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Laser microdissection and microarray analysis of breast tumors reveal estrogen receptor related genes and pathways

A technology of estrogen receptors and genes, which is applied in the field of laser microdissection and microarray analysis of breast tumors to reveal estrogen receptor-related genes and pathways, and can solve the problem of harmful gene expression data and large differences in the proportion of tumor cells, etc. question

Inactive Publication Date: 2011-02-02
VERIDEX LCC
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Furthermore, the proportion of tumor cells in clinical samples varies widely
These issues may compromise gene expression data associated with ER specifically expressed on epithelial cells

Method used

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  • Laser microdissection and microarray analysis of breast tumors reveal estrogen receptor related genes and pathways
  • Laser microdissection and microarray analysis of breast tumors reveal estrogen receptor related genes and pathways
  • Laser microdissection and microarray analysis of breast tumors reveal estrogen receptor related genes and pathways

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0079] Continuity of 21 consecutively expressed genes between bulk tumor datasets and LCM-captured sample datasets Comparison of expression intensity of home genes

[0080] To gain insights into estrogen-triggered mechanisms in mammary epithelial cells, we applied the LCM technique to a cohort of 28 early-stage primary breast tumors consisting of 17 ER+ and 11 ER- tumors. Then their gene expression profiles were analyzed using Affymetrix gene chip Hul33A.

[0081]Each tumor used in this study was selected from the Erasmus Medical Center Tumor Bank in Rotterdam, The Netherlands. These tumor samples were sent to the laboratory for routine assessment of steroid hormone receptor status and thereafter stored in liquid nitrogen for preservation. Numbered tumor tissues were used in this study, which was carried out in accordance with the relevant regulations of the Dutch Federal Academy of Medical Sciences. The study was approved by the Medical Ethics Committee of Erasmus Medic...

Embodiment 2

[0087] Unsupervised 2D Hierarchical Clustering of Global Gene Expression Data Using Gene Spring Software analyze

[0088] The gene expression intensities of approximately 23,000 probe sets on the Affymetrix U133A chip were first normalized using the quantile normalization method, and then the above data were filtered using the "current" expression determined by the Affymetrix MAS5.0 software. An unsupervised two-dimensional hierarchical clustering algorithm was applied to microarray data to classify individual genes on the basis of similarity in expression patterns and to cluster individual samples on the basis of similarity in global gene expression profiles. Such as figure 2 As shown, 56 samples (28 LCM samples plus 28 bulk tissues) were classified into two main groups according to the source of RNA extraction: LCM-captured tumor cells and mixed cell populations from bulk tumors . Samples in each group were further divided into two subgroups (Group A and Group B in LC...

Embodiment 3

[0090] Pathway Analysis of Differentially Expressed Genes Between ER+ and ER- Subgroups

[0091] To identify genes associated with ER status and pathways associated with them, we performed a t-test between each ER+ subpopulation and ER− in both datasets. Using a Bonferroni-corrected P value image 3 A; Tables 2, 3 and 4). Of the 61 common genes, 36 were relatively overexpressed and 25 were downregulated in the ER+ subgroup (Table 2). Estrogen receptor and other genes known to be involved in ER activation such as trefoil factors 1 and 3, GATA3, X-box binding protein 1 (XBP1) and keratin 18 were among the upregulated genes. Sotiriou et al. (2003); Gruvberger et al. (2001); and Sun et al. (2005). On the other hand, placental cadherin (CDH3), GABRP, and secreted Frizzled-related protein-1 (SFRP1) appeared in the list of downregulated genes.

[0092] Table 2

[0093] Common genes whose expression is altered between ER+ and ER- tumors in both the LCM dataset and the bulk tumor...

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Abstract

About 70% to 80% of breast cancers express estrogen receptor-a (ERa), and estrogens play important roles in the development and growth of hormone-dependent tumors. Together with lymph node metastasis, tumor size and histological grade, ER status is considered one of the prognostic factors in breast cancer, and an indicator for hormonal treatment. 147 genes and 112 genes with significant P- value and having significant differential expression between ER+ and ER- tumors were identified from the LCM data set and bulk tissue data set, respectively. 61 genes were found to be common in both data sets, while 85 genes were unique to the LCM data set and 51 genes were present only in the bulk tumor data set. Pathway analysis with the 85 genes using Gene Ontology suggested that genes involved in endocytosis, ceramide generation, Ras / ERK / Ark cascade, and JAT- STAT pathway may play roles related to ER. The gene profiling with LCM-captured tumpr cells provides a unique approach to characterize and study epithelial tumor cells and to gain an insight into signaling pathways associated with ER.

Description

[0001] Statement Regarding Federal Sponsorship of Research or Development: [0002] No government funding was used for this invention. [0003] REFERENCE TO SEQUENCE LISTING OR COMPUTER PROGRAM LISTING CD-ROM APPENDIX [0004] References to the sequence listing in the appendix are stated. Background technique [0005] About 70% to 80% of breast cancers express estrogen receptor α (ERα), and various estrogens play an important role in the occurrence and development of hormone-dependent tumors. Along with lymph node metastasis, tumor volume, and histological grade, estrogen receptor status is considered one of the prognostic factors in breast cancer and an indication for hormone therapy. Breast cancer is the most commonly diagnosed cancer and the second leading cause of cancer death in American women. Estrogen plays an important role in the growth and differentiation of normal mammary glands, and also plays an important role in the occurrence and development of breast canc...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): A61K38/00
CPCC12Q2600/112C12Q1/6806C12Q2600/154C12Q2600/158C12Q1/6886C12Q2600/106A61P35/00A61P37/04
Inventor Y·王J·于Y·江F·杨
Owner VERIDEX LCC
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