Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain

Cell Systems - Tập 13 - Trang 58-70.e5 - 2022
Francisco Jose Grisanti Canozo1,2, Zhen Zuo1, James F. Martin1,2, Md. Abul Hassan Samee1
1Baylor College of Medicine, Houston, TX 77030 USA
2Texas Heart Institute, Houston, TX 77030, USA

Tài liệu tham khảo

Abadi, 2016, Tensorflow: a system for large-scale machine learning, 265 Aibar, 2017, SCENIC: single-cell regulatory network inference and clustering, Nat. Methods, 14, 1083, 10.1038/nmeth.4463 Alquicira-Hernandez, 2019, scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data, Genome Biol., 20, 264, 10.1186/s13059-019-1862-5 Andersson, 2020, Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography, Commun. Biol., 3, 565, 10.1038/s42003-020-01247-y Angermueller, 2016, Deep learning for computational biology, Mol. Syst. Biol., 12, 878, 10.15252/msb.20156651 Arnol, 2019, Modeling cell-cell interactions from spatial molecular data with spatial variance component analysis, Cell Rep., 29, 202, 10.1016/j.celrep.2019.08.077 Baccin, 2020, Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization, Nat. Cell Biol., 22, 38, 10.1038/s41556-019-0439-6 Bair, 2006, Prediction by supervised principal components, J. Am. Stat. Assoc., 101, 119, 10.1198/016214505000000628 Barraud, 2013, Olfactory ensheathing glia are required for embryonic olfactory axon targeting and the migration of gonadotropin-releasing hormone neurons, Biol. Open, 2, 750, 10.1242/bio.20135249 Bialas, 2013, TGF-β signaling regulates neuronal C1q expression and developmental synaptic refinement, Nat. Neurosci., 16, 1773, 10.1038/nn.3560 Biancalani, 2021, Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram, bioRxiv Bolstad, 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185, 10.1093/bioinformatics/19.2.185 Burton, 2017, Inhibitory circuits of the mammalian main olfactory bulb, J. Neurophysiol., 118, 2034, 10.1152/jn.00109.2017 Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat. Biotechnol., 36, 411, 10.1038/nbt.4096 Cable, 2021, Robust decomposition of cell type mixtures in spatial transcriptomics, Nat. Biotechnol. Chacón, 2018 Chollet, 2015 Clarke, 2021, Regionally encoded functional heterogeneity of astrocytes in health and disease: a perspective, Glia, 69, 20, 10.1002/glia.23877 Cohen, 2018, Lung single-cell signaling interaction map reveals basophil role in macrophage imprinting, Cell, 175, 1031, 10.1016/j.cell.2018.09.009 Crosetto, 2015, Spatially resolved transcriptomics and beyond, Nat. Rev. Genet., 16, 57, 10.1038/nrg3832 Defelipe, 2011, The evolution of the brain, the human nature of cortical circuits, and intellectual creativity, Front. Neuroanat., 5, 29, 10.3389/fnana.2011.00029 Dumitrascu, 2021, Optimal marker gene selection for cell type discrimination in single cell analyses, Nat. Commun., 12, 1186, 10.1038/s41467-021-21453-4 Duong Efremova, 2020, CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes, Nat. Protoc., 15, 1484, 10.1038/s41596-020-0292-x Elosua-Bayes, 2021, SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes, Nucleic Acids Res., 49, e50, 10.1093/nar/gkab043 Eng, 2019, Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH, Nature, 568, 235, 10.1038/s41586-019-1049-y Filipp, 2019, Opportunities for artificial intelligence in advancing precision medicine, Curr. Genet. Med. Rep., 7, 208, 10.1007/s40142-019-00177-4 Glasser, 2016, A multi-modal parcellation of human cerebral cortex, Nature, 536, 171, 10.1038/nature18933 Gower-Winter, 2013, Zinc deficiency regulates hippocampal gene expression and impairs neuronal differentiation, Nutr. Neurosci., 16, 174, 10.1179/1476830512Y.0000000043 Grebien, 2008, Stat5 activation enables erythropoiesis in the absence of EpoR and Jak2, Blood, 111, 4511, 10.1182/blood-2007-07-102848 Hébert, 2003, FGF signaling through FGFR1 is required for olfactory bulb morphogenesis, Development, 130, 1101, 10.1242/dev.00334 Herculano-Houzel, 2009, The human brain in numbers: a linearly scaled-up primate brain, Front. Hum. Neurosci., 3, 31, 10.3389/neuro.09.031.2009 Herculano-Houzel, 2015, Mammalian brains are made of these: a dataset of the numbers and densities of neuronal and nonneuronal cells in the brain of Glires, Primates, Scandentia, Eulipotyphlans, Afrotherians and artiodactyls, and their relationship with body mass, Brain Behav. Evol., 86, 145, 10.1159/000437413 Holubarsch, 1992, Cellular and molecular alterations in the failing human heart, Basic Res. Cardiol., 87, 331 Ji, 2020, Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma, Cell, 182, 497, 10.1016/j.cell.2020.05.039 Jolliffe, 2016, Principal component analysis: a review and recent developments, Philos. Trans. A Math. Phys. Eng. Sci., 374, 20150202 Keren-Shaul, 2017, A unique microglia type associated with restricting development of Alzheimer’s disease, Cell, 169, 1276, 10.1016/j.cell.2017.05.018 Kleshchevnikov, 2020, Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics, bioRxiv Lein, 2017, The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing, Science, 358, 64, 10.1126/science.aan6827 Lein, 2007, Genome-wide atlas of gene expression in the adult mouse brain, Nature, 445, 168, 10.1038/nature05453 Li, 2020, Crosstalk Between liver macrophages and surrounding cells in nonalcoholic steatohepatitis, Front. Immunol., 11, 1169, 10.3389/fimmu.2020.01169 Li, 2018, Hyperband: a novel bandit-based approach to hyperparameter optimization, J. Mach. Learn. Res., 18, 1 Liao, 2021, Uncovering an Organ’s molecular architecture at single-cell resolution by spatially resolved transcriptomics, Trends Biotechnol., 39, 43, 10.1016/j.tibtech.2020.05.006 Luecken, 2019, Current best practices in single-cell RNA-seq analysis: a tutorial, Mol. Syst. Biol., 15, e8746, 10.15252/msb.20188746 Ma, 2020, ActinN: automated identification of cell types in single cell RNA sequencing, Bioinformatics, 36, 533, 10.1093/bioinformatics/btz592 Maier, 2011, A balance of BMP and notch activity regulates neurogenesis and olfactory nerve formation, PLoS One, 6, e17379, 10.1371/journal.pone.0017379 Manders, 1993, Measurement of co-localization of objects in dual-colour confocal images, J. Microsc., 169, 375, 10.1111/j.1365-2818.1993.tb03313.x Marei, 2012, Gene expression profile of adult human olfactory bulb and embryonic neural stem cell suggests distinct signaling pathways and epigenetic control, PLoS One, 7, e33542, 10.1371/journal.pone.0033542 Martin, 2012, Cardiac intercellular communication: are myocytes and fibroblasts fair-weather friends?, J. Cardiovasc. Transl. Res., 5, 768, 10.1007/s12265-012-9404-5 Moffitt, 2018, Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region, Science, 362, 10.1126/science.aau5324 Moncada, 2020, Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas, Nat. Biotechnol., 38, 333, 10.1038/s41587-019-0392-8 Mueller, 2012, Promiscuity and specificity in BMP receptor activation, FEBS Lett., 586, 1846, 10.1016/j.febslet.2012.02.043 Nagayama, 2014, Neuronal organization of olfactory bulb circuits, Front. Neural Circuits, 8, 98, 10.3389/fncir.2014.00098 O’Malley, 2019 Ortiz, 2020, Molecular atlas of the adult mouse brain, Sci. Adv., 6, eabb3446, 10.1126/sciadv.abb3446 Patel, 2014, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma, Science, 344, 1396, 10.1126/science.1254257 Pedregosa, 2011, Scikit-learn: machine learning in Python, J. Mach. Learn. Res., 12, 2825 Qian, 2020, Probabilistic cell typing enables fine mapping of closely related cell types in situ, Nat. Methods, 17, 101, 10.1038/s41592-019-0631-4 Ramel, 2012, Spatial regulation of BMP activity, FEBS Lett., 586, 1929, 10.1016/j.febslet.2012.02.035 Rumelhart, 1986, Learning representations by back-propagating errors, Nature, 323, 533, 10.1038/323533a0 Skelly, 2018, Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart, Cell Rep., 22, 600, 10.1016/j.celrep.2017.12.072 Stuart, 2019, Integrative single-cell analysis, Nat. Rev. Genet., 20, 257, 10.1038/s41576-019-0093-7 Tepe, 2018, Single-cell RNA-Seq of mouse olfactory bulb reveals cellular heterogeneity and activity-dependent molecular census of adult-born neurons, Cell Rep., 25, 2689, 10.1016/j.celrep.2018.11.034 Quake, 2021, The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors, bioRxiv Tirosh, 2016, Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq, Science, 352, 189, 10.1126/science.aad0501 Traag, 2019, From Louvain to Leiden: guaranteeing well-connected communities, Sci. Rep., 9, 5233, 10.1038/s41598-019-41695-z Vickovic, 2019, High-definition spatial transcriptomics for in situ tissue profiling, Nat. Methods, 16, 987, 10.1038/s41592-019-0548-y Vieth, 2019, A systematic evaluation of single cell RNA-seq analysis pipelines, Nat. Commun., 10, 4667, 10.1038/s41467-019-12266-7 Virtanen, 2020, SciPy 1.0: fundamental algorithms for scientific computing in Python, Nat. Methods, 17, 261, 10.1038/s41592-019-0686-2 Wang, 2020, Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function, Nat. Cell Biol., 22, 108, 10.1038/s41556-019-0446-7 Wolf, 2018, SCANPY: large-scale single-cell gene expression data analysis, Genome Biol., 19, 15, 10.1186/s13059-017-1382-0 Ximerakis, 2019, Single-cell transcriptomic profiling of the aging mouse brain, Nat. Neurosci., 22, 1696, 10.1038/s41593-019-0491-3 Xiong, 2019, Landscape of intercellular crosstalk in healthy and NASH liver revealed by single-cell secretome gene analysis, Mol. Cell, 75, 644, 10.1016/j.molcel.2019.07.028 Yang, 2019, Predicting gene regulatory interactions based on spatial gene expression data and deep learning, PLoS Comput. Biol., 15, e1007324, 10.1371/journal.pcbi.1007324 Yousef, 2015, Systemic attenuation of the TGF-β pathway by a single drug simultaneously rejuvenates hippocampal neurogenesis and myogenesis in the same old mammal, Oncotarget, 6, 11959, 10.18632/oncotarget.3851 Yu, 2020, Hyper-parameter optimization: a review of algorithms and applications, arXiv Zakin, 2010, Extracellular regulation of BMP signaling, Curr. Biol., 20, R89, 10.1016/j.cub.2009.11.021 Zeisel, 2018, Molecular architecture of the mouse nervous system, Cell, 174, 999, 10.1016/j.cell.2018.06.021 Zhang, 2019, Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling, Nat Methods, 16, 1007, 10.1038/s41592-019-0529-1 Zhao, 2020, Evaluation of single-cell classifiers for single-cell RNA sequencing data sets, Brief. Bioinform., 21, 1581, 10.1093/bib/bbz096 Zhu, 2018, Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data, Nat. Biotechnol., 36, 1183, 10.1038/nbt.4260