Spatial Transcriptomics Unveils Regional Heterogeneity and Subclonal Dynamics in the Lung Adenocarcinoma Microenvironment

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Cancer statistics, 2023

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Integrated analysis of multimodal single-cell data

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Inference and analysis of cell-cell communication using CellChat

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Molecular mechanisms of epithelial–mesenchymal transition

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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

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Reversed graph embedding resolves complex single-cell trajectories

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Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

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Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

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New insights into the mechanisms of epithelial–mesenchymal transition and implications for cancer

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EMT Transition States during Tumor Progression and Metastasis

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Clonal heterogeneity and tumor evolution: past, present, and the future

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Single-cell mRNA quantification and differential analysis with Census

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oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data

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A single-cell and spatially resolved atlas of human breast cancers

Wu, S. Z., Al-Eryani, G., Roden, D. L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J. R., Bartonicek, N., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00911-1 · Cited by 1,775 · see citing works

The global burden of lung cancer: current status and future trends

Leiter, A., Veluswamy, R. R., & Wisnivesky, J. P. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00798-3 · Cited by 1,544 · see citing works

Robust decomposition of cell type mixtures in spatial transcriptomics

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CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

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Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

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Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

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Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

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Intra-tumor heterogeneity from a cancer stem cell perspective

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Epithelial–mesenchymal transition in tumor metastasis

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CD44 Is the Signaling Component of the Macrophage Migration Inhibitory Factor-CD74 Receptor Complex

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Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma

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Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma

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Macrophage migration inhibitory factor (MIF) promotes cell survival by activation of the Akt pathway and role for CSN5/JAB1 in the control of autocrine MIF activity

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Validation of a Histology-Independent Prognostic Gene Signature for Early-Stage, Non–Small-Cell Lung Cancer Including Stage IA Patients

Der, S. D., Sykes, J. R., Pintilie, M., Zhu, C., Strumpf, D., Liu, G., Jurišica, I., Shepherd, F. A., & Tsao, M. (2013) · Journal of Thoracic Oncology · doi:10.1097/jto.0000000000000042 · Cited by 373 · see citing works

The Evolving Role of Histology in the Management of Advanced Non–Small-Cell Lung Cancer

Langer, C. J., Besse, B., Gualberto, A., Brambilla, E., & Soria, J. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2010.28.8126 · Cited by 299 · see citing works

Overview of CDK9 as a target in cancer research

Morales, F., & Giordano, A. (2016) · Cell Cycle · doi:10.1080/15384101.2016.1138186 · Cited by 200 · see citing works

Antigen processing and immune regulation in the response to tumours

Reeves, E., & James, E. (2016) · Immunology · doi:10.1111/imm.12675 · Cited by 199 · see citing works

The pivotal role of pathology in the management of lung cancer.

Davidson, M. R., Gazdar, A. F., & Clarke, B. E. (2013) · Europe PMC (PubMed Central) · doi:10.3978/j.issn.2072-1439.2013.08.43 · Cited by 193 · see citing works

Differential roles for membrane-bound and soluble syndecan-1 (CD138) in breast cancer progression

Nikolova, V. D., Koo, C.-Y., Ibrahim, S., Wang, Z., Spillmann, D., Dreier, R., Kelsch, R., Fischgräbe, J., Smollich, M., Rossi, L. H., et al. (2009) · Carcinogenesis · doi:10.1093/carcin/bgp001 · Cited by 183 · see citing works

CellChat for systematic analysis of cell-cell communication from single-cell and spatially resolved transcriptomicsPreprint

Jin, S., Plikus, M. V., & Nie, Q. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.05.565674 · Cited by 178 · see citing works

MIF interacts with CXCR7 to promote receptor internalization, ERK1/2 and ZAP‐70 signaling, and lymphocyte chemotaxis

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A single-cell tumor immune atlas for precision oncologyPreprint

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Intratumoral Heterogeneity of ALK-Rearranged and ALK/EGFR Coaltered Lung Adenocarcinoma

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Role for dipeptidyl peptidase IV in tumor suppression of human non small cell lung carcinoma cells

Wesley, U. V., Tiwari, S., & Houghton, A. N. (2004) · International Journal of Cancer · doi:10.1002/ijc.20091 · Cited by 128 · see citing works

Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

Raredon, M. S. B., Yang, J., Kothapalli, N., Lewis, W., Kaminski, N., Niklason, L. E., & Kluger, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac775 · Cited by 125 · see citing works

Overexpressed ITGA2 promotes malignant tumor aggression by up-regulating PD-L1 expression through the activation of the STAT3 signaling pathway

Ren, D., Zhao, J., Sun, Y., Li, D., Meng, Z., Wang, B., Fan, P., Liu, Z., Jin, X., & Wu, H. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1496-1 · Cited by 122 · see citing works

Vinblastine resets tumor-associated macrophages toward M1 phenotype and promotes antitumor immune response

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Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues

Ahmed, R., Zaman, T., Chowdhury, F., Mraiche, F., Tariq, M., Ahmad, I. S., & Hasan, A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23063042 · Cited by 101 · see citing works

Advances in the molecular functions of syndecan-1 (SDC1/CD138) in the pathogenesis of malignancies

Gharbaran, R. (2014) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2014.12.003 · Cited by 98 · see citing works

Reversed graph embedding resolves complex single-cell developmental trajectoriesPreprint

Qiu, X., Mao, Q., Tang, Y., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/110668 · Cited by 90 · see citing works

In vivo Dynamics and Distinct Functions of Hypoxia in Primary Tumor Growth and Organotropic Metastasis of Breast Cancer

Lü, X., Yan, C. H., Yuan, M., Wei, Y., Hu, G., & Kang, Y. (2010) · Cancer Research · doi:10.1158/0008-5472.can-09-3739 · Cited by 86 · see citing works

Th17 Cells Secrete TWEAK to Trigger Epithelial–Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis

Liu, X., Wang, X. M., Yang, Q., Luo, L., Liu, Z., Ren, X., Lei, K., Li, S., Xie, Z., Zheng, G., et al. (2024) · Cancer Research · doi:10.1158/0008-5472.can-23-2123 · Cited by 77 · see citing works

The correlations of tumor mutational burden among single-region tissue, multi-region tissues and blood in non-small cell lung cancer

Zhang, Y., Chang, L., Yang, Y., Fang, W., Guan, Y., Wu, A., Hong, S., Zhou, H., Chen, G., Chen, X., et al. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0581-5 · Cited by 69 · see citing works

Contribution of upregulated dipeptidyl peptidase 9 (DPP9) in promoting tumoregenicity, metastasis and the prediction of poor prognosis in non‐small cell lung cancer (NSCLC)

Tang, Z., Li, J., Shen, Q., Feng, J., Liu, H., Wang, W., Xu, L., Shi, G., Ye, X., Ge, M., et al. (2016) · International Journal of Cancer · doi:10.1002/ijc.30571 · Cited by 58 · see citing works

CXCR4/MIF axis amplifies tumor growth and epithelial-mesenchymal interaction in non-small cell lung cancer

Jäger, B., Klatt, D., Plappert, L., Golpon, H. A., Lienenklaus, S., Barbosa, P. D., Schambach, A., & Prasse, A. (2020) · Cellular Signalling · doi:10.1016/j.cellsig.2020.109672 · Cited by 56 · see citing works

Annual report to the nation on the status of cancer

Nierengarten, M. B. (2022) · Cancer · doi:10.1002/cncr.34586 · Cited by 56 · see citing works

Hypoxic microenvironment induced spatial transcriptome changes in pancreatic cancer

Sun, H., Zhang, D., Huang, C., Guo, Y., Yang, Z., Yao, N., Dong, X., Cheng, R.-F., Zhao, N., Meng, J., et al. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2021.0158 · Cited by 49 · see citing works

Relationship between SDC1 and cadherin signalling activation in cancer

Liao, S., Liu, C., Zhu, G.-Y., Wang, K., Yang, Y. C., & Wang, C. (2019) · Pathology - Research and Practice · doi:10.1016/j.prp.2019.152756 · Cited by 34 · see citing works

Actinomycin D and Telmisartan Combination Targets Lung Cancer Stem Cells Through the Wnt/Beta Catenin Pathway

Green, R. J., Howell, M., Khalil, R., Nair, R. R., Yan, J., Foran, E. A., Katiri, S., Banerjee, J., Singh, M. S., Bharadwaj, S. N., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-54266-z · Cited by 32 · see citing works

The G-Protein–Coupled Receptor CLR Is Upregulated in an Autocrine Loop with Adrenomedullin in Clear Cell Renal Cell Carcinoma and Associated with Poor Prognosis

Nikitenko, L. L., Leek, R., Henderson, S. R., Pillay, N., Turley, H., Generali, D., Gunningham, S. P., Morrin, H. R., Pellagatti, A., REES, M. C. P., et al. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-1712 · Cited by 26 · see citing works

SEMA4C is a novel target to limit osteosarcoma growth, progression, and metastasis

Smeester, B. A., Slipek, N. J., Pomeroy, E. J., Bomberger, H. E., Shamsan, G. A., Peterson, J. J., Crosby, M. R., Draper, G. M., Becklin, K. L., Rahrmann, E. P., et al. (2019) · Oncogene · doi:10.1038/s41388-019-1041-x · Cited by 21 · see citing works

The relevance between hypoxia-dependent spatial transcriptomics and the prognosis and efficacy of immunotherapy in claudin-low breast cancer

Sun, H., Li, Y., Zhang, Y., Zhao, X., Dong, X., Guo, Y., Mo, J., Che, N., Ban, X., Li, F., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1042835 · Cited by 19 · see citing works

Integrin α2 promotes immune escape in non-small-cell lung cancer by enhancing PD-L1 expression in exosomes to inhibit CD8 + T-cell activity

Jing, H., Meng, M., Ye, M., Liu, S., Cao, X., Li, K., Liu, Y., Zhang, J., & Wu, Y. (2023) · Journal of Investigative Medicine · doi:10.1177/10815589231207801 · Cited by 15 · see citing works

Negative regulation of NEP expression by hypoxia

Mitra, R., Chao, O. S., Nanus, D. M., & Goodman, O. B. (2012) · The Prostate · doi:10.1002/pros.22613 · Cited by 12 · see citing works

Specificity protein 1-induced serine peptidase inhibitor, Kunitz Type 1 antisense RNA1 regulates colorectal cancer cell proliferation, migration, invasion and apoptosis through targeting heparin binding growth factor via sponging microRNA-214

Fang, Y., & Yang, Q. (2022) · Bioengineered · doi:10.1080/21655979.2022.2026859 · Cited by 12 · see citing works

CALCR knockdown inhibits the development and progression of non-small-cell lung cancer

He, T., & Feng, L. (2021) · Carcinogenesis · doi:10.1093/carcin/bgab076 · Cited by 11 · see citing works

Spatial transcriptome sequencing revealed spatial trajectory in the Non-Small Cell Lung CarcinomaPreprint

Zhang, L., Mao, S., Yao, M., Chao, N., Yang, Y., Ni, Y., Song, T., Liu, Z., Yang, Y., & Li, W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.26.441394 · Cited by 10 · see citing works

Multi-omics investigation reveals functional specialization of transcriptional cyclin dependent kinases in cancer biology

Donovan, M. G., Galbraith, M. D., & Espinosa, J. M. (2022) · Scientific Reports · doi:10.1038/s41598-022-26860-1 · Cited by 5 · see citing works

Quantitative comparison of the efficacies and safety profiles of three first-line non-platinum chemotherapy regimens for advanced non-small cell lung cancer

Yang, Q., Zhu, L., Liu, H., Zheng, Q., & Li, L. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.806728 · Cited by 3 · see citing works

Spatial and Temporal Heterogeneity in Clonal Evolution of Nonsmall-cell Lung Cancer: Implications for Therapy

Koulouris, A., Tsagkaris, C., & Mountzios, G. (2022) · Forum of Clinical Oncology · doi:10.2478/fco-2023-0005 · Cited by 2 · see citing works

Case report: Metastatic adenocarcinoma of the lung with filiform “ciliated” tumor cells in the cerebrospinal fluid

Zlotoff, D. A., Kelly, C., Kierson, M., McGrath, C. M., & Gupta, P. K. (2013) · Case Reports in Clinical Medicine · doi:10.4236/crcm.2013.23055 · Cited by 1 · see citing works

Abstract 5165: Patterning of individual cellular behavior in collective invasion

Guo, C., Sanchez, E., & Fong, E. W. M. (2018) · Cancer Research · doi:10.1158/1538-7445.am2018-5165 · Cited by 1 · see citing works

Abstract 692: Patient-derived co-cultures of TRACERx lung cancer organoids and autologous T-cells reveal heterogeneity in immune evasion between cancer subclones

Dijkstra, K. K., Vendramin, R., Hynds, R. E., Pearce, D. R., Karagianni, D., Gálvez‐Cancino, F., Pich, O., Hill, M. S., Barbè, V., Rowan, A., et al. (2022) · Cancer Research · doi:10.1158/1538-7445.am2022-692 · Cited by 1 · see citing works

Artificial Intelligence in Clinical Oncology: From Productivity Enhancement to Creative Discovery

Kuno, M., Osumi, H., Udagawa, S., Yoshikawa, K., Ooki, A., Shinozaki, E., Ishikawa, T., Oba, J., Yamaguchi, K., & Sakurada, K. (2025) · Current Oncology · doi:10.3390/curroncol32110588 · Cited by 7 · see citing works

Synergistic mechanotransduction via the ΔP–EPPK1/DDR2– PI3K/AKT axis drives cell invasion and migrationPreprint

Zhao, L., Liu, C. B., Du, R., Gao, Q., Yang, Y., Han, Y., Du, J., Li, L., & Zhao, X. (2026) · Research Square · doi:10.21203/rs.3.rs-8929917/v1

Advances in deciphering lung cancer immune microenvironment heterogeneity and immunotherapy response using single-cell and multi-omics technologies

Lu, X., Zhao, G., Tang, Y., Li, F., & Cheng, M. M. H. (2026) · Current Proteomics · doi:10.1016/j.curpro.2026.100139

Systematic evaluation of spatial transcriptomic annotation methods reveals conserved tumor microenvironment programs in NSCLC

Wu, M., Zhou, Y., & Xu, D. (2026) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2026.1880333

Single-cell and spatial transcriptomic technologies for lung cancer tumor microenvironment analysis

Braicu, C., Pîrlog, R., Nutu, A. M., Pruteanu, L.-L., Berindan‐Neagoe, I., & Bender, A. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189710

Decoding genomic heterogeneity in ground-glass nodule lung adenocarcinoma before radiotherpay: Subtype-driven biomarkers and therapeutic vulnerabilities

Yao, F., WANG, Y., Li, Z., & Li, D. (2026) · International Journal of Radiation Research · doi:10.66224/ijrr.24.3.38

Decoding spatial transcriptomics-based heterogeneity of TME in early-stage invasive pulmonary adenocarcinoma.

Liu, X., Tian, J., Shang, Z., Xiang, C., Teng, F., Zhang, J., & Han, Y. (2025) · Journal of Clinical Oncology · doi:10.1200/jco.2025.43.16_suppl.e20030

Spatial transcriptomics uncovers immune-cell plasticity and dedifferentiation signatures in aggressive lung adenocarcinoma subtypes

Deng, H., Liu, Q., Tian, Z., Liu, G., Wang, S., Liang, D., Wang, Y., Han, Y., & Xie, S. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1620886 · Cited by 3 · see citing works

Abstract 4622: Tumor microenvironment differences between lung cancer subtypes revealed by spatial transcriptomics

Wilkerson, M. D., Kounelis-Wuillaume, S., Alba, C., Franks, T. J., Doughty, M. L., Kortum, R. L., Browning, R. F., Dalgard, C. L., & Shriver, C. D. (2023) · Cancer Research · doi:10.1158/1538-7445.am2023-4622

Resolving the spatial and cellular architecture of intra-tumor heterogeneity by multi-region dissection of lung adenocarcinoma

Mei, S., Wang, X., Zhao, M., Huang, Q., Huang, Y., Su, M., Zhang, X., Wang, X., Hao, X., Wang, T., et al. (2025) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2025.02.006 · Cited by 5 · see citing works

Abstract 130: Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing

Sinjab, A. F., Han, G., Treekitkarnmongkol, W., Hara, K., Brennan, P. M., Dang, M., Hao, D., Wang, R., Dai, E., Dejima, H., et al. (2021) · Cancer Research · doi:10.1158/1538-7445.am2021-130