Biomedical subjects

Edward K Lobenhofer

Publications and source records attributed to Edward K Lobenhofer.

4 recordsLinked to original sources

PubMed2003

Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference.

We propose an algorithm for selecting and clustering genes according to their time-course or dose-response profiles using gene expression data. The proposed algorithm is based on the order-restricted inference methodology developed in statistics. We describe the methodology for time-course experiments although it is applicable to any ordered set of treatments. Candidate temporal profiles are defined in terms of inequalities among mean expression levels at the time points. The proposed algorithm selects genes when they meet a bootstrap-based criterion for statistical significance and assigns each selected gene to the best fitting candidate profile. We illustrate the methodology using data from a cDNA microarray experiment in which a breast cancer cell line was stimulated with estrogen for different time intervals. In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal.

Algorithms↗

PubMed2003

Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells.

Tamoxifen is a widely used breast cancer therapeutic and preventative agent. Although functioning as an estrogen antagonist at the cellular level, transcriptional profiling revealed that at the molecular level, tamoxifen functions largely as an agonist, virtually recapitulating the gene expression profile induced in breast cancer cells by estrogen. Remarkably, tamoxifen induces transcription factors and genes involved in promoting cell cycle progression including fos, myc, myb, cdc25a, cyclins E and A2, and stk15 with kinetics that paralleled that of cells cycling in response to estrogen, even though tamoxifen-treated cells are not transiting through the cell cycle. Induction of cell cycle-associated genes was specific for tamoxifen, and did not occur with raloxifene. However, cyclin D1 was a key estrogen-induced gene not expressed in response to tamoxifen or raloxifene but constitutively expressed in tamoxifen-resistant cells.

Antineoplastic Agents↗

PubMed2002

BRCA2 monoclonal antibodies react with differentiating epithelium.

The BRCA2 gene has previously been suggested to play a role in proliferation and DNA repair. Germline mutations in the BRCA2 gene predispose individuals to early onset, hereditary breast cancer. To better understand the expression pattern and function of the BRCA2 gene product, we have developed immunological reagents specific for BRCA2. These reagents recognize full-length (384 kDa) recombinant human BRCA2 proteins in transfected cell lysates as well as multiple smaller recombinant BRCA2 polypeptides. Detection of native BRCA2 protein in most tissue types, including breast epithelium, requires sensitive techniques such as immunoprecipitation-Western blot analysis. However, we have demonstrated strong reactivity of our immunological reagents with differentiating epithelium, including epidermis, thymic epithelium, and squamous cell carcinoma. These data suggest that BRCA2 may play a role in processes associated with cellular differentiation, in addition to its previously suggested roles in proliferation and DNA repair.

Animals↗

PubMed2002

Regulation of DNA replication fork genes by 17beta-estradiol.

The steroid hormone estrogen can stimulate mitogenesis in hormone-responsive breast cancer epithelial cells. This action is attributed to the transcriptional activity of the ER, a ligand-dependent transcription factor. However, the exact molecular mechanism underlying estrogen-induced proliferation has yet to be completely elucidated. Using custom cDNA microarrays containing many genes implicated in cell cycle progression and DNA replication, we examined the gene expression of a hormone-responsive breast cancer cell line (MCF-7) treated with a mitogenic dose of estrogen in the absence of confounding growth factors found in serum. Gene expression changes were monitored 1, 4, 12, 24, 36, and 48 h after estrogen stimulation so that RNA levels at critical times throughout cell cycle progression could be monitored. Significant changes include the altered transcript levels of genes implicated in transcription, cellular signaling, and cell cycle checkpoints. At time points during which increased numbers of cells were progressing through S phase, a majority of the genes associated with the DNA replication fork were also found to be induced. The coexpression of DNA replication fork genes by estrogen without the support of serum growth factors indicates an important estrogen regulatory component of the molecular mechanism driving estrogen-induced mitogenesis.

Cell Division↗