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Sizek H, Deritei D, Fleig K, Harris M, Regan PL, Glass K, Regan ER. Unlocking mitochondrial dysfunction-associated senescence (MiDAS) with NAD + - A Boolean model of mitochondrial dynamics and cell cycle control. Transl Oncol 2024; 49:102084. [PMID: 39163758 PMCID: PMC11380032 DOI: 10.1016/j.tranon.2024.102084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 05/14/2024] [Accepted: 05/25/2024] [Indexed: 08/22/2024] Open
Abstract
The steady accumulation of senescent cells with aging creates tissue environments that aid cancer evolution. Aging cell states are highly heterogeneous. 'Deep senescent' cells rely on healthy mitochondria to fuel a strong proinflammatory secretome, including cytokines, growth and transforming signals. Yet, the physiological triggers of senescence such as reactive oxygen species (ROS) can also trigger mitochondrial dysfunction, and sufficient energy deficit to alter their secretome and cause chronic oxidative stress - a state termed Mitochondrial Dysfunction-Associated Senescence (MiDAS). Here, we offer a mechanistic hypothesis for the molecular processes leading to MiDAS, along with testable predictions. To do this we have built a Boolean regulatory network model that qualitatively captures key aspects of mitochondrial dynamics during cell cycle progression (hyper-fusion at the G1/S boundary, fission in mitosis), apoptosis (fission and dysfunction) and glucose starvation (reversible hyper-fusion), as well as MiDAS in response to SIRT3 knockdown or oxidative stress. Our model reaffirms the protective role of NAD+ and external pyruvate. We offer testable predictions about the growth factor- and glucose-dependence of MiDAS and its reversibility at different stages of reactive oxygen species (ROS)-induced senescence. Our model provides mechanistic insights into the distinct stages of DNA-damage induced senescence, the relationship between senescence and epithelial-to-mesenchymal transition in cancer and offers a foundation for building multiscale models of tissue aging.
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Affiliation(s)
- Herbert Sizek
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Dávid Deritei
- Channing Division of Network Medicine, Brigham and Women's Hospital / Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Fleig
- Neuroscience, The College of Wooster, Wooster, OH 44691, USA
| | - Marlayna Harris
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Peter L Regan
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital / Harvard Medical School, Boston, MA 02115, USA
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2
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Zhou Q, Cao T, Li F, Zhang M, Li X, Zhao H, Zhou Y. Mitochondria: a new intervention target for tumor invasion and metastasis. Mol Med 2024; 30:129. [PMID: 39179991 PMCID: PMC11344364 DOI: 10.1186/s10020-024-00899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Mitochondria, responsible for cellular energy synthesis and signal transduction, intricately regulate diverse metabolic processes, mediating fundamental biological phenomena such as cell growth, aging, and apoptosis. Tumor invasion and metastasis, key characteristics of malignancies, significantly impact patient prognosis. Tumor cells frequently exhibit metabolic abnormalities in mitochondria, including alterations in metabolic dynamics and changes in the expression of relevant metabolic genes and associated signal transduction pathways. Recent investigations unveil further insights into mitochondrial metabolic abnormalities, revealing their active involvement in tumor cell proliferation, resistance to chemotherapy, and a crucial role in tumor cell invasion and metastasis. This paper comprehensively outlines the latest research advancements in mitochondrial structure and metabolic function. Emphasis is placed on summarizing the role of mitochondrial metabolic abnormalities in tumor invasion and metastasis, including alterations in the mitochondrial genome (mutations), activation of mitochondrial-to-nuclear signaling, and dynamics within the mitochondria, all intricately linked to the processes of tumor invasion and metastasis. In conclusion, the paper discusses unresolved scientific questions in this field, aiming to provide a theoretical foundation and novel perspectives for developing innovative strategies targeting tumor invasion and metastasis based on mitochondrial biology.
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Affiliation(s)
- Quanling Zhou
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Tingping Cao
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Fujun Li
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Ming Zhang
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Xiaohui Li
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Hailong Zhao
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China
| | - Ya Zhou
- Department of Pathophysiology, Zunyi Medical University, Zunyi Guizhou, 563000, China.
- Department of Physics, Zunyi Medical University, Zunyi Guizhou, 563000, China.
- Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Guizhou, 563000, China.
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Contini C, Manconi B, Olianas A, Guadalupi G, Schirru A, Zorcolo L, Castagnola M, Messana I, Faa G, Diaz G, Cabras T. Combined High-Throughput Proteomics and Random Forest Machine-Learning Approach Differentiates and Classifies Metabolic, Immune, Signaling and ECM Intra-Tumor Heterogeneity of Colorectal Cancer. Cells 2024; 13:1311. [PMID: 39195201 DOI: 10.3390/cells13161311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024] Open
Abstract
Colorectal cancer (CRC) is a frequent, worldwide tumor described for its huge complexity, including inter-/intra-heterogeneity and tumor microenvironment (TME) variability. Intra-tumor heterogeneity and its connections with metabolic reprogramming and epithelial-mesenchymal transition (EMT) were investigated with explorative shotgun proteomics complemented by a Random Forest (RF) machine-learning approach. Deep and superficial tumor regions and distant-site non-tumor samples from the same patients (n = 16) were analyzed. Among the 2009 proteins analyzed, 91 proteins, including 23 novel potential CRC hallmarks, showed significant quantitative changes. In addition, a 98.4% accurate classification of the three analyzed tissues was obtained by RF using a set of 21 proteins. Subunit E1 of 2-oxoglutarate dehydrogenase (OGDH-E1) was the best classifying factor for the superficial tumor region, while sorting nexin-18 and coatomer-beta protein (beta-COP), implicated in protein trafficking, classified the deep region. Down- and up-regulations of metabolic checkpoints involved different proteins in superficial and deep tumors. Analogously to immune checkpoints affecting the TME, cytoskeleton and extracellular matrix (ECM) dynamics were crucial for EMT. Galectin-3, basigin, S100A9, and fibronectin involved in TME-CRC-ECM crosstalk were found to be differently variated in both tumor regions. Different metabolic strategies appeared to be adopted by the two CRC regions to uncouple the Krebs cycle and cytosolic glucose metabolism, promote lipogenesis, promote amino acid synthesis, down-regulate bioenergetics in mitochondria, and up-regulate oxidative stress. Finally, correlations with the Dukes stage and budding supported the finding of novel potential CRC hallmarks and therapeutic targets.
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Affiliation(s)
- Cristina Contini
- Department of Medical Sciences and Public Health, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Giulia Guadalupi
- Department of Surgical Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Alessandra Schirru
- Department of Life and Environmental Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Luigi Zorcolo
- Department of Surgical Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, 00143 Roma, Italy
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168 Roma, Italy
| | - Gavino Faa
- Department of Medical Sciences and Public Health, Statal University of Cagliari, 09042 Monserrato (CA), Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Giacomo Diaz
- Department of Biomedical Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, Statal University of Cagliari, 09042 Monserrato (CA), Italy
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Mouillet-Richard S, Cazelles A, Sroussi M, Gallois C, Taieb J, Laurent-Puig P. Clinical Challenges of Consensus Molecular Subtype CMS4 Colon Cancer in the Era of Precision Medicine. Clin Cancer Res 2024; 30:2351-2358. [PMID: 38564259 PMCID: PMC11145159 DOI: 10.1158/1078-0432.ccr-23-3964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Over the past decade, our understanding of the diversity of colorectal cancer has expanded significantly, raising hopes of tailoring treatments more precisely for individual patients. A key achievement in this direction was the establishment of the consensus molecular classification, particularly identifying the challenging consensus molecular subtype (CMS) CMS4 associated with poor prognosis. Because of its aggressive nature, extensive research is dedicated to the CMS4 subgroup. Recent years have unveiled molecular and microenvironmental features at the tissue level specific to CMS4 colorectal cancer. This has paved the way for mechanistic studies and the development of preclinical models. Simultaneously, efforts have been made to easily identify patients with CMS4 colorectal cancer. Reassessing clinical trial results through the CMS classification lens has improved our understanding of the therapeutic challenges linked to this subtype. Exploration of the biology of CMS4 colorectal cancer is yielding potential biomarkers and novel treatment approaches. This overview aims to provide insights into the clinico-biological characteristics of the CMS4 subgroup, the molecular pathways driving this subtype, and available diagnostic options. We also emphasize the therapeutic challenges associated with this subtype, offering potential explanations. Finally, we summarize the current tailored treatments for CMS4 colorectal cancer emerging from fundamental and preclinical studies.
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Affiliation(s)
- Sophie Mouillet-Richard
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Antoine Cazelles
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Marine Sroussi
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Gallois
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Taieb
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Pierre Laurent-Puig
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
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Sizek H, Deritei D, Fleig K, Harris M, Regan PL, Glass K, Regan ER. Unlocking Mitochondrial Dysfunction-Associated Senescence (MiDAS) with NAD + - a Boolean Model of Mitochondrial Dynamics and Cell Cycle Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572194. [PMID: 38187609 PMCID: PMC10769269 DOI: 10.1101/2023.12.18.572194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The steady accumulation of senescent cells with aging creates tissue environments that aid cancer evolution. Aging cell states are highly heterogeneous. 'Deep senescent' cells rely on healthy mitochondria to fuel a strong proinflammatory secretome, including cytokines, growth and transforming signals. Yet, the physiological triggers of senescence such as the reactive oxygen species (ROS) can also trigger mitochondrial dysfunction, and sufficient energy deficit to alter their secretome and cause chronic oxidative stress - a state termed Mitochondrial Dysfunction-Associated Senescence (MiDAS). Here, we offer a mechanistic hypothesis for the molecular processes leading to MiDAS, along with testable predictions. To do this we have built a Boolean regulatory network model that qualitatively captures key aspects of mitochondrial dynamics during cell cycle progression (hyper-fusion at the G1/S boundary, fission in mitosis), apoptosis (fission and dysfunction) and glucose starvation (reversible hyper-fusion), as well as MiDAS in response to SIRT3 knockdown or oxidative stress. Our model reaffirms the protective role of NAD + and external pyruvate. We offer testable predictions about the growth factor- and glucose-dependence of MiDAS and its reversibility at different stages of reactive oxygen species (ROS)-induced senescence. Our model provides mechanistic insights into the distinct stages of DNA-damage induced senescence, the relationship between senescence and epithelial-to-mesenchymal transition in cancer and offers a foundation for building multiscale models of tissue aging. Highlights Boolean regulatory network model reproduces mitochondrial dynamics during cell cycle progression, apoptosis, and glucose starvation. Model offers a mechanistic explanation for the positive feedback loop that locks in Mitochondrial Dysfunction-Associated Senescence (MiDAS), involving autophagy-resistant, hyperfused, dysfunctional mitochondria. Model reproduces ROS-mediated mitochondrial dysfunction and suggests that MiDAS is part of the early phase of damage-induced senescence. Model predicts that cancer-driving mutations that bypass the G1/S checkpoint generally increase the incidence of MiDAS, except for p53 loss.
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Palma FR, Gantner BN, Sakiyama MJ, Kayzuka C, Shukla S, Lacchini R, Cunniff B, Bonini MG. ROS production by mitochondria: function or dysfunction? Oncogene 2024; 43:295-303. [PMID: 38081963 DOI: 10.1038/s41388-023-02907-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 01/31/2024]
Abstract
In eukaryotic cells, ATP generation is generally viewed as the primary function of mitochondria under normoxic conditions. Reactive oxygen species (ROS), in contrast, are regarded as the by-products of respiration, and are widely associated with dysfunction and disease. Important signaling functions have been demonstrated for mitochondrial ROS in recent years. Still, their chemical reactivity and capacity to elicit oxidative damage have reinforced the idea that ROS are the products of dysfunctional mitochondria that accumulate during disease. Several studies support a different model, however, by showing that: (1) limited oxygen availability results in mitochondria prioritizing ROS production over ATP, (2) ROS is an essential adaptive mitochondrial signal triggered by various important stressors, and (3) while mitochondria-independent ATP production can be easily engaged by most cells, there is no known replacement for ROS-driven redox signaling. Based on these observations and other evidence reviewed here, we highlight the role of ROS production as a major mitochondrial function involved in cellular adaptation and stress resistance. As such, we propose a rekindled view of ROS production as a primary mitochondrial function as essential to life as ATP production itself.
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Affiliation(s)
- Flavio R Palma
- Department of Medicine, Division of Hematology Oncology, Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Northwestern University, Chicago, IL, USA
| | - Benjamin N Gantner
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Marcelo J Sakiyama
- Department of Medicine, Division of Hematology Oncology, Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Northwestern University, Chicago, IL, USA
| | - Cezar Kayzuka
- Department of Pharmacology, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Brian Cunniff
- Department of Pathology and Laboratory Medicine, Larner School of Medicine, University of Vermont, Burlington, VT, USA
| | - Marcelo G Bonini
- Department of Medicine, Division of Hematology Oncology, Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Northwestern University, Chicago, IL, USA.
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Ježek P. Pitfalls of Mitochondrial Redox Signaling Research. Antioxidants (Basel) 2023; 12:1696. [PMID: 37759999 PMCID: PMC10525995 DOI: 10.3390/antiox12091696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Redox signaling from mitochondria (mt) to the cytosol and plasma membrane (PM) has been scarcely reported, such as in the case of hypoxic cell adaptation or (2-oxo-) 2-keto-isocaproate (KIC) β-like-oxidation stimulating insulin secretion in pancreatic β-cells. Mutual redox state influence between mitochondrial major compartments, the matrix and the intracristal space, and the cytosol is therefore derived theoretically in this article to predict possible conditions, when mt-to-cytosol and mt-to-PM signals may occur, as well as conditions in which the cytosolic redox signaling is not overwhelmed by the mitochondrial antioxidant capacity. Possible peroxiredoxin 3 participation in mt-to-cytosol redox signaling is discussed, as well as another specific case, whereby mitochondrial superoxide release is diminished, whereas the matrix MnSOD is activated. As a result, the enhanced conversion to H2O2 allows H2O2 diffusion into the cytosol, where it could be a predominant component of the H2O2 release. In both of these ways, mt-to-cytosol and mt-to-PM signals may be realized. Finally, the use of redox-sensitive probes is discussed, which disturb redox equilibria, and hence add a surplus redox-buffering to the compartment, where they are localized. Specifically, when attempts to quantify net H2O2 fluxes are to be made, this should be taken into account.
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Affiliation(s)
- Petr Ježek
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
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