Multiplexed digital spatial profiling of invasive breast tumors from Black and White women

Abstract

The NanoString GeoMx Digital Spatial Profiling (DSP) is a new multiplexed platform that quantifies the abundance of tumor-and immune-related proteins in a spatially resolved manner. We performed DSP for the simultaneous assessment of 52 analytes within spatially resolved tissue compartments defined by pancytokeratin expression. We compared protein targets between 94 African American/Black and 65 European American/White cases, tumor and stromal tissue compartments, estrogen receptor alpha (ER)-positive and ER-negative cases, and explored potential biomarkers of survival. Of 33 analytes with robust signal for analysis, results were highly replicable. For a subset of markers, correlative analyses between DSP analytes and traditional immunohistochemistry (IHC) scores revealed moderate to very strong associations between the two platforms. Similarly, DSP analytes and gene expression scores were concordant for 21 of 25 markers with overlap between the two datasets. Several analytes varied by ER status, and across the 25 immune markers surveyed, 14 had a significant inverse association with ER expression. B7 homolog 3 (B7-H3; encoded by CD276) was the only analyte to show a significant difference by race, being lower in both the tumor and stromal compartments in Black women. DSP markers that were associated with survival included CD8, CD25, CD56, CD127, EpCAM, ER, Ki-67, and STING. We conclude that DSP is an efficient tool for screening tumorand immune-related markers in a simultaneous fashion and yields results that are concordant with established immune profiling assays. DSP immune analytes were inversely associated with ER expression, in agreement with a substantial body of previous work that documents higher immune infiltration in ERnegative breast cancers. This technology revealed that scores of the B7-H3 protein were significantly lower in breast cancers from Black women compared with White women, an intriguing finding that requires replication in independent and racially diverse female populations.

Association of B7‐H3 expression with racial ancestry, immune cell density, and androgen receptor activation in prostate cancer

“…Importantly, B7‐H3 remained significantly lower among BL men even after adjustment for ERG, PTEN, and clinicopathologic features, and there was no significant interaction between race and ERG or PTEN with respect to B7‐H3 expression. Corroborating this finding in other tumor types, previous studies have suggested significantly lower B7‐H3 expression in breast and colorectal cancers from self‐identified BL patients compared with WH patients 33‐35 . Whether these ancestry‐related differences in B7‐H3 expression are physiologically or clinically significant must be tested in future studies.…”

“…Corroborating this finding in other tumor types, previous studies have suggested significantly lower B7-H3 expression in breast and colorectal cancers from selfidentified BL patients compared with WH patients. [33][34][35] Whether these ancestry-related differences in B7-H3 expression are physiologically or clinically significant must be tested in future studies.…”

Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx® Digital Spatial Profiler

“…The ROI profiling strategies can be customized for the specific spatial compartments for profiling. With these key advantages, GeoMx allows researchers to achieve a wide spectrum of spatially resolved transcriptomic and proteomic characterizations of breast cancer samples [4,35,[45][46][47]. Furthermore, the GeoMx spatial profiling is applicable for other tumor types, such as melanoma, lung, prostate, or liver cancers, characterized by high clinical and histological heterogeneity [48][49][50][51][52][53][54][55][56][57][58][59][60].…”

“…In this study, GeoMx DSP was used to profile tumor-and immune-related proteins in FFPE TMA tissue sections of invasive breast tumors from black and white women [45].…”

Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx® Digital Spatial Profiler

“…As in most of carcinomas, many of these studies rely in panCK as a VM to highlight epithelial tumor cells. Some of them segmented the ROIs in tumor and stroma based on the expression of panCK ( 44 , 45 ) while others collected probes from non-segmented ROIs ( 46 , 47 ). The performance of the DSP was assessed in this tumor type by assessing levels of protein or RNA signal and associating the DSP counts of different biomarkers to traditional IHC scores for DSP protein panels or bulk RNA data for DSP RNA panels; overall, the results show a robust protein signal and moderate to strong associations between protein DSP counts and IHC and RNA DSP counts with Bulk RNA data for the majority of the targets ( 45 ).…”