Breast Cancer Molecular Subtyping in Practice: A Real-World Study of the APIS Breast Cancer Subtyping Assay in a Consecutive Series of Breast Core Biopsies

Abstract

The APIS Breast Cancer Subtyping Kit is an mRNA-based assessment of the seven parameters including three biomarkers routinely assessed in all the newly diagnosed breast cancers (BC), oestrogen receptor (ER), progesterone receptor (PR) and HER-2 and an additional four genes that create a novel proliferation signature, MKI67, PCNA, CCNA2 and KIF23. Taken together, the data are used to produce a molecular subtype for every sample. The kit was evaluated against the current standard protocol of immunohistochemistry (IHC) and/or in situ hybridisation (ISH) in breast cancer patients. The data were presented at the weekly breast multidisciplinary team (MDT) meeting. A total of 98 consecutive cases of pre-operative breast cancer core biopsies and two core biopsies of nodal metastases yielding 100 cases were assessed. IHC and APIS results were available for 100 and 99 cases. ER was concordant in 97% cases, PR was concordant in 89% and HER-2 results were concordant with IHC/ISH in 100% of the cases. Ki-67 IHC was discordant in 3% of cases when compared with MK167 alone but discordant in 24% when compared with the four-gene proliferation signature. In conclusion, our study indicates that the APIS Breast Cancer Subtyping Kit is highly concordant when compared to the results produced for ER/PR/HER-2 by IHC and/or ISH. The assay could play a role in the routine assessment of newly diagnosed breast cancer (BC) specimens.

Keywords: APIS mRNA molecular assessment; ER; HER-2; Ki-67; PR; breast cancer; immunohistochemistry.

Figure 1

Case 1 discordant case between IHC (luminal ER and PR-positive) and APIS TNBC. (a) Breast core biopsy showing an invasive carcinoma Grade 3 with basaloid architecture (H&E 10×); (b) tumour cells show palisaded architecture at the periphery of tumour islands; (c) estrogen receptors detected nuclear staining in >75% with a moderate nuclear intensity of staining; (d) progesterone receptor >75% of cells show positive and moderate staining; (e) there is no HER-2 protein overexpression (HER-2-negative); (f) Ki-67 is noted in almost 100% of nuclei of the tumour cells. (b–f): 400×.

Figure 2

Case 2 discordant IHC ER and PR-positive and APIS ER/PR-negative. Core biopsy of recurrent breast carcinoma. (a) Prominent scar tissue on the left and tumour tissue on the right (H&E 10×); (b) recurrence is seen in the cutaneous scar and subcutaneous fat of the surgical specimen (H&E whole mounted section); (c) oestrogen receptor-positive; (d) progesterone-positive; (e) Ki-67 up to 20% of hotspot areas; (f) HER-2 protein low weak cytoplasmic membrane staining (score 1+). (c–f) 400×.

Figure 3

Discordant APIS/IHC case for the oestrogen receptor. (a) Core biopsy of a pleomorphic invasive lobular carcinoma, with solid and diffuse tumour architecture (H&E 20×); (b) subsequent surgical specimen confirms nodular and diffuse architecture (H&E whole mounted section); (c) IHC for oestrogen receptor with no (bottom) and strong (top) nuclear staining; (d) androgen receptor; (e) discrete infiltration of tumour cells; (f) HER-2 protein strong and complete circumferential cytoplasmic membrane staining (score 3+). (c–f) 400×.