Assessment of Tumor Heterogeneity, as Evidenced by Gene Expression Profiles, Pathway Activation, and Gene Copy Number, in Patients with Multifocal Invasive Lobular Breast Tumors

Abstract

BackgroundInvasive lobular carcinoma (ILC) comprises approximately ~10–20% of breast cancers. In general, multifocal/multicentric (MF/MC) breast cancer has been associated with an increased rate of regional lymph node metastases. Tumor heterogeneity between foci represents a largely unstudied source of genomic variation in those rare patients with MF/MC ILC.MethodsWe characterized gene expression and copy number in 2 or more foci from 11 patients with MF/MC ILC (all ER+, HER2-) and adjacent normal tissue. RNA and DNA were extracted from 3x1.5mm cores from all foci. Gene expression (730 genes) and copy number (80 genes) were measured using Nanostring PanCancer and Cancer CNV panels. Linear mixed models were employed to compare expression in tumor versus normal samples from the same patient, and to assess heterogeneity (variability) in expression among multiple ILC within an individual.Results35 and 34 genes were upregulated (FC>2) and down-regulated (FC<0.5) respectively in ILC tumor relative to adjacent normal tissue, q<0.05. 9/34 down-regulated genes (FIGF, RELN, PROM1, SFRP1, MMP7, NTRK2, LAMB3, SPRY2, KIT) had changes larger than CDH1, a hallmark of ILC. Copy number changes in these patients were relatively few but consistent across foci within each patient. Amplification of three genes (CCND1, FADD, ORAOV1) at 11q13.3 was present in 2/11 patients in both foci. We observed significant evidence of within-patient between-foci variability (heterogeneity) in gene expression for 466 genes (p<0.05 with FDR 8%), including CDH1, FIGF, RELN, SFRP1, MMP7, NTRK2, LAMB3, SPRY2 and KIT.ConclusionsThere was substantial variation in gene expression between ILC foci within patients, including known markers of ILC, suggesting an additional level of complexity that should be addressed.

An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles

“…Because alterations in genome and epigenome profiles often lead to heterogeneous gene expression profiles in tumors, defining ITH based on gene expression profiles is a viable approach 21 – 23 . Park et al proposed a method (tITH) for evaluating transcriptome-based ITH using RNA-Seq data 24 .…”

Expression analysis of colon adenocarcinoma in the South Indian population reveals novel signals of pathogenesis

“…Signals included are COL1A1, COL11A1, SPP1, COMP, SFRP4, and INHBA. Numerous studies have shown the proliferative role of collagen in gastric 32,36 , breast 37 , and colon cancers 38,39 . Previous studies have also demonstrated that the upregulation of MMPs (MMP7 and 9) along with other collagen proteins are important for tumor vascular invasion 40 .…”

Targeted Transcriptional Profiling of Kidney Transplant Biopsies

“…These variations in gene expression might be related to intrinsic factors that are connected to platform efficiency and the process of direct detection without the need of amplification in the NS platform, but which are needed for preamplification on the FD platform. 17 , 27 , 28 …”

“… 14 , 15 Recently, a new platform for low-throughput gene expression based on molecular barcoding to quantify mRNA that does not require amplification has become available. 16 , 17 , 18 Previous studies have favorably compared the barcoded-oligo assay to QPCR in other clinical settings 19 , 20 Recently, a study by Adam et al. quantified the expression of a literature-derived, antibody-mediated rejection 34-gene panel in fresh-preserved and FFPE kidney tissues with QPCR and the barcoded-oligo assay, respectively.…”