biostudies-literatureUnknown2(17)Priedigkeit NBone metastases (BoM) are a significant cause of morbidity in patients with estrogen receptor-positive (ER-positive) breast cancer; yet, characterizations of human specimens are limited. In this study, exome-capture RNA sequencing (ecRNA-seq) on aged (8-12 years), formalin-fixed, paraffin-embedded (FFPE), and decalcified cancer specimens was evaluated. Gene expression values and ecRNA-seq quality metrics from FFPE or decalcified tumor RNA showed minimal differences when compared with matched flash-frozen or nondecalcified tumors. ecRNA-seq was then applied on a longitudinal collection of 11 primary breast cancers and patient-matched synchronous or recurrent BoMs. Overtime, BoMs exhibited gene expression shifts to more Her2 and LumB PAM50 subtype profiles, temporally influenced expression eJCI insight95703https://www.ebi.ac.uk/biostudies/studies/S-EPMC5621874biostudies-literatureExome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases.PMC5621874Lee AVBasudan ALucas PCBrufsky AMBhargava ROesterreich SWatters RJKolls JKPriedigkeit NFang ZRosenzweig MQHorne WWeiss KRfalseExome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases.Bone metastases (BoM) are a significant cause of morbidity in patients with estrogen receptor-positive (ER-positive) breast cancer; yet, characterizations of human specimens are limited. In this study, exome-capture RNA sequencing (ecRNA-seq) on aged (8-12 years), formalin-fixed, paraffin-embedded (FFPE), and decalcified cancer specimens was evaluated. Gene expression values and ecRNA-seq quality metrics from FFPE or decalcified tumor RNA showed minimal differences when compared with matched flash-frozen or nondecalcified tumors. ecRNA-seq was then applied on a longitudinal collection of 11 primary breast cancers and patient-matched synchronous or recurrent BoMs. Overtime, BoMs exhibited gene expression shifts to more Her2 and LumB PAM50 subtype profiles, temporally influenced expression e2017-01-01T00:00:00Z2017 Sep2025-04-22T07:41:41.826Z2019-03-27T02:57:48ZS-EPMC56218742887813310.1172/jci.insight.95703