Oncogenic Chromatin Modifier KAT2A Activates MCT1 to Drive the Glycolytic Process and Tumor Progression in Renal Cell Carcinoma

ObjectivesThis study aims to investigate the underlying mechanisms of KAT2A/MCT1 axis in renal cell carcinoma (RCC), providing potential therapeutic targets.MethodsWe obtained the expression data of KAT2A and MCT1 from The Cancer Genome Atlas Kidney Clear Cell Carcinoma (TCGA-KIRC) and International Cancer Genome Consortium (ICGC) databases. Differential analysis was conducted via the limma package. The CCK8 assay, soft agar assay, clone formation assay, and patients-derived organoid models were used to detect cell growth. The transwell and wound-healing assays were utilized to detect cell migration. The in vitro and in vivo assays were further conducted to assess the oncogenic roles of KAT2A. The transcriptome sequencing and chromatin immunoprecipitation (ChIP) sequencing were conducted to screen KAT2A downstream targets. The dose-effect curves were used to detect the 50% inhibiting concentration (IC50) of AZD3965. Data analysis was performed in the Graphpad Prism (Version 8.3.0) and R software (Version 3.6.1).ResultsOur study found that KAT2A was highly expressed in RCC versus normal samples. Prognostic analysis indicated that a high KAT2A was an independent biomarker and associated with poor survival outcomes. KAT2A could promote RCC proliferation and distal metastasis in vitro and in vivo. Transcriptome analysis and ChIP-seq were combined to find that KAT2A mainly regulated the glycolytic process. Validation and rescue assays revealed that MCT1 was the downstream target of KAT2A, and KAT2A depended on MCT1 to promote RCC malignant phenotypes. Lastly, MCT1 inhibitor (AZD3965) was effective to treat KAT2A-induced RCC progression.ConclusionOur study indicated that KAT2A was an oncogenic chromatin modifier that promotes RCC progression by inducing MCT1 expression. We proposed that MCT1 inhibitor (AZD3965) was useful for suppressing RCC.

Genomic Landscape of Acute Myeloid Leukemia (AML) on the Basis of 2017 ELN Classification and Other Mutations in Adult AML - Single Healthcare System Data

Introduction Recently, genomic mutation profiling of leukemic cells has been actively studied and some results have been integrated into the 2017 ELN classification with cytogenetic analysis for risk assessment of AML populations.1 However, only a few mutations are well identified and included in the 2017 ELN classification. In addition, except interaction between NPM1 and FLT-ITD, correlation and co-occurrence among various mutations have not been well studied. Here we describe our single center genomic landscapes of 2017 ELN guideline components with other NGS mutations in adult AML. Methodology We performed hematopoietic tumor profiling assay by next generation sequencing (NGS) testing and cytogenetic chromosome analyses in 193 AML patients diagnosed from 2018-08-01 to 2020-03-10. Treatment-related AML patients were excluded. All NGS and cytogenetic analyses were performed before starting chemotherapy. On the basis on 2017 ELN cytogenetic and mutations components, we analyzed significantly other co-occurred and exclusively occurred NGS mutations by using Fischer's exact test. Based on 2017 ELN classification, either one of t(6;9), t(v;11q23.3), t(9;22), inv(3) or t(3;3),-5, del(5q), -7, -17, or complex/monsoonal karyotype meeting the ELN criteria positive was grouped as Adverse Karyotype. 43 AML related genes, including 6 ELN components of NPM1, FLT-ITD low, CEBPA biallelic, TP53, RUNX1, ASXL1 and other 37 mutations including DNMT3A, NRAS and KRAS were analyzed as a single component. In addition, we grouped some mutations into larger sets or pathways and analyzed them in the same way. DNMT3A, TET2, IDH1, IDH2, and SETBP1 were grouped as DNA methylation. SFSB1, SRSF2, U2AF1, and ZRSR2 were grouped as spliceosome. BCOR, CBORL1, EXH2, and KDM6A were grouped as chromatin modifier. ASXL1, which is also chromatin modifier, was analyzed as a separated component because it is a part of the 2017 ELN. NRAS and KRAS were analyzed separately and also as one group. One-tailed statistical significance is at level of 5% for statistical analysis. Results Our cohort was male predominant (57%, 110/193) with median age of 64 YO (range 18 - 93). 29%, 25% and 46% of patients were 2017 ELN favorable, intermediate, and adverse group respectively. 27.5% and 40% were Adverse and Normal Karyotype respectively. 4%, 4% and 1% of patients were RUNX1-RUNX1T1, CBFB-MYH11 and MLLT3-KMT2A positive respectively. Figure1 describes the occurrence rate of significantly occurred mutations. Regarding 2017 ELN components, 37 patients (19.2%) were positive to NPM1, 34 patients (17.6%) had FLT-ITD low, 3 (1.6%) had CEBPA biallelic, 40 (20.7%) had TP53, 27 (14.0%) had ASXL, and 24 (12.4%) had RUNX. There was no FLT-ITD high mutation in our cohort. In total 63 patients (32.6%) had at least one DNA methylation mutation. 44 patients (22.8%) had at least one spliceosome mutation and 9 patients (4.6%) had at least one chromatin modifier mutation other than ASXL1. In activated signaling, NRAS, KRAS, FLT-TKD were significantly occurred. Table 1 describes significantly co-occurred and exclusively occurred mutations and Figure 2 visualizes significantly co-occurred and exclusively occurred mutations. TP53 exclusively occurred with normal karyotype and many different mutations including NPM1, FLT-ITD low, DNA methylation group, and KRAS/NRAS, and significantly co-occurred with Adverse Karyotype. NPM1 significantly co-occurred with Normal Karyotype and FLT-ITD mutations. Interestingly, DNA methylation group and especially IDH2 and DNMT3A significantly co-occurred with NPM1. Also, RUNX1, ASXL1 and Spliceosome group co-occurred with each other. KRAS/NRAS co-occurred with CBFB-MYH1. KIT co-occurred with CBFB-MYH1 and RUNX-RUNX1T1, although the sample sizes were relatively small. Discussion Based on strong accumulated evidence, ELN established new guidelines in 2017. Therefore, it would be a sophisticated way to find other significant mutations and their interactions on the basis of already well established 2017 ELN components. Our findings suggest DNA methylation regulatory genes, especially DNMT3A and IDH2, significantly co-occurred with NPM1, which is a component of the favorable group. Also, spliceosome mutations significantly co-occurred with RUNX1 and ASXL1, which are components of the adverse group. Further research is needed to determine whether those cooccurrences affect each group's prognosis. Figure Disclosures No relevant conflicts of interest to declare.

Chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing

Dysregulated alternative splicing (AS) driving carcinogenetic mitosis remains poorly understood. Here, we demonstrate that cancer metastasis-associated antigen 1 (MTA1), a well-known oncogenic chromatin modifier, broadly interacts and co-expresses with RBPs across cancers, contributing to cancerous mitosis-related AS. Using developed fCLIP-seq technology, we show that MTA1 binds abundant transcripts, preferentially at splicing-responsible motifs, influencing the abundance and AS pattern of target transcripts. MTA1 regulates the mRNA level and guides the AS of a series of mitosis regulators. MTA1 deletion abrogated the dynamic AS switches of variants for ATRX and MYBL2 at mitotic stage, which are relevant to mitosis-related tumorigenesis. MTA1 dysfunction causes defective mitotic arrest, leads to aberrant chromosome segregation, and results in chromosomal instability (CIN), eventually contributing to tumorigenesis. Currently, little is known about the RNA splicing during mitosis; here, we uncover that MTA1 binds transcripts and orchestrates dynamic splicing of mitosis regulators in tumorigenesis.

The Genetic Basis of Transcriptional and Spatial Heterogeneity of Squamous Features in Pancreatic Ductal Adenocarcinoma

SummaryRecent studies indicate that pancreatic cancer expression profiles are variable and largely reflect a classical or basal-type phenotype. We performed genetic sequencing, RNA-seq, and histologic review of multiregion sampled pancreatic cancers and found that squamous and squamoid features, indicators of poor prognosis, correlate with a “basal-like” expressional type. Cancers with squamous features were more likely to have truncal mutations in chromatin modifier genes and intercellular heterogeneity for MYC amplification that was associated with entosis. In most patients the basal phenotype coexisted with a glandular component, and phylogenetic studies indicated that it arose from a subclonal population in the tumor. These data provide a unifying paradigm for understanding the interrelationship of basal-type features, squamous histology, and somatic mutations in chromatin modifier genes in the context of the clonal evolution of pancreatic cancer.