Biomedical subjects

Arun Seth

Publications and source records attributed to Arun Seth.

26 records · Page 2Linked to original sources

PubMed2003

Comparison of two quantitative polymerase chain reaction methods for detecting HER2/neu amplification.

Two quantitative polymerase chain reaction (PCR) methods for HER2/neu gene quantification were evaluated for implementation into a clinical laboratory. Assays were developed using sequence-specific hybridization probes to detect a target (HER2/neu) and a reference gene (beta-globin) simultaneously. One method utilizes real-time quantification while the second uses internal competitors and melting curves to quantify the unknown sample. These two methods were evaluated using three cell lines and 97 breast tumor samples. Two hundred ninety-four samples were subsequently evaluated using the real-time quantification and immunohistochemical (IHC) staining. Real-time PCR gave HER2/neu gene doses of 10 for SKBR3 and 2 for T47D while the competitive PCR gave doses of 11 for SKBR3 and 2.2 for T47D. Both methods produced coefficients of variation (CV) of less than 3% for within-run and less than 6% for between-run analysis. Examination of 97 breast tumors found a correlation of r = 0.974 between the two methods. IHC and PCR results agreed for 234 of the subsequent 294 samples analyzed (79% concordance). A subset of ten discrepant samples was microdissected. After microdissection all ten were positive by PCR, thus resolving the discrepancy. Real-time quantification and microdissection is useful clinically for HER2/neu quantification. Its ease of use and broad dynamic range allows screening for amplification of HER2/neu.

Base Sequence↗

PubMed2003

Apolipoprotein E expression in localized prostate cancers.

Although prostate cancer has become the most common solid tumor diagnosed in men and the second leading cause of death due to malignancy, the progression of the disease is still somewhat unpredictable, until it becomes locally advanced or metastatic. The clinical problem to distinguish between dormant and progressive cancers is essential to patient care, as surgical and medical therapies have significant risk of morbidity and disability. Multiple gene expression in prostate cancer was surveyed by differential display cloning between the undifferentiated hormone refractory human prostate cancer cell line PC-3 (highly tumorigenic in nude mice) the hormone responsive LNCaP cell line (weakly tumorigenic in nude mice), and the poorly differentiated DU-145 cell line (moderately tumorigenic). ApoE mRNA was found to be highly expressed only in PC-3 cell-line. We further examined its protein expression by immunohistochemistry in 20 prostatectomy specimens and an association between Gleason score for each sample and ApoE expression was determined. ApoE expression correlates directly with the Gleason score in tissue sections, hormone independence as well as local and distant invasiveness. Prostatic intraepithelial neoplasias (PINs) adjacent to clinically manifested cancer were positive whereas more distant PINs were negative for ApoE. ApoE may represent a marker of more aggressive cells in human prostate cancers.

Aged↗

PubMed2002

Transcriptional regulation of a contractile gene by mechanical forces applied through integrins in osteoblasts.

We examined mechanotranscriptional regulation of the contractile gene, alpha-smooth muscle actin (SMA), in osteoblastic cells. Tensile forces were applied through collagen-coated magnetite beads to ROS17/2.8 cells. These cells were desmin-, vimentin+ and expressed low levels of SMA. After force application (480 piconewton/cell), SMA protein and mRNA were increased but beta-actin was unchanged. Beads coated with bovine serum albumin or poly-L-lysine produced no change of SMA. In cells transiently transfected with plasmids containing the SMA promoter fused to beta-galactosidase or green fluorescent protein coding sequences, SMA promoter activity was increased by approximately 60% after 4 h of force, whereas control (Rous sarcoma virus) promoter activity was unaffected. Transfections with beta-galactosidase or green fluorescent protein reporter constructs showed that force-loaded cells exhibited higher beta-galactosidase activity than cells without force. Cytochalasin D and latrunculin B inhibited force-induced increases of SMA promoter activity. Deletion analyses showed that SMA promoter activity was increased approximately 70% after force with a minimal construct containing 155 bp upstream of the translation start site. The force effect on the SMA promoter was abrogated in cells transfected with CArG-B box mutants. Gel mobility shift analyses of nuclear extracts showed strong binding to the CArG-B motif after force. We conclude that the CArG-B box is a force-responsive element in the SMA promoter.

Actins↗

PubMed2002

Coordinate gene expression patterns during osteoblast maturation and retinoic acid treatment of MC3T3-E1 cells.

The clonal osteoblast-like cell line MC3T3-E1 undergoes time-dependent morphological changes leading to the formation of bone nodules in vitro. Serial analysis of gene expression was used to identify genes expressed in MC3T3-E1 cells, including known osteoblast markers, structural and matrix proteins, transcription factors, cell-cycle regulators, and housekeeping genes. Relative changes in the expression of 92 representative transcripts were determined by arrayed cDNA hybridization. Complex probes were derived from MC3T3-E1 cells during the proliferation, differentiation, and matrix mineralization stages, and from cells grown with all- trans-retinoic acid (RA), a potent bone morphogen. We found that the relative expression of 68 of these genes was higher during differentiation than in the earlier proliferative phase. In the mineralization phase, all but 16 cDNAs had lower normalized hybridization intensity ratios as compared with the differentiation phase. cDNAs for vimentin (Vim), presenilin 2 (Psen2), guanine nucleotide binding protein alpha stimulating (Gnas), gap-junction membrane channel protein beta 1 (Gjb1), fibroblast growth factor receptor 1 (Fgfr1), eukaryotic translation elongation factor 2 (Eef2), and calponin 2 (Cnn2) had higher normalized hybridization intensities in both differentiation and mineralization than in proliferation. RA treatment during the differentiation phase appeared to reduce the expression of the 92 genes examined, as 62 cDNAs had lower hybridization intensities with complex cDNA probes derived from RA-treated cells than with the probe from untreated cells. Several cDNAs representing genes with previously unrecognized RA responsiveness were identified by this comparison, including the receptor for bone morphogenetic proteins 2 and 4 (Bmp2/Bmp4) and hemoglobin Y.

Activin Receptors, Type I↗

PubMed2002

Lumican is a major proteoglycan component of the bone matrix.

MC3T3-E1 mouse calvaria cells are a clonal population of committed osteoprogenitors that in the presence of appropriate supplements form a mineralized bone matrix. The development of the MC3T3-E1 cells can be divided into three major stages, namely, proliferation, differentiation, and mineralization. Recently, using the cDNA microarray technology we found lumican to be abundantly expressed during the mineralization and differentiation stages of the MC3T3-E1 development and not during the proliferation stage. Lumican has been shown to play essential roles in regulating collagen fibril formation in different extracellular matrices but its expression in the developing bone matrix remains elusive. By examining the expression profile of this gene during the different stages of MC3T3-E1 development, utilizing the 'real-time' PCR technology, we observed that the expression of lumican increases as the osteoblast culture differentiates and matures, suggesting that lumican may be involved in regulating collagen fibrillogenesis in bone matrices. Using immunostaining, we observed that during the early embryonic development of mouse (E11 to E13), lumican is mainly expressed in the cartilaginous matrices. However, in the older embryos (E14 to E16), the expression of lumican is more prominent in the developing bone matrices. Our data suggest that lumican is a significant proteoglycan component of bone matrix, which is secreted by differentiating and mature osteoblasts only and therefore it can be used as a marker to distinguish proliferating pre-osteoblasts from the differentiating osteoblasts.

Animals↗

PubMedDate not supplied

The breast cancer-associated gene Di12 has oncogenic activity.

The breast cancer-associated gene Di12 encodes a novel protein, which was found overexpressed in invasive ductal carcinomas of the breast. In experiments designed to assess the role of the Di12 gene in oncogenesis, the overexpression of 339 N-terminal amino acids of this gene in NIH3T3 cells resulted in cellular transformation and in vivo tumorigenesis. NIH3T3-Di12 tumor cell growth was partly reversible upon Di12 antisense treatment. In addition, transformation of the ER+ human breast cancer cell line MCF-7 resulted in hormone independent growth of these tumors in nude mice. Di12 expression in NIH3T3 and MCF-7 tumor cells was confirmed by RT-PCR and mabDi12 immunostaining. Immunohistochemistry using mabDi12 on an arrayed collection of 106 invasive breast tumors further underlined the expression of the gene in over 75% of advanced stage breast cancers. Our data indicate that Di12 expression is oncogenic in in vitro transformation and in vivo tumorigenic assays.

3T3 Cells↗

PubMedDate not supplied

Gene expression profiling of ductal carcinomas in situ and invasive breast tumors.

UNLABELLED: Comparative and functional genomics are powerful tools to advance the understanding of the molecular basis of cancer. It is believed that genes are epigenetically regulated and, thus, each tumor type and stage will be characterized by a gene expression fingerprint. In this study we identified genes that are differentially expressed in ductal carcinoma in situ and invasive ductal carcinoma of the breast. To isolate genes that are associated with progression of breast cancer we performed differential display and subtractive cloning procedures using matched RNA from normal and tumor tissue. cDNA microarray analysis generated gene expression profiles typical of the transition from in situ to invasive breast cancer when we used mRNA extracted from a case of low- to intermediate-grade DCIS and a case of high-grade DCIS/IDC. cDNAs from these samples were the probes in a cDNA microarray hybridization to 9183 unique cDNAs representing 8507 genes. Signals from both transcriptomes were obtained for 8083 genes, and the balanced differential expression values between pure DCIS and DCIS/invasive tumors revealed 303 distinct cDNAs with a ratio of > 2. Interferon inducible genes were found to be expressed at the highest level in the pure DCIS sample. Genes most abundantly expressed in the invasive tumor were immunoglobulin heavy constant gamma 3 and calgranulin B. Further analysis of RNA and protein expression in breast tumor cell lines and patient tissue samples revealed that: IGFBP-rP1 is down-regulated in invasive tumors whereas cyclin I protein is regulated by ubiquitination and is associated with ER-negative breast cancers. CONCLUSION: The known and novel genes discussed here represent targets for molecular characterization during breast cancer development as well as for designing novel strategies for diagnosis and treatment.

Biomarkers, Tumor↗

PubMedDate not supplied

Ets2 transcription factor inhibits mineralization and affects target gene expression during osteoblast maturation.

Our goal is to understand how Ets family transcription factors affect the genetic programs that control bone development. Modest overexpression of Ets2 in transgenic mice leads to Down's syndrome-like bone abnormalities. We observed that in the MC3T3-E1 in vitro model of osteoblast development, mature osteoblasts have very high levels of Ets2 relative to the immature preosteoblasts. We hypothesized that overexpression of Ets2 could have noticeable effects on gene expression, and found that exogenous Ets2 expression results in a complete lack of mineralized matrix in stable Ets2 transfected cells. Our cDNA microarray-based expression profiling of preosteoblasts vs. differentiated osteoblasts revealed several genes previously unrecognized as having roles in osteoblast maturation and up-regulated only in the mature osteoblasts. The promoters of these genes and known osteoblast marker genes were examined for Ets transcription factor binding sites (EBSs). Interactions of these sites with Ets2 protein were tested by EMSA. In vitro expressed Ets2 protein was able to form a protein:DNA complex with both known (Bsp, Opn, ON) and novel (Btg2, CysC, Lum) bone-related genes. In addition, Cbfa1 was found to interact with Ets2, forming a complex on the Opn promoter.

Animals↗