Prediction and analysis of a regulatory SNP map of Major Depressive Disorder
Lead Research Organisation:
University of Aberdeen
Department Name: Cal Unit (Medical Faculty)
Abstract
Major depressive disorder (MDD) constitutes the most frequently occurring mental health problem in the world and will affect up to 25% of us during our lifetimes. Worryingly, MDD is on the increase.
This study will set out to find the genetic causes of MDD by examining changes in the DNA sequence of people who are more susceptible to depression. In addition, this study will determine why certain MDD sufferers do not respond to current treatments.
Previous studies of this type have examined possible changes in the regions the genome that make protein.
Recently, however, it has been demonstrated that the majority of differences between individuals, including disease susceptibility, may be caused by changes, not in the genes themselves, but in the poorly understood DNA sequences that act as switches for these genes. These switches ensure that genes essential to healthy brain function are only used in the correct parts of the brain at the proper times and in the right dose.
Unlike genes, little is known of these switches as, up to now they have been very hard to find. However, teams led by Dr. MacKenzie have had considerable success in identifying switches responsible for driving the expression of genes known to be involved in depression, addiction and inflammatory pain.
This project will combine Dr. Mackenzies ability to detect important switch sequences, that make up less than 5% of the genome, with our new ability to detect harmful mutations within these switches. Professor McGuffin and Dr. Breen will then analyse the DNA of over 1000 individuals suffering MDD to determine whether the occurrence of particular switch differences can be associated with susceptibility to MDD. Dr MacKenzie and Prof. Quinn will then carry out molecular biological studies of these switch differences to determine the biochemical pathways affected. In addition, Prof Quinn will evaluate how the activity of variants of these switches are affected by a number of known antidepressant drugs to determine the genetic causes of variation in MDD drug treatments.
By combining a number of newly developed computer based, patent sample based and molecular biology techniques this study has the real potential of hugely expanding our understanding of the mechanisms regulating the use of key genes in the brain and how changes on these mechanisms may contribute to susceptibility to MDD. Furthermore, this study will allow us to examine why many MDD sufferers do not respond to current anti-depressive medications.
This study will set out to find the genetic causes of MDD by examining changes in the DNA sequence of people who are more susceptible to depression. In addition, this study will determine why certain MDD sufferers do not respond to current treatments.
Previous studies of this type have examined possible changes in the regions the genome that make protein.
Recently, however, it has been demonstrated that the majority of differences between individuals, including disease susceptibility, may be caused by changes, not in the genes themselves, but in the poorly understood DNA sequences that act as switches for these genes. These switches ensure that genes essential to healthy brain function are only used in the correct parts of the brain at the proper times and in the right dose.
Unlike genes, little is known of these switches as, up to now they have been very hard to find. However, teams led by Dr. MacKenzie have had considerable success in identifying switches responsible for driving the expression of genes known to be involved in depression, addiction and inflammatory pain.
This project will combine Dr. Mackenzies ability to detect important switch sequences, that make up less than 5% of the genome, with our new ability to detect harmful mutations within these switches. Professor McGuffin and Dr. Breen will then analyse the DNA of over 1000 individuals suffering MDD to determine whether the occurrence of particular switch differences can be associated with susceptibility to MDD. Dr MacKenzie and Prof. Quinn will then carry out molecular biological studies of these switch differences to determine the biochemical pathways affected. In addition, Prof Quinn will evaluate how the activity of variants of these switches are affected by a number of known antidepressant drugs to determine the genetic causes of variation in MDD drug treatments.
By combining a number of newly developed computer based, patent sample based and molecular biology techniques this study has the real potential of hugely expanding our understanding of the mechanisms regulating the use of key genes in the brain and how changes on these mechanisms may contribute to susceptibility to MDD. Furthermore, this study will allow us to examine why many MDD sufferers do not respond to current anti-depressive medications.
Technical Summary
Major Depressive Disorders (MDD) make up the most prevalent class of psychiatric disorders and will affect ~25% of us. The social and economic costs of these disorders are enormous with an estimated loss to the UK economy alone of some #9 billion per year. An additional problem facing the treatment of sufferers is variability in the efficacy of the drugs used to treat MDD.
These disorders have a strong genetic basis. Although many of these studies are still ongoing it is becoming clear that studying the effects of polymorphisms on coding regions alone will not give us a complete picture of the underlying causes.
We will explore the hypothesis that susceptibility to MDD and variation in drug efficacy may also involve polymorphisms within the gene regulatory regions responsible for maintaining normal gene expression of components of systems including the serotoninergic, dopaminergic, tachykininergic, and NPY pathways.
The objectives of this project will be to use a predictive systems biology approach to identify regulatory regions within the human genome by comparative genomics. The tissue specific and inducible status of these enhancer candidates will be analysed initially in primary cell lines and subsequently in transgenic animals in both the MacKenzie and Quinn labs.
By concentrating on SNPs within highly conserved and thus functional regions of the genome this novel approach will greatly accelerate the association of SNPs within these regions with susceptibility to MDD that will be examined in large MDD patient samples in the Institute of Psychiatry by a team headed by McGuffin and Breen.
Molecular analysis of protein-DNA interactions affected by these polymorphic ECRs will also be examined using a combination of EMSA and ChIP assay in the MacKenzie and Quinn labs. Finally, translational pharmacogenomic studies of the affects of a number of different psychoactive compounds on positively associated regulatory polymorphisms will be further examined using primary culture and in transgenic animals in the Quinn lab.
This is a novel, ambitious and multi-disciplined approach involving a unique collaboration between 3 laboratories that are individually recognised as being international leaders in their respective fields. By applying a unique combination of systems biology, patient based association study and translational pharmacogenomics this exciting collaboration has the potential of changing our understanding of the causes of MDD and will act as a translational platform that will allow for the development of more effective and specific anti-depressive therapies.
These disorders have a strong genetic basis. Although many of these studies are still ongoing it is becoming clear that studying the effects of polymorphisms on coding regions alone will not give us a complete picture of the underlying causes.
We will explore the hypothesis that susceptibility to MDD and variation in drug efficacy may also involve polymorphisms within the gene regulatory regions responsible for maintaining normal gene expression of components of systems including the serotoninergic, dopaminergic, tachykininergic, and NPY pathways.
The objectives of this project will be to use a predictive systems biology approach to identify regulatory regions within the human genome by comparative genomics. The tissue specific and inducible status of these enhancer candidates will be analysed initially in primary cell lines and subsequently in transgenic animals in both the MacKenzie and Quinn labs.
By concentrating on SNPs within highly conserved and thus functional regions of the genome this novel approach will greatly accelerate the association of SNPs within these regions with susceptibility to MDD that will be examined in large MDD patient samples in the Institute of Psychiatry by a team headed by McGuffin and Breen.
Molecular analysis of protein-DNA interactions affected by these polymorphic ECRs will also be examined using a combination of EMSA and ChIP assay in the MacKenzie and Quinn labs. Finally, translational pharmacogenomic studies of the affects of a number of different psychoactive compounds on positively associated regulatory polymorphisms will be further examined using primary culture and in transgenic animals in the Quinn lab.
This is a novel, ambitious and multi-disciplined approach involving a unique collaboration between 3 laboratories that are individually recognised as being international leaders in their respective fields. By applying a unique combination of systems biology, patient based association study and translational pharmacogenomics this exciting collaboration has the potential of changing our understanding of the causes of MDD and will act as a translational platform that will allow for the development of more effective and specific anti-depressive therapies.
Organisations
- University of Aberdeen, United Kingdom (Collaboration, Lead Research Organisation)
- The University of Iowa, United States (Collaboration)
- National Center for Biotechnology Information (NCBI) (Collaboration)
- Virginia Polytechnic Institute & State U, United States (Collaboration)
- University of Manchester, Manchester, United Kingdom (Collaboration)
Publications
Schosser A
(2010)
NRG1 gene in recurrent major depression: no association in a large-scale case-control association study.
in American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
Ball HA
(2010)
Epidemiology and symptomatology of depression in Sri Lanka: a cross-sectional population-based survey in Colombo District.
in Journal of affective disorders
Uher R
(2010)
Genome-wide pharmacogenetics of antidepressant response in the GENDEP project.
in The American journal of psychiatry
Cosgrave AS
(2010)
The effects of nitric oxide inhibition prior to kainic acid treatment on neuro- and gliogenesis in the rat dentate gyrus in vivo and in vitro.
in Histology and histopathology
Uher R
(2010)
Trajectories of change in depression severity during treatment with antidepressants.
in Psychological medicine
Butler AW
(2010)
A genomewide linkage study on suicidality in major depressive disorder confirms evidence for linkage to 2p12.
in American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
Grozeva D
(2010)
Rare copy number variants: a point of rarity in genetic risk for bipolar disorder and schizophrenia.
in Archives of general psychiatry
Green EK
(2010)
The bipolar disorder risk allele at CACNA1C also confers risk of recurrent major depression and of schizophrenia.
in Molecular psychiatry
Schosser A
(2010)
Association of DISC1 and TSNAX genes and affective disorders in the depression case-control (DeCC) and bipolar affective case-control (BACCS) studies.
in Molecular psychiatry
Lewis CM
(2010)
Genome-wide association study of major recurrent depression in the U.K. population.
in The American journal of psychiatry
Butler AW
(2011)
Response to the letter from Dr. Maher and colleagues re. Linkage on Suicidality.
in American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
Schosser A
(2011)
Genomewide association scan of suicidal thoughts and behaviour in major depression.
in PloS one
Shanley L
(2011)
Evidence for regulatory diversity and auto-regulation at the TAC1 locus in sensory neurones.
in Journal of neuroinflammation
Davidson S
(2011)
Differential activity by polymorphic variants of a remote enhancer that supports galanin expression in the hypothalamus and amygdala: implications for obesity, depression and alcoholism.
in Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology
Kohli MA
(2011)
The neuronal transporter gene SLC6A15 confers risk to major depression.
in Neuron
Haddley K
(2011)
Lithium chloride regulation of the substance P encoding preprotachykinin a, Tac1 gene in rat hippocampal primary cells.
in Journal of molecular neuroscience : MN
Brotons O
(2011)
Modulation of orbitofrontal response to amphetamine by a functional variant of DAT1 and in vitro confirmation.
in Molecular psychiatry
Gillies SG
(2011)
Distinct gene expression profiles directed by the isoforms of the transcription factor neuron-restrictive silencer factor in human SK-N-AS neuroblastoma cells.
in Journal of molecular neuroscience : MN
Breen G
(2011)
A genome-wide significant linkage for severe depression on chromosome 3: the depression network study.
in The American journal of psychiatry
Psychiatric GWAS Consortium Bipolar Disorder Working Group
(2011)
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
in Nature genetics
Rivera M
(2012)
Depressive disorder moderates the effect of the FTO gene on body mass index.
in Molecular psychiatry
Vasiliou SA
(2012)
The SLC6A4 VNTR genotype determines transcription factor binding and epigenetic variation of this gene in response to cocaine in vitro.
in Addiction biology
Nicoll G
(2012)
Allele-specific differences in activity of a novel cannabinoid receptor 1 (CNR1) gene intronic enhancer in hypothalamus, dorsal root ganglia, and hippocampus.
in The Journal of biological chemistry
Hing B
(2012)
A polymorphism associated with depressive disorders differentially regulates brain derived neurotrophic factor promoter IV activity.
in Biological psychiatry
Paredes UM
(2012)
Intronic tandem repeat in the serotonin transporter gene in Old World monkeys: a new transcriptional regulator?
in Journal of molecular neuroscience : MN
Aboonq MS
(2012)
Activity-dependent neuroprotective protein modulates its own gene expression.
in Journal of molecular neuroscience : MN
Perroud N
(2012)
Genome-wide association study of increasing suicidal ideation during antidepressant treatment in the GENDEP project.
in The pharmacogenomics journal
Rucker JJ
(2013)
Genome-wide association analysis of copy number variation in recurrent depressive disorder.
in Molecular psychiatry
MacKenzie
(2013)
Glucocorticoid receptor modulation of the TAC1 promoter in amygdala; polymorphisms, decoys stress and anxiety
in 10th congress of the European Neuropeptide Club, Gdynia, Poland
R. Ware W
(2013)
Does cholesterol drive atherosclerosis?
in Translational Medicine
MacKenzie, Alasdair
(2013)
Exploring the impact of regulatory polymorphisms on drug response and disease; the future of stratified and personalized medicine?
in 16th international symposium on Molecular Medicine, Crete, Greece.
MacKenzie A
(2013)
Exploring the effects of polymorphisms on cis-regulatory signal transduction response.
in Trends in molecular medicine
Fowler P
(2014)
In utero exposure to cigarette smoke dysregulates human fetal ovarian developmental signalling
in Human Reproduction
Hay CW
(2014)
Negative regulation of the androgen receptor gene through a primate-specific androgen response element present in the 5' UTR.
in Hormones & cancer
Hay CW
(2014)
Functional effects of polymorphisms on glucocorticoid receptor modulation of human anxiogenic substance-P gene promoter activity in primary amygdala neurones.
in Psychoneuroendocrinology
Richardson TG
(2014)
Evaluating the role of a galanin enhancer genotype on a range of metabolic, depressive and addictive phenotypes.
in American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
Davidson S
(2016)
Analysis of the effects of depression associated polymorphisms on the activity of the BICC1 promoter in amygdala neurones.
in The pharmacogenomics journal
Hay EA
(2017)
Determining Epigenetic Targets: A Beginner's Guide to Identifying Genome Functionality Through Database Analysis.
in Methods in molecular biology (Clifton, N.J.)
Hay EA
(2017)
Using the CRISPR/Cas9 system to understand neuropeptide biology and regulation.
in Neuropeptides
MacKenzie A
(2017)
Neuropeptides-2015, Aberdeen University, Scotland.
in Neuropeptides
Hing, Ben
Identification and analysis of a highly conserved enhancer region within the CGRP locus
in PLoS One
Davidson, Scott
Depression associated allelic variants within the BICC1 locus differentially regulate the BICC1 promoter in amygdala neurones.
in Neuropsychopharmacology
| Description | A novel in-vivo CRISPR enhancer screen to identify polymorphic regulatory regions controlling the hypothalamic expression of appetite regulating neuropeptides. |
| Amount | £25,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 04/2018 |
| Description | Determining the effects of genetic variation and early life stress on the regulation of the galanin gene in fat and alcohol selection. |
| Amount | £418,914 (GBP) |
| Funding ID | BB/N017544/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 09/2019 |
| Description | Effects of stress, genetic and epigenetic variation on the control of the cannaboinnoid receptor gene; possible roles in disease and drug response stratification. |
| Amount | £104,000 (GBP) |
| Organisation | Medical Research Scotland |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2014 |
| End | 09/2017 |
| Description | Wellcome trust ISSF fund |
| Amount | £20,000 (GBP) |
| Organisation | Wellcome Trust |
| Department | Wellcome Trust Pump Prime Award |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2015 |
| End | 03/2016 |
| Title | BDNF promoter 4 lacZ transgenic line. |
| Description | Several transgenic lines werw generated using a plasmid containing the BDNF promoter 4 fused to the LacZ gene. |
| Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
| Provided To Others? | No |
| Impact | Non-coding polymorphisms within the BDNF gene have been associated with conditions as diverse as MDD, obesity and BD. In addition removal of BDNF promoter 4 has been shown to cause a reduction in cognition and memory in mice. However, Nothing is known of how many of the non-coding SNPs in and around the BDNF locus modulates the regulation of the BDNF gene. Using comparitive genomics we identified and isolated the BDNF gene promoter. This promoter was used to make reporter constructs which were then used to make transgenic mouse lines. These transgenic mouse lines expressed lacZ in many areas of the limbic system including the amygdala, hippocampus and cortex. By establishing the BDNF promoter-4 as being tissue specific we have established a platform for establishing the possible effects of non-coding SNPs in and around the BDNF gene on the activity of its promoter in amygdala, hippocampal and cortical cells. |
| Title | BICC1 overexpressing cell line |
| Description | BicC1 over expression A plasmid expressing a myc/DDK-tagged human BicC1 protein driven by a CMV promoter is being transfected into human neuroblastoma and HEK293 clonal lines. The mRNA message and protein expressed from this construct is being assessed by QPCR and western blotting, respectively, to determine the functionality of the construct. Western blotting is being performed with anti myc and anti DDK antibodies to confirm expression of the tagged protein. In addition, transfected cells are also being tested with the BicC1 antibodies to help boost the signal for optimising these antibodies. The tagged construct will allow determination of the localisation of the BicC1 protein within the cells. BicC1 has mostly been considered as an RNA binding protein and is chiefly located in the cytoplasm in other species. It is not yet been determined whether BicC1 can act as a DNA binding protein although it has KH domains similar to the hnRNPK single stranded nucleic acid binding protein which is a known regulator of DNA transcription. Localisation studies in combination with ChIP assays will go some way to determine whether BicC1 can act as a transcriptional regulator of gene expression in addition to its role in mRNA stability. Furthermore, changes in distribution of the BicC1 protein within the cellular environment will be assessed following specific challenges to the cells. |
| Type Of Material | Cell line |
| Year Produced | 2010 |
| Provided To Others? | Yes |
| Impact | Having a reliable source of BICC1 protein produced from mammalian cells will be vital to efforts to characterise the function and mechamism of this protein in disease |
| Title | BICC1 promoter transgenic mice |
| Description | Transgenic lines containing the BICC1 promoter driving expression of the LacZ marker gene. |
| Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
| Provided To Others? | No |
| Impact | Non-coding polymorphisms within the BICC1 gene have been associated with MDD. Nothing is known of the regulation of the BICC1 gene. Using comparitive genomics we identified and isolated the BICC1 gene promoter. This promoter was used to make reporter constructs which were then used to make transgenic mouse lines. These transgenic mouse lines expressed lacZ in many areas of the limbic system including the amygdala, hippocampus and cortex. By establishing the BICC1 promoter as being tissue specific we have established a platform for establishing the possible effects of non-coding SNPs in and around the BICC1 gene on the activity of its promoter in amygdala, hippocampal and cortical cells. |
| Title | CACNA1c promoter transgenic line |
| Description | Transgenic lines produced by pro-nuclear microinjection |
| Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
| Provided To Others? | No |
| Impact | CACNA1c has been associated with bipolar disorder and schizophrenia by multiple GWAS analysis. By isolating and identifying the tissue specific properties of this promoter using transgenic analysis we have provided a platform for understanding the possible differential effects of non-coding SNPs on the expression of the CACNA1c gene in MDD. |
| Title | Expansion of the HPC array facility |
| Description | The MRC award allowed us to exapnd the capacity of our existing high performance computer (HPC) array. This has been of enormous benefit to our research effort and has profitted a number of other research groups around the University who require HPC array technology to carry out complex system biology type projects. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2008 |
| Provided To Others? | Yes |
| Impact | The provision of an expanded HPC systems has resulted in the publication of a manuscript in the high profile journal BMC genomics. We also hope to publish a number of other papers in BMC bioinformatics in the near future. |
| Title | Magnetofection of primary neurones |
| Description | We optimized a novel method for the recovery, transfection and culture of primary neuonal cell lines derived from the amygdala, hypothalamus and hippocampus. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2009 |
| Provided To Others? | Yes |
| Impact | The development of this technique removed much of the need to carry out experiments in whole animals. |
| Title | Rabbit anti human BICC1 antibody |
| Description | An antibody raised against the human BICC1 proteins |
| Type Of Material | Antibody |
| Provided To Others? | No |
| Impact | Detecting changes in the expression of the BICC1 protein will be critical to determining the mechanisms by which the BICC1 gene, that we have associated with major depressive disorder (MDD) using GWa studies, induces the symptoms of MDD. There are no commercial antibodies available against the human form Bicaudal C 1 homologue (BicC1). Two distinct antibodies raised in rabbit against the human homologue are being assessed for their potential to recognise the human form of BicC1 for future use in immunostaining and chromatin Immunoprecipitation assays. The human neuroblastoma cell lines used for assessing BicC1 ECR activity, SK-N-AS and SH SY5Y, were tested for the presence of BicC1 mRNA. A positive result in both cell lines suggested the presence of BicC1 in these cells lines. Furthermore, both the long isoform and the hypothetical short isoform were detected. Validation of the presence of BicC1 protein in these cell lines is now underway to confirm the existence of the BicC1 protein and to assess the antigenic potential of eight serum bleeds and four purified forms of the antibody that have been generated. Protein extracted from the neuroblastoma cell lines as well as that extracted from human embryonic kidney cells lines (HEK293), which should express BicC1 at high levels, is currently being used in western blot analysis. Initial results have shown a number of protein bands detected by both antibodies. One of these antibodies (recognising the epitope IKPKPKQPSKSVIVKSVER) would recognise both the long and the putative short isoform of BicC1. The purified from of this antibody gave a good signal with a band in the range of the expected size for the long form of BicC1. The second antibody that should only recognise the long isoform (recognising the epitope AAQGEPGYLAAQSDPGSNS), which gave poor ELISA results and was pooled from two sources, has failed to work in the purified form although serum bleeds of this antibody have identified a number of bands. Peptide competition of the antibody to determine specificity of the bands has thus far failed to compete bands although this is problematic for serum bleeds as antibody concentrations cannot be determined. For all antibodies generating bands one band in the kDa range for BicC1 appears consistently and this band is being prepared for identification by mass spectrophotometery using immunoprecipitation (IP) for enrichment. The BicC1 antibodies are currently being used for IP in human neuroblastoma cell lines. These IP will be subsequently run on western blotting gels to isolate and enrich specific bands to be sent for mass spectrophotometery analysis at the proteomics facilities at the IOP, king's college, London. |
| Title | RegSNP |
| Description | RegSNP is a new computer algorithm for the prediction of the effects of SNPs on transcription factor binding to DNA. The algorithm was released on line in the form of an easily usable web site. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2009 |
| Provided To Others? | Yes |
| Impact | The use of RegSNP allowed us to predict the effects of SNPs identified within the regulatory regions under study. We are also aware of the use of this web site by other researchers overseas. |
| Title | Reporter gene transgenic lines |
| Description | The material consists of a number of trangenic lines that contain reporter gene constructs made with enhancers identified during the time frame of the current projecty |
| Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
| Year Produced | 2008 |
| Provided To Others? | Yes |
| Impact | The material provided allow for the assessment of the tissue specific and inducible properties of enhancers identified by comparitive genomics in vivo. These novel models allow for the production of persuasive in vivo data on the properties of novel enhancers. The regulatory regions currently being modelled in these lines include enhancers and promoters for Galanin, TAC1, CGRP, NPY, BDNF and CNR1. |
| Description | Bioinformatic analysis, Virginia Tech |
| Organisation | Virginia Tech |
| Department | Virginia Bioinformatics Institute |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Harold Skip Garner, Director of Virignia Tech Bioinformatic Institute |
| Collaborator Contribution | New skills set |
| Impact | Functional analysis of genetic analysis defining important genetic variants associated with neuroscience and cancer. |
| Start Year | 2011 |
| Description | Development of a novel Algorithm to define SNP effects on DNA binding sites |
| Organisation | University of Aberdeen |
| Department | School of Engineering |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have provided intellectual input and have guided the project from the biological perspective. |
| Collaborator Contribution | Dr Starkey has brought expertise in Computer software engineering. |
| Impact | We have one paper in press (BMC genomics) and one to be submitted very soon in BMC computational biology that describes the development of a novel web site that allows researchers to predict the effects of non-coding polymorphisms on the binding of transcription factors |
| Start Year | 2006 |
| Description | Regulation of hypothalamic galanin expression |
| Organisation | University of Aberdeen |
| Department | The Rowett Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | A collaboration to understand the systems that regulate the expression of Galanin in the PVN of the hypothalamus and the amygdala. |
| Collaborator Contribution | Dr Perry Barrett brings expertise in hypothalamic function and in-situ hybridisation |
| Impact | We have used comparitive genomics to identify a gene regulatory region that supports expression of the galanin gene in the hypothalamus, amygdala and in sensory neurones. We have also found that this enhancer is highly polymorphic ans that polymorphisms affect the ability of the enhancer to activate transcription of a marker gene in primar hypothalamic neurones. We are in the process of completeing our studies and a paper has been published in the highly respected journal Neuropsychopharmocology |
| Start Year | 2007 |
| Description | Regulation of the CGRP gene |
| Organisation | University of Iowa |
| Department | Department of Molecular Physiology and Biophysics |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We made a transgenic line containing a reporter construct with the enhancer region previously identified and studied in the Russo lab. We also carried out immunohistochemical co-localisation between the activity of this enhancer and expression of the endogenous gene. |
| Collaborator Contribution | Working with Prof Russo we have identified and generated transgenic models with a novel CGRP enhancer region. The activity of this enhancer replicates many of the expression characteristics of the endogenous cgrp gene and overlaps the expression of Calcetonin in the thyroid gland. This work is currently in preperation for submision to PLOS one. |
| Impact | A manuscript is currently in preperation. |
| Start Year | 2009 |
| Description | Shared Studentship |
| Organisation | National Center for Biotechnology Information (NCBI) |
| Country | United States |
| Sector | Public |
| PI Contribution | We have a shared WT/NIH PhD student which is addressing DNA structure in areas of regulatory domains relevant for transcription |
| Collaborator Contribution | We have a shared WT/NIH PhD student which is addressing DNA structure in areas of regulatory domains relevant for transcription |
| Impact | We have a shared WT/NIH PhD student which is addressing DNA structure in areas of regulatory domains relevant for transcription |
| Start Year | 2008 |
| Description | determining the mechanisms of BDNF enhancer polymorphisms on cognitive decline in the elderly. |
| Organisation | University of Manchester |
| Department | School of Medicine Manchester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We carried out the bioinformatic analysis, cloning and reproduction of the associated alleles using site directed mutatgenesis. We cloned promoter 4 of the BDNF gene and showed that this promoter drove marker gene expression in the limbic system including the amygdala and the hippocampus. Using luciferease assays in primary hippocampal cultures we were able to show that the associated polymorphism could significantly reduce the ability of the enhancer in which it was contained to activate promoter 4 in hippocampal neurones following depolarisation |
| Collaborator Contribution | The University of Manchester provided association data for a SNP within a BDNF enahancer element that was associated with cognitive decline in the elderly. We have now show that this SNP affects the ability of the enhancer to activate BDNF promoter 4 in primary hippocampal neurones depolarised by KCl. Considering the important role played by BDNF in hippocampal plasticity the mechanistic linking of a cognitive disorder linked SNP and cell depolarisation in the hippocampus is highly significant. |
| Impact | A paper describing this research has been invited for resubmission by Biological Psychiatry |
| Start Year | 2008 |
| Description | GWA Studies, Gene Regulatory Variation and Disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Seminar/workshop no actual impacts realised to date |
| Year(s) Of Engagement Activity | 2011 |
| Description | Gene regulation, SNPs and disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Many interesting questions were asked and views shared I hope to have stimulated young people in the audience to pursue science as a career |
| Year(s) Of Engagement Activity | 2011,2012 |
| Description | Gene regulatory variation in health and disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Seminar/workshop The talk stimulated a great deal of interest from the audience |
| Year(s) Of Engagement Activity | 2011 |
| Description | Invited speaker to the Wellcome Trust, London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I was one of three invited speakers involved in presenting a Wellcome trust exhibition entitled "Gut Reactions" which aimed to inform the general public about research into the genetics of appetite. The occation generated a great deal of audience interest and many questions and was reported in the Observer. The occation generated an article in the Observer and was also reported in a number of other newspapers. |
| Year(s) Of Engagement Activity | 2011 |
| Description | Newspaper articles |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Articles published in the following news papers; PRESS & JOURNAL, THE SCOTTISH SUN, DAILY RECORD, THE SCOTSMAN, DAILY RECORD, METRO SCOTLAND, ABERDEEN EVENING EXPRESS, THE SCOTSMAN, THE HERALD (10.06.08) I was subsequently invited to contribute to several radio programmes. |
| Year(s) Of Engagement Activity | 2008 |
| Description | Radio programmes |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Interviewed on BBC RADIO ABERDEEN - NORTH EAST NEWS, NORTHSOUND 2 - NEWS, BBC RADIO SCOTLAND - NEWSDRIVE (06.06.08) Invites to take part in television programmes. |
| Year(s) Of Engagement Activity | 2008,2009,2010,2011,2012 |
| Description | RegSNP - Predicting Allele Specific Differences in Transcription Factor - DNA binding |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This website permits non-expert in biotechnology to identify the transcription factor bindingsites most affected by specific SNPs. The website also displays LD data, information on disease data and whether a particular SNP is GWAS associated or alters suceptibility to epigenetic modifiation. Our web site has informed the research of many other researchers. |
| Year(s) Of Engagement Activity | 2009,2010,2011,2012,2013,2014 |
| URL | http://viis.abdn.ac.uk/regsnp/Home.aspx |
| Description | School Visit-Glasgow |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | I gave a presentation of the importance of gene regulation on disease and evolution. I hope that I motivated the students to learn more about biology |
| Year(s) Of Engagement Activity | 2008 |
| Description | Speaker at the Bradford Science festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Over 40 reporters from all of the main newspapers and a number of science based magasines were present. This resulted in the production of a number of blogs, newspaper articles in papers such as the Guardian and articles in a number of magazines. The publication of the work sparked a great deal of media interest. |
| Year(s) Of Engagement Activity | 2011 |
| Description | Television appearances |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Gave an interview about my work to BBC television. Wider interest in my work. |
| Year(s) Of Engagement Activity | 2008,2009 |