Question

18. A study used cDNA microarray profiling to compare the expression profiles for 6900 genes in normal and malignant breast tissue from rats. RNA was extracted from the following tissues:

a. Breast tissue from virgin rats

b. Breast tissue from pregnant rats

c. Breast tissue from lactating rats

d. Breast carcinoma induced by the meat-derived carcinogen PhIP

e. Breast carcinoma induced by the experimental carcinogen DMBA

After the microarray slides were hybridized with labeled cDNAs derived from these 5 populations of RNAs, the data were analyzed by several different comparisons. In Comparison 1, tissues a, b, and c were grouped together as “normal” tissue samples, and D and e were grouped as “carcinoma” samples. Genes that were either induced (more than twofold increase in expression) or repressed (more than twofold decrease in expression) in both carcinoma samples relative to all three normal samples were determined. A partial listing of differentially expressed genes is shown below:

Induced Genes

Cell-Growth and Cell-Cycle-Related Genes

1. Platelet-derived growth factor A chain (PDGF-A)

2. Cclin-dependent kinase (Cdk4)

3. Cyclin D

Signal-Transduction and Transcription-Related Gene - STAT5a

Repressed Genes

Extracellular Matrix Genes

1. Alpha 1 type V collagen

2. Fibronectin 1

3. Desmin

Answer the following:

a. What was the purpose of analyzing breast tissue from pregnant and lactating rats?

b. What characteristic of cancer is promoted by the overexpression of PDGF-A, Cdk4, and Cyclin D?

c. What characteristic of cancer might be promoted by the repression of extracellular matrix genes?

d. STAT5a is a transcription factor that regulates the expression of cyclin D, Bcl-X1, and other genes. Why is it possible for these carcinomas that no mutation occurs in the Cyclin D gene despite its overexpression? Why are mutations in transcription-factor genes like STAT5a commonly found in cancer cells?

In Comparison 2, expression profiles of carcinomas induced by Ph1P and DMBA were compared with each other. In this analysis, some distinctions were found, but the number of differentially expressed genes was far less than the number of genes identified when comparing the grouped “normal” samples to the grouped “carcinoma” samples.

a. On the basis of this information, what can be generalized about the molecular profile of breast carcinomas?

b. Would you anticipate greater or fewer differences in gene expression if two distinct types of cancer (e.g., breast carcinoma vs. B-cell lymphoma) induced by the same carcinogen were compared by microarray analysis?

Answer 1

18. a) Breasts are very plastic organs and its development is related to vast changes in the expression of different genes. Their development is also age-dependent as well as also dependent on pregnancy and lactation period. So, the study and characterization of the expression of different genes during normal breast development from pregnant and lactating rats will help us to understand cancer development.

b). Overexpression of PDGF-A, CDK4, and cyclin D will lead to the unregulated growth of cancer cells, will increase metastasis that is the migration of cancer cells from one place to other, as well decrease the apoptosis. There are several types of cyclins D, which is an allosteric regulator of CDK 4 and CDK 6. CDK regulates the cell cycle and helps transition from G1 to S phase. Any error in this process will lead to cell cycle dysregulation in cancer cells.

C) Extracellular matric is composed of a lot of proteins that provide a base to cells as well as helps in cell adherence. If ECM genes are repressed then several proteins present IN ECM will be either absent or be defected and hence the cancerous cells will be loosely bound and would be able to easily migrate and lead to metastasis.

d). when the cell receptor interacts with cytokines, growth factors, or hormones, STATs are activated by phosphorylation at tyrosine residues. after activation, STAT dimerizes and enters nucleus where it serves as a transcription factor for several genes like cyclin D, BCLx1 etc. Therefore, even if there is no mutation found in Cyclin D, it will be overexpressed because of the activation of its transcription factor STAT 5.

STAT 5 results in cell growth, proliferation and differentiation, therefore it is upregulated in most of the cancers.