The RUNX Family of Proteins, DNA Repair, and Cancer

Abstract

The RUNX family of transcription factors, including RUNX1, RUNX2, and RUNX3, are key regulators of development and can function as either tumor suppressors or oncogenes in cancer. Emerging evidence suggests that the dysregulation of RUNX genes can promote genomic instability in both leukemia and solid cancers by impairing DNA repair mechanisms. RUNX proteins control the cellular response to DNA damage by regulating the p53, Fanconi anemia, and oxidative stress repair pathways through transcriptional or non-transcriptional mechanisms. This review highlights the importance of RUNX-dependent DNA repair regulation in human cancers.

Keywords: DNA damage; DNA repair; Fanconi anemia; RUNX1; RUNX2; RUNX3; TGF-β; leukemia; p53; reactive oxygen species.

Figure 1

RUNX1 leukemic fusion proteins, DNA repair, and cancer. RUNX1-ETO attenuates the expression of genes involved in base excision repair, DSB repair, and the HR/FA pathways. RUNX1-ETO overexpression also reduces the efficiency of oxidative stress repair and induces the accumulation of γH2AX marked DSBs. In mouse models, RUNX1-ETO expression elevates mutation rates, while in human cancers, RUNX1-ETO expression induces a ROS-associated mutation signature. The leukemogenic fusion protein ETV6-RUNX1 blocks the expression of DNA repair genes and attenuates p53 signaling by increasing MDM2 expression. RUNX1-EVI1 was shown to reduce the expression of genes involved in MMR and NER in a zebrafish model.

Figure 2

RUNX1 deletions, mutations, DNA repair, and cancer. A C-terminal deletion mutant of RUNX1 (RUNX1dc), as well as the DNA-binding point mutant of RUNX1 (R174Q), has been shown to increase DNA DSBs in the cells. Moreover, RUNT domain point mutations in blast crisis CML induce the mutational signature 9, which is attributed to polymerase η and AID activity during somatic hypermutation (SHM).

Figure 3

RUNX3 and RUNX3 dysregulation, DNA repair, and cancer. Lower RUNX3 transcript levels correlated with higher copy number alterations (CNAs) in bladder, urothelial carcinoma, and lung adenocarcinoma and with high mutation rate in esophageal carcinoma and liver hepatocellular carcinoma. In contrast, the higher levels of RUNX3 correlated with reduced DNA repair gene expression in AML and with higher levels of MYC in ovarian cancer and NKT cell lymphoma. While the expression of RUNX2 promoted the repair of UV-induced DNA damage and induced greater chemoresistance to adriamycin, the relationship between RUNX2 levels and mutational accumulation in the context of human malignancy remains unknown.

Figure 4

RUNX-p53 crosstalk and regulation of the DNA damage response. Both RUNX1 and RUNX3 form a complex with p53 and promote the transactivation of p53 target genes upon exposure to DNA damage. In addition, RUNX1 stimulates the acetylation of p53 at Lys-373/382, while RUNX3 promotes p53 phosphorylation at the serine 15 residue. The interaction of RUNX2 with p53, on the other hand, suppresses the transactivation of p53 target genes in response to the chemotherapeutic adriamycin.

Figure 5

RUNX proteins and the FA pathway of DNA repair. The multiple lines of evidence linking RUNX proteins with the FA pathway of DNA repair are summarized here. 1. Runx1/Runx3 (DKO) mice experienced mortality due to either BMF or a myeloproliferative disease, and cells derived from such mice had an elevated sensitivity to DNA ICLs, reminiscent of phenotypes manifested by FA patients. 2. RUNX proteins were poly(ADP) ribosylated or PARylated after DNA damage in a PARP-dependent manner. RUNX proteins interacted and promoted the recruitment of mono-ubiquitinated FANCD2 to sites of DNA ICLs and promoted efficient DNA repair. 3. In the presence of DNA ICLs, RUNX3 has an increased interaction with the kinetochore complex (AURB, DSN1, CASC5, MIS12, ZWINT, PMF1, NSL1, and TPX2), the E2F7 transcription factor, and BLM (adapted from Tayet et al. [60]), of which the RUNX3-BLM interaction was shown to promote FANCD2 recruitment to sites of DNA ICLs. 4. RUNX1 walker domain mutations (G141 and R142 residues) from breast cancers were defective for DNA damage-dependent RUNX PARylation.

Figure 6

The interaction of RUNX3 with DNA replication and DNA repair factors in the absence of exogenous DNA damage. The SILAC mass spectrometry methodology was used to dissect the RUNX3 interactome in the absence of exogenous DNA damage. The list of RUNX3 interacting proteins from Tay et al., [60], Table S1, was analyzed using the EnrichR database [80]. Proteins indicated within green circles were retrieved as RUNX3-interacting proteins in co-immunoprecipitation studies. For the complete list of RUNX3-interacting proteins, please refer to [60].

Figure 7

RUNX proteins guard genomic integrity after TGFβ exposure. The loss of RUNX proteins triggers dramatic DNA damage cells in lung epithelial cells undergoing TGFβ-dependent EMT. RUNX proteins reduce TGFβ induced-oxidative stress by the transcriptional induction of the antioxidant HMOX1. However, upon RUNX loss, TGFβ induced much higher levels of oxidative damage, DSBs, and acquisition of the senescence-associated secretory phenotype (SASP), represented by CXCL1, INHBA, BMP2, CCL2, CXCL3, CXCL2, IL32, IL8, AREG, GDF15, and IL1A upregulation. Since inflammation can induce DNA damage, RUNX3 deficiency creates a self-re-enforcing feedback loop of inflammation and genomic instability.