Fig. 7: Independent Validation of Black American (BA) and White American (WA) Niches Using Spatial Transcriptomics and GeoMX DSP System (NanoString). | Nature Communications

Fig. 7: Independent Validation of Black American (BA) and White American (WA) Niches Using Spatial Transcriptomics and GeoMX DSP System (NanoString).

From: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC

Fig. 7

a Spatial Transcriptomics Validation in Baylor Scott & White (BSW) 2 Cohort: Top panel: Spatial transcriptomics analysis of 4 independent FFPE BA tumors and 5 WA tumors from the BSW2 validation cohort verifies the elevated expression of extended gene signatures (ESGs) associated with BA-community 1 in BA TNBC compared to WA. Bottom panel: The same analysis verifies the elevated expression of ESGs associated with WA-community 1 in WA TNBC compared to BA. P-values were derived from 1-sided paired t test. b Spatial Transcriptomics Validation in Georgia Cohort: Top panel: Spatial transcriptomics analysis of 6 FFPE BA tumors and 4 WA tumors from the Georgia validation cohort confirms the elevated expression of ESGs associated with BA-community 1 in BA compared to WA TNBC. Bottom panel: The same analysis verifies the elevated expression of ESGs associated with WA-community 1 in WA compared to BA TNBC. P-values were derived from 1-sided paired t test. c Representative Co-localization of ESGs Associated with BA-Niche: Spatial co-localization of ESGs associated with BA-niche is observed in BA TNBC (left), but not in WA TNBC (right). Representative images of 4 tumors per group are shown. d GeoMX Validation of BA and WA Niche Enrichment: Community analysis of Nanostring GeoMx data from M = 46 BA ROIs (26 BA patients) and M = 51 WA ROIs (31 WA patients), which are the same TNBC tumors used for IMC in Fig. 1. Results show significantly higher enrichment of BA-community 1 (Endo-Mac-EMT) in the immune compartments (CD45 positive) of BA compared to WA TNBC. Similar analysis shows significantly higher enrichment of WA-community 1 (exhausted T cells) in the immune compartments of WA compared to BA TNBC. Significance was computed using T-tests. Box plots represent the median (center line), interquartile range (25–75%; bounds of the box), and whiskers extending to the 1.5 IQRs. Points that fall outside this range are displayed independently. Source data are provided as a Source Data file.

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