Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8+ T-cell large granular lymphocytic leukemia

Funding Information: This project was funded by the European Research Council (Project: M-IMM 647355), Academy of Finland Heal-Art consortium (314442), and ERA PerMed (JAKSTAT-TARGET consortium), Sigrid Juselius Foundation, Signe and Ane Gyllenberg Foundation, Helsinki Institute for Life Science, Cancer Foundation Finland, and Ministry of Education, Culture, Sports, Science and Technology of Japan (Kaken 20K08709). J.H. was supported by Finnish Hematology Association, Blood Disease Research Foundation, Helsinki Institute for Life Science, Biomedicum Helsinki Foundation, Finnish Medical Foundation. T.L. was supported by Academy of Finland (Decision 311081). RZ was supported by Italian Association for Cancer Research (AIRC #20216).?F.I. was supported by KAKEN 20K08709. from Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Single-cell RNA sequencing and amplicon sequencing were performed at the Institute for Molecular Medicine Finland FIMM Technology Centre and Finnish Functional Genomics Centre, Turku Bioscience, which are supported by Biocenter Finland. We acknowledge Jay Klievink, Sofie Lundgren, Anita Kumari, and Ella Piekkari for the processing of samples from healthy controls. We acknowledge Emmi Rehn for providing a modified script of GLIPH that was used for the previous version of the findings. We acknowledge the computational resources provided by the Aalto Science-IT project. Funding Information: This project was funded by the European Research Council (Project: M-IMM 647355), Academy of Finland Heal-Art consortium (314442), and ERA PerMed (JAKSTAT-TARGET consortium), Sigrid Juselius Foundation, Signe and Ane Gyllenberg Foundation, Helsinki Institute for Life Science, Cancer Foundation Finland, and Ministry of Education, Culture, Sports, Science and Technology of Japan (Kaken 20K08709). J.H. was supported by Finnish Hematology Association, Blood Disease Research Foundation, Helsinki Institute for Life Science, Biomedicum Helsinki Foundation, Finnish Medical Foundation. T.L. was supported by Academy of Finland (Decision 311081). RZ was supported by Italian Association for Cancer Research (AIRC #20216). F.I. was supported by KAKEN 20K08709. from Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Single-cell RNA sequencing and amplicon sequencing were performed at the Institute for Molecular Medicine Finland FIMM Technology Centre and Finnish Functional Genomics Centre, Turku Bioscience, which are supported by Biocenter Finland. We acknowledge Jay Klievink, Sofie Lundgren, Anita Kumari, and Ella Piekkari for the processing of samples from healthy controls. We acknowledge Emmi Rehn for providing a modified script of GLIPH that was used for the previous version of the findings. We acknowledge the computational resources provided by the Aalto Science-IT project. Funding Information: T.L. is a member of the scientific advisory boards and hold stock options of Keystone Nano, Dren Bio, and Kymera Therapeutics (not related to this project). S.M. has received honoraria and research funding from BMS and research funding from Novartis and Pfizer (not related to this project). The remaining authors declare no competing interests. Publisher Copyright: © 2022, The Author(s). T cell large granular lymphocytic leukemia (T-LGLL) is a rare lymphoproliferative disorder of mature, clonally expanded T cells, where somatic-activating STAT3 mutations are common. Although T-LGLL has been described as a chronic T cell response to an antigen, the function of the non-leukemic immune system in this response is largely uncharacterized. Here, by utilizing single-cell RNA and T cell receptor profiling (scRNA+TCRαβ-seq), we show that irrespective of STAT3 mutation status, T-LGLL clonotypes are more cytotoxic and exhausted than healthy reactive clonotypes. In addition, T-LGLL clonotypes show more active cell communication than reactive clones with non-leukemic immune cells via costimulatory cell–cell interactions, monocyte-secreted proinflammatory cytokines, and T-LGLL-clone-secreted IFNγ. Besides the leukemic repertoire, the non-leukemic T cell repertoire in T-LGLL is also more mature, cytotoxic, and clonally restricted than in other cancers and autoimmune disorders. Finally, 72% of the leukemic T-LGLL clonotypes share T cell receptor similarities with their non-leukemic repertoire, linking the leukemic and non-leukemic repertoires together via possible common target antigens. Our results provide a rationale to prioritize therapies that target the entire immune repertoire and not only the T-LGLL clonotype.