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Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [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: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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2
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Mott PD, Zea AH, Lewis J, Mirzalieva O, Aiyar AA. Serine deamination by human serine racemase synergizes with antibiotics to curtail the replication of Chlamydia trachomatis. J Biol Chem 2024; 300:107350. [PMID: 38718865 PMCID: PMC11140210 DOI: 10.1016/j.jbc.2024.107350] [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: 11/30/2023] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/28/2024] Open
Abstract
The obligate intracellular bacterium, Chlamydia trachomatis, has evolved to depend on its human host for many metabolites, including most amino acids and three of the four nucleotides. Given this, it is not surprising that depletion of a single amino acid in the host cell growth medium blocks chlamydial replication. Paradoxically, supra-normal levels of some amino acids also block productive replication of Chlamydia. Here, we have determined how elevated serine levels, generated by exogenous supplementation, impede chlamydial inclusion development and reduce the generation of infectious progeny. Our findings reveal that human serine racemase, which is broadly expressed in multiple tissues, potentiates the anti-chlamydial effect of elevated serine concentrations. In addition to reversibly converting l-serine to d-serine, serine racemase also deaminates serine via β-elimination. We have determined that d-serine does not directly impact Chlamydia; rather, ammonia generated by serine deamination limits the productive chlamydial replication. Our findings imply that ammonia produced within host cells can traverse the chlamydial inclusion membrane. Further, this property of serine deaminase can be exploited to sensitize Chlamydia to concentrations of doxycycline that are otherwise not bactericidal. Because exogenously elevated levels of serine can be tolerated over extended periods, the broad expression pattern of serine racemase indicates it to be a host enzyme whose activity can be directed against multiple intracellular bacterial pathogens. From a therapeutic perspective, demonstrating host metabolism can be skewed to generate an anti-bacterial metabolite that synergizes with antibiotics, we believe our results provide a new approach to target intracellular pathogens.
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Affiliation(s)
- Patricia D Mott
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.
| | - Arnold H Zea
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Jamiya Lewis
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Oygul Mirzalieva
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Ashok A Aiyar
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.
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3
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Sun M, Chang X, Gao Y, Zou S, Wang S, Liu H. GC/MS-Based Metabolomic Analysis of A549 Cells Exposed to Emerging Organophosphate Flame Retardants. TOXICS 2024; 12:384. [PMID: 38922064 PMCID: PMC11207991 DOI: 10.3390/toxics12060384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/27/2024]
Abstract
Emerging organophosphate flame retardants (eOPFRs) have attracted attention in recent times and are expected to gain extensive usage in the coming years. However, they may have adverse effects on organisms. Due to their novel nature, there are few relevant articles dealing with toxicological studies of the above eOPFRs, especially their information on the perturbation of cellular metabolism, which is, thus far, marginally understood. Our research initially assessed the cytotoxicity of eOPFRs, which include compounds like cresyl diphenyl phosphate (CDP), resorcinol bis(diphenyl phosphate) (RDP), triallyl phosphate (TAP), and pentaerythritol phosphate alcohol (PEPA). This evaluation was conducted using the methyl thiazolyl tetrazolium (MTT) assay. Subsequently, we utilized a gas chromatography/mass spectrometry (GC/MS)-based metabolomic approach to investigate the metabolic disruptions induced by these four eOPFRs in A549 cells. The MTT results showed that, at high concentrations of 1 mM, their cytotoxicity was ranked as CDP > TAP > RDP > PEPA. In addition, metabolic studies at low concentrations of 10 μM showed that the metabolic interference of CDP, TAP, and PEPA focuses on oxidative stress, amino acid metabolism, and energy metabolism, while RDP mainly affects energy metabolism-galactose metabolism and gluconeogenesis. Therefore, from the perspective of cytotoxicity and metabolic analysis, RDP may be a more promising alternative. Our experiments provide important insights into the possible metabolic effects of potential toxic substances and complement the evidence on the human health risks of eOPFRs.
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Affiliation(s)
- Mengyao Sun
- School of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, China
- College of Chemistry, Zhengzhou University, Zhengzhou 450052, China
| | - Xiao Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Gao
- College of Chemistry, Zhengzhou University, Zhengzhou 450052, China
| | - Sisi Zou
- College of Chemistry, Zhengzhou University, Zhengzhou 450052, China
| | - Shaomin Wang
- College of Chemistry, Zhengzhou University, Zhengzhou 450052, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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4
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Aquilani R, Brugnatelli S, Maestri R, Iadarola P, Corallo S, Pagani A, Serra F, Bellini A, Buonocore D, Dossena M, Boschi F, Verri M. Chemotherapy-Induced Changes in Plasma Amino Acids and Lipid Oxidation of Resected Patients with Colorectal Cancer: A Background for Future Studies. Int J Mol Sci 2024; 25:5300. [PMID: 38791339 PMCID: PMC11121634 DOI: 10.3390/ijms25105300] [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: 04/13/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Previous studies have documented that FOLFOX and XELOX therapies negatively impact the metabolism of skeletal muscle and extra-muscle districts. This pilot study tested whether three-month FOLFOX or XELOX therapy produced changes in plasma amino acid levels (PAAL) (an estimation of whole-body amino acid metabolism) and in plasma levels of malondialdehyde (MDA), a marker of lipid hyper oxidation. Fourteen ambulatory, resected patients with colorectal cancer scheduled to receive FOLFOX (n = 9) or XELOX (n = 5) therapy, after overnight fasting, underwent peripheral venous blood sampling, to determine PAAL and MDA before, during, and at the end of three-month therapy. Fifteen healthy matched subjects (controls) only underwent measures of PAAL at baseline. The results showed changes in 87.5% of plasma essential amino acids (EAAs) and 38.4% of non-EAAs in patients treated with FOLFOX or XELOX. These changes in EAAs occurred in two opposite directions: EAAs decreased with FOLFOX and increased or did not decrease with XELOX (interactions: from p = 0.034 to p = 0.003). Baseline plasma MDA levels in both FOLFOX and XELOX patients were above the normal range of values, and increased, albeit not significantly, during therapy. In conclusion, three-month FOLFOX or XELOX therapy affected plasma EAAs differently but not the baseline MDA levels, which were already high.
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Affiliation(s)
- Roberto Aquilani
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
| | - Silvia Brugnatelli
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (S.B.); (S.C.); (A.P.); (F.S.)
| | - Roberto Maestri
- Department of Biomedical Engineering of the Montescano Institute, Istituti Clinici Scientifici Maugeri IRCCS, 27040 Montescano, Italy;
| | - Paolo Iadarola
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
| | - Salvatore Corallo
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (S.B.); (S.C.); (A.P.); (F.S.)
| | - Anna Pagani
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (S.B.); (S.C.); (A.P.); (F.S.)
| | - Francesco Serra
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (S.B.); (S.C.); (A.P.); (F.S.)
| | - Anna Bellini
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
| | - Daniela Buonocore
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
| | - Maurizia Dossena
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
| | - Federica Boschi
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Manuela Verri
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (R.A.); (P.I.); (A.B.); (D.B.); (M.D.)
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5
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Luo W, Zou Z, Nie Y, Luo J, Ming Z, Hu X, Luo T, Ouyang M, Liu M, Tang H, Xie Y, Peng K, Chen L, Zhou J, Luo Z. ASS1 inhibits triple-negative breast cancer by regulating PHGDH stability and de novo serine synthesis. Cell Death Dis 2024; 15:319. [PMID: 38710705 PMCID: PMC11074131 DOI: 10.1038/s41419-024-06672-z] [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: 08/02/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024]
Abstract
Argininosuccinate synthase (ASS1), a critical enzyme in the urea cycle, acts as a tumor suppressor in many cancers. To date, the anticancer mechanism of ASS1 has not been fully elucidated. Here, we found that phosphoglycerate dehydrogenase (PHGDH), a key rate-limiting enzyme in serine synthesis, is a pivotal protein that interacts with ASS1. Our results showed that ASS1 directly binds to PHGDH and promotes its ubiquitination-mediated degradation to inhibit serine synthesis, consequently suppressing tumorigenesis. Importantly, the tumor suppressive effects of ASS1 were strongly abrogated by PHGDH knockout. In addition, ASS1 knockout and knockdown partially rescued cell proliferation when serine and glycine were depleted, while the inhibitory effect of ASS1 overexpression on cell proliferation was restored by the addition of serine and glycine. These findings unveil a novel role of ASS1 and suggest that the ASS1/PHGDH serine synthesis pathway is a promising target for cancer therapy.
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Affiliation(s)
- Wensong Luo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Zizheng Zou
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
- Yiyang Key Laboratory of Chemical Small Molecule Anti-Tumor Targeted Therapy, Department of Scientific Research, Yiyang Medical College, Yiyang, 413000, China
| | - Yuan Nie
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Junli Luo
- The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhengnan Ming
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiyuan Hu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Tiao Luo
- Hunan Key Laboratory of Oral Health Research & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, China
| | - Min Ouyang
- Department of Pharmacy, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Mingquan Liu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Huicheng Tang
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuanzhu Xie
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Kunjian Peng
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Ling Chen
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Zhou
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China
| | - Zhiyong Luo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha, China.
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6
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Hameed KM, Bollino DR, Shetty AC, Carter-Cooper B, Lapidus RG, Emadi A. Dual targeting of glutamine and serine metabolism in acute myeloid leukemia. Front Oncol 2024; 14:1326754. [PMID: 38690164 PMCID: PMC11059989 DOI: 10.3389/fonc.2024.1326754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy characterized by disrupted blood cell production and function. Recent investigations have highlighted the potential of targeting glutamine metabolism as a promising therapeutic approach for AML. Asparaginases, enzymes that deplete circulating glutamine and asparagine, are approved for the treatment of acute lymphoblastic leukemia, but are also under investigation in AML, with promising results. We previously reported an elevation in plasma serine levels following treatment with Erwinia-derived asparaginase (also called crisantaspase). This led us to hypothesize that AML cells initiate the de novo serine biosynthesis pathway in response to crisantaspase treatment and that inhibiting this pathway in combination with crisantaspase would enhance AML cell death. Here we report that in AML cell lines, treatment with the clinically available crisantaspase, Rylaze, upregulates the serine biosynthesis enzymes phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase (PSAT1) through activation of the Amino Acid Response (AAR) pathway, a cellular stress response mechanism that regulates amino acid metabolism and protein synthesis under conditions of nutrient limitation. Inhibition of serine biosynthesis through CRISPR-Cas9-mediated knockout of PHGDH resulted in a ~250-fold reduction in the half-maximal inhibitory concentration (IC50) for Rylaze, indicating heightened sensitivity to crisantaspase therapy. Treatment of AML cells with a combination of Rylaze and a small molecule inhibitor of PHGDH (BI4916) revealed synergistic anti-proliferative effects in both cell lines and primary AML patient samples. Rylaze-BI4916 treatment in AML cell lines led to the inhibition of cap-dependent mRNA translation and protein synthesis, as well as a marked decrease in intracellular glutathione levels, a critical cellular antioxidant. Collectively, our results highlight the clinical potential of targeting serine biosynthesis in combination with crisantaspase as a novel therapeutic strategy for AML.
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Affiliation(s)
- Kanwal M. Hameed
- School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
| | - Dominique R. Bollino
- School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Amol C. Shetty
- Institute of Genome Sciences, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Brandon Carter-Cooper
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
| | - Rena G. Lapidus
- School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Ashkan Emadi
- School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Institute of Genome Sciences, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
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7
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Marchesani F, Comani VB, Bruno S, Mozzarelli A, Carcelli M, Pollegioni L, Caldinelli L, Peracchi A, Campanini B. Effect of l-serine and magnesium ions on the functional properties of human phosphoserine phosphatase and its pathogenetic variants. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167034. [PMID: 38278334 DOI: 10.1016/j.bbadis.2024.167034] [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: 11/26/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
L-Ser supply in the central nervous system of mammals mostly relies on its endogenous biosynthesis by the phosphorylated pathway (PP). Defects in any of the three enzymes operating in the pathway result in a group of neurometabolic diseases collectively known as serine deficiency disorders (SDDs). Phosphoserine phosphatase (PSP) catalyzes the last, irreversible step of the PP. Here we investigated in detail the role of physiological modulators of human PSP activity and the properties of three natural PSP variants (A35T, D32N and M52T) associated with SDDs. Our results, partially contradicting previous reports, indicate that: i. PSP is almost fully saturated with Mg2+ under physiological conditions and fluctuations in Mg2+ and Ca2+ concentrations are unlikely to play a modulatory role on PSP activity; ii. Inhibition by L-Ser, albeit at play on the isolated PSP, does not exert any effect on the flux through the PP unless the enzyme activity is severely impaired by inactivating substitutions; iii. The so-far poorly investigated A35T substitution was the most detrimental, with a 50-fold reduction in catalytic efficiency, and a reduction in thermal stability (as well as an increase in the IC50 for L-Ser). The M52T substitution had similar, but milder effects, while the D32N variant behaved like the wild-type enzyme. iv. Predictions of the structural effects of the A35T and M52T substitutions with ColabFold suggest that they might affect the structure of the flexible helix-loop region.
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Affiliation(s)
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
| | | | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Loredano Pollegioni
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Laura Caldinelli
- The Protein Factory 2.0, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; Biopharmanet-TEC, University of Parma, 43124 Parma, Italy.
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8
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Frungillo L. Serine biosynthetic pathways signal to diverse outputs in plants. THE PLANT CELL 2024; 36:221-222. [PMID: 37877455 PMCID: PMC10827311 DOI: 10.1093/plcell/koad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023]
Affiliation(s)
- Lucas Frungillo
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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9
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Wang M, Tabeta H, Ohtaka K, Kuwahara A, Nishihama R, Ishikawa T, Toyooka K, Sato M, Wakazaki M, Akashi H, Tsugawa H, Shoji T, Okazaki Y, Yoshida K, Sato R, Ferjani A, Kohchi T, Hirai MY. The phosphorylated pathway of serine biosynthesis affects sperm, embryo, and sporophyte development, and metabolism in Marchantia polymorpha. Commun Biol 2024; 7:102. [PMID: 38267515 PMCID: PMC10808223 DOI: 10.1038/s42003-023-05746-6] [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: 04/03/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
Serine metabolism is involved in various biological processes. Here we investigate primary functions of the phosphorylated pathway of serine biosynthesis in a non-vascular plant Marchantia polymorpha by analyzing knockout mutants of MpPGDH encoding 3-phosphoglycerate dehydrogenase in this pathway. Growth phenotypes indicate that serine from the phosphorylated pathway in the dark is crucial for thallus growth. Sperm development requires serine from the phosphorylated pathway, while egg formation does not. Functional MpPGDH in the maternal genome is necessary for embryo and sporophyte development. Under high CO2 where the glycolate pathway of serine biosynthesis is inhibited, suppressed thallus growth of the mutants is not fully recovered by exogenously-supplemented serine, suggesting the importance of serine homeostasis involving the phosphorylated and glycolate pathways. Metabolomic phenotypes indicate that the phosphorylated pathway mainly influences the tricarboxylic acid cycle, the amino acid and nucleotide metabolism, and lipid metabolism. These results indicate the importance of the phosphorylated pathway of serine biosynthesis in the dark, in the development of sperm, embryo, and sporophyte, and metabolism in M. polymorpha.
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Affiliation(s)
- Mengyao Wang
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiromitsu Tabeta
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Kinuka Ohtaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | | | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tsubasa Shoji
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresource, Mie University, Tsushi, Japan
| | - Keisuke Yoshida
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Ryoichi Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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10
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Murray BA, Machin KL. Utilizing NMR fecal metabolomics as a novel technique for detecting the physiological effects of food shortages in waterfowl. Front Physiol 2024; 14:1229152. [PMID: 38269059 PMCID: PMC10806059 DOI: 10.3389/fphys.2023.1229152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Metabolomics is the study of small, endogenous metabolites that participate in metabolic reactions, including responses to stressors. Anthropogenic and environmental changes that alter habitat and food supply can act as stressors in wild waterfowl. These alterations invoke a series of physiological processes to provide energy to restore homeostasis and increase survival. In this study, we utilized fecal metabolomics to measure metabolites and identify pathways related to a 6-day feed restriction in captive mallard ducks (Anas platyrhynchos, n = 9). Fecal samples were collected before (baseline) and during feed restriction (treatment). H1 Nuclear Magnetic Resonance (NMR) spectroscopy was performed to identify metabolites. We found that fecal metabolite profiles could be used to distinguish between the feed-restricted and baseline samples. We identified metabolites related to pathways for energy production and metabolism endpoints, and metabolites indicative of gut microbiota changes. We also demonstrated that mallard ducks could utilize endogenous reserves in times of limited caloric intake. Fecal metabolomics shows promise as a non-invasive novel tool in identifying and characterizing physiological responses associated with stressors in a captive wild bird species.
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Affiliation(s)
| | - Karen L. Machin
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Shan Y, Liu D, Li Y, Wu C, Ye Y. The expression and clinical significance of serine hydroxymethyltransferase2 in gastric cancer. PeerJ 2024; 12:e16594. [PMID: 38188143 PMCID: PMC10771762 DOI: 10.7717/peerj.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024] Open
Abstract
Background Gastric cancer (GC) is one of the most common malignant tumours in the digestive system. Serine hydroxymethyltransferase 2 (SHMT2) is one of the key enzymes associated with serine metabolism. However, the prognostic role of SHMT2 in GC carcinogenesis has yet to be studied. Methods The expression of SHMT2 in human tumors and normal tissues was detected by the Assistant for Clinical Bioinformatics and Immunohistochemistry (IHC). The relationship of the expression of SHMT2 with clinical characteristics and survival data was analysed by the chi-square test, survival analysis and online databases. Finally, the correlation between SHMT2 expression and associated signalling channels, and molecules was analysed by online databases. Results SHMT2 was strongly expressed in numerous human cancers. The expression rate of SHMT2 was 56.44% in GC (P = 0.018). The survival analysis indicated that patients with high expression of SHMT2 had the worse overall survival (OS; log-rank P = 0.007). The expression of SHMT2 was correlated with tumour size (P = 0.034) and, TNM stage (P = 0.042). In particular, SHMT2, vessel invasion and M stage were independent factors for OS in GC (P = 0.044, P < 0.001, P < 0.001). The SHMT2 gene was substantially correlated with cell signalling pathways. Conclusions SHMT2 is highly expressed in GC and is associated with a poor prognosis. The exploration of its mechanism may be related to tumour proliferation, DNA repair and replication. SHMT2 is an independent prognostic risk factor and a potential biomarker for the diagnosis and treatment of GC.
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Affiliation(s)
- Yiming Shan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dongdong Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yingze Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chu Wu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yanwei Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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12
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Ali S, Bai Y, Zhang J, Zada S, Khan N, Hu Z, Tang Y. Discovering Nature's shield: Metabolomic insights into green zinc oxide nanoparticles Safeguarding Brassica parachinensis L. from cadmium stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108126. [PMID: 38147709 DOI: 10.1016/j.plaphy.2023.108126] [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: 04/28/2023] [Revised: 08/06/2023] [Accepted: 10/19/2023] [Indexed: 12/28/2023]
Abstract
Heavy metal cadmium (Cd) hinders plants' growth and productivity by causing different morphological and physiological changes. Nanoparticles (NPs) are promising for raising plant yield and reducing Cd toxicity. Nonetheless, the fundamental mechanism of nanoparticle-interfered Cd toxicity in Brassica parachineses L. remains unknown. A novel ZnO nanoparticle (ZnO-NPs) was synthesized using a microalgae strain (Chlorella pyrenoidosa) through a green process and characterized by different standard parameters through TEM, EDX, and XRD. This study examines the effect of different concentrations of ZnO-NPs (50 and 100 mgL-1) in B. parachineses L. under Cd stress through ultra-high-performance liquid chromatography/high-resolution mass spectrometry-based untargeted metabolomics profiling. In the presence of Cd toxicity, foliar spraying with ZnO-NPs raised Cu, Fe, Zn, and Mg levels in the roots and/or leaves, improved seedling development, as demonstrated by increased plant height, root length, and shoot and root fresh weight. Furthermore, the ZnO-NPs significantly enhanced the photosynthetic pigments and changed the antioxidant activities of the Cd-treated plants. Based on a metabolomics analysis, 481 untargeted metabolites were accumulated in leaves under normal and Cd-stressed conditions. These metabolites were highly enriched in producing organic acids, amino acids, glycosides, flavonoids, nucleic acids, and vitamin biosynthesis. Surprisingly, ZnO-NPs restored approximately 60% of Cd stress metabolites to normal leaf levels. Our findings suggest that green synthesized ZnO-NPs can balance ions' absorption, modulate the antioxidant activities, and restore more metabolites associated with plant growth to their normal levels under Cd stress. It can be applied as a plant growth regulator to alleviate heavy metal toxicity and improve crop yield in heavy metal-contaminated regions.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Junliang Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Shah Zada
- Guangdong Laboratory of Artificial Intelligence & Digital Economy (SZ), Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL32611, USA
| | - Zhangli Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China.
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13
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Ladiwala P, Dhara VG, Jenkins J, Kuang B, Hoang D, Yoon S, Betenbaugh MJ. Addressing amino acid-derived inhibitory metabolites and enhancing CHO cell culture performance through DOE-guided media modifications. Biotechnol Bioeng 2023; 120:2542-2558. [PMID: 37096798 DOI: 10.1002/bit.28403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Previously, we identified six inhibitory metabolites (IMs) accumulating in Chinese hamster ovary (CHO) cultures using AMBIC 1.0 community reference medium that negatively impacted culture performance. The goal of the current study was to modify the medium to control IM accumulation through design of experiments (DOE). Initial over-supplementation of precursor amino acids (AAs) by 100% to 200% in the culture medium revealed positive correlations between initial AA concentrations and IM levels. A screening design identified 5 AA targets, Lys, Ile, Trp, Leu, Arg, as key contributors to IMs. Response surface design analysis was used to reduce initial AA levels between 13% and 33%, and these were then evaluated in batch and fed-batch cultures. Lowering AAs in basal and feed medium and reducing feed rate from 10% to 5% reduced inhibitory metabolites HICA and NAP by up to 50%, MSA by 30%, and CMP by 15%. These reductions were accompanied by a 13% to 40% improvement in peak viable cell densities and 7% to 50% enhancement in IgG production in batch and fed-batch processes, respectively. This study demonstrates the value of tuning specific AA levels in reference basal and feed media using statistical design methodologies to lower problematic IMs.
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Affiliation(s)
- Pranay Ladiwala
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jackson Jenkins
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bingyu Kuang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Duc Hoang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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14
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Zdrazilova L, Rakosnikova T, Himmelreich N, Ondruskova N, Pasak M, Vanisova M, Volfova N, Honzik T, Thiel C, Hansikova H. Metabolic adaptation of human skin fibroblasts to ER stress caused by glycosylation defect in PMM2-CDG. Mol Genet Metab 2023; 139:107629. [PMID: 37392701 DOI: 10.1016/j.ymgme.2023.107629] [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: 03/21/2023] [Revised: 05/16/2023] [Accepted: 06/18/2023] [Indexed: 07/03/2023]
Abstract
PMM2-CDG is the most prevalent type of congenital disorders of glycosylation (CDG). It is caused by pathogenic variants in the gene encoding phosphomannomutase 2 (PMM2), which converts mannose-6-phosphate to mannose-1-phosphate and thus activates this saccharide for further glycosylation processes. Defective glycosylation can lead to an abnormal accumulation of unfolded proteins in endoplasmic reticulum (ER) and cause its stress. The ER is a key compartment for glycosylation, and its connection and communication with mitochondria has been described extensively in literature. Their crosstalk is important for cell proliferation, calcium homeostasis, apoptosis, mitochondrial fission regulation, bioenergetics, autophagy, lipid metabolism, inflammasome formation and unfolded protein response. Therefore, in the present study we posed a question, whether defective glycosylation leads to bioenergetic disruption. Our data reveal possible chronic stress in ER and activated unfolded protein response via PERK pathway in PMM2-CDG fibroblasts. Presumably, it leads to bioenergetic reorganization and increased assembly of respiratory chain complexes into supercomplexes together with suppressed glycolysis in PMM2-CDG patient cells. These changes cause alterations in Krebs cycle, which is tightly connected to electron transport system in mitochondria. In summary, we present data showing metabolic adaptation of cells to glycosylation defect caused by various pathogenic variants in PMM2.
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Affiliation(s)
- L Zdrazilova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - T Rakosnikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - N Himmelreich
- Centre for Child and Adolescent Medicine Heidelberg, Department 1, Heidelberg, Germany
| | - N Ondruskova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - M Pasak
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - M Vanisova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - N Volfova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - T Honzik
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - C Thiel
- Centre for Child and Adolescent Medicine Heidelberg, Department 1, Heidelberg, Germany
| | - H Hansikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
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15
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Phone Myint SMM, Sun LY. L-serine: Neurological Implications and Therapeutic Potential. Biomedicines 2023; 11:2117. [PMID: 37626614 PMCID: PMC10452085 DOI: 10.3390/biomedicines11082117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
L-serine is a non-essential amino acid that plays a vital role in protein synthesis, cell proliferation, development, and sphingolipid formation in the central nervous system. It exerts its effects through the activation of glycine receptors and upregulation of PPAR-γ, resulting in neurotransmitter synthesis, neuroprotection, and anti-inflammatory effects. L-serine shows potential as a protective agent in various neurological diseases and neurodegenerative disorders. Deficiency of L-serine and its downstream products has been linked to severe neurological deficits. Despite its crucial role, there is limited understanding of its mechanistic production and impact on glial and neuronal cells. Most of the focus has been on D-serine, the downstream product of L-serine, which has been implicated in a wide range of neurological diseases. However, L-serine is approved by FDA for supplemental use, while D-serine is not. Hence, it is imperative that we investigate the wider effects of L-serine, particularly in relation to the pathogenesis of several neurological deficits that, in turn, lead to diseases. This review aims to explore current knowledge surrounding L-serine and its potential as a treatment for various neurological diseases and neurodegenerative disorders.
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Affiliation(s)
| | - Liou Y. Sun
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
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16
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Hashemi M, Moieni A, Sabet MS. Improving the isolated microspore culture in eggplant (Solanum melongena L.) with amino acid nutrition. PLoS One 2023; 18:e0286809. [PMID: 37289731 PMCID: PMC10249880 DOI: 10.1371/journal.pone.0286809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
It has been proposed that the composition of the culture medium, especially its amino acids, is an important part of getting microspore androgenesis to occur in some plants. However, there have been far fewer studies done on the Solanaceae family. In this study, we studied what happened to eggplant microspore culture when we mixed casein hydrolysate (0 and 100 mg L-1) with four amino acids: proline (0, 100, 500, and 900 mg L-1), glutamine (0 and 800 mg L-1), serine (0 and 100 mg L-1), and alanine (0 and 100 mg L-1). The results showed that a combination of 800 mg L-1 of glutamine, 100 mg L-1 of serine, 100 mg L-1 of casein hydrolysate, and 500 mg L-1 of proline produced the maximum number of calli per Petri dish (938). Calli had a globular shape and a compact appearance when formed in media containing 500 mg L-1 of proline (alone or combined with serine, alanine, and/or casein hydrolysate). Most of these structures were observed in a medium with 500 mg L-1 of proline, 100 mg L-1 of casein hydrolysate, and 100 mg L-1 of serine. We also investigated what happened when gum arabic (2400, 2600, 3600, 4600, and 5600 mg L-1) was combined with proline (0 and 500 mg L-1), casein hydrolysate (0 and 100 mg L-1), and glutamine (0, 400, and 800 mg L-1). The findings demonstrated the involvement of proline in the increase of calli. Overall, the results give us new information about how amino acids work in eggplant microspore culture and suggest that proline can move this plant's microspore androgenesis pathway forward.
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Affiliation(s)
- Mozhgan Hashemi
- Faculty of Agriculture, Department of Plant Genetics and Breeding, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Moieni
- Faculty of Agriculture, Department of Plant Genetics and Breeding, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Sadegh Sabet
- Faculty of Agriculture, Department of Plant Genetics and Breeding, Tarbiat Modares University, Tehran, Iran
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17
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Roychaudhuri R, Atashi H, Snyder SH. Serine Racemase mediates subventricular zone neurogenesis via fatty acid metabolism. Stem Cell Reports 2023:S2213-6711(23)00194-7. [PMID: 37352848 PMCID: PMC10362503 DOI: 10.1016/j.stemcr.2023.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/25/2023] Open
Abstract
The adult subventricular zone (SVZ) is a neurogenic niche that continuously produces newborn neurons. Here we show that serine racemase (SR), an enzyme that catalyzes the racemization of L-serine to D-serine and vice versa, affects neurogenesis in the adult SVZ by controlling de novo fatty acid synthesis. Germline and conditional deletion of SR (nestin precursor cells) leads to diminished neurogenesis in the SVZ. Nestin-cre+ mice showed reduced expression of fatty acid synthase and its substrate malonyl-CoA, which are involved in de novo fatty acid synthesis. Global lipidomic analyses revealed significant alterations in different lipid subclasses in nestin-cre+ mice. Decrease in fatty acid synthesis was mediated by phospho Acetyl-CoA Carboxylase that was AMP-activated protein kinase independent. Both L- and D-serine supplementation rescued defects in SVZ neurogenesis, proliferation, and levels of malonyl-CoA in vitro. Our work shows that SR affects adult neurogenesis in the SVZ via lipid metabolism.
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Affiliation(s)
- Robin Roychaudhuri
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Hasti Atashi
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Solomon H Snyder
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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18
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Asghar M, Lakhani A, Asif M, Sheikh NS, Hashmi MA, Ludwig R, Hammud HH, Ayub K. Chiral Recognition of Amino Acids Using CC2 Porous Organic Cages. J Phys Chem A 2023; 127:4245-4258. [PMID: 37155274 DOI: 10.1021/acs.jpca.2c08859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Enantiomers have the same physical properties but different chemical properties due to the difference in the orientation of groups in space and thus Chiral discrimination is quite necessary, as an enantiomer of drug can have lethal effects. In this study, we used the CC2 cage for chiral discrimination of amino acids using density functional theory. The results indicated the physisorption of amino acids in the central cavity of the cage. Among the four selected amino acids, proline showed maximum interactions with the cage and maximum chiral discrimination energy is also observed in the case of proline that is 2.78 kcal/mol. Quantum theory of atoms in molecules and noncovalent interaction index analyses showed that the S enantiomer in each case has maximum interactions. The charge transfer between the analyte and surface is further studied through natural bond orbital analysis. It showed sensitivity of cage for both enantiomers, but a more pronounced effect is seen for S enantiomers. In frontier molecular orbital analysis, the least EH-L gap is observed in the case of R proline with a maximum charge transfer of -0.24 e-. Electron density difference analysis is carried out to analyze the pattern of the charge distribution. The partial density of state analysis is computed to understand the contribution of each enantiomer in overall density of the complexes. Our results show that S-CC2 porous organic cages have a good ability to differentiate between two enantiomers. S-CC2 porous organic cages efficiently differentiated the S enantiomer from the R enantiomers of selected amino acids.
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Affiliation(s)
- Maria Asghar
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Abbottabad 22060, Pakistan
| | - Ahmed Lakhani
- Department of Biomedical and Health Sciences, Calumet College of St. Joseph, 2400, New York Avenue, Whiting, Indiana 46394, United States
| | - Misbah Asif
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Abbottabad 22060, Pakistan
| | - Nadeem S Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei Darussalam
| | - Muhammad Ali Hashmi
- Department of Chemistry, Division of Science & Technology, University of Education, Lahore 54770, Pakistan
| | - Ralf Ludwig
- University of Rostock, Institute of Chemistry, Physical and Theoretical Chemistry, Albert-Einstein-Straße 27, Rostock 18059, Germany
- University of Rostock, Faculty of Interdisciplinary Research, Department "Science and Technology of Life, Light and Matter", Rostock 18059, Germany
- Leibniz Institute for Catalysis, Rostock 18059, Germany
| | - Hassan H Hammud
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Abbottabad 22060, Pakistan
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19
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Sun W, Liu R, Gao X, Lin Z, Tang H, Cui H, Zhao E. Targeting serine-glycine-one-carbon metabolism as a vulnerability in cancers. Biomark Res 2023; 11:48. [PMID: 37147729 PMCID: PMC10161514 DOI: 10.1186/s40364-023-00487-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
The serine-glycine-one-carbon (SGOC) metabolic pathway is critical for DNA methylation, histone methylation, and redox homeostasis, in addition to protein, lipid, and nucleotide biosynthesis. The SGOC pathway is a crucial metabolic network in tumorigenesis, wherein the outputs are required for cell survival and proliferation and are particularly likely to be co-opted by aggressive cancers. SGOC metabolism provides an integration point in cell metabolism and is of crucial clinical significance. The mechanism of how this network is regulated is the key to understanding tumor heterogeneity and overcoming the potential mechanism of tumor recurrence. Herein, we review the role of SGOC metabolism in cancer by focusing on key enzymes with tumor-promoting functions and important products with physiological significance in tumorigenesis. In addition, we introduce the ways in which cancer cells acquire and use one-carbon unit, and discuss the recently clarified role of SGOC metabolic enzymes in tumorigenesis and development, as well as their relationship with cancer immunotherapy and ferroptosis. The targeting of SGOC metabolism may be a potential therapeutic strategy to improve clinical outcomes in cancers.
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Affiliation(s)
- Wei Sun
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xinyue Gao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China
| | - Zini Lin
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China
| | - Hongao Tang
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei District, 400716, Chongqing, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
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20
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Wang W, Wang M, Du T, Hou Z, You S, Zhang S, Ji M, Xue N, Chen X. SHMT2 Promotes Gastric Cancer Development through Regulation of HIF1α/VEGF/STAT3 Signaling. Int J Mol Sci 2023; 24:ijms24087150. [PMID: 37108312 PMCID: PMC10138966 DOI: 10.3390/ijms24087150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The metabolic enzymes involved in one-carbon metabolism are closely associated with tumor progression and could be potential targets for cancer therapy. Recent studies showed that serine hydroxymethyltransferase 2 (SHMT2), a crucial enzyme in the one-carbon metabolic pathway, plays a key role in tumor proliferation and development. However, the precise role and function of SHMT2 in gastric cancer (GC) remain poorly understood. In this study, we presented evidence that SHMT2 was necessary for hypoxia-inducible factor-1α (HIF1α) stability and contributed to GC cells' hypoxic adaptation. The analysis of datasets retrieved from The Cancer Genome Atlas and the experimentation with human cell lines revealed a marked increase in SHMT2 expression in GC. The SHMT2 knockdown in MGC803, SGC7901, and HGC27 cell lines inhibited cell proliferation, colony formation, invasion, and migration. Notably, SHMT2 depletion disrupted redox homeostasis and caused glycolytic function loss in GC cells under hypoxic circumstances. Mechanistically, we discovered SHMT2 modulated HIF1α stability, which acted as a master regulator of hypoxia-inducible genes under hypoxic conditions. This, in turn, regulated the downstream VEGF and STAT3 pathways. The in vivo xenograft experiments showed that SHMT2 knockdown markedly reduced GC growth. Our results elucidate the novel function of SHMT2 in stabilizing HIF1α under hypoxic conditions, thus providing a potential therapeutic strategy for GC treatment.
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Affiliation(s)
- Weida Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Mingjin Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Tingting Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Zhenyan Hou
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Shen You
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Sen Zhang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Ming Ji
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Nina Xue
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
| | - Xiaoguang Chen
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
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21
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Wei J, Lu J, Nie Y, Li C, Du H, Xu Y. Amino Acids Drive the Deterministic Assembly Process of Fungal Community and Affect the Flavor Metabolites in Baijiu Fermentation. Microbiol Spectr 2023; 11:e0264022. [PMID: 36943039 PMCID: PMC10100711 DOI: 10.1128/spectrum.02640-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Nutrient fluctuation is ubiquitous in fermentation ecosystems. However, the microbial community assembly mechanism and metabolic characteristics in response to nutrient variation are still unclear. Here, we used Baijiu fermentation as a case example to study the responses of microbial community assembly and metabolic characteristics to the variation of amino acids using high-throughput sequencing and metatranscriptomics analyses. We chose two fermentation groups (group A with low amino acid and group B with high amino acid contents). The two groups showed similar succession patterns in the bacterial community, whereas they showed different succession in the fungal community wherein Pichia was dominant in group A and Zygosaccharomyces was dominant in group B. The β-nearest taxon index (βNTI) revealed that bacterial community was randomly formed, whereas fungal community assembly was a deterministic process. Variance partitioning analysis and redundancy analysis revealed that amino acids showed the largest contribution to the fungal community (37.64%, P = 0.005) and were more tightly associated with it in group B. Further study revealed that serine was positively related to Zygosaccharomyces and promoted its growth and ethanol production. Metatranscriptomic analysis revealed that the differential metabolic pathways between the two groups mainly included carbohydrate metabolism and amino acid metabolism, which explained the differences of ethanol production and volatile metabolites (such as isoamylol, isobutanol, and 2-methyl-1-butanol). Then these metabolic pathways were constructed and related gene expression and active microorganisms were listed. Our study provides a systematical understanding of the roles of amino acids in both ecological maintenance and flavor metabolism in fermentation ecosystems. IMPORTANCE In spontaneous fermented foods production, nutrient fluctuation is a critical factor affecting microbial community assembly and metabolic function. Revealing the microbial community assembly mechanism and how it regulates its metabolic characteristics in response to nutrient variation is helpful to the management of the fermentation process. This study provides a systematical understanding of the effect of amino acids on the microbial community assembly and flavor metabolisms using Baijiu fermentation as a case example. The data of this study highlight the importance of the nutrient management in fermentation ecosystems.
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Affiliation(s)
- Junlin Wei
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jun Lu
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Changwen Li
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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22
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Salzano A, Fioriniello S, D'Onofrio N, Balestrieri ML, Aiese Cigliano R, Neglia G, Della Ragione F, Campanile G. Transcriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage. BMC Genomics 2023; 24:133. [PMID: 36941576 PMCID: PMC10029215 DOI: 10.1186/s12864-023-09215-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Green feed diet in ruminants exerts a beneficial effect on rumen metabolism and enhances the content of milk nutraceutical quality. At present, a comprehensive analysis focused on the identification of genes, and therefore, biological processes modulated by the green feed in buffalo rumen has never been reported. We performed RNA-sequencing in the rumen of buffaloes fed a total mixed ration (TMR) + the inclusion of 30% of ryegrass green feed (treated) or TMR (control), and identified differentially expressed genes (DEGs) using EdgeR and NOISeq tools. RESULTS We found 155 DEGs using EdgeR (p-values < 0.05) and 61 DEGs using NOISeq (prob ≥0.8), 30 of which are shared. The rt-qPCR validation suggested a higher reliability of EdgeR results as compared with NOISeq data, in our biological context. Gene Ontology analysis of DEGs identified using EdgeR revealed that green feed modulates biological processes relevant for the rumen physiology and, then, health and well-being of buffaloes, such as lipid metabolism, response to the oxidative stress, immune response, and muscle structure and function. Accordingly, we found: (i) up-regulation of HSD17B13, LOC102410803 (or PSAT1) and HYKK, and down-regulation of CDO1, SELENBP1 and PEMT, encoding factors involved in energy, lipid and amino acid metabolism; (ii) enhanced expression of SIM2 and TRIM14, whose products are implicated in the immune response and defense against infections, and reduced expression of LOC112585166 (or SAAL1), ROR2, SMOC2, and S100A11, encoding pro-inflammatory factors; (iii) up-regulation of NUDT18, DNAJA4 and HSF4, whose products counteract stressful conditions, and down-regulation of LOC102396388 (or UGT1A9) and LOC102413340 (or MRP4/ABCC4), encoding detoxifying factors; (iv) increased expression of KCNK10, CACNG4, and ATP2B4, encoding proteins modulating Ca2+ homeostasis, and reduced expression of the cytoskeleton-related MYH11 and DES. CONCLUSION Although statistically unpowered, this study suggests that green feed modulates the expression of genes involved in biological processes relevant for rumen functionality and physiology, and thus, for welfare and quality production in Italian Mediterranean dairy buffaloes. These findings, that need to be further confirmed through the validation of additional DEGs, allow to speculate a role of green feed in the production of nutraceutical molecules, whose levels might be enhanced also in milk.
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Affiliation(s)
- Angela Salzano
- Department of Veterinary Medicine and Animal Production, Federico II University, Naples, Italy
| | | | - Nunzia D'Onofrio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | | | - Gianluca Neglia
- Department of Veterinary Medicine and Animal Production, Federico II University, Naples, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy.
- IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia, Italy.
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Production, Federico II University, Naples, Italy
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23
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Jang J, Chang JH. Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065139. [PMID: 36982214 PMCID: PMC10049462 DOI: 10.3390/ijms24065139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.
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Affiliation(s)
- Jiyeon Jang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5913; Fax: +82-53-950-6809
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24
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Zhang X, Wu J, Zhou C, Wang M, Tan Z, Jiao J. Temporal changes in muscle characteristics during growth in the goat. Meat Sci 2023; 200:109145. [PMID: 36863254 DOI: 10.1016/j.meatsci.2023.109145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/02/2023] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Abstract
This study aimed to explore the temporal accumulative process of functional components and take insight into their dynamic regulatory metabolic pathways in the longissimus during growth in goats. Results showed that the intermuscular fat content, cross-sectional area and fast- to slow-switch fiber ratio of the longissimus were synchronously increased from d1 to d90. The dynamic profiles of functional components and transcriptomic pathways of the longissimus both exhibited two distinct phases during animal development. Expression of genes involved in de novo lipogenesis was increased from birth to weaning, leading to the accumulation of palmitic acid in the first phase. Accumulation of functional oleic acid, linoleic acid and linolenic acid in the second phase was dominatingly driven by enhancement in expression of genes related to fatty acid elongation and desaturation after weaning. A shift from serine to glycine production was observed after weaning, which was linked to the expression profile of genes involved in their interconversion. Our findings systematically reported the key window and pivotal targets of the functional components' accumulation process in the chevon.
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Affiliation(s)
- Xiaoli Zhang
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China; University of the Chinese Academy of Sciences, Beijing 100193, PR China
| | - Jian Wu
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Chuanshe Zhou
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Min Wang
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Zhiliang Tan
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China
| | - Jinzhen Jiao
- CAS Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, PR China.
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25
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Zhu C, Zhang Q, Zhao X, Yang Z, Yang F, Yang Y, Tang J, Laghi L. Metabolomic Analysis of Multiple Biological Specimens (Feces, Serum, and Urine) by 1H-NMR Spectroscopy from Dairy Cows with Clinical Mastitis. Animals (Basel) 2023; 13:ani13040741. [PMID: 36830529 PMCID: PMC9952568 DOI: 10.3390/ani13040741] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Due to huge economic losses to the dairy industry worldwide, mastitis can be considered as one of the most common diseases in dairy cows. This work aimed to study this disease by comparing multiple biological specimens (feces, serum, and urine) from individuals with or without clinical mastitis. This was performed by a single analytical platform, namely 1H-NMR, through a multi-matrix strategy. Thanks to the high reproducibility of 1H-NMR, we could characterize 120 molecules across dairy cow feces, serum, and urine. Among them, 23 molecules were in common across the three biofluids. By integrating the results of multi-matrix metabolomics, several pathways pertaining to energy metabolism and amino acid metabolism appeared to be affected by clinical mastitis. The present work wished to deepen the understanding of dairy cow mastitis in its clinical form. Simultaneous analysis of metabolome changes across several key biofluids could facilitate knowledge discovery and the reliable identification of potential biomarkers, which could be, in turn, used to shed light on the early diagnosis of dairy cow mastitis in its subclinical form.
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Affiliation(s)
- Chenglin Zhu
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Qian Zhang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Xin Zhao
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Zhibo Yang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Falong Yang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yang Yang
- Farming and Animal Husbandry Bureau of Ganzi County, Ganzi 626700, China
| | - Junni Tang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
- Correspondence: (J.T.); (L.L.); Tel.: +86-028-85928243 (J.T.); +39-0547-338106 (L.L.)
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, 47521 Cesena, Italy
- Correspondence: (J.T.); (L.L.); Tel.: +86-028-85928243 (J.T.); +39-0547-338106 (L.L.)
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26
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Hesse T, Nachev M, Khaliq S, Jochmann MA, Franke F, Scharsack JP, Kurtz J, Sures B, Schmidt TC. A new technique to study nutrient flow in host-parasite systems by carbon stable isotope analysis of amino acids and glucose. Sci Rep 2023; 13:1054. [PMID: 36658208 PMCID: PMC9852285 DOI: 10.1038/s41598-022-24933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/22/2022] [Indexed: 01/20/2023] Open
Abstract
Stable isotope analysis of individual compounds is emerging as a powerful tool to study nutrient origin and conversion in host-parasite systems. We measured the carbon isotope composition of amino acids and glucose in the cestode Schistocephalus solidus and in liver and muscle tissues of its second intermediate host, the three-spined stickleback (Gasterosteus aculeatus), over the course of 90 days in a controlled infection experiment. Similar linear regressions of δ13C values over time and low trophic fractionation of essential amino acids indicate that the parasite assimilates nutrients from sources closely connected to the liver metabolism of its host. Biosynthesis of glucose in the parasite might occur from the glucogenic precursors alanine, asparagine and glutamine and with an isotope fractionation of - 2 to - 3 ‰ from enzymatic reactions, while trophic fractionation of glycine, serine and threonine could be interpreted as extensive nutrient conversion to fuel parasitic growth through one-carbon metabolism. Trophic fractionation of amino acids between sticklebacks and their diets was slightly increased in infected compared to uninfected individuals, which could be caused by increased (immune-) metabolic activities due to parasitic infection. Our results show that compound-specific stable isotope analysis has unique opportunities to study host and parasite physiology.
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Affiliation(s)
- Tobias Hesse
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Milen Nachev
- Aquatic Ecology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Shaista Khaliq
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Maik A Jochmann
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany. .,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.
| | - Frederik Franke
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany.,Bavarian State Institute of Forestry, Hans-Carl-Von-Carlowitz-Platz 1, 85354, Freising, Germany
| | - Jörn P Scharsack
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany.,Thünen Institute of Fisheries Ecology, Herwigstr. 31, 27572, Bremerhaven, Germany
| | - Joachim Kurtz
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany
| | - Bernd Sures
- Aquatic Ecology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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27
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Role of Impaired Glycolysis in Perturbations of Amino Acid Metabolism in Diabetes Mellitus. Int J Mol Sci 2023; 24:ijms24021724. [PMID: 36675238 PMCID: PMC9863464 DOI: 10.3390/ijms24021724] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The most frequent alterations in plasma amino acid concentrations in type 1 and type 2 diabetes are decreased L-serine and increased branched-chain amino acid (BCAA; valine, leucine, and isoleucine) levels. The likely cause of L-serine deficiency is decreased synthesis of 3-phosphoglycerate, the main endogenous precursor of L-serine, due to impaired glycolysis. The BCAA levels increase due to decreased supply of pyruvate and oxaloacetate from glycolysis, enhanced supply of NADH + H+ from beta-oxidation, and subsequent decrease in the flux through the citric acid cycle in muscles. These alterations decrease the supply of α-ketoglutarate for BCAA transamination and the activity of branched-chain keto acid dehydrogenase, the rate-limiting enzyme in BCAA catabolism. L-serine deficiency contributes to decreased synthesis of phospholipids and increased synthesis of deoxysphinganines, which play a role in diabetic neuropathy, impaired homocysteine disposal, and glycine deficiency. Enhanced BCAA levels contribute to increased levels of aromatic amino acids (phenylalanine, tyrosine, and tryptophan), insulin resistance, and accumulation of various metabolites, whose influence on diabetes progression is not clear. It is concluded that amino acid concentrations should be monitored in patients with diabetes, and systematic investigation is needed to examine the effects of L-serine and glycine supplementation on diabetes progression when these amino acids are decreased.
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28
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Gao D, Tang S, Cen Y, Yuan L, Lan X, Li QH, Lin GQ, Huang M, Tian P. Discovery of Novel Drug-like PHGDH Inhibitors to Disrupt Serine Biosynthesis for Cancer Therapy. J Med Chem 2023; 66:285-305. [PMID: 36594670 DOI: 10.1021/acs.jmedchem.2c01202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Being the rate-limiting enzyme within the serine biosynthesis pathway, phosphoglycerate dehydrogenase (PHGDH) is abnormally overexpressed in numerous malignant tumor cells and is a promising target for cancer treatment. Here, we report a series of novel PHGDH inhibitors using a focused compound screening and structural optimization approach. The lead compound D8 displayed good enzymatic inhibitory activity (IC50 = 2.8 ± 0.1 μM), high binding affinity (Kd = 2.33 μM), and sensitivity to the cell lines with the PHGDH gene amplification or overexpression. Furthermore, D8 was proven to restrict the de novo serine synthesis from glucose within MDA-MB-468 cells. X-ray crystallographic analysis, molecular dynamics simulations, and mutagenesis experiments on PHGDH revealed the binding site at D175 inside the NAD+-binding pocket. Finally, D8 exhibited excellent in vivo pharmacokinetic properties (F = 82.0%) and exerted evident antitumor efficacy in the PC9 xenograft mouse model.
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Affiliation(s)
- Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shuai Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Liang Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaojing Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qing-Hua Li
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Min Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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29
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The ovine conceptus utilizes extracellular serine, glucose, and fructose to generate formate via the one carbon metabolism pathway. Amino Acids 2023; 55:125-137. [PMID: 36383272 DOI: 10.1007/s00726-022-03212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022]
Abstract
Highly proliferative cells rely on one carbon (1C) metabolism for production of formate required for synthesis of purines and thymidine for nucleic acid synthesis. This study was to determine if extracellular serine and/or glucose and fructose contribute the production of formate in ovine conceptuses. Suffolk ewes (n = 8) were synchronized to estrus, bred to fertile rams, and conceptuses were collected on Day 17 of gestation. Conceptuses were either snap frozen in liquid nitrogen (n = 3) or placed in culture in medium (n = 5) containing either: 1) 4 mM D-glucose + 2 mM [U-13C]serine; 2) 6 mM glycine + 4 mM D-glucose + 2 mM [U-13C]serine; 3) 4 mM D-fructose + 2 mM [U-13C]serine; 4) 6 mM glycine + 4 mM D-fructose + 2 mM [U-13C]serine; 5) 4 mM D-glucose + 4 mM D-fructose + 2 mM [U-13C]serine; or 6) 6 mM glycine + 4 mM D-glucose + 4 mM D-fructose + 2 mM [U-13C]serine. After 2 h incubation, conceptuses in their respective culture medium were homogenized and the supernatant analyzed for 12C- and 13C-formate by gas chromatography and amino acids by high performance liquid chromatography. Ovine conceptuses produced both 13C- and 12C-formate, indicating that the [U-13C]serine, glucose, and fructose were utilized to generate formate, respectively. Greater amounts of 12C-formate than 13C-formate were produced, indicating that the ovine conceptus utilized more glucose and fructose than serine to produce formate. This study is the first to demonstrate that both 1C metabolism and serinogenesis are active metabolic pathways in ovine conceptuses during the peri-implantation period of pregnancy, and that hexose sugars are the preferred substrate for generating formate required for nucleotide synthesis for proliferating trophectoderm cells.
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30
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Islam A, Shaukat Z, Hussain R, Gregory SL. One-Carbon and Polyamine Metabolism as Cancer Therapy Targets. Biomolecules 2022; 12:biom12121902. [PMID: 36551330 PMCID: PMC9775183 DOI: 10.3390/biom12121902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer metabolic reprogramming is essential for maintaining cancer cell survival and rapid replication. A common target of this metabolic reprogramming is one-carbon metabolism which is notable for its function in DNA synthesis, protein and DNA methylation, and antioxidant production. Polyamines are a key output of one-carbon metabolism with widespread effects on gene expression and signaling. As a result of these functions, one-carbon and polyamine metabolism have recently drawn a lot of interest for their part in cancer malignancy. Therapeutic inhibitors that target one-carbon and polyamine metabolism have thus been trialed as anticancer medications. The significance and future possibilities of one-carbon and polyamine metabolism as a target in cancer therapy are discussed in this review.
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Affiliation(s)
- Anowarul Islam
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Zeeshan Shaukat
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Rashid Hussain
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Stephen L. Gregory
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Correspondence: ; Tel.: +61-0466987583
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Arshad HM, Ahmad FUD, Lodhi AH. Methanolic Extract of Aerva javanica Leaves Prevents LPS-Induced Depressive Like Behavior in Experimental Mice. Drug Des Devel Ther 2022; 16:4179-4204. [PMID: 36514526 PMCID: PMC9741839 DOI: 10.2147/dddt.s383054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Aim Depression is a chronic recurrent neuropsychiatric disorder associated with inflammation. This study explored the pharmacological activities of Aerva javanica leaves crude extract (Aj.Cr) on lipopolysaccharide (LPS)-induced depressive-like behavior in experimental mice. Methods Aj.Cr was evaluated for its phenolic and flavonoid contents, bioactive potential, amino acid profiling and enzyme inhibition assays using different analytical techniques followed by in-silico molecular docking was performed. In addition, three ligands identified in HPLC analysis and standard galantamine were docked to acetyl cholinesterase (AchE) enzyme to assess the ligand interaction along with their binding affinities. In in-vivo analysis, mice were given normal saline (10 mL/kg), imipramine (10 mg/kg) and Aj.Cr (100, 300, and 500 mg/kg) orally for 14-consecutive days. On the 14th day, respective treatment was given 30-minutes before intra-peritoneal administration of (0.83 mg/kg) LPS. Open field, forced swim and tail suspension tests were performed 24-hours after LPS injection, followed by a sucrose preference test 48-hours later. Serum corticosterone levels, as well as levels of nitric oxide (NO), malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), tumor necrosis factor-alpha (TNF-), interleukin-1β (IL-1β), interleukin-6 (IL-6), brain-derived neurotrophic factor (BDNF) and catecholamines were determined in brain tissues. Results In-vitro results revealed that crude extract of Aj.Cr possesses anti-depressant agents with solid antioxidant potential. In-vivo analysis showed that LPS significantly increased depressive-like behavior followed by alteration in serum and tissue biomarkers as compared to normal control (p < 0.001). While imipramine and Aj.Cr (100, 300, and 500 mg/kg) treated groups significantly (p<0.05) improved the depressive-like behavior and biomarkers when compared to the LPS group. Conclusion The mitigation of LPS-induced depressive-like behavior by Aj.Cr may be linked to the modulation of oxidative stress, neuro-inflammation and catecholamines due to the presence of potent bioactive compounds exerting anti-depressant effects.
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Affiliation(s)
- Hafiza Maida Arshad
- Department of Pharmacology, Faculty of Pharmacy, the Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Fiaz-ud-Din Ahmad
- Department of Pharmacology, Faculty of Pharmacy, the Islamia University of Bahawalpur, Bahawalpur, Pakistan,Correspondence: Fiaz-ud-Din Ahmad, Department of Pharmacology, the Islamia University of Bahawalpur, Pakistan Khawaja Fareed Campus, Railway Road, Bahawalpur, 63100, Pakistan, Tel +92-320-8402376, Email
| | - Arslan Hussain Lodhi
- Department of Pharmacology, Faculty of Pharmacy, the Islamia University of Bahawalpur, Bahawalpur, Pakistan
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Kim G, Yoon Y, Park JH, Park JW, Noh MG, Kim H, Park C, Kwon H, Park JH, Kim Y, Sohn J, Park S, Kim H, Im SK, Kim Y, Chung HY, Nam MH, Kwon JY, Kim IY, Kim YJ, Baek JH, Kim HS, Weinstock GM, Cho B, Lee C, Fang S, Park H, Seong JK. Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity. MICROBIOME 2022; 10:188. [PMID: 36333752 PMCID: PMC9635107 DOI: 10.1186/s40168-022-01374-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/18/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Comparisons of the gut microbiome of lean and obese humans have revealed that obesity is associated with the gut microbiome plus changes in numerous environmental factors, including high-fat diet (HFD). Here, we report that two species of Bifidobacterium are crucial to controlling metabolic parameters in the Korean population. RESULTS Based on gut microbial analysis from 99 Korean individuals, we observed the abundance of Bifidobacterium longum and Bifidobacterium bifidum was markedly reduced in individuals with increased visceral adipose tissue (VAT), body mass index (BMI), blood triglyceride (TG), and fatty liver. Bacterial transcriptomic analysis revealed that carbohydrate/nucleoside metabolic processes of Bifidobacterium longum and Bifidobacterium bifidum were associated with protecting against diet-induced obesity. Oral treatment of specific commercial Bifidobacterium longum and Bifidobacterium bifidum enhanced bile acid signaling contributing to potentiate oxidative phosphorylation (OXPHOS) in adipose tissues, leading to reduction of body weight gain and improvement in hepatic steatosis and glucose homeostasis. Bifidobacterium longum or Bifidobacterium bifidum manipulated intestinal sterol biosynthetic processes to protect against diet-induced obesity in germ-free mice. CONCLUSIONS Our findings support the notion that treatment of carbohydrate/nucleoside metabolic processes-enriched Bifidobacterium longum and Bifidobacterium bifidum would be a novel therapeutic strategy for reprograming the host metabolic homeostasis to protect against metabolic syndromes, including diet-induced obesity. Video Abstract.
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Affiliation(s)
- Gihyeon Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Youngmin Yoon
- Division of Nephrology, Department of Medicine, Chosun University Hospital, Chosun University School of Medicine, Gwangju, Korea
| | - Jin Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Won Park
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Myung-Guin Noh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Hyun Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Changho Park
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Hyuktae Kwon
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Yena Kim
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Jinyoung Sohn
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Shinyoung Park
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Hyeonhui Kim
- Graduate school of Medical Science, Brain Korea 21 Project, Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sun-Kyoung Im
- Graduate school of Medical Science, Brain Korea 21 Project, Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yeongmin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Ha Yung Chung
- Korea Basic Science Institute, Seoul Center, Seoul, South Korea
| | - Myung Hee Nam
- Korea Basic Science Institute, Seoul Center, Seoul, South Korea
| | - Jee Young Kwon
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, 06032, USA
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea
| | - Yong Jae Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea
| | - Ji Hyeon Baek
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea
| | - Hak Su Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, 06032, USA
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, 06032, USA
- Department of Life Science, Ewha Womans University, Seoul, 03760, Korea
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Sungsoon Fang
- Graduate school of Medical Science, Brain Korea 21 Project, Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
| | - Hansoo Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea.
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea.
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea.
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Korea.
- Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul, Korea.
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Moss DY, McCann C, Kerr EM. Rerouting the drug response: Overcoming metabolic adaptation in KRAS-mutant cancers. Sci Signal 2022; 15:eabj3490. [PMID: 36256706 DOI: 10.1126/scisignal.abj3490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mutations in guanosine triphosphatase KRAS are common in lung, colorectal, and pancreatic cancers. The constitutive activity of mutant KRAS and its downstream signaling pathways induces metabolic rewiring in tumor cells that can promote resistance to existing therapeutics. In this review, we discuss the metabolic pathways that are altered in response to treatment and those that can, in turn, alter treatment efficacy, as well as the role of metabolism in the tumor microenvironment (TME) in dictating the therapeutic response in KRAS-driven cancers. We highlight metabolic targets that may provide clinical opportunities to overcome therapeutic resistance and improve survival in patients with these aggressive cancers.
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Affiliation(s)
- Deborah Y Moss
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE Northern Ireland, UK
| | - Christopher McCann
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE Northern Ireland, UK
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE Northern Ireland, UK
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Perea-Gil I, Seeger T, Bruyneel AAN, Termglinchan V, Monte E, Lim EW, Vadgama N, Furihata T, Gavidia AA, Arthur Ataam J, Bharucha N, Martinez-Amador N, Ameen M, Nair P, Serrano R, Kaur B, Feyen DAM, Diecke S, Snyder MP, Metallo CM, Mercola M, Karakikes I. Serine biosynthesis as a novel therapeutic target for dilated cardiomyopathy. Eur Heart J 2022; 43:3477-3489. [PMID: 35728000 PMCID: PMC9794189 DOI: 10.1093/eurheartj/ehac305] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
AIMS Genetic dilated cardiomyopathy (DCM) is a leading cause of heart failure. Despite significant progress in understanding the genetic aetiologies of DCM, the molecular mechanisms underlying the pathogenesis of familial DCM remain unknown, translating to a lack of disease-specific therapies. The discovery of novel targets for the treatment of DCM was sought using phenotypic sceening assays in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that recapitulate the disease phenotypes in vitro. METHODS AND RESULTS Using patient-specific iPSCs carrying a pathogenic TNNT2 gene mutation (p.R183W) and CRISPR-based genome editing, a faithful DCM model in vitro was developed. An unbiased phenotypic screening in TNNT2 mutant iPSC-derived cardiomyocytes (iPSC-CMs) with small molecule kinase inhibitors (SMKIs) was performed to identify novel therapeutic targets. Two SMKIs, Gö 6976 and SB 203580, were discovered whose combinatorial treatment rescued contractile dysfunction in DCM iPSC-CMs carrying gene mutations of various ontologies (TNNT2, TTN, LMNA, PLN, TPM1, LAMA2). The combinatorial SMKI treatment upregulated the expression of genes that encode serine, glycine, and one-carbon metabolism enzymes and significantly increased the intracellular levels of glucose-derived serine and glycine in DCM iPSC-CMs. Furthermore, the treatment rescued the mitochondrial respiration defects and increased the levels of the tricarboxylic acid cycle metabolites and ATP in DCM iPSC-CMs. Finally, the rescue of the DCM phenotypes was mediated by the activating transcription factor 4 (ATF4) and its downstream effector genes, phosphoglycerate dehydrogenase (PHGDH), which encodes a critical enzyme of the serine biosynthesis pathway, and Tribbles 3 (TRIB3), a pseudokinase with pleiotropic cellular functions. CONCLUSIONS A phenotypic screening platform using DCM iPSC-CMs was established for therapeutic target discovery. A combination of SMKIs ameliorated contractile and metabolic dysfunction in DCM iPSC-CMs mediated via the ATF4-dependent serine biosynthesis pathway. Together, these findings suggest that modulation of serine biosynthesis signalling may represent a novel genotype-agnostic therapeutic strategy for genetic DCM.
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Affiliation(s)
- Isaac Perea-Gil
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Timon Seeger
- Department of Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Arne A N Bruyneel
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Vittavat Termglinchan
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Emma Monte
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Takaaki Furihata
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra A Gavidia
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Jennifer Arthur Ataam
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nike Bharucha
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Noel Martinez-Amador
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Mohamed Ameen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Pooja Nair
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Ricardo Serrano
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Balpreet Kaur
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Dries A M Feyen
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark Mercola
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
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Swanson MA, Miller K, Young SP, Tong S, Ghaloul‐Gonzalez L, Neira‐Fresneda J, Schlichting L, Peck C, Gabel L, Friederich MW, Van Hove JLK. Cerebrospinal fluid amino acids glycine, serine, and threonine in nonketotic hyperglycinemia. J Inherit Metab Dis 2022; 45:734-747. [PMID: 35357708 PMCID: PMC9543955 DOI: 10.1002/jimd.12500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/30/2023]
Abstract
Nonketotic hyperglycinemia (NKH) is caused by deficient glycine cleavage enzyme activity and characterized by elevated brain glycine. Metabolism of glycine is connected enzymatically to serine through serine hydroxymethyltransferase and shares transporters with serine and threonine. We aimed to evaluate changes in serine and threonine in NKH patients, and relate this to clinical outcome severity. Age-related reference values were developed for cerebrospinal fluid (CSF) serine and threonine from 274 controls, and in a cross-sectional study compared to 61 genetically proven NKH patients, categorized according to outcome. CSF d-serine and l-serine levels were stereoselectively determined in seven NKH patients and compared to 29 age-matched controls. In addition to elevated CSF glycine, NKH patients had significantly decreased levels of CSF serine and increased levels of CSF threonine, even after age-adjustment. The CSF serine/threonine ratio discriminated between NKH patients and controls. The CSF glycine/serine aided in discrimination between severe and attenuated neonates with NKH. Over all ages, the CSF glycine, serine and threonine had moderate to fair correlation with outcome classes. After age-adjustment, only the CSF glycine level provided good discrimination between outcome classes. In untreated patients, d-serine was more reduced than l-serine, with a decreased d/l-serine ratio, indicating a specific impact on d-serine metabolism. We conclude that in NKH the elevation of glycine is accompanied by changes in l-serine, d-serine and threonine, likely reflecting a perturbation of the serine shuttle and metabolism, and of one-carbon metabolism. This provides additional guidance on diagnosis and prognosis, and opens new therapeutic avenues to be explored.
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Affiliation(s)
- Michael A. Swanson
- Section of Clinical Genetics and Metabolism, Department of PediatricsUniversity of ColoradoAuroraColoradoUSA
| | - Kristen Miller
- Department of Pediatrics, Child Health Biostatistics CoreUniversity of Colorado and Children's Hospital ColoradoAuroraColoradoUSA
| | - Sarah P. Young
- Division of Medical Genetics, Department of PediatricsDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Suhong Tong
- Department of Pediatrics, Child Health Biostatistics CoreUniversity of Colorado and Children's Hospital ColoradoAuroraColoradoUSA
| | - Lina Ghaloul‐Gonzalez
- Division of Genetic and Genomic Medicine, Department of PediatricsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Human GeneticsGraduate School of Public Health, University of PittsburghPittsburghPennsylvaniaUSA
| | | | - Lisa Schlichting
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Cheryl Peck
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Linda Gabel
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Marisa W. Friederich
- Section of Clinical Genetics and Metabolism, Department of PediatricsUniversity of ColoradoAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Johan L. K. Van Hove
- Section of Clinical Genetics and Metabolism, Department of PediatricsUniversity of ColoradoAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
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Lee S, Hwang SK, Nam HS, Cho JS, Chung JY. Population Pharmacokinetic Model of AST-001, L-Isomer of Serine, Combining Endogenous Production and Exogenous Administration in Healthy Subjects. Front Pharmacol 2022; 13:891227. [PMID: 35814222 PMCID: PMC9263096 DOI: 10.3389/fphar.2022.891227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
AST-001 is an L-isomer of serine that has protective effects on neurological disorders. This study aimed to establish a population pharmacokinetic (PK) model of AST-001 in healthy Korean to further propose a fixed-dose regimen in pediatrics. The model was constructed using 648 plasma concentrations from 24 healthy subjects, including baseline endogenous levels during 24 h and concentrations after a single dose of 10, 20, and 30 g of AST-001. For the simulation, an empirical allometric power model was applied to the apparent clearance and volume of distribution with body weight. The PK characteristics of AST-001 after oral administration were well described by a two-compartment model with zero-order absorption and linear elimination. The endogenous production of AST-001 was well explained by continuous zero-order production at a rate of 0.287 g/h. The simulation results suggested that 2 g, 4 g, 7 g, 10 g, and 14 g twice-daily regimens for the respective groups of 10–14 kg, 15–24 kg, 25–37 kg, 38–51 kg, 52–60 kg were adequate to achieve sufficient exposure to AST-001. The current population PK model well described both observed endogenous production and exogenous administration of AST-001 in healthy subjects. Using the allometric scaling approach, we suggested an optimal fixed-dose regimen with five weight ranges in pediatrics for the upcoming phase 2 trial.
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Affiliation(s)
- Soyoung Lee
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine, Seoul, South Korea
- Kidney Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Su-Kyeong Hwang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
- Astrogen Inc., Daegu, South Korea
| | | | | | - Jae-Yong Chung
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine, Seoul, South Korea
- Department of Clinical Pharmacology and Therapeutics, Seoul National University Bundang Hospital, Seongnam, South Korea
- *Correspondence: Jae-Yong Chung,
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Endogenous glutamine is rate-limiting for anti-CD3 and anti-CD28 induced CD4+ T-cell proliferation and glycolytic activity under hypoxia and normoxia. Biochem J 2022; 479:1221-1235. [PMID: 35695514 PMCID: PMC9246347 DOI: 10.1042/bcj20220144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022]
Abstract
To meet the demand for energy and biomass, T lymphocytes (T cells) activated to proliferation and clonal expansion, require uptake and metabolism of glucose (Gluc) and the amino acid (AA) glutamine (Gln). Whereas exogenous Gln is converted to glutamate (Glu) by glutaminase (GLS), Gln is also synthesized from the endogenous pool of AA through Glu and activity of glutamine synthase (GS). Most of this knowledge comes from studies on cell cultures under ambient oxygen conditions (normoxia, 21% O2). However, in vivo, antigen induced T-cell activation often occurs under moderately hypoxic (1-4% O2) conditions and at various levels of exogenous nutrients. Here, CD4+ T cells were stimulated for 72 h with antibodies targeting the CD3 and CD28 markers at normoxia and hypoxia (1% O2). This was done in the presence and absence of the GLS and GS inhibitors, Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl) ethyl sulfide (BPTES) and methionine sulfoximine (MSO) and at various combinations of exogenous Gluc, Gln and pyruvate (Pyr) for the last 12 h of stimulation. We found that T-cell proliferation, viability and levels of endogenous AA were significantly influenced by the availability of exogenous Gln, Gluc and Pyr as well as inhibition of GLS and GS. Moreover, inhibition of GLS and GS and levels of oxygen differentially influenced oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). Finally, BPTES-dependent down-regulation of ECAR was associated with reduced hexokinase (HK) activity at both normoxia and hypoxia. Our results demonstrate that Gln availability and metabolism is rate-limiting for CD4+ T-cell activity.
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Kumar V, Singh P, Gupta SK, Ali V, Jyotirmayee, Verma M. Alterations in cellular metabolisms after Imatinib therapy: a review. Med Oncol 2022; 39:95. [DOI: 10.1007/s12032-022-01699-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022]
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Asgher M, Sehar Z, Rehaman A, Rashid S, Ahmed S, Per TS, Alyemeni MN, Khan NA. Exogenously-applied L-glutamic acid protects photosynthetic functions and enhances arsenic tolerance through increased nitrogen assimilation and antioxidant capacity in rice (Oryza sativa L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119008. [PMID: 35189299 DOI: 10.1016/j.envpol.2022.119008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/22/2022] [Accepted: 02/14/2022] [Indexed: 05/25/2023]
Abstract
L-Glutamic acid (Glu) is used as an effective bio-stimulant to reduce arsenic (As) stress in plants. The role of Glu was studied in the protection of photosynthesis and growth of rice (Oryza sativa L. Japonica Type Taipie-309) plants grown with 50 μM As stress by studying the oxidative stress, photosynthetic and growth characteristics. Among the Glu concentrations (0, 2.5, 5 and 10 μM), 10 μM Glu maximally enhanced photosynthesis and growth parameters with the least cellular oxidative stress level. The supplementation of 10 μM Glu resulted in the reduced effects of As stress on gas exchange parameters, PSII activity and growth attributes through enhancement of antioxidant and proline metabolism. The enzymes of nitrogen (N) assimilation, such as nitrate reductase, nitrite reductase, glutamine synthetase and glutamate synthase were increased with Glu treatment under As stress. The Glu-induced metabolite synthesis showed the role of various metabolites in As stress responses. The role of Glu as a signalling molecule in reducing the adverse effects of As through accelerating the antioxidant enzymes, PSII activity, proline metabolism and nitrogen assimilation has been discussed.
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Affiliation(s)
- Mohd Asgher
- Plant Physiology and Biochemistry Laboratory, Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, 185234, India
| | - Zebus Sehar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Abdul Rehaman
- Plant Physiology and Biochemistry Laboratory, Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, 185234, India
| | - Shaista Rashid
- Plant Physiology and Biochemistry Laboratory, Department of Botany, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, 185234, India
| | - Sajad Ahmed
- Plant Biotechnology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Jammu and Kashmir, 180001, India
| | - Tasir S Per
- Department of Botany, Government Degree College, Doda, Jammu and Kashmir, 182202, India
| | - Mohammed Nasser Alyemeni
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Nafees A Khan
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
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Liu Y, Liu C, Wu H, Meng Q, Zhou Z. Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers. Front Microbiol 2022; 13:862151. [PMID: 35531283 PMCID: PMC9069012 DOI: 10.3389/fmicb.2022.862151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
The gastrointestinal tract (GIT) contains complex microbial communities and plays an essential role in the overall health of the host. Previous studies of beef cattle feed efficiency have primarily concentrated on the ruminal microbiota because it plays a key role in energy production and nutrient supply in the host. Although the small intestine is the important site of post-ruminal digestion and absorption of nutrients, only a few studies have explored the relationship between the microbial populations in the small intestine and feed efficiency. Moreover, variations in GIT metabolites contribute to differences in feed efficiency. The objective of this study was to investigate relationships among bacterial populations of duodenum, jejunum, ileum; microbial metabolites; and RFI phenotype of beef cattle. We carried out by using Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC–MS). In the duodenum, the relative abundances of Firmicutes ( p < 0.01), Lachnospiraceae, Ruminococcaceae, Family_XIII, Christensenellaceae, Christensenellaceae_R-7_group ( p < 0.05), and Lachnospiraceae_NK3A20_group ( p < 0.05) were higher in the low residual feed intake (LRFI) group compared with the high residual feed intake (HRFI) group, whereas the HRFI group had higher abundances of Proteobacteria and Acinetobacter ( p < 0.01). In the jejunum, the relative abundances of Lachnospiraceae and Lachnospiraceae_NK3A20_group were higher in the LRFI group ( p < 0.05). In the ileum, the relative abundances of Ruminococcaceae ( p < 0.01), Christensenellaceae, Christensenellaceae_R-7_group, and Ruminococcus_2 were also higher in the LRFI group ( p < 0.05). Moreover, the genera Lachnospiraceae_NK3A20_group, Christensenellaceae_R-7_group, and Ruminococcus_2 were negatively associated with RFI, while the genus Acinetobacter was positively associated with RFI. The metabolomics analysis revealed that the LRFI group significantly improved protein digestion and absorption, as well as glycerophospholipid metabolism in the duodenum, jejunum, ileum. The correlation between intestinal microorganisms and metabolites revealed that some microorganisms play an important role in amino acid metabolism, glycerophospholipid metabolism, nutrient digestion and absorption, and antioxidant enhancement. The present study provides a better understanding of the small intestinal microbiota and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chang Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Holeček M. Serine Metabolism in Health and Disease and as a Conditionally Essential Amino Acid. Nutrients 2022; 14:nu14091987. [PMID: 35565953 PMCID: PMC9105362 DOI: 10.3390/nu14091987] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
L-serine plays an essential role in a broad range of cellular functions including protein synthesis, neurotransmission, and folate and methionine cycles and synthesis of sphingolipids, phospholipids, and sulphur containing amino acids. A hydroxyl side-chain of L-serine contributes to polarity of proteins, and serves as a primary site for binding a phosphate group to regulate protein function. D-serine, its D-isoform, has a unique role. Recent studies indicate increased requirements for L-serine and its potential therapeutic use in some diseases. L-serine deficiency is associated with impaired function of the nervous system, primarily due to abnormal metabolism of phospholipids and sphingolipids, particularly increased synthesis of deoxysphingolipids. Therapeutic benefits of L-serine have been reported in primary disorders of serine metabolism, diabetic neuropathy, hyperhomocysteinemia, and amyotrophic lateral sclerosis. Use of L-serine and its metabolic products, specifically D-serine and phosphatidylserine, has been investigated for the therapy of renal diseases, central nervous system injury, and in a wide range of neurological and psychiatric disorders. It is concluded that there are disorders in which humans cannot synthesize L-serine in sufficient quantities, that L-serine is effective in therapy of disorders associated with its deficiency, and that L-serine should be classified as a “conditionally essential” amino acid.
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Affiliation(s)
- Milan Holeček
- Department of Physiology, Faculty of Medicine in Hradec Králové, Charles University, Šimkova 870, 500 03 Hradec Králové, Czech Republic
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Zhao Y, Yuan Z, Wang S, Wang H, Chao Y, Sederoff RR, Sederoff H, Yan H, Pan J, Peng M, Wu D, Borriss R, Niu B. Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus. Front Microbiol 2022; 13:870519. [PMID: 35602027 PMCID: PMC9121001 DOI: 10.3389/fmicb.2022.870519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhibo Yuan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shuang Wang
- Administrative Office of the Summer Palace, Beijing Municipal Administration Center of Parks, Beijing, China
| | - Haoyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - He Yan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Jialiang Pan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Mu Peng
- College of Biological Science and Technology, Hubei Minzu University, Enshi, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Rainer Borriss
- Nord Reet UG, Greifswald, Germany
- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
- *Correspondence: Rainer Borriss,
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Ben Niu,
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López-Gonzales E, Lehmann L, Ruiz-Ojeda FJ, Hernández-Bautista R, Altun I, Onogi Y, Khalil AE, Liu X, Israel A, Ussar S. L-Serine Supplementation Blunts Fasting-Induced Weight Regain by Increasing Brown Fat Thermogenesis. Nutrients 2022; 14:1922. [PMID: 35565889 PMCID: PMC9104834 DOI: 10.3390/nu14091922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Weight regain after fasting, often exceeding the pre-fasting weight, is a common phenomenon and big problem for the treatment of obesity. Thus, novel interventions maintaining reduced body weight are critically important to prevent metabolic disease. Here we investigate the metabolic effects of dietary L-serine supplementation, known to modulate various organ functions. C57BL/6N-Rj male mice were supplemented with or without 1% L-serine in their drinking water and fed with a chow or high-fat diet. Mice were fed either ad libitum or subjected to repeated overnight fasting. Body weight, body composition, glucose tolerance and energy metabolism were assessed. This was combined with a detailed analysis of the liver and adipose tissues, including the use of primary brown adipocytes to study mitochondrial respiration and protein expression. We find that L-serine supplementation has little impact on systemic metabolism in ad libitum-fed mice. Conversely, L-serine supplementation blunted fasting-induced body weight regain, especially in diet-induced obese mice. This reduction in body weight regain is likely due to the increased energy expenditure, based on elevated brown adipose tissue activity. Thus, L-serine supplementation during and after weight-loss could reduce weight regain and thereby help tackle one of the major problems of current obesity therapies.
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Affiliation(s)
- Elena López-Gonzales
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Lisa Lehmann
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Francisco Javier Ruiz-Ojeda
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | - René Hernández-Bautista
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Irem Altun
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Yasuhiro Onogi
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Ahmed Elagamy Khalil
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Xue Liu
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Andreas Israel
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
| | - Siegfried Ussar
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity, Helmholtz Center Munich, 85764 Munich, Germany; (E.L.-G.); (L.L.); (F.J.R.-O.); (R.H.-B.); (I.A.); (Y.O.); (A.E.K.); (X.L.); (A.I.)
- German Center for Diabetes Research (DZD), 85764 Munich, Germany
- Department of Medicine, Technical University of Munich, 80333 Munich, Germany
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44
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Zhang FM, Yuan L, Shi XW, Feng KR, Lan X, Huang C, Lin GQ, Tian P, Huang M, Tang S, Gao D. Discovery of PHGDH inhibitors by virtual screening and preliminary structure–activity relationship study. Bioorg Chem 2022; 121:105705. [DOI: 10.1016/j.bioorg.2022.105705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/02/2022]
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45
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Lucia A, Ferrarese E, Uygun K. Modeling energy depletion in rat livers using Nash equilibrium metabolic pathway analysis. Sci Rep 2022; 12:3496. [PMID: 35241684 PMCID: PMC8894355 DOI: 10.1038/s41598-022-06966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
The current gold standard of Static Cold Storage (SCS), which is static cold storage on ice (about + 4 °C) in a specialized media such as the University of Wisconsin solution (UW), limits storage to few hours for vascular and metabolically active tissues such as the liver and the heart. The liver is arguably the pinnacle of metabolism in human body and therefore metabolic pathway analysis immediately becomes very relevant. In this article, a Nash Equilibrium (NE) approach, which is a first principles approach, is used to model and simulate the static cold storage and warm ischemia of a proposed model of liver cells. Simulations of energy depletion in the liver in static cold storage measured by ATP content and energy charge are presented along with comparisons to experimental data. In addition, conversion of Nash Equilibrium iterations to time are described along with an uncertainty analysis for the parameters in the model. Results in this work show that the Nash Equilibrium approach provides a good match to experimental data for energy depletion and that the uncertainty in model parameters is very small with percent variances less than 0.1%.
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Affiliation(s)
- Angelo Lucia
- Department of Chemical Engineering, University of Rhode Island, Kington, RI, 02881, USA.
| | - Emily Ferrarese
- Department of Chemical Engineering, University of Rhode Island, Kington, RI, 02881, USA
| | - Korkut Uygun
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
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46
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Agwunobi DO, Pei T, Bai R, Wang Z, Shi X, Zhang M, Yu Z, Liu J. miR-2a and miR-279 are functionally associated with cold tolerance in Dermacentor silvarum (Acari: Ixodidae). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100946. [PMID: 34872025 DOI: 10.1016/j.cbd.2021.100946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Ticks are obligate blood-sucking ectoparasites that can attack mammals, birds, reptiles as well as amphibians. Dermacentor silvarum, an important vector of various pathogenic bacteria, viruses, and protozoans, is widely distributed in China. MicroRNAs (miRNAs) are ~22 nucleotide non-coding small RNA molecules, involved in the regulation of various physiological and cellular processes. Previous studies demonstrated the vital roles of miRNAs during the reproduction and development of ticks, whereas, the regulatory/functional roles of microRNAs during the cold response of ticks remain unexplored. Here, we identified and functionally explored D. silvarum miRNAs involved in cold response to gain further understanding of the molecular regulatory mechanisms underlying cold stress in ticks. The microRNA libraries of D. silvarum were established via high-throughput sequencing after exposure to different cold treatments. A total of 147 miRNAs, including 44 known miRNAs and 103 new miRNAs, were identified. The verification of six highly differentially expressed miRNAs (miR-2a, miR-5305, miR-7, miR-279, miR-993, and novel-3) via RT-qPCR were consistent with the high-throughput sequence results. miR-2a peaked by day 6 and miR-279 expression was lowest by day 3 after cold treatment. The potential target genes of miR-2a and miR-279 were the glycogen phosphorylase (GPase) gene and serine gene, respectively. After injecting D. silvarum ticks with miR-2a and miR-279 antagonists, their respective target genes were up-regulated and vice-versa after injection with the agonists. These results indicated that these two miRNAs and their target genes may be involved in the cold response of D. silvarum ticks.
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Affiliation(s)
- Desmond O Agwunobi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ruwei Bai
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zihao Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xinyue Shi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Miao Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
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Zhang Y, Gong R, Liu Y, Sun X, Liang J, Zhou Y, Wang Y, Yu W, Wang Y, Tang L, He A, Shen Z, Yao Y, Hu H, Liu X, Zhang J. Ailanthone Inhibits Proliferation, Migration and Invasion of Osteosarcoma Cells by Downregulating the Serine Biosynthetic Pathway. Front Oncol 2022; 12:842406. [PMID: 35186770 PMCID: PMC8850634 DOI: 10.3389/fonc.2022.842406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Osteosarcoma (OS) is the most common primary bone sarcoma, chemoresistance becomes an obstacle to its treatment. Metabolic reprogramming is a hallmark of malignancy, targeting the metabolic pathways might provide a reasonable therapeutic strategy for OS. Here we demonstrated that Ailanthone (AIL), a major component of the Chinese medicine Ailanthus altissima, significantly suppressed OS cell growth in vitro and in vivo. Furthermore, AIL dose-dependently inhibited cell migration and invasion, induced cell cycle arrest and apoptosis in OS cells. Combined transcriptomics, proteomics and metabolomics analyses revealed that AIL induced widespread changes in metabolic programs in OS cells, while the serine biosynthetic pathway (SSP) was the most significantly altered pathway. qRT-PCR and Western blot assay confirmed that the transcript and protein levels of the SSP genes (PHGDH, PSAT1 and PSPH) were downregulated dose-dependently by AIL. In addition, we found out that many downstream pathways of the SSP including the one-carbon pool by folate, purine metabolism, pyrimidine metabolism, DNA replication and sphingolipid metabolism were downregulated after AIL treatment. In the revere test, PHGDH overexpression but not exogenous serine supplementation clearly attenuated the effects of AIL on OS cells. Taken together, AIL exerts antitumor effects on OS through mediating metabolic reprogramming, at least in part, by suppressing the SSP. Our findings suggest that AIL could emerge as a potential therapeutic strategy in OS.
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Affiliation(s)
- Yawen Zhang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Runze Gong
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yong Liu
- School of Artificial Intelligence, Guangxi University for Nationalities, Nanning, China
| | - Xipeng Sun
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jinrong Liang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yan Zhou
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yaling Wang
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai, China
| | - Wenxi Yu
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yonggang Wang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lina Tang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Aina He
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zan Shen
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yang Yao
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Haiyan Hu
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xin Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianjun Zhang
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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48
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Mallet D, Dufourd T, Decourt M, Carcenac C, Bossù P, Verlin L, Fernagut PO, Benoit-Marand M, Spalletta G, Barbier EL, Carnicella S, Sgambato V, Fauvelle F, Boulet S. A metabolic biomarker predicts Parkinson's disease at the early stages in patients and animal models. J Clin Invest 2022; 132:e146400. [PMID: 34914634 PMCID: PMC8843749 DOI: 10.1172/jci146400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
BackgroundCare management of Parkinson's disease (PD) patients currently remains symptomatic, mainly because diagnosis relying on the expression of the cardinal motor symptoms is made too late. Earlier detection of PD therefore represents a key step for developing therapies able to delay or slow down its progression.MethodsWe investigated metabolic markers in 3 different animal models of PD, mimicking different phases of the disease assessed by behavioral and histological evaluation, and in 3 cohorts of de novo PD patients and matched controls (n = 129). Serum and brain tissue samples were analyzed by nuclear magnetic resonance spectroscopy and data submitted to advanced multivariate statistics.ResultsOur translational strategy reveals common metabolic dysregulations in serum of the different animal models and PD patients. Some of them were mirrored in the tissue samples, possibly reflecting pathophysiological mechanisms associated with PD development. Interestingly, some metabolic dysregulations appeared before motor symptom emergence and could represent early biomarkers of PD. Finally, we built a composite biomarker with a combination of 6 metabolites. This biomarker discriminated animals mimicking PD from controls, even from the first, nonmotor signs and, very interestingly, also discriminated PD patients from healthy subjects.ConclusionFrom our translational study, which included 3 animal models and 3 de novo PD patient cohorts, we propose a promising biomarker exhibiting a high accuracy for de novo PD diagnosis that may possibly predict early PD development, before motor symptoms appear.FundingFrench National Research Agency (ANR), DOPALCOMP, Institut National de la Santé et de la Recherche Médicale, Université Grenoble Alpes, Association France Parkinson.
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Affiliation(s)
- David Mallet
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
| | - Thibault Dufourd
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
| | - Mélina Decourt
- Université de Poitiers, INSERM U1084, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Carole Carcenac
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
| | - Paola Bossù
- Dipartimento di Neurologia Clinica e Comportamentale, Laboratorio di Neuropsicobiologia Sperimentale, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Laure Verlin
- University Grenoble Alpes, INSERM, US17, CNRS, UMS 3552, CHU Grenoble Alpes, IRMaGe, Grenoble, France
| | - Pierre-Olivier Fernagut
- Université de Poitiers, INSERM U1084, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Marianne Benoit-Marand
- Université de Poitiers, INSERM U1084, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | | | - Emmanuel L. Barbier
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
- University Grenoble Alpes, INSERM, US17, CNRS, UMS 3552, CHU Grenoble Alpes, IRMaGe, Grenoble, France
| | - Sebastien Carnicella
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
| | - Véronique Sgambato
- Université de Lyon, CNRS UMR5229, Institut des Sciences Cognitives Marc Jeannerod, Bron, France
| | - Florence Fauvelle
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
- University Grenoble Alpes, INSERM, US17, CNRS, UMS 3552, CHU Grenoble Alpes, IRMaGe, Grenoble, France
| | - Sabrina Boulet
- University Grenoble Alpes, INSERM, U1216, Grenoble Institut Neurosciences, Grenoble, France
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Shafat Z, Hamza A, Deeba F, Parvez MK, Parveen S. Molecular insights into the Y-domain of hepatitis E virus using computational analyses. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Hepatitis E virus (HEV) of the family Hepeviridae is a major causative agent of acute hepatitis in developing countries. The Y-domain is derived from multi-domain non-structural polyprotein encoded by open reading frame 1 (ORF1). Previous studies have demonstrated the essentiality of Y-domain sequences in HEV life cycle; however, its function remains completely unexplored. The following study was thus conceptualized to examine the detailed computational investigation for the putative Y-domain to estimate its phylogenetic assessment, physiochemical properties, structural and functional characteristics using in silico analyses.
Results
The phylogenetic assessment of Y-domain with a vast range of hosts indicated that the protein was very well conserved throughout the course of evolution. The Y-domain was found to be unstable, hydrophilic and basic in nature with high thermostability value. Structural analysis of Y-domain revealed mixed α/β structural fold of the protein having higher percentage of alpha-helices. The three-dimensional (3D) protein model generated through homology modelling revealed the presence of clefts, tunnels and pore. Gene ontology analysis predicted Y-domain protein’s involvement in several binding and catalytic activities as well as significant biological processes. Mutations in the conserved amino acids of the Y-domain suggested that it may stabilize or de-stabilize the protein structure that might affect its structure–function relationship.
Conclusions
This theoretical study will facilitate towards deciphering the role of unexplored Y-domain, thereby providing better understanding towards the pathogenesis of HEV infection.
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Chen J, Zhou X, Jia H, Wu Z. Serine Supplementation Alleviates Doxorubicin-Induced Oxidative Damage in Skeletal Muscle of Mice. Front Physiol 2021; 12:727093. [PMID: 34566689 PMCID: PMC8458867 DOI: 10.3389/fphys.2021.727093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023] Open
Abstract
Muscle weakness affects physical activity and quality of life of patients. Serine, a nutritionally non-essential amino acid has been reported to enhance protein synthesis and implicate in biosynthesis of multiple bioactive molecules. It remains unknown whether it can protect mice against oxidative stress-induced muscles weakness. This study was conducted to test the hypothesis that serine administration alleviates doxorubicin-induced oxidative damage in skeletal muscle of mice. Mice pre-treated with or without serine were intraperitoneally injected with either doxorubicin or equal volume of saline. Reactive oxygen species (ROS) accumulation, activity of antioxidant enzymes, oxidation product of protein, DNA, and lipid, activity of mitochondrial complex, and protein level of nuclear-factor-erythroid-2-related factor 2 (NRF2)/constitutive-androstane-receptor (CAR) signaling in skeletal muscle of mice were determined. Compared with the control, doxorubicin exposure led to oxidative damage as shown by increased ROS accumulation, decreased activity of antioxidant enzymes, and enhanced oxidative product of protein, DNA, and lipid in the skeletal muscle of mice. These effects of doxorubicin were associated with increased activity of complex I and reduced glutathione. Interestingly, doxorubicin-induced oxidative damage was alleviated by serine administration. Further study showed that the beneficial effect of serine was associated with enhanced NRF2/CAR signaling. Our result showed that serine attenuated doxorubicin-induced muscle weakness in mice. Serine supplementation might be a nutritional strategy to improve the function of skeletal muscle in patients exposed to doxorubicin.
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Affiliation(s)
- Jingqing Chen
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China.,Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Xihong Zhou
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China.,Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hai Jia
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
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