Cell Spatial Distribution Patterns of Human Distal Lung

Despite the resolution of scRNA sequencing, there is no information about the location of cells within a tissue. Now by stRNA sequencing, studying cell type locations is possible to research tumor microenvironment, tumor development, invasion, and metastasis that is so functional to understand tumor progression (Wei et al., ۲۰۲۲). The aim of this study is to investigate the tissue structure and cell-type locations on it in Human distal lung (Kadur Lakshminarasimha Murthy et al., ۲۰۲۲) through bioinformatics analysis which can be e↵ective to diagnose the disease in earlier stages. MethodsThe information related to normal adult lung tissue was obtained by GEO database with GSE۱۷۸۳۶۱. Spatial transcriptomics has been done using the protocol of ۱۰x Genomics Visium Spatial Gene Expression assay (۱۰x Genomics) for spatial RNA-seq (۳’ enrichment). Data analysis consisting of quality control, preprocessing, dimensionality reduction and clustering top expressed genes for normalization was performed by python software. ۱۱ clusters were identified in the tissue surface. Afterwards in order to visualize cell-type distribution and spatial organization in the human distal lung tissue, the gene expression patterns of individual cells were specified. Results and discussionWe visualized total counts per spot and number of genes by counts in UMAP space in human distal lung that are projected onto the spatial coordinates to gain insights into tissue structure and intercellular communication. Then, we removed the lncRNA gene MALAT۱, mitochondrial genes that are among the top expressed, and hemoglobin genes (blood contamination) if they exist. According to our findings, a wide area of studied tissue is occupied by LTF, FDCSP, and SERPINA۳. Also spots belonging to other clusters seem always to be surrounded by spots belonging to mentioned clusters. ”

کلیدواژه ها:

Human distal lung ، Cancer ، Spatial coordinates ، Spatial transcriptomics (ST)