Dr Augustine Chen
My current research focus involves the co-development of a transformative diagnostic test using Next-Generation Sequencing (NGS) with applications in medical, agriculture and environmental sensing sectors. This innovation has attracted pre-seed funding to undertake proof-of-concept experiments towards multimodal signal detection (genetic and epigenetic changes) in circulating tumour DNA. Through minor modification, this test could also be expanded to include other sample types in non-medical sectors and I am currently pursuing collaborations towards such applications.
My speciality has always centred around developing, using or combining existing and emerging methodologies to answer a variety of research questions. This included technical expertise utilising
Next Generation Sequencing, high-throughput imaging and drug screening assays, siRNA and miRNA delivery, mouse necropsy as well as standard molecular biology and cell culture techniques.
To date, I have undertaken a range of biomedical research, investigating various aspects of gene regulation in human diseases such as cancer and virus infection (HBV, HPV and norovirus). Such approaches have enabled the identification of disease states and targetable vulnerabilities and has led to the discovery of putative therapeutic drugs (which led to a provisional patent filing) and the development of a diagnostic test for a NZ company (which attracted joint funding from the Ministry of Science and Innovation Technology Transfer Voucher Scheme).
Growing up in Malaysia
Augustine grew up in Malaysia, he always liked biology and was just curious about things around him. His Dad was a nurse and became a trainer for medical assistants and then principal of a training school. Medical assistants were hugely valued in Malaysia due to the shortage of doctors. Based in a rural setting Augustine was able to visit his Dad at work and just look around. An ideal environment to spark an interest in biology.
Outside the lab Augustine likes fly fishing, socialising with family and friends, and gardening.
Publications
Hannah, S. J., Chen, A., Day, R. C., & Black, M. A. (2022). Improvising read accuracy for ctDNA diagnostics. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Conference Contribution - Published proceedings: Abstract
Clarke, R. M., Hess, A., Caulton, A., Brauning, R., McRae, K., Chen, A., & Clarke, S. (2022, August). Simultaneous investigation of genomic regions of interest: The use of adaptive sampling. Poster session presented at the Applied Genetics/Genomics in Breeding Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Conference Contribution - Poster Presentation (not in published proceedings)
Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461
Journal - Research Article
Bougen-Zhukov, N., Nouri, Y., Godwin, T., Taylor, M., Hakkaart, C., Single, A., Brew, T., Permina, E., Chen, A., Black, M. A., & Guilford, P. (2019). Allosteric AKT inhibitors target synthetic lethal vulnerabilities in E-cadherin-deficient cells. Cancers, 11(9), 1359. doi: 10.3390/cancers11091359
Journal - Research Article
Beetham, H., Chen, A., Telford, B. J., Single, A., Jarman, K. E., Lackovic, K., … Guilford, P. (2019). A high-throughput screen to identify novel synthetic lethal compounds for the treatment of E-cadherin-deficient cells. Scientific Reports, 9, 12511. doi: 10.1038/s41598-019-48929-0
Journal - Research Article
Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461
Journal - Research Article
Beetham, H., Chen, A., Telford, B. J., Single, A., Jarman, K. E., Lackovic, K., … Guilford, P. (2019). A high-throughput screen to identify novel synthetic lethal compounds for the treatment of E-cadherin-deficient cells. Scientific Reports, 9, 12511. doi: 10.1038/s41598-019-48929-0
Journal - Research Article
Bougen-Zhukov, N., Nouri, Y., Godwin, T., Taylor, M., Hakkaart, C., Single, A., Brew, T., Permina, E., Chen, A., Black, M. A., & Guilford, P. (2019). Allosteric AKT inhibitors target synthetic lethal vulnerabilities in E-cadherin-deficient cells. Cancers, 11(9), 1359. doi: 10.3390/cancers11091359
Journal - Research Article
Godwin, T. D., Kelly, S. T., Brew, T. P., Bougen-Zhukov, N. M., Single, A. B., Chen, A., Stylianou, C. E., … Currie, S. K., Telford, B. J., Beetham, H. G., … Black, M. A., & Guilford, P. J. (2019). E-cadherin-deficient cells have synthetic lethal vulnerabilities in plasma membrane organisation, dynamics and function. Gastric Cancer, 22(2), 273-286. doi: 10.1007/s10120-018-0859-1
Journal - Research Article
Single, A., Beetham, H., Telford, B. J., Guilford, P., & Chen, A. (2015). A comparison of real-time and endpoint cell viability assays for improved synthetic lethal drug validation. Journal of Biomolecular Screening, 20(10), 1286-1293. doi: 10.1177/1087057115605765
Journal - Research Article
Telford, B. J., Chen, A., Beetham, H., Frick, J., Brew, T. P., Gould, C. M., Single, A., Godwin, T., … Guilford, P. (2015). Synthetic lethal screens identify vulnerabilities in GPCR signalling and cytoskeletal organization in E-cadherin-deficient cells. Molecular Cancer Therapeutics, 14(5), 1213-1223. doi: 10.1158/1535-7163.mct-14-1092
Journal - Research Article
Chen, A., Beetham, H., Black, M. A., Priya, R., Telford, B. J., Guest, J., Wiggins, G. A. R., Godwin, T. D., … Guilford, P. J. (2014). E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition. BMC Cancer, 14, 552. doi: 10.1186/1471-2407-14-552
Journal - Research Article
Chen, A., T-Thienprasert, N. P., & Brown, C. M. (2014). Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus. World Journal of Gastroenterology, 20(25), 7993-8004. doi: 10.3748/wjg.v20.i25.7993
Journal - Research Article
Waugh, E., Chen, A., Baird, M. A., Brown, C. M., & Ward, V. K. (2014). Characterization of the chemokine response of RAW264.7 cells to infection by murine norovirus. Virus Research, 181, 27-34. doi: 10.1016/j.virusres.2013.12.025
Journal - Research Article
Chen, A., & Brown, C. (2012). Distinct families of cis-acting RNA replication epsilon elements from hepatitis B viruses. RNA Biology, 9(2), 130-136. doi: 10.4161/rna.18649
Journal - Research Article
Jacobs, G. H., Chen, A., Stevens, S. G., Stockwell, P. A., Black, M. A., Tate, W. P., & Brown, C. M. (2009). Transterm: A database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Research, 37(Database issue), D72-D76. doi: 10.1093/nar/gkn763
Journal - Research Article
Chen, A., Kao, Y. F., & Brown, C. M. (2005). Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons. Nucleic Acids Research, 33(4), 1169-1181.
Journal - Research Article
Chen, A., Grigor, M. R., Thompson, C. M., & Harris, E. L. (1997). Kallikrein binding protein (KBP) maps to rat Chromosome 6 but does not cosegregate with blood pressure in a GH x BN cross. Mammalian Genome, 8(9), 701-703.
Journal - Research Article
Hannah, S. J., Chen, A., Day, R. C., & Black, M. A. (2022). Improvising read accuracy for ctDNA diagnostics. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Conference Contribution - Published proceedings: Abstract
Guilford, P. J., Chen, A., Telford, B., Single, A., Beetham, H., & Godwin, T. (2017). Synthetic lethal targeting of E-cadherin-deficient cancers. Clinical Cancer Research, 23(1, Suppl.), B04. doi: 10.1158/1557-3265.PMCCAVULN16-B04
Conference Contribution - Published proceedings: Abstract
Single, A., Chen, A., Telford, B., Beetham, H., & Guilford, P. (2017). Statins show synthetic lethality in E-cadherin-deficient cells and are synergistic with SRC and HDAC inhibitors. Clinical Cancer Research, 23(1, Suppl. ), B41. doi: 10.1158/1557-3265.PMCCAVULN16-B41
Conference Contribution - Published proceedings: Abstract
Chen, A., Telford, B. J., Single, A., Beetham, H., Simpson, K. J., & Guilford, P. J. (2016). Synthetic lethal approaches targeting E-cadherin-deficient cancers. Cancer Research, 76(14, Suppl.), 3814. doi: 10.1158/1538-7445.AM2016-3814
Conference Contribution - Published proceedings: Abstract
Beetham, H., Chen, A., Jarman, K. E., Falk, H., & Guilford, P. J. (2015). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Proceedings of the Diagnostic Drug Device Discovery (D4) Conference. Retrieved from https://www.regonline.com.au/builder/site/Default.aspx?EventID=1758070
Conference Contribution - Published proceedings: Abstract
Chen, A., Telford, B., Beetham, H., Single, A., Godwin, T., & Guilford, P. (2013). Synthetic lethal interactions with the tumour suppressor protein E-cadherin. Proceedings of the New Zealand Society for Oncology (NZSO) Conference. Retrieved from http://www.nzsoncology.org.nz/conference_2013
Conference Contribution - Published proceedings: Abstract
Single, A., Chen, A., Telford, B., & Guilford, P. (2013). Synthetic lethal interactions for the treatment of E-cadherin negative tumours. New Zealand Medical Journal, 126(1374). Retrieved from http://www.nzma.org.nz/journal
Conference Contribution - Published proceedings: Abstract
Brown, C. M., Wilkinson, T., Panjaworayan, N., Firth, A. E., Chen, A., Stevens, S. G., Wong, A., Black, M., … Roessner, S. K. (2009). Analysis of virus and human genome sequences for RNA regulatory elements. Proceedings of the Webster Centre for Infectious Diseases Symposium. WCID. Retrieved from http://www.webstercentre.otago.ac.nz/WCIDSymposiumProgramme.pdf
Conference Contribution - Published proceedings: Abstract
Panjaworayan, N., Rackham, O., Chen, A., Kao, A. Y.-F., & Brown, C. M. (2005). Post-transcriptional regulation of gene expression in hepatitis B virus. Proceedings of the Meeting on the Molecular Biology of Hepatitis B Viruses. (pp. 30). Heidelberg, Germany. [Abstract]
Conference Contribution - Published proceedings: Abstract
Clarke, R. M., Hess, A., Caulton, A., Brauning, R., McRae, K., Chen, A., & Clarke, S. (2022, August). Simultaneous investigation of genomic regions of interest: The use of adaptive sampling. Poster session presented at the Applied Genetics/Genomics in Breeding Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Conference Contribution - Poster Presentation (not in published proceedings)
Beetham, H., Chen, A., Single, A., Telford, B. J., & Guilford, P. J. (2015, August-September). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Poster Presentation (not in published proceedings)
Beetham, H., Chen, A., Single, A., Telford, B., & Guilford, P. (2015, October). The discovery of novel synthetic lethal compounds for the treatment of E-cadherin deficient tumours. Poster session presented at the Otago Spotlight Series: Cancer Research, Wellington, New Zealand.
Conference Contribution - Poster Presentation (not in published proceedings)