Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case-control study

Background: Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited.
Methods: A case-control design including 1357 primary breast cancers was used to study three distinct clinical
patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous
spread, bone-only, and visceral-only metastasis. Whole-genome expression profiles were obtained using whole genome
(WG)-DASL assays from formalin-fixed paraffin-embedded (FFPE) samples. A systematic protocol was developed for
handling FFPE samples together with stringent data quality controls to identify robust expression profiling data. A panel
of published and novel gene sets were tested for association with these specific patterns of metastatic spread and odds
ratios (ORs) were calculated.
Results: Metasynchronous metastasis to bone and viscera was found in all intrinsic breast cancer subtypes, while
immunohistochemically (IHC)-defined receptor status and specific IntClust subgroups were risk factors for visceral-only or
bone-only first metastases. Among gene modules, those related to proliferation increased the risk of metasynchronous
metastasis (OR (95% CI) = 2.3 (1.1–4.8)) and visceral-only first metastasis (OR (95% CI) = 2.5 (1.2–5.1)) but not bone-only
metastasis (OR (95% CI) = 0.97 (0.56–1.7)). A 21-gene module (BV) was identified in estrogen-receptor-positive breast
cancers with metasynchronous metastasis to bone and viscera (area under the curve = 0.77), and its expression increased
the risk of bone and visceral metasynchronous spread in this population. BV was further orthogonally validated with
NanoString nCounter in primary breast cancers, and was reproducible in their matched lymph nodes metastases and an
external cohort.
Conclusion: This case-control study of WG-DASL global expression profiles from FFPE tumour samples, after careful
quality control and RNA selection, revealed that gene modules in the primary tumour have differing risks for clinical
patterns of metasynchronous first metastases. Moreover, a novel gene module was identified as a putative risk factor for
metasynchronous bone and visceral first metastatic spread, with potential implications for disease monitoring and
treatment planning.