Identification of RUNX1T1 as a potential epigenetic modifier in small‐cell lung cancer

Abstract

Small cell lung cancer (SCLC) can be sub-grouped into common 'pure' and rare 'combined' SCLC (c-SCLC). c-SCLC features a mixed tumor histology of both SCLC and non-small cell lung cancer (NSCLC). We performed targeted exon sequencing on 90 SCLC patients, including two with c-SCLC, and discovered RUNX1T1 amplification specific to small cell tumors of both c-SCLC patients, but in only 2 of 88 'pure' SCLC patients. RUNX1T1 was first identified in the fusion transcript AML1/ETO, which occurs in 12%-15% of acute myelogenous leukemia (AML). We further show higher expression of RUNX1T1 in the SCLC component of another c-SCLC tumor by in situ hybridization. RUNX1T1 expression was enriched in SCLC compared to all other cancers, including NSCLC, in both cell lines and tumor specimens, as shown by mRNA level and western blotting. Transcriptomic analysis of hallmark genes decreased by stable RUNX1T1 overexpression revealed a significant change in E2F targets. Validation experiments in multiple lung cancer cell lines showed that RUNX1T1 overexpression consistently decreased CDKN1A (p21) expression and increased E2F transcriptional activity, which is commonly altered in SCLC. Chromatin immunoprecipitation (ChIP) in these overexpressing cells demonstrated that RUNX1T1 interacts with the CDKN1A (p21) promoter region, which displayed parallel reductions in histone 3 acetylation. Furthermore, reduced p21 expression could be dramatically restored by HDAC inhibition using Trischostatin A. Reanalysis of ChIP-seq data in Kasumi-1 AML cells showed that knockdown of the RUNX1T1 fusion protein was associated with increased global acetylation, including the CDKN1A (p21) promoter. Thus, our study identifies RUNX1T1 as a biomarker and potential epigenetic regulator of SCLC.

Comprehensive Analysis of Tripterine Anti-Ovarian Cancer Effects Using Weighted Gene Co-Expression Network Analysis and Molecular Docking

“…Studies have shown that the upregulation of RUNX1T1 can inhibit the proliferation, migration, and invasion of ovarian cancer [ 34 ]. Another study found that RUNX1T1 is highly expressed in non-small cell lung cancer through in situ hybridization [ 35 ]. Further research is needed to determine the role of this gene in cancer.…”

RUNX1T1 function in cell fate

“…NHR3, containing a putative amphipathic helix, features in the interaction of A-kinase anchor proteins with RIIα and functions by partially binding to co-repressors [ 13 ]. The NHR4 domain, also regarded as a myeloid-Nervy-DEAF1 homology domain (MYND), exhibits two zinc structures at the C terminal, which assist in the combination of RUNX1T1 with the nuclear core repressor (N-CoR) and DNMTs to further recruit HDACs and form a co-repressive compound [ 14 ]. After the binding of the CRD with mSin3A and effective recruitment of HDACs, histone is methylated to induce a closer bind with DNA, which tightens the spatial structure of the chromosome and makes it difficult for transcription to be triggered.…”

“…Even though RUNX1T1 is downregulated in most cases of carcinogenesis, its upregulation has also been revealed in research on small cell lung cancer (SCLC) and bladder cancer [ 14 , 52 ]. By binding to the promoter of CDKN1A, RUNX1T1 inhibits histone acetylation, which leads to E2F upregulation and carcinogenesis acceleration, an expected modulation accompanying the loss of tumor-repressor RB1 in SCLC [ 14 ].…”

“…Even though RUNX1T1 is downregulated in most cases of carcinogenesis, its upregulation has also been revealed in research on small cell lung cancer (SCLC) and bladder cancer [ 14 , 52 ]. By binding to the promoter of CDKN1A, RUNX1T1 inhibits histone acetylation, which leads to E2F upregulation and carcinogenesis acceleration, an expected modulation accompanying the loss of tumor-repressor RB1 in SCLC [ 14 ]. RUNX1T1 is also involved in the progression of bladder cancer via the positive RUNX1T1/TCF4/miR-625-5p feedback loop, closely relating to RNA-binding motif protein 24 (RBM24), a determinant of carcinogenesis.…”

Identification of Novel Prognostic Biomarkers to Predict Pembrolizumab Response in Gastric Cancer by Bioinformatics Analysis

“…In addition, RUNX1T1 also participates in the regulation of numerous biological processes, such as protein interactions [9], proliferation and differentiation of hematopoietic stem cells [11], adipocyte proliferation [12], and hippocampal neuronal differentiation [13]. Increasingly, reports indicate that RUNX1T1 is a candidate biomarker that is related to diagnosis and prognosis in various solid tumors, including pancreatic endocrine tumors, small cell lung cancer, and colorectal cancer [14][15][16]. However, the underlying functions and mechanisms of RUNX1T1 in ICIs treatment of GC are still unclear.…”