CSI Singapore congratulates our PhD graduate students and staff for receiving several awards during the 3rd NCIS Annual Research Meeting (NCAM) 2016. This conference, co-organised by National University Cancer Institute, Singapore (NCIS) and CSI Singapore, was held on 1st July 2016 at National University Health System, Singapore. This annual meeting is a full day program attended by participants with varied scientific backgrounds.
This event showcases excellent cancer research by local investigators and provide an excellent platform to develop need collaborations.
BASIC SCIENCE
Leong Wei Zhong
Best Oral Presentation
Oncogenic Role of ARID5B in the Molecular Pathogenesis of T-Cell Acute Lymphoblastic Leukemia
T-cell acute lymphoblastic leukemia (T-ALL) is a malignant disorder characterized by the clonal proliferation of T-cell precursors. It accounts for approximately 15% and 25% of all childhood and adult ALL cases, respectively. The most frequent molecular abnormality in T-ALL is the dysregulation of transcription factor genes, including the overexpression of TAL1/SCL that is found in 40-60% of T-ALL cases. However, the oncogenic mechanisms controlled by TAL1, in particular, downstream targets and their roles in T-ALL pathogenesis are largely unknown. Here we report that TAL1 and its regulatory partners (GATA3 and RUNX1) directly regulate the ARID5B gene, which is one of members of the ARID family protein. Knockdown of TAL1 resulted in downregulation of ARID5B protein. mRNA and protein expressions of ARID5B were positively correlated with TAL1 expression among T-ALL cell samples examined. Importantly, knockdown of ARID5B inhibited cell growth and induced apoptosis in TAL1-positive T-ALL cell lines, showing requirement of this protein in T-ALL pathogenesis. Microarray analysis revealed that ARID5B regulates genes involved in T-cell homeostasis and hematopoietic cell function as well as many genes that are directly controlled by TAL1. Chromatin immunoprecipitation with DNA sequencing (ChIP-seq) analysis revealed that ARID5B frequently co-occupies enhancer regions of target genes with the TAL1 complex in T-ALL cells. Consequently, ARID5B positively regulates the major components of the TAL1 complex (TAL1, GATA3 and RUNX1) as well as the MYC oncogene. Zebrafish transgenic study showed that overexpression of the human ARID5B gene in thymus could induce T-cell lymphoma albeit with low penetrance. Taken together, our results indicate that ARID5B reinforces oncogenic transcriptional program in T-ALL cells by positively regulating the oncogenic transcription factors, thereby promoting T-cell leukemogenesis.
Patrick Jaynes
Best Oral Presentation (Runner-up)
Loss of OTUD4 Impairs TGF? Signaling and Confers Poorer Overall Survival in Luminal A Breast Cancer
The Transforming Growth Factor ? (TGF?) pathway plays an important role in development and adult tissue homeostasis. TGF? has been shown to regulate proliferation, differentiation, cell survival, migration, and adhesion. We have identified a deubiquitinating enzyme, OTU, as being a potent modulator of this pathway. Furthermore, we have subsequently found that OTU is able to deubiquitinate SMAD7. SMAD7 is critical for the recruitment of E3 ligase SMURF2 to the TGF? receptor complex resulting in receptor degradation and the consequent inhibition of signaling. Interestingly, OTU is able to induce stabilization of SMURF2 though this appears to correlate with the reduced function of the latter. As OTU is able to deubiquitinate SMAD7, it is possible that this results in the disruption of the functional relationship between SMAD7 and SMURF2, promoting the activation of the TGF? pathway. TGF? has well known tumour suppressor properties. In relation to this, a bioinformatic meta-analysis demonstrates that low expression of OTU correlates with poorer overall survival in luminal A breast cancer. Our results demonstrate that OTU can regulate the TGF? pathway and is potentially a key determinant in breast cancer pathogenesis.
Dr Avinash Bahirvani
Best Poster Award
Highly Efficient Runx1 Enhancer Er1-Mediated Genetic Engineering for Hematopoietic Stem Cells and Leukemogenesis
A cis–regulatory genetic element which targets gene expression to stem cells, termed stem cell enhancer, serves as a molecular handle for stem cell-specific genetic engineering. Here we show the generation and characterization of a tamoxifen (TM)-inducible CreERT2 transgenic (Tg) mouse employing previously identified hematopoietic stem cell (HSC) enhancer for Runx1, eR1 (+24m). Kinetics analysis of labeled cells after TM injection and transplantation assays revealed that eR1-driven CreERT2 activity marks dormant adult HSCs which slowly but steadily contribute to unperturbed hematopoiesis. Fetal and child HSCs which are uniformly or intermediately active were also efficiently targeted. Notably, a gene ablation at distinct developmental stages, enabled by this system, resulted in different phenotypes. Similarly, an oncogenic Kras induction at distinct ages caused different spectrums of malignant diseases. These results demonstrate that the eR1-CreERT2 Tg mouse serves as a powerful resource for the analyses of both normal and malignant HSCs at all developmental stages.
Dr Fang Yiwen
Best Poster Award (Runner-up)
The 3-dimensional Genome Organization of Super-Enhancers and Target Genes
Abstract – Super-enhancers are characterized by extensive large regions with dense H3K27Ac marks, and previously have been associated with key oncogenes. To investigate long-range super-enhancer looping to target genes, we connected super-enhancers in the K562 Chronic Myelogenous Leukemia cell line with chromatin interactions identified from Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data. Super-enhancers are more highly associated with chromatin interactions than typical enhancers, and super-enhancers can connect with multiple gene promoters. Surprisingly, super-enhancers can loop to tumor suppressor genes as well as oncogenes. Super-enhancers overlap with broad H3K4me3 peaks, which associate with tumor suppressor genes. Besides K562, we could observe such chromatin interactions by EpiSwitchTM, a Chromosome Conformation Capture (3C)-based method, in primary human samples. Taken together, these results reveal a new layer of complexity in gene regulation by super-enhancers, particularly in the control of tumor suppressor genes and oncogenes by super-enhancers in cancer.
TRANSLATIONAL SCIENCE
Dr Liu Bee Hui
Best Oral Presentation
Structure Guided Design of a Therapeutic Inhibitor of SALL4 Positive Liver Cancer
BACKGROUND: SALL4 is a nuclear factor central to the maintenance of stem cell pluripotency. It is specifically expressed in fetal cells, absent in adult tissues but is re-activated in cancers associated with poor prognosis. Activation of SALL4 was recently described as a key component driving up to 55% of hepatocellular carcinoma (HCC), a malignancy with no suitable treatment regime. In cancer cells, SALL4 recruits remodelling complex NuRD to PTEN promoter, resulting in transcriptional repression. This SALL4–NuRD interaction offers an intriguing therapeutic target for HCC. RESULTS: Here, we report the development of a potent anti-tumor therapeutic peptide (FFW) based on our elucidation of the crystal structure of SALL4-RBBp4 complex at 2.7Å. The crystal complex reveal a large binding groove suitable for the development of peptide as therapeutic agent, where we subsequently design over 40 peptides using systematic truncation and amino acid substitution studies. The final FFW peptide has 56- fold increase in binding affinity compared to wild-type, and exhibits superior anti-proliferative effect in SALL4+ HCC cells, where it conferred a 4-fold improvement in cell viability. It also exhibits potent anti-tumor activity in HCC xenograft mouse models (tumor growth inhibition 85%), supporting FFW as a highly viable drug candidate. CONCLUSION: FFW peptide could potentially fulfill the unmet need in liver cancer and other malignancies characterized by SALL4 expression. This report also highlights an effective strategy to accurately design a therapeutic approach against candidate genes that are otherwise considered undruggable.
Mr Azad Saei
Best Oral Presentation (Runner-up)
Loss of USP28 Mediated BRAF Degradation Drives Resistance to RAF Cancer Therapies
Evidences indicate that nearly 50% of melanoma patients have somatic mutations in BRAF with the majority of these pertaining to a single hotspot BRAF V600E, which results in hyperactivation of MAPK pathway. As such, various inhibitors which target mutant BRAF have been developed including vemurafenib and dabrafenib both of which have demonstrated significant clinical outcomes. Nevertheless overall patient responses are limited by both primary and acquired resistance. So the search of a suitable and efficient treatment in the drug resistant melanoma patients has become an imperative subject of research. The mechanism of ubiquitination in controlling various functions such as stabilization of a protein cannot be neglected. In order to investigate the role of deubiquitinating enzymes (DUBs) in MAPK signaling, we performed an RNAi screen using a shRNA library targeting all known human DUBs. Interestingly, USP has been reported to be deleted in a 10% of melanoma patients. We demonstrate that loss of USP in melanoma cell lines stabilizes BRAF resulting in vemurafenib resistance. Taken together our results identify USP as a novel biomarker for vemurafenib resistance in BRAF600E mutant melanoma.
Dr Tim Chan Hon Man
Best Oral Presentation (Runner-up)
ADAR-Mediated RNA Editing Predicts Progression and Prognosis Of Gastric Cancer
BACKGROUD AND AIMS: Gastric cancer (GC) is the third leading cause of global cancer mortality. Adenosine-to-Inosine (A-to-I) RNA editing is a recently-described novel epigenetic mechanism involving sequence alterations at the RNA but not DNA level, primarily mediated by ADAR enzymes (Adenosine DeAminase that act on RNA). Emerging evidence suggests a role for RNA editing and ADARs in cancer, however the relation between RNA editing and GC development and progression remains unknown. RESULTS: Relative to normal gastric tissues, almost all GCs displayed a clear RNA misediting phenotype with ADAR1/2 dysregulation, arising from the genomic gain and loss of the ADAR1 and ADAR2 gene in primary GCs, respectively. Clinically, patients with GCs exhibiting ADAR1/2 imbalance demonstrated extremely poor prognoses in multiple independent cohorts. Functionally, we demonstrate in vitro and in vivo that ADAR-mediated RNA misediting is closely associated with GC pathogenesis, with ADAR1 and ADAR2 playing reciprocal oncogenic and tumor suppressive roles through their catalytic deaminase domains, respectively. Using an exemplary target gene PODXL (podocalyxin-like), we demonstrate that the ADAR2-regulated recoding editing at codon 241 (His?Arg) confers a loss-of-function phenotype that neutralizes the tumorigenic ability of the unedited PODXL. CONCLUSIONS: Our study highlights a major role for RNA editing in GC disease and progression, an observation potentially missed by previous NGS analyses of GC focused on DNA alterations alone. Our findings also suggest new GC therapeutic opportunities, through ADAR1 enzymatic inhibition or the potential restoration of ADAR2 activity.
Jane Anthony
Best Poster Award
Gas6/AXL Signaling Network as a Mes Molecular Subtype Specific Therapeutic Target for Ovarian Cancer
The mesenchymal subtype relies on the AXL/Gas6 signaling node to sustain signal propagation, effecting RTK clustering, ERK/FRA-1 signaling, motility and consequently sensitization to AXL inhibition; this highlights the intrinsic role of EMT in sustaining oncogenic signaling, and the relevance of identifying specific therapeutic targets for the EMT molecular subtypes.