Journal: NPJ Precision Oncology

Article Title: High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints

doi: 10.1038/s41698-023-00441-5

Figure Lengend Snippet: The patient characteristics ( a ) of the six ccRCC patients ( n = 3 LG and n = 3 HG) include: patient LG_2 with a vena cava thrombus (VCT) for which we collected primary tumour microenvironment (TME) and thrombi separately but processed in the one capture array for ST-seq; patient HG_1 that we collected and processed tissues from para-TME (pTME) and TME; and patient HG_3 that we collected tissues from pTME and TME. For this experimental workflow ( b ), ten tissue regions were sampled from pTME, TME and VCT that excluded fibrotic and necrotic regions. ST-seq was completed using 10x Genomics Visium Gene Expression microarrayed glass slides with unique spatially barcoded ST-spots that captured the mRNA released from the overlaying thin ccRCC tissue sections. Annotation of immune ST-spots was completed with data integration of six published single-cell RNA-sequencing (scRNA-seq) datasets. Further immune cell sub-typing was completed with a scRNA and T-cell receptor (TCR) sequencing dataset. Integrated analysis was completed on CD8 + T cells, TAM and monocytes.

Article Snippet: To profile the transcriptome within the ccRCC TME, we performed ST-seq using Visium Spatial Gene Expression (CG000239 Rev D, 2020 October, 10x Genomics, USA) on ten fresh frozen tissue sections collected in the operating theatre from six patients with ccRCC ( n = 2 pTME, n = 4 LG and n = 4 HG) presenting at a tertiary referral hospital from June 2021 to January 2022 (Fig. ).

Techniques: Gene Expression, RNA Sequencing, Sequencing