1
|
Kim LC, Lesner NP, Simon MC. Cancer Metabolism under Limiting Oxygen Conditions. Cold Spring Harb Perspect Med 2024; 14:a041542. [PMID: 37848248 PMCID: PMC10835619 DOI: 10.1101/cshperspect.a041542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Molecular oxygen (O2) is essential for cellular bioenergetics and numerous biochemical reactions necessary for life. Solid tumors outgrow the native blood supply and diffusion limits of O2, and therefore must engage hypoxia response pathways that evolved to withstand acute periods of low O2 Hypoxia activates coordinated gene expression programs, primarily through hypoxia inducible factors (HIFs), to support survival. Many of these changes involve metabolic rewiring such as increasing glycolysis to support ATP generation while suppressing mitochondrial metabolism. Since low O2 is often coupled with nutrient stress in the tumor microenvironment, other responses to hypoxia include activation of nutrient uptake pathways, metabolite scavenging, and regulation of stress and growth signaling cascades. Continued development of models that better recapitulate tumors and their microenvironments will lead to greater understanding of oxygen-dependent metabolic reprogramming and lead to more effective cancer therapies.
Collapse
Affiliation(s)
- Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
2
|
Li F, Liu P, Mi W, Li L, Anderson NM, Lesner NP, Burrows M, Plesset J, Majer A, Wang G, Li J, Zhu L, Keith B, Simon MC. Blocking methionine catabolism induces senescence and confers vulnerability to GSK3 inhibition in liver cancer. Nat Cancer 2024; 5:131-146. [PMID: 38168934 DOI: 10.1038/s43018-023-00671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/16/2023] [Indexed: 01/05/2024]
Abstract
Availability of the essential amino acid methionine affects cellular metabolism and growth, and dietary methionine restriction has been implicated as a cancer therapeutic strategy. Nevertheless, how liver cancer cells respond to methionine deprivation and underlying mechanisms remain unclear. Here we find that human liver cancer cells undergo irreversible cell cycle arrest upon methionine deprivation in vitro. Blocking methionine adenosyl transferase 2A (MAT2A)-dependent methionine catabolism induces cell cycle arrest and DNA damage in liver cancer cells, resulting in cellular senescence. A pharmacological screen further identified GSK3 inhibitors as senolytics that selectively kill MAT2A-inhibited senescent liver cancer cells. Importantly, combined treatment with MAT2A and GSK3 inhibitors therapeutically blunts liver tumor growth in vitro and in vivo across multiple models. Together, methionine catabolism is essential for liver tumor growth, and its inhibition can be exploited as an improved pro-senescence strategy for combination with senolytic agents to treat liver cancer.
Collapse
Affiliation(s)
- Fuming Li
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Pingyu Liu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Wen Mi
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Liucheng Li
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Nicole M Anderson
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Burrows
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Plesset
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariana Majer
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanlin Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jinyang Li
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Lingzhi Zhu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Brian Keith
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research 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.
| |
Collapse
|
3
|
Missiaen R, Lesner NP, Simon MC. HIF: a master regulator of nutrient availability and metabolic cross-talk in the tumor microenvironment. EMBO J 2023; 42:e112067. [PMID: 36808622 PMCID: PMC10015374 DOI: 10.15252/embj.2022112067] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 02/22/2023] Open
Abstract
A role for hypoxia-inducible factors (HIFs) in hypoxia-dependent regulation of tumor cell metabolism has been thoroughly investigated and covered in reviews. However, there is limited information available regarding HIF-dependent regulation of nutrient fates in tumor and stromal cells. Tumor and stromal cells may generate nutrients necessary for function (metabolic symbiosis) or deplete nutrients resulting in possible competition between tumor cells and immune cells, a result of altered nutrient fates. HIF and nutrients in the tumor microenvironment (TME) affect stromal and immune cell metabolism in addition to intrinsic tumor cell metabolism. HIF-dependent metabolic regulation will inevitably result in the accumulation or depletion of essential metabolites in the TME. In response, various cell types in the TME will respond to these hypoxia-dependent alterations by activating HIF-dependent transcription to alter nutrient import, export, and utilization. In recent years, the concept of metabolic competition has been proposed for critical substrates, including glucose, lactate, glutamine, arginine, and tryptophan. In this review, we discuss how HIF-mediated mechanisms control nutrient sensing and availability in the TME, the competition for nutrients, and the metabolic cross-talk between tumor and stromal cells.
Collapse
Affiliation(s)
- Rindert Missiaen
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
4
|
Bezwada D, Lesner NP, Brooks B, Vu HS, Wu Z, Cai L, Kasitinon S, Kelekar S, Cai F, Aurora AB, Patrick M, Leach A, Ghandour R, Zhang Y, Do D, Sudderth J, Dumesnil D, House S, Rosales T, Poole AM, Lotan Y, Woldu S, Bagrodia A, Meng X, Cadeddu JA, Mishra P, Pedrosa I, Kapur P, Courtney KD, Malloy CR, Margulis V, DeBerardinis RJ. Mitochondrial metabolism in primary and metastatic human kidney cancers. bioRxiv 2023:2023.02.06.527285. [PMID: 36798172 PMCID: PMC9934542 DOI: 10.1101/2023.02.06.527285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Most kidney cancers display evidence of metabolic dysfunction1-4 but how this relates to cancer progression in humans is unknown. We used a multidisciplinary approach to infuse 13C-labeled nutrients during surgical tumour resection in over 70 patients with kidney cancer. Labeling from [U-13C]glucose varies across cancer subtypes, indicating that the kidney environment alone cannot account for all metabolic reprogramming in these tumours. Compared to the adjacent kidney, clear cell renal cell carcinomas (ccRCC) display suppressed labelling of tricarboxylic acid (TCA) cycle intermediates in vivo and in organotypic slices cultured ex vivo, indicating that suppressed labeling is tissue intrinsic. Infusions of [1,2-13C]acetate and [U-13C]glutamine in patients, coupled with respiratory flux of mitochondria isolated from kidney and tumour tissue, reveal primary defects in mitochondrial function in human ccRCC. However, ccRCC metastases unexpectedly have enhanced labeling of TCA cycle intermediates compared to primary ccRCCs, indicating a divergent metabolic program during ccRCC metastasis in patients. In mice, stimulating respiration in ccRCC cells is sufficient to promote metastatic colonization. Altogether, these findings indicate that metabolic properties evolve during human kidney cancer progression, and suggest that mitochondrial respiration may be limiting for ccRCC metastasis but not for ccRCC growth at the site of origin.
Collapse
Affiliation(s)
| | | | | | - Hieu S. Vu
- Children’s Medical Center Research Institute
| | - Zheng Wu
- Children’s Medical Center Research Institute
| | - Ling Cai
- Children’s Medical Center Research Institute
- Quantitative Biomedical Research Center
| | | | | | - Feng Cai
- Children’s Medical Center Research Institute
| | | | | | | | | | | | - Duyen Do
- Children’s Medical Center Research Institute
| | | | | | - Sara House
- Children’s Medical Center Research Institute
| | | | - Alan M. Poole
- Children’s Medical Center Research Institute
- Department of Pediatrics
| | | | | | | | | | | | - Prashant Mishra
- Children’s Medical Center Research Institute
- Department of Pediatrics
| | - Ivan Pedrosa
- Department of Urology
- Department of Radiology
- Kidney Cancer Program
| | - Payal Kapur
- Department of Urology
- Kidney Cancer Program
- Department of Pathology
| | | | - Craig R. Malloy
- Department of Radiology
- Department of Internal Medicine
- Advanced Imaging Research Center
| | | | - Ralph J. DeBerardinis
- Children’s Medical Center Research Institute
- Department of Pediatrics
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
5
|
Chen Z, Bordieanu B, Kesavan R, Lesner NP, Venigalla SSK, Shelton SD, DeBerardinis RJ, Mishra P. Lactate metabolism is essential in early-onset mitochondrial myopathy. Sci Adv 2023; 9:eadd3216. [PMID: 36598990 PMCID: PMC9812384 DOI: 10.1126/sciadv.add3216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Myopathies secondary to mitochondrial electron transport chain (ETC) dysfunction can result in devastating disease. While the consequences of ETC defects have been extensively studied in culture, little in vivo data are available. Using a mouse model of severe, early-onset mitochondrial myopathy, we characterized the proteomic, transcriptomic, and metabolic characteristics of disease progression. Unexpectedly, ETC dysfunction in muscle results in reduced expression of glycolytic enzymes in our animal model and patient muscle biopsies. The decrease in glycolysis was mediated by loss of constitutive Hif1α signaling, down-regulation of the purine nucleotide cycle enzyme AMPD1, and activation of AMPK. In vivo isotope tracing experiments indicated that myopathic muscle relies on lactate import to supply central carbon metabolites. Inhibition of lactate import reduced steady-state levels of tricarboxylic acid cycle intermediates and compromised the life span of myopathic mice. These data indicate an unexpected mode of metabolic reprogramming in severe mitochondrial myopathy that regulates disease progression.
Collapse
Affiliation(s)
- Zhenkang Chen
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bogdan Bordieanu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rushendhiran Kesavan
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas P. Lesner
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Siva Sai Krishna Venigalla
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D. Shelton
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J. DeBerardinis
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
6
|
Wang X, Jia Y, Zhao J, Lesner NP, Menezes CJ, Shelton SD, Venigalla SSK, Xu J, Cai C, Mishra P. A mitofusin 2/HIF1α axis sets a maturation checkpoint in regenerating skeletal muscle. J Clin Invest 2022; 132:e161638. [PMID: 36125902 PMCID: PMC9711883 DOI: 10.1172/jci161638] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
A fundamental issue in regenerative medicine is whether there exist endogenous regulatory mechanisms that limit the speed and efficiency of the repair process. We report the existence of a maturation checkpoint during muscle regeneration that pauses myofibers at a neonatal stage. This checkpoint is regulated by the mitochondrial protein mitofusin 2 (Mfn2), the expression of which is activated in response to muscle injury. Mfn2 is required for growth and maturation of regenerating myofibers; in the absence of Mfn2, new myofibers arrested at a neonatal stage, characterized by centrally nucleated myofibers and loss of H3K27me3 repressive marks at the neonatal myosin heavy chain gene. A similar arrest at the neonatal stage was observed in infantile cases of human centronuclear myopathy. Mechanistically, Mfn2 upregulation suppressed expression of hypoxia-induced factor 1α (HIF1α), which is induced in the setting of muscle damage. Sustained HIF1α signaling blocked maturation of new myofibers at the neonatal-to-adult fate transition, revealing the existence of a checkpoint that delays muscle regeneration. Correspondingly, inhibition of HIF1α allowed myofibers to bypass the checkpoint, thereby accelerating the repair process. We conclude that skeletal muscle contains a regenerative checkpoint that regulates the speed of myofiber maturation in response to Mfn2 and HIF1α activity.
Collapse
Affiliation(s)
- Xun Wang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yuemeng Jia
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiawei Zhao
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicholas P. Lesner
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Cameron J. Menezes
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Spencer D. Shelton
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Siva Sai Krishna Venigalla
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jian Xu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Comprehensive Cancer Center
- Hamon Center for Regenerative Science and Medicine
- Department of Pediatrics, and
| | - Chunyu Cai
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Comprehensive Cancer Center
- Department of Pediatrics, and
| |
Collapse
|
7
|
Nascentes Melo LM, Lesner NP, Sabatier M, Ubellacker JM, Tasdogan A. Emerging metabolomic tools to study cancer metastasis. Trends Cancer 2022; 8:988-1001. [PMID: 35909026 DOI: 10.1016/j.trecan.2022.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]
Abstract
Metastasis is responsible for 90% of deaths in patients with cancer. Understanding the role of metabolism during metastasis has been limited by the development of robust and sensitive technologies that capture metabolic processes in metastasizing cancer cells. We discuss the current technologies available to study (i) metabolism in primary and metastatic cancer cells and (ii) metabolic interactions between cancer cells and the tumor microenvironment (TME) at different stages of the metastatic cascade. We identify advantages and disadvantages of each method and discuss how these tools and technologies will further improve our understanding of metastasis. Studies investigating the complex metabolic rewiring of different cells using state-of-the-art metabolomic technologies have the potential to reveal novel biological processes and therapeutic interventions for human cancers.
Collapse
Affiliation(s)
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Sabatier
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessalyn M Ubellacker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany.
| |
Collapse
|
8
|
Garg A, Keng WT, Chen Z, Sathe AA, Xing C, Kailasam PD, Shao Y, Lesner NP, Llamas CB, Agarwal AK, Mishra P. Autosomal recessive progeroid syndrome due to homozygosity for a TOMM7 variant. J Clin Invest 2022; 132:e156864. [PMID: 36282599 PMCID: PMC9711873 DOI: 10.1172/jci156864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Multiple genetic loci have been reported for progeroid syndromes. However, the molecular defects in some extremely rare forms of progeria have yet to be elucidated. Here, we report a 21-year-old man of Chinese ancestry who has an autosomal recessive form of progeria, characterized by severe dwarfism, mandibular hypoplasia, hyperopia, and partial lipodystrophy. Analyses of exome sequencing data from the entire family revealed only 1 rare homozygous missense variant (c.86C>T; p.Pro29Leu) in TOMM7 in the proband, while the parents and 2 unaffected siblings were heterozygous for the variant. TOMM7, a nuclear gene, encodes a translocase in the outer mitochondrial membrane. The TOMM complex makes up the outer membrane pore, which is responsible for importing many preproteins into the mitochondria. A proteomic comparison of mitochondria from control and proband-derived cultured fibroblasts revealed an increase in abundance of several proteins involved in oxidative phosphorylation, as well as a reduction in abundance of proteins involved in phospholipid metabolism. We also observed elevated basal and maximal oxygen consumption rates in the fibroblasts from the proband as compared with control fibroblasts. We concluded that altered mitochondrial protein import due to biallelic loss-of-function TOMM7 can cause severe growth retardation and progeroid features.
Collapse
Affiliation(s)
- Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Wee-Teik Keng
- Medical Genetics Department, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | | | | | - Chao Xing
- McDermott Center for Human Growth and Development, and
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Yanqiu Shao
- McDermott Center for Human Growth and Development, and
| | | | | | - Anil K. Agarwal
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute
- Department of Pediatrics and
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
9
|
Lesner NP, Wang X, Chen Z, Frank A, Menezes CJ, House S, Shelton SD, Lemoff A, McFadden DG, Wansapura J, DeBerardinis RJ, Mishra P. Differential requirements for mitochondrial electron transport chain components in the adult murine liver. eLife 2022; 11:e80919. [PMID: 36154948 PMCID: PMC9648974 DOI: 10.7554/elife.80919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial electron transport chain (ETC) dysfunction due to mutations in the nuclear or mitochondrial genome is a common cause of metabolic disease in humans and displays striking tissue specificity depending on the affected gene. The mechanisms underlying tissue-specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for basal respiration and maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function, redox and oxygen status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, impaired oxygen handling, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes use alternative electron donors to fuel the mitochondrial ETC.
Collapse
Affiliation(s)
- Nicholas P Lesner
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Xun Wang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Zhenkang Chen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anderson Frank
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - Cameron J Menezes
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sara House
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Spencer D Shelton
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - David G McFadden
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Janaka Wansapura
- Advanced Imaging Research Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
| |
Collapse
|
10
|
Lesner NP, Gokhale AS, Kota K, DeBerardinis RJ, Mishra P. α-ketobutyrate links alterations in cystine metabolism to glucose oxidation in mtDNA mutant cells. Metab Eng 2020; 60:157-167. [PMID: 32330654 PMCID: PMC7310915 DOI: 10.1016/j.ymben.2020.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 11/08/2022]
Abstract
Pathogenic mutations in the mitochondrial genome (mtDNA) impair organellar ATP production, requiring mutant cells to activate metabolic adaptations for survival. Understanding how metabolism adapts to clinically relevant mtDNA mutations may provide insight into cellular strategies for metabolic flexibility. In this study, we use 13C isotope tracing and metabolic flux analysis to investigate central carbon and amino acid metabolic reprogramming in isogenic cells containing mtDNA mutations. We identify alterations in glutamine and cystine transport which indirectly regulate mitochondrial metabolism and electron transport chain function. Metabolism of cystine can promote glucose oxidation through the transsulfuration pathway and the production of α-ketobutyrate. Intriguingly, activating or inhibiting α-ketobutyrate production is sufficient to modulate both glucose oxidation and mitochondrial respiration in mtDNA mutant cells. Thus, cystine-stimulated transsulfuration serves as an adaptive mechanism linking glucose oxidation and amino acid metabolism in the setting of mtDNA mutations.
Collapse
Affiliation(s)
- Nicholas P Lesner
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Amrita S Gokhale
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalyani Kota
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
11
|
Venkateswaran N, Lafita-Navarro MC, Hao YH, Kilgore JA, Perez-Castro L, Braverman J, Borenstein-Auerbach N, Kim M, Lesner NP, Mishra P, Brabletz T, Shay JW, DeBerardinis RJ, Williams NS, Yilmaz OH, Conacci-Sorrell M. MYC promotes tryptophan uptake and metabolism by the kynurenine pathway in colon cancer. Genes Dev 2019; 33:1236-1251. [PMID: 31416966 PMCID: PMC6719621 DOI: 10.1101/gad.327056.119] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/12/2019] [Indexed: 11/24/2022]
Abstract
Tumors display increased uptake and processing of nutrients to fulfill the demands of rapidly proliferating cancer cells. Seminal studies have shown that the proto-oncogene MYC promotes metabolic reprogramming by altering glutamine uptake and metabolism in cancer cells. How MYC regulates the metabolism of other amino acids in cancer is not fully understood. Using high-performance liquid chromatography (HPLC)-tandem mass spectrometry (LC-MS/MS), we found that MYC increased intracellular levels of tryptophan and tryptophan metabolites in the kynurenine pathway. MYC induced the expression of the tryptophan transporters SLC7A5 and SLC1A5 and the enzyme arylformamidase (AFMID), involved in the conversion of tryptophan into kynurenine. SLC7A5, SLC1A5, and AFMID were elevated in colon cancer cells and tissues, and kynurenine was significantly greater in tumor samples than in the respective adjacent normal tissue from patients with colon cancer. Compared with normal human colonic epithelial cells, colon cancer cells were more sensitive to the depletion of tryptophan. Blocking enzymes in the kynurenine pathway caused preferential death of established colon cancer cells and transformed colonic organoids. We found that only kynurenine and no other tryptophan metabolite promotes the nuclear translocation of the transcription factor aryl hydrocarbon receptor (AHR). Blocking the interaction between AHR and kynurenine with CH223191 reduced the proliferation of colon cancer cells. Therefore, we propose that limiting cellular kynurenine or its downstream targets could present a new strategy to reduce the proliferation of MYC-dependent cancer cells.
Collapse
Affiliation(s)
- Niranjan Venkateswaran
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - M Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi-Heng Hao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Kilgore
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Lizbeth Perez-Castro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jonathan Braverman
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nofit Borenstein-Auerbach
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Min Kim
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Nicholas P Lesner
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Prashant Mishra
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Thomas Brabletz
- Nikolaus-Fiebiger-Center for Molecular Medicine, University Erlangen-Nurnberg, Erlangen 91054, Germany
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, Dallas, Texas 75390, USA
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Omer H Yilmaz
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Pathology, Massachusetts General Hospital Boston, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
12
|
Addepalli B, Lesner NP, Limbach PA. Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia. RNA 2015; 21:1746-1756. [PMID: 26221047 PMCID: PMC4574751 DOI: 10.1261/rna.052472.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/28/2015] [Indexed: 06/06/2023]
Abstract
A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA(Tyr I). Analysis of MC1 digestion products by ion-pairing reverse phase liquid-chromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5'-termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.
Collapse
Affiliation(s)
- Balasubrahmanym Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Nicholas P Lesner
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA Department of Chemistry, The College of Wooster, Wooster, Ohio 44691-2393, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| |
Collapse
|