Auckland Cancer Society Research Centre

Escaping the PARP trap - hypoxia activated prodrugs of talazoparib

Supervisor

Benjamin Dickson
Michael Hay

Discipline

Auckland Cancer Society Research Centre

Project code: MHS058

Talazoparib is the most potent PARP inhibitor currently in clinical development. PARP inhibitors are known to act via a combination of catalytic inhibition and trapping of PARP-DNA complexes; the relative contributions of these mechanisms are still being explored. It has been demonstrated that although talazoparib has similar IC50 values in isolated enzyme assays to other PARP inhibitors, it is significantly more potent in cell culture (100x vs. olaparib). This difference has been attributed to the ability of talazoparib to trap PARP-DNA complexes more efficiently than other PARP inhibitors. Recent research indicates that the trapping mechanism is a double edged blade, along with the increase in potency comes an increase in toxicity. This project aims to explore hypoxia activated prodrugs of talazoparib analogues in order to secure targeted activation of the PARP inhibitor within tumours and thus reduce off-target toxicity.

Students interested in this medicinal chemistry project should have at least second year organic chemistry knowledge (Chem230). The Auckland Cancer Society Research Centre provides a multidisciplinary and collaborative environment.

Opportunities exist for the right candidate to pursue further studies in cancer drug discovery.

Exploring the PARP trap – hybridising PARP inhibitors

Supervisor

Benjamin Dickson
Michael Hay

Discipline

Auckland Cancer Society Research Centre

Project code: MHS059

PARP inhibitors are known to act via a combination of catalytic inhibition and trapping of PARP-DNA complexes; the relative contributions of these mechanisms are still being explored. Of the PARP inhibitors in clinical development talazoparib provides the most potent PARP-DNA trapping. Through hybridisation of talazoparib and olaparib (a PARP inhibitor registered for clinical use) we hope to explore features of binding which may lead to increased PARP trapping.

Students interested in this medicinal chemistry project should have at least second year organic chemistry knowledge (Chem230). The Auckland Cancer Society Research Centre provides a multidisciplinary and collaborative environment.

Opportunities exist for the right candidate to pursue further studies in cancer drug discovery.

Targeting amino acid homeostasis in cancers with oncogenic KRAS mutations

Supervisor

Dr Dean Singleton

Discipline

Auckland Cancer Society Research Centre

Project code: MHS203

Many cancer types develop oncogenic driver mutations in KRAS that activate the RAF-MEK-ERK signalling pathway to drive malignancy. Downstream signalling through this axis promotes a number of biosynthetic changes, particularly amino acid transport and metabolism, to allow cell growth and proliferation. However, these changes in metabolic demand can lead to dependence on a stress regulated transcription factor, ATF4. ATF4 is highly expressed in KRAS mutant cells and acts to maintain levels of protein synthesis, but can also promote apoptosis when severe nutrient limitation occurs. In this project the candidate will assess the therapeutic utility of modulating ATF4 activity using RNAi or small molecule inhibitors/activators of the eIF2a-ATF4 pathway. Effects on growth and survival of KRAS mutant cancer cell lines under conditions of nutrient abundance or depletion will be characterised.

This project will utilise techniques including cell culture, RT-qPCR, western immunoblotting, RNAi, microscopy and drug sensitivity assays.

Understanding CP-506, a new hypoxia-targeted cancer drug

Supervisor

Dr Kevin Hicks
Victoria Jackson-Patel

Discipline

Auckland Cancer Society Research Centre

Project code: MHS168

Regions of low oxygen (tumour hypoxia) are a common feature of cancer. We have developed a new anticancer drug the selectively kills cancer cells at low oxygen. This drug (CP-506) is about to undergo clinical trials. CP-506 releases a cellular cytotoxin that has the potential to diffuse to and kill surrounding cells cancer cells that are at higher oxygen levels (called the “bystander effect”), thus selectively targeting more of the tumour. In this project we will investigate the efficiency of this bystander effect by assessing cell killing in 3-dimensional co-cultures containing CP-506 activating and non-activating (target) cells.

Skills
Skills learned will include cell and tissue culture, drug exposure studies and pharmacology principles, together with an understanding of how anticancer drugs are developed and tumour selective drug targeting. This project could lead to Honours or Masters level research.

Re-educating macrophages towards fighting cancer

Supervisor

Dr Kimiora Henare
Dr Cherie Blenkiron
Professor Lai-Ming Ching

Discipline

Auckland Cancer Society Research Centre

Project code: MHS131

Macrophages are a common feature of the complex tumour microenvironment for many tumour types. Within this niche, cancer cells (and other normal cells caught in the mix) produce a range of signals that encourage macrophages to adopt wound healing and immunosuppressive phenotypes. These innate abilities that macrophages normally use to restore homeostasis (i.e. following injury and infection) are exploited to facilitate tumour growth, immune evasion, metastasis, and resistance to therapy. However, their functional plasticity also means that macrophages can be pharmacologically "re-educated" towards an immune-stimulatory, anti-tumour phenotype.

One such strategy is to trigger stimulator of interferon genes (STING), a cytoplasmic DNA sensor that plays a critical role in the body's defence against DNA viruses and tumour cells. Activation of STING rapidly results in type I interferon signalling and the production of proinflammatory cytokines; many of which are hallmark cytokines of the antitumour macrophage phenotype. We will explore the effects of STING activation on human macrophages at a gene level and examine the potential implications for therapy in the future.

Suitable candidates will learn a range of technical and analytical skills essential to oncoimmunology and genomic medicine; two key areas at the forefront of research into cancer care. Specifically, these include cell culture and in vitro experimentation, gene expression analysis, and bioethics associated with these techniques. The Auckland Cancer Society Research Centre, where the project will be based, provides a multidisciplinary and collaborative environment.

Whole genome CRISPR/Cas9 screens to identify tumour acidity tolerance genes

Supervisor

Dr Tet-Woo Lee
Dr Stephen Jamieson

Discipline

Auckland Cancer Society Research Centre

Project code: MHS086

The tumour microenvironment (TME) is characterised by a low extracellular pH (pHe) due to increased production of lactic acid and poor perfusion, while tumour cells must maintain a neutral to alkaline intracellular pH (pHi) to survive. Genes responsible for survival of tumour cells in an acidic environment may provide molecular targets that can be exploited to develop anti-tumour agents. We are attempting to identify such genes using whole genome CRISPR/Cas9 technology to knock out every gene individually (i.e. one gene per cell) in head and neck cancer cells exposed to low extracellular pH. This project will involve identifying appropriate experimental conditions that allow growth of head and neck cancer cells to be modulated by low extracellular pH. If time permits, a forward genetic screen will be conducted by exposing cells transduced with a CRISPR/Cas9 library to these conditions to identify genes that promote survival under low pHe.

Skills:
Mammalian cell culture including maintenance of cell lines and assays for cell survival; molecular biology techniques

Bioinformatics analysis of whole genome CRISPR/Cas9 knockout screen data

Supervisor

Dr Tet-Woo Lee
Dr Stephen Jamieson
Dr Francis Hunter

Discipline

Auckland Cancer Society Research Centre

Project code: MHS190

We have established the ability within our laboratory to conduct whole genome knockout screens in human cancer cells using CRISPR/Cas9 technology. Using this technology, we have conducted several forward genetic screens to identify genes that may contribute to resistance and sensitivity to various anti-tumour therapeutic agents. Analyses of these datasets have provided many candidate genes that may contribute to anti-cancer drug sensitivity. To maximise our returns from these screens, however, we are looking to conduct more detailed analyses and visualisation of these datasets, and also implement additional analysis tools in our pipeline. As part of this project, the student is expected to gain experience in the analysis and visualisation of large experimental datasets, as well as in contributing to the development of an analysis pipeline for these data.

This project would suit a student who has a background in computer science or bioinformatics and is comfortable working with shell scripts, and programming in R and Python.

Skills gained: Data analysis and visualisation, development of data analysis pipeline, application of computer science to biomedical research
Background required: Shell scripting, programming (particularly R and Python)

PERK up! A cancer drug design project

Supervisor

Lydia Liew
AP Michael Hay

Discipline

Auckland Cancer Society Research Centre

Project code: MHS140

Aims
PERK receptors on the endoplasmic reticulum are involved in a cell's response to stress. The activated PERK pathway produces responses that support the survival of cells under stressful conditions. Tumour cells utilise the PERK pathway to thrive under stressful cellular conditions typical of the tumour microenvironment. We are able to inhibit this survival mechanism by switching-off the PERK receptors in tumour cells. Incidentally, PERK receptors are highly expressed in the pancreas and are essential for normal functioning. We aim to shut-down the PERK pathway in tumours without affecting the normal functioning of PERK in the pancreas.
We are interested in designing novel PERK inhibitors with the necessary properties for tumour-selective prodrug delivery. In this project, you will learn basic research methods and gain experience in the design and synthesis of small drug molecules. The Auckland Cancer Society Research Centre has an international track-record in drug development and you will have the opportunity to participate in a multidisciplinary and collaborative research environment.

Skills
The preferred candidates are self-motivated individuals who are looking to pursue postgraduate research in the near future. Experience working in a chemistry laboratory is essential (minimum CHEM230).

Functional characterization of non-protein coding genes in cancer

Supervisor

Marjan Askarian-Amiri

Discipline

Auckland Cancer Society Research Centre and Molecular Medicine and Pathology

Project code: MHS092

Research proposal
RNAs were long thought to act mainly as carriers of genetic information between DNA and the protein-synthesising machinery of the cell. Recent whole genome sequencing technology has demonstrated that protein coding open reading frames comprise only about 1.2% of the human genome. On the other hand, 70-90% of the genome is transcribed as non-protein coding RNA (ncRNA). Initially regarded as ‘junk’, these transcripts have been found to possess many regulatory roles and represent a largely unexplored area of cell biology.
Recent studies have revealed that the RNAs transcribed in cell are replete with long ncRNAs (lncRNAs), which have similar structure to mRNA. The emerging role of lncRNAs in different aspects of biology provides encouragement for further studies on their roles in normal cell development and disease.
The major goal of our research group is to investigate functional roles of selected number of lncRNAs in different cancer. Here several projects are proposed, however the selected student will work on one project based his/her interest.
Proposed projects are:
1. Functional analysis of ribosome bound lncRNA (Hansji, et al., 2016).
2. Investigation in functional role of circular RNA in cancer progression (Sarkar, et al., 2017)
3. Identify and functionally characterise lncRNAs (either linear or circular) secreted from cancer cell and use them as potential biomarker (Yin, etal., 2017; Bayoumi, et al., 2018; Li et al., 2015).
4. Identify circular RNA derived from translocated gene in solid tumour and leukaemia (Guarnerio, et al., 2015).

If you are interested to any of the proposed project, please contact me before 27 July to discuss the further details.

Skills
The project involves application of basic molecular biology techniques including mammalian cell culture, RNA and DNA extraction, cloning techniques, PCR and reverse transcription (RT) followed by PCR, quantitative RT-PCR as well as isolation of extra cellular vesicle. These techniques will provide the candidate great basic skills required for performing experiments in molecular biology laboratories.

Reference:
Bayoumi AS, Aonuma T, Teoh JP, Tang YL, and Kim IM1. (2018) Circular noncoding RNAs as potential therapies and circulating biomarkers for cardiovascular diseases, Acta Pharmacol Sin.

Guarnerio, J., Bezzi, M., Jeong, J. C., Paffenholz, S. V., Berry, K., Naldini, M. M., Lo-Coco, F., Tay, Y., Beck, A. H., and Pandolfi, P. P. (2016) Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations, Cell 166, 1055-1056.

Hansji, H., Leung, E. Y., Baguley, B. C., Finlay, G. J., Cameron-Smith, D., Figueiredo, V. C., and Askarian-Amiri, M. E. (2016) ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells, Biol Direct 11, 62.

Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J, Chen D, Gu J, He X, and S., H. (2015) Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis, Cell Res. 25, 981-984.

Sarkar, D., Oghabian, A., Bodiyabadu, P. K., Joseph, W. R., Leung, E. Y., Finlay, G. J., Baguley, B. C., and Askarian-Amiri, M. E. (2017) Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing, Int J Mol Sci 18.

Yin WB, Yan MG, Fang X, Guo JJ, Xiong W, and RP., Z. (2017) Circulating circular RNA hsa_circ_0001785 acts as a diagnostic biomarker for breast cancer detection., Clin Chim Acta. pii: S0009-8981, 30407-30402.

Death by a thousand cuts: Drugging the DNA damage response

Supervisor

Michael Hay
Lydia Liew

Discipline

Auckland Cancer Society Research Centre

Project code: MHS117

Cancer cells use DNA repair mechanisms to escape the full effects of cytotoxic chemotherapy and radiotherapy. DNA-Protein Kinase (DNA-PK) plays a crucial role in repairing DNA damage caused by radiotherapy and some chemotherapy drugs. Consequently, DNA-PK represents a new drug target where inhibition will potentiate cytotoxic therapy. Currently, there are few selective inhibitors of this enzyme or strategies for their selective delivery to tumours. The discovery of new selective inhibitors of DNA-PK would be a dramatic innovation with potential to impact on current cancer treatment.
This project will explore novel pharmacophore models to design, synthesize and evaluate new inhibitors of DNA-PK.
The Auckland Cancer Society Research Centre provides an exciting, multidisciplinary and collaborative environment. The preferred candidate will be a high achiever with synthetic chemistry experience and ambitions to pursue a career in cutting edge drug discovery.
Skills
Medicinal chemistry
Drug design

Organelle selective fluorescent probes for studying cancer cell lines

Supervisor

Peter Choi
Jiney Jose

Discipline

Auckland Cancer Society Research Centre

Project code: MHS124

Organelle selective fluorescent probes are useful tools for delineating functional and morphological changes of various organelles, especially in a diseased state.1
There is a growing need for development of organelle selective fluorescent probes in the near infrared region (700-1000 nm) for studying disease initiation at a cellular level. With our group’s recent success in synthesising mitochondria selective near infrared emitting fluorescent dye with a heptamethine cyanine scaffold,2 this project will aim to synthesize analogues of such class to selectively target mitochondria.
This is a medicinal chemistry project with emphasis on synthetic organic chemistry. Prospective students should have experience with chemistry papers CHEM230 and CHEM330 (preferred).

References:
1. Jose, J.; Loudet, A.; Ueno, Y.; Barhoumi, R.; Burghardt, R. C.; Burgess, K., Org. Biomol. Chem. 2010, 8, 2052-2059.
2. Choi, P.; Noguchi, K.; Ishiyama, M.; Denny, W. A.; Jose, J., Bioorg Med Chem Lett 2018, 28, 2013-2017.