Taiwan Partnering Award: Artificial intelligence applications to identify regulatory genomic signatures of diet and lifestyle disease risk factors
Lead Research Organisation:
King's College London
Department Name: Genetics and Molecular Medicine
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
People |
ORCID iD |
| Jordana Bell (Principal Investigator) | |
| Sarah Berry (Co-Investigator) |
Publications
Christiansen C
(2024)
Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications.
in EBioMedicine
Christiansen C
(2022)
Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers.
in Genome medicine
Costeira R
(2023)
Metabolomic biomarkers of habitual B vitamin intakes unveil novel differentially methylated positions in the human epigenome.
in Clinical epigenetics
Hellbach F
(2023)
Pooled analysis of epigenome-wide association studies of food consumption in KORA, TwinsUK and LLS.
in European journal of nutrition
Hellbach F
(2023)
Usual dietary intake and change in DNA methylation over years: EWAS in KORA FF4 and KORA fit.
in Frontiers in nutrition
Hung RKY
(2024)
Epigenetic associations with kidney disease in individuals of African ancestry with APOL1 high-risk genotypes and Human Immunodeficiency Virus.
in Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association
Karabegovic I
(2021)
Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.
in Nature communications
| Title | Additional file 1 of Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers |
| Description | Additional file 1: Supplementary Figures 1 - 5. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2022 |
| URL | https://springernature.figshare.com/articles/presentation/Additional_file_1_of_Adipose_methylome_int... |
| Title | Additional file 1 of Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers |
| Description | Additional file 1: Supplementary Figures 1 - 5. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2022 |
| URL | https://springernature.figshare.com/articles/presentation/Additional_file_1_of_Adipose_methylome_int... |
| Description | The UK-Taiwan award analyses a subset of the data generated in the DIMENSION project. The key findings to date contributed to a publication on epigenetic signatures of caffeine intakes (Karabegovic et al. 2021). On-going work includes epigenetic exploration of B-vitamins intake and dynamic diet-epigenetic links related to the postprandial response. |
| Exploitation Route | Basis of diet biomarkers, as well as basis for validation and replication studies, and for future experimental work on the molecular signatures of nutrition. |
| Sectors | Agriculture Food and Drink Healthcare |
| Title | Additional file 2 of Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers |
| Description | Additional file 2: Table S1. Statistically significant adipose tissue CpGs in relation to visceral fat accumulation at Bonferroni 5% (VF-DMPs). Table S2. Pathway Analysis (IPA) results. Table S3. Statistically significant associations between methylation and gene expression at VF-DMPs. Table S4. meQTLs. Table S5. Diet VF-DMPs. Table S6. Diet-VF mediation by methylation. Table S7. Effect sizes for statistically significant associations with metabolites. Table S8. Metabolic Phenotype results and Replication. Table S9. Validation and Replication Cohort Characteristics. Table S10. GTEx median expression levels in SAT, VAT and Whole Blood. Table S11. Results from Differentially methylated region analysis. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Adipose_methylome_integrat... |
| Title | Additional file 2 of Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers |
| Description | Additional file 2: Table S1. Statistically significant adipose tissue CpGs in relation to visceral fat accumulation at Bonferroni 5% (VF-DMPs). Table S2. Pathway Analysis (IPA) results. Table S3. Statistically significant associations between methylation and gene expression at VF-DMPs. Table S4. meQTLs. Table S5. Diet VF-DMPs. Table S6. Diet-VF mediation by methylation. Table S7. Effect sizes for statistically significant associations with metabolites. Table S8. Metabolic Phenotype results and Replication. Table S9. Validation and Replication Cohort Characteristics. Table S10. GTEx median expression levels in SAT, VAT and Whole Blood. Table S11. Results from Differentially methylated region analysis. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Adipose_methylome_integrat... |
| Title | Genetic impacts on DNA methylation help elucidate regulatory genomic processes |
| Description | Background: Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. Results: We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2,358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1,520 co-localisations across 1,325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs, (e.g. through disruption of transcription factor binding sites for CTCF and SMC3), and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). Conclusions: Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk/. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/doi/10.5281/zenodo.8047777 |
| Title | Genetic impacts on DNA methylation help elucidate regulatory genomic processes |
| Description | Background: Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. Results: We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2,358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1,520 co-localisations across 1,325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs, (e.g. through disruption of transcription factor binding sites for CTCF and SMC3), and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). Conclusions: Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk/. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/doi/10.5281/zenodo.8047776 |
| Description | "Genetic impacts on human methylome variation", CANSSI Ontario STAGE program International Speaker Seminar Series, Toronto, Canada, November 2021 (delivered online). |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at an international seminar series host by University of Toronto |
| Year(s) Of Engagement Activity | 2021 |
| Description | "Genetic impacts on human methylome variation", Epigenetic Inheritance Symposium, ETH Zurich, Switzerland, August 2021 (delivered online). |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a symposium on epigenetics |
| Year(s) Of Engagement Activity | 2021 |
| Description | "Genetic impacts on human methylome variation", FASEB conference "The Epigenome in Human Health and Diseases", University of Lorraine, October 2021 (delivered online). |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at an international conference |
| Year(s) Of Engagement Activity | 2021 |
| Description | "Twin studies for epigenomic markers in obesity", European Association for the Study of Obesity (EASO)'s 28th annual European Congress on Obesity (ECO2021), May 2021 (delivered online). |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a scientific conference on obesity |
| Year(s) Of Engagement Activity | 2021 |
| Description | Body responses after food intake: Impact of gene expression and epigenetics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Oral presentation by Dr Jordana Bell "Body responses after food intake: Impact of gene expression and epigenetics", Vitafoods Europe Conference 2024, Switzerland, May 2024. Participation in expert panel discussion |
| Year(s) Of Engagement Activity | 2024 |
| Description | Body responses after food intake: Impact of gene expression and epigenetics (BH) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at a conference- "Body responses after food intake: Impact of gene expression and epigenetics", Clinical Epigenetics Conference (CLEPIC), Poland, May 2024. (delivered by Prof Bastiaan Heijsman) |
| Year(s) Of Engagement Activity | 2024 |
| Description | Diet and the human epigenome: the molecular response to food intake |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited talk at the Festival of Genomics event in London by Dr Jordana Bell Diet and the human epigenome: the molecular response to food intake. Festival of Genomics, London, January 2025. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Diet and the human epigenome: the molecular response to food intake |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation and discussion by Dr Jordana Bell at the University of Essex 1-day national Genomics meeting: "Diet and the human epigenome: the molecular response to food intake", University of Essex, UK, September 2024. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Diet and the human methylome: towards improvement of cardio-metabolic health |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the seminar series 'Paediatric Allergy and Nutrition Research' across multiple departments at King's College London, March 2023. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Dr Tsai's seminar at the Department of Twin Research |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Tsai and her research team members undertook a research visit to Dr Bell's research group at King's College London in September 2023. Dr Tsai gave a seminar to the department. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Epigenetics in twins: drivers and consequences |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the International Society for Twin Studies, Twin Congress 2023, Budapest, Hungary, June 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Epigenomics and human nutrition |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk at the University of Naples Federico II (UNINA), Italy, January 2024. (delivered online). |
| Year(s) Of Engagement Activity | 2023 |
| Description | Genetic and environmental impacts on the human methylome: towards improvement of cardio-metabolic health |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the Department of Molecular and Medical Genetics, King's College London, November 2023. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Genetic impacts on DNA methylation levels in the context of DOHAD |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the international DOHAD congress, Vancouver, August 2022. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Genetic impacts on DNA methylation variance (XZ) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Selected oral presentation at the FASEB conference on The Epigenome in Human Health and Diseases, University of Lorraine, France, November 2021. Zhang* and Bell. Genetic impacts on DNA methylation variance |
| Year(s) Of Engagement Activity | 2021 |
| Description | Genetic impacts on DNA methylation variance in monozygotic twins capture gene-environment interactions and cell-type effects (XZ) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Conference presentation at the Epigenomics of Common Diseases conference in Hinxton, November 2023. Zhang*, Yet, Villicaña, Hottenga, Boomsma, van Dongen, and Bell. Genetic impacts on DNA methylation variance in monozygotic twins capture gene-environment interactions and cell-type effects. |
| Year(s) Of Engagement Activity | 2023 |
| Description | High-dimensional integrative data analysis for personalized medicine |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk at the Karolinska Institute, Stockholm, Sweden, October 2023. (delivered online) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Human DNA methylation trajectories of the postprandial metabolic response to food (RC) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Selected talk at the 22nd International Congress of Nutrition (22nd IUNS-ICN) - in Tokyo, Japan. December 2022: Ricardo Costeira*, Lidia Daimiel Ruiz, Lucy Sinke, Colette Christiansen, Bastiaan Heijmans, Eline Slagboom, Melanie Waldenberger, Sarah Berry, José M Ordovás, Jordana T Bell. Human DNA methylation trajectories of the postprandial metabolic response to food. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Networking event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Tsai and members of her research group visited Dr Bell's research group at King's College London in September 2023. During this time, we organised a networking event where Dr Tsai's group met and discussed research ideas with members of the Department of Twin Research. |
| Year(s) Of Engagement Activity | 2023 |
| Description | The effect of diet on the human epigenome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at University College London Biosocial collective seminar - by Dr Jordana Bell: "The effect of diet on the human epigenome", University College London, UK, November 2024. |
| Year(s) Of Engagement Activity | 2024 |