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Microarray and RNA in situ hybridization assay for recurrence risk markers of breast carcinoma and ductal carcinoma in situ: Evidence supporting the use of diverse pathways panels
Author(s) -
Evans Mark Francis,
Vacek Pamela Mary,
Sprague Brian Lee,
Stein Gary Stephen,
Stein Janet Lee,
Weaver Donald Lee
Publication year - 2020
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.29409
Subject(s) - tissue microarray , in situ hybridization , ductal carcinoma , microarray , breast cancer , biology , microarray analysis techniques , pathology , cancer research , carcinoma in situ , carcinoma , downregulation and upregulation , cancer , oncology , medicine , gene expression , immunohistochemistry , gene , genetics
Breast tumor stratification by recurrence‐risk is critical for deciding patient treatment. Here an approach combining cancer pathways microarray data complemented by RNA in situ hybridization (ISH) was investigated as a means for recurrence marker discovery and visualization in pathology specimens. LncRNA and mRNA expressions in breast carcinomas with low (n = 8) vs intermediate/high (n = 10) recurrence‐scores as estimated by 21‐gene assay and pathology review were compared by microarray assay. Tissue microarrays were prepared from breast carcinomas (n = 20) and ductal carcinoma in situ (DCIS) specimens (n = 84 patients) with known outcomes. Thirteen RNA ISH assays were performed: lncRNAs ( BBC3‐1 , FER3 , RAD21‐AS1 , ZEB1‐2 ) and mRNAs ( GLO1 , GLTSCR2 , TGFB1 , TLR2 ) (implicated by the microarray data); MKI67 ; a pooled panel of recurrence‐associated proliferation markers ( BIRC5 , Cyclin B1 , MKI67 , MYBL2 , STK15 ); a pooled panel of non‐proliferation recurrence‐associated markers ( CEACAM5 , HTF9C , NDRG1 , TP53 , SLC7A5 ); and lncRNAs H19 and HOTAIR . Seven lncRNAs and 10 mRNAs showed significantly ( P < .05) altered upregulation or downregulation by microarray assay: carcinoma RNA ISH staining did not mirror these patterns. HOTAIR staining was associated with a higher breast cancer recurrence score ( P = .0152); qualitatively, H19 was massively expressed in a metaplastic triple negative breast carcinoma. Among the DCIS cohort, significant associations with multiple outcome variables were noted for TGFB1 and the non‐proliferation panel ( P ‐value range: .0001 to .047); proliferation panel staining showed an association with increasing DCIS grade ( P = .0269) but not with outcomes. The findings support recurrence‐risk estimation by the use of multi‐marker panels that are representative of diverse cellular pathways rather than over‐reliance on proliferation targets. H19 , HOTAIR , and TGFB1 RNA ISH show potential for selective diagnostics.