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Biology subjects

Heng, Y.

Publications and source records attributed to Heng, Y..

3 recordsLinked to original sources

Integrated analysis of spatial multi-omics with SpatialGlue

Integration of multiple data modalities in a spatially informed manner remains an unmet need for exploiting spatial multi-omics data. We introduce SpatialGlue, a graph neural network with dual-attention mechanism, to learn each modalitys significance at cross-omics and intra-omics integration. We demonstrate that SpatialGlue can accurately aggregate cell types into spatial domains at a higher resolution on different tissue types and technology platforms, as well as gain insights into cross-modality spatial correlations.

bioinformatics↗

Integrated Spatial Transcriptomic and Proteomic Analysis of Fresh Frozen Tissue Based on Stereo-seq

To simultaneously detect whole transcriptomes and protein markers on the same tissue section, we combined Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Stereo-seq to develop the Stereo-CITE-seq workflow. Here, we demonstrated that Stereo-CITE-seq can co-detect mRNAs and proteins in immune organs with high spatial resolution, reproducibility and accuracy.

molecular biology↗

Intravital microscopy of satellite cell dynamics and their interaction with myeloid cells during skeletal muscle regeneration

Skeletal muscle regeneration requires the highly coordinated cooperation of muscle satellite cells (MuSCs) with other cellular components. However, due to technical limitations, it remains unclear how MuSCs dynamically interact with non-myogenic cells, especially myeloid cells, in live animals. In this work, we developed a dual-laser multimodal nonlinear optical microscope platform to serve as an effective tool for studying the real-time interaction between MuSCs and non-myogenic cells during the early phase of muscle regeneration. Increased cell volume and mitochondrial mass, cell density, and myotube formation are indicative of MuSCs activation/growth, proliferation, and differentiation, respectively. Using 3D time-lapse imaging on live reporter mice containing both red fluorescence protein (RFP)-labeled macrophages and yellow fluorescence protein (YFP)-labeled MuSCs, and taking advantages of the autofluorescence of reduced nicotinamide adenine dinucleotide (NADH), we monitored the real-time spatiotemporal interaction between RFP+ macrophages/RFP- non-myogenic cells and YFP+ muscle stem/progenitor cells during the activation and the proliferation stages of regeneration. Our results indicated that their cell-cell contact was transient in nature. By inhibiting macrophage infiltration, we further showed that direct cell-cell contact between macrophages and MuSCs was not required for early activation of MuSCs before the proliferation stage. However, decreased macrophage infiltration impeded the proliferation and differentiation of MuSCs and also led to intramuscular fibrosis. Besides, neutrophil depletion in the CCR2 deficient mice did not delay the initial growth of MuSCs. These findings provide a new perspective on myeloid cells role during muscle regeneration.

cell biology↗