Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers
Justina X Caushi1,2,3, Jiajia Zhang1,2,3, Zhicheng Ji4,5
1Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA.
Abstract:
PD-1 blockade unleashes CD8 T cells1, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction programs in tumour-infiltrating lymphocytes (TIL). However, the majority of TIL do not recognize tumour antigens2, and little is known about transcriptional programs of MANA-specific TIL. Here, we identify MANA-specific T cell clones using the MANA functional expansion of specific T cells assay3 in neoadjuvant anti-PD-1-treated non-small cell lung cancers (NSCLC). We use their T cell receptors as a 'barcode' to track and analyse their transcriptional programs in the tumour microenvironment using coupled single-cell RNA sequencing and T cell receptor sequencing. We find both MANA- and virus-specific clones in TIL, regardless of response, and MANA-, influenza- and Epstein-Barr virus-specific TIL each have unique transcriptional programs. Despite exposure to cognate antigen, MANA-specific TIL express an incompletely activated cytolytic program. MANA-specific CD8 T cells have hallmark transcriptional programs of tissue-resident memory (TRM) cells, but low levels of interleukin-7 receptor (IL-7R) and are functionally less responsive to interleukin-7 (IL-7) compared with influenza-specific TRM cells. Compared with those from responding tumours, MANA-specific clones from non-responding tumours express T cell receptors with markedly lower ligand-dependent signalling, are largely confined to HOBIThigh TRM subsets, and coordinately upregulate checkpoints, killer inhibitory receptors and inhibitors of T cell activation. These findings provide important insights for overcoming resistance to PD-1 blockade.
Insights
PD-1 blockade can unleash CD8 T cells specific for mutation-associated neoantigens (MANA), but the tumor microenvironment hinders their function. This study reveals unique transcriptional programs in MANA-specific T cells, offering insights into overcoming resistance to immunotherapy.
Area of Science:
- Immunology
- Cancer Research
- Molecular Biology
Background:
- Programmed cell death protein 1 (PD-1) blockade immunotherapy activates CD8 T cells, including those targeting mutation-associated neoantigens (MANA).
- Tumor microenvironment factors and global T cell dysfunction can limit anti-tumor T cell responses.
- Transcriptional programs of MANA-specific tumor-infiltrating lymphocytes (TIL) remain largely uncharacterized.
Purpose of the Study:
- To identify and analyze the transcriptional programs of MANA-specific T cell clones within the tumor microenvironment of non-small cell lung cancer (NSCLC) patients treated with neoadjuvant anti-PD-1 therapy.
- To compare the transcriptional profiles and functional states of MANA-specific TILs with virus-specific TILs.
- To elucidate mechanisms of T cell dysfunction and resistance to PD-1 blockade.
Main Methods:
- Identification of MANA-specific T cell clones using the MANA functional expansion of specific T cells assay.
- Utilizing coupled single-cell RNA sequencing and T cell receptor sequencing to analyze transcriptional programs of identified T cell clones within the tumor microenvironment.
- Comparison of transcriptional programs between MANA-specific, influenza-specific, and Epstein-Barr virus-specific TILs.
Main Results:
- Both MANA-specific and virus-specific T cell clones were identified in TILs, irrespective of treatment response.
- MANA-specific TILs exhibited unique transcriptional programs, characterized by an incompletely activated cytolytic program and hallmarks of tissue-resident memory (TRM) cells with diminished interleukin-7 receptor (IL-7R) expression and responsiveness.
- MANA-specific T cells from non-responding tumors showed reduced T cell receptor signaling, enrichment in HOBIThigh TRM subsets, and increased expression of inhibitory checkpoints and receptors.
Conclusions:
- MANA-specific CD8 T cells possess distinct transcriptional signatures and functional impairments within the tumor microenvironment, even after PD-1 blockade.
- Impaired IL-7 signaling and upregulation of inhibitory molecules contribute to the dysfunction of MANA-specific T cells, particularly in non-responding tumors.
- These findings provide critical insights into the mechanisms of resistance to PD-1 blockade and suggest potential strategies for enhancing anti-tumor T cell responses.
