Abstract P3-01-26: Comparison of PAM50 intrinsic subtype profiles in matched primary and metastatic breast cancer samples from the CTC-MBC trial (NCT01322893) shows a significant shift towards more aggressive subtypes throughout tumor progression
Authors: Jörgensen Charlotte Levin Tykjär , Forsare Carina , Bendahl Pär-Ola , Larsson Anna-Maria , Lövgren Kristina , Aaltonen Kristina , Jansson Sara , Rydén Lisa 
Published: March 2020

Abstract
Background: At time of diagnosis of metastatic disease, a biopsy of the metastatic lesion is recommended to confirm diagnosis and as a basis for systemic treatment decision.Numerous papers have reported discrepancy between routinely used biomarker status of the primary tumor and corresponding metastases in a relatively large proportion of patients, but less is known about gene expression profiles throughout tumor progression. Differences between biomarker status of the primary tumor lesion and its metastasis could be a major cause of treatment failure, and the molecular alterations that occur during tumor progression are still incompletely described. The main objective of this study was to use tumor specimens collected from a prospective observational trial to determine the PAM50 breast cancer intrinsic subtype in matched pairs of tumor samples from primary tumor (PT), synchronous lymph node metastases (LNMs), and distant metastases (DMs), to investigate if subtype classification changes during tumor progression, and the putative implication of a shift in inherence on prognosis.
Materials and Methods: RNA was isolated from archival formalin-fixed, paraffin-embedded tumor tissue from newly diagnosed metastatic breast cancer patients (N=156) enrolled in the CTC-MBC trial (NCT01322893), and run with the NanoString Breast Cancer 360 assay on the NanoString nCounter Sprint Profiler. PAM50 breast cancer intrinsic subtyping analysis was completed at NanoString, and the statistical analysis at Lund University. Exact McNemar tests and exact tests of symmetry were used to compare subtype inherence at two locations, i.e. matched pairs of PTs and LNMs or DMs.
Results: RNA from 143 patients was evaluable. A PAM50 breast cancer intrinsic subtype could be assigned to 124 PT samples, 68 synchronous LNMs and 76 DMs (Table 1), of which 59 and 63 had paired data, respectively. The evidence for a difference in PAM50 breast cancer intrinsic subtype between matched pairs (PT and LNM; PT and DM) was generally strong (Table 2).
A PAM50 conversion was seen in 21/59 (36%) cases considering the luminal A vs non-luminal A subtype between matched pairs of PT and LNM, 17/21 (81%) of which changed from luminal A to non-luminal A subtype (P=0.007). In matched pairs of PT and DM a PAM50 conversion was seen in 27/63 (43%) cases comparing the luminal A vs non-luminal A subtype, 25/27 (93%) of which changed from luminal A to non-luminal A subtype (P&lt;0.001).
Conclusion: The present study shows that PAM50 breast cancer intrinsic subtype is not stable throughout tumor progression. A significant shift towards a non-luminal A subtype profile was observed in both LNMs and DMs. The shift towards a non-favorable subtype from PT to DM confirms previous data on biomarker status, whereas the significant shift towards a non-luminal A subtype in LNM has to our knowledge not previously been described. Survival analysis is ongoing on the prognostic implication of a shift in PAM50 breast cancer intrinsic subtype.
Table 1. Distribution of PAM50 breast cancer intrinsic subtype at different tumor progression stagesPAM50 subtypeIncluded N (%)Luminal A, N (%)Luminal B, N (%)HER2-enriched N (%)Basal N (%)Primary tumors12447 (38)46 (37)15 (12)16 (13)Synchrounous lymph node metastases6818 (27)37 (54)9 (13)4 (6)Distant metastases767 (9)41 (54)20 (26)8 (11)
Table 2. PAM50 breast cancer intrinsic subtype concordance at different stages of tumor progressionPAM50 subtype Lymph node metastasis Luminal ALuminal BHER2-enrichedBasalTotalP *P **Luminal A131700300.0070.002Primary tumorLuminal B3152121HER2-enriched10405Basal01023 Total17336359 Distant metastasis Luminal ALuminal BHER2-enrichedBasalTotalP *P **Luminal A5167230&lt;0.001&lt;0.0001Primary tumorLuminal B2173123HER2-enriched00505Basal00145 Total73316763 *Exact McNemar test for Luminal A versus non-Luminal A subtype**Exact test of symmetry
Citation Format: Charlotte Levin Tykjär Jörgensen, Carina Forsare, Pär-Ola Bendahl, Anna-Maria Larsson, Kristina Lövgren, Kristina Aaltonen, Sara Jansson, Lisa Rydén. Comparison of PAM50 intrinsic subtype profiles in matched primary and metastatic breast cancer samples from the CTC-MBC trial (NCT01322893) shows a significant shift towards more aggressive subtypes throughout tumor progression [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-01-26.