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Huang M, Prasad RB, Coral DE, Hjort L, Minja DT, Mulder H, Franks PW, Kalamajski S. Human Genetic Variation at rs10071329 Correlates With Adiposity-Related Traits, Modulates PPARGC1B Expression, and Alters Brown Adipocyte Function. Diabetes 2024; 73:637-645. [PMID: 38190589 PMCID: PMC10958585 DOI: 10.2337/db23-0531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024]
Abstract
Human genetic variation in PPARGC1B has been associated with adiposity, but the genetic variants that affect PPARGC1B expression have not been experimentally determined. Here, guided by previous observational data, we used clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to scarlessly edit the alleles of the candidate causal genetic variant rs10071329 in a human brown adipocyte cell line. Switching the rs10071329 genotype from A/A to G/G enhanced PPARGC1B expression throughout the adipogenic differentiation, identifying rs10071329 as a cis-expression quantitative trait loci (eQTL). The higher PPARGC1B expression in G/G cells coincided with greater accumulation of triglycerides and higher expression of mitochondria-encoded genes, but without significant effects on adipogenic marker expression. Furthermore, G/G cells had improved basal- and norepinephrine-stimulated mitochondrial respiration, possibly relating to enhanced mitochondrial gene expression. The G/G cells also exhibited increased norepinephrine-stimulated glycerol release, indicating improved lipolysis. Altogether, our results showed that rs10071329 is a cis-eQTL, with the G/G genotype conferring enhanced PPARGC1B expression, with consequent improved mitochondrial function and response to norepinephrine in brown adipocytes. This genetic variant, and as yet undetermined eQTLs, at PPARGC1B could prove useful in genotype-based precision medicine for obesity treatment. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Mi Huang
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Rashmi B. Prasad
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
- Institute for Molecular Medicine, Helsinki University, Helsinki, Finland
| | - Daniel E. Coral
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Line Hjort
- Department of Obstetrics, Center for Pregnant Women with Diabetes, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel T.R. Minja
- National Institute for Medical Research, Tanga Center, Tanga, Tanzania
| | - Hindrik Mulder
- Unit of Molecular Metabolism, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
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Gebreyesus LH, Choi S, Neequaye P, Mahmoud M, Mahmoud M, Ofosu-Boateng M, Twum E, Nnamani DO, Wang L, Yadak N, Ghosh S, Gonzalez FJ, Gyamfi MA. Pregnane X receptor knockout mitigates weight gain and hepatic metabolic dysregulation in female C57BL/6 J mice on a long-term high-fat diet. Biomed Pharmacother 2024; 173:116341. [PMID: 38428309 PMCID: PMC10983615 DOI: 10.1016/j.biopha.2024.116341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024] Open
Abstract
Obesity is a significant risk factor for several chronic diseases. However, pre-menopausal females are protected against high-fat diet (HFD)-induced obesity and its adverse effects. The pregnane X receptor (PXR, NR1I2), a xenobiotic-sensing nuclear receptor, promotes short-term obesity-associated liver disease only in male mice but not in females. Therefore, the current study investigated the metabolic and pathophysiological effects of a long-term 52-week HFD in female wild-type (WT) and PXR-KO mice and characterized the PXR-dependent molecular pathways involved. After 52 weeks of HFD ingestion, the body and liver weights and several markers of hepatotoxicity were significantly higher in WT mice than in their PXR-KO counterparts. The HFD-induced liver injury in WT female mice was also associated with upregulation of the hepatic mRNA levels of peroxisome proliferator-activated receptor gamma (Pparg), its target genes, fat-specific protein 27 (Fsp27), and the liver-specific Fsp27b involved in lipid accumulation, apoptosis, and inflammation. Notably, PXR-KO mice displayed elevated hepatic Cyp2a5 (anti-obesity gene), aldo-keto reductase 1b7 (Akr1b7), glutathione-S-transferase M3 (Gstm3) (antioxidant gene), and AMP-activated protein kinase (AMPK) levels, contributing to protection against long-term HFD-induced obesity and inflammation. RNA sequencing analysis revealed a general blunting of the transcriptomic response to HFD in PXR-KO compared to WT mice. Pathway enrichment analysis demonstrated enrichment by HFD for several pathways, including oxidative stress and redox pathway, cholesterol biosynthesis, and glycolysis/gluconeogenesis in WT but not PXR-KO mice. In conclusion, this study provides new insights into the molecular mechanisms by which PXR deficiency protects against long-term HFD-induced severe obesity and its adverse effects in female mice.
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Affiliation(s)
- Lidya H Gebreyesus
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Sora Choi
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Prince Neequaye
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Mattia Mahmoud
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Mia Mahmoud
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA
| | - Malvin Ofosu-Boateng
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Elizabeth Twum
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Daniel O Nnamani
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Lijin Wang
- Center for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
| | - Nour Yadak
- Department of Pathology and Laboratory Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sujoy Ghosh
- Center for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore; Bioinformatics and Computational Biology Core, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Frank J Gonzalez
- Center for Cancer Research, National Cancer Institute, Building 37, Room 3106, Bethesda, MD 20892, USA
| | - Maxwell A Gyamfi
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA; Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA.
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Doughan A, Adingo W, Salifu SP. RNA-seq research landscape in Africa: systematic review reveals disparities and opportunities. Eur J Med Res 2023; 28:244. [PMID: 37480073 PMCID: PMC10362609 DOI: 10.1186/s40001-023-01206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
RNA sequencing has emerged as the standard method for transcriptome profiling of several human diseases. We performed a systematic review detailing the state of RNA-seq analyses in Africa from its inception till February 2022. Our goal was to provide an update on the state of RNA-seq analyses in Africa, including research gaps, funding information, participants information, authorship and collaborations. Following the PRISMA guidelines, we performed an exhaustive literature search for RNA-seq studies conducted in Africa, using PubMed, Scopus and Academic Search Complete (EBSCOhost). The output was exported to Endnote X9 for analyses. The initial literature search yielded 10,369 articles spread across PubMed (4916), Scopus (4847) and EBSCOhost (580). By applying our exclusion criteria, 28 full-text articles remained and were thoroughly analyzed. Overall, 17 human diseases were studied, including cancers (10/28), infectious disease (4/28), parasitic disease (4/28), autoimmune disorders (2/28) and neglected tropical diseases (2/28). Majority of the articles were published in PLoS Pathogens, BioMed Central and Nature. The National Institutes of Health (42.4%), the Bill & Melinda Gates Foundation (7.5%) and the Wellcome Trust (7.5%) were the top funders of the research studies. Eleven African countries contributed to the participant group, with 57% located in Eastern Africa, 23.1% from Western and 16.7% from Southern Africa. The extremely low number of RNA-seq research studies in Africa is worrying and calls for an immediate investment in research by the African governments. The funding agencies and institutional review boards should also ensure that African collaborators are treated equitably in the course of the research projects.
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Affiliation(s)
- Albert Doughan
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wisdom Adingo
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Samson Pandam Salifu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.
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Yajnik CS, Wagh R, Kunte P, Asplund O, Ahlqvist E, Bhat D, Shukla SR, Prasad RB. Polygenic scores of diabetes-related traits in subgroups of type 2 diabetes in India: a cohort study. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 14:100182. [PMID: 37492423 PMCID: PMC10363502 DOI: 10.1016/j.lansea.2023.100182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/08/2022] [Accepted: 03/09/2023] [Indexed: 07/27/2023]
Abstract
Background A machine-learning approach identified five subgroups of diabetes in Europeans which included severe autoimmune diabetes (SAID), severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD) and mild age-related diabetes (MARD) with partially distinct genetic aetiologies. We previously validated four of the non-autoimmune subgroups in people with young-onset type 2 diabetes (T2D) from the Indian WellGen study. Here, we aimed to apply European-derived centroids and genetic risk scores (GRSs) to the unselected (for age) WellGen to test their applicability and investigate the genetic aetiology of the Indian T2D subgroups. Methods We applied European derived centroids and GRSs to T2D participants of Indian ancestry (WellGen, n = 2217, 821 genotyped) and compared them with normal glucose tolerant controls (Pune Maternal Nutrition Study, n = 461). Findings SIDD was the predominant subgroup followed by MOD, whereas SIRD and MARD were less frequent. Weighted-GRS for T2D, obesity and lipid-related traits associated with T2D. We replicated some of the previous associations of GRS for T2D, insulin secretion, and BMI with SIDD and MOD. Unique to Indian subgroups was the association of GRS for (a) proinsulin with MOD and MARD, (b) liver-lipids with SIDD, SIRD and MOD, and (c) opposite effect of beta-cell GRS with SIDD and MARD, obesity GRS with MARD compared to Europeans. Genetic variants of fucosyltransferases were associated with T2D and MOD in Indians but not Europeans. Interpretation The similarities emphasise the applicability of some of the European-derived GRSs to T2D and its subgroups in India while the differences highlight the need for large-scale studies to identify aetiologies in diverse ancestries. The data provide robust evidence for genetically distinct aetiologies for the T2D subgroups and at least partly mirror those seen in Europeans. Funding Vetenskapsrådet, Diabetes Wellness, and Hjärt-Lungfonden (Sweden), DST (India), Wellcome Trust, Crafoord Foundation and Albert Påhlsson Foundation.
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Affiliation(s)
- Chittaranjan S. Yajnik
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Rucha Wagh
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed) University, Pune, 411021, India
| | - Pooja Kunte
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown Campus, Sydney, 2560, NSW, Australia
| | - Olof Asplund
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Dattatrey Bhat
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Sharvari R. Shukla
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis Statistical Institute, Symbiosis International University, Pune, 411005, India
| | - Rashmi B. Prasad
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
- Institute for Molecular Medicine Finland FIMM, Helsinki University, 00290, Helsinki, Finland
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Christensen DL, Mutabingwa TK, Bygbjerg IC, Vaag AA, Grunnet LG, Lajeunesse-Trempe F, Nielsen J, Schmiegelow C, Ramaiya KL, Myburgh KH. Skeletal muscle fibre type and enzymatic activity in adult offspring following placental and peripheral malaria exposure in foetal life. Front Public Health 2023; 11:1122393. [PMID: 37333553 PMCID: PMC10275361 DOI: 10.3389/fpubh.2023.1122393] [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: 12/12/2022] [Accepted: 05/12/2023] [Indexed: 06/20/2023] Open
Abstract
Background Maternal malaria may restrict foetal growth. Impaired utero-placental blood flow due to malaria infection may cause hypoxia-induced altered skeletal muscle fibre type distribution in the offspring, which may contribute to insulin resistance and impaired glucose metabolism. This study assessed muscle fibre distribution 20 years after placental and/or peripheral in-utero malaria exposure compared to no exposure, i.e., PPM+, PM+, and M-, respectively. Methods We traced 101 men and women offspring of mothers who participated in a malaria chemosuppression study in Muheza, Tanzania. Of 76 eligible participants, 50 individuals (29 men and 21 women) had skeletal muscle biopsy taken from m. vastus lateralis in the right leg. As previously reported, fasting and 30 min post-oral glucose challenge plasma glucose values were higher, and insulin secretion disposition index was lower, in the PPM+ group. Aerobic capacity (fitness) was estimated by an indirect VO2max test on a stationary bicycle. Muscle fibre sub-type (myosin heavy chain, MHC) distribution was analysed, as were muscle enzyme activities (citrate synthase (CS), 3-hydroxyacyl-CoA dehydrogenase, myophosphorylase, phosphofructokinase, lactate dehydrogenase, and creatine kinase activities. Between-group analyses were adjusted for MHC-I %. Results No differences in aerobic capacity were found between groups. Despite subtle elevations of plasma glucose levels in the PPM+ group, there was no difference in MHC sub-types or muscle enzymatic activities between the malaria-exposed and non-exposed groups. Conclusion The current study did not show differences in MHC towards glycolytic sub-types or enzymatic activity across the sub-groups. The results support the notion of the mild elevations of plasma glucose levels in people exposed to placental malaria in pregnancy being due to compromised pancreatic insulin secretion rather than insulin resistance.
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Affiliation(s)
| | | | - Ib C. Bygbjerg
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Allan A. Vaag
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Translational Type 2 Diabetes Research, Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Louise G. Grunnet
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Clinical Prevention Research, Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Jannie Nielsen
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kathryn H. Myburgh
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
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Christensen DL, Hjort L, Mpagama SG, Ramaiya KL. Environmental exposures are important for type 2 diabetes pathophysiology in sub-Saharan African populations. Diabetologia 2023; 66:777-779. [PMID: 36656321 DOI: 10.1007/s00125-022-05867-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 01/20/2023]
Affiliation(s)
- Dirk L Christensen
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Line Hjort
- Department of Obstetrics, Copenhagen University Hospital, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stellah G Mpagama
- Kibong'oto Infectious Diseases Hospital, Sanya Juu, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Kaushik L Ramaiya
- Department of Internal Medicine, Shree Hindu Mandal Hospital, Dar es Salaam, Tanzania
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Wang JH, Wong RCB, Liu GS. Retinal Transcriptome and Cellular Landscape in Relation to the Progression of Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2022; 63:26. [PMID: 36006018 PMCID: PMC9424969 DOI: 10.1167/iovs.63.9.26] [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] [Indexed: 11/26/2022] Open
Abstract
Purpose Previous studies that identify putative genes associated with diabetic retinopathy are only focusing on specific clinical stages, thus resulting genes are not necessarily reflective of disease progression. This study identified genes associated with the severity level of diabetic retinopathy using the likelihood-ratio test (LRT) and ordinal logistic regression (OLR) model, as well as to profile immune and retinal cell landscape in progressive diabetic retinopathy using a machine learning deconvolution approach. Methods This study used a published transcriptomic dataset (GSE160306) from macular regions of donors with different degrees of diabetic retinopathy (10 healthy controls, 10 cases of diabetes, 9 cases of nonproliferative diabetic retinopathy, and 10 cases of proliferative diabetic retinopathy or combined with diabetic macular edema). LRT and OLR models were applied to identify severity-associated genes. In addition, CIBERSORTx was used to estimate proportional changes of immune and retinal cells in progressive diabetic retinopathy. Results By controlling for gender and age using LRT and OLR, 50 genes were identified to be significantly increased in expression with the severity of diabetic retinopathy. Functional enrichment analyses suggested these severity-associated genes are related to inflammation and immune responses. CCND1 and FCGR2B are further identified as key regulators to interact with many other severity-associated genes and are crucial to inflammation. Deconvolution analyses demonstrated that the proportions of memory B cells, M2 macrophages, and Müller glia were significantly increased with the progression of diabetic retinopathy. Conclusions These findings demonstrate that deep analyses of transcriptomic data can advance our understanding of progressive ocular diseases, such as diabetic retinopathy, by applying LRT and OLR models as well as bulk gene expression deconvolution.
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Affiliation(s)
- Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia
| | - Guei-Sheung Liu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia.,Aier Eye Institute, Changsha, Hunan, China
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