DNMT3A mutations define a unique biological and prognostic subgroup associated with cytotoxic T cells in PTCL-NOS

• Published in: Blood Vol. 140; no. 11; pp. 1278 - 1290
• Main Authors: Herek, Tyler A, Bouska, Alyssa, Lone, Waseem, Sharma, Sunandini, Amador, Catalina, Heavican, Tayla B, Li, Yuping, Wei, Qi, Jochum, Dylan, Greiner, Timothy C, Smith, Lynette, Pileri, Stefano, Feldman, Andrew L, Rosenwald, Andreas, Ott, German, Lim, Soon Thye, Ong, Choon Kiat, Song, Joo, Jaffe, Elaine S, Wang, Gang Greg, Staudt, Louis, Rimsza, Lisa M, Vose, Julie, d'Amore, Francesco, Weisenburger, Dennis D, Chan, Wing C, Iqbal, Javeed
• Format: Journal Article
• Language: English
• Published: United States American Society of Hematology 15-09-2022
• Subjects: Animals; Interferon-gamma - genetics; Lymphoid Neoplasia; Lymphoma, T-Cell, Peripheral - pathology; Methyltransferases - genetics; Mice; Mutation; Prognosis; Receptors, Antigen, T-Cell - genetics
• ISSN: 0006-4971; 1528-0020; 1528-0020
• DOI: 10.1182/blood.2021015019

Peripheral T-cell lymphomas (PTCLs) are heterogenous T-cell neoplasms often associated with epigenetic dysregulation. We investigated de novo DNA methyltransferase 3A (DNMT3A) mutations in common PTCL entities, including angioimmunoblastic T-cell lymphoma and novel molecular subtypes identified within PTCL-not otherwise specified (PTCL-NOS) designated as PTCL-GATA3 and PTCL-TBX21. DNMT3A-mutated PTCL-TBX21 cases showed inferior overall survival (OS), with DNMT3A-mutated residues skewed toward the methyltransferase domain and dimerization motif (S881-R887). Transcriptional profiling demonstrated significant enrichment of activated CD8+ T-cell cytotoxic gene signatures in the DNMT3A-mutant PTCL-TBX21 cases, which was further validated using immunohistochemistry. Genomewide methylation analysis of DNMT3A-mutant vs wild-type (WT) PTCL-TBX21 cases demonstrated hypomethylation in target genes regulating interferon-γ (IFN-γ), T-cell receptor signaling, and EOMES (eomesodermin), a master transcriptional regulator of cytotoxic effector cells. Similar findings were observed in a murine model of PTCL with Dnmt3a loss (in vivo) and further validated in vitro by ectopic expression of DNMT3A mutants (DNMT3A-R882, -Q886, and -V716, vs WT) in CD8+ T-cell line, resulting in T-cell activation and EOMES upregulation. Furthermore, stable, ectopic expression of the DNMT3A mutants in primary CD3+ T-cell cultures resulted in the preferential outgrowth of CD8+ T cells with DNMT3AR882H mutation. Single-cell RNA sequencing(RNA-seq) analysis of CD3+ T cells revealed differential CD8+ T-cell subset polarization, mirroring findings in DNMT3A-mutated PTCL-TBX21 and validating the cytotoxic and T-cell memory transcriptional programs associated with the DNMT3AR882H mutation. Our findings indicate that DNMT3A mutations define a cytotoxic subset in PTCL-TBX21 with prognostic significance and thus may further refine pathological heterogeneity in PTCL-NOS and suggest alternative treatment strategies for this subset.