Background
Renal cell carcinoma (RCC) has been ranked as the seventh leading cancer type in the developed world [
1]. RCC is classified into several histological subtypes such as clear cell renal cell carcinomas, papillary renal cell carcinomas and chromophobe renal cell carcinomas. Among them, KIRC is the most common and lethal subtype of RCC [
2]. Surgical and targeted immunotherapy therapies are indispensable treatment options for RCC [
3‐
5]. However, tumor recurrence and drug resistance are the main problems in the treatment of RCC. Exploring predictive biomarkers is very important for the early diagnosis and prognosis of RCC.
The Histone acetyltransferases (HATs) of the MYST family are highly conserved from yeast to humans and function exclusively in multisubunit protein complexes [
6]. Their main feature is the existence of a highly conserved MYST domain, which is composed of an acetyl CoA binding motif and a zinc ring. The HATs of the MYST family comprise five members: KAT5 (Tip60), KAT6A (MOZ/MYST3), KAT6B (MORF/MYST4), KAT7 (HBO1/MYST2) and KAT8 (MOF/MYST1) [
7]. MYST family HATs can catalyze protein acetylation in both the nucleus and cytoplasm. MYST HATs are involved in various biological functions, including nuclear processes, transcription, DNA damage response, DNA repair, DNA replication, stress response and metabolism [
8]. Abnormally expressed MYST HATs are closely associated with some human cancers and neurodegenerative diseases [
9,
10].
To date, the significance of the expression of MYST HATs in relation to the clinicopathological and prognostic variables of patients with KIRC has not yet been fully revealed. In this study, we performed an integrative analysis of MYST HATs in KIRC based on the public database.
Methods
Gene correlation and prognostic significance analysis in GEPIA
The online database Gene Expression Profiling Interactive Analysis (GEPIA) (
http://gepia.cancer-pku.cn/index.html) [
11] was used to obtain information on differential expression analysis, gene profiling, correlation analysis, and patient survival analysis of MYST HATs based on TCGA and GTEx data (*
P < 0.05, FDR adjustment).
Gene expression analysis
The correlations of MYST HAT expression with the clinicopathological characteristics of patients with KIRC were determined using the UALCAN database [
12] (
http://ualcan.path.uab.edu/index.html). Pancancer analysis was performed using the TIMER web server (
http://timer.comp-genomics.org/). The statistical significance computed by the Wilcoxon test is annotated by the number of stars (*:
P value < 0.05; **:
P value < 0.01; ***:
P value < 0.001). Immunohistochemical images of cancer and normal tissue were downloaded from Human Protein Atlas (
http://www.proteinatlas.org/).
GSEA
Gene set enrichment analysis (GSEA) is a method for analyzing microarray data of whole genome expression profiles, which compare genes with predefined gene sets. The LinkedOmics online database was used to perform a GSEA analysis [
13], which explored the correlation between the potential functions of MYST HAT expression and the pathogenesis of KIRC based on the TCGA and GTEx data (FDR < 0.05) (
http://linkedomics.org/login.php).
Immune infiltrate analysis
The TIMER web server is a comprehensive resource for systematic analysis of immune infiltrates in various types of cancer [
14]. The Gene module on the TIMER web was used to explore the correlation between gene expression and abundance of immune infiltrates (
https://cistrome.shinyapps.io/timer/).
Western blot analysis of KIRC tissue samples
KIRC tissue samples and adjacent paired non-cancerous tissues were obtained from 20 KIRC patients. All samples were stored at the Affiliated Hospital of Hebei University. The number of subjects, the age range, the sex ratio, the criteria used for the diagnosis, and the description of any control subjects were shown in Additional File 1. All procedures follow the ethical guidelines for the storage and use of human biological samples. The tissue samples were rapidly frozen in liquid nitrogen and stored at -80 ° C. The Ethics Committee of the Affiliated Hospital of Hebei University approved the present investigation (NO.2020-KY-021). Tissue samples were collected and dissolved in RIPA lysis buffer. After centrifugation, the supernatant was quantified by the Bradford method. 20 µg of the supernatant was subjected to SDS-PAGE and transferred to a PVDF membrane, then incubated with antibodies, KAT5 (ab137518), KAT6B (ab246879) KAT7 (ab190908) (ABCAM, MA, USA), and KAT6A (sc-293,283) (Santa Cruz Biotechnology, MA, USA) (dilution 1:500). Anti-actin antibody (sc-8432) (dilution 1:1000) was used to ensure equal protein loading (Santa Cruz Biotechnology, MA, USA). Anti-rabbit IgG, HRP-linked antibody (sc-2357) and anti-goat IgG, HRP-linked antibody (sc-2354) were used as secondary antibody (dilution 1:1000) (Santa Cruz Biotechnology, MA, USA). Densitometry intensity was calculated using image J software.
Statistical analysis
The expression results were displayed in the fold change with the P values. Survival curves were made using the Kaplan-Meier method. Spearman rank correlation was performed to investigate the correlation of gene expression. P < 0.05 was considered statistically significant.
Discussion
MYST HATs play an important role in transcription regulation, DNA repair, and DNA replication through the acetylation of histone lysine residues [
6]. We studied the relationships between MYST HATs and clinical status, and found that MYST HATs except KAT8 are favorable prognostic maker markersfor KIRC patients.
KAT5 plays an important role in genomic instability, gene transcription, and DNA damage repair [
16]. Silencing of KAT5 in cells leads to early embryonic lethality [
17]. The KAT5 gene is a haplo-insufficient tumor suppressor required for an oncogene-induced DNA damage response [
18]. The expression of KAT5 was downregulated in colon, lung, breast, and other cancers [
19]. KAT5 and KAT6A were associated with prognosis and tumor mutation burden in KIRC [
20]. In our study, low expression of KAT5 predicted advanced TNM stage and was significantly correlated with poor overall survival and disease-free survival in KIRC patients. TCGA data showed that the transcription level of KAT5 in KIRC was higher than that in normal tissues, but the protein level detected by immune histochemistry and western blotting was not significantly different. The mRNA level and the protein level of KAT5 expression exhibited a different trend in KIRC, but the reason was not entirely clear. The gene correlation analysis showed that KAT5 was negatively correlated with T cell activation and the immune response in KIRC. However, TIME database analysis found that KAT5 was weakly correlated with tumor infiltrating lymphocytes. The two types of data explored the relationship between KAT5 and immunity at different levels. Although there were some contradictions, these data indicated that KAT5 could not improve the immune response. In view of some contradictions in the results of KAT5, it is necessary to further study whether KAT5 is a prognostic marker of KIRC.KAT6A and KAT6B have a similar structure with 60% amino acid identity and 66% similarity [
21]. Both KAT6A and KAT6B are composed of tandem PHD fingers, a MYST domain, an acid region, and an SM-rich domain [
22]. KAT6A and KAT6B play an important role in vertebrate development. The human KAT6A and KAT6B genes mutated recurrently in leukemia, nonhematologic malignancies, and multiple developmental disorders [
23]. These two acetyltransferases are considered as good targets for cancer therapy [
24]. Inhibition of KAT6A and KAT6B could induce senescence and arrest tumor growth [
25]. In our study, the function of KAT6A and KAT6B in KIRC is different from that of other types of tumors. Up-regulation of
KAT6A and
KAT6B showed good overall survival benefits in KIRC. We also found that
KAT6A showed a strong positive correlation with CD4
+ T cells, macrophages, and neutrophils, which may make it as a favorable marker in KIRC (Fig.
8).
KAT7 complexes are the major acetyltransferase responsible for the histone H4 and H3 acetylation and regulate various cellular functions, such as DNA replication, gene transcription, protein ubiquitination and immune regulation [
26]. KAT7 is also involved in cell senescence and is a therapeutic target for ageing [
27]. KAT7 is up-regulated in a variety of cancers such as breast, prostate, bladder and gastric cancer [
28]. KAT7 is reported to be an anticancer target. Our results are different from previous reports. We found that
KAT7 decreased in KIRC and low expression of
KAT7 was significantly associated with poor overall survival in patients with KIRC. KAT7 also showed positive associations with immune infiltration level.
KAT8 plays an important role in different cell functions, including autophagy, carbon metabolism, gene transcription, DNA damage repair, cell cycle regulation, and early embryonic development [
29‐
32]. KAT8 plays a dual role in the tumor, acting as a suppressor or promoting tumor growth [
33‐
36]. In our study, the high expression of
KAT8 was not related to good overall survival and disease-free survival rate in KIRC (Additional File 4). GESA analysis showed that the function of KAT8 was obviously different from that of other MYST HATs in KIRC.
We also found that the expression of MYST HATs (
KAT5,
KAT6A,
KAT6B and
KAT7) showed a strong correlation with each other in KIRC. However, the correlation was rare in other cancers. This phenomenon may be related to the special function of MYST HATs in KIRC. MYST HATs function in multiunit protein complexes. We speculated that the antitumor function of MYST HATs may be due to the existence of a tumor suppressor protein in the functional complex. The relationship between MYST HATs and the ING family has been studied extensively. The ING family has been reported as tumor suppressor gene that regulate chromatin function through interaction with histone acetyltransferase or histone deacetylase protein complexes [
37]. In our study, ING3 showed a strong correlation with MYST HATs except
KAT8. It is unclear whether the regulatory effect of
ING3 on MYST HATs can inhibit tumor progression in KIRC. Human MORF4L1(MRG15) is a transcription factor involved in cellular senescence [
38]. However, little is known about the role of
MORF4L1 in KIRC. We found that
MORF4L1 showed a strong correlation with MYST HATs except
KAT8, which implied that MYST HATs may be involved in cellular senescence. More studies were needed to explore the detailed relationship between MYST HATs and
ING3 or
MORF4L1 in KIRC.
Our study has some limitations that need further discussion. First, there is no in-depth study on the relationship between MYST HATs and histone methylation in KIRC. Second, although MYST HATs affect the metastasis and development of KIRC, the specific mechanism has not been explored. Although our analysis is still preliminary and more details need to be improved with experiments, our investigation may help guide a further study of MYST HATs, especially for the role of these genes in immune infiltration.
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