RUNX3 explained

Runt-related transcription factor 3 is a protein that in humans is encoded by the RUNX3 gene.^[1]

Function

This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-YGYGGT-3' found in a number of enhancers and promoters,^[2] and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene.^[3]

In melanocytic cells RUNX3 gene expression may be regulated by MITF.^[4]

RUNX3 plays a fundamental role in defense against early tumor formation. In response to growth factors, RUNX3 is acetylated by p300 to complex with bromodomain-containing protein 2 (BRD2; a member of the BET family of transcription co-regulators)^[5] and to subsequent transient induction of CDKN1A and ARF.^[6] CDKN1A (also known as CIP1 or p21) inhibits the cell cycle, and ARF inhibits MDM2, increasing the stability of the cancer-suppressing gene p53.

The expression of CDKN1A and ARF under wild-type cell cycles is temporary, which results from the RUNX3-BRD2 complex replacing the RUNX3-cyclinD1 complex. However, oncogenic mitogen signals such as KRAS^G12D cause the RUNX3-BRD2 complex to be maintained continuously, resulting in the continuous expression of p21, ARF, and p53. Therefore, RUNX3 can function as a sensor for unregulated mitogenic signals, and its inactivation can ultimately lead to cancer due to the loss of function as a sensor.

Knockout mouse

Runx3 null mouse gastric mucosa exhibits hyperplasia due to stimulated proliferation and suppressed apoptosis in epithelial cells, and the cells are resistant to TGF-beta stimulation.^[7]

The RUNX3 controversy and resolution

In 2011 doubt was cast over the tumor suppressor function of Runx3 originated from the earlier publication by Li and co-workers.^[8] On the basis of the original study by Li and co-workers (2002), the majority of later literature citing Li and co-workers (2002) assumed that RUNX3 was expressed in the normal gut epithelium and that it is therefore likely to act as a tumor suppressor in the particular epithelial cancer investigated. Most of this literature used RUNX3 promoter methylation status in various cancers as a proxy for its expression. However, quite many genes are known to be methylated in tumor cell genomes, and the majority of these genes are not expressed in the normal tissue of origin of these cancers. Others used poorly characterized (or fully invalidated) antibodies to detect the RUNX3 protein, or used RT-PCR or validated antibodies and failed to detect RUNX3 in the gut epithelium but still did not question the original finding by Li and co-workers (2002). This facts have recently been discussed in a book by Ülo Maiväli.^[9]

In late 2009, a report written by Kosei Ito and his co-workers resolved the controversy by verifying that RUNX3 is indeed expressed in human and mouse gastrointestinal tract (GIT) epithelium and it functions as a tumor suppressor in gastric and colorectal tissues.^[10] The authors of the paper suggested that the previous conflicting report might be caused by use of a specific antibody, known as G-poly. Ito and his team generated multiple anti-RUNX3 monoclonal antibodies recognizing the RUNX3 N-terminal region (residues 1-234). The researchers found that the antibodies react with RUNX3 in gastric epithelial cells, whereas those recognizing the C-terminal region did not. G-poly primarily recognizes the region beyond 234 and hence, is unable to detect Runx3 in this tissue.

Interactions

RUNX3 has been shown to interact with TLE1.^[11]

See also

• Core binding factor
• RUNX1
• RUNX2

Further reading

• Vogiatzi P, De Falco G, Claudio PP, Giordano A . How does the human RUNX3 gene induce apoptosis in gastric cancer? Latest data, reflections and reactions . Cancer Biology & Therapy . 5 . 4 . 371–374 . April 2006 . 16627973 . 10.4161/cbt.5.4.2748 . free .
• Wijmenga C, Speck NA, Dracopoli NC, Hofker MH, Liu P, Collins FS . Identification of a new murine runt domain-containing gene, Cbfa3, and localization of the human homolog, CBFA3, to chromosome 1p35-pter . Genomics . 26 . 3 . 611–614 . April 1995 . 7607690 . 10.1016/0888-7543(95)80185-O . free .
• Bae SC, Takahashi E, Zhang YW, Ogawa E, Shigesada K, Namba Y, Satake M, Ito Y . Cloning, mapping and expression of PEBP2 alpha C, a third gene encoding the mammalian Runt domain . Gene . 159 . 2 . 245–248 . July 1995 . 7622058 . 10.1016/0378-1119(95)00060-J .
• Bae SC, Yamaguchi-Iwai Y, Ogawa E, Maruyama M, Inuzuka M, Kagoshima H, Shigesada K, Satake M, Ito Y . Isolation of PEBP2 alpha B cDNA representing the mouse homolog of human acute myeloid leukemia gene, AML1 . Oncogene . 8 . 3 . 809–814 . March 1993 . 8437866 .
• Levanon D, Goldstein RE, Bernstein Y, Tang H, Goldenberg D, Stifani S, Paroush Z, Groner Y . Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors . Proceedings of the National Academy of Sciences of the United States of America . 95 . 20 . 11590–11595 . September 1998 . 9751710 . 21685 . 10.1073/pnas.95.20.11590 . free . 1998PNAS...9511590L .
• Bangsow C, Rubins N, Glusman G, Bernstein Y, Negreanu V, Goldenberg D, Lotem J, Ben-Asher E, Lancet D, Levanon D, Groner Y . The RUNX3 gene--sequence, structure and regulated expression . Gene . 279 . 2 . 221–232 . November 2001 . 11733147 . 10.1016/S0378-1119(01)00760-0 .
• Waki T, Tamura G, Sato M, Terashima M, Nishizuka S, Motoyama T . Promoter methylation status of DAP-kinase and RUNX3 genes in neoplastic and non-neoplastic gastric epithelia . Cancer Science . 94 . 4 . 360–364 . April 2003 . 12824905 . 11160204 . 10.1111/j.1349-7006.2003.tb01447.x . 22030810 .
• Puig-Kröger A, Sanchez-Elsner T, Ruiz N, Andreu EJ, Prosper F, Jensen UB, Gil J, Erickson P, Drabkin H, Groner Y, Corbi AL . RUNX/AML and C/EBP factors regulate CD11a integrin expression in myeloid cells through overlapping regulatory elements . Blood . 102 . 9 . 3252–3261 . November 2003 . 12855590 . 10.1182/blood-2003-02-0618 . free . free . 10171/18733 .
• Kato N, Tamura G, Fukase M, Shibuya H, Motoyama T . Hypermethylation of the RUNX3 gene promoter in testicular yolk sac tumor of infants . The American Journal of Pathology . 163 . 2 . 387–391 . August 2003 . 12875960 . 1868235 . 10.1016/S0002-9440(10)63668-1 .
• Yang N, Zhang L, Zhang Y, Kazazian HH . An important role for RUNX3 in human L1 transcription and retrotransposition . Nucleic Acids Research . 31 . 16 . 4929–4940 . August 2003 . 12907736 . 169909 . 10.1093/nar/gkg663 .
• Li QL, Kim HR, Kim WJ, Choi JK, Lee YH, Kim HM, Li LS, Kim H, Chang J, Ito Y, Youl Lee K, Bae SC . Transcriptional silencing of the RUNX3 gene by CpG hypermethylation is associated with lung cancer . Biochemical and Biophysical Research Communications . 314 . 1 . 223–228 . January 2004 . 14715269 . 10.1016/j.bbrc.2003.12.079 .
• Xiao WH, Liu WW . Hemizygous deletion and hypermethylation of RUNX3 gene in hepatocellular carcinoma . World Journal of Gastroenterology . 10 . 3 . 376–380 . February 2004 . 14760761 . 4724901 . 10.3748/wjg.v10.i3.376 . free .
• Oshimo Y, Oue N, Mitani Y, Nakayama H, Kitadai Y, Yoshida K, Ito Y, Chayama K, Yasui W . Frequent loss of RUNX3 expression by promoter hypermethylation in gastric carcinoma . Pathobiology . 71 . 3 . 137–143 . 2004 . 15051926 . 10.1159/000076468 . 25618007 .
• Jin YH, Jeon EJ, Li QL, Lee YH, Choi JK, Kim WJ, Lee KY, Bae SC . Transforming growth factor-beta stimulates p300-dependent RUNX3 acetylation, which inhibits ubiquitination-mediated degradation . The Journal of Biological Chemistry . 279 . 28 . 29409–29417 . July 2004 . 15138260 . 10.1074/jbc.M313120200 . free .
• Ku JL, Kang SB, Shin YK, Kang HC, Hong SH, Kim IJ, Shin JH, Han IO, Park JG . Promoter hypermethylation downregulates RUNX3 gene expression in colorectal cancer cell lines . Oncogene . 23 . 40 . 6736–6742 . September 2004 . 15273736 . 10.1038/sj.onc.1207731 . 28548483 .
• Sakakura C, Hagiwara A, Miyagawa K, Nakashima S, Yoshikawa T, Kin S, Nakase Y, Ito K, Yamagishi H, Yazumi S, Chiba T, Ito Y . Frequent downregulation of the runt domain transcription factors RUNX1, RUNX3 and their cofactor CBFB in gastric cancer . International Journal of Cancer . 113 . 2 . 221–228 . January 2005 . 15386419 . 10.1002/ijc.20551 . 34944735 . free .

Notes and References

1. Levanon D, Negreanu V, Bernstein Y, Bar-Am I, Avivi L, Groner Y . AML1, AML2, and AML3, the human members of the runt domain gene-family: cDNA structure, expression, and chromosomal localization . Genomics . 23 . 2 . 425–432 . September 1994 . 7835892 . 10.1006/geno.1994.1519 .
2. Levanon D, Eisenstein M, Groner Y . Site-directed mutagenesis supports a three-dimensional model of the runt domain . Journal of Molecular Biology . 277 . 3 . 509–512 . April 1998 . 9533875 . 10.1006/jmbi.1998.1633 . 13139512 .
3. Web site: Entrez Gene: RUNX3 runt-related transcription factor 3.
4. Hoek KS, Schlegel NC, Eichhoff OM, Widmer DS, Praetorius C, Einarsson SO, Valgeirsdottir S, Bergsteinsdottir K, Schepsky A, Dummer R, Steingrimsson E . Novel MITF targets identified using a two-step DNA microarray strategy . Pigment Cell & Melanoma Research . 21 . 6 . 665–676 . December 2008 . 19067971 . 10.1111/j.1755-148X.2008.00505.x . free .
5. Lee YS, Lee JW, Jang JW, Chi XZ, Kim JH, Li YH, Kim MK, Kim DM, Choi BS, Kim EG, Chung JH, Lee OJ, Lee YM, Suh JW, Chuang LS, Ito Y, Bae SC . Runx3 inactivation is a crucial early event in the development of lung adenocarcinoma . Cancer Cell . 24 . 5 . 603–616 . November 2013 . 24229708 . 10.1016/j.ccr.2013.10.003 . free .
6. Lee JW, Kim DM, Jang JW, Park TG, Song SH, Lee YS, Chi XZ, Park IY, Hyun JW, Ito Y, Bae SC . RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction-point . Nature Communications . 10 . 1 . 1897 . April 2019 . 31015486 . 6479060 . 10.1038/s41467-019-09810-w . free . 2019NatCo..10.1897L .
7. Li QL, Ito K, Sakakura C, Fukamachi H, Inoue K, Chi XZ, Lee KY, Nomura S, Lee CW, Han SB, Kim HM, Kim WJ, Yamamoto H, Yamashita N, Yano T, Ikeda T, Itohara S, Inazawa J, Abe T, Hagiwara A, Yamagishi H, Ooe A, Kaneda A, Sugimura T, Ushijima T, Bae SC, Ito Y . Causal relationship between the loss of RUNX3 expression and gastric cancer . Cell . 109 . 1 . 113–124 . April 2002 . 11955451 . 10.1016/S0092-8674(02)00690-6 . 11362226 . free .
8. Levanon D, Bernstein Y, Negreanu V, Bone KR, Pozner A, Eilam R, Lotem J, Brenner O, Groner Y . Absence of Runx3 expression in normal gastrointestinal epithelium calls into question its tumour suppressor function . EMBO Molecular Medicine . 3 . 10 . 593–604 . October 2011 . 21786422 . 3258485 . 10.1002/emmm.201100168 .
9. Book: Maiväli, Ülo . 2015 . Interpreting Biomedical Science . Academic Press . 44–45 . 9780124186897 .
10. Ito K, Inoue KI, Bae SC, Ito Y . Runx3 expression in gastrointestinal tract epithelium: resolving the controversy . Oncogene . 28 . 10 . 1379–1384 . March 2009 . 19169278 . 10.1038/onc.2008.496 .
11. Levanon D, Goldstein RE, Bernstein Y, Tang H, Goldenberg D, Stifani S, Paroush Z, Groner Y . Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors . Proceedings of the National Academy of Sciences of the United States of America . 95 . 20 . 11590–11595 . September 1998 . 9751710 . 21685 . 10.1073/pnas.95.20.11590 . free . 1998PNAS...9511590L .