[1] |
Ståhl PL, Salmén F, Vickovic S, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics[J]. Science, 2016,353(6294):78⁃82. doi: 10.1126/science.aaf 2403.
|
[2] |
Wang X, Allen WE, Wright MA, et al. Three⁃dimensional intact⁃tissue sequencing of single⁃cell transcriptional states[J]. Science, 2018,361(6400):eaat5691. doi: 10.1126/science.aat5691.
|
[3] |
Larsson L, Frisén J, Lundeberg J. Spatially resolved transcriptomics adds a new dimension to genomics[J]. Nat Methods, 2021,18(1):15⁃18. doi: 10.1038/s41592⁃020⁃01038⁃7.
|
[4] |
Rao A, Barkley D, França GS, et al. Exploring tissue architecture using spatial transcriptomics[J]. Nature, 2021,596(7871):211⁃220. doi: 10.1038/s41586⁃021⁃03634⁃9.
|
[5] |
Savulescu AF, Jacobs C, Negishi Y, et al. Pinpointing cell identity in time and space[J]. Front Mol Biosci, 2020,7:209. doi: 10.3389/fmolb.2020.00209.
|
[6] |
Lee J, Yoo M, Choi J. Recent advances in spatially resolved transcriptomics: challenges and opportunities[J]. BMB Rep, 2022,55(3):113⁃124. doi: 10.5483/BMBRep.2022.55.3.014.
|
[7] |
Gyllborg D, Langseth CM, Qian X, et al. Hybridization⁃based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue[J]. Nucleic Acids Res, 2020,48(19):e112. doi: 10.1093/nar/gkaa792.
|
[8] |
Longo SK, Guo MG, Ji AL, et al. Integrating single⁃cell and spatial transcriptomics to elucidate intercellular tissue dynamics[J]. Nat Rev Genet, 2021,22(10):627⁃644. doi: 10.1038/s41576⁃021⁃00370⁃8.
|
[9] |
Stubbington M, Rozenblatt⁃Rosen O, Regev A, et al. Single⁃cell transcriptomics to explore the immune system in health and disease[J]. Science, 2017,358(6359):58⁃63. doi: 10.1126/science.aan6828.
|
[10] |
Lawson DA, Kessenbrock K, Davis RT, et al. Tumour heterogeneity and metastasis at single⁃cell resolution[J]. Nat Cell Biol, 2018,20(12):1349⁃1360. doi: 10.1038/s41556⁃018⁃0236⁃7.
|
[11] |
Papalexi E, Satija R. Single⁃cell RNA sequencing to explore immune cell heterogeneity[J]. Nat Rev Immunol, 2018,18(1):35⁃45. doi: 10.1038/nri.2017.76.
|
[12] |
Lohoff T, Ghazanfar S, Missarova A, et al. Integration of spatial and single⁃cell transcriptomic data elucidates mouse organogenesis[J]. Nat Biotechnol, 2022,40(1):74⁃85. doi: 10. 1038/s41587⁃021⁃01006⁃2.
|
[13] |
Zhou X, Lu Y, Zhao F, et al. Deciphering the spatial⁃temporal transcriptional landscape of human hypothalamus development[J]. Cell Stem Cell, 2022,29(2):328⁃343. doi: 10.1016/j.stem. 2021.11.009.
|
[14] |
Moor AE, Itzkovitz S. Spatial transcriptomics: paving the way for tissue⁃level systems biology[J]. Curr Opin Biotechnol, 2017,46:126⁃133. doi: 10.1016/j.copbio.2017.02.004.
|
[15] |
Hampel H, Nisticò R, Seyfried NT, et al. Omics sciences for systems biology in Alzheimer's disease: State⁃of⁃the⁃art of the evidence[J]. Ageing Res Rev, 2021,69:101346. doi: 10.1016/j.arr.2021.101346.
|
[16] |
Wu Y, Cheng Y, Wang X, et al. Spatial omics: navigating to the golden era of cancer research[J]. Clin Transl Med, 2022,12(1):e696. doi: 10.1002/ctm2.696.
|
[17] |
Veenstra J, Dimitrion P, Yao Y, et al. Research techniques made simple: use of imaging mass cytometry for dermatological research and clinical applications[J]. J Invest Dermatol, 2021,141(4):705⁃712. doi: 10.1016/j.jid.2020.12.008.
|
[18] |
Solé⁃Boldo L, Raddatz G, Schütz S, et al. Single⁃cell transcriptomes of the human skin reveal age⁃related loss of fibroblast priming[J]. Commun Biol, 2020,3(1):188. doi: 10. 1038/s42003⁃020⁃0922⁃4.
|
[19] |
Joost S, Annusver K, Jacob T, et al. The molecular anatomy of mouse skin during hair growth and rest[J]. Cell Stem Cell, 2020,26(3):441⁃457.e7. doi: 10.1016/j.stem.2020.01.012.
|
[20] |
Jin S, Ramos R. Computational exploration of cellular communication in skin from emerging single⁃cell and spatial transcriptomic data[J]. Biochem Soc Trans, 2022,50(1):297⁃308. doi: 10.1042/BST20210863.
|
[21] |
Foster DS, Januszyk M, Yost KE, et al. Integrated spatial multiomics reveals fibroblast fate during tissue repair[J]. Proc Natl Acad Sci U S A, 2021,118(41):e2110025118. doi: 10.1073/pnas.2110025118.
|
[22] |
Wu J, Fang Z, Liu T, et al. Maximizing the utility of transcriptomics data in inflammatory skin diseases[J]. Front Immunol, 2021,12:761890. doi: 10.3389/fimmu.2021.761890.
|
[23] |
Cheng JB, Sedgewick AJ, Finnegan AI, et al. Transcriptional programming of normal and inflamed human epidermis at single⁃cell resolution[J]. Cell Rep, 2018,25(4):871⁃883. doi: 10.1016/j.celrep.2018.09.006.
|
[24] |
Hughes TK, Wadsworth MH 2nd, Gierahn TM, et al. Second⁃strand synthesis⁃based massively parallel scRNA⁃Seq reveals cellular states and molecular features of human inflammatory skin pathologies[J]. Immunity, 2020,53(4):878⁃894. doi: 10. 1016/j.immuni.2020.09.015.
|
[25] |
Gudjonsson JE, Tsoi LC, Ma F, et al. Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis[J]. JCI Insight, 2020,5(19):e139930. doi: 10.1172/jci.insight.139930.
|
[26] |
Gutowska⁃Owsiak D, Schaupp AL, Salimi M, et al. IL⁃17 downregulates filaggrin and affects keratinocyte expression of genes associated with cellular adhesion[J]. Exp Dermatol, 2012,21(2):104⁃110. doi: 10.1111/j.1600⁃0625.2011.01412.x.
|
[27] |
Belkaid Y, Segre JA. Dialogue between skin microbiota and immunity[J]. Science, 2014,346(6212):954⁃959. doi: 10.1126/science.1260144.
|
[28] |
Xiang Y, Ye Y, Zhang Z, et al. Maximizing the utility of cancer transcriptomic data[J]. Trends Cancer, 2018,4(12):823⁃837. doi: 10.1016/j.trecan.2018.09.009.
|
[29] |
Ji AL, Rubin AJ, Thrane K, et al. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma[J]. Cell, 2020,182(2):497⁃514. doi: 10.1016/j.cell. 2020.05.039.
|
[30] |
Jin MZ, Jin WL. The updated landscape of tumor microenvironment and drug repurposing[J]. Signal Transduct Target Ther, 2020,5(1):166. doi: 10.1038/s41392⁃020⁃00280⁃x.
|
[31] |
Gatenby RA, Brown JS. Integrating evolutionary dynamics into cancer therapy[J]. Nat Rev Clin Oncol, 2020,17(11):675⁃686. doi: 10.1038/s41571⁃020⁃0411⁃1.
|
[32] |
Quek C, Bai X, Long GV, et al. High⁃dimensional single⁃cell transcriptomics in melanoma and cancer immunotherapy[J]. Genes (Basel), 2021,12(10):1629. doi: 10.3390/genes12101629.
|
[33] |
Dagogo⁃Jack I, Shaw AT. Tumour heterogeneity and resistance to cancer therapies[J]. Nat Rev Clin Oncol, 2018,15(2):81⁃94. doi: 10.1038/nrclinonc.2017.166.
|
[34] |
Thrane K, Eriksson H, Maaskola J, et al. Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage Ⅲ cutaneous malignant melanoma[J]. Cancer Res, 2018,78(20):5970⁃5979. doi: 10.1158/0008⁃5472.CAN⁃18⁃0747.
|
[35] |
Hunter MV, Moncada R, Weiss JM, et al. Spatially resolved transcriptomics reveals the architecture of the tumor⁃microenvironment interface[J]. Nat Commun, 2021,12(1):6278. doi: 10.1038/s41467⁃021⁃26614⁃z.
|
[36] |
Rambow F, Rogiers A, Marin⁃Bejar O, et al. Toward minimal residual disease⁃directed therapy in melanoma[J]. Cell, 2018,174(4):843⁃855. doi: 10.1016/j.cell.2018.06.025.
|
[37] |
Lee H, Quek C, Silva I, et al. Integrated molecular and immunophenotypic analysis of NK cells in anti⁃PD⁃1 treated metastatic melanoma patients[J]. Oncoimmunology, 2019,8(2):e1537581. doi: 10.1080/2162402X.2018.1537581.
|
[38] |
Pourmaleki M, Jones CJ, Ariyan CE, et al. Tumor MHC class Ⅰ expression associates with intralesional IL2 response in melanoma[J]. Cancer Immunol Res, 2022,10(3):303⁃313. doi: 10.1158/2326⁃6066.CIR⁃21⁃1083.
|
[39] |
Gadeyne L, Van Herck Y, Milli G, et al. A multi⁃omics analysis of metastatic melanoma identifies a germinal center⁃like tumor microenvironment in HLA⁃DR⁃positive tumor areas[J]. Front Oncol, 2021,11:636057. doi: 10.3389/fonc.2021.636057.
|
[40] |
Pheasant K, Möller⁃Levet CS, Jones J, et al. Nuclear⁃cytoplasmic compartmentalization of the herpes simplex virus 1 infected cell transcriptome is co⁃ordinated by the viral endoribonuclease vhs and cofactors to facilitate the translation of late proteins[J]. PLoS Pathog, 2018,14(11):e1007331. doi: 10.1371/journal.ppat. 1007331.
|
[41] |
Atta L, Fan J. Computational challenges and opportunities in spatially resolved transcriptomic data analysis[J]. Nat Commun, 2021,12(1):5283. doi: 10.1038/s41467⁃021⁃25557⁃9.
|