High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

Abstract

Spatial gene expression heterogeneity plays an essential role in a range of biological, physiological and pathological processes but it remains a scientific challenge to conduct highspatial-resolution, genome-wide, unbiased biomolecular profiling over a large tissue area. Herein, we present a fundamentally new approachmicrofluidic Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq). Parallel microfluidic channels (10μm, 25μm, or 50μm in width) are used to deliver molecular barcodes to the surface of a formaldehyde fixed tissue slide in a spatially confined manner. Crossflow of two sets of barcodes A1-A50 and B1-B50 followed by ligation in situ yields a 2D mosaic of tissue pixels, each containing a unique combination of full barcode AiBj (i=1-50, j=1-50). It permits simultaneous barcoding of mRNAs, proteins, or even other omics on a fixed tissue slide, enabling the construction of a high-spatial-resolution multiomics atlas by NGS sequencing. Applying it to mouse embryo tissues revealed all major tissue types in early organogenesis, distinguished brain microvascular networks, discovered new developmental patterning in forebrain, and demonstrated the ability to detect a single-cell-layer of melanocytes lining an optical vesicle and asymmetric expression of Rorb and Aldh1a1 within it, presumably associated with the onset of retina and lens, respectively. Automated feature identification using spatial differential expression further identified dozens of developmental features. DBiT-seq is a highly versatile technology that may become a universal method for spatial barcoding and sequencing of a range of molecular information at a high resolution and the genome scale. It can be readily adopted by biologists with no experience in microfluidics or advanced imaging, and could be quickly disseminated for broader impacts in a variety of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.

Teratoma Growth Retardation by HDACi Treatment of the Tumor Embryonal Source

“…The detected discrepancy between mRNA and protein data could also be explained by the fact that embryo cells are less competent in protein translation due to a lack of ribosomes in comparison to the present mRNA quantity [ 72 , 73 ]. Indeed, dissonances between proteome and transcriptome are often reported in embryo and embryo-related models [ 74 ]. Congruently, in this study, the detected phenomenon of the RNA expression and protein expression assessments giving different results can be potentially explained by the HDACi-induced change in mRNA level still overwhelming the translation machinery present in the 7-day-old embryo-derived teratomas, or by other mechanisms described to disturb the linearity of the transcription–translation axis.…”

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

“…A spatial method that attempts to combine spatially resolved mRNA and protein expression on the same tissue section, utilizing microfluidics and imaging, was recently presented in a preprint. [50] This method, named microfluidic Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq), is performed by first placing a microfluidics chip containing multiple parallel channels on top of a tissue section. For each channel, oligo-dT-tagged barcodes and/or antibody-tagged barcodes are streamed over the tissue.…”

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

“…In particular single-cell RNA sequencing (scRNAseq) methods allow transcriptome profiling in a highly parallel manner, resulting in the quantification of thousands of genes across thousands of cells of the same tissue. However, with a few exceptions [1, 2, 3, 4, 5] current high-throughput scRNAseq methods share the drawback of losing the information relative to the spatial arrangement of the cells in the tissue during the cell dissociation step.…”