Dr. Owen Donohoe

Position: Technical Postdoctoral Research Officer
Department: Research Hub, BRI and MRI
Room Location: RH209
Email: odonohoe@ait.ie
Ext. No.: 8099
Teaching: Genetics

Research Interests: Virology (Herpesviruses and Influenza), RNA-interference, Viral Vaccines, Innate Immune Stimulation, Adaptive immunity, Molecular Diagnostics, Viral Engineering, Oncolytic Viral Therapy.

Expertise: Novel viral MicroRNA Prediction and Discovery, Molecular Biology, Genetics, Molecular Diagnostics, Assay Development, Test Method Validation (INAB Accredited Diagnostic and Biopharma QC environments), Virology incl. Viral Culture, Titration (Plaque Assay, TCID 50, hemagglutination assay, hemagglutination inhibition assay), Viral Harvesting (from cell culture and live chicken embryos), Isolation form infected tissue, Cell Culture, RNA/DNA extraction, PCR, PAGE, Northern Blotting, Sequencing, Gene Cloning, Gene Mutagenesis, Transfection, Deep Sequencing Library Preparation, ELISA, Cell-based Bioassays, Antibody Bioactivity Testing, Tissue dissection, QC testing, miRNA Target-Site Prediction and Validation, Staff training, Tech-Transfer, Analysis of Deep Sequnecing Datasets, Linux Terminal Interface, Bioinformatics (SeqMap, Bowtie, Cufflinks, FastxToolKit, MiRDeep, miReap, TargetScan, PITA)

 

Biography

 

Owen is an early stage researcher having joined AIT in 2017, with a background in Diagnostics, Virology, Molecular Biology, Bioinformatics, Vaccines and Quality Control.

After graduation from DCU in 2008 (BSc in Genetics and Cell Biology), he joined the Marine Institute (MI) where he worked as a Diagnostics Analyst in the Fish Health and Molecular Biology Unit. While here, he gained 4 ½ years experience in nationwide disease surveillance and molecular diagnostics including field sampling, tissue dissection, test method development and test method validation (sensitivity, repeatability, specificity, reproducibility, accuracy, precision, tissue/matrix inhibition) for INAB testing accreditation. While in the MI, he also did a PhD. through the MI Research Fellowship Program, as part of this he registered with DCU in 2009 under the supervision of Dr. Dermot Walls and graduated in 2013. After this he worked briefly in NUIG in the Molecular Diagnostic Research Group under Prof. Terry Smith on the development of point of care diagnostic device for breast cancer. In 2014, he joined Elanco (part of the Eli Lilly Group), a vaccine biotech company in Sligo, where he worked in both QC and Process Development labs. As part of this position he carried out routine QC in-process, release, and stability testing. he also carried out test method validation, tech transfer to CROs and subsequent on-site training of CRO staff. He also took part in lab investigation reports and root cause analysis. As part of Process Development Lab activities, he also contributed to production process validation work packages related to the introduction of new mycoplasma and influenza vaccines, as such, he was the primary person responsible for establishing influenza and mycoplasma growth/inactivation kinetics in preliminary engineering runs for production of new vaccines. he was also responsible for generating experimental data on vaccine dose-response studies in guinea pigs. He also conducted and co-ordinated vaccine stability studies to establish antibody response in guinea pigs receiving vaccine batches at various time-points post production. He was also the primary person responsible for management of the cell culture facilities in the QC labs, providing a constant supply of 9 animal cells lines for QC and stability testing of legacy vaccine products.

Owen’s expertise lies primarily is in the field of virology, (specifically herpesviruses & influenza), RNA-interference mechanisms, molecular biology and bioinformatics. His PhD project involved an investigation into the existence of Cyprinid Herpesvirus-3 (CyHV-3) encoded microRNAs (miRNAs) and was proposed on the basis of an initial bioinformatic study he carried out on the CyHV-3 genome, which suggested that specific non-coding regions of the genome could theoretically gave rise to RNA transcripts that folded into stable stem-loop structures consistent with precursor-miRNAs (pre-miRNAs). To investigate these predictions, he used deep-sequencing to profile the types of small RNA transcripts that were produced during CyHV-3 infections in common carp brain cells (CCBs), accumulating over 35 million RNA sequence reads between separate infections using two different CyHV-3 isolates. He then used bioinformatics analysis and a suite of other molecular methods to verify and functionally characterise putative novel viral miRNAs identified in deep sequencing data. Newly designed PCR assays were used to show that these miRNAs observed in infected cell lines were also present in naturally infected host tissue. This was the first study to show that members of the Alloherpesviridae family have also evolved to use RNA-interference as mechanism to regulate gene expression during infection and also the among some of the earliest studies to observe microRNA-offset-RNAs (moRNAs), a newly described class of small non-coding transcript related to miRNAs.

A. Genomic locations of confirmed and high probability CyHV-3 Precursor-microRNA (Pre-miRNA) genes. B. Structures of CyHV-3 pre-miRNAs, locations of 5' and 3' miRNAs are indicated in in Red and Yellow respectively, locations of 5' and 3' miRNA-offset-RNAs (moRNAs) are indicated in Green and Purple respectively (http://dx.doi.org/10.1371/journal.pone.0125434)

A. Genomic locations of confirmed and high probability CyHV-3 Precursor-microRNA (Pre-miRNA) genes. B. Structures of CyHV-3 pre-miRNAs, locations of 5′ and 3′ miRNAs are indicated in in Red and Yellow respectively, locations of 5′ and 3′ miRNA-offset-RNAs (moRNAs) are indicated in Green and Purple respectively (http://dx.doi.org/10.1371/journal.pone.0125434)



 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

From 2014-2015 while working in NUIG and Elanco, Owen proposed and developed a similar miRNA discovery project to investigate the existence of Oyster Herpesvirus (OsHV-1) encoded miRNAs, with a view to integrating NUIG as a partner in the Vivaldi research consortium with the support of Prof. Terry Smith (NUIG) and Deberah Chesslett (MI). The consortium consists of 21 partners from 10 countries was formed in 2011 (then called Bivalife) to address the diagnosis and management of infectious diseases in oysters and mussels at an EU level. This is a major issue identified by the European commission in light of large increases in international and intra-EU trade and exchange of such animals which has resulted in an increase in the incidence of pathogen transfer and infectious disease outbreaks. The identification of latently infected animals (pathogen in “dormant” state, no clinical symptoms, low/undetectable levels of pathogen), is a significant issue in disease monitoring and control. The identification of alternative diagnostic biomarkers for latent stages of viral infection is crucial. Unlike viral genomic DNA and coding transcripts, viral miRNAs can remain present at high levels during latent infections, thus they should represent a much more readily detectable diagnostic target than viral DNA or coding transcripts in latent carriers. For this reason, Owen proposed to the consortium (in a presentation at the annual meeting Paris 2014) that it would be useful to work towards identifying OsHV-1 encoded miRNAs with a view to evaluating their significance as diagnostic biomarkers for the identification of latently infected carriers. This idea was subsequently included as a work package as part of a much larger research program submitted to the EU commission for H2020 funding in 2015 and subsequently funded later that year (Call H2020-SFS-2015-2, Sub Topic SFS-10b-2015). This OsHV-1 miRNA discovery study was officially launched in April 2017 with work packages currently taking place in NUIG and the MI with elements of the bioinformatic analysis to be carried out by Owen in AIT. Owen currently co-ordinate this study from AIT in close collaboration with Deborah Cheslett (MI) and Prof. Terry Smith (NUIG).

Owen has recently been successful in securing Marie Curie Fellowship funding for an idea he developed and proposed while working in Elanco (Funding Call H2020-MSCA-IF-2016). This Marie Curie project, entitled  “Super-Vaccine”  will explore an idea for a new type of vaccine technology aimed at enhancing live-viral-vaccine safety and efficacy. The proposed project involves genetically modifying live-attenuated-vaccine strains to allow them to inhibit WT-virus replication during vaccination via RNA-interference resulting in less WT progeny being available for potential homologous recombination with vaccine strains during these periods, thus reducing the risk of novel strains emerging as a result of widespread routine live-vaccine use. The potential for recombination with circulating WT strains is a major safety concern among regulatory bodies when assessing new live-viral-vaccines, and novel vaccine design strategies that dramatically reduce such risks would represent a significant contribution to the field in terms of safety. The second part of Owen’s idea involves introducing an additional modification to the same same live-attenuated-vaccine strains enabling them to express potent novel RNA-based “molecular-adjuvants” as agonists of innate-immune receptors, improving their intrinsic ability to stimulate the innate immune response leading to increased IFN-I expression and increased tendency towards a Th1-polarized adaptive immune response (i.e. involving both antibody and CD8+ T-Cell adaptive elements). This novel vaccine design strategy has the potential to increase the intrinsic potency of attenuated vaccine strain and thus may potentially allow the use of much lower vaccine doses to achieve the same long-term protection, reducing the production resources required to meet annual market needs. In addition to improving the performance of existing adequately functioning vaccines, this may also potentially be used to improve under-performing vaccine prototypes and may be of particular importance for replication deficient attenuated vaccine strains. The use of such “molecular-adjuvants”  should also eliminate the need to include potentially toxic adjuvants in vaccine formulations, something which has been the focus of some negative attention in recent years. This two-year project will explore this novel vaccine design concept by monitoring the WT-inhibitory and immune-stimulatory effects of these proposed vaccine modifications in-vitro using an existing live-attenuated CyHV-3 vaccine prototype as a test subject. This existing test vaccine was developed by Prof. Alain Vanderplasschen and his team at the Laboratory of Immunology and Vaccinology in the University of Liège, Belgium, a world-renowned vaccine development lab and recent recipients of the prestigious GSK Vaccines Award
This Marie Curie Fellowship will commence in 2018 in conjunction with the Laboratory of Immunology and Vaccinology in the University of Liège, with a view to ultimately using it to drive the establishment of a novel virology and vaccine research group here in AIT, centered on the utilization of this new and innovative viral vaccine design strategy. Vaccine innovation is an important EU priority-research area recognized through the establishment of The Innovation Partnership for a Roadmap on Vaccines in Europe (IPROVE), an initiative tasked with creating a clear vision on how to maintain Europe’s preeminent position as a global leader in vaccine innovation. Accordingly, IPROVE recently launched The Strategic European Roadmap for the Vaccines of Tomorrow which emphasises the need to prioritise research on novel interdisciplinary and rational approaches to vaccine design and the acceleration of research into novel adjuvant systems, underscoreing the importance of continued EU-led research and innovation in this area.

 

Awards and Research Funding

 
  • Moate Community School Science Student of the Year (2004)
  • Marine Institute Research Fellowship (2008)
  • Best Research Poster Presentation, DCU School of Biotechnology Research Day (2011)
  • H2020 funding under SFS-10b-2015 call: Scientific basis and tools for preventing and mitigating farmed mollusc diseases (H2020-SFS-2015-2, Sub Topic SFS-10b-2015) as partner in Vivaldi Research Consortium (2015)
  • Marie Skłodowska Curie Individual Fellowship – (Call H2020-MSCA-IF-2016) (2017)
  • Marine Institute Infrastructure Award, AIT group submission (2017)

Publications

 

Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D (2015) Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS ONE10(4): e0125434. https://doi.org/10.1371/journal.pone.0125434