ATF3 Repression of BCL-XL Determines Apoptotic Sensitivity to HDAC Inhibitors across Tumor Types.
Chüeh, A.C., Janson, W.T., Dickinson, M., Ioannidis, P., Jenkins, L., Tögel, L., Tan, B., Luk, I., Dávalos-Salas, M., Nightingale, R. et al., 2017.
Clinical cancer research, 23(18), pp.5573–5584. (6 citations)
Histone deacetylase inhibitors (HDACi) are one of earliest first-in-class epigenome-targeting small molecules that are clinically approved for the treatment of cancer. Clinical activity was established in several hematological malignancies (such as cutaneous T-cell lymphoma) but was somewhat limited in solid tumours with the exception of breast and lung cancers. This latest first-author paper of mine summarizes a 5-year comprehensive study that identifies a novel transcriptional axis by which HDACi induce apoptosis in tumor cells through induction of the ATF3 transcription factor and subsequent repression of pro-survival BCL-xL protein. This mechanism transcends tumor type, is measurable in patient samples in vivo, and defines the basis for sensitivity or resistance to HDACi. These findings establish a strategy for overcoming inherent resistance to HDACi by rational combination with BCL-xL inhibitors, and define a framework for the identification of biomarkers predictive of HDACi response, including rapid assessment of ATF3 induction.
Promoter hypomethylation of NY-ESO-1, association with clinicopathological features and PD-L1 expression in non-small cell lung cancer.
Chüeh, A.C., Liew, M.-S., Russell, P.A., Walkiewicz, M., Jayachandran, A., Starmans, M.H.W., Boutros, P.C., Wright, G., Barnett, S.A., Mariadason, J.M. and John, T., 2017. Oncotarget, 8(43), pp.74036–74048. (0 citations)
Cancer-testis (CT) antigens are immunogenic molecules with normal tissue expression restricted to testes but with aberrant expression in up to 30% of lung cancers and other tumour types. These CT antigens are attractive therapeutic targets for cancer vaccine development. Cancer vaccines targeting CT antigen NY-ESO-1 and MAGE-A3 are undergoing active development in CSL and GSK respectively. Here in this recent first-author paper of mine identified a novel mechanism by which normal cells utilized promoter methylation as means to induce epigenetic silencing of NY-ESO-1. In lung cancer cells and tumour tissues, NY-ESO-1 promoter hypomethylation was evident and highly correlated with the re-expression of NY-ESO-1 in both mRNA and protein level. A quantitative methylation detection methodology and associated biomarker was developed for NY-ESO-1 that accurately predicted NY-ESO-1 expression in tumour cells and patient samples. These results provided a novel predictive biomarker for identifying NY-ESO-1 positive tumours and have direct implications in the clinical development of NY-ESO-1 targeting cancer vaccine. We have also demonstrated that DNA methyltransferase inhibitor (DNMTi) 5-azacytidine can be used to induce NY-ESO-1 hypomethylation and re-expression, as well as PD-L1 re-expression in lung cancer cells, which is identified as a novel combinational strategy to boost cancer immunotherapy response.
Variable and hierarchical size distribution of L1-retroelement-enriched CENP-A clusters within a functional human neocentromere.
Chüeh, A.C., Wong, L.H., Wong, N. and Choo, K.H.A., 2005.
Human molecular genetics, 14(1), pp.85–93. (60 citations)
The centromere complex was first identified in 1880s by Walter Fleming as the primary constriction on human chromosomes that is essential for proper chromosome segregation and cell division. The precise mechanism underlying the mitotic stability and faithful inheritance of the centromere loci has been a century old unresolved mystery, especially when comparative genomics identified stable inheritance of centromere with rapidly evolving centromere associated DNA throughout eukaryote evolution in early 1990s. Seminal discoveries made by KH Andy Choo and his teams in 1990s identified a new form of centromeres (i.e. neocentromeres) that are assembled epigenetically at ectopic chromosomal regions without the presence of canonical human centromere-associated alpha satellite DNA. Here in this first-author paper of mine, together with other co-authors, I developed a novel technology where high-resolution genomic tiling PCR-fragment microarray was assembled in-house and coupled with chromatin immunoprecipitations (ChIP) to map human neocentromere chromatin structures as part of my PhD study. Importantly, our technology was developed prior Affymetrix entering Australian diagnostics market and provided a >20-fold increase in mapping resolution compared to traditional bacterial artificial chromosome (BAC) arrays. This was the first study to use such genomics technology to precisely elucidate the complete structural domain of centromere-associated histones (i.e. CENP-A) along a functional human centromere. We were the first to make the observation that the human neocentromere chromatin is structured to contain the interspersion of CENP-A and histone H3 nucleosomal blocks. These results formed the basis of a well-recognised 3D model of chromatin folding at human centromeres, which is cited as a key reference in centromere biology section of the famous ‘Epigenetics’ textbook written by David Allis, Thomas Jenuwein and Danny Reinberg (Cold Spring Harbor Laboratory Press, 2007).
LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin.
Chüeh, A.C., Northrop, E.L., Brettingham-Moore, K.H., Choo, K.H.A. and Wong, L.H., 2009.
PLoS genetics, 5(1), p.e1000354. (115 citations)
The identity of centromere was determined epigenetically by the deposition of CENP-A nucleosomes. This mechanism is conserved among eukaryotic species throughout evolution and only realized in early 2000s. However, the key components of the epigenetic machinery that contribute to the deposition of CENP-A nucleosomes at centromeres was largely uncharacterized. Here in this first-author paper of mine, we used a fully functional human neocentromere as the model system to study the epigenetic mechanisms by which centromere are formed. We were the first in the world to identify LINE-1 retrotransposon RNA as an essential structural and functional component of human neocentromere chromatin, and that retrotransposable elements serve as a critical epigenetic determinants in the chromatin remodelling events that lead to neocentromere formation. Importantly, this study described for the first time in the literature that RNAi-mediated knockdown of a single retrotransposon in human cells can be achieved using the novel methodology that I developed. This is significant undertaking that has not been previously documented prior to this study. This work attracted 115 citations and I was invited to make an oral presentation at the prestigious Keystone Conference in Cancer Genomics and Epigenomics in 2008 in Taos, New Mexico, USA.
Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution.
Marshall, O.J.#, Chüeh, A.C.#, Wong, L.H. and Choo, K.H.A., 2008.
American journal of human genetics, 82(2), pp.261–282. (# equal contribution) (263 citations)
This is a joint-first paper of mine that nicely summarized and reviewed our insights into centromere structure, disease development, and karyotype evolution based the collective findings of our group and others on neocentromere biology since the first discovery in 1993. This a highly-cited comprehensive review article that discussed the mechanism of epigenetic regulation of centromere identity, which is one of the central theme in the field of human genetics. This article has been cited 263 times despite being a very specialized topic of interest. Being one of the highest cited reviews on centromere biology, this work provided the foundation for future work on the centromere epigenetics and has been considered a landmark paper in the respective field.
Mechanisms of Histone Deacetylase Inhibitor-Regulated Gene Expression in Cancer Cells.
Chüeh, A.C., Tse, J.W.T., Tögel, L. and Mariadason, J.M., 2015.
Antioxidants & redox signaling, 23(1), pp.66–84. (27 citations)
Histone deacetylase inhibitors (HDACi) are one of earliest first-in-class epigenome-targeting small molecules that are clinically approved for the treatment of cancer. However, the mechanistic basis for how HDACi activate, and in particular repress gene expression, is not well understood. In addition, whether subsets of genes are reproducibly regulated by these agents both within and across tumor types has not been systematically addressed. Here in this first-author paper of mine, we provide a comprehensive review of a detailed understanding of the transcriptional changes elicited by HDACi in various tumor types, and the mechanistic basis for these effects, which may in term provide further insights into the specificity of these drugs for transformed cells and specific tumor types. These knowledge could inform the design of rational drug combinations involving HDACi, and facilitate the identification of mechanism-based biomarkers of response.
BAC-based PCR fragment microarray: high-resolution detection of chromosomal deletion and duplication breakpoints.
Ren, H., Francis, W., Boys, A., Chüeh, A.C., Wong, N., La, P., Wong, L.H., Ryan, J., Slater, H.R. and Choo, K.H.A., 2005.
Human mutation, 25(5), pp.476–482. (38 citations)
This study was one of the earliest studies to describe the use of a high-resolution PCR-fragment array comparative genomic hybridization (CGH) platform to map chromosomal deletion and duplication breakpoints in humans. The first-author of this paper was a medical scientist developing tools to identify chromosomal deletions and duplication breakpoints, as part of the Victorian Clinical Genetics Services (VCGS)’s investment in molecular cytogenetics. As part of my PhD, I developed a high-resolution PCR-fragment array methodology for my investigation on centromere structures. The first-author and I worked together to transform my technology to a 2-colour microarray platform and applied it to clinical patient samples for the detection of chromosomal deletion and duplication breakpoints. This is a significant advancement in molecular cytogenetics that achieved a 10-40X increase in mapping resolution compared to BAC-based array CGH (where as little as 5-20 kb deletion could be identified). Imporantly, this technology was transferred to VCGS and was in routine use in the molecular cytogenetics laboratory until it was replaced by the Affymetrix aCGH platform when it entered Australian market.
A beacon of hope in stroke therapy—Blockade of pathologically activated cellular events in excitotoxic neuronal death as potential neuroprotective strategies.
Hoque, A., Hossain, M.I., Ameen, S.S., Ang, C.-S., Williamson, N., Ng, D.C., Chüeh, A.C., Roulston, C. and Cheng, H.-C., 2016. Pharmacology and Therapeutics, 160, pp.159–179. (15 citations)
This is a comprehensive review that summarized the current understandings on key cellular events directing neuronal death in the neurotoxic signaling pathways and identified potential targets for the development of neuroprotectant therapeutics. We provided updates on promising small molecules that have been developed to protect neuronal death and discussed their precise mechanism of actions. The involvement of epigenetic regulators REST and LSD1 have recently attracted much attention when it comes to the neuronal death pathways. I was invited as the drug development expert by the senior author to contribute the section on the potential strategy to target the epigenetic regulators as means to provide neuroprotection and reduce stroke-induced clinical brain damage.
Apoptotic sensitivity of colon cancer cells to histone deacetylase inhibitors is mediated by an Sp1/Sp3-activated transcriptional program involving immediate-early gene induction.
Wilson, A.J., Chüeh, A.C., Tögel, L., Corner, G.A., Ahmed, N., Goel, S., Byun, D.-S., Nasser, S., Houston, M.A., Jhawer, M. et al., 2010. Cancer research, 70(2), pp.609–620. (79 citations)
This study identifies a subset of genes selectively induced by HDACi in colorectal cancer cell lines that are sensitive to these drugs. Using a large panel of 30 colorectal cancer cell lines that encompasses different genetic mutations, we identified a novel Sp1-regulated gene-signature that associates with HDACi-mediated apoptotic response. This paper was highly cited (79 citations) because it is earliest report where systematic approach was taken to study HDACi induced apoptotic sensitivity in a single disease. The findings was consistent and reproducible among all multiple HDACi known at the time. The identified gene-signature in cell line was linked to observed HDACi mediated in vivo response in mouse model and patient samples.
Molecular imaging of death receptor 5 occupancy and saturation kinetics in vivo by humanized monoclonal antibody CS-1008.
Burvenich, I.J.G., Lee, F.T., Cartwright, G.A., O'Keefe, G.J., Makris, D., Cao, D., Gong, S., Chüeh, A.C., Mariadason, J.M., Brechbiel, M.W., Beckman, R.A., Fujiwara, K., Roemeling, von, R. and Scott, A.M., 2013.
Clinical cancer research, 19(21), pp.5984–5993. (12 citations)
This is a recent translational cancer research study that describe a novel molecular imaging technique that can be used to determine receptor occupancy and the effective dose level of an antibody that acts as an agonist for the death receptor 5 (DR5) protein. I collaborated with the first-author and guided the choice of cell lines and contributed to the design, experimentation of the cell-based assays including apoptosis detection and in vitro growth rate estimation. These findings will help inform the design of a clinical trial involving this antibody.
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