Cancer Epigenetics & Experimental Therapeutics

Section Leader
Shujun Liu, PhD
Assistant Director of Research

  • Epigenetics and genetics equally contribute to cancer pathogenesis
  • Epigenetics bridges the gap between human cancer and environmental exposure
  • Due to the promptness and reversibility, epigenetic modifications rapidly turn on cell fate determinators helping a subpopulation of cells escape drug-mediated killing


  1. Discover a dynamic and reversible FTO/m6A axis in drug resistance

The discovery of activating mutations in receptor tyrosine kinases (RTKs) led to clinical testing of RTK inhibitors (TKIs) in many cancers, but the rapid acquisition of resistance limits TKI effectiveness and remains a major scientific and clinical challenge. N6-methyladenosine (m6A), erased by demethylases (e.g., FTO), is the most prevalent internal modification of mRNAs, and influences all fundamental aspects of mRNA metabolism (e.g., mRNA stability) regulating cell fate determination. However, its physiological function in drug resistance is still unknown. We modeled and characterized TKI resistance in distinct leukemia models and directly mapped m6A in the transcriptomes of leukemia cells. We show that survival and propagation of leukemia cells under TKI selection requires a dynamic change in m6A methylome. Notably, the distinct m6A modification exists in naïve cancer cell populations that are genetically homogenous. Exposure to TKIs induces m6A hypomethylation through FTO upregulation, whereas the removal of TKIs results in reversal of the m6A marks. Mechanically, m6A depletion upregulates proliferation/ anti-apoptotic oncogenes bearing m6A sites through the enhanced RNA stability and protein translation. When the m6A modification is restored, the resistant cells re-gain sensitivity to TKIs. Our study identifies for the first time, to our knowledge, an epitranscriptomic mechanism in regulating cancer cell fate decision during TKI selection. Our findings support that m6A modulation could be considered for use in a neo-adjuvant manner to prevent emergence of resistant clones, or to eradicate TKI resistance by impairing aberrant FTO demethylase activity that resistant clones rely on to outcompete with therapy-sensitive clones.


  1. Discover the FABP4-IL-6-DNMT1 cascade as a hitherto unknown molecular link between obesity and cancer

Cancer is the representatively systemic lesions taking over the first place of lethal diseases throughout the world. Obesity, a chronic disease, is an important risk factor for many types of human illnesses. The World Health Organization estimates that one-quarter of the world’s population are obese. While it is a well-established concept that obesity is strongly associated with an increased incidence of breast cancer, colon cancer, pancreatic cancer and prostate cancer etc., whether and how obesity contributes to leukemia remain unexplored. Our findings reveal that dietary-induced obesity mediates aggressive leukemia growth in vitro and in vivo, thus, for the first time, experimentally demonstrating obesity-leukemia association. We present compelling evidence that FABP4, a member of fatty acid binding proteins (FABPs) family, is responsible for the aggressive leukemic phenotypes in obesity, because a single change of FABP4 in host or in leukemia cells is sufficient to alter leukemia cell fate. Mechanistically, the obese environment educates leukemia cells via FABP4 overproduction followed by DNMT1 upregulation, DNA hypermethylation and further silencing of tumor suppressor genes.

Theoretically, our findings identify FABP4 as an entirely new type of epigenetic modulator, in line with other members, such as TET (ten-eleven-translocation) proteins, cytidine deaminases or IDH (isocitrate dehydrogenase) mutations. Our discoveries unravel the FABP4-IL-6-DNMT1 cascade as a novel molecular rule behind obesity-cancer association. In terms of practical use, our findings open a novel window of targeting the FABP4/DNMT1 axis for treating leukemia, and, potentially, other types of cancer.


  1. Discover a crosstalk of epigenome and kinome in cancers

DNA methylation occurs at the 5-position of cytosine in a CpG dinucleotide context and is a major epigenetic mechanism regulating chromosomal stability and gene expression. DNA methylation is under control of DNA methyltransferases (DNMTs) that are highly expressed in cancers. Our findings suggest that DNMT overexpression is attributed to Sp1/miR29 network, miR101, nucleolin, and recently, cytokines (e.g., IL-6/IL-15). In addition, abnormal kinase activities are essential in cancer initiation and metastasis. While kinase mutations are crucial, our main focus is shifted to kinase overamplification, which significantly contributes to the development, progression and drug resistance of cancers. Our discoveries support that receptor tyrosine kinases are regulated by the Sp1/miR29 network. Because Sp1/miR29 is also involved in DNMT gene regulation, we proposed that aberrant DNMT activities may control kinase signaling. Indeed, we demonstrated that KIT and DNMT1 form a regulatory circuit, in which KIT regulates DNMT1 expression through STAT3 pathway, whereas DNMT1 modulates KIT expression through the Sp1/miR29 loop. Functionally, KIT and DNMT1 synergistically enhance cancer cell survival and proliferation, implicating the effectiveness of dual inhibition. The crosstalk of KIT and DNMT1 also exists in leukemia, liver cancer and breast cancer. These findings identify the regulatory and functional interactions between kinases and DNA methyltransferases, and highlight the key role of the crosstalk between the dysregulated KIT signaling and DNA hypermethylation in cancer cell survival and proliferation.


  1. Discover receptor tyrosine kinases as epigenetic activators in leukemia

Receptor tyrosine kinases (RTKs) are membrane-spanning proteins that exhibit intrinsic phosphotyrosine kinase activity. RTKs are frequently dysregulated in leukemia, yet the biological consequences of this dysregulation are largely unclear. Further, because hyperactive RTKs crucially contribute to leukemia pathogenesis, their inhibitors (TKIs) have been broadly tested against leukemia. However, the molecular mechanisms by which TKIs suppress leukemia growth remain elusive. We found that upregulation of RTKs paralleled DNMT overexpression in leukemia cell lines and patient blasts. Knockdown of RTKs disrupted, whereas enforced expression increased, DNMT expression and DNA methylation. Treatment with the RTK inhibitor, nilotinib, resulted in a reduction of Sp1-dependent DNMT1 expression, the diminution of global DNA methylation and the upregulation of tumor suppressor genes (TSG) through promoter hypomethylation in AML cell lines and patient blasts. This led to disruption of AML cell clonogenicity and promotion of cellular apoptosis without obvious changes in cell cycle. Importantly, nilotinib administration in mice and human patients with AML impaired expression of DNMTs followed by DNA hypomethylation, TSG re-expression, and leukemia regression. Our study provides the first evidence that RTKs are modulators of DNMT1-dependent DNA methylation in leukemia cells. Our study has for the first time documented that TKIs impair DNMT1 expression resulting in global and gene specific DNA hypomethylation. These findings demonstrate RTKs as new types of epigenetic regulators and unravel a signaling interaction between RTKs and DNMTs in leukemia pathogenesis, shedding light on leukemia molecular biology. Our data identify the DNA hypomethylating activities of TKIs, thus significantly expanding the pool of DNA methylation inhibitors. Our discoveries provide a mechanistic explanation why TKIs show therapeutic efficacy in patients without target mutations, and suggest that altered DNA methylation profile might be alternative predictors of responses in patients without RTK mutations. Altogether, our work provides the preclinical rationale for using TKIs to benefit patient subpopulations characterized by aberrant DNA methylation including those who relapse from current epigenetic therapy.


  1. Discover the FABP4-DNMT1 loop as a new epigenetic target for leukemia therapy

Acute myeloid leukemia (AML) is a highly aggressive hematologic malignancy characterized by the swift uncontrolled growth of immature myeloblasts. It is a lethal disease that lacks effective treatment. Although the precise molecular causes that are responsible for AML development and disease progression are unclear, it seems to result from an interplay of genetic and environmental factors that are largely unidentified. Aberrant DNA methylation mediated by dysregulation of DNA methyltransferases (DNMT) is a key hallmark of AML, yet efforts to target DNMT dysregulation for drug development have lagged. We previously demonstrated that FABP4 upregulation promotes AML aggressiveness through an increase of DNMT1-dependent DNA methylation. Here we demonstrate that FABP4 upregulation in AML cells occurs through vascular endothelial growth factor (VEGF) signaling, thus elucidating a crucial FABP4-DNMT1 regulatory feedback loop in AML biology. We show that FABP4 dysfunction by a selective inhibitor BMS309403 leads to downregulation of DNMT1, decrease of global DNA methylation and re-expression of p15INK4B gene by promoter DNA hypomethylation in vitro, ex vivo and in vivo. Functionally, BMS309403 suppresses cell colony formation, induces cell differentiation, and, importantly, impairs leukemic disease progression in mouse models of leukemia. Our findings highlight AML-promoting properties of the FABP4-DNMT1 vicious loop, and identify an attractive class of therapeutic agents with a high potential for clinical use in AML patients. The results will also assist in establishing the FABP4-DNMT1 loop as a target for therapeutic discovery to enhance the index of current epigenetic therapies.


  1. Discover fusion proteins as epigenetic modulators through multiple mechanisms

The oncogenic fusion proteins (e.g., AML1/ETO), resulting from chromosomal translocations [e.g., t(8;21)], are leukemia-initiating transcription factors, and tightly associated with aberrant DNA methylation signature that predicts worse clinical outcomes. We were the first to show that AML1/ETO recruits DNMT1 to repress AML1 target genes in leukemia, but these findings are insufficient to explain why the promotors of many genes without AML1/ETO binding elements are hypermethylated. Recently, we identified a positive feedback loop, AML1/ETO-HIF1α, which are enriched at DNMT3a gene promoter and upregulates DNMT3a expression leading to an increase of global and gene specific DNA methylation. These findings provide additional mechanisms behind AML1/ETO-driven DNA hypermethylation, supporting that fusion proteins modify epigenetic landscapes in leukemia cells through both protein interaction with DNMTs and gene upregulation of DNMT3a.


Selected Publications

  • Yan F, Al-Kali A, Zhang Z, Liu J, Pang J, Zhao N, He C, Litzow M, Liu S. A dynamic N6-methyladenosine methylome regulates intrinsic and acquired resistance to tyrosine kinase inhibitors. Cell Research. 2018 (accepted)
  • Hao J, Yan F, Zhang Y, Triplett A, Zhang Y, Schultz D, Sun Y, Zeng J, Silverstein K, Zheng Q, Bernlohr D, Cleary M, Egilmez N, Sauter E, Liu S*, Suttles J*, Li B*. Expression of adipocyte/macrophage fatty acid binding protein in tumor associated macrophages promotes breast cancer progression. Cancer Research. 2018 May 1;78(9):2343-2355. (*Corresponding Author)
  • Yan F, Shen N, Pang J, Zhao N, Zhang Y, Bode A, Al-Kali A, Litzow M, Li B, Liu S. A Vicious Loop of Fatty Acid-Binding Protein 4 and DNA Methyltransferase 1 Promotes Acute Myeloid Leukemia and Acts as a Therapeutic Target. Leukemia.  2017 Oct 10.
  • Yan F, Shen N, Pang J, Zhao N, Deng B, Li B, Yang Y, Yang P, Molina J, Liu S. A Regulatory Circuit Composed of DNA Methyltransferases and Receptor Tyrosine Kinases Controls Lung Cancer Cell Aggressiveness. Oncogene. 2017 Dec 14;36(50):6919-6928.
  • Shen N, Yan F, Pang J, Zhao N, Gangat N, Wu L, Bode A, Al-Kali A, Litzow M, Liu S. Inactivation of Receptor Tyrosine Kinases Reverts Aberrant DNA Methylation in Acute Myeloid Leukemia. Clinical Cancer Research. 2017 Oct 15;23(20):6254-6266. (Cover Article)
  • Yan F, Shen N, Pang J, Zhang Y, Rao E, Bode A, Al-Kali A, Zhang D, Litzow M, Li B, Liu S. Fatty Acid Binding Protein FABP4 Mechanistically Links Obesity with Aggressive AML by Enhancing Aberrant DNA Methylation in AML Cells. Leukemia.  2017 Jun;31(6):1434-1442.
  • Yan F, Pang J, Peng Y, Molina J, Yang P, Liu S. Elevated Cellular PD1/PD-L1 Expression Confers Acquired Resistance to Cisplatin in Small Cell Lung Cancer Cells. PLoS One. 2016 Sep 9;11(9):e0162925. (Featured in PLOS journal and included in the PLOS Editor’s Picks Collection, Cancer Immunotherapy)
  • Gao X, Yan F, Lin J, Gao L, Lu X, Wei S, Shen N, Pang J, Ning Q, Komeno Y, Deng A, Xu Y, Shi J, Li Y, Zhang D, Nervi C, *Liu S, Yu L. AML1/ETO Cooperates with HIF1α to Promote Leukemogenesis through DNMT3a Transactivation. Leukemia.  2015 Aug;29(8):1730-40. (*Corresponding Author/Lead Contact)
  • Liu S. Epigenetics Advancing Personalized Nanomedicine in Cancer Therapy. Advanced Drug Delivery Reviews.2012 Oct;64(13):1532-43.
  • Mishra A, Liu S, Santhanam R, Deanna S, Jackie J, Yang X, Wu L, Chandler J, Wu, Y, Heerema N, Chan K, Perrotti D, Zhang J, Pierluigi P, Garzon R, Racke F, Hickey C, Lee R, Marcucci G, Caligiuri M. Aberrant Overexpression of IL-15 Initiates Large Granular Lymphocyte Leukemia through Chromosomal Instability and DNA Hypermethylation. Cancer Cell. 2012 Nov 13;22(5):645-55.
  • *Liu S, Wu L, Pang J, Santhanam R, Schwind S, Wu Y, Hickey C, Yu J, Becker H, Maharry K, Radmacher M, Li CL, Whitman S, Eiring A, Briesewitz R, Caligiuri M, Byrd J, Croce C, Bloomfield C, Perrotti D, Garzon R, *Marcucci G. Sp1/NFkB/HDAC/miR-29b Regulatory Network in KIT-driven Myeloid Leukemia. Cancer Cell. 2010 Apr 13;17(4):333-47. (*Corresponding Author)


Complete List of Published Work in MyBibliography