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Home › Dataset Library › BRCA1-related gene signature in breast cancer: the role of ER status and molecular type

Dataset: BRCA1-related gene signature in breast cancer: the role of ER status and molecular type

We have analyzed, using DNA microarrays, putative differences in gene-expression level between hereditary BRCA1 mutation-linked and...

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We have analyzed, using DNA microarrays, putative differences in gene-expression level between hereditary BRCA1 mutation-linked and sporadic breast cancer. Our results show that a previously reported marked difference between BRCA1-mutation linked and sporadic breast cancer was probably due to uneven stratification of samples with different ER status and basal-like versus luminal-like subtype. We observed that apparent difference between BRCA1-linked and other types of breast cancer found in univariate analysis was diminished when data were corrected for ER status and molecular subtype in multivariate analyses. In fact, the difference in gene expression pattern of BRCA1-mutated and sporadic cancer is very discrete. These conclusions were supported by the results of Q-PCR validation. We also found that BRCA1 gene inactivation due to promoter hypermethylation had similar effect on general gene expression profile as mutation-induced protein truncation. This suggests that in the molecular studies of hereditary breast cancer, BRCA1 gene methylation should be recognized and considered together with gene mutation. We analyzed 35 breast cancer specimens. Surgical samples obtained during mastectomy were flash-frozen in liquid nitrogen and stored at -80°C. Only samples from patients without neoadjuvant chemotherapy were used in this study as chemotherapy may seriously affect gene expression profile. All tissue samples were collected at the Pomeranian Medical University in Szczecin. Seventeen tumor samples were collected from patients with hereditary breast cancer: 12 were derived from tumors affecting women with hereditary BRCA1 mutation, the only one from a woman with BRCA2 mutation, while another eight cases had familial history of breast/ovarian cancer, but were negative for the BRCA1/2 mutations (so called BRCAx cases). Proportion of BRCA1 and BRCA2 mutated tumors was typical for the Polish population. Ten samples were derived from patients with apparently sporadic disease (no familial history of cancer) while 4 patients had a history of familial cancer aggregation (FCA) but without prevalence of breast/ovarian cancers. Thus, these samples were merged with sporadic samples in most of the analyses. All BRCA1 mutation-linked tumors in our study were negative for estrogen receptor (by immunohistochemistry, standard procedures for ER, PGR and HER2 staining were applied), while the only BRCA2-mutated tumor was ER-positive. There were 26 ductal and 5 medullary carcinomas within the study group, which is consistent with the distribution of histopathological types in BRCA1 mutation carriers. Patients were diagnosed at stage T1-2, N0-1 and M0. Caution: this submission contains the data from 6 microarrays done on the normal/pathologically unchanged breast tissue from breast cancer patiets. The data from normal tissues was not analyzed in the paper BRCA1-related gene signature in breast cancer is strongly influenced by ER status and molecular type by Lisowska et al., 2011, Front Biosci (Elite Ed). 2011 Jan 1;3:125-36

Species:
human

Samples:
41

Source:
E-GEOD-50567

PubMed:
21196292

Updated:
Dec.12, 2014

Registered:
Jul.12, 2014


Factors: (via ArrayExpress)
Sample HISTOPATHOLOGY BRCA1 PROMOTER METHYLATION AGE CLINICAL SAMPLE MOLECULAR SUBTYPE ACCORDING TO SORLIE ET AL., PNAS 100, 8418-23 2003 ESTROGEN RECEPTOR STATUS BY IMMUNOHISTOCHEMISTRY BRCA1/2 MUTATION
GSM1223693 normal breast not analyzed 48 surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM1223692 normal breast not analyzed 49 surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM122369 normal breast not analyzed 55 surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM1223690 normal breast not analyzed 39 surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM1223689 normal breast not analyzed not specified surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM1223689 normal breast not analyzed not specified surgical sample of pathologically unchanged breast tissue, adjacent to the tumor not specified not analyzed No mutation
GSM1223687 ductal breast ca. methylated 52 surgical tumor sample basal-like ER(-) No mutation
GSM1223687 ductal breast ca. methylated 52 surgical tumor sample basal-like ER(-) No mutation
GSM1223685 ductal breast ca. unmethylated 51 surgical tumor sample luminal-like ER(+) No mutation
GSM1223684 ductal breast ca. unmethylated 61 surgical tumor sample luminal-like ER(-) No mutation
GSM1223683 ductal breast ca. unmethylated 48 surgical tumor sample luminal-like ER(+) No mutation
GSM1223682 ductal breast ca. unmethylated not specified surgical tumor sample basal-like ER(-) No mutation
GSM122368 ductal breast ca. methylated not specified surgical tumor sample basal-like ER(-) No mutation
GSM1223680 ductal breast ca. unmethylated 57 surgical tumor sample luminal-like ER(-) No mutation
GSM1223679 ductal breast ca. unmethylated 59 surgical tumor sample luminal-like ER(-) No mutation
GSM1223678 ductal breast ca. unmethylated 74 surgical tumor sample luminal-like ER(-) No mutation
GSM1223677 ductal breast ca. unmethylated 27 surgical tumor sample luminal-like ER(-) No mutation
GSM1223676 medullary breast ca. unmethylated 70 surgical tumor sample basal-like ER(-) No mutation
GSM1223675 ductal breast ca. methylated 39 surgical tumor sample basal-like ER(-) No mutation
GSM1223674 medullary breast ca. methylated 45 surgical tumor sample basal-like ER(-) No mutation
GSM1223673 ductal breast ca. unmethylated 76 surgical tumor sample luminal-like ER(+) No mutation
GSM1223672 ductal breast ca. unmethylated 50 surgical tumor sample luminal-like ER(+) No mutation
GSM122367 ductal breast ca. unmethylated not specified surgical tumor sample luminal-like ER(+) No mutation
GSM1223670 ductal breast ca. unmethylated 50 surgical tumor sample luminal-like ER(-) No mutation
GSM1223669 ductal breast ca. unmethylated not specified surgical tumor sample luminal-like ER(-) No mutation
GSM1223668 ductal breast ca. unmethylated 50 surgical tumor sample basal-like ER(-) No mutation
GSM1223667 ductal breast ca. methylated 58 surgical tumor sample basal-like ER(-) No mutation
GSM1223666 ductal breast ca. unmethylated 56 surgical tumor sample basal-like ER(-) No mutation
GSM1223665 ductal breast ca. unmethylated not specified surgical tumor sample luminal-like ER(+) BRCA2 9631delC Ex25
GSM1223664 ductal breast ca. unmethylated 62 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223664 ductal breast ca. unmethylated 62 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223662 ductal breast ca. unmethylated not specified surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM122366 ductal breast ca. unmethylated 48 surgical tumor sample basal-like ER(-) BRCA1 C61G Ex5
GSM1223660 ductal breast ca. unmethylated 41 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223659 medullary breast ca. unmethylated 52 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223658 ductal breast ca. unmethylated 49 surgical tumor sample basal-like ER(-) BRCA1 4153delA Ex11
GSM1223657 medullary breast ca. unmethylated 55 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223656 ductal breast ca. unmethylated 51 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223656 ductal breast ca. unmethylated 51 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223662 ductal breast ca. unmethylated not specified surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20
GSM1223653 medullary breast ca. unmethylated 42 surgical tumor sample basal-like ER(-) BRCA1 5382insC Ex20

Tags

  • basal
  • brca1
  • breast
  • breast cancer
  • cancer
  • disease
  • estrogen
  • liquid
  • luminal
  • ovarian cancer
  • protein
  • sporadic breast cancer

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