cells (hMSCs) through adipogenesis, a tightly controlled differentiation process involving close interplay between metabolic transitions and sequential programs of gene expression. However, the specific gears driving this interplay remain largely obscure. Additionally, the metabolite nicotinamide adenine dinucleotide (NAD+) is becoming increasingly recognized as a regulator of lipid metabolism, and a promising therapeutic target for dyslipidemia and obesity. Here, we explored how NAD+ bioavailability controls adipogenic differentiation from hMSC. We found a previously unappreciated repressive role for NAD+ on adipocyte commitment, while a functional NAD+-dependent deacetylase SIRT1 appeared crucial for terminal differentiation of pre-adipocytes. Repressing NAD+ biosynthesis during adipogenesis promoted the adipogenic transcriptional program, while two-photon microscopy and extracellular flux analyses suggest that SIRT1 activity mostly relies on the metabolic switch. Interestingly, SIRT1 controls subcellular compartmentalization of redox metabolism during adipogenesis.
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Affiliation(s)
- Edgar Sánchez-Ramírez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Alejandro Alarcón del Carmen
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ximena del Toro-Ríos
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guadalupe R. Fajardo-Orduña
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lilia G. Noriega
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Victor A. Cortés-Morales
- Mesenchymal Stem Cells Laboratory, Oncology Research Unit, Oncology Hospital, National Medical Center, Mexico City, Mexico
| | - Armando R. Tovar
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan José Montesinos
- Mesenchymal Stem Cells Laboratory, Oncology Research Unit, Oncology Hospital, National Medical Center, Mexico City, Mexico
| | - Ricardo Orozco-Solís
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France,Chiara Stringari:
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico,Correspondence to Lorena Aguilar-Arnal:
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12
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Solano A, Lou J, Scipioni L, Gratton E, Hinde E. Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture. Biophys J 2022; 121:2152-2167. [PMID: 35490296 PMCID: PMC9247470 DOI: 10.1016/j.bpj.2022.04.030] [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: 06/08/2021] [Revised: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nuclear proteins can modulate their DNA binding activity and the exploration volume available during DNA target search by self-associating into higher-order oligomers. Directly tracking this process in the nucleoplasm of a living cell is, however, a complex task. Thus, here we present a microscopy method based on radial pair correlation of molecular brightness fluctuations (radial pCOMB) that can extract the mobility of a fluorescently tagged nuclear protein as a function of its oligomeric state and spatiotemporally map the anisotropy of this parameter with respect to nuclear architecture. By simply performing a rapid frame scan acquisition, radial pCOMB has the capacity to detect, within each pixel, protein oligomer formation and the size-dependent obstruction nuclear architecture imparts on this complex's transport across sub-micrometer distances. From application of radial pCOMB to an oligomeric transcription factor and DNA repair protein, we demonstrate that homo-oligomer formation differentially regulates chromatin accessibility and interaction with the DNA template.
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Affiliation(s)
- Ashleigh Solano
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Jieqiong Lou
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California, Irvine
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne.
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13
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Linear Combination Properties of the Phasor Space in Fluorescence Imaging. SENSORS 2022; 22:s22030999. [PMID: 35161742 PMCID: PMC8840623 DOI: 10.3390/s22030999] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
The phasor approach to fluorescence lifetime imaging, and more recently hyperspectral fluorescence imaging, has increased the use of these techniques, and improved the ease and intuitiveness of the data analysis. The fit-free nature of the phasor plots increases the speed of the analysis and reduces the dimensionality, optimization of data handling and storage. The reciprocity principle between the real and imaginary space-where the phasor and the pixel that the phasor originated from are linked and can be converted from one another-has helped the expansion of this method. The phasor coordinates calculated from a pixel, where multiple fluorescent species are present, depends on the phasor positions of those components. The relative positions are governed by the linear combination properties of the phasor space. According to this principle, the phasor position of a pixel with multiple components lies inside the polygon whose vertices are occupied by the phasor positions of these individual components and the distance between the image phasor to any of the vertices is inversely proportional to the fractional intensity contribution of that component to the total fluorescence from that image pixel. The higher the fractional intensity contribution of a vertex, the closer is the resultant phasor. The linear additivity in the phasor space can be exploited to obtain the fractional intensity contribution from multiple species and quantify their contribution. This review details the various mathematical models that can be used to obtain two/three/four components from phasor space with known phasor signatures and then how to obtain both the fractional intensities and phasor positions without any prior knowledge of either, assuming they are mono-exponential in nature. We note that other than for blind components, there are no restrictions on the type of the decay or their phasor positions for linear combinations to be valid-and they are applicable to complicated fluorescence lifetime decays from components with intensity decays described by multi-exponentials.
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14
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Mendoza M, Egervari G, Sidoli S, Donahue G, Alexander DC, Sen P, Garcia BA, Berger SL. Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites. SCIENCE ADVANCES 2022; 8:eabj5688. [PMID: 35061542 PMCID: PMC8782443 DOI: 10.1126/sciadv.abj5688] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
Histone acetylation is governed by nuclear acetyl-CoA pools generated, in part, from local acetate by metabolic enzyme acetyl-CoA synthetase 2 (ACSS2). We hypothesize that during gene activation, a local transfer of intact acetate occurs via sequential action of epigenetic and metabolic enzymes. Using stable isotope labeling, we detect transfer between histone acetylation sites both in vitro using purified mammalian enzymes and in vivo using quiescence exit in Saccharomyces cerevisiae as a change-of-state model. We show that Acs2, the yeast ortholog of ACSS2, is recruited to chromatin during quiescence exit and observe dynamic histone acetylation changes proximal to Acs2 peaks. We find that Acs2 is preferentially associated with the most up-regulated genes, suggesting that acetyl group transfer plays an important role in gene activation. Overall, our data reveal direct transfer of acetate between histone lysine residues to facilitate rapid transcriptional induction, an exchange that may be critical during changes in nutrient availability.
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Affiliation(s)
- Mariel Mendoza
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Greg Donahue
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Desi C. Alexander
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Payel Sen
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L. Berger
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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15
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Chellappa K, Baur JA. Reducing NAD(H) to amplify rhythms. Nat Metab 2021; 3:1589-1590. [PMID: 34903882 DOI: 10.1038/s42255-021-00494-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Karthikeyani Chellappa
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Levine DC, Kuo HY, Hong HK, Cedernaes J, Hepler C, Wright AG, Sommars MA, Kobayashi Y, Marcheva B, Gao P, Ilkayeva OR, Omura C, Ramsey KM, Newgard CB, Barish GD, Peek CB, Chandel NS, Mrksich M, Bass J. NADH inhibition of SIRT1 links energy state to transcription during time-restricted feeding. Nat Metab 2021; 3:1621-1632. [PMID: 34903884 PMCID: PMC8688143 DOI: 10.1038/s42255-021-00498-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022]
Abstract
In mammals, circadian rhythms are entrained to the light cycle and drive daily oscillations in levels of NAD+, a cosubstrate of the class III histone deacetylase sirtuin 1 (SIRT1) that associates with clock transcription factors. Although NAD+ also participates in redox reactions, the extent to which NAD(H) couples nutrient state with circadian transcriptional cycles remains unknown. Here we show that nocturnal animals subjected to time-restricted feeding of a calorie-restricted diet (TRF-CR) only during night-time display reduced body temperature and elevated hepatic NADH during daytime. Genetic uncoupling of nutrient state from NADH redox state through transduction of the water-forming NADH oxidase from Lactobacillus brevis (LbNOX) increases daytime body temperature and blood and liver acyl-carnitines. LbNOX expression in TRF-CR mice induces oxidative gene networks controlled by brain and muscle Arnt-like protein 1 (BMAL1) and peroxisome proliferator-activated receptor alpha (PPARα) and suppresses amino acid catabolic pathways. Enzymatic analyses reveal that NADH inhibits SIRT1 in vitro, corresponding with reduced deacetylation of SIRT1 substrates during TRF-CR in vivo. Remarkably, Sirt1 liver nullizygous animals subjected to TRF-CR display persistent hypothermia even when NADH is oxidized by LbNOX. Our findings reveal that the hepatic NADH cycle links nutrient state to whole-body energetics through the rhythmic regulation of SIRT1.
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Affiliation(s)
- Daniel C Levine
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hsin-Yu Kuo
- Departments of Chemistry, Biomedical Engineering, and Cell and Molecular Biology, Northwestern University, Evanston, IL, USA
| | - Hee-Kyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jonathan Cedernaes
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Departments of Medical Sciences and Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Chelsea Hepler
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexandra G Wright
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Meredith A Sommars
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peng Gao
- Robert H. Lurie Cancer Center Metabolomics Core, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC, USA
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kathryn M Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher B Newgard
- Duke Molecular Physiology Institute, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC, USA
| | - Grant D Barish
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Clara Bien Peek
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Milan Mrksich
- Departments of Chemistry, Biomedical Engineering, and Cell and Molecular Biology, Northwestern University, Evanston, IL, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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17
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Guido ME, Monjes NM, Wagner PM, Salvador GA. Circadian Regulation and Clock-Controlled Mechanisms of Glycerophospholipid Metabolism from Neuronal Cells and Tissues to Fibroblasts. Mol Neurobiol 2021; 59:326-353. [PMID: 34697790 DOI: 10.1007/s12035-021-02595-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022]
Abstract
Along evolution, living organisms developed a precise timekeeping system, circadian clocks, to adapt life to the 24-h light/dark cycle and temporally regulate physiology and behavior. The transcriptional molecular circadian clock and metabolic/redox oscillator conforming these clocks are present in organs, tissues, and even in individual cells, where they exert circadian control over cellular metabolism. Disruption of the molecular clock may cause metabolic disorders and higher cancer risk. The synthesis and degradation of glycerophospholipids (GPLs) is one of the most highly regulated metabolisms across the 24-h cycle in terms of total lipid content and enzyme expression and activity in the nervous system and individual cells. Lipids play a plethora of roles (membrane biogenesis, energy sourcing, signaling, and the regulation of protein-chromatin interaction, among others), making control of their metabolism a vital checkpoint in the cellular organization of physiology. An increasing body of evidence clearly demonstrates an orchestrated and sequential series of events occurring in GPL metabolism across the 24-h day in diverse retinal cell layers, immortalized fibroblasts, and glioma cells. Moreover, the clock gene Per1 and other circadian-related genes are tightly involved in the regulation of GPL synthesis in quiescent cells. However, under proliferation, the metabolic oscillator continues to control GPL metabolism of brain cancer cells even after molecular circadian clock disruption, reflecting the crucial role of the temporal metabolism organization in cell preservation. The aim of this review is to examine the control exerted by circadian clocks over GPL metabolism, their synthesizing enzyme expression and activities in normal and tumorous cells of the nervous system and in immortalized fibroblasts.
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Affiliation(s)
- Mario E Guido
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.
| | - Natalia M Monjes
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Paula M Wagner
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
- Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Gabriela A Salvador
- INIBIBB-UNS-CONICET, Departamento de Biología, Bioquímica y Farmacia, UNS, Bahía Blanca, Argentina
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18
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Pham DL, Miller CR, Myers MS, Myers DM, Hansen LA, Nichols MG. Development and characterization of phasor-based analysis for FLIM to evaluate the metabolic and epigenetic impact of HER2 inhibition on squamous cell carcinoma cultures. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210187R. [PMID: 34628733 PMCID: PMC8501457 DOI: 10.1117/1.jbo.26.10.106501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
SIGNIFICANCE Deranged metabolism and dysregulated growth factor signaling are closely associated with abnormal levels of proliferation, a recognized hallmark in tumorigenesis. Fluorescence lifetime imaging microscopy (FLIM) of endogenous nicotinamide adenine dinucleotide (NADH), a key metabolic coenzyme, offers a non-invasive, diagnostic indicator of disease progression, and treatment response. The model-independent phasor analysis approach leverages FLIM to rapidly evaluate cancer metabolism in response to targeted therapy. AIM We combined lifetime and phasor FLIM analysis to evaluate the influence of human epidermal growth factor receptor 2 (HER2) inhibition, a prevalent cancer biomarker, on both nuclear and cytoplasmic NAD(P)H of two squamous cell carcinoma (SCC) cultures. While better established, the standard lifetime analysis approach is relatively slow and potentially subject to intrinsic fitting errors and model assumptions. Phasor FLIM analysis offers a rapid, model-independent alternative, but the sensitivity of the bound NAD(P)H fraction to growth factor signaling must also be firmly established. APPROACH Two SCC cultures with low- and high-HER2 expression, were imaged using multiphoton-excited NAD(P)H FLIM, with and without treatment of the HER2 inhibitor AG825. Cells were challenged with mitochondrial inhibition and uncoupling to investigate AG825's impact on the overall metabolic capacity. Phasor FLIM and lifetime fitting analyses were compared within nuclear and cytoplasmic compartments to investigate epigenetic and metabolic impacts of HER2 inhibition. RESULTS NAD(P)H fluorescence lifetime and bound fraction consistently decreased following HER2 inhibition in both cell lines. High-HER2 SCC74B cells displayed a more significant response than low-HER2 SCC74A in both techniques. HER2 inhibition induced greater changes in nuclear than cytoplasmic compartments, leading to an increase in NAD(P)H intensity and concentration. CONCLUSIONS The use of both, complementary FLIM analysis techniques together with quantitative fluorescence intensity revealed consistent, quantitative changes in NAD(P)H metabolism associated with inhibition of growth factor signaling in SCC cell lines. HER2 inhibition promoted increased reliance on oxidative phosphorylation in both cell lines.
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Affiliation(s)
- Dan L. Pham
- Creighton University, Department of Physics, Omaha, Nebraska, United States
| | | | - Molly S. Myers
- Creighton University, Department of Physics, Omaha, Nebraska, United States
| | - Dominick M. Myers
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
| | - Laura A. Hansen
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
| | - Michael G. Nichols
- Creighton University, Department of Physics, Omaha, Nebraska, United States
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
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19
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Sato T, Greco CM. Expanding the link between circadian rhythms and redox metabolism of epigenetic control. Free Radic Biol Med 2021; 170:50-58. [PMID: 33450380 DOI: 10.1016/j.freeradbiomed.2021.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Circadian rhythms play a central role in physiological and metabolic processes. This is mostly achieved through rhythmic regulation of myriad genes via dynamic epigenome changes. Accumulating evidence indicates that oxidative stress and redox balance are under circadian control and feedback on the clock system. Circadian perturbations induce oxidative stress accumulation and disturb redox balance. Along with these changes, epigenomic landscape changes are a remarkable hallmark of clock disruption. This review aims to summarize evidence supporting the link between the circadian clock and redox metabolism, focusing on possible connections through epigenetic mechanisms.
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Affiliation(s)
- Tomoki Sato
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Carolina Magdalen Greco
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, 92697, USA.
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20
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Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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21
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Maniyadath B, Sandra US, Kolthur-Seetharam U. Metabolic choreography of gene expression: nutrient transactions with the epigenome. J Biosci 2020. [DOI: 10.1007/s12038-019-9987-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Chung JY, Jeong JH, Song J. Resveratrol Modulates the Gut-Brain Axis: Focus on Glucagon-Like Peptide-1, 5-HT, and Gut Microbiota. Front Aging Neurosci 2020; 12:588044. [PMID: 33328965 PMCID: PMC7732484 DOI: 10.3389/fnagi.2020.588044] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Resveratrol is a natural polyphenol that has anti-aging and anti-inflammatory properties against stress condition. It is reported that resveratrol has beneficial functions in various metabolic and central nervous system (CNS) diseases, such as obesity, diabetes, depression, and dementia. Recently, many researchers have emphasized the connection between the brain and gut, called the gut-brain axis, for treating both CNS neuropathologies and gastrointestinal diseases. Based on previous findings, resveratrol is involved in glucagon-like peptide 1 (GLP-1) secreted by intestine L cells, the patterns of microbiome in the intestine, the 5-hydroxytryptamine (5-HT) level, and CNS inflammation. Here, we review recent evidences concerning the relevance and regulatory function of resveratrol in the gut-brain axis from various perspectives. Here, we highlight the necessity for further study on resveratrol's specific mechanism in the gut-brain axis. We present the potential of resveratrol as a natural therapeutic substance for treating both neuropathology and gastrointestinal dysfunction.
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Affiliation(s)
- Ji Yeon Chung
- Department of Neurology, Chosun University Medical School, Gwangju, South Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, South Korea
| | - Juhyun Song
- Department of Anatomy, Chonnam National University Medical School, Gwangju, South Korea
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23
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Vallmitjana A, Torrado B, Dvornikov A, Ranjit S, Gratton E. Blind Resolution of Lifetime Components in Individual Pixels of Fluorescence Lifetime Images Using the Phasor Approach. J Phys Chem B 2020; 124:10126-10137. [PMID: 33140960 PMCID: PMC9272785 DOI: 10.1021/acs.jpcb.0c06946] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phasor approach is used in fluorescence lifetime imaging microscopy for several purposes, notably to calculate the metabolic index of single cells and tissues. An important feature of the phasor approach is that it is a fit-free method allowing immediate and easy to interpret analysis of images. In a recent paper, we showed that three or four intensity fractions of exponential components can be resolved in each pixel of an image by the phasor approach using simple algebra, provided the component phasors are known. This method only makes use of the rule of linear combination of phasors rather than fits. Without prior knowledge of the components and their single exponential decay times, resolution of components and fractions is much more challenging. Blind decomposition has been carried out only for cuvette experiments wherein the statistics in terms of the number of photons collected is very good. In this paper, we show that using the phasor approach and measurements of the decay at phasor harmonics 2 and 3, available using modern electronics, we could resolve the decay in each pixel of an image in live cells or mice liver tissues with two or more exponential components without prior knowledge of the values of the components. In this paper, blind decomposition is achieved using a graphical method for two components and a minimization method for three components. This specific use of the phasor approach to resolve multicomponents in a pixel enables applications where multiplexing species with different lifetimes and potentially different spectra can provide a different type of super-resolved image content.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Belén Torrado
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
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24
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Ranjit S, Lanzanò L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol 2020; 17:128-144. [PMID: 32948857 DOI: 10.1038/s41581-020-00337-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, in particular immunofluorescence microscopy, has been used extensively for the assessment of kidney function and pathology for both research and diagnostic purposes. The development of confocal microscopy in the 1950s enabled imaging of live cells and intravital imaging of the kidney; however, confocal microscopy is limited by its maximal spatial resolution and depth. More recent advances in fluorescence microscopy techniques have enabled increasingly detailed assessment of kidney structure and provided extraordinary insights into kidney function. For example, nanoscale precise imaging by rapid beam oscillation (nSPIRO) is a super-resolution microscopy technique that was originally developed for functional imaging of kidney microvilli and enables detection of dynamic physiological events in the kidney. A variety of techniques such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) enable assessment of interaction between proteins. The emergence of other super-resolution techniques, including super-resolution stimulated emission depletion (STED), photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM), has enabled functional imaging of cellular and subcellular organelles at ≤50 nm resolution. The deep imaging via emission recovery (DIVER) detector allows deep, label-free and high-sensitivity imaging of second harmonics, enabling assessment of processes such as fibrosis, whereas fluorescence lifetime imaging microscopy (FLIM) enables assessment of metabolic processes.
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Affiliation(s)
- Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA. .,Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA.
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25
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Vallmitjana A, Dvornikov A, Torrado B, Jameson DM, Ranjit S, Gratton E. Resolution of 4 components in the same pixel in FLIM images using the phasor approach. Methods Appl Fluoresc 2020; 8:035001. [PMID: 32235070 DOI: 10.1088/2050-6120/ab8570] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In several cellular systems, the phasor FLIM approach has shown the existence of more than 2 components in the same pixel, a typical example being free and bound NADH. In order to properly quantify the concentrations and the spatial distributions of fluorescence components associated with different molecular species we developed a general method to resolve 3 and 4 components in the same pixel using the phasor approach. The method is based on the law of linear combination of components valid after transformation of the decay curves to phasors for each pixel in the image. In principle, the linear combination rule is valid for an arbitrary number of components. For 3 components we use only the phasor position for the first harmonic, which has a small error, while for 4 components we need the phasor location at higher harmonics that have intrinsically more noise. As a result of the noise in the higher harmonics, caused by limited photon statistics, we are able to use linear algebra to resolve 4 components given the position of the phasors of 4 independent components in mixtures of dyes and 3 components for dyes in cellular systems.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, United States of America
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26
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Edatt L, Poyyakkara A, Raji GR, Ramachandran V, Shankar SS, Kumar VBS. Role of Sirtuins in Tumor Angiogenesis. Front Oncol 2020; 9:1516. [PMID: 32010617 PMCID: PMC6978795 DOI: 10.3389/fonc.2019.01516] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Generally, changes in the metabolic status of cells under conditions like hypoxia and accumulation of lactate can be sensed by various sensing mechanisms, leading to modulation of a number of signal transduction pathways and transcription factors. Several of the proangiogenic cytokines like VEGF, FGF, PDGF, TGF-β, Ang-2, ILs, etc. are secreted by cancer cells, under hypoxic microenvironment. These cytokines bind to their receptors on the endothelial cells and activates a number of signaling pathways including Akt/PIP3, Src, p38/MAPK, Smad2/3, etc., which ultimately results in the proliferation and migration of endothelial cells. Transcription factors that are activated in response to the metabolic status of tumors include HIFs, NF-κb, p53, El-2, and FOXO. Many of these transcription factors has been reported to be regulated by a class of histone deacetylase called sirtuins. Sirtuins are NAD+ dependent histone deacetylases that play pivotal role in the regulation of tumor cell metabolism, proliferation, migration and angiogenesis. The major function of sirtuins include, deacetylation of histones as well as some non-histone proteins like NF-κB, FOXOs, PPAR⋎, PGC1-α, enzymes like acetyl coenzymeA and structural proteins like α tubulin. In the cell, sirtuins are generally considered as the redox sensors and their activities are dependent on the metabolic status of the cell. Understanding the intricate regulatory mechanisms adopted by sirtuins, is crucial in devising effective therapeutic strategies against angiogenesis, metastasis and tumor progression. Keeping this in mind, the present review focuses on the role of sirtuins in the process of tumor angiogenesis and the regulatory mechanisms employed by them.
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Affiliation(s)
| | | | | | | | | | - V. B. Sameer Kumar
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasaragod, India
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27
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Maniyadath B, Sandra US, Kolthur-Seetharam U. Metabolic choreography of gene expression: nutrient transactions with the epigenome. J Biosci 2020; 45:7. [PMID: 31965985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Eukaryotic complexity and thus their ability to respond to diverse cues are largely driven by varying expression of gene products, qualitatively and quantitatively. Protein adducts in the form of post-translational modifications, most of which are derived from metabolic intermediates, allow fine tuning of gene expression at multiple levels. With the advent of high-throughput and high-resolution mapping technologies there has been an explosion in terms of the kind of modifications on chromatin and other factors that govern gene expression. Moreover, even the classical notion of acetylation and methylation dependent regulation of transcription is now known to be intrinsically coupled to biochemical pathways, which were otherwise regarded as 'mundane'. Here we have not only reviewed some of the recent literature but also have highlighted the dependence of gene regulatory mechanisms on metabolic inputs, both direct and indirect. We have also tried to bring forth some of the open questions, and how our understanding of gene expression has changed dramatically over the last few years, which has largely become metabolism centric. Finally, metabolic regulation of epigenome and gene expression has gained much traction due to the increased incidence of lifestyle and age-related diseases.
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Affiliation(s)
- Babukrishna Maniyadath
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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28
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Ma R, Wu Y, Zhai Y, Hu B, Ma W, Yang W, Yu Q, Chen Z, Workman JL, Yu X, Li S. Exogenous pyruvate represses histone gene expression and inhibits cancer cell proliferation via the NAMPT-NAD+-SIRT1 pathway. Nucleic Acids Res 2019; 47:11132-11150. [PMID: 31598701 PMCID: PMC6868375 DOI: 10.1093/nar/gkz864] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 09/21/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022] Open
Abstract
Pyruvate is a glycolytic metabolite used for energy production and macromolecule biosynthesis. However, little is known about its functions in tumorigenesis. Here, we report that exogenous pyruvate inhibits the proliferation of different types of cancer cells. This inhibitory effect of pyruvate on cell growth is primarily attributed to its function as a signal molecule to repress histone gene expression, which leads to less compact chromatin and misregulation of genome-wide gene expression. Pyruvate represses histone gene expression by inducing the expression of NAD+ biosynthesis enzyme, nicotinamide phosphoribosyltransferase (NAMPT) via myocyte enhancer factor 2C (MEF2C), which then increases NAD+ levels and activates the histone deacetylase activity of SIRT1. Chromatin immunoprecipitation analysis indicates that pyruvate enhances SIRT1 binding at histone gene promoters where it reduces histone acetylation. Although pyruvate delays cell entry into S phase, pyruvate represses histone gene expression independent of cell cycle progression. Moreover, we find that administration of pyruvate reduces histone expression and retards tumor growth in xenograft mice without significant side effects. Using tissues from cervical and lung cancer patients, we find intracellular pyruvate concentrations inversely correlate with histone protein levels. Together, we uncover a previously unknown function of pyruvate in regulating histone gene expression and cancer cell proliferation.
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Affiliation(s)
- Rui Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yinsheng Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yansheng Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Bicheng Hu
- The Central Laboratory, Wuhan No.1 Hospital, Wuhan, Hubei 430022, China
| | - Wei Ma
- The Central Laboratory, Wuhan No.1 Hospital, Wuhan, Hubei 430022, China
| | - Wenqiang Yang
- The Central Laboratory, Wuhan No.1 Hospital, Wuhan, Hubei 430022, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhen Chen
- Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, China
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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Ranjit S, Datta R, Dvornikov A, Gratton E. Multicomponent Analysis of Phasor Plot in a Single Pixel to Calculate Changes of Metabolic Trajectory in Biological Systems. J Phys Chem A 2019; 123:9865-9873. [PMID: 31638388 DOI: 10.1021/acs.jpca.9b07880] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phasor FLIM in cells undergoing oxidative stress and in mice liver sections have shown the presence of a third autofluorescent component indicative of lipid droplets along with free and enzyme-bound NADH with similar emissions. This third component affects the position and shape of the phasor distribution, pushing it away from the metabolic trajectory. Phasor rule of addition is still valid and was exploited here to create a multicomponent analysis where the phasor distribution can be reassigned to the metabolic trajectory and changes in metabolism can be detected independently of the intensity of this third component. Calculation of multiple components from FLIM imaging data of biological systems is a difficult process, especially if different fluorescent species are present at the same pixel. This paper describes the methodology that can be used to separate these multiple components when they are present in the phasor signature acquired in a single pixel of an image.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States.,Department of Biochemistry and Molecular & Cellular Biology , Georgetown University , Washington , D.C. 20057 , United States
| | - Rupsa Datta
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States.,Morgridge Institute for Research , 330 North Orchard Street , Madison , Wisconsin 53715 , United States
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States
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30
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Ranjit S, Malacrida L, Stakic M, Gratton E. Determination of the metabolic index using the fluorescence lifetime of free and bound nicotinamide adenine dinucleotide using the phasor approach. JOURNAL OF BIOPHOTONICS 2019; 12:e201900156. [PMID: 31194290 PMCID: PMC6842045 DOI: 10.1002/jbio.201900156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 05/05/2023]
Abstract
The fluorescence lifetime of nicotinamide adenine dinucleotide (NADH) is commonly used in conjunction with the phasor approach as a molecular biomarker to provide information on cellular metabolism of autofluorescence imaging of cells and tissue. However, in the phasor approach, the bound and free lifetime defining the phasor metabolic trajectory is a subject of debate. The fluorescence lifetime of NADH increases when bound to an enzyme, in contrast to the short multiexponential lifetime displayed by NADH in solution. The extent of fluorescence lifetime increase depends on the enzyme to which NADH is bound. With proper preparation of lactate dehydrogenase (LDH) using oxalic acid (OA) as an allosteric factor, bound NADH to LDH has a lifetime of 3.4 ns and is positioned on the universal semicircle of the phasor plot, inferring a monoexponential lifetime for this species. Surprisingly, measurements in the cellular environments with different metabolic states show a linear trajectory between free NADH at about 0.37 ns and bound NADH at 3.4 ns. These observations support that in a cellular environment, a 3.4 ns value could be used for bound NADH lifetime. The phasor analysis of many cell types shows a linear combination of fractional contributions of free and bound species NADH.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
| | - Milka Stakic
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
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31
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Logan RW, Parekh PK, Kaplan G, Becker-Krail D, Williams W, Yamaguchi S, Yoshino J, Shelton MA, Zhu X, Zhang H, Waplinger S, Fitzgerald E, Oliver-Smith J, Sundarvelu P, Enwright JF, Huang YH, McClung CA. NAD+ cellular redox and SIRT1 regulate the diurnal rhythms of tyrosine hydroxylase and conditioned cocaine reward. Mol Psychiatry 2019; 24:1668-1684. [PMID: 29728703 PMCID: PMC6215755 DOI: 10.1038/s41380-018-0061-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/12/2018] [Accepted: 02/19/2018] [Indexed: 12/21/2022]
Abstract
The diurnal regulation of dopamine is important for normal physiology and diseases such as addiction. Here we find a novel role for the CLOCK protein to antagonize CREB-mediated transcriptional activity at the tyrosine hydroxylase (TH) promoter, which is mediated by the interaction with the metabolic sensing protein, Sirtuin 1 (SIRT1). Additionally, we demonstrate that the transcriptional activity of TH is modulated by the cellular redox state, and daily rhythms of redox balance in the ventral tegmental area (VTA), along with TH transcription, are highly disrupted following chronic cocaine administration. Furthermore, CLOCK and SIRT1 are important for regulating cocaine reward and dopaminergic (DAergic) activity, with interesting differences depending on whether DAergic activity is in a heightened state and if there is a functional CLOCK protein. Taken together, we find that rhythms in cellular metabolism and circadian proteins work together to regulate dopamine synthesis and the reward value for drugs of abuse.
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Affiliation(s)
- Ryan W. Logan
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Puja K. Parekh
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gabrielle Kaplan
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Darius Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wilbur Williams
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Shintaro Yamaguchi
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Jun Yoshino
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Micah A. Shelton
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Xiyu Zhu
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Hui Zhang
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,School of Medicine, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Spencer Waplinger
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Ethan Fitzgerald
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Jeffrey Oliver-Smith
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Poornima Sundarvelu
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - John F. Enwright
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | | | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609,Correspondence: (C.A.M.)
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32
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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33
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Dvornikov A, Malacrida L, Gratton E. The DIVER Microscope for Imaging in Scattering Media. Methods Protoc 2019; 2:E53. [PMID: 31234383 PMCID: PMC6632175 DOI: 10.3390/mps2020053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 01/31/2023] Open
Abstract
We describe an advanced DIVER (Deep Imaging Via Emission Recovery) detection system for two-photon fluorescence microscopy that allows imaging in multiple scattering media, including biological tissues, up to a depth of a few mm with micron resolution. This detection system is more sensitive to low level light signals than conventional epi-detection used in two-photon fluorescence microscopes. The DIVER detector efficiently collects scattered emission photons from a wide area of turbid samples at almost any entrance angle in a 2π spherical angle. Using an epi-detection scheme only photons coming from a relatively small area of a sample and at narrow acceptance angle can be detected. The transmission geometry of the DIVER imaging system makes it exceptionally suitable for Second and Third Harmonic Generation (SHG, THG) signal detection. It also has in-depth fluorescence lifetime imaging (FLIM) capability. Using special optical filters with sin-cos spectral response, hyperspectral analysis of images acquired in-depth in scattering media can be performed. The system was successfully employed in imaging of various biological tissues. The DIVER detector can be plugged into a standard microscope stage and used as an external detector with upright commercial two-photon microscopes.
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Affiliation(s)
- Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA.
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA.
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República-Uruguay, Montevideo 11400, Uruguay.
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA.
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Theurey P, Connolly NMC, Fortunati I, Basso E, Lauwen S, Ferrante C, Moreira Pinho C, Joselin A, Gioran A, Bano D, Park DS, Ankarcrona M, Pizzo P, Prehn JHM. Systems biology identifies preserved integrity but impaired metabolism of mitochondria due to a glycolytic defect in Alzheimer's disease neurons. Aging Cell 2019; 18:e12924. [PMID: 30793475 PMCID: PMC6516149 DOI: 10.1111/acel.12924] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 12/14/2018] [Accepted: 01/21/2019] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial dysfunction is implicated in most neurodegenerative diseases, including Alzheimer's disease (AD). We here combined experimental and computational approaches to investigate mitochondrial health and bioenergetic function in neurons from a double transgenic animal model of AD (PS2APP/B6.152H). Experiments in primary cortical neurons demonstrated that AD neurons had reduced mitochondrial respiratory capacity. Interestingly, the computational model predicted that this mitochondrial bioenergetic phenotype could not be explained by any defect in the mitochondrial respiratory chain (RC), but could be closely resembled by a simulated impairment in the mitochondrial NADH flux. Further computational analysis predicted that such an impairment would reduce levels of mitochondrial NADH, both in the resting state and following pharmacological manipulation of the RC. To validate these predictions, we utilized fluorescence lifetime imaging microscopy (FLIM) and autofluorescence imaging and confirmed that transgenic AD neurons had reduced mitochondrial NAD(P)H levels at rest, and impaired power of mitochondrial NAD(P)H production. Of note, FLIM measurements also highlighted reduced cytosolic NAD(P)H in these cells, and extracellular acidification experiments showed an impaired glycolytic flux. The impaired glycolytic flux was identified to be responsible for the observed mitochondrial hypometabolism, since bypassing glycolysis with pyruvate restored mitochondrial health. This study highlights the benefits of a systems biology approach when investigating complex, nonintuitive molecular processes such as mitochondrial bioenergetics, and indicates that primary cortical neurons from a transgenic AD model have reduced glycolytic flux, leading to reduced cytosolic and mitochondrial NAD(P)H and reduced mitochondrial respiratory capacity.
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Affiliation(s)
- Pierre Theurey
- Department of Biomedical Sciences University of Padua Padua Italy
| | - Niamh M. C. Connolly
- Department of Physiology & Medical Physics Royal College of Surgeons in Ireland Dublin Ireland
| | | | - Emy Basso
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute – Italian National Research Council (CNR) Padua Italy
| | - Susette Lauwen
- Department of Physiology & Medical Physics Royal College of Surgeons in Ireland Dublin Ireland
| | | | - Catarina Moreira Pinho
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society Karolinska Institutet Stockholm Sweden
| | - Alvin Joselin
- Brain & Mind Research Institute University of Ottawa Ottawa Ontario Canada
| | - Anna Gioran
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - David S. Park
- Brain & Mind Research Institute University of Ottawa Ottawa Ontario Canada
| | - Maria Ankarcrona
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society Karolinska Institutet Stockholm Sweden
| | - Paola Pizzo
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute – Italian National Research Council (CNR) Padua Italy
| | - Jochen H. M. Prehn
- Department of Physiology & Medical Physics Royal College of Surgeons in Ireland Dublin Ireland
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Dyar KA, Lutter D, Artati A, Ceglia NJ, Liu Y, Armenta D, Jastroch M, Schneider S, de Mateo S, Cervantes M, Abbondante S, Tognini P, Orozco-Solis R, Kinouchi K, Wang C, Swerdloff R, Nadeef S, Masri S, Magistretti P, Orlando V, Borrelli E, Uhlenhaut NH, Baldi P, Adamski J, Tschöp MH, Eckel-Mahan K, Sassone-Corsi P. Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks. Cell 2019; 174:1571-1585.e11. [PMID: 30193114 DOI: 10.1016/j.cell.2018.08.042] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/20/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022]
Abstract
Metabolic diseases are often characterized by circadian misalignment in different tissues, yet how altered coordination and communication among tissue clocks relate to specific pathogenic mechanisms remains largely unknown. Applying an integrated systems biology approach, we performed 24-hr metabolomics profiling of eight mouse tissues simultaneously. We present a temporal and spatial atlas of circadian metabolism in the context of systemic energy balance and under chronic nutrient stress (high-fat diet [HFD]). Comparative analysis reveals how the repertoires of tissue metabolism are linked and gated to specific temporal windows and how this highly specialized communication and coherence among tissue clocks is rewired by nutrient challenge. Overall, we illustrate how dynamic metabolic relationships can be reconstructed across time and space and how integration of circadian metabolomics data from multiple tissues can improve our understanding of health and disease.
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Affiliation(s)
- Kenneth A Dyar
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Dominik Lutter
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Anna Artati
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764 Neuherberg Germany
| | - Nicholas J Ceglia
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Danny Armenta
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Martin Jastroch
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Sandra Schneider
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Sara de Mateo
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Serena Abbondante
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paola Tognini
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Ricardo Orozco-Solis
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Christina Wang
- Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90509, USA
| | - Ronald Swerdloff
- Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90509, USA
| | - Seba Nadeef
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Selma Masri
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Magistretti
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Valerio Orlando
- BESE Division, KAUST Environmental Epigenetics Program, King Abdullah University Science and Technology, Thuwal, Saudi Arabia
| | - Emiliana Borrelli
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764 Neuherberg Germany; Chair of Experimental Genetics, Technical University of Munich, 85350 Freising-Weihenstephan, Germany.
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Division of Metabolic Diseases, Technical University of Munich, 80333 Munich, Germany.
| | - Kristin Eckel-Mahan
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
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Pacheco-Bernal I, Becerril-Pérez F, Aguilar-Arnal L. Circadian rhythms in the three-dimensional genome: implications of chromatin interactions for cyclic transcription. Clin Epigenetics 2019; 11:79. [PMID: 31092281 PMCID: PMC6521413 DOI: 10.1186/s13148-019-0677-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Circadian rhythms orchestrate crucial physiological functions and behavioral aspects around a day in almost all living forms. The circadian clock is a time tracking system that permits organisms to predict and anticipate periodic environmental fluctuations. The circadian system is hierarchically organized, and a master pacemaker located in the brain synchronizes subsidiary clocks in the rest of the organism. Adequate synchrony between central and peripheral clocks ensures fitness and potentiates a healthy state. Conversely, disruption of circadian rhythmicity is associated with metabolic diseases, psychiatric disorders, or cancer, amongst other pathologies. Remarkably, the molecular machinery directing circadian rhythms consists of an intricate network of feedback loops in transcription and translation which impose 24-h cycles in gene expression across all tissues. Interestingly, the molecular clock collaborates with multitude of epigenetic remodelers to fine tune transcriptional rhythms in a tissue-specific manner. Very exciting research demonstrate that three-dimensional properties of the genome have a regulatory role on circadian transcriptional rhythmicity, from bacteria to mammals. Unexpectedly, highly dynamic long-range chromatin interactions have been revealed during the circadian cycle in mammalian cells, where thousands of regulatory elements physically interact with promoter regions every 24 h. Molecular mechanisms directing circadian dynamics on chromatin folding are emerging, and the coordinated action between the core clock and epigenetic remodelers appears to be essential for these movements. These evidences reveal a critical epigenetic regulatory layer for circadian rhythms and pave the way to uncover molecular mechanisms triggering pathological states associated to circadian misalignment.
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Affiliation(s)
- Ignacio Pacheco-Bernal
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Royer CA. Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy. Protein Sci 2019; 28:1210-1221. [PMID: 31012169 DOI: 10.1002/pro.3630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 11/12/2022]
Abstract
Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super-resolution.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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38
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Off the Clock: From Circadian Disruption to Metabolic Disease. Int J Mol Sci 2019; 20:ijms20071597. [PMID: 30935034 PMCID: PMC6480015 DOI: 10.3390/ijms20071597] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian timekeeping allows appropriate temporal regulation of an organism’s internal metabolism to anticipate and respond to recurrent daily changes in the environment. Evidence from animal genetic models and from humans under circadian misalignment (such as shift work or jet lag) shows that disruption of circadian rhythms contributes to the development of obesity and metabolic disease. Inappropriate timing of food intake and high-fat feeding also lead to disruptions of the temporal coordination of metabolism and physiology and subsequently promote its pathogenesis. This review illustrates the impact of genetically or environmentally induced molecular clock disruption (at the level of the brain and peripheral tissues) and the interplay between the circadian system and metabolic processes. Here, we discuss some mechanisms responsible for diet-induced circadian desynchrony and consider the impact of nutritional cues in inter-organ communication, with a particular focus on the communication between peripheral organs and brain. Finally, we discuss the relay of environmental information by signal-dependent transcription factors to adjust the timing of gene oscillations. Collectively, a better knowledge of the mechanisms by which the circadian clock function can be compromised will lead to novel preventive and therapeutic strategies for obesity and other metabolic disorders arising from circadian desynchrony.
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Cacabelos R, Carril JC, Cacabelos N, Kazantsev AG, Vostrov AV, Corzo L, Cacabelos P, Goldgaber D. Sirtuins in Alzheimer's Disease: SIRT2-Related GenoPhenotypes and Implications for PharmacoEpiGenetics. Int J Mol Sci 2019; 20:ijms20051249. [PMID: 30871086 PMCID: PMC6429449 DOI: 10.3390/ijms20051249] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Sirtuins (SIRT1-7) are NAD+-dependent protein deacetylases/ADP ribosyltransferases with important roles in chromatin silencing, cell cycle regulation, cellular differentiation, cellular stress response, metabolism and aging. Sirtuins are components of the epigenetic machinery, which is disturbed in Alzheimer’s disease (AD), contributing to AD pathogenesis. There is an association between the SIRT2-C/T genotype (rs10410544) (50.92%) and AD susceptibility in the APOEε4-negative population (SIRT2-C/C, 34.72%; SIRT2-T/T 14.36%). The integration of SIRT2 and APOE variants in bigenic clusters yields 18 haplotypes. The 5 most frequent bigenic genotypes in AD are 33CT (27.81%), 33CC (21.36%), 34CT (15.29%), 34CC (9.76%) and 33TT (7.18%). There is an accumulation of APOE-3/4 and APOE-4/4 carriers in SIRT2-T/T > SIRT2-C/T > SIRT2-C/C carriers, and also of SIRT2-T/T and SIRT2-C/T carriers in patients who harbor the APOE-4/4 genotype. SIRT2 variants influence biochemical, hematological, metabolic and cardiovascular phenotypes, and modestly affect the pharmacoepigenetic outcome in AD. SIRT2-C/T carriers are the best responders, SIRT2-T/T carriers show an intermediate pattern, and SIRT2-C/C carriers are the worst responders to a multifactorial treatment. In APOE-SIRT2 bigenic clusters, 33CC carriers respond better than 33TT and 34CT carriers, whereas 24CC and 44CC carriers behave as the worst responders. CYP2D6 extensive metabolizers (EM) are the best responders, poor metabolizers (PM) are the worst responders, and ultra-rapid metabolizers (UM) tend to be better responders that intermediate metabolizers (IM). In association with CYP2D6 genophenotypes, SIRT2-C/T-EMs are the best responders. Some Sirtuin modulators might be potential candidates for AD treatment.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Juan C Carril
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Natalia Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Aleksey G Kazantsev
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Alex V Vostrov
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Lola Corzo
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Pablo Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Dmitry Goldgaber
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
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Abstract
SIGNIFICANCE NAD+ and NADP+ are important cosubstrates in redox reactions and participate in regulatory networks operating in adjustment of metabolic pathways. Moreover, NAD+ is a cosubstrate in post-translational modification of proteins and is involved in DNA repair. NADPH is indispensable for reductive syntheses and the redox chemistry involved in attaining and maintaining correct protein conformation. Recent Advances: Within a couple of decades, a wealth of information has been gathered on NAD(H)+/NADP(H) redox imaging, regulatory role of redox potential in assembly of spatial protein structures, and the role of ADP-ribosylation of regulatory proteins affecting both gene expression and metabolism. All these have a bearing also on disease, healthy aging, and longevity. CRITICAL ISSUES Knowledge of the signal propagation pathways of NAD+-dependent post-translational modifications is still fragmentary for explaining the mechanism of cellular stress effects and nutritional state on these actions. Evaluation of the cosubstrate and regulator roles of NAD(H) and NADP(H) still suffers from some controversies in experimental data. FUTURE DIRECTIONS Activating or inhibiting interventions in NAD+-dependent protein modifications for medical purposes has shown promise, but restraining tumor growth by inhibiting DNA repair in tumors by means of interference in sirtuins is still in the early stage. The same is true for the use of this technology in improving health and healthy aging. New genetically encoded specific NAD and NADP probes are expected to modernize the research on redox biology.
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Affiliation(s)
- Ilmo E Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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Mechanisms of Communication in the Mammalian Circadian Timing System. Int J Mol Sci 2019; 20:ijms20020343. [PMID: 30650649 PMCID: PMC6359556 DOI: 10.3390/ijms20020343] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/17/2022] Open
Abstract
24-h rhythms in physiology and behaviour are organized by a body-wide network of endogenous circadian clocks. In mammals, a central pacemaker in the hypothalamic suprachiasmatic nucleus (SCN) integrates external light information to adapt cellular clocks in all tissues and organs to the external light-dark cycle. Together, central and peripheral clocks co-regulate physiological rhythms and functions. In this review, we outline the current knowledge about the routes of communication between the environment, the main pacemakers and the downstream clocks in the body, focusing on what we currently know and what we still need to understand about the communication mechanisms by which centrally and peripherally controlled timing signals coordinate physiological functions and behaviour. We highlight recent findings that shed new light on the internal organization and function of the SCN and neuroendocrine mechanisms mediating clock-to-clock coupling. These findings have implications for our understanding of circadian network entrainment and for potential manipulations of the circadian clock system in therapeutic settings.
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42
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Mah EJ, Lefebvre AEYT, McGahey GE, Yee AF, Digman MA. Collagen density modulates triple-negative breast cancer cell metabolism through adhesion-mediated contractility. Sci Rep 2018; 8:17094. [PMID: 30459440 DOI: 10.2139/ssrn.3188427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/30/2018] [Indexed: 05/21/2023] Open
Abstract
Extracellular matrix (ECM) mechanical properties upregulate cancer invasion, cell contractility, and focal adhesion formation. Alteration in energy metabolism is a known characteristic of cancer cells (i.e., Warburg effect) and modulates cell invasion. There is little evidence to show if collagen density can alter cancer cell metabolism. We investigated changes in energy metabolism due to collagen density in five breast cell lines by measuring the fluorescence lifetime of NADH. We found that only triple-negative breast cancer cells, MDA-MB231 and MDA-MB468 cells, had an increased population of bound NADH, indicating an oxidative phosphorylation (OXPHOS) signature, as collagen density decreased. When inhibiting ROCK and cell contractility, MDA-MB231 cells on glass shifted from glycolysis (GLY) to OXPHOS, confirming the intricate relationship between mechanosensing and metabolism. MCF10A cells showed less significant changes in metabolism, shifting towards GLY as collagen density decreased. The MCF-7 and T-47D, less invasive breast cancer cells, compared to the MDA-MB231 and MDA-MB468 cells, showed no changes regardless of substrate. In addition, OXPHOS or GLY inhibitors in MDA-MB231 cells showed dramatic shifts from OXPHOS to GLY or vice versa. These results provide an important link between cellular metabolism, contractility, and collagen density in human breast cancer.
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Affiliation(s)
- Emma J Mah
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, USA
| | - Austin E Y T Lefebvre
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, USA
| | - Gabrielle E McGahey
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, USA
| | - Albert F Yee
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Michelle A Digman
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA.
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, USA.
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Collagen density modulates triple-negative breast cancer cell metabolism through adhesion-mediated contractility. Sci Rep 2018; 8:17094. [PMID: 30459440 PMCID: PMC6244401 DOI: 10.1038/s41598-018-35381-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extracellular matrix (ECM) mechanical properties upregulate cancer invasion, cell contractility, and focal adhesion formation. Alteration in energy metabolism is a known characteristic of cancer cells (i.e., Warburg effect) and modulates cell invasion. There is little evidence to show if collagen density can alter cancer cell metabolism. We investigated changes in energy metabolism due to collagen density in five breast cell lines by measuring the fluorescence lifetime of NADH. We found that only triple-negative breast cancer cells, MDA-MB231 and MDA-MB468 cells, had an increased population of bound NADH, indicating an oxidative phosphorylation (OXPHOS) signature, as collagen density decreased. When inhibiting ROCK and cell contractility, MDA-MB231 cells on glass shifted from glycolysis (GLY) to OXPHOS, confirming the intricate relationship between mechanosensing and metabolism. MCF10A cells showed less significant changes in metabolism, shifting towards GLY as collagen density decreased. The MCF-7 and T-47D, less invasive breast cancer cells, compared to the MDA-MB231 and MDA-MB468 cells, showed no changes regardless of substrate. In addition, OXPHOS or GLY inhibitors in MDA-MB231 cells showed dramatic shifts from OXPHOS to GLY or vice versa. These results provide an important link between cellular metabolism, contractility, and collagen density in human breast cancer.
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45
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Goodman RP, Calvo SE, Mootha VK. Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. J Biol Chem 2018; 293:7508-7516. [PMID: 29514978 PMCID: PMC5961030 DOI: 10.1074/jbc.tm117.000258] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Compartmentalization is a fundamental design principle of eukaryotic metabolism. Here, we review the compartmentalization of NAD+/NADH and NADP+/NADPH with a focus on the liver, an organ that experiences the extremes of biochemical physiology each day. Historical studies of the liver, using classical biochemical fractionation and measurements of redox-coupled metabolites, have given rise to the prevailing view that mitochondrial NAD(H) pools tend to be oxidized and important for energy homeostasis, whereas cytosolic NADP(H) pools tend to be highly reduced for reductive biosynthesis. Despite this textbook view, many questions still remain as to the relative size of these subcellular pools and their redox ratios in different physiological states, and to what extent such redox ratios are simply indicators versus drivers of metabolism. By performing a bioinformatic survey, we find that the liver expresses 352 known or predicted enzymes composing the hepatic NAD(P)ome, i.e. the union of all predicted enzymes producing or consuming NADP(H) or NAD(H) or using them as a redox co-factor. Notably, less than half are predicted to be localized within the cytosol or mitochondria, and a very large fraction of these genes exhibit gene expression patterns that vary during the time of day or in response to fasting or feeding. A future challenge lies in applying emerging new genetic tools to measure and manipulate in vivo hepatic NADP(H) and NAD(H) with subcellular and temporal resolution. Insights from such fundamental studies will be crucial in deciphering the pathogenesis of very common diseases known to involve alterations in hepatic NAD(P)H, such as diabetes and fatty liver disease.
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Affiliation(s)
- Russell P Goodman
- From the Division of Gastroenterology and
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
| | - Sarah E Calvo
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
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46
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Lou PH, Lucchinetti E, Scott KY, Huang Y, Gandhi M, Hersberger M, Clanachan AS, Lemieux H, Zaugg M. Alterations in fatty acid metabolism and sirtuin signaling characterize early type-2 diabetic hearts of fructose-fed rats. Physiol Rep 2018; 5:5/16/e13388. [PMID: 28830979 PMCID: PMC5582268 DOI: 10.14814/phy2.13388] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/24/2017] [Indexed: 01/25/2023] Open
Abstract
Despite the fact that skeletal muscle insulin resistance is the hallmark of type‐2 diabetes mellitus (T2DM), inflexibility in substrate energy metabolism has been observed in other tissues such as liver, adipose tissue, and heart. In the heart, structural and functional changes ultimately lead to diabetic cardiomyopathy. However, little is known about the early biochemical changes that cause cardiac metabolic dysregulation and dysfunction. We used a dietary model of fructose‐induced T2DM (10% fructose in drinking water for 6 weeks) to study cardiac fatty acid metabolism in early T2DM and related signaling events in order to better understand mechanisms of disease. In early type‐2 diabetic hearts, flux through the fatty acid oxidation pathway was increased as a result of increased cellular uptake (CD36), mitochondrial uptake (CPT1B), as well as increased β‐hydroxyacyl‐CoA dehydrogenase and medium‐chain acyl‐CoA dehydrogenase activities, despite reduced mitochondrial mass. Long‐chain acyl‐CoA dehydrogenase activity was slightly decreased, resulting in the accumulation of long‐chain acylcarnitine species. Cardiac function and overall mitochondrial respiration were unaffected. However, evidence of oxidative stress and subtle changes in cardiolipin content and composition were found in early type‐2 diabetic mitochondria. Finally, we observed decreased activity of SIRT1, a pivotal regulator of fatty acid metabolism, despite increased protein levels. This indicates that the heart is no longer capable of further increasing its capacity for fatty acid oxidation. Along with increased oxidative stress, this may represent one of the earliest signs of dysfunction that will ultimately lead to inflammation and remodeling in the diabetic heart.
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Affiliation(s)
- Phing-How Lou
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Eliana Lucchinetti
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Katrina Y Scott
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Yiming Huang
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Manoj Gandhi
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Martin Hersberger
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zürich, Zurich, Switzerland
| | | | - Hélène Lemieux
- Faculty Saint-Jean, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Zaugg
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada .,Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta, Canada
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47
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Sant'Anna-Silva ACB, Santos GC, Campos SPC, Oliveira Gomes AM, Pérez-Valencia JA, Rumjanek FD. Metabolic Profile of Oral Squamous Carcinoma Cell Lines Relies on a Higher Demand of Lipid Metabolism in Metastatic Cells. Front Oncol 2018; 8:13. [PMID: 29456966 PMCID: PMC5801303 DOI: 10.3389/fonc.2018.00013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/16/2018] [Indexed: 01/10/2023] Open
Abstract
Tumor cells are subjected to a broad range of selective pressures. As a result of the imposed stress, subpopulations of surviving cells exhibit individual biochemical phenotypes that reflect metabolic reprograming. The present work aimed at investigating metabolic parameters of cells displaying increasing degrees of metastatic potential. The metabolites present in cell extracts fraction of tongue fibroblasts and of cell lines derived from human tongue squamous cell carcinoma lineages displaying increasing metastatic potential (SCC9 ZsG, LN1 and LN2) were analyzed by 1H NMR (nuclear magnetic resonance) spectroscopy. Living, intact cells were also examined by the non-invasive method of fluorescence lifetime imaging microscopy (FLIM) based on the auto fluorescence of endogenous NADH. The cell lines reproducibly exhibited distinct metabolic profiles confirmed by Partial Least-Square Discriminant Analysis (PLS-DA) of the spectra. Measurement of endogenous free and bound NAD(P)H relative concentrations in the intact cell lines showed that ZsG and LN1 cells displayed high heterogeneity in the energy metabolism, indicating that the cells would oscillate between glycolysis and oxidative metabolism depending on the microenvironment’s composition. However, LN2 cells appeared to have more contributions to the oxidative status, displaying a lower NAD(P)H free/bound ratio. Functional experiments of energy metabolism, mitochondrial physiology, and proliferation assays revealed that all lineages exhibited similar energy features, although resorting to different bioenergetics strategies to face metabolic demands. These differentiated functions may also promote metastasis. We propose that lipid metabolism is related to the increased invasiveness as a result of the accumulation of malonate, methyl malonic acid, n-acetyl and unsaturated fatty acids (CH2)n in parallel with the metastatic potential progression, thus suggesting that the NAD(P)H reflected the lipid catabolic/anabolic pathways.
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Affiliation(s)
- Ana Carolina B Sant'Anna-Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilson C Santos
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro Nacional de Biologia Estrutural e Bioimagem I (CENABIO I)/Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Laboratório de Ressonância Magnética Nuclear de Biomoléculas (bioNMR), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Samir P Costa Campos
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Marco Oliveira Gomes
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juan Alberto Pérez-Valencia
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Franklin David Rumjanek
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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48
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Wang XX, Wang D, Luo Y, Myakala K, Dobrinskikh E, Rosenberg AZ, Levi J, Kopp JB, Field A, Hill A, Lucia S, Qiu L, Jiang T, Peng Y, Orlicky D, Garcia G, Herman-Edelstein M, D'Agati V, Henriksen K, Adorini L, Pruzanski M, Xie C, Krausz KW, Gonzalez FJ, Ranjit S, Dvornikov A, Gratton E, Levi M. FXR/TGR5 Dual Agonist Prevents Progression of Nephropathy in Diabetes and Obesity. J Am Soc Nephrol 2018; 29:118-137. [PMID: 29089371 PMCID: PMC5748904 DOI: 10.1681/asn.2017020222] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022] Open
Abstract
Bile acids are ligands for the nuclear hormone receptor farnesoid X receptor (FXR) and the G protein-coupled receptor TGR5. We have shown that FXR and TGR5 have renoprotective roles in diabetes- and obesity-related kidney disease. Here, we determined whether these effects are mediated through differential or synergistic signaling pathways. We administered the FXR/TGR5 dual agonist INT-767 to DBA/2J mice with streptozotocin-induced diabetes, db/db mice with type 2 diabetes, and C57BL/6J mice with high-fat diet-induced obesity. We also examined the individual effects of the selective FXR agonist obeticholic acid (OCA) and the TGR5 agonist INT-777 in diabetic mice. The FXR agonist OCA and the TGR5 agonist INT-777 modulated distinct renal signaling pathways involved in the pathogenesis and treatment of diabetic nephropathy. Treatment of diabetic DBA/2J and db/db mice with the dual FXR/TGR5 agonist INT-767 improved proteinuria and prevented podocyte injury, mesangial expansion, and tubulointerstitial fibrosis. INT-767 exerted coordinated effects on multiple pathways, including stimulation of a signaling cascade involving AMP-activated protein kinase, sirtuin 1, PGC-1α, sirtuin 3, estrogen-related receptor-α, and Nrf-1; inhibition of endoplasmic reticulum stress; and inhibition of enhanced renal fatty acid and cholesterol metabolism. Additionally, in mice with diet-induced obesity, INT-767 prevented mitochondrial dysfunction and oxidative stress determined by fluorescence lifetime imaging of NADH and kidney fibrosis determined by second harmonic imaging microscopy. These results identify the renal signaling pathways regulated by FXR and TGR5, which may be promising targets for the treatment of nephropathy in diabetes and obesity.
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MESH Headings
- Albuminuria/etiology
- Animals
- Bile Acids and Salts/pharmacology
- Chenodeoxycholic Acid/analogs & derivatives
- Chenodeoxycholic Acid/pharmacology
- Cholesterol/metabolism
- Cholic Acids/pharmacology
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 2/metabolism
- Diabetic Nephropathies/complications
- Diabetic Nephropathies/metabolism
- Diabetic Nephropathies/pathology
- Diabetic Nephropathies/prevention & control
- Disease Progression
- Endoplasmic Reticulum Stress
- Fibrosis
- Glomerular Mesangium/pathology
- Humans
- Kidney Tubules/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred DBA
- Mitochondria/metabolism
- Obesity/complications
- Obesity/metabolism
- Oxidative Stress
- Podocytes/pathology
- RNA, Messenger/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Signal Transduction/drug effects
- Triglycerides/metabolism
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Affiliation(s)
- Xiaoxin X Wang
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Dong Wang
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Yuhuan Luo
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Komuraiah Myakala
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Evgenia Dobrinskikh
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Avi Z Rosenberg
- National Institute of Diabetes and Digestive and Kidney Diseases and
- Division of Pathology and
| | - Jonathan Levi
- National Institute of Diabetes and Digestive and Kidney Diseases and
| | - Jeffrey B Kopp
- National Institute of Diabetes and Digestive and Kidney Diseases and
| | - Amanda Field
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Medical Center and the George Washington University School of Medicine and Health Sciences, Washington, DC
- Department of Nephrology and Hypertension, Rabin Medical Center, Tel Aviv, Israel
| | - Ashley Hill
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Medical Center and the George Washington University School of Medicine and Health Sciences, Washington, DC
- Department of Nephrology and Hypertension, Rabin Medical Center, Tel Aviv, Israel
| | - Scott Lucia
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Liru Qiu
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Tao Jiang
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Yingqiong Peng
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - David Orlicky
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Gabriel Garcia
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
| | - Michal Herman-Edelstein
- Department of Nephrology and Hypertension, Rabin Medical Center, Tel Aviv, Israel
- Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vivette D'Agati
- Department of Pathology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Kammi Henriksen
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | - Mark Pruzanski
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Cen Xie
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kristopher W Krausz
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank J Gonzalez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Moshe Levi
- Departments of Medicine and
- Pathology, University of Colorado Denver and Department of Veterans Affairs Medical Center, Aurora, Colorado
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49
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Bhattacharjee A, Datta R, Gratton E, Hochbaum AI. Metabolic fingerprinting of bacteria by fluorescence lifetime imaging microscopy. Sci Rep 2017; 7:3743. [PMID: 28623341 PMCID: PMC5473825 DOI: 10.1038/s41598-017-04032-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial populations exhibit a range of metabolic states influenced by their environment, intra- and interspecies interactions. The identification of bacterial metabolic states and transitions between them in their native environment promises to elucidate community behavior and stochastic processes, such as antibiotic resistance acquisition. In this work, we employ two-photon fluorescence lifetime imaging microscopy (FLIM) to create a metabolic fingerprint of individual bacteria and populations. FLIM of autofluorescent reduced nicotinamide adenine dinucleotide (phosphate), NAD(P)H, has been previously exploited for label-free metabolic imaging of mammalian cells. However, NAD(P)H FLIM has not been established as a metabolic proxy in bacteria. Applying the phasor approach, we create FLIM-phasor maps of Escherichia coli, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus epidermidis at the single cell and population levels. The bacterial phasor is sensitive to environmental conditions such as antibiotic exposure and growth phase, suggesting that observed shifts in the phasor are representative of metabolic changes within the cells. The FLIM-phasor approach represents a powerful, non-invasive imaging technique to study bacterial metabolism in situ and could provide unique insights into bacterial community behavior, pathology and antibiotic resistance with sub-cellular resolution.
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Affiliation(s)
- Arunima Bhattacharjee
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Rupsa Datta
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Allon I Hochbaum
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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