The NSD2 p.E1099K Mutation Is Enriched at Relapse and Confers Drug Resistance in a Cell Context–Dependent Manner in Pediatric Acute Lymphoblastic Leukemia

Abstract

The NSD2 p.E1099K (EK) mutation is observed in 10% of acute lymphoblastic leukemia (ALL) samples with enrichment at relapse indicating a role in clonal evolution and drug resistance. To discover mechanisms that mediate clonal expansion, we engineered B-ALL cell lines (Reh, 697) to overexpress wildtype (WT) and EK NSD2, but observed no differences in proliferation, clonal growth, or chemosensitivity. To address whether NSD2 EK acts collaboratively with other pathways, we used shRNAs to knockdown expression of NSD2 in B-ALL cell lines heterozygous for NSD2 EK (RS4;11, RCH-ACV, SEM). Knockdown resulted in decreased proliferation in all lines, decreased clonal growth in RCH-ACV, and increased sensitivity to cytotoxic chemotherapeutic agents, although the pattern of drug sensitivity varied among cell lines implying that the oncogenic properties of NSD2 mutations are likely cell context specific and rely on cooperative pathways. Knockdown of both Type II and REIIBP EK isoforms had a greater impact than knockdown of Type II alone, suggesting that both SET containing EK isoforms contribute to phenotypic changes driving relapse. Furthermore, in vivo models using both cell lines and patient samples revealed dramatically enhanced proliferation of NSD2 EK compared to WT and reduced sensitivity to 6-mercaptopurine in the relapse sample relative to diagnosis. Finally, EK-mediated changes in chromatin state and transcriptional output differed dramatically among cell lines further supporting a cell context specific role of NSD2 EK. These results demonstrate a unique role of NSD2 EK in mediating clonal fitness through pleiotropic mechanisms dependent on the genetic and epigenetic landscape. IMPLICATIONSNSD2 p.E1099K mutation leads to drug resistance and a clonal advantage in childhood B-ALL.

Clonal dynamics in pediatric B‐cell precursor acute lymphoblastic leukemia with very early relapse

“…We have identified a hotspot WHSC1 E1099K mutation in two patients with very early relapse and 42,59 Among pediatric tumors, the frequency of WHSC1 mutations is highest in BCP-ALL, especially in ETV6-RUNX1 (20%) and TCF3-PBX1 (15%) ALL subtypes. 42 Therefore, a WHSC1 mutation is unlikely to be a strong risk factor for relapse in these subtypes by itself.…”

Epigenomic reprogramming via HRP2-MINA dictates response to proteasome inhibitors in multiple myeloma with t(4;14) translocation

“…NSD2 is involved in the proliferation, apoptosis, and adhesion of MM cells, and the HMT activity of NSD2 is critical for its biological function in tumorigenicity (7). Overexpression or gain-of-function mutation in NSD2 results in drug resistance in multiple cancers (8)(9)(10) and drives endocrine resistance via the reprogramming of metabolism by coordinating pentose phosphate pathway enzymes (11). Although a recent retrospective study showed that t(4;14) translocations are associated with high-risk disease characteristics in patients with MM, they are also associated with better responses to PI-based treatments (12).…”

Structure-based Discovery of a Series of NSD2-PWWP1 Inhibitors

“…As shown in Table 1, compound 5 with two methoxy groups displayed a good binding affinity to NSD2 PWWP1 domain, with an IC 50 value of 4.44 μM，which is much better than MR837 (4). This encouraged us to synthesize analogs 6 -12.…”

“…2 Notably, NSD2 is closely related to accelerated disease progression and rapid relapse in 15-20% of multiple myeloma (MM) harboring the t(4;14) chromosomal translocation with increased levels of H3K36me2, 3 and among the most frequently mutated genes in pediatric cancer genomes, E1099K mutant of NSD2 is hyperactivated in acute lymphoblastic leukemia. 4 Recent studies have revealed that overexpression of NSD2 occurred in several solid tumors including bladder, prostate, glioblastoma and gastrointestinal. 5,6 NSD2 is a multi-domain protein, consists of the SET domain performing the catalytic methylation function and two PWWP (proline-tryptophan-tryptophan-proline) domains.…”