Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

Abstract

Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.

A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2

“…These phenotypic dissimilarities are expected, given the opposite cellular effects of GoF and LoF variants. Utilizing publically available omics data from the Cancer Cell Line Encyclopedia (CCLE) 12 we confirm 15,31 dysregulated methylation of histone H3 at the lysine residue 36, especially increased dimethylation, (H3K36me2) as primary molecular effect of the c.3295G>A, p.Glu1099Lys variant. Looking at differential promoter methylation, we identified extensive DNA hypermethylation in GoF cell lines (Fig.…”

“…Next to the p.Glu1099Lys missense substitution, other NSD2 missense variants causing similar GoF effects have either been described in blood malignancies (T1150A; c.3448A>G, p.Thr1150Ala) or investigated in vitro 14,15 . Also structural variants like the recurrent somatic t(4;14) translocation, can result in overexpression and increased activity of NSD2.…”

“…11 Recent investigations using cryo-electron microscopy solved the structure of NSD2 bound to the nucleosome and indicated that the oncogenic p.Glu1099Lys NSD2 missense variant destabilizes the autoinhibitory loop of the protein to enhance substrate recognition and increase the nucleosomal H3K36 methyltransferase activity of NSD2. 14,15…”

“…11 Recent investigations using cryo-electron microscopy solved the structure of NSD2 bound to the nucleosome and indicated that the oncogenic p.Glu1099Lys NSD2 missense variant destabilizes the autoinhibitory loop of the protein to enhance substrate recognition and increase the nucleosomal H3K36 methyltransferase activity of NSD2. 14,15 It is known 16 that genes involved in clonal hematopoiesis, hematologic malignancy and other types of cancer are also overrepresented in curated NDD databases. On a variant level, there is a significant overlap between somatic driver mutations in (hematologic) malignancies and (de novo) germline variants causing NDD.…”

Structural and functional specificity of H3K36 methylation

“…Carcinogenesis associated with changes in the expression of NSD2 is also linked with cell cycle dysregulation [ 102 ], VEGF-A-mediated angiogenesis [ 104 ], hematopoietic stem cell differentiation [ 105 ], metastasis [ 91 ], chemoresistance (in osteosarcoma) [ 106 ], and the expression of various oncogenes (e.g., SYK , PTPN13 and ETV5 in multiple myeloma) [ 107 ]. Gain-of-function mutations (E1099K and T1150A) in the SET domain of NSD2 have been associated with the enhanced enzymatic activity of NSD2 in mantle cell lymphoma and pediatric acute lymphoblastic leukemia, in which they cause destabilization of the auto-inhibitory loop responsible for keeping signaling in check (refer below) [ 108 , 109 ]. E1099K mutation is also found in 70% of patients with leukemia who experience relapse, and has been linked with aberrant global DNA methylation profiles in these patients [ 108 , 110 ].…”