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For: Smith EA, Hodges HC. The Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies. Trends Cancer 2019;5:411-25. [PMID: 31311656 DOI: 10.1016/j.trecan.2019.05.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 12/23/2022]
Number Cited by Other Article(s)
1
Sheng L, Xu H, Wang Y, Ni J, Xiang T, Xu H, Zhou X, Wei K, Dai J. Systematic analysis of lysine lactylation in nucleus pulposus cells. iScience 2024;27:111157. [PMID: 39524337 PMCID: PMC11546124 DOI: 10.1016/j.isci.2024.111157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/28/2024] [Accepted: 10/09/2024] [Indexed: 11/16/2024]  Open
2
Wang Y, Thottappillil N, Gomez-Salazar M, Tower RJ, Qin Q, Del Rosario Alvia IC, Xu M, Cherief M, Cheng R, Archer M, Arondekar S, Reddy S, Broderick K, Péault B, James AW. Integrated transcriptomics of human blood vessels defines a spatially controlled niche for early mesenchymal progenitor cells. Dev Cell 2024;59:2687-2703.e6. [PMID: 39025061 PMCID: PMC11496018 DOI: 10.1016/j.devcel.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/28/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024]
3
Zeng S, Chen L, Tian J, Liu Z, Liu X, Tang H, Wu H, Liu C. Integrative analysis of pan-cancer single-cell data reveals a tumor ecosystem subtype predicting immunotherapy response. NPJ Precis Oncol 2024;8:205. [PMID: 39277681 PMCID: PMC11401940 DOI: 10.1038/s41698-024-00703-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 09/04/2024] [Indexed: 09/17/2024]  Open
4
Jones A, Cai D, Li D, Engelhardt BE. Optimizing the design of spatial genomic studies. Nat Commun 2024;15:4987. [PMID: 38862492 PMCID: PMC11166654 DOI: 10.1038/s41467-024-49174-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2024] [Indexed: 06/13/2024]  Open
5
Zhou M, He X, Mei C, Ou C. Exosome derived from tumor-associated macrophages: biogenesis, functions, and therapeutic implications in human cancers. Biomark Res 2023;11:100. [PMID: 37981718 PMCID: PMC10658727 DOI: 10.1186/s40364-023-00538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]  Open
6
Chitra U, Arnold BJ, Sarkar H, Ma C, Lopez-Darwin S, Sanno K, Raphael BJ. Mapping the topography of spatial gene expression with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561757. [PMID: 37873258 PMCID: PMC10592770 DOI: 10.1101/2023.10.10.561757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
7
Zhao C, Germain RN. Multiplex imaging in immuno-oncology. J Immunother Cancer 2023;11:e006923. [PMID: 37899132 PMCID: PMC10619056 DOI: 10.1136/jitc-2023-006923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 10/31/2023]  Open
8
Cephas AT, Hwang WL, Maitra A, Parnas O, DelGiorno KE. It is better to light a candle than to curse the darkness: single-cell transcriptomics sheds new light on pancreas biology and disease. Gut 2023;72:1211-1219. [PMID: 36997301 PMCID: PMC10988578 DOI: 10.1136/gutjnl-2022-329313] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
9
Bärthel S, Falcomatà C, Rad R, Theis FJ, Saur D. Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy. NATURE CANCER 2023;4:454-467. [PMID: 36959420 DOI: 10.1038/s43018-023-00526-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/08/2023] [Indexed: 03/25/2023]
10
Chen L, Li Z, Wu H. CeDAR: incorporating cell type hierarchy improves cell type-specific differential analyses in bulk omics data. Genome Biol 2023;24:37. [PMID: 36855165 PMCID: PMC9972684 DOI: 10.1186/s13059-023-02857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 01/17/2023] [Indexed: 03/02/2023]  Open
11
Jones A, Cai D, Li D, Engelhardt BE. Optimizing the design of spatial genomic studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526115. [PMID: 36778332 PMCID: PMC9915499 DOI: 10.1101/2023.01.29.526115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
12
Sharma A, Blériot C, Currenti J, Ginhoux F. Oncofetal reprogramming in tumour development and progression. Nat Rev Cancer 2022;22:593-602. [PMID: 35999292 DOI: 10.1038/s41568-022-00497-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/12/2022]
13
Li X, Yang Y, Zhang B, Lin X, Fu X, An Y, Zou Y, Wang JX, Wang Z, Yu T. Lactate metabolism in human health and disease. Signal Transduct Target Ther 2022;7:305. [PMID: 36050306 PMCID: PMC9434547 DOI: 10.1038/s41392-022-01151-3] [Citation(s) in RCA: 337] [Impact Index Per Article: 168.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/17/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022]  Open
14
Hobbs EA, Chen N, Kuriakose A, Bonefas E, Lim B. Prognostic/predictive markers in systemic therapy resistance and metastasis in breast cancer. Ther Adv Med Oncol 2022;14:17588359221112698. [PMID: 35860831 PMCID: PMC9290149 DOI: 10.1177/17588359221112698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/23/2022] [Indexed: 01/12/2023]  Open
15
Peng L, Wang F, Wang Z, Tan J, Huang L, Tian X, Liu G, Zhou L. Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies. Brief Bioinform 2022;23:6618236. [PMID: 35753695 DOI: 10.1093/bib/bbac234] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022]  Open
16
Simonson PD, Valencia I, Patel SS. Tyramide-conjugated DNA barcodes enable signal amplification for multiparametric CODEX imaging. Commun Biol 2022;5:627. [PMID: 35754060 PMCID: PMC9234042 DOI: 10.1038/s42003-022-03558-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/06/2022] [Indexed: 01/09/2023]  Open
17
Xu H, Clemenceau JR, Park S, Choi J, Lee SH, Hwang TH. Spatial heterogeneity and organization of tumor mutation burden with immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer. J Pathol Inform 2022;13:100105. [PMID: 36268064 PMCID: PMC9577053 DOI: 10.1016/j.jpi.2022.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023]  Open
18
LaFave LM, Savage RE, Buenrostro JD. Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
19
Museum of spatial transcriptomics. Nat Methods 2022;19:534-546. [PMID: 35273392 DOI: 10.1038/s41592-022-01409-2] [Citation(s) in RCA: 398] [Impact Index Per Article: 199.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
20
Li K, Yan C, Li C, Chen L, Zhao J, Zhang Z, Bao S, Sun J, Zhou M. Computational elucidation of spatial gene expression variation from spatially resolved transcriptomics data. MOLECULAR THERAPY - NUCLEIC ACIDS 2022;27:404-411. [PMID: 35036053 PMCID: PMC8728308 DOI: 10.1016/j.omtn.2021.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
21
Spatial components of molecular tissue biology. Nat Biotechnol 2022;40:308-318. [PMID: 35132261 DOI: 10.1038/s41587-021-01182-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
22
Wu Y, Cheng Y, Wang X, Fan J, Gao Q. Spatial omics: Navigating to the golden era of cancer research. Clin Transl Med 2022;12:e696. [PMID: 35040595 PMCID: PMC8764875 DOI: 10.1002/ctm2.696] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/11/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022]  Open
23
Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021;40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
24
Khera E, Dong S, Huang H, de Bever L, Delft FLV, Thurber GM. Cellular-Resolution Imaging of Bystander Payload Tissue Penetration from Antibody-Drug Conjugates. Mol Cancer Ther 2021;21:310-321. [PMID: 34911819 DOI: 10.1158/1535-7163.mct-21-0580] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/16/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022]
25
Mortezaee K, Majidpoor J. Key promoters of tumor hallmarks. Int J Clin Oncol 2021;27:45-58. [PMID: 34773527 DOI: 10.1007/s10147-021-02074-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023]
26
Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell 2021;184:5482-5496.e28. [PMID: 34597583 DOI: 10.1016/j.cell.2021.09.014] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/21/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
27
Furman SA, Stern AM, Uttam S, Taylor DL, Pullara F, Chennubhotla SC. In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence. CELL REPORTS METHODS 2021;1:100072. [PMID: 34888541 PMCID: PMC8653984 DOI: 10.1016/j.crmeth.2021.100072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 04/21/2023]
28
Wang Y, Li X, Peng S, Hu H, Wang Y, Shao M, Feng G, Liu Y, Bai Y. Single-Cell Analysis Reveals Spatial Heterogeneity of Immune Cells in Lung Adenocarcinoma. Front Cell Dev Biol 2021;9:638374. [PMID: 34513820 PMCID: PMC8424094 DOI: 10.3389/fcell.2021.638374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 07/13/2021] [Indexed: 01/18/2023]  Open
29
Surman DR, Xu Y, Lee MJ, Trepel J, Brown K, Ramineni M, Splawn TG, Diggs LP, Hodges HC, Davis JL, Lee HS, Burt BM, Ripley RT. Therapeutic Synergy in Esophageal Cancer and Mesothelioma Is Predicted by Dynamic BH3 Profiling. Mol Cancer Ther 2021;20:1469-1480. [PMID: 34088830 PMCID: PMC8338890 DOI: 10.1158/1535-7163.mct-20-0887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/09/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
30
Rao A, Barkley D, França GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature 2021;596:211-220. [PMID: 34381231 PMCID: PMC8475179 DOI: 10.1038/s41586-021-03634-9] [Citation(s) in RCA: 574] [Impact Index Per Article: 191.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 02/08/2023]
31
Li Z, Song T, Yong J, Kuang R. Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion. PLoS Comput Biol 2021;17:e1008218. [PMID: 33826608 PMCID: PMC8055040 DOI: 10.1371/journal.pcbi.1008218] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/19/2021] [Accepted: 03/19/2021] [Indexed: 12/02/2022]  Open
32
Seita A, Nakaoka H, Okura R, Wakamoto Y. Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug. PLoS One 2021;16:e0236534. [PMID: 33524064 PMCID: PMC7850478 DOI: 10.1371/journal.pone.0236534] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/14/2021] [Indexed: 11/18/2022]  Open
33
Sharma A, Seow JJW, Dutertre CA, Pai R, Blériot C, Mishra A, Wong RMM, Singh GSN, Sudhagar S, Khalilnezhad S, Erdal S, Teo HM, Khalilnezhad A, Chakarov S, Lim TKH, Fui ACY, Chieh AKW, Chung CP, Bonney GK, Goh BKP, Chan JK, Chow PK, Ginhoux F, DasGupta R. Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma. Cell 2020;183:377-394.e21. [DOI: 10.1016/j.cell.2020.08.040] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/29/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022]
34
Jin MZ, Jin WL. The updated landscape of tumor microenvironment and drug repurposing. Signal Transduct Target Ther 2020;5:166. [PMID: 32843638 PMCID: PMC7447642 DOI: 10.1038/s41392-020-00280-x] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]  Open
35
Yang F, Zhao Z, Sun B, Chen Q, Sun J, He Z, Luo C. Nanotherapeutics for Antimetastatic Treatment. Trends Cancer 2020;6:645-659. [PMID: 32448754 DOI: 10.1016/j.trecan.2020.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 02/08/2023]
36
Liu D, Zhao X, Tang A, Xu X, Liu S, Zha L, Ma W, Zheng J, Shi M. CRISPR screen in mechanism and target discovery for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2020;1874:188378. [PMID: 32413572 DOI: 10.1016/j.bbcan.2020.188378] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
37
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. Cell Rep 2020;30:1767-1779.e6. [DOI: 10.1016/j.celrep.2020.01.049] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/07/2019] [Accepted: 01/15/2020] [Indexed: 12/16/2022]  Open
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