ABSTRACT
High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ~2-35 co-expressed genes (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
Subject(s)
Gene Expression Profiling , Transcriptome , Animals , Mice , Humans , In Situ Hybridization, Fluorescence/methods , Gene Expression Profiling/methods , Transcriptome/geneticsABSTRACT
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.
Subject(s)
Algorithms , Benchmarking , Animals , Mice , Gene Expression Profiling , RNA , Transcriptome , Data AnalysisABSTRACT
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
ABSTRACT
We present split-FISH, a multiplexed fluorescence in situ hybridization method that leverages a split-probe design to achieve enhanced specificity. Split-FISH reduces off-target background fluorescence, decreases false positives and enables accurate RNA profiling in uncleared tissues. We demonstrate the efficacy of split-FISH on various mouse tissues by quantifying the distribution and abundance of 317 genes in single cells and reveal diverse localization patterns for spatial regulation of the transcriptome in complex tissues.
Subject(s)
In Situ Hybridization, Fluorescence/methods , RNA/analysis , Animals , Cells, Cultured , Humans , Mice , Single-Cell Analysis , TranscriptomeABSTRACT
Assays that can determine the response of tumor cells to cancer therapeutics could greatly aid the selection of drug regimens for individual patients. However, the utility of current functional assays is limited, and predictive genetic biomarkers are available for only a small fraction of cancer therapies. We found that the single-cell mass accumulation rate (MAR), profiled over many hours with a suspended microchannel resonator, accurately defined the drug sensitivity or resistance of glioblastoma and B-cell acute lymphocytic leukemia cells. MAR revealed heterogeneity in drug sensitivity not only between different tumors, but also within individual tumors and tumor-derived cell lines. MAR measurement predicted drug response using samples as small as 25 µl of peripheral blood while maintaining cell viability and compatibility with downstream characterization. MAR measurement is a promising approach for directly assaying single-cell therapeutic responses and for identifying cellular subpopulations with phenotypic resistance in heterogeneous tumors.
Subject(s)
Antineoplastic Agents/administration & dosage , Drug Screening Assays, Antitumor/instrumentation , Lab-On-A-Chip Devices , Micro-Electrical-Mechanical Systems/instrumentation , Neoplasms, Experimental/drug therapy , Neoplasms, Experimental/physiopathology , Cell Proliferation/drug effects , Cells, Cultured , Dose-Response Relationship, Drug , Drug Resistance, Neoplasm , Drug Screening Assays, Antitumor/methods , Equipment Design , Equipment Failure Analysis , Humans , Micro-Electrical-Mechanical Systems/methods , Neoplasms, Experimental/pathology , Treatment OutcomeABSTRACT
Brain extraction is an important preprocessing step for further processing (e.g., registration and morphometric analysis) of brain MRI data. Due to the operator-dependent and time-consuming nature of manual extraction, automated or semi-automated methods are essential for large-scale studies. Automatic methods are widely available for human brain imaging, but they are not optimized for rodent brains and hence may not perform well. To date, little work has been done on rodent brain extraction. We present an extended pulse-coupled neural network algorithm that operates in 3-D on the entire image volume. We evaluated its performance under varying SNR and resolution and tested this method against the brain-surface extractor (BSE) and a level-set algorithm proposed for mouse brain. The results show that this method outperforms existing methods and is robust under low SNR and with partial volume effects at lower resolutions. Together with the advantage of minimal user intervention, this method will facilitate automatic processing of large-scale rodent brain studies.