Investigating cellular plasticity in the avian primitive streak
Lead Research Organisation:
University of East Anglia
Department Name: Biological Sciences
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.
Planned Impact
INTRODUCTION: This is a basic science project; it addresses fundamental questions about molecular signaling mechanisms that control embryonic development. Similar mechanisms will be important for stem cells and discoveries made are therefore relevant for human and animal health. The project is most likely to have longer-term impacts in the biomedical and health science areas.
HUMAN (AND ANIMAL) HEALTH AND APPLIED RESEARCH: BMP and Wnt signaling pathways are major biological mechanisms for cell-to-cell communication in humans and animals. Deregulated signaling contributes to developmental abnormalities, for example cardia bifida, and diseases in the adult such as colorectal cancer. Understanding the molecular mechanisms that regulate the specificity of the transcriptional and cellular response in different cells is of fundamental importance in order to develop strategies aimed at the use of stem cell-based therapies in regenerative medicine. This includes, but is not limited to cardiomyocyte (heart muscle) regeneration.
GENERATION OF A SCIENTIFICALLY LITERATE WORKFORCE: This project will train the next generation of biomedical researchers by directly supporting the academic research career of Dr McColl and by training an RA in chick embryology. Indirect benefits will come from the team's contributions to a research-led environment for teaching of postgraduate and undergraduate students, who enter many science related careers.
THE WIDER PUBLIC: Members of the public are interested in scientific progress and embryo development is a fascinating topic that people can easily relate to. Understanding how genes regulate and drive this process has become easier to tackle with the recent advances in genomics technologies. This project will contribute discoveries towards this intriguing issue by focusing on two highly relevant signaling pathways that govern discrete cellular responses in the very early embryo.
PHARMA AND BIOTECH INDUSTRY: Context-specific signaling mechanisms are important for drug development and longer-term beneficiaries will be biotech and pharmaceutical industry. The project will increase our knowledge base, a prerequisite to design more sophisticated drugs targeting specific pathways in specific contexts. Detailed insights into the control of cellular behaviour will also benefit regenerative medicine and tissue engineering.
OVERALL this study will contribute to health improvements and to economic wealth generation in the UK and beyond, both directly and indirectly.
HUMAN (AND ANIMAL) HEALTH AND APPLIED RESEARCH: BMP and Wnt signaling pathways are major biological mechanisms for cell-to-cell communication in humans and animals. Deregulated signaling contributes to developmental abnormalities, for example cardia bifida, and diseases in the adult such as colorectal cancer. Understanding the molecular mechanisms that regulate the specificity of the transcriptional and cellular response in different cells is of fundamental importance in order to develop strategies aimed at the use of stem cell-based therapies in regenerative medicine. This includes, but is not limited to cardiomyocyte (heart muscle) regeneration.
GENERATION OF A SCIENTIFICALLY LITERATE WORKFORCE: This project will train the next generation of biomedical researchers by directly supporting the academic research career of Dr McColl and by training an RA in chick embryology. Indirect benefits will come from the team's contributions to a research-led environment for teaching of postgraduate and undergraduate students, who enter many science related careers.
THE WIDER PUBLIC: Members of the public are interested in scientific progress and embryo development is a fascinating topic that people can easily relate to. Understanding how genes regulate and drive this process has become easier to tackle with the recent advances in genomics technologies. This project will contribute discoveries towards this intriguing issue by focusing on two highly relevant signaling pathways that govern discrete cellular responses in the very early embryo.
PHARMA AND BIOTECH INDUSTRY: Context-specific signaling mechanisms are important for drug development and longer-term beneficiaries will be biotech and pharmaceutical industry. The project will increase our knowledge base, a prerequisite to design more sophisticated drugs targeting specific pathways in specific contexts. Detailed insights into the control of cellular behaviour will also benefit regenerative medicine and tissue engineering.
OVERALL this study will contribute to health improvements and to economic wealth generation in the UK and beyond, both directly and indirectly.
Organisations
People |
ORCID iD |
| Simon Moxon (Principal Investigator) |
Publications
Hatch VL
(2016)
The positive transcriptional elongation factor (P-TEFb) is required for neural crest specification.
in Developmental biology
| Description | RNAseq is a transcriptomic approach where the total complement of RNAs from a given sample is isolated and sequenced using high-throughput sequencing technology. The RNA fragments provide a snapshot of a sample's messenger RNA content which can be mapped to a reference gene model and gene expression quantification obtained. Experimentalists collaborating on this project provided the RNAseq read out from a total of 32 samples across two time-points in the embryonic development of Chicken (Gallus gallus). The two time-points were Hamburger Hamilton stages 3 and 4 (HH3 and HH4). 16 samples were provided for time point HH3 and 16 samples provided for time point HH4. The time point sample groups comprised RNAseq from cells transfected with GFP (control), or cells transfected with constitutively active Smad1 (Smad-EVE), BMP2 or Wnt3a expression plasmids. In total there are 4 experimental conditions (GFP, Smad-EVE, BMP2 and Wnt3a) each with 4 repeats (2 stages x 4 conditions x 4 repeats = 32 samples in total). To identify genes that were differentially expressed we conducted computational RNAseq differential expression (DE) analyses. The HH3 sample group and the HH4 sample group were analysed independently and the same analysis was carried out for both groups. For each group, the RNAseq reads were aligned to the Chicken reference genome (galgal5) using the STAR read aligner (Dobin et al. 2013). The total number of reads that uniquely mapped to the reference genome was between 87.24% and 90.68% varying slightly between the samples. The resulting alignments were provided to the work flow for the count-based statistical method DESeq2 (Love, Huber, and Anders 2014) and the following comparisons were conducted: GFP vs BMP2, GFP vs Smad1 and GFP vs Wnt3a. From these comparisons, the DE analysis reported a number of genes as differentially expressed, and those DE genes assigned a Benjamini-Hochberg adjusted p-value (padj) of less or equal to 0.05 were accepted as candidates for further assessment. More specifically, for time point HH3 the following contrasts of GFP vs BMP2, GFP vs Smad1 and GFP vs Wnt3a identified a total of 44, 78 and 32 differentially expressed genes respectively (padj < 0.05). Using the same contrasts as HH3, analysis of the HH4 time point revealed a total of 2412, 1533 and 320 differentially expressed genes respectively (padj < 0.05). These candidate DE genes will be further investigated for their potential involvement in BMP/Smad or Wnt/GSK3b signaling. REFERENCES: Dobin, Alexander, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. 2013. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29 (1):15-21. Love, Michael I., John B. Hogenesch, and Rafael A. Irizarry. 2016. "Modeling of Rna-Seq Fragment Sequence Bias Reduces Systematic Errors in Transcript Abundance Estimation." Nature Biotechnology 34 (12):1287-91. |
| Exploitation Route | The differentially expressed genes, are being assessed further and candidates are being experimentally validated by collaborators on this project. |
| Sectors | Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology |