Xenium In Situ Gene and Protein Expression data for FFPE Human Renal Cell Carcinoma

Overview

This human FFPE renal cell carcinoma dataset was generated following the Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining workflow. The Xenium Human Multi-Tissue and Cancer Pre-designed Panel, supplemented with custom genes, was used to profile gene expression. The 27-plex Cell Typing & Functional State Marker Set was used to profile protein expression (immune cell types, functional states, and tissue microenvironment context). This set includes six subpanels and individually imaged cell segmentation markers.

The combined gene and protein expression data reveal that the sample’s composition differs from healthy kidney tissue. There are neoplastic "clear cells", which lack normal kidney cell type expression signatures. They are surrounded by extensive, expanded vasculature, numerous immune cells types, and exhausted T cells. There are distinct heterogenous cellular neighborhoods that vary in tumor and immune cell infiltration surrounded by stromal cells. The Ki-67 protein marker identifies proliferating cells and a rare subset of apoptotic endothelial cells. This pattern aligns with the MKI67 gene expression, potentially indicating rapid proliferation, gene expression, and cell death in this cell population.

How to view data

Interactively explore this dataset with the Xenium Explorer web demo, a preview of the upcoming desktop version of Xenium Explorer software.

See the Getting Started with Xenium Explorer page for more details. Follow these instructions to view the post-Xenium H&E image or image alignment file in Xenium Explorer.

Biomaterials

FFPE tissue blocks were purchased from Discovery Life Sciences (kidney cancer, Renal Cell Carcinoma: Stage III (T3a N1 MX)).

Tissue preparation

Tissue was prepared following the Demonstrated Protocols Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578) and Xenium In Situ for FFPE Tissues – Deparaffinization & Decrosslinking (CG000580).

Probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following the upcoming Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining User Guide.

Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).

Gene panel

The Xenium Human Multi-Tissue and Cancer Panel (377 genes) was pre-designed by 10x Genomics. The panel design was informed using single cell RNA sequencing data curated and reprocessed for standardization by the Human Protein Atlas. Genes were chosen to accurately type cells, and identify select immune, proliferation, and tumor markers, in human breast, lung, skin, liver, colon, kidney, lung cancer, and heart.

We added 28 new RNA targets to enable detection of genes that are translated into the assayed protein targets and genes useful for identifying relevant cell types. This includes probes targeting the splice isoforms that are translated into the CD45RA and CD45RO isoforms of the PTPRC gene. We also added probe sets to boost sensitivity for 25 genes in the Human Multi-Tissue and Cancer Panel that are associated with protein panel markers. Boosting genes in v1 gene panels can be requested via an advanced custom design.

Protein panel

The protein panel for this dataset consists of all six protein subpanels:

• Xenium Protein Immune Cell Subpanel A (CD4, CD20, CD8A, CD3E)
• Xenium Protein Immune Cell Subpanel B (CD138, HLA-DR, CD11c, CD68)
• Xenium Protein Immune Cell Subpanel C (CD16, GranzymeB, CD163)
• Xenium Protein Proliferation & Differentiation Subpanel (CD45RA, PCNA, CD45RO, Ki-67)
• Xenium Protein Immune Checkpoint Subpanel (PD-1, VISTA, PD-L1, LAG-3)
• Xenium Protein Tumor Subpanel (Beta-catenin, CD31, PTEN, PanCK)

It also includes separately imaged cell segmentation (Xenium Multi-Tissue Stain Mix) markers (E-cadherin, Vimentin, alphaSMA, CD45), which are labeled "Cellular Localization" markers in outputs.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide (CG000584). The on-instrument analysis was run with upcoming Xenium Onboard Analysis v4.0.

This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.