Encyclopedia of Signaling Molecules

2018 Edition
| Editors: Sangdun Choi


  • Hidenori Shiraha
  • Shigeru Horiguchi
  • Hiroyuki Okada
Reference work entry
DOI: https://doi.org/10.1007/978-3-319-67199-4_101799


Historical Background

In studies on murine polyoma and leukemia viruses, mammalian core-binding factors (CBFs) were identified as proteins regulating viral replication (Boral et al. 1989; Speck and Terryl 1995). Investigating the regulatory mechanism of viral replication led to the identification of the polyomavirus enhancer-binding protein 2 (PEBP2), also known as core-binding factor-β (CBF-β) (Katinka et al. 1980; Tanaka et al. 1982). Further study revealed that PEBP2/CBFB was composed of dimers of a DNA-binding subunit (CBF-α) and a non-DNA-binding subunit (CBF-β). Gene cloning investigations discovered that CBF-α was encoded by RUNX genes (RUNX1/CBFA2/PEBPA2B, RUNX2/CBFA1/PEBPA2A, and RUNX3/CBFA3/PEBPA2C) (Levanon and Groner 2004). Bae et al. also identified RUNX3 gene as PEBPA2C (Bae et al. 1995).

Gene Structure and Function

RUNX3, located on human chromosome 1p36, is approximately 67 kb long. It is composed of two promoters and six exons. The two promoter regions, designated P1 and P2, regulate RUNX3 expression in a cell-typic manner. The proximal promoter, P2, is located before exon 2 and contains a large CpG island that is frequently methylated in solid tumors.

The protein product of RUNX3 is a heterodimer of alpha and beta subunits containing 415 amino acids. The alpha subunit is a homolog of the product of the Drosophila melanogaster segmentation gene, runt, which contains a conserved region of 128 amino acids called the runt domain. This domain is responsible for binding to DNA and for heterodimerization with the beta subunit. The runt domain is located at the N-terminus of RUNX3 and mediates sequence-specific binding to the target DNA motif of PyGPyGGT, which is found in a number of enhancers and promoters. The runt domain can either activate or suppress transcription.

RUNX3 is ubiquitously expressed in many tissues. Its functions have mainly been understood through studies on RUNX3-null mice. RUNX3 plays an important role in the development of various cell types including gastric epithelial cells, osteoblasts, and hematopoietic cells via interacting with transforming growth factor (TGF)-β signaling. TGF-β is a family of multifunctional cytokines that regulates the growth, differentiation, apoptosis, motility, angiogenesis, epithelial–mesenchymal transition (EMT), and extracellular matrix production of wide varieties of cells (Blobe et al. 2000). TGF-β acts as a potent growth inhibitor of many types of cells, including epithelial cells, endothelial cells, hematopoietic cells, and lymphocytes. Ligands of the TGF-β superfamily initiate signal transduction through complex ligand–receptor interactions. TGF-β type I and II transmembrane receptor serine/threonine kinases transduce downstream signals via cytoplasmic transcription factors called Smad proteins (Fig. 1). The TGF-β receptor phosphorylates receptor substrate Smads (Rsmads) including Smads 2 and 3, and the activated Rsmads shuttle to the nucleus and form a complex with Smad 4. Smad 4–Rsmad complexes associate with RUNX3 to achieve binding with specific target genes. Consequently, RUNX3 regulates cell growth, differentiation, apoptosis in the developmental process, carcinogenesis, neurogenesis, and hematopoietic cell differentiation.
RUNX3, Fig. 1

RUNX3 cooperates with Smad 4 to activate TGF-β-induced signaling

RUNX3 in Cancer

The chromosome 1p36, in which RUNX3 is located, is a deletion hotspot in various cancers, suggesting its tumor-suppressor function. Transcription of RUNX3 is also frequently decreased in cancer. RUNX3 inactivation in cancer is due to hemizygous deletion, promoter hypermethylation, and mislocalization of the gene. The transcriptional inactivation is the result of hypermethylation of the CpG islands at the RUNX3 promoter. RUNX3 was first described in 2005 as a potential tumor suppressor gene for gastric cancer (Chi et al. 2005). Decreased expression of RUNX3 has also been demonstrated in other human cancers, such as those of the lung, breast, cervix, thyroid, pancreas, colon, bile duct, and liver as well as glioma, meningioma, neuroblastoma, melanoma, acute myeloid leukemia, chronic myeloid leukemia, and non-Hodgkin lymphoma.

RUNX3-null mouse gastric mucosa exhibits hyperplasia due to stimulated proliferation and suppressed apoptosis in epithelial cells, and the cells are resistant to TGF-β stimulation. TGF-β is involved in cell-growth control; it induces cell-growth arrest through activating cyclin-dependent kinase inhibitor 1A. In a study on RUNX3-null mice, the sensitivity to TGF-β was suppressed, resulting in enhanced cell proliferation and suppressed apoptosis in epithelial cells. Thus, RUNX3 is considered an apoptosis inducer. TGF-β-induced apoptosis requires Bim activation. Given that the Bim promoter contains a RUNX binding site, RUNX3 has been considered responsible for the transcriptional upregulation of Bim (Yano et al. 2006).

RUNX3 regulates angiogenesis, cancer stem cells, EMT, cell migration and metastasis, and apoptosis in cancer development. Vascular endothelial growth factor (VEGF) plays a major role in cancer angiogenesis, because it stimulates proliferation and migration of vascular endothelial cells. The VEGF promotor region contains a RUNX3 binding site. The restoration of RUNX3 in gastric cancer cells has demonstrated reduced VEGF expression (Peng et al. 2006). RUNX3 is also involved in the regulation of EMT. EMT is closely related to cancer cell migration and metastasis and is involved in the progression of noninvasive tumor cells into malignant metastatic carcinoma cells. RUNX3 is considered an EMT suppressor, and loss of RUNX3 contributes to EMT progression due to dysregulated TGF-β and Wnt signaling (Voon et al. 2012).

Although RUNX3 is considered a tumor suppressor, it can be oncogenic in certain cancers. RUNX3 overexpression has been frequently observed and is correlated with malignant behaviors in head and neck cancer (Kudo et al. 2011) and skin cancer. In these cancer cells, RUNX3 enhanced cell proliferation and inhibited apoptosis.

RUNX3 in Hematopoietic Cells

The RUNX family genes are also known as acute myeloid leukemia (AML) genes and are implicated in leukemogenesis. Several studies have demonstrated the downregulation of RUNX3 expression in inv.(16) AML, while it has been overexpressed in patients with acute promyelocytic leukemia (t15;17). Although RUNX3 hypermethylation is frequently seen in leukemia cell lines, it is highly variable among patient samples. RUNX3 hypermethylation has also been proven frequent in AML patients with inv.(16)(p13.1q22) and acute lymphoblastic leukemia (Estecio et al. 2015). Others have reported that RUNX3 sites mediate transcriptional repression of RUNX3 by the t(8:21) and inv.(16) fusion proteins in AML (Cheng et al. 2008).

RUNX3 is also involved in the development and differentiation of normal blood cells, including dendritic cells (DCs), Langhans cells (LCs), T lymphocytes, and natural killer (NK) cytotoxic lymphocytes.

RUNX3 is highly expressed in mature DCs and mediates their response to TGF-β. In RUNX3-null mice, DCs and epidermal LCs do not respond to TGF-β. These findings suggest the role of RUNX3 in the TGF-β signaling cascade and development of DC and LC (Fainaru et al. 2004). Lack of RUNX3 has accelerated DC maturation and resulted in an increased efficacy to stimulate T lymphocytes. Consequently, lung alveoli of RUNX3-null mice exhibit a primary immune system defect leading to the development of lung inflammation and asthma-like conditions.

Furthermore, RUNX3 is a key player in T-cell development and function, being highly expressed in mature CD8+ T lymphocytes and NK cytotoxic lymphocytes, and regulates their proliferation and activation. Hematopoietic precursors lacking CD4 and CD8 receptors progress through a double positive stage (CD4+CD8+) and are then selected to become either a CD4+ helper cell or CD8+ cytotoxic cell through the silencing of either CD8 or CD4 expression, respectively. Two consensus RUNX binding sites have been found in the regulatory element required for CD4 silencing during T-cell development. Thus, experiments involving RUNX3-null mice indicate that RUNX3 is required for cytotoxic T-lymphocyte specification, CD4 downregulation, and CD8 upregulation.

RUNX3 is highly expressed in NK cells, but its function in these cells has not yet been clearly elucidated. A recent study has revealed that RUNX3 cooperates with ETS and T-box transcription factors to drive the interleukin-15-mediated transcription program during activation of these cells (Levanon et al. 2014).

RUNX3 also regulates B-lymphocyte function, being highly expressed in B lymphocytes, by regulating TGF-β-induced immunoglobulin class switching.

RUNX3 in Development

The runt domain is an evolutionarily conserved protein domain, and RUNX is a key regulator of lineage-specific gene expression in major developmental pathways. Given that runt-related genes, including RUNX3, regulate cell differentiation, RUNX3 plays an important role in the development of various organs. In fact, RUNX3 is strongly expressed in neuronal, hematopoietic, cartilaginous, and gastrointestinal tract tissues in the developing embryo.

There are three major subpopulations of dorsal root ganglion (DRG) neurons – nociceptive, mechanoreceptive, and proprioceptive. RUNX3-null mice have demonstrated a similar phenotype to neurotrophin-3 knockout (KO) and its receptor tropomyosin receptor kinase (Trk) C KO mice. In these KO mice, DRG neurons fail to form stretch reflex circuits with motor neurons in the spinal cord. In DRG development, RUNX3 functions by repressing Trk B and acquiring Trk C+ identity (Inoue et al. 2003). In addition, RUNX3 regulates the axonal projections of a specific subpopulation of DRG neurons.

As mentioned above, RUNX3 controls the generation of T-cell sub-lineage, particularly being involved in the transcriptional regulation of the CD4 silencer in T-cell development. RUNX3 is also involved in the development of skin dendritic epidermal T-cell development (Woolf et al. 2007). RUNX3 is required for the proper development of embryonal Vgamma3 thymocytes. When RUNX3 is knocked out, the maturation and proliferation of these thymocytes are impaired, resulting in a complete absence of skin dendritic epidermal T cells in adult KO mice.

Although RUNX3 is considered a tumor suppressor and primarily regulates neurogenesis, all three RUNX genes are involved in skeletogenesis. RUNX3 is expressed along with RUNX1 in bone cells such as osteoblasts and chondrocytes and is involved in skeletal development and differentiation (Stein et al. 2004). Furthermore, RUNX3-null mice demonstrate posture abnormalities with severe limb ataxia.

RUNX3 is associated with gastrointestinal tract development. Because RUNX3-null gastric epithelial cells become less sensitive to TGF-β-induced growth inhibition and apoptosis, RUNX3 is considered a major growth regulator of gastric epithelial cells (Fukamachi and Ito 2004).


RUNX3 is a transcription factor that can either activate or suppress transcription to induce various biological effects in carcinogenesis, hematopoietic development, and neurogenesis.

RUNX3 is deeply involved in normal developmental processes such as hematopoiesis, neurogenesis, and osteogenesis via interacting with other developmental molecules. The runt domain is highly conserved during evolution. Many of the genes regulating development are highly conserved, which indicates a major role for RUNX3 in the developmental process.

The accumulating evidence demonstrates that RUNX3 is a tumor suppressor in various solid cancers and leukemia. RUNX3 is inactivated by reduced copy number, promoter hypermethylation, hemizygous deletion, and protein mislocalization. RUNX3 may be a prognostic marker, because its expression in a tumor is associated with a more favorable prognosis with reduced recurrence and better survival rates. RUNX3 is considered to regulate the cell cycle and is an apoptosis enhancer. In addition to those functions, RUNX3 plays a significant role in angiogenesis, EMT, migration, and invasion in cancers. Taken together, RUNX3 may be a promising therapeutic target for cancers and leukemia.

See Also


  1. Bae SC, Takahashi E, Zhang YW, Ogawa E, Shigesada K, Namba Y, et al. Cloning, mapping and expression of PEBP2 alpha C, a third gene encoding the mammalian Runt domain. Gene. 1995;159:245–8.PubMedCrossRefGoogle Scholar
  2. Blobe GC, Schiemann WP, Lodish HF. Role of transforming growth factor beta in human disease. N Engl J Med. 2000;342:1350–8. doi:10.1056/NEJM200005043421807.PubMedCrossRefGoogle Scholar
  3. Boral AL, Okenquist SA, Lenz J. Identification of the SL3-3 virus enhancer core as a T-lymphoma cell-specific element. J. Virol. 1989;63:76–84.PubMedPubMedCentralGoogle Scholar
  4. Cheng CK, Li L, Cheng SH, Lau KM, Chan NP, Wong RS, et al. Transcriptional repression of the RUNX3/AML2 gene by the t(8;21) and inv.(16) fusion proteins in acute myeloid leukemia. Blood. 2008;112:3391–402. doi:10.1182/blood-2008-02-137083.PubMedCrossRefGoogle Scholar
  5. Chi XZ, Yang JO, Lee KY, Ito K, Sakakura C, Li QL, et al. RUNX3 suppresses gastric epithelial cell growth by inducing p21(WAF1/Cip1) expression in cooperation with transforming growth factor {beta}-activated SMAD. Mol. Cell. Biol. 2005;25:8097–107. doi:10.1128/MCB.25.18.8097-8107.2005.PubMedPubMedCentralCrossRefGoogle Scholar
  6. Estecio MR, Maddipoti S, Bueso-Ramos C, DiNardo CD, Yang H, Wei Y, et al. RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype. Br J Haematol. 2015;169:344–51. doi:10.1111/bjh.13299.PubMedPubMedCentralCrossRefGoogle Scholar
  7. Fainaru O, Woolf E, Lotem J, Yarmus M, Brenner O, Goldenberg D, et al. Runx3 regulates mouse TGF-beta-mediated dendritic cell function and its absence results in airway inflammation. The EMBO journal. 2004;23:969–79. doi:10.1038/sj.emboj.7600085.PubMedPubMedCentralCrossRefGoogle Scholar
  8. Fukamachi H, Ito K. Growth regulation of gastric epithelial cells by Runx3. Oncogene. 2004;23:4330–5. doi:10.1038/sj.onc.1207121.PubMedCrossRefGoogle Scholar
  9. Inoue K, Ozaki S, Ito K, Iseda T, Kawaguchi S, Ogawa M, et al. Runx3 is essential for the target-specific axon pathfinding of trkc-expressing dorsal root ganglion neurons. Blood Cells Mol Dis. 2003;30:157–60.PubMedCrossRefGoogle Scholar
  10. Katinka M, Yaniv M, Vasseur M, Blangy D. Expression of polyoma early functions in mouse embryonal carcinoma cells depends on sequence rearrangements in the beginning of the late region. Cell. 1980;20:393–9.PubMedCrossRefGoogle Scholar
  11. Kudo Y, Tsunematsu T, Takata T. Oncogenic role of RUNX3 in head and neck cancer. J Cell Biochem. 2011;112:387–93. doi:10.1002/jcb.22967.PubMedCrossRefGoogle Scholar
  12. Levanon D, Groner Y. Structure and regulated expression of mammalian RUNX genes. Oncogene. 2004;23:4211–9. doi:10.1038/sj.onc.1207670.PubMedCrossRefGoogle Scholar
  13. Levanon D, Negreanu V, Lotem J, Bone KR, Brenner O, Leshkowitz D, et al. Transcription factor Runx3 regulates interleukin-15-dependent natural killer cell activation. Mol. Cell. Biol. 2014;34:1158–69. doi:10.1128/MCB.01202-13.PubMedPubMedCentralCrossRefGoogle Scholar
  14. Peng Z, Wei D, Wang L, Tang H, Zhang J, Le X, et al. RUNX3 inhibits the expression of vascular endothelial growth factor and reduces the angiogenesis, growth, and metastasis of human gastric cancer. Clin Cancer Res. 2006;12:6386–94. doi:10.1158/1078-0432.CCR-05-2359.PubMedCrossRefGoogle Scholar
  15. Speck NA, Terryl S. A new transcription factor family associated with human leukemias. Crit. Rev. Eukaryot. Gene Expr. 1995;5:337–64.PubMedCrossRefGoogle Scholar
  16. Stein GS, Lian JB, van Wijnen AJ, Stein JL, Montecino M, Javed A, et al. Runx2 control of organization, assembly and activity of the regulatory machinery for skeletal gene expression. Oncogene. 2004;23:4315–29. doi:10.1038/sj.onc.1207676.PubMedCrossRefGoogle Scholar
  17. Tanaka K, Chowdhury K, Chang KS, Israel M, Ito Y. Isolation and characterization of polyoma virus mutants which grow in murine embryonal carcinoma and trophoblast cells. The EMBO journal. 1982;1:1521–7.PubMedPubMedCentralGoogle Scholar
  18. Voon DC, Wang H, Koo JK, Nguyen TA, Hor YT, Chu YS, et al. Runx3 protects gastric epithelial cells against epithelial-mesenchymal transition-induced cellular plasticity and tumorigenicity. Stem Cells. 2012;30:2088–99. doi:10.1002/stem.1183.PubMedCrossRefGoogle Scholar
  19. Woolf E, Brenner O, Goldenberg D, Levanon D, Groner Y. Runx3 regulates dendritic epidermal T cell development. Dev Biol. 2007;303:703–14. doi:10.1016/j.ydbio.2006.12.005.PubMedCrossRefGoogle Scholar
  20. Yano T, Ito K, Fukamachi H, Chi XZ, Wee HJ, Inoue K, et al. The RUNX3 tumor suppressor upregulates Bim in gastric epithelial cells undergoing transforming growth factor beta-induced apoptosis. Mol. Cell. Biol. 2006;26:4474–88. doi:10.1128/MCB.01926-05.PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Hidenori Shiraha
    • 1
  • Shigeru Horiguchi
    • 1
  • Hiroyuki Okada
    • 1
  1. 1.Department of Gastroenterology and HepatologyOkayama University Faculty of MedicineOkayamaJapan