Single-cell RNA sequencing presents the sophisticated delineation of cell transcriptomes in many cancer types and highlights the tumor heterogeneity at higher resolution, which provides a new chance to explore the molecular mechanism in a minority of cells. In this study, we utilized publicly available single-cell RNA-seq data to discover and comprehensively dissect rare genes existing in few glioblastoma (GBM) cells. Moreover, we designed a framework to systematically identify 51 rare protein-coding genes (PCGs) and 47 rare long non-coding RNAs (lncRNAs) in GBM. Patients with high expression levels of rare genes like CYB5R2 and TPPP3 had worse overall survival and disease-free survival, implying their potential implication in GBM progression and prognosis. We found that these rare genes tended to be specifically expressed in GBM cancer stem cells, which emphasized their ability to characterize stem-like cancer cells and implied their contribution to GBM growth. Furthermore, rare genes were enriched in a 17-cell subset, which was located in an individual branch of the pseudotime trajectory of cancer progression and exhibited high cell cycle activity and invasive potential. Our study captures the rare genes highly expressed in few cells, deepens our understanding of special states during GBM tumorigenesis and progression such as cancer stemness and invasion, and proposes potential targets for cancer therapy.

Objectives Homologous recombination repair (HRR) deficiency is associated with improved immunotherapy responses in non-small cell lung cancer (NSCLC) patients. The HRR genes BRCA1/2 are key regulators of DNA repair, yet their impact on the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Methods Using single-cell sequencing and multi-omics data, we characterized BRCA1/2 mutation-associated transcriptional programs, immune cell composition, and functional alterations in T cells, investigating the molecular and immune architecture of BRCA-mutant LUAD patients. Results BRCA1/2 mutations were associated with increased genomic instability and poor prognosis in LUAD patients, but predicted better clinical outcomes following immune checkpoint blockade (ICB) treatment. BRCA1 mutations correlated with an upregulated type I IFN/IFN-γ signature and CD8+ T cell activation. BRCA2 mutations were associated with alveolar/stress/inflammatory responses and enhanced MHC-II antigen presentation, linked to CD4+ T cell differentiation. Both alterations coincided with reduced CD28 co-stimulation and CTL activity, hinting of immune evasion. We identified two tissue-resident memory T cell (Trm) subsets as predictors of clinical outcomes and ICB response. BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity. Furthermore, a cancer-promoting program activated by BRCA1 mutation was vulnerable to histone deacetylase inhibitors, which inhibited LUAD tumor growth. Conclusions This study provides a preliminary characterization of the BRCA-mutant TME in LUAD patients, revealing distinct transcriptional and immune patterns that highlight differences in BRCA1/2-associated molecular architecture and offer a framework for improving therapy efficacy in LUAD.

Homologous recombination repair (HRR) deficiency is associated with improved immunotherapy responses in non-small cell lung cancer (NSCLC) patients. The HRR genes BRCA1 / 2 are key regulators of DNA repair, yet their impact on the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Using single-cell sequencing and multi-omics data, we characterized BRCA1/2 mutation-associated transcriptional programs, immune cell composition, and functional alterations in T cells, investigating the molecular and immune architecture of BRCA-mutant LUAD patients. BRCA1 / 2 mutations were associated with increased genomic instability and poor prognosis in LUAD patients, but predicted better clinical outcomes following immune checkpoint blockade (ICB) treatment. BRCA1 mutations correlated with an upregulated type I IFN/IFN-γ signature and CD8 ⁺ T cell activation. BRCA2 mutations were associated with alveolar/stress/inflammatory responses and enhanced MHC-II antigen presentation, linked to CD4 ⁺ T cell differentiation. Both alterations coincided with reduced CD28 co-stimulation and CTL activity, hinting at immune evasion. We identified two tissue-resident memory T cell (Trm) subsets as predictors of clinical outcomes and ICB response. BRCA1 mutations were associated with CD8 ⁺ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4 ⁺ Trm expansion and peripheral T/NK cell cytotoxicity. Furthermore, a cancer-promoting program activated by BRCA1 mutation was vulnerable to histone deacetylase inhibitors, which inhibited LUAD tumor growth. This study provides a preliminary characterization of the BRCA-mutant TME in LUAD patients, revealing distinct transcriptional and immune patterns that highlight differences in BRCA1/2 -associated molecular architecture and offer a framework for improving therapy efficacy in LUAD.

Background Radiation pneumonitis (RP) is a deleterious complication of thoracic radiotherapy, yet the cellular mechanisms driving its onset and progression remain unclear. Here we constructed a single-cell dynamic architecture of RP rats with acute lung injury at multiple time points after radiation from 84,865 high-quality cells through single-cell RNA sequencing. Results Endothelial and epithelial cells are damaged within 24 hours after radiation, while epithelial-mesenchymal transitions (EMT) occur in RP lesions at 1–2 weeks. Identification of radiation-induced EMT signature highly correlated with and superior to known EMT signature. Radiation induces oxidative stress and promotes apoptosis in monocytes one week after radiation exposure, and the induced inflammation persists. Macrophage components enhance the pro-inflammatory response following radiation via MIF signaling and exhibit four distinct intercellular communication patterns. The ligand Mif was associated with radiation-induced expression enhancement, and its blockade alleviated pneumonia symptoms. The dynamics and differentiation of lymphocytes reveal that effector and helper T cells activate within 2–4 weeks post-radiation, while tissue-resident memory T cells proliferate at 6 weeks. Conclusions This RP architecture provides a comprehensive view of the cellular architecture and dynamics following radiation exposure, enhancing our understanding of RP’s pathogenesis and offering biomarkers and potential therapeutic targets for early diagnosis and intervention.

Objectives: Homologous recombination repair (HRR) deficiency is associated with improved immunotherapy responses in non-small cell lung cancer (NSCLC) patients. The HRR genes BRCA1 / 2 are key regulators of DNA repair, yet their impact on the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Methods: Using single-cell sequencing and multi-omics data, we characterized BRCA1/2 mutation-associated transcriptional programs, immune cell composition, and functional alterations in T cells, investigating the molecular and immune architecture of BRCA-mutant LUAD patients. Results: BRCA1 / 2 mutations were associated with increased genomic instability and poor prognosis in LUAD patients, but predicted better clinical outcomes following immune checkpoint blockade (ICB) treatment. BRCA1 mutations correlated with an upregulated type I IFN/IFN-γ signature and CD8 ⁺ T cell activation. BRCA2 mutations were associated with alveolar/stress/inflammatory responses and enhanced MHC-II antigen presentation, linked to CD4 ⁺ T cell differentiation. Both alterations coincided with reduced CD28 co-stimulation and CTL activity, hinting of immune evasion. We identified two tissue-resident memory T cell (Trm) subsets as predictors of clinical outcomes and ICB response. BRCA1 mutations were associated with CD8 ⁺ Trm expansion, whereas BRCA2 mutations linked to tumor CD4 ⁺ Trm expansion and peripheral T/NK cell cytotoxicity. Furthermore, a cancer-promoting program activated by BRCA1 mutation was vulnerable to histone deacetylase inhibitors, which inhibited LUAD tumor growth. Conclusions: This study provides a preliminary characterization of the BRCA-mutant TME in LUAD patients, revealing distinct transcriptional and immune patterns that highlight differences in BRCA1/2 -associated molecular architecture and offer a framework for improving therapy efficacy in LUAD.

Background Tissue-resident memory T cells (Trm) are crucial local sentinels in cancer immunity; yet, their functional diversity and the role in non-small cell lung cancer (NSCLC) immune checkpoint blockade (ICB) therapy remain incompletely understood. Methods In this study, we conducted an integrated multidimensional analysis, incorporating single-cell RNA and TCR sequencing, as well as large-scale omics data to elucidate the functions of CD8⁺ Trm subsets in NSCLC patients receiving anti-PD-1/PD-L1 therapy. Results The Trm subsets, Trm-CD103, Trm-ZNF683, and Trm-NR4A1, expressed high levels of tissue-residency markers ITGAE (CD103) and ITGA1 (CD49a), alongside their respective key transcriptional regulators ZNF683 (Hobit) or NR4A1 (Nur77), respectively, while sharing core functional features of cytotoxicity and tissue residency. Importantly, CD103⁺ Trm cells were significantly enriched in anti-PD-1/PD-L1 therapy responders and their abundance correlated with improved survival after treatment. Repertoire analysis revealed clonal expansion and TCR overlap between Trm and effector/memory CD8⁺ T-cell subsets, underscoring their differentiation origins and integrated role in the antitumor immune response. We further developed a core gene signature associated with Trm-CD103 cells that can predict anti-PD-1/PD-L1 therapy response and patient prognosis and found it to be associated with an immunologically active tumor microenvironment. Mechanistically, we identified the transcription factor RBPJ as a key driver of Trm proliferation through integrated single-cell analyses and cross-referencing of a previous knockout mouse experiment dataset, linking its expression to enhanced ICB efficacy. Conclusions Together, our findings elucidate the multifaceted functions of Trm cells in NSCLC patients, establishing them as critical mediators of antitumor immunity and promising biomarkers and therapeutic targets for immunotherapy.