Table 1 Differential expression of immune proteins as a function of spatial distribution in intraepithelial and stromal segments and recurrence

From: Distinct spatial immune microlandscapes are independently associated with outcomes in triple-negative breast cancer

Protein	Intraepithelial (cytokeratin-positive) segments								Stroma (cytokeratin-negative) segments
Protein	All segments fold change	p-value	CD45ENR fold change	p-value	CD68ENR fold change	p-value	TumorENR fold change	p-value	All segments fold change	p-value	CD45ENR fold change	p-value	CD68ENR fold change	p-value
B7-H3	1.2	0.038	1.2	0.212	1.2	0.237	1.2	0.249	1.0	0.784	0.9	0.234	1.0	0.841
*B2M*	1.7	0.000	1.8	0.000	1.6	0.000	1.6	0.000	1.3	0.000	1.2	0.013	1.3	0.001
*CD11c*	1.4	0.000	1.8	0.000	1.2	0.116	1.0	0.630	1.0	0.519	1.2	0.126	0.9	0.493
CD127	1.0	0.373	1.0	0.700	0.9	0.380	1.0	0.745	1.2	0.013	1.0	0.613	1.0	0.992
*CD20*	2.1	0.000	2.5	0.000	1.6	0.000	1.7	0.000	1.3	0.018	1.1	0.559	1.2	0.128
CD25	1.3	0.000	1.4	0.001	1.2	0.022	1.3	0.011	1.2	0.000	1.1	0.181	1.1	0.109
CD3	1.6	0.000	1.8	0.000	1.3	0.063	1.3	0.116	1.1	0.216	1.1	0.196	1.0	0.783
CD4	1.3	0.000	1.5	0.000	1.2	0.145	1.1	0.364	1.0	0.629	1.0	0.699	0.9	0.434
*CD40*	1.9	0.000	1.9	0.000	1.8	0.000	2.2	0.000	1.2	0.004	1.1	0.142	1.4	0.003
CD44	1.3	0.024	1.1	0.653	1.3	0.183	1.5	0.029	1.0	0.723	0.9	0.507	1.2	0.189
CD45	1.4	0.001	1.5	0.000	1.1	0.341	1.2	0.325	1.1	0.413	1.1	0.489	1.1	0.368
*CD56*	3.1	0.000	2.9	0.000	2.5	0.000	4.1	0.000	1.3	0.000	1.2	0.002	1.3	0.003
CD68	1.0	0.946	1.1	0.300	0.9	0.619	0.9	0.647	0.9	0.080	0.8	0.036	0.9	0.275
CD8	1.5	0.000	1.7	0.000	1.2	0.175	1.5	0.004	1.1	0.259	1.1	0.404	1.1	0.654
CTLA4	1.2	0.000	1.4	0.001	1.0	0.744	1.3	0.001	0.8	0.013	0.9	0.412	0.6	0.000
FN	1.4	0.005	1.4	0.083	1.9	0.001	0.9	0.454	1.6	0.000	1.1	0.524	2.1	0.000
*GZMB*	1.9	0.000	1.9	0.000	1.8	0.000	1.8	0.000	1.6	0.000	1.5	0.000	1.5	0.000
*HLA-DR*	2.8	0.000	2.4	0.000	2.6	0.000	3.7	0.000	1.0	0.556	1.0	0.766	1.0	0.916
*ICOS*	1.9	0.000	2.0	0.000	1.8	0.000	1.7	0.000	1.2	0.004	1.1	0.242	1.4	0.003
*IDO1*	1.8	0.000	2.2	0.000	1.6	0.034	1.6	0.029	1.8	0.000	1.5	0.004	2.7	0.000
Ki-67	1.2	0.052	1.2	0.224	1.3	0.050	1.0	0.930	1.1	0.351	1.1	0.473	1.3	0.030
PanCk	1.0	0.639	1.1	0.533	0.9	0.617	1.1	0.510	1.2	0.041	1.1	0.331	1.0	0.670
PD-L1	1.7	0.000	1.9	0.000	1.6	0.000	1.6	0.000	1.5	0.000	1.3	0.001	1.5	0.000
*PD-L2*	4.0	0.000	3.9	0.000	3.6	0.000	4.4	0.000	3.3	0.000	3.2	0.000	3.2	0.000
SMA	1.3	0.006	1.5	0.011	0.9	0.369	1.8	0.001	0.7	0.000	0.8	0.058	0.5	0.000
STING	1.2	0.012	1.4	0.000	0.9	0.602	1.1	0.326	1.0	0.940	1.0	0.639	1.1	0.235
*TGFB1*	1.6	0.000	2.0	0.000	1.5	0.000	1.4	0.000	1.2	0.001	1.2	0.014	1.1	0.181
Tim-3	1.0	0.591	1.2	0.109	1.0	0.692	1.0	0.686	0.9	0.289	0.9	0.390	0.9	0.417
VISTA	1.4	0.000	1.5	0.001	1.3	0.027	1.3	0.042	1.3	0.000	1.0	0.911	1.2	0.019

Differential expression, given as estimated fold change (FC), was calculated from normalized protein counts for RFS = YES/RFS = NO tumors. The linear mixed model was used to calculate the estimated fold change and significance, defined as nominal two-sided p < 0.05 with FC > 1.5 or < −0.5, shown in bold font. Proteins with Benjamini–Yekutieli adjusted p < 0.05 in one or more segment types are shown in italic font. PD-L2 alone was significant at BYadj p < 0.05 in any stroma segment (All Segments, stroma and CD45EnR, stroma). “All Intraepithelial” data are averaged for all categories of intraepithelial segments (CD45EnR, CD68EnR, and TumorEnr, n = 12 ROI/sample). “All Stroma” are averaged data from stromal segments (CD45EnR and CD68EnR, n = 8 ROI/sample). Source data are given in Supplementary Data 1.
B2M beta-2-microglobulin, FN fibronectin, GZMB granzyme B, PanCK pan-cytokeratin, SMA smooth muscle actin.

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Table 1 Differential expression of immune proteins as a function of spatial distribution in intraepithelial and stromal segments and recurrence

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