Single-cell data analysis of malignant epithelial cell heterogeneity in lung adenocarcinoma for patient classification and prognosis prediction

Siegel, 2022, Cancer statistics, 2022, CA Cancer J Clin, 72, 7, 10.3322/caac.21708 Herbst, 2018, The biology and management of non-small cell lung cancer, Nature, 553, 446, 10.1038/nature25183 Costa, 2013, Comprehensive molecular screening: from the RT-PCR to the RNA-seq, Transl. Lung Cancer Res., 2, 87 Yoshihara, 2013, Inferring tumour purity and stromal and immune cell admixture from expression data, Nat. Commun., 4, 2612, 10.1038/ncomms3612 Newman, 2015, Robust enumeration of cell subsets from tissue expression profiles, Nat. Methods, 12, 453, 10.1038/nmeth.3337 Becht, 2016, Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression, Genome Biol., 17, 218, 10.1186/s13059-016-1070-5 Dagogo-Jack, 2018, Tumour heterogeneity and resistance to cancer therapies, Nat. Rev. Clin. Oncol., 15, 81, 10.1038/nrclinonc.2017.166 Vitale, 2021, Intratumoral heterogeneity in cancer progression and response to immunotherapy, Nat Med, 27, 212, 10.1038/s41591-021-01233-9 Prasetyanti, 2017, Intra-tumor heterogeneity from a cancer stem cell perspective, Mol. Cancer, 16, 41, 10.1186/s12943-017-0600-4 Lei, 2021, Applications of single-cell sequencing in cancer research: progress and perspectives, J. Hematol. Oncol., 14, 91, 10.1186/s13045-021-01105-2 Gohil, 2021, Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy, Nat. Rev. Clin. Oncol., 18, 244, 10.1038/s41571-020-00449-x Zilionis, 2019, Single-cell Transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species, Immunity, 50, 1317, 10.1016/j.immuni.2019.03.009 Wu, 2021, Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer, Nat. Commun., 12, 2540, 10.1038/s41467-021-22801-0 Maynard, 2020, Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing, Cell, 182, 1232, 10.1016/j.cell.2020.07.017 Leader, 2021, Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification, Cancer Cell, 39, 1594, 10.1016/j.ccell.2021.10.009 Kim, 2020, Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma, Nat. Commun., 11, 2285, 10.1038/s41467-020-16164-1 Kashima, 2021, Single-cell analyses reveal diverse mechanisms of resistance to EGFR Tyrosine kinase inhibitors in lung cancer, Cancer Res., 81, 4835, 10.1158/0008-5472.CAN-20-2811 Guo, 2018, Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing, Nat Med, 24, 978, 10.1038/s41591-018-0045-3 Chen, 2020, Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer, Genome Biol., 21, 152, 10.1186/s13059-020-02064-6 Rowbotham, 2014, Diverse cells at the origin of lung adenocarcinoma, Proc Natl Acad Sci U S A, 111, 4745, 10.1073/pnas.1401955111 Sarode, 2020, Epithelial cell plasticity defines heterogeneity in lung cancer, Cell. Signal., 65, 10.1016/j.cellsig.2019.109463 Xu, 2022, Delving into the heterogeneity of different breast cancer subtypes and the prognostic models utilizing scRNA-seq and bulk RNA-seq, Int. J. Mol. Sci., 23, 10.3390/ijms23179936 Chen, 2022, Single cell RNA-seq reveals the CCL5/SDC1 receptor-ligand interaction between T cells and tumor cells in pancreatic cancer, Cancer Lett., 545, 10.1016/j.canlet.2022.215834 Chen, 2022, Development and validation of prognostic and diagnostic model for pancreatic ductal adenocarcinoma based on scRNA-seq and bulk-seq datasets, Hum. Mol. Genet., 31, 1705, 10.1093/hmg/ddab343 Patel, 2014, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma, Science, 344, 1396, 10.1126/science.1254257 Yokota, 1991, Chromosomal localization of putative tumor-suppressor genes in several human cancers, Environ. Health Perspect., 93, 121, 10.1289/ehp.9193121 Tamura, 1997, Deletion of three distinct regions on chromosome 13q in human non-small-cell lung cancer, Int. J. Cancer, 74, 45, 10.1002/(SICI)1097-0215(19970220)74:1<45::AID-IJC8>3.0.CO;2-0 Kwong, 2003, Genetic alterations detected on chromosomes 13 and 14 in Chinese non-small cell lung carcinomas, Cancer Lett., 192, 189, 10.1016/S0304-3835(02)00698-5 Cheung, 2015, Lineage factors and differentiation states in lung cancer progression, Oncogene, 34, 5771, 10.1038/onc.2015.85 Nanashima, 2017, Hair keratin KRT81 is expressed in normal and breast cancer cells and contributes to their invasiveness, Oncol. Rep., 37, 2964, 10.3892/or.2017.5564 Zhang, 2021, KRT81 knockdown inhibits malignant progression of melanoma through regulating interleukin-8, DNA Cell Biol., 40, 1290, 10.1089/dna.2021.0317 La Manno, 2018, RNA velocity of single cells, Nature, 560, 494, 10.1038/s41586-018-0414-6 Yuanhua, 2019, TFAP2A induced KRT16 as an oncogene in lung adenocarcinoma via EMT, Int. J. Biol. Sci., 15, 1419, 10.7150/ijbs.34076 Xiong, 2021, TFAP2A potentiates lung adenocarcinoma metastasis by a novel miR-16 family/TFAP2A/PSG9/TGF-beta signaling pathway, Cell Death Dis., 12, 352, 10.1038/s41419-021-03606-x Guoren, 2020, TFAP2A induced ITPKA serves as an oncogene and interacts with DBN1 in lung adenocarcinoma, Int. J. Biol. Sci., 16, 504, 10.7150/ijbs.40435 Zhang, 2020, Chromatin accessibility analysis reveals that TFAP2A promotes angiogenesis in acquired resistance to anlotinib in lung cancer cells, Acta Pharmacol. Sin., 41, 1357, 10.1038/s41401-020-0421-7 Mano, 2007, Fibroblast growth factor receptor 1 oncogene partner as a novel prognostic biomarker and therapeutic target for lung cancer, Cancer Sci., 98, 1902, 10.1111/j.1349-7006.2007.00610.x Jiang, 2019, miR-22 enhances the radiosensitivity of small-cell lung cancer by targeting the WRNIP1, J. Cell. Biochem., 120, 17650, 10.1002/jcb.29032 Efremova, 2020, CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes, Nat. Protoc., 15, 1484, 10.1038/s41596-020-0292-x Casazza, 2013, Impeding macrophage entry into hypoxic tumor areas by Sema3A/Nrp1 signaling blockade inhibits angiogenesis and restores antitumor immunity, Cancer Cell, 24, 695, 10.1016/j.ccr.2013.11.007 Tokunaga, 2018, CXCL9, CXCL10, CXCL11/CXCR3 axis for immune activation - a target for novel cancer therapy, Cancer Treat Rev., 63, 40, 10.1016/j.ctrv.2017.11.007 Cambien, 2009, Organ-specific inhibition of metastatic colon carcinoma by CXCR3 antagonism, Br. J. Cancer, 100, 1755, 10.1038/sj.bjc.6605078 Zhu, 2015, CXCR3 as a molecular target in breast cancer metastasis: inhibition of tumor cell migration and promotion of host anti-tumor immunity, Oncotarget, 6, 43408, 10.18632/oncotarget.6125 Walser, 2006, Antagonism of CXCR3 inhibits lung metastasis in a murine model of metastatic breast cancer, Cancer Res., 66, 7701, 10.1158/0008-5472.CAN-06-0709 Pradelli, 2009, Antagonism of chemokine receptor CXCR3 inhibits osteosarcoma metastasis to lungs, Int. J. Cancer, 125, 2586, 10.1002/ijc.24665 Zhang, 2023, A novel basement membrane-related gene signature for prognosis of lung adenocarcinomas, Comput. Biol. Med., 154, 10.1016/j.compbiomed.2023.106597 Zhang, 2023, Mast cell marker gene signature: prognosis and immunotherapy response prediction in lung adenocarcinoma through integrated scRNA-seq and bulk RNA-seq, Front. Immunol., 14 Zhang, 2023, T cell-related prognostic risk model and tumor immune environment modulation in lung adenocarcinoma based on single-cell and bulk RNA sequencing, Comput. Biol. Med., 152, 10.1016/j.compbiomed.2022.106460 Huang, 2023, Integrating single-cell and bulk RNA sequencing to develop a cancer-associated fibroblast-related signature for immune infiltration prediction and prognosis in lung adenocarcinoma, J. Thorac. Dis., 15, 1406, 10.21037/jtd-23-238 Kurahara, 2020, Lung recurrence and its therapeutic strategy in patients with pancreatic cancer, Pancreatology, 20, 89, 10.1016/j.pan.2019.11.015 Kobayashi, 2005, EGFR mutation and resistance of non-small-cell lung cancer to gefitinib, N. Engl. J. Med., 352, 786, 10.1056/NEJMoa044238 Shukla, 2017, Development of a RNA-seq based prognostic signature in lung adenocarcinoma, J Natl Cancer Inst, 109, 10.1093/jnci/djw200 Marjanovic, 2020, Emergence of a high-plasticity cell state during lung cancer evolution, Cancer Cell, 38, 229, 10.1016/j.ccell.2020.06.012 Lim, 2019, Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy, J. Hematol. Oncol., 12, 134, 10.1186/s13045-019-0818-2 Jamal-Hanjani, 2017, Tracking the evolution of non-small-cell lung cancer, N. Engl. J. Med., 376, 2109, 10.1056/NEJMoa1616288 de Sousa, 2018, Heterogeneity in lung cancer, Pathobiology, 85, 96, 10.1159/000487440 Fang, 2021, Intratumoral heterogeneity as a predictive biomarker in anti-PD-(L)1 therapies for non-small cell lung cancer, Mol. Cancer, 20, 37, 10.1186/s12943-021-01331-9 Chong, 2021, Single-cell RNA sequencing in human lung cancer: applications, challenges, and pathway towards personalized therapy, J. Chin. Med. Assoc., 84, 563, 10.1097/JCMA.0000000000000535 Mendez, 2013, Copy number gains of FGFR1 and 3q chromosome in squamous cell carcinoma of the lung, Transl. Lung Cancer Res., 2, 101 Sangaletti, 2021, Myeloid cell heterogeneity in lung cancer: implication for immunotherapy, Cancer Immunol. Immunother., 70, 2429, 10.1007/s00262-021-02916-5 Azevedo, 2018, Cross-talk between lung cancer and bones results in neutrophils that promote tumor progression, Cancer Metastasis Rev., 37, 779, 10.1007/s10555-018-9759-4 Pan, 2021, EMT-associated microRNAs and their roles in cancer stemness and drug resistance, Cancer Commun., 41, 199, 10.1002/cac2.12138 Mittal, 2018, Epithelial mesenchymal transition in tumor metastasis, Annu. Rev. Pathol., 13, 395, 10.1146/annurev-pathol-020117-043854 Wang, 2021, Role of hypoxiainducible factor2alpha in lung cancer (Review). Oncol Rep, 45 Ancel, 2021, Hypoxia in lung cancer management: a Translational approach, Cancers, 13, 10.3390/cancers13143421 Tirpe, 2019, Hypoxia: overview on hypoxia-mediated mechanisms with a focus on the role of HIF genes, Int. J. Mol. Sci., 20, 10.3390/ijms20246140 Dumond, 2020, Neuropilins, as relevant oncology target: their role in the tumoral microenvironment, Front. Cell Dev. Biol., 8, 662, 10.3389/fcell.2020.00662 Liu, 2020, Identification and validation of two lung adenocarcinoma-development characteristic gene sets for diagnosing lung adenocarcinoma and predicting prognosis, Front. Genet., 11, 10.3389/fgene.2020.565206 Laughney, 2020, Regenerative lineages and immune-mediated pruning in lung cancer metastasis, Nat Med, 26, 259, 10.1038/s41591-019-0750-6 Hao, 2021, Integrated analysis of multimodal single-cell data, Cell, 184, 3573, 10.1016/j.cell.2021.04.048 Puram, 2017, Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer, Cell, 171, 1611, 10.1016/j.cell.2017.10.044 Trapnell, 2014, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells, Nat. Biotechnol., 32, 381, 10.1038/nbt.2859 Yu, 2012, clusterProfiler: an R package for comparing biological themes among gene clusters, OMICS, 16, 284, 10.1089/omi.2011.0118 Wu, 2021, clusterProfiler 4.0: a universal enrichment tool for interpreting omics data, Innovation, 2 Newman, 2019, Determining cell type abundance and expression from bulk tissues with digital cytometry, Nat. Biotechnol., 37, 773, 10.1038/s41587-019-0114-2 Aibar, 2017, SCENIC: single-cell regulatory network inference and clustering, Nat. Methods, 14, 1083, 10.1038/nmeth.4463 Wilkerson, 2010, ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking, Bioinformatics, 26, 1572, 10.1093/bioinformatics/btq170 Schneider, 2012, NIH Image to ImageJ: 25 years of image analysis, Nat. Methods, 9, 671, 10.1038/nmeth.2089