Immune Infiltration Correlates with Transcriptomic Subtypes in Primary ER+ Invasive Lobular Breast Cancer

Understanding interplay of breast cancer and microenvironment is critical. Here we identified two transcriptomic subtypes and five immune infiltration patterns from RNA-seq and multiplex immunohistochemistry from 21 ER+/HER2- ILCs. We found proliferative subtype associated with increased suppressive immune infiltration, and defined a signature associated with lower proliferative, pro-inflammatory TAM infiltration, and improved survival in ER+ breast cancer. Our work identified genes related to ILC immune microenvironment and prognosis. This GEO submission is related to RNA-seq section of this study. For the 21 cases, formalin-fixed paraffin-embedded (FFPE) blocks of primary ER+/HER2- ILC tumors were acquired from University of Pittsburgh Biospecimen Core, and clinical information was queried from the UPMC Cancer Registry. For each block, three sections (at the top, bottom and middle of the block) were stained with hematoxylin and eosin (H&E) and inspected by pathologist to circle out regions with tumor epithelial cell proportion ≥40%. 5 sections (of 10uM thickness each) were used for RNA extraction and sequencing at these circled regions. Sample RNA was extracted with Qiagen tissue DNA/RNA kit from FFPE sections, assessed with High Sensitivity RNA TapeStation for quality and concentration, and sequenced with Illumina Nextseq 500 75 bp pair-end in 150 cycles at University of Pittsburgh Health Sciences Sequencing Core. For RNA-seq data, we used FastQC for FASTQ data quality control, trimmomatic for adapter trimming, Hisat2 for alignment to human genome 38 (hg38), and HTSeq for quantification, to generate normalized expression in transcripts per million (TPM).