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O'Leary TJ, Jackson S, Izard RM, Walsh NP, Carswell AT, Oliver SJ, Tang JCY, Fraser WD, Greeves JP. Iron status is associated with tibial structure and vitamin D metabolites in healthy young men. Bone 2024; 186:117145. [PMID: 38838798 DOI: 10.1016/j.bone.2024.117145] [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: 01/13/2024] [Revised: 04/16/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
The influence of iron on collagen synthesis and vitamin D metabolism has implications for bone health. This cross-sectional observational study investigated associations between markers of iron status and tibial structure, vitamin D metabolites, and circulating biochemical markers of bone metabolism in young healthy men. A total of 343 male British Army recruits participated (age 22 ± 3 y, height 1.77 ± 0.06 m, body mass 75.5 ± 10.1 kg). Circulating biochemical markers of iron status, vitamin D metabolites, and bone metabolism, and tibial structure and density by high-resolution peripheral quantitative computed tomography scans (HRpQCT) were measured in participants during week 1 of basic military training. Associations between markers of iron status and HRpQCT outcomes, bone metabolism, and vitamin D metabolites were tested, controlling for age, height, lean body mass, and childhood exercise volume. Higher ferritin was associated with higher total, trabecular, and cortical volumetric bone mineral density, trabecular volume, cortical area and thickness, stiffness, and failure load (all p ≤ 0.037). Higher soluble transferrin receptor (sTfR) was associated with lower trabecular number, and higher trabecular thickness and separation, cortical thickness, and cortical pore diameter (all p ≤ 0.033). Higher haemoglobin was associated with higher cortical thickness (p = 0.043). Higher ferritin was associated with lower βCTX, PINP, total 25(OH)D, and total 24,25(OH)2D, and higher 1,25(OH)2D:24,25(OH)2D ratio (all p ≤ 0.029). Higher sTfR was associated with higher PINP, total 25(OH)D, and total 24,25(OH)2D (all p ≤ 0.025). The greater density, size, and strength of the tibia, and lower circulating concentrations of markers of bone resorption and formation with better iron stores (higher ferritin) are likely as a result of the direct role of iron in collagen synthesis.
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Affiliation(s)
- Thomas J O'Leary
- Army Health and Performance Research, Army Headquarters, Andover, United Kingdom; Division of Surgery and Interventional Science, UCL, London, United Kingdom
| | - Sarah Jackson
- Army Health and Performance Research, Army Headquarters, Andover, United Kingdom
| | - Rachel M Izard
- Defence Science and Technology, Ministry of Defence, Porton Down, United Kingdom
| | - Neil P Walsh
- Faculty of Science, Liverpool John Moores University, Liverpool, United Kingdom
| | - Alexander T Carswell
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom; School of Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Samuel J Oliver
- College of Human Sciences, Bangor University, Bangor, United Kingdom
| | - Jonathan C Y Tang
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom; Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - William D Fraser
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom; Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Julie P Greeves
- Army Health and Performance Research, Army Headquarters, Andover, United Kingdom; Division of Surgery and Interventional Science, UCL, London, United Kingdom; Norwich Medical School, University of East Anglia, Norwich, United Kingdom.
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2
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Bologna-Molina R, Schuch L, Niklander SE. Comprehensive insights into the understanding of hypoxia in ameloblastoma. Histol Histopathol 2024; 39:983-989. [PMID: 38362601 DOI: 10.14670/hh-18-718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Hypoxia is characterized by a disparity between supply and demand of oxygen. The association between hypoxia and head and neck tumors is a topic of significant interest. Tumors frequently encounter areas with inadequate oxygen supply, resulting in a hypoxic microenvironment. Ameloblastoma is one of the most common benign odontogenic tumors of the maxillofacial region. It is a slow-growing but locally invasive tumor with a high recurrence rate. The literature has demonstrated the correlation between hypoxia and ameloblastoma, revealing a discernible link between the heightened expression of hypoxic markers in low oxygen conditions. This association is intricately tied to the tumoral potential for invasion, progression, and malignant transformation. Hypoxia profoundly influences the molecular and cellular landscape within ameloblastic lesions. The present review sheds light on the mechanisms, implications, and emerging perspectives in understanding this intriguing association to clarify the dynamic relationship between hypoxia and ameloblastoma.
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Affiliation(s)
- Ronell Bologna-Molina
- Diagnostic in Oral Pathology and Oral Medicine Department, Faculty of Dentistry, Universidad de la República, Uruguay.
- Research Department, School of Dentistry, Universidad Juarez del Estado de Durango, Mexico
| | - Lauren Schuch
- Diagnostic in Oral Pathology and Oral Medicine Department, Faculty of Dentistry, Universidad de la República, Uruguay
| | - Sven Eric Niklander
- Unit of Oral Pathology and Oral Medicine, Faculty of Dentistry, Universidad Andres Bello, Viña del Mar, Chile
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3
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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4
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Thomas M, Jaber Sathik Rifayee SB, Chaturvedi SS, Gorantla KR, White W, Wildey J, Schofield CJ, Christov CZ. The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A. Inorg Chem 2024; 63:10737-10755. [PMID: 38781256 PMCID: PMC11168414 DOI: 10.1021/acs.inorgchem.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
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Affiliation(s)
- Midhun
George Thomas
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | | | - Shobhit S. Chaturvedi
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Koteswara Rao Gorantla
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Walter White
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Jon Wildey
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K.
| | - Christo Z. Christov
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
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5
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Krishnan A, Waheed SO, Melayikandy S, LaRouche C, Paik M, Schofield CJ, Karabencheva-Christova TG. Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH. Chemphyschem 2024:e202400303. [PMID: 38839574 DOI: 10.1002/cphc.202400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post-translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single-point mutations in the Second Coordination Sphere (SCS) and long-range (LR) residues of AspH have been linked to pathological conditions such as the ophthalmologic condition Traboulsi syndrome and chronic kidney disease (CKD). Although the clinical impacts of these mutations are established, there is a critical knowledge gap regarding their specific atomistic effects on the catalytic mechanism of AspH. In this study, we report integrated computational investigations on the potential mechanistic implications of four mutant forms of human AspH with clinical importance: R735W, R735Q, R688Q, and G434V. All the mutant forms exhibited altered binding interactions with the co-substrate 2-oxoglutarate (2OG) and the main substrate in the ferric-superoxo and ferryl complexes, which are critical for catalysis, compared to the wild-type (WT). Importantly, the mutations strongly influence the energetics of the frontier molecular orbitals (FMOs) and, thereby, the activation energies for the hydrogen atom transfer (HAT) step compared to the WT AspH. Insights from our study can contribute to enzyme engineering and the development of selective modulators for WT and mutants of AspH, ultimately aiding in treating cancers, Traboulsi syndrome and, CKD.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sreerag Melayikandy
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Techno, Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
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6
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Cordonnier C, Mandalasi M, Gigley J, Wohlfert EA, West CM, Blader IJ. The Toxoplasma oxygen-sensing protein, TgPhyA, is required for resistance to interferon gamma-mediated nutritional immunity in mice. PLoS Biol 2024; 22:e3002690. [PMID: 38857298 PMCID: PMC11192375 DOI: 10.1371/journal.pbio.3002690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/21/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
As Toxoplasma gondii disseminates through its host, the parasite must sense and adapt to its environment and scavenge nutrients. Oxygen (O2) is one such environmental factor and cytoplasmic prolyl 4-hydroxylases (PHDs) are evolutionarily conserved O2 cellular sensing proteins that regulate responses to changes in O2 availability. Toxoplasma expresses 2 PHDs. One of them, TgPHYa hydroxylates SKP1, a subunit of the SCF-E3 ubiquitin ligase complex. In vitro, TgPHYa is important for growth at low O2 levels. However, studies have yet to examine the role that TgPHYa or any other pathogen-encoded PHD plays in virulence and disease. Using a type II ME49 Toxoplasma TgPHYa knockout, we report that TgPHYa is important for Toxoplasma virulence and brain cyst formation in mice. We further find that while TgPHYa mutant parasites can establish an infection in the gut, they are unable to efficiently disseminate to peripheral tissues because the mutant parasites are unable to survive within recruited immune cells. Since this phenotype was abrogated in IFNγ knockout mice, we studied how TgPHYa mediates survival in IFNγ-treated cells. We find that TgPHYa is not required for release of parasite-encoded effectors into host cells that neutralize anti-parasitic processes induced by IFNγ. In contrast, we find that TgPHYa is required for the parasite to scavenge tryptophan, which is an amino acid whose levels are decreased after IFNγ up-regulates the tryptophan-catabolizing enzyme, indoleamine dioxygenase (IDO). We further find, relative to wild-type mice, that IDO knockout mice display increased morbidity when infected with TgPHYa knockout parasites. Together, these data identify the first parasite mechanism for evading IFNγ-induced nutritional immunity and highlight a novel role that oxygen-sensing proteins play in pathogen growth and virulence.
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Affiliation(s)
- Charlotte Cordonnier
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Msano Mandalasi
- Department of Biochemistry & Molecular Biology, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Jason Gigley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Elizabeth A. Wohlfert
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Christopher M. West
- Department of Biochemistry & Molecular Biology, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Ira J. Blader
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
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7
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Ziki RA, Colnot S. Glutamine metabolism, a double agent combating or fuelling hepatocellular carcinoma. JHEP Rep 2024; 6:101077. [PMID: 38699532 PMCID: PMC11063524 DOI: 10.1016/j.jhepr.2024.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 05/05/2024] Open
Abstract
The reprogramming of glutamine metabolism is a key event in cancer more generally and in hepatocellular carcinoma (HCC) in particular. Glutamine consumption supplies tumours with ATP and metabolites through anaplerosis of the tricarboxylic acid cycle, while glutamine production can be enhanced by the overexpression of glutamine synthetase. In HCC, increased glutamine production is driven by activating mutations in the CTNNB1 gene encoding β-catenin. Increased glutamine synthesis or utilisation impacts tumour epigenetics, oxidative stress, autophagy, immunity and associated pathways, such as the mTOR (mammalian target of rapamycin) pathway. In this review, we will discuss studies which emphasise the pro-tumoral or tumour-suppressive effect of glutamine overproduction. It is clear that more comprehensive studies are needed as a foundation from which to develop suitable therapies targeting glutamine metabolic pathways, depending on the predicted pro- or anti-tumour role of dysregulated glutamine metabolism in distinct genetic contexts.
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Affiliation(s)
- Razan Abou Ziki
- INSERM, Sorbonne Université, Centre de Recherche des Cordeliers (CRC), Paris, F-75006, France
- Équipe labellisée Ligue Nationale Contre le Cancer, France
| | - Sabine Colnot
- INSERM, Sorbonne Université, Centre de Recherche des Cordeliers (CRC), Paris, F-75006, France
- Équipe labellisée Ligue Nationale Contre le Cancer, France
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8
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Egorova KS, Kibardin AV, Posvyatenko AV, Ananikov VP. Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms. Chem Rev 2024; 124:4679-4733. [PMID: 38621413 DOI: 10.1021/acs.chemrev.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.
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Affiliation(s)
- Ksenia S Egorova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey V Kibardin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Health of Russian Federation, Moscow 117198, Russia
| | - Alexandra V Posvyatenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Health of Russian Federation, Moscow 117198, Russia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
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9
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Wang H, Chen Q, Feng W. The Emerging Role of 2OGDs as Candidate Targets for Engineering Crops with Broad-Spectrum Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1129. [PMID: 38674537 PMCID: PMC11054871 DOI: 10.3390/plants13081129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Plant diseases caused by pathogens result in a marked decrease in crop yield and quality annually, greatly threatening food production and security worldwide. The creation and cultivation of disease-resistant cultivars is one of the most effective strategies to control plant diseases. Broad-spectrum resistance (BSR) is highly preferred by breeders because it confers plant resistance to diverse pathogen species or to multiple races or strains of one species. Recently, accumulating evidence has revealed the roles of 2-oxoglutarate (2OG)-dependent oxygenases (2OGDs) as essential regulators of plant disease resistance. Indeed, 2OGDs catalyze a large number of oxidative reactions, participating in the plant-specialized metabolism or biosynthesis of the major phytohormones and various secondary metabolites. Moreover, several 2OGD genes are characterized as negative regulators of plant defense responses, and the disruption of these genes via genome editing tools leads to enhanced BSR against pathogens in crops. Here, the recent advances in the isolation and identification of defense-related 2OGD genes in plants and their exploitation in crop improvement are comprehensively reviewed. Also, the strategies for the utilization of 2OGD genes as targets for engineering BSR crops are discussed.
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Affiliation(s)
- Han Wang
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
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10
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Tvaroška I. Glycosylation Modulates the Structure and Functions of Collagen: A Review. Molecules 2024; 29:1417. [PMID: 38611696 PMCID: PMC11012932 DOI: 10.3390/molecules29071417] [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: 02/26/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Collagens are fundamental constituents of the extracellular matrix and are the most abundant proteins in mammals. Collagens belong to the family of fibrous or fiber-forming proteins that self-assemble into fibrils that define their mechanical properties and biological functions. Up to now, 28 members of the collagen superfamily have been recognized. Collagen biosynthesis occurs in the endoplasmic reticulum, where specific post-translational modification-glycosylation-is also carried out. The glycosylation of collagens is very specific and adds β-d-galactopyranose and β-d-Glcp-(1→2)-d-Galp disaccharide through β-O-linkage to hydroxylysine. Several glycosyltransferases, namely COLGALT1, COLGALT2, LH3, and PGGHG glucosidase, were associated the with glycosylation of collagens, and recently, the crystal structure of LH3 has been solved. Although not fully understood, it is clear that the glycosylation of collagens influences collagen secretion and the alignment of collagen fibrils. A growing body of evidence also associates the glycosylation of collagen with its functions and various human diseases. Recent progress in understanding collagen glycosylation allows for the exploitation of its therapeutic potential and the discovery of new agents. This review will discuss the relevant contributions to understanding the glycosylation of collagens. Then, glycosyltransferases involved in collagen glycosylation, their structure, and catalytic mechanism will be surveyed. Furthermore, the involvement of glycosylation in collagen functions and collagen glycosylation-related diseases will be discussed.
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Affiliation(s)
- Igor Tvaroška
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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11
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Yuan X, Ruan W, Bobrow B, Carmeliet P, Eltzschig HK. Targeting hypoxia-inducible factors: therapeutic opportunities and challenges. Nat Rev Drug Discov 2024; 23:175-200. [PMID: 38123660 DOI: 10.1038/s41573-023-00848-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
Hypoxia-inducible factors (HIFs) are highly conserved transcription factors that are crucial for adaptation of metazoans to limited oxygen availability. Recently, HIF activation and inhibition have emerged as therapeutic targets in various human diseases. Pharmacologically desirable effects of HIF activation include erythropoiesis stimulation, cellular metabolism optimization during hypoxia and adaptive responses during ischaemia and inflammation. By contrast, HIF inhibition has been explored as a therapy for various cancers, retinal neovascularization and pulmonary hypertension. This Review discusses the biochemical mechanisms that control HIF stabilization and the molecular strategies that can be exploited pharmacologically to activate or inhibit HIFs. In addition, we examine medical conditions that benefit from targeting HIFs, the potential side effects of HIF activation or inhibition and future challenges in this field.
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Affiliation(s)
- Xiaoyi Yuan
- Department of Anaesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Wei Ruan
- Department of Anaesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Anaesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bentley Bobrow
- Department of Emergency Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Peter Carmeliet
- Laboratory of Angiogenesis & Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis & Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Holger K Eltzschig
- Department of Anaesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- Outcomes Research Consortium, Cleveland, OH, USA.
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12
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Diptiman D, Jalan A, Pal R, Dodwani S, Bandyopadhyay D. Hist-i-fy-a multiple histidine post-translational-modification (PTM) prediction server based on protein sequences using convolution neural network: a case study on mass spectroscopy data. J Biomol Struct Dyn 2024:1-10. [PMID: 38285683 DOI: 10.1080/07391102.2024.2310200] [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: 07/24/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024]
Abstract
Computational characterization of multiple Histidine (His) post-translational-modifications (PTM) at enzyme active sites complements tedious experimental characterization in proteins-of-unknown-functions (PUFs) and domain-of-unknown-functions (DUFs). There are only a handful of Histidine-PTM-prediction-tools and those also annotate only a single function. Here, we addressed the problem using artificial neural networks on functional histidine dataset curated from enzyme (protein) sequences available in UniProt database (sample size n = 1584). The convolution-neural-network (CNN) model ('Hist-i-fy') performed the best with 75% overall accuracy/F1-score. A case study was performed on histidine-phosphorylation (n = 34) obtained from mass spectroscopy data. For the first time, we report multiple His-PTM-prediction-tool (https://histify.streamlit.app/& https://github.com/dibyansu24-maker/Histify), with optimal performance. The inputs to the tool are (i) protein sequence containing histidine, and (ii) the histidine residue number. Prediction output is one out of the eight histidine functions-acetylation, ribosylation, glycosylation, hydroxylation, methylation, oxidation, phosphorylation, and protein splicing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dibyansu Diptiman
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Rishabh Pal
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Sachin Dodwani
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
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Chumak V, Rajacharya GH, Singh PK. Metabolomic Investigations into Hypoxia-Mediated Metabolic Reprogramming of Pancreatic Cancer Cells. Methods Mol Biol 2024; 2755:191-200. [PMID: 38319579 PMCID: PMC10915399 DOI: 10.1007/978-1-0716-3633-6_14] [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] [Indexed: 02/07/2024]
Abstract
Hypoxia is a crucial microenvironmental factor that defines tumor cell growth and aggressiveness. Cancer cells adapt to hypoxia by altering their metabolism. These alterations impact various cellular and physiological functions, including energy metabolism, vascularization, invasion and metastasis, genetic instability, cell immortalization, stem cell maintenance, and resistance to chemotherapy (Li et al. Technol Cancer Res Treat 20:15330338211036304, 2021). Hypoxia-inducible factor-1α (HIF-1α) is known to be a critical regulator of glycolysis that directly regulates the transcription of multiple key enzymes of the glycolysis pathway. Moreover, HIF-1α stabilization can be directly modulated by TCA-derived metabolites, including 2-ketoglutarate and succinate (Infantino et al, Int J Mol Sci 22(22), https://doi.org/10.3390/ijms22115703 , 2021). Overall, the molecular mechanisms underlying the adaptation of cellular metabolism to hypoxia impact the metabolic phenotype of cancer cells. Such adaptations include increased glucose uptake, increased lactate production, and increased levels of other metabolites that stabilize HIF-1α, leading to a vicious circle of hypoxia-induced tumor growth.
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Affiliation(s)
- Vira Chumak
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Girish H Rajacharya
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Pankaj K Singh
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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14
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Kim TD, Gu R, Janknecht R. Methylation of the JMJD2B epigenetic regulator differentially affects its ability to coactivate the ETV1 and JUN transcription factors. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 14:101-115. [PMID: 38213775 PMCID: PMC10776875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
OBJECTIVES Jumonji C domain-containing (JMJD) 2B (JMJD2B) is a transcriptional cofactor and histone demethylase that is involved in prostate cancer formation. However, how its function is regulated by posttranslational modification has remained elusive. Hence, we examined if JMJD2B would be regulated by lysine methylation. METHODS Through in vitro methylation assays and Western blotting with methyl-lysine specific antibodies, we analyzed lysine methylation within JMJD2B. Identified methylated lysine residues were mutated to arginine residues and the respective impact on JMJD2B transcriptional activity measured with a reporter gene assay in human LNCaP prostate cancer cells. RESULTS We discovered that JMJD2B is methylated on up to six different lysine residues. Further, we identified the suppressor of variegation 3-9/enhancer of zeste/trithorax (SET) domain-containing protein 7/9 (SET7/9) as the methyltransferase being responsible for this posttranslational modification. Mutating the methylation sites in JMJD2B to arginine residues led to diminished coactivation of the Ju-nana (JUN) transcription factor, which is a known oncogenic protein in prostate tumors. In contrast, methylation of JMJD2B had no impact on its ability to coactivate another transcription factor associated with prostate cancer, the DNA-binding protein E26 transformation-specific (ETS) variant 1 (ETV1). Consistent with a potential joint action of JMJD2B, SET7/9 and JUN in prostate cancer, the expression of JMJD2B in human prostate tumors was positively correlated with both SET7/9 and JUN levels. CONCLUSIONS The identified SET7/9-mediated methylation of JMJD2B appears to impact its cooperation with selected interacting transcription factors in prostate cancer cells. Given the implicated roles of JMJD2B beyond prostate tumorigenesis, SET7/9-mediated methylation of JMJD2B possibly also influences the development of other cancers, while its impairment might have relevance for obesity or a global developmental delay that can be elicited by reduced JMJD2B activity.
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Affiliation(s)
- Tae-Dong Kim
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma, OK, USA
| | - Ruicai Gu
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma, OK, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma, OK, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences CenterOklahoma, OK, USA
- Department of Pathology, University of Oklahoma Health Sciences CenterOklahoma, OK, USA
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15
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Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. SCIENCE ADVANCES 2023; 9:eadj4884. [PMID: 38064566 PMCID: PMC10708181 DOI: 10.1126/sciadv.adj4884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Abstract
Oxygen deprivation and excess are both toxic. Thus, the body's ability to adapt to varying oxygen tensions is critical for survival. While the hypoxia transcriptional response has been well studied, the post-translational effects of oxygen have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to varying oxygen tensions. In particular, several extracellular matrix (ECM) proteins are stabilized in the lung under both hypoxia and hyperoxia. Furthermore, we show that complex 1 of the electron transport chain is destabilized in hyperoxia, in accordance with the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a hyperoxia transcriptional regulator, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of varying oxygen tensions on protein turnover rates and identifies tissue-specific mediators of oxygen-dependent responses.
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Affiliation(s)
- Xuewen Chen
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Augustinus G. Haribowo
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan H. Baik
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Fossati
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Erica Stevenson
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yiwen R. Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Nabora S. Reyes
- Department of Medicine and Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Tien Peng
- Department of Medicine and Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michael A. Matthay
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Departments of Medicine and Anesthesia, University of California San Francisco, San Francisco, CA, USA
| | - Michela Traglia
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Alexander R. Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, CA, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sina Ghaemmaghami
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Danielle L. Swaney
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Isha H. Jain
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
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16
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Grandi E, Feyza Özgen F, Schmidt S, Poelarends GJ. Enzymatic Oxy- and Amino-Functionalization in Biocatalytic Cascade Synthesis: Recent Advances and Future Perspectives. Angew Chem Int Ed Engl 2023; 62:e202309012. [PMID: 37639631 DOI: 10.1002/anie.202309012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Biocatalytic cascades are a powerful tool for building complex molecules containing oxygen and nitrogen functionalities. Moreover, the combination of multiple enzymes in one pot offers the possibility to minimize downstream processing and waste production. In this review, we illustrate various recent efforts in the development of multi-step syntheses involving C-O and C-N bond-forming enzymes to produce high value-added compounds, such as pharmaceuticals and polymer precursors. Both in vitro and in vivo examples are discussed, revealing the respective advantages and drawbacks. The use of engineered enzymes to boost the cascades outcome is also addressed and current co-substrate and cofactor recycling strategies are presented, highlighting the importance of atom economy. Finally, tools to overcome current challenges for multi-enzymatic oxy- and amino-functionalization reactions are discussed, including flow systems with immobilized biocatalysts and cascades in confined nanomaterials.
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Affiliation(s)
- Eleonora Grandi
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Fatma Feyza Özgen
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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17
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Yoo S, Choi S, Kim I, Kim IS. Hypoxic regulation of extracellular vesicles: Implications for cancer therapy. J Control Release 2023; 363:201-220. [PMID: 37739015 DOI: 10.1016/j.jconrel.2023.09.034] [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: 03/01/2023] [Revised: 08/18/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Extracellular vesicles (EVs) play a pivotal role in intercellular communication and have been implicated in cancer progression. Hypoxia, a pervasive hallmark of cancer, is known to regulate EV biogenesis and function. Hypoxic EVs contain a specific set of proteins, nucleic acids, lipids, and metabolites, capable of reprogramming the biology and fate of recipient cells. Enhancing the intrinsic therapeutic efficacy of EVs can be achieved by strategically modifying their structure and contents. Moreover, the use of EVs as drug delivery vehicles holds great promise for cancer treatment. However, various hurdles must be overcome to enable their clinical application as cancer therapeutics. In this review, we aim to discuss the current knowledge on the hypoxic regulation of EVs. Additionally, we will describe the underlying mechanisms by which EVs contribute to cancer progression in hypoxia and outline the progress and limitations of hypoxia-related EV therapeutics for cancer.
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Affiliation(s)
- Seongkyeong Yoo
- Department of Pharmacology and Program in Biomedical Science and Engineering, Inha University College of Medicine, Incheon 22212, South Korea; Research Center for Controlling Intercellular Communication, Inha University College of Medicine, Incheon 22212, South Korea
| | - Sanga Choi
- Department of Pharmacology and Program in Biomedical Science and Engineering, Inha University College of Medicine, Incheon 22212, South Korea; Research Center for Controlling Intercellular Communication, Inha University College of Medicine, Incheon 22212, South Korea
| | - Iljin Kim
- Department of Pharmacology and Program in Biomedical Science and Engineering, Inha University College of Medicine, Incheon 22212, South Korea; Research Center for Controlling Intercellular Communication, Inha University College of Medicine, Incheon 22212, South Korea.
| | - In-San Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, South Korea; Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute Science and Technology, Seoul 02792, South Korea.
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18
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Curieses Andrés CM, Pérez de la Lastra JM, Andrés Juan C, Plou FJ, Pérez-Lebeña E. From reactive species to disease development: Effect of oxidants and antioxidants on the cellular biomarkers. J Biochem Mol Toxicol 2023; 37:e23455. [PMID: 37437103 DOI: 10.1002/jbt.23455] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/14/2023]
Abstract
The influence of modern lifestyle, diet, exposure to chemicals such as phytosanitary substances, together with sedentary lifestyles and lack of exercise play an important role in inducing reactive stress (RS) and disease. The imbalance in the production and scavenging of free radicals and the induction of RS (oxidative, nitrosative, and halogenative) plays an essential role in the etiology of various chronic pathologies, such as cardiovascular diseases, diabetes, neurodegenerative diseases, and cancer. The implication of free radicals and reactive species injury in metabolic disturbances and the onset of many diseases have been accumulating for several decades, and are now accepted as a major cause of many chronic diseases. Exposure to elevated levels of free radicals can cause molecular structural impact on proteins, lipids, and DNA, as well as functional alteration of enzyme homeostasis, leading to aberrations in gene expression. Endogenous depletion of antioxidant enzymes can be mitigated using exogenous antioxidants. The current interest in the use of exogenous antioxidants as adjunctive agents for the treatment of human diseases allows a better understanding of these diseases, facilitating the development of new therapeutic agents with antioxidant activity to improve the treatment of various diseases. Here we examine the role that RS play in the initiation of disease and in the reactivity of free radicals and RS in organic and inorganic cellular components.
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Affiliation(s)
| | | | - Celia Andrés Juan
- Department of Organic Chemistry, Cinquima Institute, Faculty of Sciences, Valladolid University, Valladolid, Spain
| | - Francisco J Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, Madrid, Spain
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19
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Geng Y, Hu Y, Zhang F, Tuo Y, Ge R, Bai Z. Mitochondria in hypoxic pulmonary hypertension, roles and the potential targets. Front Physiol 2023; 14:1239643. [PMID: 37645564 PMCID: PMC10461481 DOI: 10.3389/fphys.2023.1239643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023] Open
Abstract
Mitochondria are the centrol hub for cellular energy metabolisms. They regulate fuel metabolism by oxygen levels, participate in physiological signaling pathways, and act as oxygen sensors. Once oxygen deprived, the fuel utilizations can be switched from mitochondrial oxidative phosphorylation to glycolysis for ATP production. Notably, mitochondria can also adapt to hypoxia by making various functional and phenotypes changes to meet the demanding of oxygen levels. Hypoxic pulmonary hypertension is a life-threatening disease, but its exact pathgenesis mechanism is still unclear and there is no effective treatment available until now. Ample of evidence indicated that mitochondria play key factor in the development of hypoxic pulmonary hypertension. By hypoxia-inducible factors, multiple cells sense and transmit hypoxia signals, which then control the expression of various metabolic genes. This activation of hypoxia-inducible factors considered associations with crosstalk between hypoxia and altered mitochondrial metabolism, which plays an important role in the development of hypoxic pulmonary hypertension. Here, we review the molecular mechanisms of how hypoxia affects mitochondrial function, including mitochondrial biosynthesis, reactive oxygen homeostasis, and mitochondrial dynamics, to explore the potential of improving mitochondrial function as a strategy for treating hypoxic pulmonary hypertension.
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Affiliation(s)
- Yumei Geng
- Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Research Center for High Altitude Medicine, Qinghai University, Xining, China
- Department of Respiratory and Critical Care Medicine, Qinghai Provincial People’s Hospital, Xining, China
| | - Yu Hu
- Department of Pharmacy, Qinghai Provincial Traffic Hospital, Xining, China
| | - Fang Zhang
- Department of Respiratory and Critical Care Medicine, Qinghai Provincial People’s Hospital, Xining, China
| | - Yajun Tuo
- Department of Respiratory and Critical Care Medicine, Qinghai Provincial People’s Hospital, Xining, China
| | - Rili Ge
- Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Research Center for High Altitude Medicine, Qinghai University, Xining, China
| | - Zhenzhong Bai
- Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Research Center for High Altitude Medicine, Qinghai University, Xining, China
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20
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Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. eLife 2023; 12:e87705. [PMID: 37494095 PMCID: PMC10371230 DOI: 10.7554/elife.87705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/09/2023] [Indexed: 07/27/2023] Open
Abstract
The ability to sense and respond to changes in cellular oxygen levels is critical for aerobic organisms and requires a molecular oxygen sensor. The prototypical sensor is the oxygen-dependent enzyme PHD: hypoxia inhibits its ability to hydroxylate the transcription factor HIF, causing HIF to accumulate and trigger the classic HIF-dependent hypoxia response. A small handful of other oxygen sensors are known, all of which are oxygen-dependent enzymes. However, hundreds of oxygen-dependent enzymes exist among aerobic organisms, raising the possibility that additional sensors remain to be discovered. This review summarizes known and potential hypoxia sensors among human O2-dependent enzymes and highlights their possible roles in hypoxia-related adaptation and diseases.
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Affiliation(s)
- Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Susan Shen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Department of Psychiatry, University of California, San FranciscoSan FranciscoUnited States
| | - Philip Bickler
- Hypoxia Research Laboratory, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Center for Health Equity in Surgery and Anesthesia, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Anesthesia and Perioperative Care, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
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21
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Rajesh R, Atallah R, Bärnthaler T. Dysregulation of metabolic pathways in pulmonary fibrosis. Pharmacol Ther 2023; 246:108436. [PMID: 37150402 DOI: 10.1016/j.pharmthera.2023.108436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/09/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disorder of unknown origin and the most common interstitial lung disease. It progresses with the recruitment of fibroblasts and myofibroblasts that contribute to the accumulation of extracellular matrix (ECM) proteins, leading to the loss of compliance and alveolar integrity, compromising the gas exchange capacity of the lung. Moreover, while there are therapeutics available, they do not offer a cure. Thus, there is a pressing need to identify better therapeutic targets. With the advent of transcriptomics, proteomics, and metabolomics, the cellular mechanisms underlying disease progression are better understood. Metabolic homeostasis is one such factor and its dysregulation has been shown to impact the outcome of IPF. Several metabolic pathways involved in the metabolism of lipids, protein and carbohydrates have been implicated in IPF. While metabolites are crucial for the generation of energy, it is now appreciated that metabolites have several non-metabolic roles in regulating cellular processes such as proliferation, signaling, and death among several other functions. Through this review, we succinctly elucidate the role of several metabolic pathways in IPF. Moreover, we also discuss potential therapeutics which target metabolism or metabolic pathways.
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Affiliation(s)
- Rishi Rajesh
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Reham Atallah
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Thomas Bärnthaler
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria.
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22
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Fletcher SC, Hall C, Kennedy TJ, Pajusalu S, Wojcik MH, Boora U, Li C, Oja KT, Hendrix E, Westrip CA, Andrijes R, Piasecka SK, Singh M, El-Asrag ME, Ptasinska A, Tillmann V, Higgs MR, Carere DA, Beggs AD, Pappas J, Rabin R, Smerdon SJ, Stewart GS, Õunap K, Coleman ML. Impaired protein hydroxylase activity causes replication stress and developmental abnormalities in humans. J Clin Invest 2023; 133:e152784. [PMID: 36795492 PMCID: PMC10065073 DOI: 10.1172/jci152784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Although protein hydroxylation is a relatively poorly characterized posttranslational modification, it has received significant recent attention following seminal work uncovering its role in oxygen sensing and hypoxia biology. Although the fundamental importance of protein hydroxylases in biology is becoming clear, the biochemical targets and cellular functions often remain enigmatic. JMJD5 is a "JmjC-only" protein hydroxylase that is essential for murine embryonic development and viability. However, no germline variants in JmjC-only hydroxylases, including JMJD5, have yet been described that are associated with any human pathology. Here we demonstrate that biallelic germline JMJD5 pathogenic variants are deleterious to JMJD5 mRNA splicing, protein stability, and hydroxylase activity, resulting in a human developmental disorder characterized by severe failure to thrive, intellectual disability, and facial dysmorphism. We show that the underlying cellular phenotype is associated with increased DNA replication stress and that this is critically dependent on the protein hydroxylase activity of JMJD5. This work contributes to our growing understanding of the role and importance of protein hydroxylases in human development and disease.
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Affiliation(s)
- Sally C. Fletcher
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte Hall
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tristan J. Kennedy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Uncaar Boora
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Chan Li
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kaisa Teele Oja
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Eline Hendrix
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Christian A.E. Westrip
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Regina Andrijes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sonia K. Piasecka
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mansi Singh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mohammed E. El-Asrag
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Faculty of Science, Benha University, Benha, Egypt
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Vallo Tillmann
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Children’s Clinic, Tartu University Hospital, Tartu, Estonia
| | - Martin R. Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA
| | - Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA
| | - Stephen J. Smerdon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Mathew L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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23
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Lun J, Zhang H, Guo J, Yu M, Fang J. Hypoxia inducible factor prolyl hydroxylases in inflammatory bowel disease. Front Pharmacol 2023; 14:1045997. [PMID: 37201028 PMCID: PMC10187758 DOI: 10.3389/fphar.2023.1045997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/18/2023] [Indexed: 05/20/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease that is characterized by intestinal inflammation. Epithelial damage and loss of intestinal barrier function are believed to be the hallmark pathologies of the disease. In IBD, the resident and infiltrating immune cells consume much oxygen, rendering the inflamed intestinal mucosa hypoxic. In hypoxia, the hypoxia-inducible factor (HIF) is induced to cope with the lack of oxygen and protect intestinal barrier. Protein stability of HIF is tightly controlled by prolyl hydroxylases (PHDs). Stabilization of HIF through inhibition of PHDs is appearing as a new strategy of IBD treatment. Studies have shown that PHD-targeting is beneficial to the treatment of IBD. In this Review, we summarize the current understanding of the role of HIF and PHDs in IBD and discuss the therapeutic potential of targeting PHD-HIF pathway for IBD treatment.
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Affiliation(s)
- Jie Lun
- Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongwei Zhang
- Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, China
| | - Jing Guo
- Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengchao Yu
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, China
| | - Jing Fang
- Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Jing Fang,
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Chowdhury MN, Jin H. The RGG motif proteins: Interactions, functions, and regulations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1748. [PMID: 35661420 PMCID: PMC9718894 DOI: 10.1002/wrna.1748] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/31/2023]
Abstract
Proteins with motifs rich in arginines and glycines were discovered decades ago and are functionally involved in a staggering range of essential processes in the cell. Versatile, specific, yet adaptable molecular interactions enabled by the unique combination of arginine and glycine, combined with multiplicity of molecular recognition conferred by repeated di-, tri-, and multiple peptide motifs, allow RGG motif proteins to interact with a broad range of proteins and nucleic acids. Furthermore, posttranslational modifications at the arginines in the motif extend the RGG protein's capacity for a fine-tuned regulation. In this review, we focus on the biochemical properties of the RGG motif, its molecular interactions with RNAs and proteins, and roles of the posttranslational modification in modulating their interactions. We discuss current knowledge of the RGG motif proteins involved in mRNA transport and translation, highlight our merging understanding of their molecular functions in translational regulation and summarize areas of research in the future critical in understanding this important family of proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Mechanisms.
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Affiliation(s)
- Mashiat N. Chowdhury
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Corresponding author: Phone: (217)244-9493, Fax: (217)244-5858,
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25
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Isono T, Matsumoto T, Suzaki M, Kubota S, Kageyama S, Kawauchi A, Wada A. Transcriptome analysis of a dog model of congestive heart failure shows that collagen-related 2-oxoglutarate-dependent dioxygenases contribute to heart failure. Sci Rep 2022; 12:22569. [PMID: 36581661 PMCID: PMC9800379 DOI: 10.1038/s41598-022-26717-7] [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: 03/03/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022] Open
Abstract
Fibrosis is an important pathological mechanism in heart failure (HF) and is associated with poor prognosis. We analyzed fibrosis in HF patients using transcriptomic data. Genes differentially expressed between normal control and congestive HF (CHF) dogs included P3H1, P3H2, P3H4, P4HA2, PLOD1 and PLOD3, which belong to the 2-oxoglutarate-dependent dioxygenases (2OGD) superfamily that stabilizes collagen during fibrosis. Quantitative polymerase chain reaction analysis demonstrated 2OGD gene expression was increased in CHF samples compared with normal left ventricle (LV) samples. 2OGD gene expression was repressed in angiotensin converting enzyme inhibitor-treated samples. These genes, activated the hydroxylation of proline or lysin residues of procollagen mediated by 2-oxoglutaric acid and O2, produce succinic acid and CO2. Metabolic analysis demonstrated the concentration of succinic acid was significantly increased in CHF samples compared with normal LV samples. Fibrosis was induced in human cardiac fibroblasts by TGF-ß1 treatment. After treatment, the gene and protein expressions of 2OGD, the concentration of succinic acid, and the oxygen consumption rate were increased compared with no treatment. This is the first study to show that collagen-related 2OGD genes contribute to HF during the induction of fibrosis and might be potential therapeutic targets for fibrosis and HF.
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Affiliation(s)
- Takahiro Isono
- grid.410827.80000 0000 9747 6806Department of Urology, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan ,grid.410827.80000 0000 9747 6806Central Research Laboratory, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Takehiro Matsumoto
- Center of Cardiovascular Disease and Heart Failure, Omi Medical Center, Kusatsu, Shiga 525-8585 Japan
| | - Masafumi Suzaki
- grid.410827.80000 0000 9747 6806Central Research Laboratory, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Shigehisa Kubota
- grid.410827.80000 0000 9747 6806Department of Urology, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Susumu Kageyama
- grid.410827.80000 0000 9747 6806Department of Urology, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Akihiro Kawauchi
- grid.410827.80000 0000 9747 6806Department of Urology, Shiga University of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Atuyuki Wada
- Center of Cardiovascular Disease and Heart Failure, Omi Medical Center, Kusatsu, Shiga 525-8585 Japan
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26
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Targeting hypoxia-related metabolism molecules: How to improve tumour immune and clinical treatment? Biomed Pharmacother 2022; 156:113917. [DOI: 10.1016/j.biopha.2022.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/20/2022] Open
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Liu H, Xie Y, Wang X, Abboud MI, Ma C, Ge W, Schofield CJ. Exploring links between 2-oxoglutarate-dependent oxygenases and Alzheimer's disease. Alzheimers Dement 2022; 18:2637-2668. [PMID: 35852137 PMCID: PMC10083964 DOI: 10.1002/alz.12733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/12/2022] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
Abstract
Hypoxia, that is, an inadequate oxygen supply, is linked to neurodegeneration and patients with cardiovascular disease are prone to Alzheimer's disease (AD). 2-Oxoglutarate and ferrous iron-dependent oxygenases (2OGDD) play a key role in the regulation of oxygen homeostasis by acting as hypoxia sensors. 2OGDD also have roles in collagen biosynthesis, lipid metabolism, nucleic acid repair, and the regulation of transcription and translation. Many biological processes in which the >60 human 2OGDD are involved are altered in AD patient brains, raising the question as to whether 2OGDD are involved in the transition from normal aging to AD. Here we give an overview of human 2OGDD and critically discuss their potential roles in AD, highlighting possible relationships with synapse dysfunction/loss. 2OGDD may regulate neuronal/glial differentiation through enzyme activity-dependent mechanisms and modulation of their activity has potential to protect against synapse loss. Work linking 2OGDD and AD is at an early stage, especially from a therapeutic perspective; we suggest integrated pathology and in vitro discovery research to explore their roles in AD is merited. We hope to help enable long-term research on the roles of 2OGDD and, more generally, oxygen/hypoxia in AD. We also suggest shorter term empirically guided clinical studies concerning the exploration of 2OGDD/oxygen modulators to help maintain synaptic viability are of interest for AD treatment.
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Affiliation(s)
- Haotian Liu
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yong Xie
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationDepartment of OrthopedicsGeneral Hospital of Chinese PLABeijingChina
| | - Xia Wang
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Martine I. Abboud
- The Chemistry Research LaboratoryDepartment of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordOxfordUK
| | - Chao Ma
- Department of Human Anatomy, Histology and EmbryologyNeuroscience CenterNational Human Brain Bank for Development and FunctionInstitute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Wei Ge
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Christopher J. Schofield
- The Chemistry Research LaboratoryDepartment of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordOxfordUK
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Richard Q, Laurenge A, Mallat M, Sanson M, Castro-Vega LJ. New insights into the Immune TME of adult-type diffuse gliomas. Curr Opin Neurol 2022; 35:794-802. [PMID: 36226710 PMCID: PMC9671594 DOI: 10.1097/wco.0000000000001112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW Adult-type diffuse gliomas are highly heterogeneous tumors. Bulk transcriptome analyses suggested that the composition of the tumor microenvironment (TME) corresponds to genetic and clinical features. In this review, we highlight novel findings on the intratumoral heterogeneity of IDH-wildtype and IDH-mutant gliomas characterized at single-cell resolution, and emphasize the mechanisms shaping the immune TME and therapeutic implications. RECENT FINDINGS Emergent evidence indicates that in addition to genetic drivers, epigenetic mechanisms and microenvironmental factors influence the glioma subtypes. Interactions between glioma and immune cells contribute to immune evasion, particularly in aggressive tumors. Spatial and temporal heterogeneity of malignant and immune cell subpopulations is high in recurrent gliomas. IDH-wildtype and IDH-mutant tumors display distinctive changes in their myeloid and lymphoid compartments, and D-2HG produced by IDH-mutant cells impacts the immune TME. SUMMARY The comprehensive dissection of the intratumoral ecosystem of human gliomas using single-cell and spatial transcriptomic approaches advances our understanding of the mechanisms underlying the immunosuppressed state of the TME, supports the prognostic value of tumor-associated macrophages and microglial cells, and sheds light on novel therapeutic options.
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Affiliation(s)
- Quentin Richard
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Alice Laurenge
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Michel Mallat
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Marc Sanson
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
- Department of Neurology 2, Pitié-Salpêtrière Hospital
- Onconeurotek Tumor Bank, Paris, France
| | - Luis Jaime Castro-Vega
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
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Shao Q, Liu J, Li G, Gu Y, Guo M, Guan Y, Tian Z, Ma W, Wang C, Ji X. Proteomic Analysis Reveals That Mitochondria Dominate the Hippocampal Hypoxic Response in Mice. Int J Mol Sci 2022; 23:ijms232214094. [PMID: 36430571 PMCID: PMC9697535 DOI: 10.3390/ijms232214094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Hypoxic stress occurs in various physiological and pathological states, such as aging, disease, or high-altitude exposure, all of which pose a challenge to many organs in the body, necessitating adaptation. However, the exact mechanisms by which hypoxia affects advanced brain function (learning and memory skills in particular) remain unclear. In this study, we investigated the effects of hypoxic stress on hippocampal function. Specifically, we studied the effects of the dysfunction of mitochondrial oxidative phosphorylation using global proteomics. First, we found that hypoxic stress impaired cognitive and motor abilities, whereas it caused no substantial changes in the brain morphology or structure of mice. Second, bioinformatics analysis indicated that hypoxia affected the expression of 516 proteins, of which 71.1% were upregulated and 28.5% were downregulated. We demonstrated that mitochondrial function was altered and manifested as a decrease in NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4 expression, accompanied by increased reactive oxygen species generation, resulting in further neuronal injury. These results may provide some new insights into how hypoxic stress alters hippocampal function via the dysfunction of mitochondrial oxidative phosphorylation.
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Affiliation(s)
- Qianqian Shao
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Jia Liu
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Gaifen Li
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yakun Gu
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Mengyuan Guo
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Yuying Guan
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Zhengming Tian
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Wei Ma
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Chaoyu Wang
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
| | - Xunming Ji
- Laboratory of Brain Disorders, Beijing Institute of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Capital Medical University, Beijing 100069, China
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Correspondence: ; Tel.: +86-139-1107-7166
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30
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Impact of Reactive Species on Amino Acids-Biological Relevance in Proteins and Induced Pathologies. Int J Mol Sci 2022; 23:ijms232214049. [PMID: 36430532 PMCID: PMC9692786 DOI: 10.3390/ijms232214049] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
This review examines the impact of reactive species RS (of oxygen ROS, nitrogen RNS and halogens RHS) on various amino acids, analyzed from a reactive point of view of how during these reactions, the molecules are hydroxylated, nitrated, or halogenated such that they can lose their capacity to form part of the proteins or peptides, and can lose their function. The reactions of the RS with several amino acids are described, and an attempt was made to review and explain the chemical mechanisms of the formation of the hydroxylated, nitrated, and halogenated derivatives. One aim of this work is to provide a theoretical analysis of the amino acids and derivatives compounds in the possible positions. Tyrosine, methionine, cysteine, and tryptophan can react with the harmful peroxynitrite or •OH and •NO2 radicals and glycine, serine, alanine, valine, arginine, lysine, tyrosine, histidine, cysteine, methionine, cystine, tryptophan, glutamine and asparagine can react with hypochlorous acid HOCl. These theoretical results may help to explain the loss of function of proteins subjected to these three types of reactive stresses. We hope that this work can help to assess the potential damage that reactive species can cause to free amino acids or the corresponding residues when they are part of peptides and proteins.
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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Ascorbic Acid (Vitamin C) as a Cosmeceutical to Increase Dermal Collagen for Skin Antiaging Purposes: Emerging Combination Therapies. Antioxidants (Basel) 2022; 11:antiox11091663. [PMID: 36139737 PMCID: PMC9495646 DOI: 10.3390/antiox11091663] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Ascorbic acid (AA) is an essential nutrient and has great potential as a cosmeceutical that protects the health and beauty of the skin. AA is expected to attenuate photoaging and the natural aging of the skin by reducing oxidative stress caused by external and internal factors and by promoting collagen gene expression and maturation. In this review, the biochemical basis of AA associated with collagen metabolism and clinical evidence of AA in increasing dermal collagen and inhibiting skin aging were discussed. In addition, we reviewed emerging strategies that have been developed to overcome the shortcomings of AA as a cosmeceutical and achieve maximum efficacy. Because extracellular matrix proteins, such as collagen, have unique amino acid compositions, their production in cells is influenced by the availability of specific amino acids. For example, glycine residues occupy 1/3 of amino acid residues in collagen protein, and the supply of glycine can be a limiting factor for collagen synthesis. Experiments showed that glycinamide was the most effective among the various amino acids and amidated amino acids in stimulating collagen production in human dermal fibroblasts. Thus, it is possible to synergistically improve collagen synthesis by combining AA analogs and amino acid analogs that act at different stages of the collagen production process. This combination therapy would be useful for skin antiaging that requires enhanced collagen production.
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Ferrante F, Giaimo BD, Friedrich T, Sugino T, Mertens D, Kugler S, Gahr BM, Just S, Pan L, Bartkuhn M, Potente M, Oswald F, Borggrefe T. Hydroxylation of the NOTCH1 intracellular domain regulates Notch signaling dynamics. Cell Death Dis 2022; 13:600. [PMID: 35821235 PMCID: PMC9276811 DOI: 10.1038/s41419-022-05052-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 01/21/2023]
Abstract
Notch signaling plays a pivotal role in the development and, when dysregulated, it contributes to tumorigenesis. The amplitude and duration of the Notch response depend on the posttranslational modifications (PTMs) of the activated NOTCH receptor - the NOTCH intracellular domain (NICD). In normoxic conditions, the hydroxylase FIH (factor inhibiting HIF) catalyzes the hydroxylation of two asparagine residues of the NICD. Here, we investigate how Notch-dependent gene transcription is regulated by hypoxia in progenitor T cells. We show that the majority of Notch target genes are downregulated upon hypoxia. Using a hydroxyl-specific NOTCH1 antibody we demonstrate that FIH-mediated NICD1 hydroxylation is reduced upon hypoxia or treatment with the hydroxylase inhibitor dimethyloxalylglycine (DMOG). We find that a hydroxylation-resistant NICD1 mutant is functionally impaired and more ubiquitinated. Interestingly, we also observe that the NICD1-deubiquitinating enzyme USP10 is downregulated upon hypoxia. Moreover, the interaction between the hydroxylation-defective NICD1 mutant and USP10 is significantly reduced compared to the NICD1 wild-type counterpart. Together, our data suggest that FIH hydroxylates NICD1 in normoxic conditions, leading to the recruitment of USP10 and subsequent NICD1 deubiquitination and stabilization. In hypoxia, this regulatory loop is disrupted, causing a dampened Notch response.
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Affiliation(s)
- Francesca Ferrante
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Benedetto Daniele Giaimo
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tobias Friedrich
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany ,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany
| | - Toshiya Sugino
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Daniel Mertens
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Bridging Group Mechanisms of Leukemogenesis, B061, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Kugler
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Bernd Martin Gahr
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steffen Just
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Leiling Pan
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany ,Institute for Lung Health (ILH), Aulweg 132, 35392 Giessen, Germany
| | - Michael Potente
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany ,grid.484013.a0000 0004 6879 971XBerlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Franz Oswald
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Tilman Borggrefe
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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Hypoxia signaling in human health and diseases: implications and prospects for therapeutics. Signal Transduct Target Ther 2022; 7:218. [PMID: 35798726 PMCID: PMC9261907 DOI: 10.1038/s41392-022-01080-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 02/07/2023] Open
Abstract
Molecular oxygen (O2) is essential for most biological reactions in mammalian cells. When the intracellular oxygen content decreases, it is called hypoxia. The process of hypoxia is linked to several biological processes, including pathogenic microbe infection, metabolic adaptation, cancer, acute and chronic diseases, and other stress responses. The mechanism underlying cells respond to oxygen changes to mediate subsequent signal response is the central question during hypoxia. Hypoxia-inducible factors (HIFs) sense hypoxia to regulate the expressions of a series of downstream genes expression, which participate in multiple processes including cell metabolism, cell growth/death, cell proliferation, glycolysis, immune response, microbe infection, tumorigenesis, and metastasis. Importantly, hypoxia signaling also interacts with other cellular pathways, such as phosphoinositide 3-kinase (PI3K)-mammalian target of rapamycin (mTOR) signaling, nuclear factor kappa-B (NF-κB) pathway, extracellular signal-regulated kinases (ERK) signaling, and endoplasmic reticulum (ER) stress. This paper systematically reviews the mechanisms of hypoxia signaling activation, the control of HIF signaling, and the function of HIF signaling in human health and diseases. In addition, the therapeutic targets involved in HIF signaling to balance health and diseases are summarized and highlighted, which would provide novel strategies for the design and development of therapeutic drugs.
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Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
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Affiliation(s)
- Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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Yang J, Hu Y, Zhang B, Liang X, Li X. The JMJD Family Histone Demethylases in Crosstalk Between Inflammation and Cancer. Front Immunol 2022; 13:881396. [PMID: 35558079 PMCID: PMC9090529 DOI: 10.3389/fimmu.2022.881396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Inflammation has emerged as a key player in regulating cancer initiation, progression, and therapeutics, acting as a double edged sword either facilitating cancer progression and therapeutic resistance or inducing anti-tumor immune responses. Accumulating evidence has linked the epigenetic modifications of histones to inflammation and cancer, and histone modifications-based strategies have shown promising therapeutic potentials against cancer. The jumonji C domain-containing (JMJD) family histone demethylases have exhibited multiple regulator functions in inflammatory processes and cancer development, and a number of therapeutic strategies targeting JMJD histone demethylases to modulate inflammatory cells and their products have been successfully evaluated in clinical or preclinical tumor models. This review summarizes current understanding of the functional roles and mechanisms of JMJD histone demethylases in crosstalk between inflammation and cancer, and highlights recent clinical and preclinical progress on harnessing the JMJD histone demethylases to regulate cancer-related inflammation for future cancer therapeutics.
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Affiliation(s)
- Jia Yang
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yuan Hu
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Binjing Zhang
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiao Liang
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Xin Li
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans. Sci Rep 2022; 12:6065. [PMID: 35410347 PMCID: PMC9001643 DOI: 10.1038/s41598-022-10028-y] [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: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe JmjC family of 2-oxoglutarate dependent oxygenases catalyse a range of hydroxylation and demethylation reactions in humans and other animals. Jumonji domain-containing 7 (JMJD7) is a JmjC (3S)-lysyl-hydroxylase that catalyses the modification of Developmentally Regulated GTP Binding Proteins 1 and 2 (DRG1 and 2); JMJD7 has also been reported to have histone endopeptidase activity. Here we report biophysical and biochemical studies on JMJD7 from Drosophila melanogaster (dmJMJD7). Notably, crystallographic analyses reveal that the unusual dimerization mode of JMJD7, which involves interactions between both the N- and C-terminal regions of both dmJMJD7 monomers and disulfide formation, is conserved in human JMJD7 (hsJMJD7). The results further support the assignment of JMJD7 as a lysyl hydroxylase and will help enable the development of selective inhibitors for it and other JmjC oxygenases.
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Huang AW, Janssen PML. The Case for, and Challenges of, Human Cardiac Tissue in Advancing Phosphoprotein Research. Front Physiol 2022; 13:853511. [PMID: 35399265 PMCID: PMC8984461 DOI: 10.3389/fphys.2022.853511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
Cardiovascular disease (CVD) and stroke affect over 92 million Americans and account for nearly 1 out of 3 deaths in the US. The use of animal models in cardiovascular research has led to considerable advances in treatment and in our understanding of the pathophysiology of many CVDs. Still, animals may not fully recapitulate human disease states; species differences have long been postulated to be one of the main reasons for a failure of translation between animals and humans in drug discovery and development. Indeed, it has become increasingly clear over the past few decades that to answer certain biomedical questions, like the physiological mechanisms that go awry in many human CVDs, animal tissues may not always be the best option to use. While human cardiac tissue has long been used for laboratory research, published findings often contradict each other, leading to difficulties in interpretation. Current difficulties in utilizing human cardiac tissue include differences in acquisition time, varying tissue procurement protocols, and the struggle to define a human “control” sample. With the tremendous emphasis on translational research that continues to grow, research studies using human tissues are becoming more common. This mini review will discuss advantages, disadvantages, and considerations of using human cardiac tissue in the study of CVDs, paying specific attention to the study of phosphoproteins.
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Wolf D, Muralidharan A, Mohan S. Role of prolyl hydroxylase domain proteins in bone metabolism. Osteoporos Sarcopenia 2022; 8:1-10. [PMID: 35415275 PMCID: PMC8987327 DOI: 10.1016/j.afos.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/12/2022] [Accepted: 03/04/2022] [Indexed: 11/03/2022] Open
Abstract
Cellular metabolism requires dissolved oxygen gas. Because evolutionary refinements have constrained mammalian dissolved oxygen levels, intracellular oxygen sensors are vital for optimizing the bioenergetic and biosynthetic use of dissolved oxygen. Prolyl hydroxylase domain (PHD) homologs 1–3 (PHD1/2/3) are molecular oxygen dependent non-heme dioxygenases whose enzymatic activity is regulated by the concentration of dissolved oxygen. PHD oxygen dependency has evolved into an important intracellular oxygen sensor. The most well studied mechanism of PHD oxygen-sensing is its regulation of the hypoxia-inducible factor (HIF) hypoxia signaling pathway. Heterodimeric HIF transcription factor activity is regulated post-translationally by selective PHD proline hydroxylation of its HIF1α subunit, accelerating HIF1α ubiquitination and proteasomal degradation, preventing HIF heterodimer assembly, nuclear accumulation, and activation of its target oxygen homeostasis genes. Phd2 has been shown to be the key isoform responsible for HIF1α subunit regulation in many cell types and accordingly disruption of the Phd2 gene results in embryonic lethality. In bone cells Phd2 is expressed in high abundance and tightly regulated. Conditional disruption of the Phd1, Phd2 and/or Phd3 gene in various bone cell types using different Cre drivers reveals a major role for PHD2 in skeletal growth and development. In this review, we will summarize the state of current knowledge on the role and mechanism of action of PHD2 as oxygen sensor in regulating bone metabolism.
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Arumugam K, Sellappan M, Anand D, Anand S, Radhakrishnan SV. A Text Mining and Machine Learning Protocol for Extracting Posttranslational Modifications of Proteins from PubMed: A Special Focus on Glycosylation, Acetylation, Methylation, Hydroxylation, and Ubiquitination. Methods Mol Biol 2022; 2496:179-202. [PMID: 35713865 DOI: 10.1007/978-1-0716-2305-3_10] [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] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) of proteins impart a significant role in human cellular functions ranging from localization to signal transduction. Hundreds of PTMs act in a human cell. Among them, only the selected PTMs are well established and documented. PubMed includes thousands of papers on the selected PTMs, and it is a challenge for the biomedical researchers to assimilate useful information manually. Alternatively, text mining approaches and machine learning algorithm automatically extract the relevant information from PubMed. Protein phosphorylation is a well-established PTM and several research works are under way. Many existing systems are there for protein phosphorylation information extraction. A recent approach uses a hybrid approach using text mining and machine learning to extract protein phosphorylation information from PubMed. Some of the other common PTMs that exhibit similar features in terms of entities that are involved in PTM process, that is, the substrate, the enzymes, and the amino acid residues, are glycosylation, acetylation, methylation, hydroxylation, and ubiquitination. This has motivated us to repurpose and extend the text mining protocol and machine learning information extraction methodology developed for protein phosphorylation to these PTMs. In this chapter, the chemistry behind each of the PTMs is briefly outlined and the text mining protocol and machine learning algorithm adaption is explained for the same.
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Affiliation(s)
- Krishnamurthy Arumugam
- Department of Management Studies, Coimbatore Institute of Engineering and Technology, Coimbatore, Tamilnadu, India.
| | - Malathi Sellappan
- Department of Pharmaceutical Analysis, PSG College of Pharmacy, Coimbatore, Tamilnadu, India
| | - Dheepa Anand
- Department of Pharmacology, Cheran College of Pharmacy, Coimbatore, Tamilnadu, India
| | - Sadhanha Anand
- Department of Biomedical Engineering, PSG College of Technology, Coimbatore, Tamilnadu, India
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Teh MR, Frost JN, Armitage AE, Drakesmith H. Analysis of Iron and Iron-Interacting Protein Dynamics During T-Cell Activation. Front Immunol 2021; 12:714613. [PMID: 34880854 PMCID: PMC8647206 DOI: 10.3389/fimmu.2021.714613] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Recent findings have shown that iron is a powerful regulator of immune responses, which is of broad importance because iron deficiency is highly prevalent worldwide. However, the underlying reasons of why iron is needed by lymphocytes remain unclear. Using a combination of mathematical modelling, bioinformatic analysis and experimental work, we studied how iron influences T-cells. We identified iron-interacting proteins in CD4+ and CD8+ T-cell proteomes that were differentially expressed during activation, suggesting that pathways enriched with such proteins, including histone demethylation, may be impaired by iron deficiency. Consistent with this, iron-starved Th17 cells showed elevated expression of the repressive histone mark H3K27me3 and displayed reduced RORγt and IL-17a, highlighting a previously unappreciated role for iron in T-cell differentiation. Quantitatively, we estimated T-cell iron content and calculated that T-cell iron demand rapidly and substantially increases after activation. We modelled that these increased requirements will not be met during clinically defined iron deficiency, indicating that normalizing serum iron may benefit adaptive immunity. Conversely, modelling predicted that excess serum iron would not enhance CD8+ T-cell responses, which we confirmed by immunising inducible hepcidin knock-out mice that have very high serum iron concentrations. Therefore, iron deficiency impairs multiple aspects of T-cell responses, while iron overload likely has milder effects.
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Affiliation(s)
- Megan R. Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Joe N. Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew E. Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford, United Kingdom
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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43
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Wang Z, Li ZX, Zhao WC, Huang HB, Wang JQ, Zhang H, Lu JY, Wang RN, Li W, Cheng Z, Xu WL, Di Zhu, Zhou LS, Jiang W, Yu L, Liu JY, Luo C, Zhu H, Dan Ye, Pan WJ, Ju JH, Dang YJ. Identification and characterization of isocitrate dehydrogenase 1 (IDH1) as a functional target of marine natural product grincamycin B. Acta Pharmacol Sin 2021; 42:801-813. [PMID: 32796956 DOI: 10.1038/s41401-020-0491-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 01/07/2023] Open
Abstract
Grincamycins (GCNs) are a class of angucycline glycosides isolated from actinomycete Streptomyces strains that have potent antitumor activities, but their antitumor mechanisms remain unknown. In this study, we tried to identify the cellular target of grincamycin B (GCN B), one of most dominant and active secondary metabolites, using a combined strategy. We showed that GCN B-selective-induced apoptosis of human acute promyelocytic leukemia (APL) cell line NB4 through increase of ER stress and intracellular reactive oxygen species (ROS) accumulation. Using a strategy of combining phenotype, transcriptomics and protein microarray approaches, we identified that isocitrate dehydrogenase 1(IDH1) was the putative target of GCN B, and confirmed that GCNs were a subset of selective inhibitors targeting both wild-type and mutant IDH1 in vitro. It is well-known that IDH1 converts isocitrate to 2-oxoglutarate (2-OG), maintaining intracellular 2-OG homeostasis. IDH1 and its mutant as the target of GCN B were validated in NB4 cells and zebrafish model. Knockdown of IDH1 in NB4 cells caused the similar phenotype as GCN B treatment, and supplementation of N-acetylcysteine partially rescued the apoptosis caused by IDH1 interference in NB4 cells. In zebrafish model, GCN B effectively restored myeloid abnormality caused by overexpression of mutant IDH1(R132C). Taken together, we demonstrate that IDH1 is one of the antitumor targets of GCNs, suggesting wild-type IDH1 may be a potential target for hematological malignancies intervention in the future.
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PLOD2-driven IL-6/STAT3 signaling promotes the invasion and metastasis of oral squamous cell carcinoma via activation of integrin β1. Int J Oncol 2021; 58:29. [PMID: 33887877 PMCID: PMC8057293 DOI: 10.3892/ijo.2021.5209] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
We previously reported that high expression of procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2) leads to stabilization and plasma membrane translocation of integrin β1 to promote the invasion and metastasis of oral squamous cell carcinoma (SCC). The present study aimed to further understand the relationship between PLOD2-integrin β1 signaling and the tumor microenvironment. This study provided further advanced insights indicating that elevated interleukin (IL)-6 in the tumor microenvironment acts as a key molecule that triggers PLOD2-integrin β1 axis-derived acceleration of tumor invasion and metastasis. It was found using the dual-luciferase reporter assay system that signal transducer and activator of transcription 3 (STAT3) activation by IL-6 was essential for increasing the expression levels of PLOD2 through direct activation of the PLOD2 promoter in oral SCC, whereas IL-6 stimulation did not contribute to integrin β1 expression or the subsequent maturation process towards a functional form on the plasma membrane. Furthermore, the expression of IL-6 in oral SCC tissues was mainly observed in the tumor stroma. Finally, with double immunofluorescence staining, it was found that IL-6 expression occurred in CD163-positive M2 macrophages distributed around the tumor nest. These results combined with our previous results indicate that as IL-6 significantly increases STAT3-mediated PLOD2 promoter activity, IL-6 released by M2-type tumor-associated macrophages is a crucial factor that promotes PLOD2-integrin β1 axis-enhanced invasion and metastasis of oral SCC cells.
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Czyzyk-Krzeska MF, Landero Figueroa JA, Gulati S, Cunningham JT, Meller J, ShamsaeI B, Vemuri B, Plas DR. Molecular and Metabolic Subtypes in Sporadic and Inherited Clear Cell Renal Cell Carcinoma. Genes (Basel) 2021; 12:genes12030388. [PMID: 33803184 PMCID: PMC7999481 DOI: 10.3390/genes12030388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 01/18/2023] Open
Abstract
The promise of personalized medicine is a therapeutic advance where tumor signatures obtained from different omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics, in addition to environmental factors including metals and metalloids, are used to guide the treatments. Clear cell renal carcinoma (ccRCC), the most common type of kidney cancer, can be sporadic (frequently) or genetic (rare), both characterized by loss of the von Hippel-Lindau (VHL) gene that controls hypoxia inducible factors. Recently, several genomic subtypes were identified with different prognoses. Transcriptomics, proteomics, metabolomics and metallomic data converge on altered metabolism as the principal feature of the disease. However, in view of multiple biochemical alterations and high level of tumor heterogeneity, identification of clearly defined subtypes is necessary for further improvement of treatments. In the future, single-cell combined multi-omics approaches will be the next generation of analyses gaining deeper insights into ccRCC progression and allowing for design of specific signatures, with better prognostic/predictive clinical applications.
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Affiliation(s)
- Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Correspondence:
| | - Julio A. Landero Figueroa
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Shuchi Gulati
- Division of Hematology and Oncology, Department of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - John T. Cunningham
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - Jarek Meller
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45267, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Behrouz ShamsaeI
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Bhargav Vemuri
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - David R. Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
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Pleiotropic effects of alpha-ketoglutarate as a potential anti-ageing agent. Ageing Res Rev 2021; 66:101237. [PMID: 33340716 DOI: 10.1016/j.arr.2020.101237] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/23/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
An intermediate of tricarboxylic acid cycle alpha-ketoglutarate (AKG) is involved in pleiotropic metabolic and regulatory pathways in the cell, including energy production, biosynthesis of certain amino acids, collagen biosynthesis, epigenetic regulation of gene expression, regulation of redox homeostasis, and detoxification of hazardous substances. Recently, AKG supplement was found to extend lifespan and delay the onset of age-associated decline in experimental models such as nematodes, fruit flies, yeasts, and mice. This review summarizes current knowledge on metabolic and regulatory functions of AKG and its potential anti-ageing effects. Impact on epigenetic regulation of ageing via being an obligate substrate of DNA and histone demethylases, direct antioxidant properties, and function as mimetic of caloric restriction and hormesis-induced agent are among proposed mechanisms of AKG geroprotective action. Due to influence on mitochondrial respiration, AKG can stimulate production of reactive oxygen species (ROS) by mitochondria. According to hormesis hypothesis, moderate stimulation of ROS production could have rather beneficial biological effects, than detrimental ones, because of the induction of defensive mechanisms that improve resistance to stressors and age-related diseases and slow down functional senescence. Discrepancies found in different models and limitations of AKG as a geroprotective drug are discussed.
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Wu Z, Yuan Y, Tian J, Long F, Luo W. The associations between serum trace elements and bone mineral density in children under 3 years of age. Sci Rep 2021; 11:1890. [PMID: 33479410 PMCID: PMC7820346 DOI: 10.1038/s41598-021-81501-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/05/2021] [Indexed: 12/31/2022] Open
Abstract
We examined the associations of age and serum magnesium, iron, lead, copper, and zinc levels with bone mineral density (BMD) in 2412 children under 3 years of age in order to find a tool to monitor BMD in children without the use of expensive imaging techniques. One-way ANOVA and chi-square tests were used to determine the associations of age and serum trace elements with BMD. Multivariable logistic regression analysis was used to test the correlation of five serum trace elements with BMD after adjustments for potential confounding factors in children under 3 years of age. Significant associations between age and four serum trace elements and BMD were found. Compared to the group with the lowest serum levels detected, the adjusted odds ratio (OR) for the incidence of normal bone mineral density in the third magnesium concentration tertile, the third iron concentration tertile, the fifth copper concentration quintile, the third zinc concentration quintile, and the fifth zinc concentration quintile were 1.30 (95% confidence interval (CI) 1.02–1.67), 1.43 (95% CI 1.11–1.84), 1.42 (95% CI 1.04–1.94), 1.46 (95% CI 1.05–2.04), and 1.48 (95% CI 1.06–2.06), respectively. However, there was no significant correlation between serum lead level and BMD in this study. Age and serum magnesium, iron, copper, and zinc levels are positively associated with BMD in children under 3 years old.
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Affiliation(s)
- Ziyi Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yuhao Yuan
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jian Tian
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Feng Long
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Wei Luo
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China.
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48
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Choi I, Son H, Baek JH. Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses. Life (Basel) 2021; 11:69. [PMID: 33477822 PMCID: PMC7832849 DOI: 10.3390/life11010069] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
The tricarboxylic acid cycle (TCA) is a series of chemical reactions used in aerobic organisms to generate energy via the oxidation of acetylcoenzyme A (CoA) derived from carbohydrates, fatty acids and proteins. In the eukaryotic system, the TCA cycle occurs completely in mitochondria, while the intermediates of the TCA cycle are retained inside mitochondria due to their polarity and hydrophilicity. Under cell stress conditions, mitochondria can become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss its implication for immune activation and suppression.
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Affiliation(s)
| | | | - Jea-Hyun Baek
- School of Life Science, Handong Global University, Pohang, Gyeongbuk 37554, Korea; (I.C.); (H.S.)
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Metabolic adaptation in hypoxia and cancer. Cancer Lett 2021; 502:133-142. [PMID: 33444690 DOI: 10.1016/j.canlet.2020.12.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
The ability of tumor cells to adapt to changes in oxygen tension is essential for tumor development. Low oxygen concentration influences cellular metabolism and, thus, affects proliferation, migration, and invasion. A focal point of the cell's adaptation to hypoxia is the transcription factor HIF1α (hypoxia-inducible factor 1 alpha), which affects the expression of specific gene networks involved in cellular energetics and metabolism. This review illustrates the mechanisms by which HIF1α-induced metabolic adaptation promotes angiogenesis, participates in the escape from immune recognition, and increases cancer cell antioxidant capacity. In addition to hypoxia, metabolic inhibition of 2-oxoglutarate-dependent dioxygenases regulates HIF1α stability and transcriptional activity. This phenomenon, known as pseudohypoxia, is frequently used by cancer cells to promote glycolytic metabolism to support biomass synthesis for cell growth and proliferation. In this review, we highlight the role of the most important metabolic intermediaries that are at the center of cancer's biology, and in particular, the participation of these metabolites in HIF1α retrograde signaling during the establishment of pseudohypoxia. Finally, we will discuss how these changes affect both the development of cancers and their resistance to treatment.
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Liu T, Abboud MI, Chowdhury R, Tumber A, Hardy AP, Lippl K, Lohans CT, Pires E, Wickens J, McDonough MA, West CM, Schofield CJ. Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondii. J Biol Chem 2020; 295:16545-16561. [PMID: 32934009 PMCID: PMC7864055 DOI: 10.1074/jbc.ra120.013998] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/14/2020] [Indexed: 12/30/2022] Open
Abstract
In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, Dictyostelium discoideum, and the protozoan parasite, Toxoplasma gondii, both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, Trichoplax adhaerens, and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.
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Affiliation(s)
- Tongri Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - James Wickens
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Christopher M West
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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