Frequent Alterations of Driver Genes in Chromosome X and Their Clinical Relevance in Extranodal NK/T-Cell Lymphoma

Extranodal NK/T-cell lymphoma (ENKTCL) is a rare and aggressive mature T-cell malignancy which is invariably related to Epstein-Barr virus (EBV) infection with male predominance. Although many genetic studies of ENKTCL have revealed frequent alterations in several genes (e.g., DDX3X and TP53), they have mainly focused on mutational changes. Therefore, the landscape of somatic alterations, including copy number alterations (CNAs) and structural variations (SVs), in ENKTCL remains elusive.

Here we performed whole-exome sequencing (WES) of 66 ENKTCL patients, followed by targeted-capture sequencing (targeted-seq) of 147 lymphoma-associated genes in 168 patients from Japanese (n=64) and French (n=104) institutions. Combined analysis of WES and targeted-seq identified 25 significantly mutated genes using dNdScv. These genes included six novel genes, namely HLA-B (8%), HLA-C (6%) ROBO1 (5%), CD58 (4%), POT1 (3%), and MAP2K1 (2%). Besides them, recurrent mutations (in ≥ 3 cases) were observed in seven genes previously reported to be drivers in ENKTCL. Thus, 32 genes were recurrently mutated in our cohort. Consistent with our previous report, we detected SVs truncating the 3′-untranslated region of CD274 in 14% of cases. We also identified significant focal amplification (n = 1) and deletions (n = 10) and arm-level gains (n = 12) and losses (n = 7) by GISTIC2.0. Focal CNAs included 15 driver genes, including CD274 amplifications (18%) and CDKN2A (17%) and ARID1A (11%) deletions.

When mutations, CNAs, and SVs were combined, a total of 34 genes were recurrently altered in our cohort. CD274 (24%) was the most frequently altered, followed by TP53 (20%), CDKN2A (19%), ARID1A (15%), HLA-A (15%), BCOR (15%), and MSN (15%). The frequently altered pathways were immune surveillance (46%), epigenetic regulation (43%), and tumor suppressors (41%). Notably, several driver genes (MSN, BCOR, DDX3X, and KDM6A) were present on chromosome (chr) X. Among arm-level CNAs, chrX losses were only observed in females (39% and 37% in Xp and Xq loss, respectively). In addition, the proportion of mutations affecting these drivers on chrX was higher in males and females with chrX loss than in females without chrX loss (43% vs 23%, p = 0.02). These results suggest that driver genes on chrX are coordinately involved in ENKTCL pathogenesis and may explain its male predominance (58% in our cohort).

Among driver genes on chrX, the most frequently altered gene was MSN (15%), which was affected by loss-of-function mutations and/or deletions and specifically altered in ENKTCL among lymphoma subtypes. To assess the functional consequence of MSN alterations, we investigated the effect of MSN knockout (KO) or overexpression (OE) in NK/T cell lines. MSN OE diminished the proliferation of a MSN-null cell line (YT1), while cell growth was enhanced by CRISPR-mediated MSN KO in MSN wild-type cell lines. In line with this, transcriptomic analysis with RNA-seq demonstrated the enrichment of proliferation-related signatures in MSN-null cells. Next, we analyzed the hematopoietic system in Msn KO mice and found that Msn disruption caused an increase of a subset (CD11b^-CD27⁺) of NK cells but a decrease in a more mature subset (CD11b⁺CD27⁺) in the bone marrow. In addition, cell-cycle progression was increased in these Msn KO NK subsets. Transcriptomic analysis showed the significant enrichment of proliferation-related signatures and several signaling pathway signatures.

Finally, we integrated 34 drivers and 19 significant arm-level CNAs using consensus clustering based on non-negative matrix factorization and identified two molecular groups. In group 1 (n=33), tumor suppressors (CDKN2A and TP53), epigenetic regulators (KDM6A and BCOR), and JAK-STAT pathway genes (JAK3 and STAT5B) were more frequently altered, whereas group 2 (n=30) was enriched with MSN and CD274 alterations. Clinically, group 1 was significantly associated with a more advanced stage and worse prognosis than group 2, irrespective of the PINK score.

In summary, we have illustrated the genetic landscape of ENKTCL, which was shaped by frequent disruptions of driver genes on chrX. Particularly, we characterized the role of loss-of-function MSN alterations in NK cell function in vitro and in vivo. In addition, we proposed a novel molecular classification with biological and clinical relevance. Our findings can help improve diagnostic and therapeutic strategies in ENKTCL.

Kogure:Kyowa Kirin Co., Ltd.: Honoraria; Nippon Shinyaku Co., Ltd.: Honoraria; Daiichi Sankyo Co., Ltd.: Honoraria; Takeda Pharmaceutical Co., Ltd.: Honoraria. Koya:TOMY DIGITAL BIOLOGY CO.,LTD.: Honoraria; Scrum Inc.: Honoraria; Eisai Co., Ltd.: Honoraria. Bruneau:Innate pharma: Consultancy, Research Funding. Andre:Smart Immune: Consultancy, Current equity holder in publicly-traded company. Chaubard:Correspondances en Onco-Hématologie: Honoraria; Accord Healthcare: Other: meeting registration. Bachy:Kite, Gilead, Novartis, Roche, Incyte, Miltenyi Biotech, Takeda, Sanofi: Honoraria; Roche, Gilead, ADC Therapeutics, Takeda, Novartis, Incyte: Membership on an entity's Board of Directors or advisory committees; Amgen, BMS: Research Funding; Hospices Civils de Lyon: Current Employment. Meignin:Eusapharma: Consultancy. Michot:Sanofi: Research Funding; Roche: Other: Nonfinancial support, Research Funding; NH TherAGUuiX: Other: Nonfinancial support; Pfizer: Other: Nonfinancial support, Research Funding; Merck: Other: Nonfinancial support, Research Funding; Janssen Cilag: Research Funding; INCa: Research Funding; MedImmune: Other: Nonfinancial support; GlaxoSmithKline: Other: Nonfinancial support, Research Funding; Boehringer Ingelheim: Other: Nonfinancial support, Research Funding; Bristol Myers Squibb: Other: Nonfinancial support, support for travel to and accomodation at EHA 2022 to present CC-99282-NHL-001 study data;, Research Funding; AstraZeneca: Other: Nonfinancial support, Research Funding. Tournilhac:Securabio: Honoraria, Other: Travel grant , Research Funding; IdeoGen: Honoraria, Other: Travel grant , Research Funding; Gilead: Honoraria, Other: Travel grant , Research Funding; Janssen: Honoraria, Other: Travel grant , Research Funding; Abbvie: Honoraria, Other: Travel grant , Research Funding; Takeda: Honoraria, Other: Travel grant , Research Funding. Izutsu:Eli Lilly and Company: Consultancy, Honoraria; Merck Sharp & Dohme: Honoraria, Research Funding; Incyte: Research Funding; Eizai: Honoraria, Research Funding; Chugai: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria, Research Funding; Ono Pharmaceutical: Consultancy, Honoraria, Research Funding; AstraZeneca: Consultancy, Honoraria, Research Funding; Beigene: Consultancy, Research Funding; Yakult: Research Funding; Kyowa Kirin: Honoraria, Research Funding; Loxo Oncology: Research Funding; Bristol Myers Squibb: Consultancy, Honoraria, Research Funding; Daiichi Sankyo: Honoraria, Research Funding; Genmab: Research Funding; Takeda: Honoraria; Janssen: Research Funding; Symbio: Honoraria. Takeuchi:Nippon Shinyaku: Consultancy; Meiji Seika Pharma: Consultancy; Fujirebio: Research Funding; Daiichi Sankyo: Research Funding; Eli Lilly: Honoraria; Chugai: Honoraria; Kyowa Kirin: Honoraria; Janssen: Honoraria; Sysmex: Patents & Royalties; Nichirei Bioscience: Consultancy, Patents & Royalties. Ohshima:Bristol-Myers Squibb Co.: Research Funding; Chugai Co., Ltd.: Honoraria, Research Funding; Daiichi Sankyo Co., Ltd.: Research Funding; Kyowa Kirin Co., Ltd.: Research Funding. Gaulard:Takeda: Consultancy, Honoraria, Research Funding; Innate Pharma: Research Funding; Alderan: Research Funding; Sanofi: Research Funding; Gilead: Honoraria. Jaccard:Amgen: Honoraria; Pfizer: Honoraria; sanofi: Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding. Ogawa:2013-526957 (JP02): Patents & Royalties; The Chemo-Sero-Therapeutic Research Institute: Speakers Bureau; MSD: Speakers Bureau; 2015-239547: Patents & Royalties; Clinical Research Support Center Kyushu: Research Funding; Kirin/Chugai: Speakers Bureau; Astrazeneca: Speakers Bureau; Astellas: Speakers Bureau; Otsuka Pharmatheutical: Research Funding; Novartis: Honoraria, Speakers Bureau; Chordia Threapeutics: Consultancy, Current equity holder in publicly-traded company, Research Funding; 62/187386 (US01): Patents & Royalties; 15/353395 (US03): Patents & Royalties; PCT/JP2014/062112 (WO01): Patents & Royalties; Pfaizer: Speakers Bureau; The Mitsubishi foundation: Honoraria; 2013-096582 (JP01): Patents & Royalties; Sysmex: Honoraria; Nanpu Hospital: Research Funding; ASAHI Genomics: Current equity holder in publicly-traded company; Esai Pharmatheutical: Consultancy; DaiichiSankyo: Speakers Bureau; 2014-191287: Patents & Royalties. Hermine:Kite/Gilead: Honoraria; BMS: Honoraria, Research Funding; Novartis: Research Funding; Inatherys: Research Funding; AB Science: Current equity holder in private company, Honoraria, Research Funding. Kataoka:Kyowa Kirin: Honoraria, Research Funding; Genetic alterations as a biomarker in T-cell lymphomas licensed to Kyoto University and a patent for PD-L1 abnormalities as a predictive biomarker for immune checkpoint blockade therapy licensed to Kyoto University.: Patents & Royalties; Alexion Pharmaceuticals: Honoraria; Ono Pharmaceutical: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria; Eisai: Honoraria, Research Funding; Janssen Pharmaceutical: Honoraria; Asahi Genomics: Current equity holder in private company; Teijin Pharma: Research Funding; Shionogi: Research Funding; Takeda Pharmaceutical: Honoraria, Research Funding; Mochida Pharmaceutical: Research Funding; Japan Blood Products Organization: Research Funding; Otsuka Pharmaceutical: Honoraria, Research Funding; Novartis: Honoraria; Chugai Pharmaceutical: Honoraria, Research Funding; Sumitomo Dainippon Pharma: Honoraria, Research Funding; AstraZeneca: Honoraria; Celgene: Honoraria; JCR Pharmaceuticals: Research Funding; Chordia Therapeutics: Research Funding; Asahi Kasei Pharma: Research Funding; Astellas Pharma: Honoraria; SymBio Pharmaceuticals: Honoraria; Pfizer: Honoraria; Nippon Shinyaku: Honoraria; Daiichi Sankyo: Honoraria; AbbVie: Honoraria; Meiji Seika Pharma: Honoraria; Sanofi: Honoraria; Keio University School of Medicine: Other: NA; National Cancer Center Research Institute: Other: NA.