A Simple Analysis of Gene Expression and Variability in Gene Arrays Based on Repeated Observations

Jovanovic, Borko; Huang, Shuguang; Liu, Yuequin; Naguib, Karen N.; Bergan, Raymond C.

doi:10.2165/00129785-200101020-00007

Cited by 13 publications

(15 citation statements)

References 22 publications

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“…Evaluation for longer periods of time show a reentry into cell attachment, but of lower magnitude than observed with the first cycle (unpublished observations). Prior gene array-based studies indicated that endoglin expression increased during cell detachment (Jovanovic et al, 2001). However, array findings were never confirmed by Northern blot.…”

Section: Endoglin Is Down-regulated During Prostate Cell Detachmentmentioning

confidence: 96%

“…We found that metastatic variant PC3-M cells exhibited a unique pattern of cell adhesion, characterized by rapid attachment, followed by detachment. Focusing upon genes important in regulating cell detachment, we developed a novel statistical approach wherein multiple replicates of gene array experiments were used to calculate mean and variance of gene expression, for all genes (Jovanovic et al, 2001;. In this manner, genes whose expression was significantly up-or downregulated, as compared to that associated with normal gene variance, could be identified, and investigated further.…”

Section: Introductionmentioning

confidence: 99%

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Over expression of endoglin in human prostate cancer suppresses cell detachment, migration and invasion

et al. 2002

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The regulation of cell adhesion and motility in human prostate is not well understood. We have previously shown that the endoglin gene is differently expressed during changes in prostate cell adhesion. Endoglin is a transmembrane transforming growth factor b binding protein typically expressed by endothelial cells. In this report we demonstrate that endoglin over expression increases prostate cell attachment, while decreasing migration and invasion. Engineered decreases in endoglin expression have opposite effects. While endoglin exerted only relatively small effects upon cell adhesion, large effects upon cell migration and invasion were observed. Endoglin was shown to localize to focal adhesion plaques, consistent with its role in regulating cell adhesion and motility. Loss of endoglin expression in cancer, as compared to normal prostate, was seen in human prostate cell lines. Suppression of endoglin expression in a panel of normal human prostate cell lines led to cell detachment. Endoglin is identified as a regulator of cell adhesion, motility and invasion in human prostate. Loss of endoglin expression appears to be associated with prostate cancer progression, at least in vitro.

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Section: Endoglin Is Down-regulated During Prostate Cell Detachmentmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Over expression of endoglin in human prostate cancer suppresses cell detachment, migration and invasion

et al. 2002

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“…The metastatic behavior of cells is heavily dependent upon the cellular functions of migration and invasion (Poste and Fidler, 1980;Bissell and Radisky, 2001). Using gene arrays to identify regulators of PCa cell motility, we uniquely identified endoglin (ENG) (Jovanovic et al, 2001). ENG is a 180 kDa homodimeric type I transmembrane transforming growth factor b (TGFb) binding protein (Cheifetz et al, 1992).…”

Section: Introductionmentioning

confidence: 99%

Endoglin inhibits prostate cancer motility via activation of the ALK2-Smad1 pathway

et al. 2007

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Endoglin is a transforming growth factor b (TGFb) superfamily auxiliary receptor. We had previously shown that it suppressed prostate cancer (PCa) cell motility, and that its expression was lost during PCa progression. The mechanism by which endoglin inhibits PCa cell motility is unknown. Here we demonstrate that endoglin abrogates TGFb-mediated cell motility, but does not alter cell surface binding of TGFb. By measuring Smad-specific phosphorylation and Smad-responsive promoter activity, endoglin was shown to constitutively activate Smad1, with little-to-no effect upon Smad3. Knockdown of Smad1 increased motility and abrogated endoglin's effects. As type I activin receptor-like kinases (ALKs) are necessary for Smad activation, we went on to show that knockdown of ALK2, but not TGFbRI (ALK5), abrogated endoglinmediated decreases in cell motility and constitutively active ALK2 was sufficient to restore a low-motility phenotype in endoglin deficient cells. These findings provide the first evidence that endoglin decreases PCa cell motility through activation of the ALK2-Smad1 pathway.

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“…We have previously described similar findings before in studies involving only nonamplified (i.e., native) RNA. 22 Most importantly, when LCM was coupled to linear amplification and array data pooled across different subjects, genes were found to be differentially expressed when normal epithelial cells were compared to cancer.…”

Section: Discussionmentioning

confidence: 99%

“…In studies using only non-amplified (or native) RNA, we have previously reported that there is increased variability in gene expression profiles when comparing RNA from different, as apposed to identical RNA batches. 22 Data in Figure 3a were generated from the same batch of RNA, for each cell line tested. To further characterize sources of variability, RNA was isolated from PC3 and PC3-M cells at two separate times, aRNA generated, and aPC3/aPC3-M versus PC3/PC3-M determined, for non-trivial genes ( Figure 4).…”

Section: Evaluating Other Factors: Variability In Gene Expressionmentioning

confidence: 99%

Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification

Ding

Xu²,

Chen³

et al. 2006

Prostate Cancer Prostatic Dis

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Coupling array technology to laser capture microdissection (LCM) has the potential to yield gene expression profiles of specific cell populations within tissue. However, remaining problems with linear amplification preclude accurate expression profiling when using the low nanogram amounts of RNA recovered after LCM of human tissue. We describe a novel robust method to reliably amplify RNA after LCM, allowing direct probing of 12K gene arrays. The fidelity of amplification was demonstrated by comparing the ability of amplified RNA (aRNA) versus that of native RNA to identify differentially expressed genes between two different cell lines, demonstrating a 99.3% concordance between observations. Array findings were validated by quantitative polymerase chain reaction analysis of a randomly selected subset of 32 genes. Using LCM to recover normal (N ¼ 5 subjects) or cancer (N ¼ 3) cell populations from intact human prostate tissue, three differentially expressed genes were identified. Independent investigators have previously identified differential expression of two of these three genes, hepsin and beta-microseminoprotein, in prostate cancer. Taken together, the current study demonstrates that accurate gene expression profiling can readily be performed on specific cell populations present within complex tissue. It also demonstrates that this approach efficiently identifies biologically relevant genes.

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A Simple Analysis of Gene Expression and Variability in Gene Arrays Based on Repeated Observations

Abstract: These findings have implications relating to the use of gene arrays to detect variance of gene expression, and should be taken into consideration in the prospective design of array experiments.

Cited by 13 publications

References 22 publications

Over expression of endoglin in human prostate cancer suppresses cell detachment, migration and invasion

Over expression of endoglin in human prostate cancer suppresses cell detachment, migration and invasion

Endoglin inhibits prostate cancer motility via activation of the ALK2-Smad1 pathway

Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification

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