Integrative Genomic and Transcriptomic Analysis Reveals Targetable Vulnerabilities in Angioimmunoblastic T‐Cell Lymphoma
Alyssa Bouska, Weiwei Zhang, Sunandini Sharma, Harald Holte, Roshani Shah, Waseem Lone, Mahfuza Afroz Soma, Ruimeng Yang, Xuxiang Liu, Syed Karman Mehmood, Rakesh Chawla, Luca Vincenzo Cappelli, Danilo Fiore, Qiang Gong, Tayla B. Heavican‐Foral, Jeffrey J. Cannatella, Catalina Amador, Aiza Arif, Lynette M. Smith, Soon Thye Lim, Choon Kiat Ong, Andrew L. Feldman, Ming‐Qing Du, Anamarija M. Perry, Laurence de Leval, Timothy C. Greiner, Kai Fu, Gunhild Trøen, Daniel Vodák, Sigve Nakken, Jan Delabie, David M. Weinstock, Stefano Pileri, Antonella Laginestra, KyeongJin Kim, Utpal B. Pajvani, Julie Vose, Dennis D. Weisenburger, Steven M. Horwitz, Sandeep S. Davé, Joseph D. Khoury, Giorgio Inghirami, Wing C. Chan, Javeed Iqbal
IF 9.9
American Journal of Hematology
Nodal follicular helper T-cell (T <sub>FH</sub>) 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 <sup>R172</sup> ) and novel ones (TET3, KMT2D). TET2, IDH2 <sup>R172</sup> , DNMT3A co-mutated AITLs had poor prognosis (p < 0.0001). Genes regulating T-cell receptor (TCR) signaling (CD28, PLCG1, VAV1, FYN) or activation (RHOA <sup>G17V</sup> ) 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 (CD3<sup>+</sup>PD1<sup>+</sup>) 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 <sup>G17V</sup> , IDH2 <sup>R172</sup> , 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 <sub>FH</sub> and T <sub>CM</sub> (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<sup>+</sup> T-cells showed enhanced PI(3)K activation, thus uncovering a therapeutic target for clinical trials.
https://doi.org/10.1002/ajh.27736
Angioimmunoblastic T-cell lymphoma
Transcriptome
Lymphoma
Medicine
Cancer research
Computational biology
Oncology
Internal medicine
Biology
Immunology
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