Master transcription factors

Recent work has suggested that a relatively small set of transcription factors work cooperatively to govern the key cellular transcriptional program by binding to the majority of expressed gene enhancers, forming the unique identity of the cell (“master transcription factors”). These factors are essential for normal tissue development and cell maintenance. Importantly, when abnormally expressed, they often act as oncogenes. A prime example is TAL1, which is ectopically expressed in 40-60% of T-cell acute lymphoblastic leukemia (T-ALL) cases via various mechanisms that acquire enhancers. Notably, this factor is normally expressed in hematopoietic stem and progenitor cells and myeloid lineage, but silenced during T-cell development. Ectopic expression of TAL1 alters the transcriptional program in developing thymocytes by blocking the expression of genes that are required for normal T-cell differentiation and instead, it aberrantly activates genes that are usually not expressed in T-cells. Thus, it is important to elucidate the transcriptional program driven by master transcription factors.

Core regulatory circuit in T-ALL and neuroblastoma

Interestingly, these master transcription factors often form a “core regulatory circuitry (CRC)”, which consists of an interconnected auto-regulatory loop where the expression of each member is driven by themselves and other members of the CRC. Additionally, CRC members are often associated with a large cluster of enhancers (“super-enhancers”). We and others have demonstrated that TAL1 and its regulatory partners (GATA3 and RUNX1) form the CRC and are regulated under super-enhancers in T-ALL cells. Similarly, we reported that in the adrenergic subtype neuroblastoma, ASCL1 and several transcription factors form the CRC and are regulated by super-enhancers. We hypothesize that this structure is ideal to reinforce and stabilize gene expression program via “interlocking” regulatory loops and maintaining their expressions at high level, to keep the malignant state of cancer cells.

The CRCs in T-ALL (Sanda et al, Cancer Cell, 2012) and in adrenergic neuroblastoma (Wang et al, Nat Communications, 2019)

Multi-layered coherent feed-forward loop in adult T-cell leukemia

Another type of regulatory structure that has often been implicated in normal and malignant cells is the coherent feed-forward loop, in which the top-tier transcription factor regulates the second-tier transcription factor and both of them coordinately induce the activation of downstream targets. We recently reported that the NF-kB and IRF4-BATF3 form this type of transcriptional regulatory loop in adult T-cell leukemia (ATL) and regulate many genes that characterize cell identity and oncogenesis. Their downstream targets include various genes involved in the T-cell receptor (TCR) pathway, which in fact is the upstream regulator of the NF-?B-IRF4 axis. We hypothesize that these multi-layered feed-forward loop may act as “detectors” that respond rapidly to activating stimuli and help to filter fluctuations in input stimuli, thereby amplifying the signal and increasing the robustness of a cellular state. This structure would be critical for the maintenance of malignant cells.

Feed-forward loop in ATL (Wong & Tan et al, Blood, 2020)

Tissue-specific oncogenesis

Importantly, many of these oncogenic master transcription factors serve as oncogenes only in specific tissues and cell stages. As an example, TAL1 has been implicated as an oncogene in T-ALL but not in other cancers, while ASCL1 is abnormally expressed only in adrenergic neuroblastoma and a subtype of lung cancer. This suggests that oncogenic transcription factors need to utilize certain endogenous cellular machinery and microenvironment to exert the oncogenicity. Thus, it is critical to read the background context behind the oncogenesis driven by master transcription factors.

Our goal: “Breaking the circuit”

As a physician scientist, I am particularly motivated in areas that have the potential to improve public health, with the advancement in the understanding of cancer for the eventual development of improved therapeutics. The short-term goal of our laboratory is to identify critical oncogenic machinery involving the master transcription factors, CRC and feed-forward loop, and to elucidate the tissue-specific oncogenic mechanism. The mid-term goal would be to translate the knowledge gained from these basic studies into clinical application (diagnostics or therapeutics). And finally, our long-term goal would be to improve cancer cure rates by developing novel therapeutics. We hope to discover a novel means to break the oncogenic regulatory circuit (“circuit breaker”) in cancers. Most importantly, my mission is to train the future generation of scientists, which I believe is a major cornerstone to advance biomedical research and ultimately improve the public health. We are looking forward to working with highly motivated young scientists.

1. Amanda S, Tan TK, Ong JZL, Theardy MS, Wong RWJ, Huang XZ, Ali MZ, Li Y, Gong Z, Inagaki H, Foo EY, Pang B, Tan SY, Iida S, Sanda T. IRF4 drives clonal evolution and lineage choice in a zebrafish model of T-cell lymphoma, Nat Commun. 2022 May 3;13(1):2420

2. Zhang C, Amanda S, Wang C, Tan TK, Ali MZ, Leong WZ, Ng LM, Kitajima S, Li Z, Yeoh AEJ, Tan SH, Sanda T. Oncorequisite role of an aldehyde dehydrogenase in the pathogenesis of T-cell acute lymphoblastic leukemia. Haematologica. 2021 Jun 1;106(6):1545-1558

3. Wong RWJ, Tan TK, Amanda S, Ngoc PCT, Leong WZ, Tan SH, Asamitsu K, Hibi Y, Ueda R, Okamoto T, Ishida T, Iida S, Sanda T, Feed-forward Regulatory Loop Driven by IRF4 and NF-kB in Adult T-cell Leukemia/Lymphoma. Blood. 2020 Mar 19;135(12):934-947

4. Wang L, Tan TK, Durbin AD, Zimmerman MW, Abraham BJ, Tan SH, Ngoc PCT, Weichert N, Akahane K, Lawton LN, Rokita JL, Maris JM, Young RA, Look AT, Sanda T, ASCL1 is a MYCN- and LMO1-dependent member of the neuroblastoma adrenergic core regulatory circuitry. Nat Commun. 2019 Dec 9;10(1):5622.

5. Tan SH, Leong WZ, Ngoc PCT, Tan TK, Bertulfo FC, Lim MC, An O, Li Z, Yeoh AEJ, Fullwood MJ, Tenen DG and Sanda T. The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia. Blood. 2019 Jul 18;134(3):239-251

6. Ngoc PC, Tan SH, Tan TK, Chan MM, Li Z, Yeoh AEJ, Tenen DG, Sanda T. Identification of novel lncRNAs regulated by the TAL1 complex in T-cell acute lymphoblastic leukemia. Leukemia. 2018, Oct;32(10):2138-2151.

7. Leong WZ, Tan SH, Ngoc PCT, Amanda S, Yam AWY, Liau WS, Gong Z, Lawton LN, Tenen DG, Sanda T. ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis. Genes Dev. 2017 Dec 1;31(23-24):2343-2360.

8. Wong RWJ, Ngoc PCT, Leong WZ, Yam AWY, Zhang T, Asamitsu K, Iida S, Okamoto T, Ueda R, Gray NS, Ishida T, Sanda T. Enhancer profiling identifies critical cancer genes and characterizes cell identity in adult T-cell leukemia. Blood. 2017 Nov 23;130(21):2326-2338

9. Liau WS, Tan SH, Ngoc PC, Wang CQ, Tergaonkar V, Feng H, Gong Z, Osato M, Look AT, Sanda T. Aberrant activation of the GIMAP enhancer by oncogenic transcription factors in T-cell acute lymphoblastic leukemia. Leukemia. 2017, Aug;31(8):1798-1807.

10. Tan SH, Yam AW, Lawton LN, Wong RW, Young RA, Look AT, Sanda T. TRIB2 reinforces the oncogenic transcriptional program controlled by the TAL1 complex in T-cell acute lymphoblastic leukemia. Leukemia. 2016 Apr;30(4):959-62.