Zhang H, Jiang H, Zhu L, Li J, Ma S. Cancer-associated fibroblasts in non-small cell lung cancer: recent advances and future perspectives. Cancer Lett. 2021;514:38–47.

Article  CAS  PubMed  Google Scholar 

Rotow J, Bivona TG. Understanding and targeting resistance mechanisms in NSCLC. Nat Rev Cancer. 2017;17:637–58.

Article  CAS  PubMed  Google Scholar 

Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, Shafi S, Johnson DH, Mitter R, Rosenthal R, et al. Tracking the evolution of Non-small-cell Lung Cancer. N Engl J Med. 2017;376:2109–21.

Article  CAS  PubMed  Google Scholar 

de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014;346:251–6.

Article  PubMed  PubMed Central  Google Scholar 

Frankell AM, Dietzen M, Al Bakir M, Lim EL, Karasaki T, Ward S, Veeriah S, Colliver E, Huebner A, Bunkum A, et al. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature. 2023;616:525–33.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Martinez-Ruiz C, Black JRM, Puttick C, Hill MS, Demeulemeester J, Larose Cadieux E, Thol K, Jones TP, Veeriah S, Naceur-Lombardelli C, et al. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature. 2023;616:543–52.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qiao M, Jiang T, Liu X, Mao S, Zhou F, Li X, Zhao C, Chen X, Su C, Ren S, Zhou C. Immune checkpoint inhibitors in EGFR-Mutated NSCLC: Dusk or Dawn? J Thorac Oncol. 2021;16:1267–88.

Article  CAS  PubMed  Google Scholar 

Harrison PT, Vyse S, Huang PH. Rare epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer. Semin Cancer Biol. 2020;61:167–79.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ferrer I, Zugazagoitia J, Herbertz S, John W, Paz-Ares L, Schmid-Bindert G. KRAS-Mutant non-small cell lung cancer: from biology to therapy. Lung Cancer. 2018;124:53–64.

Article  PubMed  Google Scholar 

Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, et al. Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients. Nat Commun. 2016;7:11815.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dearden S, Stevens J, Wu YL, Blowers D. Mutation incidence and coincidence in non small-cell lung cancer: meta-analyses by ethnicity and histology (mutMap). Ann Oncol. 2013;24:2371–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cords L, Engler S, Haberecker M, Rüschoff JH, Moch H, de Souza N, Bodenmiller B. Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer.

Wu F, Fan J, He Y, Xiong A, Yu J, Li Y, Zhang Y, Zhao W, Zhou F, Li W, et al. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nat Commun. 2021;12:2540.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong N, Shi L, Wang DC, Chen C, Wang X. Role of epigenetics in lung cancer heterogeneity and clinical implication.

Hua X, Zhao W, Pesatori AC, Consonni D, Caporaso NE, Zhang T, Zhu B, Wang M, Jones K, Hicks B, et al. Genetic and epigenetic intratumor heterogeneity impacts prognosis of lung adenocarcinoma. Nat Commun. 2020;11:2459.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, Yu X, Shi S. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol. 2021;14:91.

Article  PubMed  PubMed Central  Google Scholar 

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, et al. The human tumor Atlas Network: charting Tumor transitions across Space and Time at single-cell resolution. Cell. 2020;181:236–49.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu Y, Yang S, Ma J, Chen Z, Song G, Rao D, Cheng Y, Huang S, Liu Y, Jiang S, et al. Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at single-cell level. Cancer Discov. 2022;12:134–53.

Article  CAS  PubMed  Google Scholar 

Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573–e35873529.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

Fan JA-O, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ et al. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019;566:496–502.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Croizer H, Mhaidly R, Kieffer YA-O, Gentric GA-O, Djerroudi L, Leclere RA-O, Pelon F, Robley C, Bohec MA-OX, Meng A et al. Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer.

Wang M, Liu Y, Sun R, Liu F, Li J, Yan L, Zhang J, Xie X, Li D, Wang Y, et al. Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy. Nat Genet. 2024;56:294–305.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Desai TJ, Brownfield DG, Krasnow MA. Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature. 2014;507:190–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kotliar D, Veres A, Nagy MA, Tabrizi S, Hodis E, Melton DA, Sabeti PC. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq. Elife 2019; 8.

Ni Y, Lu M, Li M, Hu X, Li F, Wang Y, Xue D. Unraveling the underlying pathogenic factors driving nonalcoholic steatohepatitis and hepatocellular carcinoma: an in-depth analysis of prognostically relevant gene signatures in hepatocellular carcinoma.

Deng X, Li M, Deng S, Wang L. Hybrid gene selection approach using XGBoost and multi-objective genetic algorithm for cancer classification. Med Biol Eng Comput. 2022;60:663–81.

Article  PubMed  Google Scholar 

Li H, Shi L, Gao W, Zhang Z, Zhang L, Zhao Y, Wang G. dPromoter-XGBoost: detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost.

Panagiotopoulos KA-OX, Korfiati A, Theofilatos KA-O, Hurwitz PA-OX, Deriu MA-O, Mavroudi SA-O. MEvA-X: a hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets. LID – 10.1093/bioinformatics/btad384 [doi] LID - btad384.

Thul PJ, Lindskog CA-O. The human protein atlas: A spatial map of the human proteome.

Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using CellChat. Nat Commun. 2021;12:1088.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature. 2023;619:585–94.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu X, Song J, Zhang H, Liu X, Zuo F, Zhao Y, Zhao Y, Yin X, Guo X, Wu X et al. Immune checkpoint HLA-E:CD94-NKG2A mediates evasion of circulating tumor cells from NK cell surveillance.

Reichart DA-O, Lindberg EA-OX, Maatz HA-O, Miranda AMA, Viveiros AA-O, Shvetsov NA-O, Gärtner AA-O, Nadelmann EA-O, Lee MA-O, Kanemaru KA-O et al. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.

He H, Ma H, Chen Z, Chen J, Wu D, Lv X, Zhu J. Chromosomal Copy Number Variation predicts EGFR-TKI response and prognosis for patients with Non-small Cell Lung Cancer.

Voutsadakis IA-O. Characteristics and prognosis of 8p11.23-Amplified squamous lung carcinomas. LID – 10.3390/jcm12051711 [doi] LID – 1711.

Camidge DR, Otterson GA, Clark JW, Ignatius Ou SH, Weiss J, Ades S, Shapiro GI, Socinski MA, Murphy DA, Conte U et al. Crizotinib in Patients With MET-Amplified NSCLC.

Liu CA-OX, Liu D, Wang SA-O, Gan L, Yang X, Ma CA-O. Identification of the SNARE complex that mediates the fusion of multivesicular bodies with the plasma membrane in exosome secretion.

Veglia F, Gabrilovich DI. Dendritic cells in cancer: the role revisited. Curr Opin Immunol. 2017;45:43–51.

Article  CAS  PubMed