Housekeeping Gene Variability in Normal and Carcinomatous Colorectal and Liver Tissues: Applications in Pharmacogenomic Gene Expression Studies

Blanquicett, Carmelo; Johnson, Martin R.; Heslin, Marty J.; Diasio, Robert B.

doi:10.1006/abio.2001.5570

Cited by 106 publications

(73 citation statements)

References 10 publications

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“…Ribosomal S9 was used as the endogenous reference (forward-5'-ATCCGCCAGCGCCATA-3', reverse-5'-TCAATGTGCTTCTGGGAATCC-3' and probe-5'-6FAMAGCAGGTGGTGAACATCCCGTCCTTTAMRA-3') in cell line assays. 31 For microdissected samples, the TaqMan ® Gene Expression Assay primer and probe set for ribosomal protein, large, P0 (RPLP0) (Hs99999902_m1) was used as the endogenous control. 31 The log-linear phase of amplification was monitored to obtain C T (threshold cycle) values.…”

Section: Methodsmentioning

confidence: 99%

“…31 For microdissected samples, the TaqMan ® Gene Expression Assay primer and probe set for ribosomal protein, large, P0 (RPLP0) (Hs99999902_m1) was used as the endogenous control. 31 The log-linear phase of amplification was monitored to obtain C T (threshold cycle) values. The standard curve method was employed to determine target expression levels.…”

Section: Methodsmentioning

confidence: 99%

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Hedgehog signaling and response to cyclopamine differs in epithelial and stromal cells in benign breast and breast cancer

Mukherjee

Frolova

Sadlonova

et al. 2006

Cancer Biology & Therapy

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147

149

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Hedgehog signaling and response to cyclopamine differs in epithelial and stromal cells in benign breast and breast cancer

Mukherjee

Frolova

Sadlonova

et al. 2006

Cancer Biology & Therapy

Self Cite

147

149

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“…To ensure that only genomic DNA was detected, the primers were designed to span an intron-exon border, and each sample was treated with an RNA-degrading enzyme during the DNA extraction process. We controlled for differences in DNA concentration between samples by normalizing against hypoxanthine phosphoribosyltransferase 1 (HPRT1; Xq26.1) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH; 12p13), both of which have been previously reported to be housekeeping genes (11).…”

Section: Methodsmentioning

confidence: 99%

Variation in the relative copy number of the TLR7 gene in patients with systemic lupus erythematosus and healthy control subjects

Kelley¹,

Johnson²,

Alarcón³

et al. 2007

Arthritis & Rheumatism

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Objective. To determine whether there is an increase in the number of TLR7 gene copies in patients diagnosed as having systemic lupus erythematosus (SLE) and whether gene amplification influences the autoantibody profiles in SLE patients, as has recently been reported in the BXSB/Yaa mouse model of lupus.Methods. We used a modified real-time quantitative polymerase chain reaction protocol to calculate the relative TLR7 gene copy number according to the comparative 2 -⌬⌬C t method in 99 SLE patients and 91 healthy controls matched for sex and ethnicity. Autoantibody profiles were determined by standard methods.Results. The relative number of TLR7 gene copies in SLE patients and healthy controls varied; however, no significant concordance between the number of relative gene copies and the SLE phenotype was found. There was also no difference in variation by ethnic group. Comparison of the relative gene copy numbers according to the presence or absence of antinuclear antibodies (ANAs), the ANA staining patterns, and the presence or absence of anti-RNA-associated antigen antibody showed no statistically significant difference in the SLE patients.Conclusion. We determined that although the relative gene copy number of TLR7 varied in both SLE patients and healthy controls, it was not significantly increased among our SLE patients as compared with our controls. We found no detectable trend for an association between the relative gene copy number and the autoantibody profile in SLE patients.A recent article in Science (1) reported that a genomic segmental duplication, which included the murine Toll-like receptor 7 (Tlr7) gene, and the translocation of this segment to the Y-linked autoimmune accelerator (Yaa) locus were associated with autoreactive B cell responses to RNA-related antigens. Similar findings of a duplication of the Yaa locus have been independently reported (2). The Yaa locus has previously been shown to increase the severity of lupus-like disease in males of the BXSB mouse strain (3) and to change their autoantibody specificity (4), leading to the suggestion that increased expression of Tlr7 due to this increase in genomic DNA may affect the autoimmune phenotype of these mice.Mouse models can provide important insights into human immune function and disease; however, the mechanisms require careful validation, since many known immunologic differences exist between the two species (5). A role of TLR7 in humans with systemic lupus erythematosus (SLE) is consistent with its ability to induce the release of interferon-␣ (IFN␣), a cytokine that has been shown to be increased in the serum of patients with SLE (6). Since TLR7 is located in a syntenic region of the X chromosome in humans and mice and since an increased prevalence of SLE in women (7) suggests an X-linked genetic component, we sought to determine whether, similar to the findings in the Yaa mouse, there were increased gene copy numbers of TLR7 in humans with SLE.

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“…1B), and at last with a probe for Ubiquitin (Fig. 1C), commonly used as internal positive control (Blanquicett et al, 2002). Signals quantification was performed and all the collected data were normalized for loading with respect to the Ubiquitin control.…”

Section: Chromatin Immunoprecipitation (Chip) Assaymentioning

confidence: 99%

The PVT‐1 oncogene is a Myc protein target that is overexpressed in transformed cells

Carramusa

Contino

Ferro

et al. 2007

Journal Cellular Physiology

134

102

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The human PVT-1 gene is located on chromosome 8 telomeric to the c-Myc gene and it is frequently involved in the translocations occurring in variant Burkitt's lymphomas and murine plasmacytomas. It has been proposed that PVT-1 regulates c-Myc gene transcription over a long distance. To get new insights into the functional relationships between the two genes, we have investigated PVT-1 and c-Myc expression in normal human tissues and in transformed cells. Our findings indicate that PVT-1 expression is restricted to a relative low number of normal tissues compared to the wide distribution of c-Myc mRNA, whereas the gene is highly expressed in many transformed cell types including neuroblastoma cells that do not express c-Myc. Reporter gene assays were used to dissect the PVT-1 promoter and to identify the region responsible for the elevated expression observed in transformed cells. This region contains two putative binding sites for Myc proteins. The results of transfection experiments in RAT1-MycER cells and chromatin immunoprecipitation (ChIP) assays in proliferating and differentiated neuroblastoma cells indicate that PVT-1 is a downstream target of Myc proteins.

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Housekeeping Gene Variability in Normal and Carcinomatous Colorectal and Liver Tissues: Applications in Pharmacogenomic Gene Expression Studies

Cited by 106 publications

References 10 publications

Hedgehog signaling and response to cyclopamine differs in epithelial and stromal cells in benign breast and breast cancer

Hedgehog signaling and response to cyclopamine differs in epithelial and stromal cells in benign breast and breast cancer

Variation in the relative copy number of the TLR7 gene in patients with systemic lupus erythematosus and healthy control subjects

The PVT‐1 oncogene is a Myc protein target that is overexpressed in transformed cells

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