Fig. 1: Spatial multi-omics analysis of the prostate tumor microenvironment reveals gene signatures discriminating between aggressive and non-aggressive disease patient groups. | Nature Communications

Fig. 1: Spatial multi-omics analysis of the prostate tumor microenvironment reveals gene signatures discriminating between aggressive and non-aggressive disease patient groups.

From: Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment

Fig. 1: Spatial multi-omics analysis of the prostate tumor microenvironment reveals gene signatures discriminating between aggressive and non-aggressive disease patient groups.

a Schematics of cancer, normal adjacent, and normal sample collection for bulk and spatial analysis of PCa tissue using bulk and spatial transcriptomics (ST), bulk metabolomics (high-resolution magic-angle spinning [HRMAS] NMR), spatial metabolomics (mass spectrometry imaging [MSI]), and histopathology staining (HE[S], immunohistochemistry [IHC] of lipopolysaccharide (LPS) and lipoteichoic acid (LTA)). The fresh frozen prostate tissue sections for sampling were selected based on pathology annotations from adjacent FFPE sections to locate cancer and normal areas. Cryo-sections from samples were obtained at 10 µm thickness and placed on slides for spatial analysis, here exemplary shown for ST and MSI. ST spots were classified according to per-section histopathology and assigned a cell count. Finally, all spatial modalities were integrated into one spatial multi-omics data set. Expression of up- and downregulated genes forming the b aggressive prostate cancer (APC) signature and c chemokine enriched gland (CEG) signature over all spots with a count >0 for the respective gene separated according to status of aggressiveness (AC069228.1 n = 1 + 1076 [non-aggressive + aggressive], ALOX15B n = 6195 + 6792, ANPEP n = 5674 + 5226, AOC1 n = 1530 + 668, CARTPT n = 775 + 305, CCL19 n = 449 + 3833, CCL20 n = 15 + 301, CST2 n = 369 + 3477, CST4 n = 116 + 421, CXCL1 n = 172 + 1373, CXCL11 n = 113 + 867, CXCL17 n = 349 + 1434, CXCL2 n = 328 + 1792, CXCL3 n = 58 + 654, CXCL5 n = 9 + 459, CXCL6 n = 193 + 669, CYP3A5 n = 1531 + 910, GABRP n = 197 + 971, IGHG3 n = 2371 + 9574, IGHG4 n = 1128 + 6009, IGKC n = 3269 + 10,999, IGLC2 n = 2598 + 9846, IGLC7 n = 6 + 1390, KRT13 n = 953 + 532, LCN2 n = 925 + 3808, LTF n = 970 + 5478, MUC5B n = 22 + 437, NCAPD3 n = 6155 + 6565, ORM1 n = 688 + 2336, PCAT4 n = 4234 + 2934, PTPRM n = 3529 + 2342, SAA1 n = 569 + 3544, SAA2 n = 105 + 1782, TGM4 n = 906 + 1766). The box and whisker plots (box spans interquartile range (IQR), centerline indicates median, whisker extend 1.5 IQR from first and third quartile, observations beyond shown as individual points) are based on the z-score of the decadic logarithm of the normalized unique molecular identifier (UMI) counts.

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