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He Y, Zhu Y, Shui X, Huang Z, Li K, Lei W. Gut microbiome and metabolomic profiles reveal the antiatherosclerotic effect of indole-3-carbinol in high-choline-fed ApoE -/- mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155621. [PMID: 38678950 DOI: 10.1016/j.phymed.2024.155621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND The metabolites produced from choline contribute to atherosclerosis (AS) pathogenesis, and the gut microbiota is redundantly essential for this process. Indole-3-carbinol (I3C), found in cruciferous vegetables such as broccoli, cabbage, cauliflower and brussels sprouts, helps prevent hyperlipidemia, maintain the gut microbiota balance, and decrease the production of trimethylamine-N-oxide (TMAO) from choline in the diet. PURPOSE The objective of this research was to investigate the impact of I3C on choline-induced AS and to further elucidate the underlying mechanism involved. METHODS AS models of high-choline-induced ApoE-/- mice and TMAO-promoted foamy macrophages were established to observe the effect of I3C on the formation of atherosclerotic plaques and foam cells and changes in AS-related indicators (including blood biochemical indicators, TMA, TMAO, SRA, and SRB1), and integrated analyses of the microbiome and metabolome were used to reveal the mechanism of action of I3C. RESULTS We found that I3C inhibited high-choline-induced atheroma formation (50-100 mg/kg/d, in vivo) and slightly improved the lipid profile (15 mg/kg/d, in vivo). Moreover, I3C suppressed lipid influx at a concentration of 40 µmol/L in vitro, enhanced the diversity of the gut microbiota and the abundance of the phylum Verrucomicrobia, and consequently modified the gut microbial metabolites at a dosage of 50 mg/kg/d in the mice. Associative analyses based on microbiome and metabolomics revealed that 1-methyladenosine was a key modulator of the protective effect of I3C against AS in high-choline-induced ApoE-/- mice. CONCLUSION These findings demonstrate for the first time that I3C ameliorates AS progression through remodeling of the gut microbiome and metabolomics, which paves the way for the possible therapeutic use of this vegetable-derived natural compound and may reduce the clinical severity of AS-related cardiovascular diseases.
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Affiliation(s)
- Yuan He
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Ying Zhu
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Xiaorong Shui
- Laboratory of Vascular Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Zufeng Huang
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Kongwei Li
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Wei Lei
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China.
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2
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Ren WT, Lv Y, He ZL, Wang HZ, Deng L, Ye SS, Wu QL, Guo WQ. Feedback of chain elongation microorganisms on iron-based conductive materials: Enhanced microbial functions and biotoxicity adaptation mechanisms. BIORESOURCE TECHNOLOGY 2024; 406:130959. [PMID: 38876286 DOI: 10.1016/j.biortech.2024.130959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Despite the increased research efforts aimed at understanding iron-based conductive materials (CMs) for facilitating chain elongation (CE) to produce medium chain fatty acids (MCFAs), the impact of these materials on microbial community functions and the adaptation mechanisms to their biotoxicity remain unclear. This study found that the supply of zero-valent iron (ZVI) and magnetite enhanced the MCFAs carbon-flow distribution by 26 % and 52 %, respectively. Metagenomic analysis revealed the upregulation of fatty acid metabolism, pyruvate metabolism and ABC transporters with ZVI and magnetite. The predominant functional microorganisms were Massilibacterium and Tidjanibacter with ZVI, and were Petrimonas and Candidatus_Microthrix with magnetite. Furthermore, it was demonstrated that CE microorganisms respond and adapt to the biotoxicity of iron-based CMs by adjusting Two-component system and Quorum sensing for the first time. In summary, this study provided a new deep-insight on the feedback mechanisms of CE microorganisms on iron-based CMs.
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Affiliation(s)
- Wei-Tong Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lv
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zi-Lin He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hua-Zhe Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lin Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shan-Shan Ye
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qing-Lian Wu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Wan-Qian Guo
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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3
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Kim YK, Won KC, Sussel L. Glucose metabolism partially regulates β-cell function through epigenomic changes. J Diabetes Investig 2024; 15:649-655. [PMID: 38436511 PMCID: PMC11143420 DOI: 10.1111/jdi.14173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
The β-cell relies predominantly on glucose utilization to generate adenosine triphosphate, which is crucial for both cell viability and insulin secretion. The β-cell has evolved remarkable metabolic flexibility to productively respond to shifts in environmental conditions and changes in glucose availability. Although these adaptive responses are important for maintaining optimal cellular function, there is emerging evidence that the resulting changes in cellular metabolites can impact the epigenome, causing transient and lasting alterations in gene expression. This review explores the intricate interplay between metabolism and the epigenome, providing valuable insights into the molecular mechanisms leading to β-cell dysfunction in diabetes. Understanding these mechanisms will be critical for developing targeted therapeutic strategies to preserve and enhance β-cell function, offering potential avenues for interventions to improve glycemic control in individuals with diabetes.
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Affiliation(s)
- Yong Kyung Kim
- Barbara Davis Center for DiabetesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Kyu Chang Won
- Department of Internal MedicineYeungnam University College of MedicineDaeguKorea
| | - Lori Sussel
- Barbara Davis Center for DiabetesUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
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4
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Li YS, Yang RR, Li XY, Liu WW, Zhao YM, Zu MM, Gao YH, Huo MQ, Jiang YT, Li BY. Fluoride impairs vascular smooth muscle A7R5 cell lines via disrupting amino acids metabolism. J Transl Med 2024; 22:528. [PMID: 38824544 PMCID: PMC11143695 DOI: 10.1186/s12967-024-05350-0] [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: 03/13/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
Given the insidious and high-fatality nature of cardiovascular diseases (CVDs), the emergence of fluoride as a newly identified risk factor demands serious consideration alongside traditional risk factors. While vascular smooth muscle cells (VSMCs) play a pivotal role in the progression of CVDs, the toxicological impact of fluoride on VSMCs remains largely uncharted. In this study, we constructed fluorosis model in SD rats and A7R5 aortic smooth muscle cell lines to confirm fluoride impaired VSMCs. Fluoride aggravated the pathological damage of rat aorta in vivo. Then A7R5 were exposed to fluoride with concentration ranging from 0 to 1200 μmol/L over a 24-h period, revealing a dose-dependent inhibition of cell proliferation and migration. The further metabolomic analysis showed alterations in metabolite profiles induced by fluoride exposure, notably decreasing organic acids and lipid molecules level. Additionally, gene network analysis underscored the frequency of fluoride's interference with amino acids metabolism, potentially impacting the tricarboxylic acid (TCA) cycle. Our results also highlighted the ATP-binding cassette (ABC) transporters pathway as a central element in VSMC impairment. Moreover, we observed a dose-dependent increase in osteopontin (OPN) and α-smooth muscle actin (α-SMA) mRNA level and a dose-dependent decrease in ABC subfamily C member 1 (ABCC1) and bestrophin 1 (BEST1) mRNA level. These findings advance our understanding of fluoride as a CVD risk factor and its influence on VSMCs and metabolic pathways, warranting further investigation into this emerging risk factor.
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MESH Headings
- Animals
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/drug effects
- Fluorides/pharmacology
- Rats, Sprague-Dawley
- Cell Line
- Amino Acids/metabolism
- Cell Proliferation/drug effects
- Rats
- Cell Movement/drug effects
- Male
- Aorta/pathology
- Aorta/drug effects
- Aorta/metabolism
- Metabolomics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/pathology
- Gene Regulatory Networks/drug effects
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Affiliation(s)
- Yan-Shu Li
- School of Public Health, Shantou University, 243 Daxue Road, Jinping District, Shantou, 515063, Guangdong Province, China
| | - Ru-Ru Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Key Lab of Etiology and Epidemiology, Harbin Medical University, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, 150081, China
| | - Xin-Ying Li
- School of Public Health, Shantou University, 243 Daxue Road, Jinping District, Shantou, 515063, Guangdong Province, China
| | - Wei-Wei Liu
- Weihai Municipal Hospital, Weihai, 264299, Shandong Province, China
| | - Yi-Ming Zhao
- Xinyi Center for Disease Control and Prevention, Xinyi, China
| | - Ming-Man Zu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Key Lab of Etiology and Epidemiology, Harbin Medical University, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, 150081, China
| | - Yi-Hong Gao
- School of Public Health, Shantou University, 243 Daxue Road, Jinping District, Shantou, 515063, Guangdong Province, China
| | - Min-Qi Huo
- School of Public Health, Shantou University, 243 Daxue Road, Jinping District, Shantou, 515063, Guangdong Province, China
| | - Yu-Ting Jiang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Key Lab of Etiology and Epidemiology, Harbin Medical University, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, 150081, China
| | - Bing-Yun Li
- School of Public Health, Shantou University, 243 Daxue Road, Jinping District, Shantou, 515063, Guangdong Province, China.
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Terry AR, Hay N. Emerging targets in lipid metabolism for cancer therapy. Trends Pharmacol Sci 2024; 45:537-551. [PMID: 38762377 PMCID: PMC11162322 DOI: 10.1016/j.tips.2024.04.007] [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: 01/26/2024] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/20/2024]
Abstract
Cancer cells perturb lipid metabolic pathways for a variety of pro-tumorigenic functions, and deregulated cellular metabolism is a hallmark of cancer cells. Although alterations in lipid metabolism in cancer cells have been appreciated for over 20 years, there are no FDA-approved cancer treatments that target lipid-related pathways. Recent advances pertaining to cancer cell fatty acid synthesis (FAS), desaturation, and uptake, microenvironmental and dietary lipids, and lipid metabolism of tumor-infiltrating immune cells have illuminated promising clinical applications for targeting lipid metabolism. This review highlights emerging pathways and targets for tumor lipid metabolism that may soon impact clinical treatment.
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Affiliation(s)
- Alexander R Terry
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA.
| | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA; Research and Development Section, Jesse Brown VA Medical Center, Chicago, IL 60612, USA.
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6
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Supplee JG, Affronti HC, Duan R, Brooks RC, Stine ZE, Nguyen PTT, Pinheiro LV, Noji MC, Drummond JM, Huang K, Schultz K, Dang CV, Marmorstein R, Wellen KE. ACLY alternative splicing correlates with cancer phenotypes. J Biol Chem 2024:107418. [PMID: 38815867 DOI: 10.1016/j.jbc.2024.107418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
ATP-citrate lyase (ACLY) links carbohydrate and lipid metabolism and provides nucleocytosolic acetyl-CoA necessary for protein acetylation. ACLY has two major splice isoforms: the full-length canonical "long" isoform and an uncharacterized "short" isoform in which exon 14 is spliced out. Exon 14 encodes 10 amino acids within a disordered region of the protein and includes at least 1 site that is dynamically phosphorylated. Both isoforms are expressed in healthy tissues to varying degrees. Analysis of human transcriptomic data revealed that the Percent Spliced In (PSI) of exon 14, i.e., the proportion of long isoform, is increased in several cancers and correlated with poorer overall survival in a pan-cancer analysis, though not in individual tumor types, which prompted us to explore potential biochemical and functional differences between ACLY isoforms. Here, we show that there are no discernible differences in enzymatic activity or stability between isoforms or phosphomutants of ACLY in vitro. Similarly, both isoforms and phosphomutants were able to rescue ACLY functions, including fatty acid synthesis and bulk histone acetylation, when re-expressed in Acly knockout cells. Deletion of Acly exon 14 in mice did not overtly impact development or metabolic physiology, nor did it attenuate tumor burden in a genetic model of intestinal cancer. Notably, expression of epithelial splicing regulatory protein 1 (ESRP1) is highly correlated with ACLY PSI. We report that ACLY splicing is regulated by ESRP1. In turn, both ESRP1 expression and ACLY PSI are correlated with specific immune signatures in tumors. Despite these intriguing patterns of ACLY splicing in healthy and cancer tissues, functional differences between the isoforms remain elusive.
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Affiliation(s)
- Julianna G Supplee
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Hayley C Affronti
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Richard Duan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | | | | | - Phuong T T Nguyen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Laura V Pinheiro
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Michael C Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Jack M Drummond
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Kevin Huang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Kollin Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Chi V Dang
- Wistar Cancer Institute, Philadelphia, PA; Johns Hopkins University School of Medicine, Baltimore, MD; Ludwig Institute for Cancer Research, New York, NY
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
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7
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Verkerke ARP, Wang D, Yoshida N, Taxin ZH, Shi X, Zheng S, Li Y, Auger C, Oikawa S, Yook JS, Granath-Panelo M, He W, Zhang GF, Matsushita M, Saito M, Gerszten RE, Mills EL, Banks AS, Ishihama Y, White PJ, McGarrah RW, Yoneshiro T, Kajimura S. BCAA-nitrogen flux in brown fat controls metabolic health independent of thermogenesis. Cell 2024; 187:2359-2374.e18. [PMID: 38653240 PMCID: PMC11145561 DOI: 10.1016/j.cell.2024.03.030] [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: 07/24/2023] [Revised: 01/07/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Brown adipose tissue (BAT) is best known for thermogenesis. Rodent studies demonstrated that enhanced BAT thermogenesis is tightly associated with increased energy expenditure, reduced body weight, and improved glucose homeostasis. However, human BAT is protective against type 2 diabetes, independent of body weight. The mechanism underlying this dissociation remains unclear. Here, we report that impaired mitochondrial catabolism of branched-chain amino acids (BCAAs) in BAT, by deleting mitochondrial BCAA carriers (MBCs), caused systemic insulin resistance without affecting energy expenditure and body weight. Brown adipocytes catabolized BCAA in the mitochondria as nitrogen donors for the biosynthesis of non-essential amino acids and glutathione. Impaired mitochondrial BCAA-nitrogen flux in BAT resulted in increased oxidative stress, decreased hepatic insulin signaling, and decreased circulating BCAA-derived metabolites. A high-fat diet attenuated BCAA-nitrogen flux and metabolite synthesis in BAT, whereas cold-activated BAT enhanced the synthesis. This work uncovers a metabolite-mediated pathway through which BAT controls metabolic health beyond thermogenesis.
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Affiliation(s)
- Anthony R P Verkerke
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Dandan Wang
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Naofumi Yoshida
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Zachary H Taxin
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Yuka Li
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Christopher Auger
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Jin-Seon Yook
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Melia Granath-Panelo
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Wentao He
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University, Durham, NC, USA
| | - Guo-Fang Zhang
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University, Durham, NC, USA
| | - Mami Matsushita
- Department of Nutrition, School of Nursing and Nutrition, Tenshi College, Sapporo, Japan
| | - Masayuki Saito
- Laboratory of Biochemistry, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Evanna L Mills
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Phillip J White
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Robert W McGarrah
- Duke Molecular Physiology Institute, Duke School of Medicine, Sarah W. Stedman Nutrition and Metabolism Center, Department of Medicine, Division of Cardiology, Duke University, Durham, NC, USA
| | - Takeshi Yoneshiro
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA.
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8
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024; 17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [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: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. RESULTS Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. CONCLUSIONS Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Loic H Steinthal
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Dias
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gladys E Zapata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA.
| | - Alli M Nuotio-Antar
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.
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9
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Schulz-Kuhnt A, Rühle K, Javidmehr A, Döbrönti M, Biwank J, Knittel S, Neidlinger P, Leupold J, Liu LJ, Dedden M, Taudte RV, Gessner A, Fromm MF, Mielenz D, Kreiss L, Waldner MJ, Schürmann S, Friedrich O, Dietel B, López-Posadas R, Plattner C, Zundler S, Becker C, Atreya R, Neurath MF, Atreya I. ATP citrate lyase (ACLY)-dependent immunometabolism in mucosal T cells drives experimental colitis in vivo. Gut 2024; 73:601-612. [PMID: 38176897 DOI: 10.1136/gutjnl-2023-330543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE Mucosal T cells play a major role in inflammatory bowel disease (IBD). However, their immunometabolism during intestinal inflammation is poorly understood. Due to its impact on cellular metabolism and proinflammatory immune cell function, we here focus on the enzyme ATP citrate lyase (ACLY) in mucosal T cell immunometabolism and its relevance for IBD. DESIGN ACLY expression and its immunometabolic impact on colitogenic T cell function were analysed in mucosal T cells from patients with IBD and in two experimental colitis models. RESULTS ACLY was markedly expressed in colon tissue under steady-state conditions but was significantly downregulated in lamina propria mononuclear cells in experimental dextran sodium sulfate-induced colitis and in CD4+ and to a lesser extent in CD8+ T cells infiltrating the inflamed gut in patients with IBD. ACLY-deficient CD4+ T cells showed an impaired capacity to induce intestinal inflammation in a transfer colitis model as compared with wild-type T cells. Assessment of T cell immunometabolism revealed that ACLY deficiency dampened the production of IBD-relevant cytokines and impaired glycolytic ATP production but enriched metabolites involved in the biosynthesis of phospholipids and phosphatidylcholine. Interestingly, the short-chain fatty acid butyrate was identified as a potent suppressor of ACLY expression in T cells, while IL-36α and resolvin E1 induced ACLY levels. In a translational approach, in vivo administration of the butyrate prodrug tributyrin downregulated mucosal infiltration of ACLYhigh CD4+ T cells and ameliorated chronic colitis. CONCLUSION ACLY controls mucosal T cell immunometabolism and experimental colitis. Therapeutic modulation of ACLY expression in T cells emerges as a novel strategy to promote the resolution of intestinal inflammation.
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Affiliation(s)
- Anja Schulz-Kuhnt
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Current address: Bionorica SE, Neumarkt in der Oberpfalz, Germany
| | - Katharina Rühle
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Asal Javidmehr
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Döbrönti
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jana Biwank
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Selina Knittel
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Neidlinger
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jannik Leupold
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Li-Juan Liu
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mark Dedden
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Regina Verena Taudte
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Core Facility for Metabolomics, Department of Medicine, Philipps-Universität Marburg, Marburg, Germany
| | - Arne Gessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin F Fromm
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lucas Kreiss
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Maximilian J Waldner
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Schürmann
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Barbara Dietel
- Department of Medicine 2 - Cardiology and Angiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rocío López-Posadas
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie DZI, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christina Plattner
- Institute for Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Zundler
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Raja Atreya
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie DZI, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Imke Atreya
- Department of Medicine 1, University Hospital of Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie DZI, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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10
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Zeaiter N, Belot L, Cunin V, Nahed RA, Tokarska-Schlattner M, Le Gouellec A, Petosa C, Khochbin S, Schlattner U. Acetyl-CoA synthetase (ACSS2) does not generate butyryl- and crotonyl-CoA. Mol Metab 2024; 81:101903. [PMID: 38369012 PMCID: PMC10906504 DOI: 10.1016/j.molmet.2024.101903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024] Open
Abstract
Acetyl and other acyl groups from different short-chain fatty acids (SCFA) competitively modify histones at various lysine sites. To fully understand the functional significance of such histone acylation, a key epigenetic mechanism, it is crucial to characterize the cellular sources of the corresponding acyl-CoA molecules required for the lysine modification. Like acetate, SCFAs such as propionate, butyrate and crotonate are thought to be the substrates used to generate the corresponding acyl-CoAs by enzymes known as acyl-CoA synthetases. The acetyl-CoA synthetase, ACSS2, which produces acetyl-CoA from acetate in the nucleocytoplasmic compartment, has been proposed to also mediate the synthesis of acyl-CoAs such as butyryl- and crotonyl-CoA from the corresponding SCFAs. This idea is now widely accepted and is sparking new research projects. However, based on our direct in vitro experiments with purified or recombinant enzymes and structural considerations, we demonstrate that ACSS2 is unable to mediate the generation of non-acetyl acyl-CoAs like butyryl- and crotonyl-CoA. It is therefore essential to re-examine published data and corresponding discussions in the light of this new finding.
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Affiliation(s)
- Nour Zeaiter
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | - Laura Belot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Valérie Cunin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Roland Abi Nahed
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | | | - Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France.
| | - Uwe Schlattner
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; Institut Universitaire de France, Paris, France.
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11
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Risbud M, Madhu V, Hernandez-Meadows M, Coleman A, Sao K, Inguito K, Haslam O, Boneski P, Sesaki H, Collins J. The loss of OPA1 accelerates intervertebral disc degeneration and osteoarthritis in aged mice. RESEARCH SQUARE 2024:rs.3.rs-3950044. [PMID: 38464287 PMCID: PMC10925423 DOI: 10.21203/rs.3.rs-3950044/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
NP cells of the intervertebral disc and articular chondrocytes reside in avascular and hypoxic tissue niches. As a consequence of these environmental constraints the cells are primarily glycolytic in nature and were long thought to have a minimal reliance on mitochondrial function. Recent studies have challenged this long-held view and highlighted the increasingly important role of mitochondria in the physiology of these tissues. However, the foundational understanding of mechanisms governing mitochondrial dynamics and function in these tissues is lacking. We investigated the role of mitochondrial fusion protein OPA1 in maintaining the spine and knee joint health in mice. OPA1 knockdown in NP cells altered mitochondrial size and cristae shape and increased the oxygen consumption rate without affecting ATP synthesis. OPA1 governed the morphology of multiple organelles, including peroxisomes, early endosomes and cis-Golgi and its loss resulted in the dysregulation of NP cell autophagy. Metabolic profiling and 13C-flux analyses revealed TCA cycle anaplerosis and altered metabolism in OPA1-deficient NP cells. Noteworthy, Opa1AcanCreERT2 mice with Opa1 deletion in disc and cartilage showed age-dependent disc degeneration, osteoarthritis, and vertebral osteopenia. Our findings underscore that OPA1 regulation of mitochondrial dynamics and multi-organelle interactions is critical in preserving metabolic homeostasis of disc and cartilage.
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12
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Smith JJ, Valentino TR, Ablicki AH, Banerjee R, Colligan AR, Eckert DM, Desjardins GA, Diehl KL. A genetically-encoded fluorescent biosensor for visualization of acetyl-CoA in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573774. [PMID: 38260544 PMCID: PMC10802309 DOI: 10.1101/2023.12.31.573774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Acetyl-coenzyme A is a central metabolite that participates in many cellular pathways. Evidence suggests that acetyl-CoA production and consumption are highly compartmentalized in mammalian cells. Yet methods to measure acetyl-CoA in living cells are lacking. In this work, we engineer an acetyl-CoA biosensor from the bacterial protein PanZ and circularly permuted green fluorescent protein (cpGFP). We biochemically characterize the sensor and demonstrate its selectivity for acetyl-CoA over other CoA species. We then deploy the biosensor in E. coli and HeLa cells to demonstrate its utility in living cells. In E. coli, we show that the biosensor enables detection of rapid changes in acetyl-CoA levels. In human cells, we show that the biosensor enables subcellular detection and reveals the compartmentalization of acetyl-CoA metabolism.
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13
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Ghilardi G, Paruzzo L, Svoboda J, Chong EA, Shestov AA, Chen L, Cohen IJ, Gabrielli G, Nasta SD, Porazzi P, Landsburg DJ, Gerson JN, Carter J, Barta SK, Yelton R, Pajarillo R, Patel V, White G, Ballard HJ, Weber E, Napier E, Chong ER, Fraietta JA, Garfall AL, Porter DL, Milone MC, O’Connor R, Schuster SJ, Ruella M. Bendamustine lymphodepletion before axicabtagene ciloleucel is safe and associates with reduced inflammatory cytokines. Blood Adv 2024; 8:653-666. [PMID: 38113468 PMCID: PMC10839610 DOI: 10.1182/bloodadvances.2023011492] [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: 08/21/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
ABSTRACT Lymphodepletion (LD) is an integral component of chimeric antigen receptor T-cell (CART) immunotherapies. In this study, we compared the safety and efficacy of bendamustine (Benda) to standard fludarabine/cyclophosphamide (Flu/Cy) LD before CD19-directed, CD28-costimulated CART axicabtagene ciloleucel (axi-cel) for patients with large B-cell lymphoma (LBCL) and follicular lymphoma (FL). We analyzed 59 patients diagnosed with LBCL (n = 48) and FL (n = 11) consecutively treated with axi-cel at the University of Pennsylvania. We also analyzed serum samples for cytokine levels and metabolomic changes before and after LD. Flu/Cy and Benda demonstrated similar efficacy, with complete remission rates of 51.4% and 50.0% (P = .981), respectively, and similar progression-free and overall survivals. Any-grade cytokine-release syndrome occurred in 91.9% of patients receiving Flu/Cy vs 72.7% of patients receiving Benda (P = .048); any-grade neurotoxicity after Flu/Cy occurred in 45.9% of patients and after Benda in 18.2% of patients (P = .031). In addition, Flu/Cy was associated with a higher incidence of grade ≥3 neutropenia (100% vs 54.5%; P < .001), infections (78.4% vs 27.3%; P < .001), and neutropenic fever (78.4% vs 13.6%; P < .001). These results were confirmed both in patients with LBCL and those with FL. Mechanistically, patients with Flu/Cy had a greater increase in inflammatory cytokines associated with neurotoxicity and reduced levels of metabolites critical for redox balance and biosynthesis. This study suggests that Benda LD may be a safe alternative to Flu/Cy for CD28-based CART CD19-directed immunotherapy with similar efficacy and reduced toxicities. Benda is associated with reduced levels of inflammatory cytokines and increased anabolic metabolites.
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Affiliation(s)
- Guido Ghilardi
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Luca Paruzzo
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
- Department of Oncology, University of Turin, Turin, Italy
| | - Jakub Svoboda
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Eise A. Chong
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Alexander A. Shestov
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Linhui Chen
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ivan J. Cohen
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Giulia Gabrielli
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Sunita D. Nasta
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Patrizia Porazzi
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Daniel J. Landsburg
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - James N. Gerson
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Jordan Carter
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Stefan K. Barta
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Rebecca Yelton
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Raymone Pajarillo
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Vrutti Patel
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Griffin White
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Hatcher J. Ballard
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Elizabeth Weber
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ellen Napier
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Emeline R. Chong
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Joseph A. Fraietta
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
| | - Alfred L. Garfall
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - David L. Porter
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Michael C. Milone
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Roderick O’Connor
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Marco Ruella
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA
- Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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14
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Uboveja A, Huang Z, Buj R, Amalric A, Wang H, Tangudu NK, Cole AR, Megill E, Kantner D, Chatoff A, Ahmad H, Marcinkiewicz MM, Disharoon JA, Graff S, Dahl ES, Hempel N, Stallaert W, Sidoli S, Bitler BG, Long DT, Snyder NW, Aird KM. αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.578742. [PMID: 38370789 PMCID: PMC10871207 DOI: 10.1101/2024.02.06.578742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases (αKGDDs), and prior work has shown that changes in αKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via αKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through αKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.
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Affiliation(s)
- Apoorva Uboveja
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Zhentai Huang
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Raquel Buj
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Amandine Amalric
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Hui Wang
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Naveen Kumar Tangudu
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Aidan R. Cole
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Emily Megill
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Daniel Kantner
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Adam Chatoff
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Hafsah Ahmad
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Mariola M. Marcinkiewicz
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Julie A. Disharoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Sarah Graff
- Department of Biochemistry, Albert Einstein College of Medicine, The Bronx, NY
| | - Erika S. Dahl
- Department of Cellular & Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Nadine Hempel
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, PA, USA
| | - Wayne Stallaert
- Department of Computational & Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, The Bronx, NY
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, University of Colorado Anschutz Medical Campus, Denver, Colorado
| | - David T. Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Nathaniel W. Snyder
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Katherine M. Aird
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
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15
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [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: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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16
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Wu J, Singh K, Shing V, Gupta AK, Huffstutler RD, Lee DY, Sack MN. The mitochondrial thiolase ACAT1 regulates monocyte/macrophage type I interferon via epigenetic control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577773. [PMID: 38410425 PMCID: PMC10896343 DOI: 10.1101/2024.01.29.577773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Lipid-derived acetyl-CoA is shown to be the major carbon source for histone acetylation. However, there is no direct evidence demonstrating lipid metabolic pathway contribututions to this process. Mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes the final step of ß-oxidation, the aerobic process catabolizing fatty acids (FA) into acetyl-CoA. To investigate this in the context of immunometabolism, we generated macrophage cell line lacking ACAT1. 13C-carbon tracing combined with mass spectrometry confirmed incorporation of FA-derived carbons into histone H3 and this incorporation was reduced in ACAT1 KO macrophage cells. RNA-seq identified a subset of genes downregulated in ACAT1 KO cells including STAT1/2 and interferon stimulated genes (ISGs). CHIP analysis demonstrated reduced acetyl-H3 binding to STAT1 promoter/enhancer regions. Increasing histone acetylation rescued STAT1/2 expression in ACAT1 KO cells. Concomitantly, ligand triggered IFNβ release was blunted in ACAT1 KO cells and rescued by reconstitution of ACAT1. Furthermore, ACAT1 promotes FA-mediated histone acetylation in an acetylcarnitine shuttle-dependent manner. In patients with obesity, levels of ACAT1 and histone acetylation are abnormally elevated. Thus, our study identified a novel link between ACAT1 mediated FA metabolism and epigenetic modification on STAT1/2 that uncovers a regulatory role of lipid metabolism in innate immune signaling and opens novel avenues for interventions in human diseases such as obesity.
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Affiliation(s)
- Jing Wu
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Komudi Singh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivian Shing
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anand K Gupta
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca D Huffstutler
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Duck-Yeon Lee
- Biochemistry Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael N Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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17
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551059. [PMID: 38328142 PMCID: PMC10849524 DOI: 10.1101/2023.07.30.551059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression data suggest a role for epigenetic modification of DNA in gene regulation in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. Taken together, our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C. Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Loic H. Steinthal
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Michelle Dias
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Hari K. Yalamanchili
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Gladys E. Zapata
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Nitesh R. Mehta
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Nicolas L. Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
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18
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Madhu V, Hernandaz-Meadows M, Coleman A, Sao K, Inguito K, Haslam O, Boneski PK, Sesaki H, Collins JA, Risbud MV. OPA1 protects intervertebral disc and knee joint health in aged mice by maintaining the structure and metabolic functions of mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576115. [PMID: 38293153 PMCID: PMC10827164 DOI: 10.1101/2024.01.17.576115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Due to their glycolytic nature and limited vascularity, nucleus pulposus (NP) cells of the intervertebral disc and articular chondrocytes were long thought to have minimal reliance on mitochondrial function. Recent studies have challenged this long-held view and highlighted the increasingly important role of mitochondria in the physiology of these tissues. We investigated the role of mitochondrial fusion protein OPA1 in maintaining the spine and knee joint health in aging mice. OPA1 knockdown in NP cells altered mitochondrial size and cristae shape and increased the oxygen consumption rate without affecting ATP synthesis. OPA1 governed the morphology of multiple organelles, and its loss resulted in the dysregulation of NP cell autophagy. Metabolic profiling and 13 C-flux analyses revealed TCA cycle anaplerosis and altered metabolism in OPA1-deficient NP cells. Noteworthy, Opa1 AcanCreERT2 mice showed age- dependent disc, and cartilage degeneration and vertebral osteopenia. Our findings suggest that OPA1 regulation of mitochondrial dynamics and multi-organelle interactions is critical in preserving metabolic homeostasis of disc and cartilage. Teaser OPA1 is necessary for the maintenance of intervertebral disc and knee joint health in aging mice.
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19
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Chi W, Kang N, Sheng L, Liu S, Tao L, Cao X, Liu Y, Zhu C, Zhang Y, Wu B, Chen R, Cheng L, Wang J, Sun X, Liu X, Deng H, Yang J, Li Z, Liu W, Chen L. MCT1-governed pyruvate metabolism is essential for antibody class-switch recombination through H3K27 acetylation. Nat Commun 2024; 15:163. [PMID: 38167945 PMCID: PMC10762154 DOI: 10.1038/s41467-023-44540-0] [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: 07/24/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Monocarboxylate transporter 1 (MCT1) exhibits essential roles in cellular metabolism and energy supply. Although MCT1 is highly expressed in activated B cells, it is not clear how MCT1-governed monocarboxylates transportation is functionally coupled to antibody production during the glucose metabolism. Here, we report that B cell-lineage deficiency of MCT1 significantly influences the class-switch recombination (CSR), rendering impaired IgG antibody responses in Mct1f/fMb1Cre mice after immunization. Metabolic flux reveals that glucose metabolism is significantly reprogrammed from glycolysis to oxidative phosphorylation in Mct1-deficient B cells upon activation. Consistently, activation-induced cytidine deaminase (AID), is severely suppressed in Mct1-deficient B cells due to the decreased level of pyruvate metabolite. Mechanistically, MCT1 is required to maintain the optimal concentration of pyruvate to secure the sufficient acetylation of H3K27 for the elevated transcription of AID in activated B cells. Clinically, we found that MCT1 expression levels are significantly upregulated in systemic lupus erythematosus patients, and Mct1 deficiency can alleviate the symptoms of bm12-induced murine lupus model. Collectively, these results demonstrate that MCT1-mediated pyruvate metabolism is required for IgG antibody CSR through an epigenetic dependent AID transcription, revealing MCT1 as a potential target for vaccine development and SLE disease treatment.
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Affiliation(s)
- Wenna Chi
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610065, China
| | - Na Kang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Linlin Sheng
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Sichen Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China
| | - Lei Tao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610065, China
| | - Xizhi Cao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Ye Liu
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Can Zhu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China
| | - Yuming Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Bolong Wu
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Ruiqun Chen
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Lili Cheng
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jing Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China
| | - Xiaolin Sun
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Xiaohui Liu
- National Center for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haiteng Deng
- National Center for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinliang Yang
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610065, China
| | - Zhanguo Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Wanli Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| | - Ligong Chen
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China.
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610065, China.
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20
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Eames A, Chandrasekaran S. Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth. PNAS NEXUS 2024; 3:pgae013. [PMID: 38292544 PMCID: PMC10825626 DOI: 10.1093/pnasnexus/pgae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/28/2023] [Indexed: 02/01/2024]
Abstract
Quiescence, a temporary withdrawal from the cell cycle, plays a key role in tissue homeostasis and regeneration. Quiescence is increasingly viewed as a continuum between shallow and deep quiescence, reflecting different potentials to proliferate. The depth of quiescence is altered in a range of diseases and during aging. Here, we leveraged genome-scale metabolic modeling (GEM) to define the metabolic and epigenetic changes that take place with quiescence deepening. We discovered contrasting changes in lipid catabolism and anabolism and diverging trends in histone methylation and acetylation. We then built a multi-cell type machine learning model that accurately predicts quiescence depth in diverse biological contexts. Using both machine learning and genome-scale flux simulations, we performed high-throughput screening of chemical and genetic modulators of quiescence and identified novel small molecule and genetic modulators with relevance to cancer and aging.
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Affiliation(s)
- Alec Eames
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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21
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Chen G, Bao B, Cheng Y, Tian M, Song J, Zheng L, Tong Q. Acetyl-CoA metabolism as a therapeutic target for cancer. Biomed Pharmacother 2023; 168:115741. [PMID: 37864899 DOI: 10.1016/j.biopha.2023.115741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023] Open
Abstract
Acetyl-coenzyme A (acetyl-CoA), an essential metabolite, not only takes part in numerous intracellular metabolic processes, powers the tricarboxylic acid cycle, serves as a key hub for the biosynthesis of fatty acids and isoprenoids, but also serves as a signaling substrate for acetylation reactions in post-translational modification of proteins, which is crucial for the epigenetic inheritance of cells. Acetyl-CoA links lipid metabolism with histone acetylation to create a more intricate regulatory system that affects the growth, aggressiveness, and drug resistance of malignancies such as glioblastoma, breast cancer, and hepatocellular carcinoma. These fascinating advances in the knowledge of acetyl-CoA metabolism during carcinogenesis and normal physiology have raised interest regarding its modulation in malignancies. In this review, we provide an overview of the regulation and cancer relevance of main metabolic pathways in which acetyl-CoA participates. We also summarize the role of acetyl-CoA in the metabolic reprogramming and stress regulation of cancer cells, as well as medical application of inhibitors targeting its dysregulation in therapeutic intervention of cancers.
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Affiliation(s)
- Guo Chen
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Banghe Bao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Yang Cheng
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Minxiu Tian
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Jiyu Song
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
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22
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Young CM, Beziaud L, Dessen P, Madurga Alonso A, Santamaria-Martínez A, Huelsken J. Metabolic dependencies of metastasis-initiating cells in female breast cancer. Nat Commun 2023; 14:7076. [PMID: 37925484 PMCID: PMC10625534 DOI: 10.1038/s41467-023-42748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Understanding the mechanisms that enable cancer cells to metastasize is essential in preventing cancer progression. Here we examine the metabolic adaptations of metastasis-initiating cells (MICs) in female breast cancer and how those shape their metastatic phenotype. We find that endogenous MICs depend on the oxidative tricarboxylic acid cycle and fatty acid usage. Sorting tumor cells based upon solely mitochondrial membrane potential or lipid storage is sufficient at identifying MICs. We further identify that mitochondrially-generated citrate is exported to the cytoplasm to yield acetyl-CoA, and this is crucial to maintaining heightened levels of H3K27ac in MICs. Blocking acetyl-CoA generating pathways or H3K27ac-specific epigenetic writers and readers reduces expression of epithelial-to-mesenchymal related genes, MIC frequency, and metastatic potential. Exogenous supplementation of a short chain carboxylic acid, acetate, increases MIC frequency and metastasis. In patient cohorts, we observe that higher expression of oxidative phosphorylation related genes is associated with reduced distant relapse-free survival. These data demonstrate that MICs specifically and precisely alter their metabolism to efficiently colonize distant organs.
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Affiliation(s)
- C Megan Young
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland
- Agora Cancer Research Center, Rue du Bugnon 25A, 1011, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Laurent Beziaud
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland
- Agora Cancer Research Center, Rue du Bugnon 25A, 1011, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Pierre Dessen
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland
- Agora Cancer Research Center, Rue du Bugnon 25A, 1011, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Angela Madurga Alonso
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland
- Agora Cancer Research Center, Rue du Bugnon 25A, 1011, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
| | - Albert Santamaria-Martínez
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland.
- Swiss Cancer Center Léman, Lausanne, Switzerland.
| | - Joerg Huelsken
- École Polytechnique Fédérale de Lausanne (EPFL), ISREC (Swiss Institute for Experimental Cancer Research), 1015, Lausanne, Switzerland.
- Agora Cancer Research Center, Rue du Bugnon 25A, 1011, Lausanne, Switzerland.
- Swiss Cancer Center Léman, Lausanne, Switzerland.
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23
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Wu M, Du Y, Zhang C, Li Z, Li Q, Qi E, Ruan W, Feng S, Zhou H. Mendelian Randomization Study of Lipid Metabolites Reveals Causal Associations with Heel Bone Mineral Density. Nutrients 2023; 15:4160. [PMID: 37836445 PMCID: PMC10574167 DOI: 10.3390/nu15194160] [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: 09/01/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Osteoporosis, which is a bone disease, is characterized by low bone mineral density and an increased risk of fractures. The heel bone mineral density is often used as a representative measure of overall bone mineral density. Lipid metabolism, which includes processes such as fatty acid metabolism, glycerol metabolism, inositol metabolism, bile acid metabolism, carnitine metabolism, ketone body metabolism, sterol and steroid metabolism, etc., may have an impact on changes in bone mineral density. While some studies have reported correlations between lipid metabolism and heel bone mineral density, the overall causal relationship between metabolites and heel bone mineral density remains unclear. OBJECTIVE to investigate the causal relationship between lipid metabolites and heel bone mineral density using two-sample Mendelian randomization analysis. METHODS Summary-level data from large-scale genome-wide association studies were extracted to identify genetic variants linked to lipid metabolite levels. These genetic variants were subsequently employed as instrumental variables in Mendelian randomization analysis to estimate the causal effects of each lipid metabolite on heel bone mineral density. Furthermore, metabolites that could potentially be influenced by causal relationships with bone mineral density were extracted from the KEGG and WikiPathways databases. The causal associations between these downstream metabolites and heel bone mineral density were then examined. Lastly, a sensitivity analysis was conducted to evaluate the robustness of the results and address potential sources of bias. RESULTS A total of 130 lipid metabolites were analyzed, and it was found that acetylcarnitine, propionylcarnitine, hexadecanedioate, tetradecanedioate, myo-inositol, 1-arachidonoylglycerophosphorine, 1-linoleoylglycerophoethanolamine, and epiandrosterone sulfate had a causal relationship with heel bone mineral density (p < 0.05). Furthermore, our findings also indicate an absence of causal association between the downstream metabolites associated with the aforementioned metabolites identified in the KEGG and WikiPathways databases and heel bone mineral density. CONCLUSION This work supports the hypothesis that lipid metabolites have an impact on bone health through demonstrating a causal relationship between specific lipid metabolites and heel bone mineral density. This study has significant implications for the development of new strategies to osteoporosis prevention and treatment.
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Affiliation(s)
- Mingxin Wu
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Yufei Du
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Chi Zhang
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Zhen Li
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Qingyang Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Enlin Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Wendong Ruan
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Shiqing Feng
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Hengxing Zhou
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
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