Polly Leilei CHEN

The human genome encodes RNA molecules that instruct the behaviour of cancer cells. Leveraging on the next-generation sequencing technologies, well-established cancer cell lines and animal models, Dr Polly Leilei Chen’s group aims to identify the harmful changes that will occur in RNA molecules after it is made from DNA. It is critical to uncover how these changes trigger a cell to develop into cancer which can eventually lead to the unsatisfactory treatment outcomes for patients with cancers (particularly esophageal, stomach, colon and liver cancer). The long-term goal of Dr Chen’s team is to develop novel cancer therapies targeting these cancer-associated RNA changes.

csicl[at]nus.edu.sg

Biosketch

Affliations

Principal Investigator, Cancer Science Institute of Singapore
Associate Professor, Department of Anatomy, NUS

Honors & Awards

2021 Yong Loo Lin School of Medicine Research Excellence Award
2019 EMBO Young Investigator Program (YIP)
2018 NUHS-Mochtar Riady Pinnacle Awards-High Achiever Award 2018
2017 Yong Loo Lin School of Medicine Young Researcher Of the Year Award
2015 President Assistant Professorship, National University of Singapore
2014 Science and Technology Award of Higher Education of China (Second Class), Ministry of Education, China
2014 NUS Young Scientist Award, National University of Singapore
2010 Li Ka Shing Prize 2009/2010, Hong Kong
2010 Young Scientist Award (Life Science Panel), Hong Kong Institution of Science
2010 Dr KP Stephen Chang Gold Medal, The University of Hong Kong

Research

My research interest has been centered on understanding the changes in RNA (particularly adenosine-to-inosine RNA editing and splicing) in human cancers and translating this new knowledge to aid early detection and intervention as well as treatment.

RNA editing and splicing share the largest overlap in time and space during processing of pre-mRNA and contribute to transcriptome diversity. RNA editing introduces changes in RNA sequences encoded by the genome. In humans, the most common type of editing is the conversion of adenosine to inosine (A-to-I), which is catalysed by the double-stranded RNA-specific adenosine deaminase that acts on RNA (ADAR) family of proteins. This process of recoding of translated exons, widespread editing of repetitive sequence elements and sequence modification of microRNA (miRNA) can lead to specific amino acid substitutions, alternative splicing, and changes in gene expression levels. With the advent of high-throughput transcriptome sequencing, many editing sites potentially associated with cancer development have been identified.

Alternative splicing and RNA editing are the two major pre-messenger RNA processing steps diversifying transcriptome in eukaryotes. ADAR1 and/or ADAR2 proteins bind to double-stranded RNAs (dsRNAs) in the nucleus and convert adenosine (A) to inosine (I). Inosine is recognized as guanosine (G) by most cellular machineries, such as splicing and translation machineries. Regulation of alternative splicing involves cis-acting elements, such as exonic/intronic splicing enhancers/silencers (ESE/S, ISE/S), and transacting factors, such as serine arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs), transcription, chromatin modification, and RNA secondary structure.

We were amongst the first to report that the dysregulated adenosine-to-inosine (A-to-I) RNA editing contributes to human liver, stomach, and oesophageal cancers. We deciphered how RNA editing enzyme ADARs regulate gene functions and other RNA processing steps (e.g., canonical linear mRNA splicing and non-canonical backsplicing) via their editing-dependent and/or independent functions in the context of cancer and identified hundreds of non-ADAR editing regulators and decipher their role in shaping the cancer editome. To translate our research into clinically applied settings, we developed antisense oligonucleotide (ASO)-based RNA editing inhibitors for cancer treatment (International Patent Application No. PCT/SG2020/050380) and identified a 29-gene RNA editing signature for guiding gastric cancer chemotherapy (International Patent Application No. PCT/SG2021/050203).

My recent research focuses have been placed on 1) identifying changes in RNAs leading to cancer initiation, relapse post treatment, and drug resistance using advanced multi-omics approaches; and 2) understanding how pre-malignant and tumour cells develop immune evasion mechanisms through impairing RNA sensing and immune activation.

Lab Members

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SONG Yangyang

Senior Research Scientist

Investigate RNA editing in Hepatocellular Carcinoma and Liver Differentiation.

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TANG Sze Jing

Research Scientist

Study Alternative Splicing in Hepatocellular Carcinoma.

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HAN Jian

Research Fellow

Elucidating the functional roles of ADAR co-factors in A-to-I RNA editing.

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Daryl Jin Tai TAY

Research Associate

Targeting RNA Editing by Triplex-Forming Oligonucleotides (TFOs) or Peptide Nucleic Acid (PNA).

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Vanessa Hui En NG

Senior Laboratory Executive

The role of COG3 editing event in human HCC.

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GAN Wei Liang

PhD Student

Understanding the role of RNA-binding proteins in modulating tumor cell-intrinsic immunity

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LEONG Ka Wai

Research Assistant

Understanding the substrate selectivity and sensitivity of ADARs.

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Larry NG Tze Hiang

PhD Student

Understanding the regulatory mechanisms contributing to the reshaping of RNA editome in cancer

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NG Yik Loong Bryan

PhD Student

Elucidating the splicing mechanisms and functional consequences of ADAR self-regulation in cancer

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Haoqing SHEN

Research Fellow

Understanding the interplay between RNA splicing and RNA editing

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Xi REN

Research Fellow (Bioinformatician)

Identifying potential targets in the cancer genome and transcriptome for personalized immunotherapy

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Apurva KULKARNI

PhD Student

Studying the role of non-coding RNAs in cancer.

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Xiaohui SUI

Laboratory Executive

Lab operation and administration with research

Selected Publications

Google Scholar Citations

1. Chen L. A-to-I editing prevents self-RNA sensing. Nature Reviews Molecular Cell Biology (2022).

2. Shen H, An Ö, Ren X, Song Y, Tang SJ, Ke X, Han J, Tay DJ, Ng VHE, Bellido Molias F, Pitcheshwar P, Leong KW, Tan KK , Yang H, Chen L. ADARs act as potent regulators of circular transcriptome in cancer. Nature Communications, 13(1):16 pages Number ARTN 1508 21 Mar 2022.

3. Han J, An Ö, Ren X, Song Y, Tang SJ, Shen H, Ke X, Ng VHE, Tay DJ, Tan HQ, Kappei D, Yang H, Chen L. Multilayered Control of Splicing Regulatory Networks by DAP3 Leads to Widespread Alternative Splicing Changes in Cancer. Nature Communications, 13(1):1793 04 Apr 2022.

4. Tay DJ, Song Y, Peng B, Toh TB, Hooi L, Toh DFK, Hong H, Tang SJ, Han J, Gan WL, Chan THM, Krishna MS, Patil KM, Maraswami M, Loh TP, Dan YY, Zhou L, Bonney GK, Chow PKH, Chen G, Chow EKH, Le MT, Chen L. Targeting RNA Editing of Antizyme Inhibitor 1: a Potential Oligonucleotide-Based Antisense Therapy for Cancer. Molecular Therapy, 2021, 29(11):3258-3273. 

5. Song Y, An O, Ren X, Chan TH, Tay DJ, Tang SJ, Han J, Hong HQ, Ng VHE, Ke X, Shen H, Pitcheshwar P, Lin SJ, Leong KW, Molias FB, Yang H, Kappei D, Chen L. RNA editing mediates the functional switch of COPA in a novel mechanism of hepatocarcinogenesis. Journal of Hepatology. Published: July 18, 2020. DOI:https://doi.org/10.1016/j.jhep.2020.07.021

6. Han J, An O, Hong H, Chan TH, Song Y, Shen H, Tang SJ, Lin JS, Ng VHE, Tay DJ, Molias FB, Pitcheshwar P, Yang H, Chen L. Suppression of Adenosine-to-Inosine (A-to-I) RNA Editome by Death Associated Protein 3 (DAP3) Promotes Cancer Progression. Science Advances,2020; 6, eaba5136.

7. Tang SJ, Shen H, An O, Hong HQ, Li J, Song Y, Han J, Tay DJ, Ng VHE, Molias FB, Leong KW, Pitcheshwar P, Yang H, Chen L. Cis- and trans-regulation of pre-mRNA splicing by RNA editing enzymes: influencing cancer development. Nature Communications. 2020;11(1):799.

8. Hong H, An O, Chan TH, Ng VHE, Kwok HS, Lin JS, Qi L, Han J, Tay DJ, Tang SJ, Yang H, Song YY, Molias FB, Tenen DG, Chen L. Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer. Nucleic Acids Res, 2018 Sep 6;46(15):7953-7969.

9. Qi L, Song Y, Chan TH, Yang H, Lin CH, Tay ST, Hong H, Tang SJ, Tan KT, Huang XX, Lin JS, Ng VHE, Maury JJP, Tenen DG, Chen L. An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer. Nucleic Acids Res. 2017 Oct 13;45 (18):10436-10451.

10. Chan TH, Qamra A, Tan KT, Guo J, Yang H, Qi L, Lin JS, Ng VH, Song Y, Hong HQ, Tay ST, Liu Y, Lee J, Rha SY, Feng Z, So JB, Tean TB, Guan YK, Rozen S, Tenen DG, Tan P, Chen L. ADAR-mediated RNA editing predicts progression and prognosis of Gastric Cancer. Gastroenterology. 2016, 151(4):637-650.



Cancer Science Institute of Singapore
Centre for Translational Medicine
14 Medical Drive, #12-01,
Singapore 117599