1
|
Musgrave JH, Han JC, Ward ML, Taberner AJ, Tran K. Measuring and Modelling the Effect of Inorganic Phosphate on Cross-bridge Mechanics in Human Cardiac Muscle. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38082686 DOI: 10.1109/embc40787.2023.10340057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Many common chronic diseases operate at the intersection of metabolic and cardiovascular dysfunction. In order to model the effects of these diseases and investigate underlying causes we are developing a cardiomyocyte model which incorporates both the mechanics and metabolic factors that underlie work done by the heart. In this paper we present the first experimental results from our study measuring mechanical properties in human cardiac trabeculae, including the effect of inorganic phosphate (Pi) on the complex modulus at 37 °C. Extending our previous mathematical model, we have developed a computationally efficient model of cardiac cross-bridge mechanics which is sensitive to changes in cellular Pi. This extended model was parameterised with human cardiac complex modulus data. It captured the changes to cardiac mechanics following an increase in Pi concentration that we measured experimentally, including a reduced elastic modulus and a right-shift in frequency. The human cardiac trabecula we studied had a low sensitivity to Pi compared to what has been previously reported in mammalian cardiac tissue, which suggests that the muscle may have cellular compensatory mechanisms to cope with elevated Pi levels. This study demonstrates the feasibility of our experimental-modelling pipeline for future investigation of mechanical and metabolic effects in the diseased human heart.Clinical Relevance- This study presents the first measurement of the effect of Pi on the stiffness frequency response of human cardiac tissue and extends an experimental-modelling framework appropriate for investigating effects of disease on the human heart.
Collapse
|
2
|
Walkon LL, Strubbe-Rivera JO, Bazil JN. Calcium Overload and Mitochondrial Metabolism. Biomolecules 2022; 12:1891. [PMID: 36551319 PMCID: PMC9775684 DOI: 10.3390/biom12121891] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Mitochondria calcium is a double-edged sword. While low levels of calcium are essential to maintain optimal rates of ATP production, extreme levels of calcium overcoming the mitochondrial calcium retention capacity leads to loss of mitochondrial function. In moderate amounts, however, ATP synthesis rates are inhibited in a calcium-titratable manner. While the consequences of extreme calcium overload are well-known, the effects on mitochondrial function in the moderately loaded range remain enigmatic. These observations are associated with changes in the mitochondria ultrastructure and cristae network. The present mini review/perspective follows up on previous studies using well-established cryo-electron microscopy and poses an explanation for the observable depressed ATP synthesis rates in mitochondria during calcium-overloaded states. The results presented herein suggest that the inhibition of oxidative phosphorylation is not caused by a direct decoupling of energy metabolism via the opening of a calcium-sensitive, proteinaceous pore but rather a separate but related calcium-dependent phenomenon. Such inhibition during calcium-overloaded states points towards mitochondrial ultrastructural modifications, enzyme activity changes, or an interplay between both events.
Collapse
Affiliation(s)
- Lauren L. Walkon
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Jasiel O. Strubbe-Rivera
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Jason N. Bazil
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
3
|
Ghosh S, Guglielmi G, Orfanidis I, Spill F, Hickey A, Hanssen E, Rajagopal V. Effects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy: an in silico study. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210323. [PMID: 36189807 PMCID: PMC9527921 DOI: 10.1098/rstb.2021.0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Abstract
Diabetic cardiomyopathy is a leading cause of heart failure in diabetes. At the cellular level, diabetic cardiomyopathy leads to altered mitochondrial energy metabolism and cardiomyocyte ultrastructure. We combined electron microscopy (EM) and computational modelling to understand the impact of diabetes-induced ultrastructural changes on cardiac bioenergetics. We collected transverse micrographs of multiple control and type I diabetic rat cardiomyocytes using EM. Micrographs were converted to finite-element meshes, and bioenergetics was simulated over them using a biophysical model. The simulations also incorporated depressed mitochondrial capacity for oxidative phosphorylation (OXPHOS) and creatine kinase (CK) reactions to simulate diabetes-induced mitochondrial dysfunction. Analysis of micrographs revealed a 14% decline in mitochondrial area fraction in diabetic cardiomyocytes, and an irregular arrangement of mitochondria and myofibrils. Simulations predicted that this irregular arrangement, coupled with the depressed activity of mitochondrial CK enzymes, leads to large spatial variation in adenosine diphosphate (ADP)/adenosine triphosphate (ATP) ratio profile of diabetic cardiomyocytes. However, when spatially averaged, myofibrillar ADP/ATP ratios of a cardiomyocyte do not change with diabetes. Instead, average concentration of inorganic phosphate rises by 40% owing to lower mitochondrial area fraction and dysfunction in OXPHOS. These simulations indicate that a disorganized cellular ultrastructure negatively impacts metabolite transport in diabetic cardiomyopathy. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
Collapse
Affiliation(s)
- Shouryadipta Ghosh
- CSIRO Data61, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, VIC 3168, Australia
- Department of Biomedical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Giovanni Guglielmi
- Department of Biomedical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
- School of Mathematics, University of Birmingham, Edgbaston B15 2TS, UK
| | - Ioannis Orfanidis
- Health Data Specialists, Grand Canal Docklands, Dublin D02 VK08, Republic of Ireland
| | - Fabian Spill
- School of Mathematics, University of Birmingham, Edgbaston B15 2TS, UK
| | - Anthony Hickey
- School of Biological Sciences, University of Auckland, Auckland, NZ 1042, New Zealand
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology, Bio21 Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
4
|
Musgrave JH, Han JC, Ward ML, Taberner AJ, Loiselle DS, Tran K. Uncovering cross-bridge properties that underlie the cardiac active complex modulus using model linearisation techniques. Math Biosci 2022; 353:108922. [DOI: 10.1016/j.mbs.2022.108922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/12/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
|
5
|
Computational Modeling and Imaging of the Intracellular Oxygen Gradient. Int J Mol Sci 2022; 23:ijms232012597. [PMID: 36293452 PMCID: PMC9604273 DOI: 10.3390/ijms232012597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022] Open
Abstract
Computational modeling can provide a mechanistic and quantitative framework for describing intracellular spatial heterogeneity of solutes such as oxygen partial pressure (pO2). This study develops and evaluates a finite-element model of oxygen-consuming mitochondrial bioenergetics using the COMSOL Multiphysics program. The model derives steady-state oxygen (O2) distributions from Fickian diffusion and Michaelis–Menten consumption kinetics in the mitochondria and cytoplasm. Intrinsic model parameters such as diffusivity and maximum consumption rate were estimated from previously published values for isolated and intact mitochondria. The model was compared with experimental data collected for the intracellular and mitochondrial pO2 levels in human cervical cancer cells (HeLa) in different respiratory states and under different levels of imposed pO2. Experimental pO2 gradients were measured using lifetime imaging of a Förster resonance energy transfer (FRET)-based O2 sensor, Myoglobin-mCherry, which offers in situ real-time and noninvasive measurements of subcellular pO2 in living cells. On the basis of these results, the model qualitatively predicted (1) the integrated experimental data from mitochondria under diverse experimental conditions, and (2) the impact of changes in one or more mitochondrial processes on overall bioenergetics.
Collapse
|
6
|
Nichenko AS, Specht KS, Craige SM, Drake JC. Sensing local energetics to acutely regulate mitophagy in skeletal muscle. Front Cell Dev Biol 2022; 10:987317. [PMID: 36105350 PMCID: PMC9465048 DOI: 10.3389/fcell.2022.987317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023] Open
Abstract
The energetic requirements of skeletal muscle to sustain movement, as during exercise, is met largely by mitochondria, which form an intricate, interconnected reticulum. Maintenance of a healthy mitochondrial reticulum is essential for skeletal muscle function, suggesting quality control pathways are spatially governed. Mitophagy, the process by which damaged and/or dysfunctional regions of the mitochondrial reticulum are removed and degraded, has emerged as an integral part of the molecular response to exercise. Upregulation of mitophagy in response to acute exercise is directly connected to energetic sensing mechanisms through AMPK. In this review, we discuss the connection of mitophagy to muscle energetics and how AMPK may spatially control mitophagy through multiple potential means.
Collapse
|
7
|
Rajagopal V, Arumugam S, Hunter PJ, Khadangi A, Chung J, Pan M. The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology? Annu Rev Biomed Data Sci 2022; 5:341-366. [PMID: 35576556 DOI: 10.1146/annurev-biodatasci-072018-021246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern biology and biomedicine are undergoing a big data explosion, needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome project: a framework and approach for creating, sharing, and using biophysics-based computational models of single-cell physiology. Using examples in calcium signaling, bioenergetics, and endosomal trafficking, we highlight the need for spatially detailed, biophysics-based computational models to uncover new mechanisms underlying cell biology. We review progress and challenges to date toward creating cell physiome models. We then introduce bond graphs as an efficient way to create cell physiome models that integrate chemical, mechanical, electromagnetic, and thermal processes while maintaining mass and energy balance. Bond graphs enhance modularization and reusability of computational models of cells at scale. We conclude with a look forward at steps that will help fully realize this exciting new field of mechanistic biomedical data science. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Senthil Arumugam
- Cellular Physiology Lab, Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences; European Molecular Biological Laboratory (EMBL) Australia; and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton/Melbourne, Victoria, Australia
| | - Peter J Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Afshin Khadangi
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Joshua Chung
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Michael Pan
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
8
|
Colman MA, Alvarez-Lacalle E, Echebarria B, Sato D, Sutanto H, Heijman J. Multi-Scale Computational Modeling of Spatial Calcium Handling From Nanodomain to Whole-Heart: Overview and Perspectives. Front Physiol 2022; 13:836622. [PMID: 35370783 PMCID: PMC8964409 DOI: 10.3389/fphys.2022.836622] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of intracellular calcium is a critical component of cardiac electrophysiology and excitation-contraction coupling. The calcium spark, the fundamental element of the intracellular calcium transient, is initiated in specialized nanodomains which co-locate the ryanodine receptors and L-type calcium channels. However, calcium homeostasis is ultimately regulated at the cellular scale, by the interaction of spatially separated but diffusively coupled nanodomains with other sub-cellular and surface-membrane calcium transport channels with strong non-linear interactions; and cardiac electrophysiology and arrhythmia mechanisms are ultimately tissue-scale phenomena, regulated by the interaction of a heterogeneous population of coupled myocytes. Recent advances in imaging modalities and image-analysis are enabling the super-resolution reconstruction of the structures responsible for regulating calcium homeostasis, including the internal structure of nanodomains themselves. Extrapolating functional and imaging data from the nanodomain to the whole-heart is non-trivial, yet essential for translational insight into disease mechanisms. Computational modeling has important roles to play in relating structural and functional data at the sub-cellular scale and translating data across the scales. This review covers recent methodological advances that enable image-based modeling of the single nanodomain and whole cardiomyocyte, as well as the development of multi-scale simulation approaches to integrate data from nanometer to whole-heart. Firstly, methods to overcome the computational challenges of simulating spatial calcium dynamics in the nanodomain are discussed, including image-based modeling at this scale. Then, recent whole-cell models, capable of capturing a range of different structures (such as the T-system and mitochondria) and cellular heterogeneity/variability are discussed at two different levels of discretization. Novel methods to integrate the models and data across the scales and simulate stochastic dynamics in tissue-scale models are then discussed, enabling elucidation of the mechanisms by which nanodomain remodeling underlies arrhythmia and contractile dysfunction. Perspectives on model differences and future directions are provided throughout.
Collapse
Affiliation(s)
- Michael A. Colman
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Blas Echebarria
- Departament de Fisica, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
| | - Daisuke Sato
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Henry Sutanto
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Jordi Heijman
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
9
|
Paradoxes of Hymenoptera flight muscles, extreme machines. Biophys Rev 2022; 14:403-412. [PMID: 35340599 PMCID: PMC8921419 DOI: 10.1007/s12551-022-00937-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2022] [Indexed: 10/29/2022] Open
Abstract
AbstractIn the Carboniferous, insects evolved flight. Intense selection drove for high performance and approximately 100 million years later, Hymenoptera (bees, wasps and ants) emerged. Some species had proportionately small wings, with apparently impossible aerodynamic challenges including a need for high frequency flight muscles (FMs), powered exclusively off aerobic pathways and resulting in extreme aerobic capacities. Modern insect FMs are the most refined and form large dense blocks that occupy 90% of the thorax. These can beat wings at 200 to 230 Hz, more than double that achieved by standard neuromuscular systems. To do so, rapid repolarisation was circumvented through evolution of asynchronous stimulation, stretch activation, elastic recoil and a paradoxically slow Ca2+ reuptake. While the latter conserves ATP, considerable ATP is demanded at the myofibrils. FMs have diminished sarcoplasmic volumes, and ATP is produced solely by mitochondria, which pack myocytes to maximal limits and have very dense cristae. Gaseous oxygen is supplied directly to mitochondria. While FMs appear to be optimised for function, several unusual paradoxes remain. FMs lack any significant equivalent to the creatine kinase shuttle, and myofibrils are twice as wide as those of within cardiomyocytes. The mitochondrial electron transport systems also release large amounts of reactive oxygen species (ROS) and respiratory complexes do not appear to be present at any exceptional level. Given that the loss of the creatine kinase shuttle and elevated ROS impairs heart function, we question how do FM shuttle adenylates at high rates and tolerate oxidative stress conditions that occur in diseased hearts?
Collapse
|
10
|
Xu C, Cao Y, Liu R, Liu L, Zhang W, Fang X, Jia S, Ye J, Liu Y, Weng L, Qiao X, Li B, Zheng M. Mitophagy-regulated mitochondrial health strongly protects the heart against cardiac dysfunction after acute myocardial infarction. J Cell Mol Med 2022; 26:1315-1326. [PMID: 35040256 PMCID: PMC8831983 DOI: 10.1111/jcmm.17190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/11/2021] [Accepted: 01/03/2022] [Indexed: 01/08/2023] Open
Abstract
Autophagy including mitophagy serves as an important regulatory mechanism in the heart to maintain the cellular homeostasis and to protect against heart damages caused by myocardial infarction (MI). The current study aims to dissect roles of general autophagy and specific mitophagy in regulating cardiac function after MI. By using Beclin1+/- , Fundc1 knockout (KO) and Fundc1 transgenic (TG) mouse models, combined with starvation and MI models, we found that Fundc1 KO caused more severe mitochondrial and cardiac dysfunction damages than Beclin1+/- after MI. Interestingly, Beclin1+/- caused notable decrease of total autophagy without detectable change to mitophagy, and Fundc1 KO markedly suppressed mitophagy but did not change the total autophagy activity. In contrast, starvation increased total autophagy without changing mitophagy while Fundc1 TG elevated total autophagy and mitophagy in mouse hearts. As a result, Fundc1 TG provided much stronger protective effects than starvation after MI. Moreover, Beclin1+/- /Fundc1 TG showed increased total autophagy and mitophagy to a level comparable to Fundc1 TG per se, and completely reversed Beclin1+/- -caused aggravation of mitochondrial and cardiac injury after MI. Our results reveal that mitophagy but not general autophagy contributes predominantly to the cardiac protective effect through regulating mitochondrial function.
Collapse
Affiliation(s)
- Chunling Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Yangpo Cao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ruxia Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Lei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Weilin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xuan Fang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Shi Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Jingjing Ye
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Yingying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Lin Weng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Xue Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Bo Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ming Zheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| |
Collapse
|
11
|
Isolation and reconstruction of cardiac mitochondria from SBEM images using a deep learning-based method. J Struct Biol 2021; 214:107806. [PMID: 34742833 DOI: 10.1016/j.jsb.2021.107806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/06/2021] [Accepted: 10/27/2021] [Indexed: 11/23/2022]
Abstract
Mitochondrial morphological defects are a common feature of diseased cardiac myocytes. However, quantitative assessment of mitochondrial morphology is limited by the time-consuming manual segmentation of electron micrograph (EM) images. To advance understanding of the relation between morphological defects and dysfunction, an efficient morphological reconstruction method is desired to enable isolation and reconstruction of mitochondria from EM images. We propose a new method for isolating and reconstructing single mitochondria from serial block-face scanning EM (SBEM) images. CDeep3M, a cloud-based deep learning network for EM images, was used to segment mitochondrial interior volumes and boundaries. Post-processing was performed using both the predicted interior volume and exterior boundary to isolate and reconstruct individual mitochondria. Series of SBEM images from two separate cardiac myocytes were processed. The highest F1-score was 95% using 50 training datasets, greater than that for previously reported automated methods and comparable to manual segmentations. Accuracy of separation of individual mitochondria was 80% on a pixel basis. A total of 2315 mitochondria in the two series of SBEM images were evaluated with a mean volume of 0.78 µm3. The volume distribution was very broad and skewed; the most frequent mitochondria were 0.04-0.06 µm3, but mitochondria larger than 2.0 µm3 accounted for more than 10% of the total number. The average short-axis length was 0.47 µm. Primarily longitudinal mitochondria (0-30 degrees) were dominant (54%). This new automated segmentation and separation method can help quantitate mitochondrial morphology and improve understanding of myocyte structure-function relationships.
Collapse
|
12
|
Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy. Proc Natl Acad Sci U S A 2021; 118:2025932118. [PMID: 34493662 PMCID: PMC8449344 DOI: 10.1073/pnas.2025932118] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022] Open
Abstract
Mitochondria form a complex, interconnected reticulum that is maintained through coordination among biogenesis, dynamic fission, and fusion and mitophagy, which are initiated in response to various cues to maintain energetic homeostasis. These cellular events, which make up mitochondrial quality control, act with remarkable spatial precision, but what governs such spatial specificity is poorly understood. Herein, we demonstrate that specific isoforms of the cellular bioenergetic sensor, 5' AMP-activated protein kinase (AMPKα1/α2/β2/γ1), are localized on the outer mitochondrial membrane, referred to as mitoAMPK, in various tissues in mice and humans. Activation of mitoAMPK varies across the reticulum in response to energetic stress, and inhibition of mitoAMPK activity attenuates exercise-induced mitophagy in skeletal muscle in vivo. Discovery of a mitochondrial pool of AMPK and its local importance for mitochondrial quality control underscores the complexity of sensing cellular energetics in vivo that has implications for targeting mitochondrial energetics for disease treatment.
Collapse
|
13
|
Prabhakar N, Belevich I, Peurla M, Heiligenstein X, Chang HC, Sahlgren C, Jokitalo E, Rosenholm JM. Cell Volume (3D) Correlative Microscopy Facilitated by Intracellular Fluorescent Nanodiamonds as Multi-Modal Probes. NANOMATERIALS 2020; 11:nano11010014. [PMID: 33374705 PMCID: PMC7822478 DOI: 10.3390/nano11010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023]
Abstract
Three-dimensional correlative light and electron microscopy (3D CLEM) is attaining popularity as a potential technique to explore the functional aspects of a cell together with high-resolution ultrastructural details across the cell volume. To perform such a 3D CLEM experiment, there is an imperative requirement for multi-modal probes that are both fluorescent and electron-dense. These multi-modal probes will serve as landmarks in matching up the large full cell volume datasets acquired by different imaging modalities. Fluorescent nanodiamonds (FNDs) are a unique nanosized, fluorescent, and electron-dense material from the nanocarbon family. We hereby propose a novel and straightforward method for executing 3D CLEM using FNDs as multi-modal landmarks. We demonstrate that FND is biocompatible and is easily identified both in living cell fluorescence imaging and in serial block-face scanning electron microscopy (SB-EM). We illustrate the method by registering multi-modal datasets.
Collapse
Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Correspondence:
| | - Ilya Belevich
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan;
| | - Cecilia Sahlgren
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Eija Jokitalo
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| |
Collapse
|
14
|
Cowley AW, Dash RK. Computational/Experimental Interrogation of the Failing Heart-A Perspective on "Impaired Myocardial Energetics Causes Mechanical Dysfunction in Decompensated Failing Hearts". FUNCTION (OXFORD, ENGLAND) 2020; 1:zqaa022. [PMID: 35330639 PMCID: PMC8788834 DOI: 10.1093/function/zqaa022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/24/2020] [Accepted: 10/07/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA,Address correspondence to A.W.C. (e-mail: )
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| |
Collapse
|
15
|
Lopez R, Marzban B, Gao X, Lauinger E, Van den Bergh F, Whitesall SE, Converso-Baran K, Burant CF, Michele DE, Beard DA. Impaired Myocardial Energetics Causes Mechanical Dysfunction in Decompensated Failing Hearts. FUNCTION 2020; 1:zqaa018. [PMID: 33074265 PMCID: PMC7552914 DOI: 10.1093/function/zqaa018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 01/06/2023] Open
Abstract
Cardiac mechanical function is supported by ATP hydrolysis, which provides the chemical-free energy to drive the molecular processes underlying cardiac pumping. Physiological rates of myocardial ATP consumption require the heart to resynthesize its entire ATP pool several times per minute. In the failing heart, cardiomyocyte metabolic dysfunction leads to a reduction in the capacity for ATP synthesis and associated free energy to drive cellular processes. Yet it remains unclear if and how metabolic/energetic dysfunction that occurs during heart failure affects mechanical function of the heart. We hypothesize that changes in phosphate metabolite concentrations (ATP, ADP, inorganic phosphate) that are associated with decompensation and failure have direct roles in impeding contractile function of the myocardium in heart failure, contributing to the whole-body phenotype. To test this hypothesis, a transverse aortic constriction (TAC) rat model of pressure overload, hypertrophy, and decompensation was used to assess relationships between metrics of whole-organ pump function and myocardial energetic state. A multiscale computational model of cardiac mechanoenergetic coupling was used to identify and quantify the contribution of metabolic dysfunction to observed mechanical dysfunction. Results show an overall reduction in capacity for oxidative ATP synthesis fueled by either fatty acid or carbohydrate substrates as well as a reduction in total levels of adenine nucleotides and creatine in myocardium from TAC animals compared to sham-operated controls. Changes in phosphate metabolite levels in the TAC rats are correlated with impaired mechanical function, consistent with the overall hypothesis. Furthermore, computational analysis of myocardial metabolism and contractile dynamics predicts that increased levels of inorganic phosphate in TAC compared to control animals kinetically impair the myosin ATPase crossbridge cycle in decompensated hypertrophy/heart failure.
Collapse
Affiliation(s)
- Rachel Lopez
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Bahador Marzban
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Gao
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Ellen Lauinger
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Françoise Van den Bergh
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Steven E Whitesall
- Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Kimber Converso-Baran
- Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Address correspondence to D.A.B. (e-mail: )
| |
Collapse
|
16
|
Drake JC, Yan Z. Precision remodeling: how exercise improves mitochondrial quality in myofibers. CURRENT OPINION IN PHYSIOLOGY 2020; 10:96-101. [PMID: 32832743 DOI: 10.1016/j.cophys.2019.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The profound energetic demand of prolonged exercise imposed upon skeletal muscle and the heart is met by oxidation of substrate within mitochondria. As such, several coordinated events are initiated in order to maintain mitochondria, collectively known as mitochondrial quality control. In this review, we discuss how mitochondrial quality control functions to maintain the integrity of the reticulum and energy production in response to prolonged exercise, as well as the relevant signaling events that dictate these responses. Based upon the prevailing data in the field, we propose a model where exercise-mediated quality control may be chiefly regulated through local mechanisms, thus allowing for the remarkable precision in mitochondrial quality control events.
Collapse
Affiliation(s)
- Joshua C Drake
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center
| | - Zhen Yan
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908
| |
Collapse
|
17
|
Maddah M, Mandegar MA, Dame K, Grafton F, Loewke K, Ribeiro AJS. Quantifying drug-induced structural toxicity in hepatocytes and cardiomyocytes derived from hiPSCs using a deep learning method. J Pharmacol Toxicol Methods 2020; 105:106895. [PMID: 32629158 DOI: 10.1016/j.vascn.2020.106895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Abstract
Cardiac and hepatic toxicity result from induced disruption of the functioning of cardiomyocytes and hepatocytes, respectively, which is tightly related to the organization of their subcellular structures. Cellular structure can be analyzed from microscopy imaging data. However, subtle or complex structural changes that are not easily perceived may be missed by conventional image-analysis techniques. Here we report the evaluation of PhenoTox, an image-based deep-learning method of quantifying drug-induced structural changes using human hepatocytes and cardiomyocytes derived from human induced pluripotent stem cells. We assessed the ability of the deep learning method to detect variations in the organization of cellular structures from images of fixed or live cells. We also evaluated the power and sensitivity of the method for detecting toxic effects of drugs by conducting a set of experiments using known toxicants and other methods of screening for cytotoxic effects. Moreover, we used PhenoTox to characterize the effects of tamoxifen and doxorubicin-which cause liver toxicity-on hepatocytes. PhenoTox revealed differences related to loss of cytochrome P450 3A4 activity, for which it showed greater sensitivity than a caspase 3/7 assay. Finally, PhenoTox detected structural toxicity in cardiomyocytes, which was correlated with contractility defects induced by doxorubicin, erlotinib, and sorafenib. Taken together, the results demonstrated that PhenoTox can capture the subtle morphological changes that are early signs of toxicity in both hepatocytes and cardiomyocytes.
Collapse
Affiliation(s)
| | | | - Keri Dame
- Division of Applied Regulatory Science, Office of Translational Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Alexandre J S Ribeiro
- Division of Applied Regulatory Science, Office of Translational Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| |
Collapse
|
18
|
Impact of global structure on diffusive exploration of organelle networks. Sci Rep 2020; 10:4984. [PMID: 32188905 PMCID: PMC7080787 DOI: 10.1038/s41598-020-61598-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023] Open
Abstract
We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures.
Collapse
|