Background
Acute myeloid leukemia (AML) is a genetically and clinically heterogeneous disorder featured by the incomplete maturation of hematopoietic stem cell and the reduction of normal blood counts [
1]. Despite great efforts have been made in new therapy development, chemotherapy with cytarabine and anthracycline remains the current treatment protocols in AML, which conduct complete remission (CR) rates of 70–80% [
2]. However, more than half of adult patients and around 80% of elder patients develop into primary refractoriness, relapse, or treatment-related mortality [
3]. In addition, tremendous individual variability in prognosis varies greatly among patients: 5-year survival varies from 18 to 82%, and relapse rate varies from 33 to 80%, which can be partly explained by disease subtype, age, somatic mutations, gene expression abnormalities, and other molecular alterations. Genetic variants in those, such as in
NPM1, FLT3-
ITD, CEBPA, WT1 have been verified to be marks of prognosis [
4‐
6], however, these factors can only explain part of individual variants for AML.
Recent studies have underscored the significant role of epigenetic mechanisms in chemotherapy sensitivity and disease prognosis of AML. Such as DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) R882 mutations, which give rise to focal hypomethylation phenotype, were associated with inferior prognosis in AML [
7,
8]. Mutations in Ten–eleven-translocation (TET)-enzymes (TET2), which catalyzed the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), confers unfavorable prognostic factor in AML patients with intermediate-risk cytogenetics [
9].
SETD2 belongs to a superfamily of lysine methyltransferase, which is a solely H3K36 trimethylation
methyltransferase in mammals. H3K36 trimethylation has also been implicated in a diverse of cellular biology functions, including transcriptional activation, alternative splicing, dosage compensation, DNA replication and repair, and homologous recombination [
10].
SETD2 is a 2-hit tumor suppressor gene, for loss-of-function mutations and deletions were detected in a series of tumor types, most notably in clear cell renal cell cancer (ccRCC) [
11] and high-grade gliomas [
12] and subsequently presents in a subset of patients with acute lymphoblastic leukemia [
13] and acute myeloid leukemia [
14]. Most of mutations or abnormalities of
SETD2 has been reported to be associated with a worse outcome among patients with ccRCC suggested a protection value of
SETD2 [
15]. Moreover, a selective enrichment of
SETD2 inactivating mutation in relapsed acute leukemia indicated an association with chemoresistance [
16]. However, whether single-nucleotide polymorphisms (SNPs) in
SETD2 related to disease progression and drug response remains unknown.
In the present study, we performed the candidate gene association study to find out whether SETD2 SNPs correlated with AML survival and chemotherapy response, which will explore factors leading to individual difference in AML prognosis and will provide new directions for new treatment.
Discussion
In this study, we studied the association between SETD2 tagSNPs with chemosensitivity response to Ara-C baseds therapy as well as disease prognosis in Chinese AML patients for the first time. We found that SETD2 rs76208147 TT genotype predicted worse OS in the AML patients, while the SETD2 rs4082155 AA genotype were associated with chemoresistance after Ara-C based therapy. Moreover, haplotype with one or two copies of GGT showed better chemotherapy response compare with individuals with no copies.
The
SETD2 gene encodes a 230 kDa protein that is non-redundantly responsible for trimethylation of lysine 36 on histone H3 (H3K36me3), a critical mark that is involved in various important cellular processes such as transcriptional elongation, alteration splicing, mismatch repair regulation and homologous recombination repair [
22‐
27]. Recently,
SETD2 was identified as tumor suppressor, as loss-of-function mutation with
SETD2 has been discovered in various tumors, including ccRCC, lung adenocarcinoma, gliomas, AML, ALL, and mastocytosis [
12,
28‐
32]. In addition, loss-of-function mutation in
SETD2 and/or decreased H3K36me3 levels have been linked to poor clinical prognosis in lung cancer and ccRCC [
15,
33]. In AML,
SETD2 mutations are recurrent events and are associated with chromosomal abnormalities that are known to be driver mutations in leukemogenesis, such as MLL-rearrangement [
14]. In the presence of chromosomal translocation, such as MLL-rearrangement, knockdown of
SETD2 promotes initiation as well as progression of tumor by expediting the potential of self-renewal of leukemic stem cell [
14]. Notably, under normal hematopoietic condition,
SETD2 is required to maintain self-renewal capability of hematopoietic stem cell,
SETD2-deleted HSCs gives rise to malignant transformation eventually [
34]. Consistent with our findings,
SETD2 rs76208147 TT genotype indicates worse prognosis of AML patient, which underlying mechanism warrants further investigation.
Recently, it is well accepted that
SETD2 was associated with chemotherapy sensitivity. Studies have identified the enrichment of mutations in
SETD2 in relapsed acute lymphoblastic leukemia and MLL-rearranged acute leukemia [
16]. In addition,
SETD2 mutations led to resistance to DNA-damaging agents, cytarabine, 6-thioguanine, doxorubicin, and etoposide, but not to a non-DNA damaging agent via impairing DNA damage recognition [
35]. Moreover, acquired loss-of-function mutations in
SETD2 enable metastatic non-small cell lung cancer to resist to cisplatin [
36]. All of these reports suggested that
SETD2 exerted a subtle impact on the DNA mismatch repair (MMR) machinery [
37]. It has been reported that MSH6, which is an essential component of the MMR machinery localizes to chromatin by binding to the H3K36 trimethyl mark that
SETD2 makes.
SETD2 knockdown has been shown to give rise to mislocalization of MSH6 and microsatellite instability and a mutator phenotype in several cell types. There are at least two possible explanations to link
SETD2 inactivation to the survival of leukemia cell. First, a mutator phenotype induced by
SETD2 inactivation could increase the mutational diversity and thus, adaptability of the leukemia, leading to clonal survival. Two, since intact MMR is important for triggering apoptosis and/or cell cycle arrest in response to many DNA damaging chemotherapies,
SETD2 loss may lead to chemotherapy tolerance [
35]. To be mentioned, the function of
SETD2 is also involved in homologous recombination which deficiency have generally led to sensitivity to DNA-damaging agents, such as cisplatin [
24]. That being said, the impact of
SETD2 alteration on homologous recombination require further investigation.
SETD2 was discovered because of its capability to catalyze H3K36 trimethyltransferase, and major researches have been confined to its role of histone modification. But, in recent studies it has become apparent that
SETD2 exerts diverse functions that unrelated to histone modification. For instance, it has been reported that
SETD2 directly mediates STAT1 methylation on lysine 525, which amplifies the antiviral immunity of IFN-a [
38], and a-tubulin methylation on lysine 40, which maintains genomic stability through microtubule methylation [
39]. Taken together, the contributions of these additional functions of
SETD2 on prognosis and treatment of AML remain to be fully elucidated.
There are several limitations in the present study. First, the outcomes of our study failed to undergo multiple test adjusting, P values lost statistical significance when Bonferroni correction was performed possibly due to the limited sample size included in our study. Second, Ara-C response is affected by various genetic factors, the contribution of single unique gene to the drug exposure might be limited.
Authors’ contributions
WSW made main contributions to specimen collection, sorting date, date analysis; YXQ analyzed the data; LYZ, ZKW, CP, YH and ZHY assisted in specimen collection, acquisition of clinical date and obtaining the follow-up information; LX gave useful advice; ZH, ZXL helped to collect specimen smoothly; CXP helped to design research and gave guidance; CS and ZG provided substantial guidance, designed the research and drafted and revised manuscript. All authors read and approved the final manuscript.