Project description:To investigate the effecs of commensal papillomavirus immunity on the homeostasis of highly mutated normal skin, spatial transcriptomics (Xenium, 10x Genomics, Pleasanton, CA) was performed on SKH-1 mouse back skin. The mice were treated with mouse papillomavirus (MmuPV1) or virus-like particles (VLP), followed by UV exposure for 25 weeks.
Project description:We developed a method that utilizes floating mounting of thin sections of fixed frozen mouse lung tissue onto Xenium slides for the fluorescent in situ hybridization (FISH) and imaging–based spatial transcriptomics analysis of gene expression using the Xenium platform provided by 10X Genomics. Spatial transcriptomics techniques provide a comprehensive view by merging gene expression data with spatial context within their native tissue architecture. However, the Xenium pipeline has been validated only for formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections by 10X Genomics. Notably, many researchers prefer paraformaldehyde-fixed cryosections for immunohistochemistry and in situ hybridization. In our study, we assessed the compatibility of standard fixed frozen mouse lung sections with the Xenium protocol. Our findings reveal that these sections not only align well with the Xenium platform but also offer superb imaging and gene expression quantification, even with limited number of genes in the Xenium panel. This protocol can serve as a valuable resource for preparing various tissues where FFPE and fresh frozen samples present challenges.
Project description:Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed Xenium in situ analysis in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.
Project description:One of the most common origins of Peritoneal metastasis (PM) is colon cancer, which occurs in about 20% of colon cancer patients. Given the cancer cell heterogeneity in PM, we first tried to dissect the spatial distribution of CAF and the associated niches at a single cell resolution, we exploited the Xenium In Situ high-plex spatial imaging platform. We performed the Xenium assays with 8 human PM samples of colon origin including one PM-adjacent tissue. Among the 8 PM samples, 3 samples carried a distinct iCMS3 epithelial signature (PM1, PM2, PM3), 2 carried iCMS2 signature (PM6, PM7), while the other 2 samples had a mix of both iCMS2 and iCMS3 signatures (PM4, PM5). We found that the presence of iCMS3 cancer cells was associated with an increase infiltration of lymphocytes and the formation of tertiary lymphoid structures (TLS).
Project description:Recent work has shown that the spatial organization of immune responses is a critical determinant of anti-tumor immunity. Here, we profiled ten head and neck squamous cell carcinoma (HNSCC) patient tumors and one ameloblastoma tumor using Xenium V1 spatial transcriptomics. The 10X genomics human multi-tissue and cancer gene expression panel targeting 377 genes was used in combination with 100 custom Xenium probes targeting patient-specific CDR3 regions of T cell receptors (TCRs) in T cells, additoinal T cell specific genes, HPV oncoprotein genes, and tumor genes of interest. This enabled the detection of 477 transcripts within each tumor sample at a single-cell resolution. For seven of the ten HNSCC samples, different tissue sections run on different days were analyzed as technical replicates. Together, these findings introduce a scalable platform for spatial clonal T cell analysis and provide new insight into the spatial relationship of cells within the HNSCC tumor microenvironment.
Project description:We conducted a multicenter, open-label, single-arm phase II trial (SCan Study) to evaluate the efficacy and safety of canakinumab in 5 Japanese patients with Schnitzler syndrome (SchS), based on a similar study conducted in Germany. As part of this study, spatial transcriptomics of urticarial rash skin lesions were performed before treatment in 2 cases to identify IL1B-expressing cells. The spatial transcriptomics analysis was conducted using the 10x Genomics Xenium platform.
Project description:Spatial organization of different cell types within prenatal skin across various anatomical sites is not well understood. To address this, here we have generated spatial transcriptomics data from prenatal facial and abdominal skin obtained from a donor at 10 post conception weeks. This in combination with our prenatal skin scRNA-seq dataset has helped us map the location of various identified cell types.