title: 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: BACKGROUND
  Invasive 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.
  
  
  METHODS
  We 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 3x1.5 mm 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.
  
  
  RESULTS
  35 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.
  
  
  CONCLUSIONS
  There 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.
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Nadine
authors.initials: N
authors.lastname: Norton
authors.affiliation: Division of Hematology/Oncology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Pooja P
authors.initials: PP
authors.lastname: Advani
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Serie
authors.affiliation: Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Xochiquetzal J
authors.initials: XJ
authors.lastname: Geiger
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Brian M
authors.initials: BM
authors.lastname: Necela
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Bianca C
authors.initials: BC
authors.lastname: Axenfeld
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Kachergus
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Feathers
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Carr
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Julia E
authors.initials: JE
authors.lastname: Crook
authors.affiliation: Division of Hematology/Oncology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Moreno-Aspitia
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Panos Z
authors.initials: PZ
authors.lastname: Anastasiadis
authors.affiliation: Division of Hematology/Oncology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Edith A
authors.initials: EA
authors.lastname: Perez
authors.affiliation: Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: E Aubrey
authors.initials: EA
authors.lastname: Thompson
mesh_terms: D000328:Adult; D001940:Breast / Q000378:metabolism / Q000473:pathology; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D018275:Carcinoma, Lobular / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D002880:Chromosomes, Human, Pair 11; D019938:Cyclin D1 / Q000235:genetics / Q000378:metabolism; D004273:DNA, Neoplasm / Q000302:isolation & purification / Q000378:metabolism; D005260:Female; D018628:Gene Dosage; D056426:Genetic Loci; D006801:Humans; D008207:Lymphatic Metastasis; D012334:RNA, Neoplasm / Q000302:isolation & purification / Q000378:metabolism; D000091042:Reelin Protein; D059467:Transcriptome
chemical_list: C530104:CCND1 protein, human; D004273:DNA, Neoplasm; D012334:RNA, Neoplasm; D000091042:Reelin Protein; D019938:Cyclin D1; C000717127:RELN protein, human