Gene Expression Profiles from Needle Biopsies Provide Useful Signatures of Non-Small Cell Lung Carcinomas

Gene expression profiles from DNA microarrays can provide molecular signatures that improve tumor classification, prognosis, and treatment options. While much of this work has focused on isolation of RNA from the resected tumor, fewer studies have utilized RNA from fine needle aspirates (FNA). In this pilot study we examined whether the gene signatures obtained from FNA samples would correlate with signatures taken from the resected tumor. Based on NSCLC gene expression profiles obtained from eleven sets of FNA and tumor samples we obtained a high concordance of FNA profiles matching their matched tumor sample. These results suggest that FNA samples may provide informative gene expression signatures regarding the potential aggressiveness of non-small-cell lung carcinomas

Alterations in gene expression and sensitivity to genotoxic stress following HdmX or Hdm2 knockdown in human tumor cells harboring wild-type p53

While half of all human tumors possess p53 mutations, inactivation of wild-type p53 can also occur through a variety of mechanisms that do not involve p53 gene mutation or deletion. Our laboratory has been interested in tumor cells possessing wild-type p53 protein and elevated levels of HdmX and/or Hdm2, two critical negative regulators of p53 function. In this study we utilized RNAi to knockdown HdmX or Hdm2 in MCF7 human breast cancer cells, which harbor wild-type p53 and elevated levels of HdmX and Hdm2 then examined gene expression changes and effects on cell growth. Cell cycle and growth assays confirmed that the loss of either HdmX or Hdm2 led to a significant growth inhibition and G1 cell cycle arrest. Although the removal of overexpressed HdmX/2 appears limited to an anti-proliferative effect in MCF7 cells, the loss of HdmX and/or Hdm2 enhanced cytotoxicity in these same cells exposed to DNA damage. Through the use of Affymetrix GeneChips and subsequent RT-qPCR validations, we uncovered a subset of anti-proliferative p53 target genes activated upon HdmX/2 knockdown. Interestingly, a second set of genes, normally transactivated by E2F1 as cells transverse the G1-S phase boundary, were found repressed in a p21-dependent manner following HdmX/2 knockdown. Taken together, these results provide novel insights into the reactivation of p53 in cells overexpressing HdmX and Hdm2

Full-Length \u3cem\u3ehdmX\u3c/em\u3e Transcripts Decrease Following Genotoxic Stress

Previous studies have suggested that the mdmX gene is constitutively transcribed, and that MdmX protein activity is instead controlled by cellular localization and DNA damage induced Mdm2-mediated ubiquitination leading to proteasomal degradation. In these studies, we report that the human mdmX (hdmX) mRNA is reproducibly decreased in various human cell lines following treatment with various DNA-damaging agents. Repression of hdmX transcripts is observed in DNA-damaged HCT116 colon cancer cells and in isogenic p53−/− cells, suggesting that this effect is p53-independent. Reduction in the amount of hdmX transcript occurs in both human tumor cell lines and primary human diploid fibroblasts, and results in a significant reduction of HdmX protein. Examination of hdmX promoter activity suggests that damage-induced repression of hdmX mRNA is not significantly impacted by transcription initiation. In contrast, changes in hdmX mRNA splicing appear to partly explain the reduction in full-length hdmX mRNA levels in tumor cell lines with the destabilization of full-length hdmX transcripts, potentially through microRNA miR-34a regulation, also impacting transcript levels. Taken together, this study uncovers previously unrecognized cellular mechanisms by which hdmX mRNA levels are kept low following genotoxic stress

Full-Length \u3cem\u3ehdmX\u3c/em\u3e Transcripts Decrease Following Genotoxic Stress

Previous studies have suggested that the mdmX gene is constitutively transcribed, and that MdmX protein activity is instead controlled by cellular localization and DNA damage induced Mdm2-mediated ubiquitination leading to proteasomal degradation. In these studies, we report that the human mdmX (hdmX) mRNA is reproducibly decreased in various human cell lines following treatment with various DNA-damaging agents. Repression of hdmX transcripts is observed in DNA-damaged HCT116 colon cancer cells and in isogenic p53−/− cells, suggesting that this effect is p53-independent. Reduction in the amount of hdmX transcript occurs in both human tumor cell lines and primary human diploid fibroblasts, and results in a significant reduction of HdmX protein. Examination of hdmX promoter activity suggests that damage-induced repression of hdmX mRNA is not significantly impacted by transcription initiation. In contrast, changes in hdmX mRNA splicing appear to partly explain the reduction in full-length hdmX mRNA levels in tumor cell lines with the destabilization of full-length hdmX transcripts, potentially through microRNA miR-34a regulation, also impacting transcript levels. Taken together, this study uncovers previously unrecognized cellular mechanisms by which hdmX mRNA levels are kept low following genotoxic stress

Why YPEL3 Represents a Novel Tumor Suppressor

Yippee-like 3 (YPEL3) was reported in 2004 as one of five family members of the Yippee protein with conservation in species down to slime molds. While reports of other YPEL family members have surfaced our laboratory was the first to report that YPEL3 is induced by the p53 tumor suppressor. Furthermore we demonstrated that YPEL3 is growth suppressive, triggering cellular senescence in human cell lines and is down-regulated in several human tumors. Studies with mouse YPEL3, originally named small unstable apoptotic protein (SUAP), confirmed that the gene encodes a growth suppressive highly unstable protein. In this review we show that transcriptionally active forms of p73 and p63, family members of p53, can transactivate the human YPEL3 gene. While there are several reported YPEL3 transcripts and potentially 2 protein isoforms, no clear protein structure has been reported. As evidence mounts that YPEL3 is a tumor suppressor gene, studies aimed at understanding its biological function, regulation of gene expression and impact on tumorigenesis will help

Why YPEL3 Represents a Novel Tumor Suppressor

Yippee-like 3 (YPEL3) was reported in 2004 as one of five family members of the Yippee protein with conservation in species down to slime molds. While reports of other YPEL family members have surfaced our laboratory was the first to report that YPEL3 is induced by the p53 tumor suppressor. Furthermore we demonstrated that YPEL3 is growth suppressive, triggering cellular senescence in human cell lines and is down-regulated in several human tumors. Studies with mouse YPEL3, originally named small unstable apoptotic protein (SUAP), confirmed that the gene encodes a growth suppressive highly unstable protein. In this review we show that transcriptionally active forms of p73 and p63, family members of p53, can transactivate the human YPEL3 gene. While there are several reported YPEL3 transcripts and potentially 2 protein isoforms, no clear protein structure has been reported. As evidence mounts that YPEL3 is a tumor suppressor gene, studies aimed at understanding its biological function, regulation of gene expression and impact on tumorigenesis will help

Why YPEL3 Represents a Novel Tumor Suppressor

Yippee-like 3 (YPEL3) was reported in 2004 as one of five family members of the Yippee protein with conservation in species down to slime molds. While reports of other YPEL family members have surfaced our laboratory was the first to report that YPEL3 is induced by the p53 tumor suppressor. Furthermore we demonstrated that YPEL3 is growth suppressive, triggering cellular senescence in human cell lines and is down-regulated in several human tumors. Studies with mouse YPEL3, originally named small unstable apoptotic protein (SUAP), confirmed that the gene encodes a growth suppressive highly unstable protein. In this review we show that transcriptionally active forms of p73 and p63, family members of p53, can transactivate the human YPEL3 gene. While there are several reported YPEL3 transcripts and potentially 2 protein isoforms, no clear protein structure has been reported. As evidence mounts that YPEL3 is a tumor suppressor gene, studies aimed at understanding its biological function, regulation of gene expression and impact on tumorigenesis will help

MicroRNA-34a Modulates MDM4 Expression via a Target Site in the Open Reading Frame

Background MDM4, also called MDMX or HDMX in humans, is an important negative regulator of the p53 tumor suppressor. MDM4 is overexpressed in about 17% of all cancers and more frequently in some types, such as colon cancer or retinoblastoma. MDM4 is known to be post-translationally regulated by MDM2-mediated ubiquitination to decrease its protein levels in response to genotoxic stress, resulting in accumulation and activation of p53. At the transcriptional level, MDM4 gene regulation has been less clearly understood. We have reported that DNA damage triggers loss of MDM4 mRNA and a concurrent increase in p53 activity. These experiments attempt to determine a mechanism for down-regulation of MDM4 mRNA. Methodology/Principal Findings Here we report that MDM4 mRNA is a target of hsa-mir-34a (miR-34a). MDM4 mRNA contains a lengthy 3′ untranslated region; however, we find that it is a miR-34a site within the open reading frame (ORF) of exon 11 that is responsible for the repression. Overexpression of miR-34a, but not a mutant miR-34a, is sufficient to decrease MDM4 mRNA levels to an extent identical to those of known miR-34a target genes. Likewise, MDM4 protein levels are decreased by miR-34a overexpression. Inhibition of endogenous miR-34a increased expression of miR-34a target genes and MDM4. A portion of MDM4 exon 11 containing this 8mer-A1 miR-34a site fused to a luciferase reporter gene is sufficient to confer responsiveness, being inhibited by additional expression of exogenous mir-34a and activated by inhibition of miR-34a. Conclusions/Significance These data establish a mechanism for the observed DNA damage-induced negative regulation of MDM4 and potentially provide a novel means to manipulate MDM4 expression without introducing DNA damage

Alterations in Gene Expression and Sensitivity to Genotoxic Stress Following HdmX or Hdm2 Knockdown in Human Tumor Cells Harboring Wild-Type p53

While half of all human tumors possess p53 mutations, inactivation of wild-type p53 can also occur through a variety of mechanisms that do not involve p53 gene mutation or deletion. Our laboratory has been interested in tumor cells possessing wild-type p53 protein and elevated levels of HdmX and/or Hdm2, two critical negative regulators of p53 function. In this study we utilized RNAi to knockdown HdmX or Hdm2 in MCF7 human breast cancer cells, which harbor wild-type p53 and elevated levels of HdmX and Hdm2 then examined gene expression changes and effects on cell growth. Cell cycle and growth assays confirmed that the loss of either HdmX or Hdm2 led to a significant growth inhibition and G1 cell cycle arrest. Although the removal of overexpressed HdmX/2 appears limited to an anti-proliferative effect in MCF7 cells, the loss of HdmX and/or Hdm2 enhanced cytotoxicity in these same cells exposed to DNA damage. Through the use of Affymetrix GeneChips and subsequent RT-qPCR validations, we uncovered a subset of anti-proliferative p53 target genes activated upon HdmX/2 knockdown. Interestingly, a second set of genes, normally transactivated by E2F1 as cells transverse the G1-S phase boundary, were found repressed in a p21-dependent manner following HdmX/2 knockdown. Taken together, these results provide novel insights into the reactivation of p53 in cells overexpressing HdmX and Hdm2