Bouska Alyssa, Zhang Weiwei, Sharma Sunandini, Holte Harald, Shah Rauf A, Lone Waseem G, Soma Mahfuza Afroz, Yang Ruimeng, Liu Xuxiang, Mehmood Syed, Chawla Ravneet Singh, Cappelli Luca Vincenzo, Fiore Danilo, Gong Qiang, Heavican-Foral Tayla B, Cannatella Jeffrey J, Amador Catalina, Arif Aiza, Smith Lynette M, Lim Soon Thye, Ong Choon Kiat, Feldman Andrew L, Du Ming-Qing, Perry Anamarija M, de Leval Laurence, Greiner Timothy C, Fu Kai, Trøen Gunhild, Vodák Daniel, Nakken Sigve, Delabie Jan, Weinstock David, Pileri Stefano, Laginestra Antonella, Kim KyeongJin, Pajvani Utpal, Vose Julie M, Weisenburger Dennis D, Horwitz Steven M, Dave Sandeep, Khoury Joseph, Inghirami Giorgio, Chan Wing C, Iqbal Javeed
Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
Department of Oncology, Oslo University Hospital, Oslo, Norway.
Am J Hematol. 2025 Sep;100(9):1486-1501. doi: 10.1002/ajh.27736. Epub 2025 Jun 13.
Nodal follicular helper T-cell (T ) lymphoma of the angioimmunoblastic (AITL) subtype has a dismal prognosis. Using whole-exome sequencing (n = 124), transcriptomic (n = 78), and methylation (n = 40) analysis, we identified recurrent mutations in known epigenetic drivers (TET2, DNMT3A, IDH2 ) and novel ones (TET3, KMT2D). TET2, IDH2 , DNMT3A co-mutated AITLs had poor prognosis (p < 0.0001). Genes regulating T-cell receptor (TCR) signaling (CD28, PLCG1, VAV1, FYN) or activation (RHOA ) or regulators of the PI3K-pathway (PIK(3)C members, PTEN, PHLPP1, PHLPP2) were mutated. CD28 mutation/fusion was associated with poor prognosis (p = 0.02). WES of purified, neoplastic T-cell (CD3PD1) demonstrated high concordance with whole tumor biopsies and validated the presence of TET2 and DNMT3A in tumor and non-lymphoid cells, but other mutations (CD28, RHOA , IDH2 , PLCG1) in neoplastic cells. Integrated DNA-methylation and mRNA expression analysis revealed epigenetic alterations in genes regulating TCR, cytokines, PI3K-signaling, and apoptosis. RNA-seq analysis identified fusion transcripts regulating TCR-activation (8%), revealed a restricted TCR-repertoire (α = 87%, β = 72%), and showed the presence of Epstein-Barr virus transcriptome (73%). GEP demonstrated the association of B-cells or dendritic cells in the tumor milieu with prognosis (p < 0.01). RNA-seq and WES analysis of 12 AITL-patient-derived-xenografts (PDX) showed that bi-allelic TET2 and DNMT3A mutations or sub-clonal mutations (PLCG1, PHLPP2) propagated in sequential passages, and gene signatures related to T and T (central-memory) were well-maintained through passages. Gene expression signatures associated with late PDX passages (3rd-5th) were enriched with proliferation and metabolic reprogramming-related genes and predicted prognosis in an independent AITL series. Low PHLPP2 mRNA expression predicted poor prognosis (p = 0.05) and engineered PHLPP2 or TET2 loss in CD4 T-cells showed enhanced PI(3)K activation, thus uncovering a therapeutic target for clinical trials.
血管免疫母细胞性（AITL）亚型的结内滤泡辅助性T细胞（TFH）淋巴瘤预后不佳。通过全外显子组测序（n = 124）、转录组分析（n = 78）和甲基化分析（n = 40），我们在已知的表观遗传驱动因子（TET2、DNMT3A、IDH2）和新发现的因子（TET3、KMT2D）中鉴定出复发性突变。TET2、IDH2、DNMT3A共同突变的AITL预后较差（p < 0.0001）。调节T细胞受体（TCR）信号传导（CD28、PLCG1、VAV1、FYN）或激活（RHOA）或PI3K通路的调节因子（PIK(3)C成员、PTEN、PHLPP1、PHLPP2）发生了突变。CD28突变/融合与预后不良相关（p = 0.02）。对纯化的肿瘤性T细胞（CD3PD1）进行的全外显子组测序显示与全肿瘤活检具有高度一致性，并证实肿瘤细胞和非淋巴细胞中存在TET2和DNMT3A，但肿瘤细胞中存在其他突变（CD28、RHOA、IDH2、PLCG1）。整合的DNA甲基化和mRNA表达分析揭示了调节TCR、细胞因子、PI3K信号传导和细胞凋亡的基因中的表观遗传改变。RNA测序分析鉴定出调节TCR激活的融合转录本（8%），揭示了受限的TCR库（α = 87%，β = 72%），并显示存在爱泼斯坦-巴尔病毒转录组（73%）。基因表达谱显示肿瘤微环境中的B细胞或树突状细胞与预后相关（p < 0.01）。对12例AITL患者来源的异种移植瘤（PDX）进行的RNA测序和全外显子组测序分析表明，双等位基因TET2和DNMT3A突变或亚克隆突变（PLCG1、PHLPP2）在连续传代中得以传播，并且与TFH和T（中央记忆）相关的基因特征在传代过程中得到很好的维持。与晚期PDX传代（第3 - 5代）相关的基因表达特征富含与增殖和代谢重编程相关的基因，并在一个独立的AITL系列中预测预后。低PHLPP2 mRNA表达预测预后不良（p = 0.05），并且在CD4 T细胞中对PHLPP2或TET2进行基因工程敲除显示PI(3)K激活增强，从而揭示了一个用于临床试验的治疗靶点。
