Transcriptional profiling as a key tool to improve marbling in beef cattle.
1 like463 views
The document presents an analysis of cellular signaling pathways and transcriptomics profiling aimed at improving marbling in beef cattle. It outlines the identification of genes and pathways related to intramuscular fat deposition, highlighting the significance of the MAPK signaling pathways in high-marbling breeds. Future research directions include the integration of various omics data and exploring environmental factors influencing meat quality.
Transcriptional profiling as a key tool to improve marbling in beef cattle.
- 1. Cellular signaling pathway analysis of transcriptomics profiling as a key tool to improve marbling in beef cattle. A possible approach for artificial meat quality improvement Susan Steinbusch-Coort, PhD Dept. Bioinformatics-BiGCaT, NUTRIM, Maastricht University susan.coort@maastrichtuniversity.nl
- 2. 1st International Symposium on Cultured Meat 19 October 2015 2 Marbling • Intramuscular fat – the fat present within a cut of meat and between the muscle fibers. • Breed, genotype, age, diet, husbandry and growth stages.
- 3. 1st International Symposium on Cultured Meat 19 October 2015 3 Aim To identify genes and biological pathways regulating marbling of muscle tissue in beef cattle. Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene 7 Gene 8
- 4. 1st International Symposium on Cultured Meat 19 October 2015 4 WikiPathways (www.wikipathways.org) Community curated pathway database o everybody can contribute and share pathways o everybody can edit and curate pathways o everybody can use the pathway collection o not just diagrams but fully annotated pathways o new findings can be added immediately
- 5. 1st International Symposium on Cultured Meat 19 October 2015 5 Bos taurus collection at WikiPathways 282 Bt pathways
- 6. 1st International Symposium on Cultured Meat 19 October 2015 6 Analysis workflow Adapted from: Kutmon M, Evelo CT, Coort SL. (2014) A network biology workflow to study transcriptomics data of the diabetic liver. BMC Genomics. 15:971. doi: 10.1186/1471-2164-15-971.
- 7. 1st International Symposium on Cultured Meat 19 October 2015 7 Transcriptomics data Limousin - Low marbling Hereford - High marbling N=4N= N=4 Agilent Two-Color Mi Bovine (V2) 4 x 44K Gene Expression Microarray T. Sadkowski et al “Transcriptional background of beef marbling – Novel genes implicated in intramuscular fat deposition,” Meat Sci., vol. 97, no. 1, pp. 32–41, 2014. Semitendinosus muscle of 15-month-old bulls Isolation RNA Gene expression Publicly available at ArrayExpress (accession number E-GEOD-46411).
- 8. 1st International Symposium on Cultured Meat 19 October 2015 8 Differential expression Differentially expressed genes comparing Hereford with Limousin - Absolute log10 fold change > 0.11 - Absolute fold change of 1.3 - P-value < 0.05 28,753 genes measured and annotated 2,873 differentially expressed genes 1421 genes 1452 genes
- 9. 1st International Symposium on Cultured Meat 19 October 2015 9 Over-representation analysis PathVisio: a tool to edit and analyze biological pathways Transcriptomics data Pathway collection Analysis collection from WikiPathways (www.wikipathways.org) Differentially expressed genes Z-score per pathway Over-representation analysis Ranking of pathways based on z-score Kutmon, M et al. PathVisio 3: An Extendable Pathway Analysis Toolbox. (Accepted for publication in PLOS Computational Biology)
- 10. 1st International Symposium on Cultured Meat 19 October 2015 10 Pathway Positive(r) Measured(n) Total Z Score P-value Marbling Hypertrophy Model 8 15 19 3.94 0.000 * MAPK signaling pathway 34 124 167 3.51 0.002 * Histone Modifications 13 35 43 3.41 0.000 - IL-1 signaling pathway 15 41 54 3.17 0.003 * P38 MAPK signaling pathway 10 27 36 2.98 0.006 * Cardiac progenitor differentiation 11 33 54 2.72 0.006 - TCR signaling pathway 19 68 89 2.70 0.011 * MicroRNAs in cardiomyocyte hypertrophy 20 73 102 2.67 0.006 * Mitochondrial gene expression 5 11 23 2.66 0.006 * Physiological and pathological hypertrophy of the heart 7 19 26 2.47 0.012 * Parkin-Ubiquitin proteasomal system pathway 13 44 64 2.45 0.022 - Insulin Signaling 27 111 157 2.41 0.012 - Transcriptional activation by NRF2 5 13 19 2.2 0.020 - The highest ranked pathways based on Z score in Hereford vs Limousin
- 11. 1st International Symposium on Cultured Meat 19 October 2015 11 Gene expression in Hereford vs Limousin visualized on the Hypertrophy model.
- 12. 1st International Symposium on Cultured Meat 19 October 2015 12 Conclusions • MAPK and P38 MAPK signaling, two pathways well known to affect lipid metabolism, were enriched in the high-marbling breed. • The signaling pathways “Hypertrophy Model”, “MicroRNAs in cardiomyocyte hypertrophy” and “Physiological and pathological hypertrophy of the heart” that play a role in tissue development were affected. • Immune response pathways - IL signaling, TCR signaling and Toll-like receptor signaling pathways – were changed.
- 13. 1st International Symposium on Cultured Meat 19 October 2015 13 Future directions • Integration of different types of omics data in pathway analysis, like proteomics and metabolomics. • Effect of environmental factors on marbling and the underlying biological processes. • Extending the analysis with network analysis to add a regulatory level. • Analyzing cultured meat quality at a molecular level.
- 14. 1st International Symposium on Cultured Meat 19 October 2015 14 Acknowledgements Chris Evelo Maastricht University (Maastricht – NL) - Lars Eijssen - Egon Willighagen - Anwesha Bohler-Dutta - Elisa Cirillo - Nuno Nunes - Jonathan Mellius - Linda Rieswijk - Frederieke Ehrhart Dept. Animal Science, University of Ferdowsi Mashhad (Mashhad – Iran) Zahra Roudbari Gladstone Institute (San Francisco - USA) - Alexander Pico - Samad Lotia - Kristina Hanspers
- 15. 1st International Symposium on Cultured Meat 19 October 2015 15 Questions