{
  "abstract": "Background T-cell activation and clonal expansion are essential to effective immunotherapy responses in non-small cell lung cancer (NSCLC). The distribution of T-cell clones may offer insights into immunogenic mechanisms and imply potential prognostic and predictive information.Methods We analyzed α/β T-cell receptor (TCR) clonality using RNA-sequencing of bulk frozen tumor tissue from 182 patients with NSCLC. The data was integrated with molecular and clinical characteristics, extensive in situ imaging, and spatial sequencing of the tumor immune microenvironment. TCR clonality was also determined in an independent cohort of nine patients with immune checkpoint-treated NSCLC.Results TCR clonality (Gini index) patterns ranged from high T-cell clone diversity with high evenness (low Gini index) to clonal dominance with low evenness (high Gini index). Generally, TCR clonality in cancer was lower than in matched normal lung parenchyma distant from the tumor (p=0.021). The TCR clonality distribution between adenocarcinoma and squamous cell carcinoma was similar; however, smokers showed a higher Gini index. While in the operated patient with NSCLC cohort, TCR clonality was not prognostic, in an immune checkpoint inhibitor-treated cohort, high TCR clonality was associated with better therapy response (p=0.016) and prolonged survival (p=0.003, median survival 13.8 vs 2.9 months). On the genomic level, a higher Gini index correlated strongly with a lower frequency of epidermal growth factor receptor (EGFR) and adenomatous polypsis coli (APC) gene mutations, but a higher frequency of P53 mutations, and a higher tumor mutation burden. In-depth characterization of the tumor tissue revealed that high TCR clonality was associated with an activated, inflamed tumor phenotype (PRF1, GZMA, GZMB, INFG) with exhaustion signatures (LAG3, TIGIT, IDO1, PD-1, PD-L1). Correspondingly, PD-1+, CD3+, CD8A+, CD163+, and CD138+immune cells infiltrated cancer tissue with high TCR clonality. In situ sequencing recovered single dominant T-cell clones within the patient tumor tissue, which were predominantly of the CD8 subtype and localized closer to tumor cells.Conclusion Our robust analysis pipeline characterized diverse TCR repertoires linked to distinct genotypes and immunologic tumor phenotypes. The spatial clustering of expanded T-cell clones and their association with immunological activation underscores a functional, clinically relevant immune response, particularly in patients with NSCLC treated with checkpoint inhibitors.",
  "authors": [
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Hui Yu"
    },
    {
      "affiliations": [
        "Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm County, Sweden"
      ],
      "name": "Anastasia Magoulopoulou"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Rose-Marie Amini"
    },
    {
      "affiliations": [
        "Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm County, Sweden"
      ],
      "name": "Maria Paraskevi Chatzinikolaou"
    },
    {
      "affiliations": [
        "Division of Molecular and Genomic Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe, Japan"
      ],
      "name": "Masafumi Horie"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Amanda Lindberg"
    },
    {
      "affiliations": [
        "Molecular Oncology Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain"
      ],
      "name": "Artur Mezheyeuski"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Max Backman"
    },
    {
      "affiliations": [
        "Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm County, Sweden",
        "Dept. of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"
      ],
      "name": "Andreas Metousis"
    },
    {
      "affiliations": [
        "Division of Pathology, Lund University, Lund, Sweden"
      ],
      "name": "Hans Brunnström"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Millaray Marincevic"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Johan Botling"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Johanna Sofia Margareta Mattsson"
    },
    {
      "affiliations": [
        "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Stockholm County, Sweden"
      ],
      "name": "Klas Kärre"
    },
    {
      "affiliations": [
        "Department of Translational Medicine, Lund University, Lund, Sweden"
      ],
      "name": "Karin Leandersson"
    },
    {
      "affiliations": [
        "Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm County, Sweden"
      ],
      "name": "Mats Nilsson"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden",
        "Center for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway"
      ],
      "name": "Carina Strell"
    },
    {
      "affiliations": [
        "Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Uppsala County, Sweden"
      ],
      "name": "Patrick Micke"
    }
  ],
  "title": "Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer",
  "uid": "4d314576-0090-5c67-b1ed-4314a9dc4d37"
}