Pluto Bioinformatics

GSE96758: Cooperative epigenetic remodeling by TET2 loss and NRAS mutation drives myeloid transformation and MEK inhibitor sensitivity [RNA-Seq]

Bulk RNA sequencing

Recent studies using next-generation sequencing technology have uncovered mutational landscapes of various myeloid malignancies (Cancer Genome Atlas Research Network, 2013; Yoshida et al., 2011). These genetic data revealed novel classes of mutations that commonly occur in patients with myeloid malignancies, including epigenetic regulators and spliceosomal genes. In addition, co-occurrence and mutual exclusivity of these disease alleles suggest convergent cooperative roles or common biological effects of specific alleles in myeloid leukemogenesis (Shih et al., 2012). Somatic deletions and loss-of-function mutations in TET2, a member of the TET family which regulates DNA methylation, were identified in 10-20% of myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN) patients, 12-24% of acute myeloid leukemia (AML) patients and 40-50% of chronic myelomonocytic leukemia (CMML) patients (Abdel-Wahab et al., 2009; Delhommeau et al., 2009; Jankowska et al., 2009; Langemeijer et al., 2009). Analysis carried out in large AML cohorts has shown that TET2 mutations are associated with adverse outcome in patients with intermediate-risk, cytogenetically normal AML (Patel et al., 2012). TET proteins (TET1-3) are Fe(II)- and a-ketoglutarate-dependent enzymes that catalyze the conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) leading to DNA demethylation (Guo et al., 2011; Tahiliani et al., 2009). Consistent with this notion, TET2 mutant AML patient samples show decreased 5-hmC levels and hypermethylation phenotype (Figueroa et al., 2010; Ko et al., 2010). Oncometabolite 2-hydroxyglutarate produced by IDH1/2 mutations inhibits TET2 function (Figueroa et al., 2010). Moreover, WT1 recruits TET2 to regulate its target gene expression (Wang et al., 2015) and WT1 mutations lead to reduced TET2 function and decreased 5-hmC levels (Rampal et al., 2014). Together, IDH1/2 mutations and WT1 mutations share, at least partially, common epigenetic pathogenesis in AML as TET2 mutations through altered DNA hydroxymethylation. A number of studies have shown that TET2 is a key regulator of hematopoietic stem cell (HSC) self-renewal and myeloid differentiation. Conditional loss of Tet2 in mouse hematopoietic compartment leads to expansion of hematopoietic stem/progenitor cells (HSPCs, LSK, lin- Sca1+ cKit+) and enhanced repopulating capacity in vivo (Li et al., 2011; Moran-Crusio et al., 2011; Quivoron et al., 2011). In addition, Tet2-mutant mice show myeloproliferation in vivo and TET2-silenced human cord blood cells show skewed differentiation towards CD14+ myelomonocytic lineage in vitro (Pronier et al., 2011), which is compatible with a high frequency of TET2 mutations in CMML patients. More recently, mutations in TET2 and in other epigenetic regulators, such as DNMT3A and ASXL1, are reported in individuals with clonal hematopoiesis without hematological malignancies (Busque et al., 2012; Xie et al., 2014). Analysis of AML and patients with nonhematologic malignancies suggest mutations in TET2 and in other epigenetic modifiers may represent early premalignant events that cause clonal hematopoietic expansion (Genovese et al., 2014; Jaiswal et al., 2014; Jan et al., 2012). These data indicate that TET2 inactivation contributes to selective clonal advantages in early leukemia initiation but requires additional genetic events to induce myeloid transformation. Ras proteins are small GTPases that cycle between active guanosine triphosphate (GTP)-bound (Ras-GTP) and inactive guanosine diphosphate (GDP)-bound (Ras-GDP) conformations (Schubbert et al., 2007). Ras-GTP binds to and activates downstream signaling effectors, such as Raf and phosphoinositide 3-kinase (PI3K), thereby transducing signals from activated growth factor receptors to the nucleus. Thus, Ras-mediated signal transduction critically regulates fundamental cellular behaviors, including proliferation, differentiation and survival (Schubbert et al., 2007). The three cellular Ras genes encode 4 highly homologous proteins, Hras, Kras4A, Kras4B and Nras, that share conserved effector binding domains and the P-loop, which binds the g-phosphate of GTP (Zhou et al., 2016). Cancer-associated RAS mutations encode proteins that accumulate in the active GTP-bound conformation due to defective intrinsic hydrolysis and resistance to guanosine triphosphatase-activating proteins (Schubbert et al., 2007). Among these isoforms, NRAS is the most common target of oncogenic signaling mutations in myeloid leukemia, including 10-15% of AML and CMML cases (Bacher et al., 2006; Ball et al., 2016). Moreover, recent study identified NRAS as one of the somatic gene mutations with adverse prognostic relevance in CMML (Elena et al., 2016). Consistent with human data, mice with hematopoietic tissue specific conditional NrasG12D allele develop fatal myeloproliferative disease in vivo (Li et al., 2011). These data underscore critical role of oncogenic NRAS mutations in myeloid leukemogenesis. Recent studies have shown that mutations in epigenetic modifiers and signaling factors commonly co-occur in AML, including the co-occurrence of TET2 mutations and NRAS mutations (Papaemmanuil et al., 2016; Patel et al., 2012). Analysis of the clonal architecture in CMML patients suggests TET2/NRAS double-mutant clones expand both within stable disease time course and in relapse after allogeneic stem cell transplantation (Itzykson et al., 2013). These evidences imply TET2 and NRAS mutation likely function together in myeloid transformation. Although previous study has shown that knockdown of Tet2 does not accelerate NrasG12D induced transplant myeloproliferative disease model (Chang et al., 2014), to date there have been no studies of the mechanistic impact caused by the combination of these high risk genetic lesions using physiologic in vivo model. Moreover, how the combination of myeloid leukemia-associated disease alleles affect sensitivity to targeted therapy has not been elucidated. Here we investigate loss of Tet2 together with NrasG12D in CMML development and specifically how they interact to affect sensitivity to targeted therapy. SOURCE: Francine,E.,Garrett-Bakelman ( - Weill Cornell Medicine

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