Applicability of Spatial Technology in Cancer Research

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참고문헌 (99)

1. Quail DF, "Microenvironmental regulation of tumor progression and metastasis", Nat Med, 19, pp.1423~1437 (2013)
2. Ren X, "Understanding tumor ecosystems by single-cell sequencing : promises and limitations", Genome Biol, 19, pp.211~ (2018)
3. Klein CA, "Parallel progression of primary tumours and meta-stases", Nat Rev Cancer, 9, pp.302~312 (2009)
4. Marusyk A, "Intratumor heterogeneity : the Rosetta stone of therapy resistance", Cancer Cell, 37, pp.471~484 (2020)
5. Efremova M, "CellPhoneDB : inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes", Nat Protoc, 15, pp.1484~1506 (2020)
6. Browaeys R, "NicheNet : modeling intercellular communication by linking ligands to target genes", Nat Methods, 17, pp.159~162 (2020)
7. Chattopadhyay PK, "Single-cell technologies for monitoring immune systems", Nat Immunol, 15, pp.128~135 (2014)
8. Puram SV, "Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer", Cell, 171, pp.1611~1624 (2017)
9. Young MD, "Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors", Sci-ence, 361, pp.594~599 (2018)
10. Elhanani O, "Spatial profiling technologies illuminate the tumor microenvironment", Cancer Cell, 41, pp.404~420 (2023)
11. Zhuang X, "Spatially resolved single-cell genomics and transcriptomics by imaging", Nat Methods, 18, pp.18~22 (2021)
12. Tan WCC, "Overview of multiplex immunohistochemistry", immunofluorescence techniques in the era of cancer immunotherapy, 2020, pp.40, 135~153
13. Hickey JW, "Spatial mapping of protein composition and tissue organization : a primer for multiplexed antibody-based imaging", Nat Methods, 19, pp.284~295 (2022)
14. Crosetto N, "Spatially resolved transcriptomics and beyond", Nat Rev Genet, 16, pp.57~66 (2015)
15. Allam M, "Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics", NPJ Precis Oncol, 4, pp.11~ (2020)
16. Wang N, "Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment", Biotechnol J, 16, pp.e2100041~ (2021)
17. Maniatis S, "Spatially resolved transcriptomics and its applications in cancer", Curr Opin Genet Dev, 66, pp.70~77 (2021)
18. Zheng B, "Spatially resolved transcriptomics provide a new method for cancer research", J Exp Clin Cancer Res, 41, pp.179~ (2022)
19. Bassiouni R, "Applicability of spatial transcriptional profiling to cancer research", Mol Cell, 81, pp.1631~1639 (2021)
20. Marx V, "Method of the Year : spatially resolved transcriptomics", Nat Methods, 18, pp.9~14 (2021)
21. Lewis SM, "Spatial omics and multiplexed imaging to explore cancer biology", Nat Methods, 18, pp.997~1012 (2021)
22. Rao A, "Exploring tissue architecture using spatial transcriptomics", Nature, 596, pp.211~220 (2021)
23. Longo SK, "Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics", Nat Rev Genet, 22, pp.627~644 (2021)
24. McGinnis LM, "Clinical and research applications of multiplexed immunohistochemistry and in situ hybridization", J Pathol, 254, pp.405~417 (2021)
25. Ahmed R, "Spatial mapping of cancer tissues by OMICS technologies", Biochim Biophys Acta Rev Cancer, 1877, pp.188663~ (2022)
26. Kuczkiewicz-Siemion O, "The role of pathology-based methods in qualitative and quantitative approaches to cancer immunotherapy", Cancers(Basel), 14, pp.3833~ (2022)
27. Akhoundova D, "Clinical application of advanced multi-omics tumor profiling : Shaping precision oncology of the future", Cancer Cell, 40, pp.920~938 (2022)
28. Wu Y, "Spatial omics : Navigating to the golden era of cancer research", Clin Transl Med, 12, pp.e696~ (2022)
29. Ahmed R, "Single-cell RNA sequencing with spatial transcriptomics of cancer tissues", Int J Mol Sci, 23, pp.3042~ (2022)
30. Walker BL, "Deciphering tissue structure and function using spatial transcriptomics", Commun Biol, 5, pp.220~ (2022)
31. Moses L, "Museum of spatial transcriptomics", Nat Methods, 19, pp.534~546 (2022)
32. Asp M, "Spatially resolved transcriptomes-next generation tools for tissue exploration", Bioessays, 42, pp.e1900221~ (2020)
33. Stahl PL, "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics", Science, 353, pp.78~82 (2016)
34. Gracia Villacampa E, "Genome-wide spatial expre-ssion profiling in formalin-fixed tissues", Cell Genom, 1, pp.100065~ (2021)
35. Harouaka RA, "Circulating tumor cell enrichment based on physical properties", J Lab Autom, 18, pp.455~468 (2013)
36. Nagasawa S, "Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast", Commun Biol, 4, pp.438~ (2021)
37. Chu Y, "Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance", Nat Med, 29, pp.1550~1562 (2023)
38. Zollinger DR, "GeoMx RNA assay : high multiplex, digital, spatial analysis of RNA in FFPE tissue", Methods Mol Biol, 2148, pp.331~345 (2020)
39. Merritt CR, "Multiplex digital spatial profiling of proteins and RNA in fixed tissue", Nat Biotechnol, 38, pp.586~599 (2020)
40. Reis PP, "mRNA transcript quantification in archival samples using multiplexed, color-coded probes", BMC Biotechnol, 11, pp.46~ (2011)
41. Vadakekolathu J, "Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia", Sci Transl Med, 12, pp.eaaz0463~ (2020)
42. Keane C, "LAG3 : a novel immune checkpoint expressed by multiple lymphocyte subsets in diffuse large B-cell lymphoma", Blood Adv, 4, pp.1367~1377 (2020)
43. Stewart RL, "Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis", Sci Rep, 10, pp.6598~ (2020)
44. Hwang WL, "Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment", Nat Genet, 54, pp.1178~1191 (2022)
45. Danaher P, "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Nat Commun, 13, pp.385~ (2022)
46. Pich-Bavastro C, "Activin A-mediated polarization of cancer-associated fibroblasts and macrophages confers resistance to checkpoint immunotherapy in Skin Cancer", Clin Cancer Res, 29, pp.3498~3513 (2023)
47. Lubeck E, "Single-cell in situ RNA profiling by sequential hybridization", Nat Methods, 11, pp.360~361 (2014)
48. Shah S, "In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus", Neuron, 92, pp.342~357 (2016)
49. Chen KH, "RNA imaging: spatially resolved, highly multiplexed RNA profiling in single cells", Science, 348, pp.aaa6090~ (2015)
50. He S, "High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging", Nat Biotechnol, 40, pp.1794~1806 (2022)
51. Lee JH, "Fluorescent in situ sequencing(FISSEQ)of RNA for gene expression profiling in intact cells and tissues", Nat Protoc, 10, pp.442~458 (2015)
52. Ke R, "In situ sequencing for RNA analysis in preserved tissue and cells", Nat Methods, 10, pp.857~860 (2013)
53. Wang X, "Three-dimensional intact-tissue sequencing of single-cell transcriptional states", Science, 361, pp.eaat5691~ (2018)
54. Chen F, "Optical imaging : expansion microscopy", Science, 347, pp.543~548 (2015)
55. Xia C, "Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression", Proc Natl Acad Sci U S A, 116, pp.19490~19499 (2019)
56. Moffitt JR, "High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing", Proc Natl Acad Sci U S A, 113, pp.14456~14461 (2016)
57. "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue" (2022)[URL]
58. Remark R, "In-depth tissue profiling using multiplexed immunohistochemical consecutive staining on single slide", Sci Immunol, 1, pp.aaf6925~ (2016)
59. Akturk G, "Multiplexed Immunohistochemical Consecutive Staining on Single Slide(MICSSS) : multiplexed chromogenic IHC assay for high-dimensional tissue analysis", Methods Mol Biol, 2055, pp.497~519 (2020)
60. Lin JR, "Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes", Elife, 7, pp.e31657~ (2018)
61. Angelo M, "Multiplexed ion beam imaging of human breast tumors", Nat Med, 20, pp.436~442 (2014)
62. Giesen C, "Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry", Nat Methods, 11, pp.417~422 (2014)
63. Goltsev Y, "Deep profiling of mouse splenic architecture with CODEX multiplexed imaging", Cell, 174, pp.968~981 (2018)
64. Schurch CM, "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front", Cell, 182, pp.1341~1359 (2020)
65. Ahmed FS, "PD-L1 protein expression on both tumor cells and macrophages are associated with response to neoadjuvant durvalumab with chemotherapy in triple-negative breast cancer", Clin Cancer Res, 26, pp.5456~5461 (2020)
66. Na HY, "Prognostic significance of natural killer cell-associated markers in gastric cancer : quantitative analysis using multiplex immunohistochemistry", J Transl Med, 19, pp.529~ (2021)
67. Park Y, "Expression of the immune checkpoint receptors PD-1, LAG3, and TIM3 in the immune context of stage II and III gastric cancer by using single and chromogenic multiplex immunohistochemistry", Oncoimmunology, 10, pp.1954761~ (2021)
68. Tsujikawa T, "Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis", Cell Rep, 19, pp.203~217 (2017)
69. Cassetta L, "Human tumor-associated macrophage and monocyte transcriptional landscapes reveal cancer-specific reprogramming, biomarkers, and therapeutic targets", Cancer Cell, 35, pp.588~602 (2019)
70. Banik G, "High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers", Methods Enzymol, 635, pp.1~20 (2020)
71. Gerdes MJ, "Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue", Proc Natl Acad Sci U S A, 110, pp.11982~11987 (2013)
72. Li C, "Excess PLAC8 promotes an unconventional ERK2-dependent EMT in colon cancer", J Clin Invest, 124, pp.2172~2187 (2014)
73. Gerdes MJ, "Single-cell heterogeneity in ductal carcinoma in situ of breast", Mod Pathol, 31, pp.406~417 (2018)
74. Stack EC, "Multiplexed immunohistochemistry, imaging, and quantitation : a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis", Methods, 70, pp.46~58 (2014)
75. Halse H, "Multiplex immunohistochemistry accurately defines the immune context of metastatic melanoma", Sci Rep, 8, pp.11158~ (2018)
76. Carstens JL, "Spatial computation of intratumoral T cells correlates with survival of patients with pancreatic cancer", Nat Commun, 8, pp.15095~ (2017)
77. Guo M, "Expression and clinical significance of LAG-3, FGL1, PD-L1 and CD8(+)T cells in hepatocellular carcinoma using multiplex quantitative analysis", J Transl Med, 18, pp.306~ (2020)
78. Majonis D, "Synthesis of a functional metal-chelating polymer and steps toward quantitative mass cytometry bioassays", Anal Chem, 82, pp.8961~8969 (2010)
79. Lou X, "Polymer-based elemental tags for sensitive bioassays", Angew Chem Int Ed Engl, 46, pp.6111~6114 (2007)
80. Han G, "Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry", Nat Protoc, 13, pp.2121~2148 (2018)
81. Rana R, "Signal amplifica-tion for imaging mass cytometry", Bioconjug Chem, 30, pp.2805~2810 (2019)
82. Wang YJ, "Multiplexed in situ imaging mass cytometry analysis of the human endocrine pancreas and immune system in type 1 diabetes", Cell Metab, 29, pp.769~783 (2019)
83. Damond N, "A map of human type 1 diabetes progression by imaging mass cytometry", Cell Metab, 29, pp.755~768 (2019)
84. Keren L, "MIBI-TOF: a multiplexed imaging platform relates cellular phenotypes and tissue structure", Sci Adv, 5, pp.eaax5851~ (2019)
85. Keren L, "A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging", Cell, 174, pp.1373~1387 (2018)
86. Williams CG, "An introduction to spatial transcriptomics for biomedical research", Genome Med, 14, pp.68~ (2022)
87. Kim TY, "Analysis of the role of tumor microenvironment on clinical outcomes of chemotherapy in patients with advanced gastric cancer using high plex digital spatial profiling", J Clin Oncol, 41(4 Suppl), pp.456~ (2023)
88. Zhao T, "Spatial genomics enables multi-modal study of clonal heterogeneity in tissues", Nature, 601, pp.85~91 (2022)
89. Schulz D, "Simultaneous multiplexed imaging of mRNA and proteins with subcellular resolution in breast cancer tissue samples by mass cytometry", Cell Syst, 6, pp.531~ (2018)
90. Hoch T, "Multiplexed imaging mass cytometry of the chemo-kine milieus in melanoma characterizes features of the res-ponse to immunotherapy", Sci Immunol, 7, pp.eabk1692~ (2022)
91. Jiang S, "Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments", Immunity, 55, pp.1118~1134 (2022)
92. Esteva A, "Deep learning-enabled medical computer vision", NPJ Digit Med, 4, pp.5~ (2021)
93. Fu Y, "Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis", Nat Cancer, 1, pp.800~810 (2020)
94. Petukhov V, "Cell segmentation in imaging-based spatial transcriptomics", Nat Biotechnol, 40, pp.345~354 (2022)
95. Zhao Y, "DIST : spatial transcriptomics enhancement using deep learning", Brief Bioinform, 24, pp.bbad013~ (2023)
96. Xu C, "DeepST : identifying spatial domains in spatial transcriptomics by deep learning", Nucleic Acids Res, 50, pp.e131~ (2022)
97. Liu T, "Graph deep learning enabled spatial domains identification for spatial transcriptomics", Brief Bioinform, 24, pp.bbad146~ (2023)
98. Lee RY, "The promise and challenge of spatial omics in dissecting tumour microenvironment and the role of AI", Front Oncol, 13, pp.1172314~ (2023)
99. Pham D, "Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues", Nat Commun, 14, pp.7739~ (2023)