RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive ductal carcinoma (IDC). ILC cells exhibit anchorage-independent growth in ultra-low attachment (ULA) suspension cultures, which is largely attributed to the loss of E-cadherin. In addition to anoikis resistance, herein we show that human ILC cell lines exhibit enhanced cell proliferation in ULA cultures as compared to IDC cells. Proteomic comparison of ILC and IDC cell lines identified induction of PI3K/Akt and p90-RSK pathways specifically in ULA culture in ILC cells. Further transcriptional profiling uncovered unique upregulation of the inhibitors of differentiation family transcription factors ID1 and ID3 in ILC ULA culture, the knockdown of which diminished the anchorage-independent growth of ILC cell lines through cell cycle arrest. We find that ID1 and ID3 expression is higher in human ILC tumors as compared to IDC, correlated with worse prognosis uniquely in patients with ILC and associated with upregulation of angiogenesis and matrisome-related genes. Altogether, our comprehensive study of anchorage independence in human ILC cell lines provides mechanistic insights and clinical implications for metastatic dissemination of ILC and implicates ID1 and ID3 as novel drivers and therapeutic targets for lobular breast cancer. Overall design: MDA-MB-134-VI (MM134) and SUM44PE (SUM44) ILC cell lines and MCF7 and T47D IDC cell lines were grown in attached (2D) and suspension (ultra-low attachment, ULA) plates for 24 hours, in triplicate. RNA-Seq was carried out using an Illumina NextSeq 500. Raw sequence data were mapped to hg38 genome (ensembl release version 82) and transcript counts were quantified with Salmon (version 0.8.2). Transcript counts were converted to gene counts using tximport and biomaRt (sep2015.archive.ensembl.org).