An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes
Vitamin B12 has multiple biochemical functions including in the one-carbon cycle generating a methyl group for DNA methylation, and metabolism of fatty acids and amino acids to generate energy via the citric acid cycle. The aim of our study was to use a combined epigenomic and transcriptomic approac...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2022-10-01
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| Series: | Epigenetics |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15592294.2021.2003043 |
| _version_ | 1797678850790916096 |
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| author | B. William Ogunkolade Antonysunil Adaikalakoteswari Shirleny Romualdo Cardoso Rob Lowe Nisha Patel Vardhman Rakyan Sarah Finer Martin Wabitsch Ponnusamy Saravanan Gyanendra Tripathi Elena Bochukova Graham A Hitman |
| author_facet | B. William Ogunkolade Antonysunil Adaikalakoteswari Shirleny Romualdo Cardoso Rob Lowe Nisha Patel Vardhman Rakyan Sarah Finer Martin Wabitsch Ponnusamy Saravanan Gyanendra Tripathi Elena Bochukova Graham A Hitman |
| author_sort | B. William Ogunkolade |
| collection | DOAJ |
| description | Vitamin B12 has multiple biochemical functions including in the one-carbon cycle generating a methyl group for DNA methylation, and metabolism of fatty acids and amino acids to generate energy via the citric acid cycle. The aim of our study was to use a combined epigenomic and transcriptomic approach to identify novel genes mediating the effect of B12 on adipogenesis. Human pre-adipocytes (CHUB-S7) were treated with a range of B12 (0–500 nM) concentrations from the day of cell seeding until harvesting in discovery and validation experiments prior to genome-wide methylation analysis using the Illumina HumanMethylation 450Beadchip. For transcriptomic analysis, RNA-seq libraries were run on the Illumina HiSeq 2500. To further investigate the expression of any genes on human adipogenesis, a second human preadipocyte strain was studied (SGBS) by real-time quantitative PCR (qRT-PCR). A combined epigenetic and transcriptomic approach in differentiated human pre-adipocyte cell line, CHUB-S7, identified that the Human cartilage chitinase 3-like protein 2 (CHI3L2) gene was hypo-methylated and had increased expression in low B12 conditions. Furthermore, there was an approximately 1000-fold increase in CHI3L2 expression in the early days of adipocyte differentiation, which paralleled an increase of lipid droplets in differentiated SGBS cells and an increased expression level of markers of mature adipocytes. In summary, we have identified a potential role of the human cartilage chitinase 3-like protein 2 (CHI3L2) in adipocyte function in the presence of low B12 levels. |
| first_indexed | 2024-03-11T23:05:57Z |
| format | Article |
| id | doaj.art-da875f7227f04099ad63049ddd7f3934 |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:05:57Z |
| publishDate | 2022-10-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-da875f7227f04099ad63049ddd7f39342023-09-21T13:23:11ZengTaylor & Francis GroupEpigenetics1559-22941559-23082022-10-0117101219123310.1080/15592294.2021.20030432003043An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytesB. William Ogunkolade0Antonysunil Adaikalakoteswari1Shirleny Romualdo Cardoso2Rob Lowe3Nisha Patel4Vardhman Rakyan5Sarah Finer6Martin Wabitsch7Ponnusamy Saravanan8Gyanendra Tripathi9Elena Bochukova10Graham A Hitman11Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonWarwick Medical School, University of WarwickBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonUlm University HospitalWarwick Medical School, University of WarwickWarwick Medical School, University of WarwickBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonBlizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonVitamin B12 has multiple biochemical functions including in the one-carbon cycle generating a methyl group for DNA methylation, and metabolism of fatty acids and amino acids to generate energy via the citric acid cycle. The aim of our study was to use a combined epigenomic and transcriptomic approach to identify novel genes mediating the effect of B12 on adipogenesis. Human pre-adipocytes (CHUB-S7) were treated with a range of B12 (0–500 nM) concentrations from the day of cell seeding until harvesting in discovery and validation experiments prior to genome-wide methylation analysis using the Illumina HumanMethylation 450Beadchip. For transcriptomic analysis, RNA-seq libraries were run on the Illumina HiSeq 2500. To further investigate the expression of any genes on human adipogenesis, a second human preadipocyte strain was studied (SGBS) by real-time quantitative PCR (qRT-PCR). A combined epigenetic and transcriptomic approach in differentiated human pre-adipocyte cell line, CHUB-S7, identified that the Human cartilage chitinase 3-like protein 2 (CHI3L2) gene was hypo-methylated and had increased expression in low B12 conditions. Furthermore, there was an approximately 1000-fold increase in CHI3L2 expression in the early days of adipocyte differentiation, which paralleled an increase of lipid droplets in differentiated SGBS cells and an increased expression level of markers of mature adipocytes. In summary, we have identified a potential role of the human cartilage chitinase 3-like protein 2 (CHI3L2) in adipocyte function in the presence of low B12 levels.http://dx.doi.org/10.1080/15592294.2021.2003043vitamin b12adipocyteepigenometranscriptomechi3l2 |
| spellingShingle | B. William Ogunkolade Antonysunil Adaikalakoteswari Shirleny Romualdo Cardoso Rob Lowe Nisha Patel Vardhman Rakyan Sarah Finer Martin Wabitsch Ponnusamy Saravanan Gyanendra Tripathi Elena Bochukova Graham A Hitman An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes Epigenetics vitamin b12 adipocyte epigenome transcriptome chi3l2 |
| title | An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes |
| title_full | An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes |
| title_fullStr | An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes |
| title_full_unstemmed | An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes |
| title_short | An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes |
| title_sort | integrative epi transcriptomic approach identifies the human cartilage chitinase 3 like protein 2 chi3l2 as a potential mediator of b12 deficiency in adipocytes |
| topic | vitamin b12 adipocyte epigenome transcriptome chi3l2 |
| url | http://dx.doi.org/10.1080/15592294.2021.2003043 |
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