Limits...
Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation.

Ji H, Wu G, Zhan X, Nolan A, Koh C, De Marzo A, Doan HM, Fan J, Cheadle C, Fallahi M, Cleveland JL, Dang CV, Zeller KI - PLoS ONE (2011)

Bottom Line: Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types.Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes.Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America. hji@jhsph.edu

ABSTRACT
The functions of key oncogenic transcription factors independent of context have not been fully delineated despite our richer understanding of the genetic alterations in human cancers. The MYC oncogene, which produces the Myc transcription factor, is frequently altered in human cancer and is a major regulatory hub for many cancers. In this regard, we sought to unravel the primordial signature of Myc function by using high-throughput genomic approaches to identify the cell-type independent core Myc target gene signature. Using a model of human B lymphoma cells bearing inducible MYC, we identified a stringent set of direct Myc target genes via chromatin immunoprecipitation (ChIP), global nuclear run-on assay, and changes in mRNA levels. We also identified direct Myc targets in human embryonic stem cells (ESCs). We further document that a Myc core signature (MCS) set of target genes is shared in mouse and human ESCs as well as in four other human cancer cell types. Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types. Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes. Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression. Annotation of this gene signature reveals Myc's primordial function in RNA processing, ribosome biogenesis and biomass accumulation as its key roles in cancer and stem cells.

Show MeSH

Related in: MedlinePlus

Trophoblastic differentiation of H9 hESCs is associated with reduced Myc.(A) Photomicrographs of H9 hESCs following exposure to BMP4 for the indicated times. Representative images are shown. (B) Flow cytometry of BMP4 treated cells stained for KRT-PE, a marker of trophoblastic differentiation. Immunoblot at right shows that Myc protein levels are drastically reduced in BMP4-treated H9 cells. Tubulin immunoblot shows equal loading of samples. (C) Expression of the indicated stem cell genes and those enriched in trophoblasts was determined by realtime PCR normalized to B-ACTIN.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3198433&req=5

pone-0026057-g003: Trophoblastic differentiation of H9 hESCs is associated with reduced Myc.(A) Photomicrographs of H9 hESCs following exposure to BMP4 for the indicated times. Representative images are shown. (B) Flow cytometry of BMP4 treated cells stained for KRT-PE, a marker of trophoblastic differentiation. Immunoblot at right shows that Myc protein levels are drastically reduced in BMP4-treated H9 cells. Tubulin immunoblot shows equal loading of samples. (C) Expression of the indicated stem cell genes and those enriched in trophoblasts was determined by realtime PCR normalized to B-ACTIN.

Mentions: MYC plays essential roles in stem cell pluripotency and self renewal, and in reprogramming adult cells to an induced pluripotent state [36]. However, the mechanisms by which Myc directs the induction of pluripotency are poorly understood. To define MYC's functional role in ESCs, we determined direct Myc transcriptional targets in these cells. In hESCs, Myc levels are high and decrease with differentiation. Embryoid body formation promotes differentiation of stem cells into all three germ layers and is an attractive model to study the multipotentiality of hESC, but this is inherently limited by the cellular heterogeneity [37]. We therefore chose a simple, robust model that drives a more homogenous differentiation program, specifically using the bone morphogenetic protein BMP4 that induces differentiation of hESCs to trophoblasts, the cells that comprise the placenta [38]. After 6 days of exposure to BMP4, greater than 80% of cells differentiate and MYC mRNA and protein levels dropped several fold (Figures 3B and 3C), allowing us to study the Myc responsive transcriptome in a more uniform cell population. BMP4-treated H9 hESCs acquired a cobblestone appearance characteristic of differentiated trophoblasts (Figure 3A), and expressed high levels of CGA, GATA2 and KRT7 and reduced levels of pluripotency markers. Flow cytometric analyses revealed >90% of cells expressed high KRT7 levels compared to untreated H9 ESCs (Figure 3B).


Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation.

Ji H, Wu G, Zhan X, Nolan A, Koh C, De Marzo A, Doan HM, Fan J, Cheadle C, Fallahi M, Cleveland JL, Dang CV, Zeller KI - PLoS ONE (2011)

Trophoblastic differentiation of H9 hESCs is associated with reduced Myc.(A) Photomicrographs of H9 hESCs following exposure to BMP4 for the indicated times. Representative images are shown. (B) Flow cytometry of BMP4 treated cells stained for KRT-PE, a marker of trophoblastic differentiation. Immunoblot at right shows that Myc protein levels are drastically reduced in BMP4-treated H9 cells. Tubulin immunoblot shows equal loading of samples. (C) Expression of the indicated stem cell genes and those enriched in trophoblasts was determined by realtime PCR normalized to B-ACTIN.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198433&req=5

pone-0026057-g003: Trophoblastic differentiation of H9 hESCs is associated with reduced Myc.(A) Photomicrographs of H9 hESCs following exposure to BMP4 for the indicated times. Representative images are shown. (B) Flow cytometry of BMP4 treated cells stained for KRT-PE, a marker of trophoblastic differentiation. Immunoblot at right shows that Myc protein levels are drastically reduced in BMP4-treated H9 cells. Tubulin immunoblot shows equal loading of samples. (C) Expression of the indicated stem cell genes and those enriched in trophoblasts was determined by realtime PCR normalized to B-ACTIN.
Mentions: MYC plays essential roles in stem cell pluripotency and self renewal, and in reprogramming adult cells to an induced pluripotent state [36]. However, the mechanisms by which Myc directs the induction of pluripotency are poorly understood. To define MYC's functional role in ESCs, we determined direct Myc transcriptional targets in these cells. In hESCs, Myc levels are high and decrease with differentiation. Embryoid body formation promotes differentiation of stem cells into all three germ layers and is an attractive model to study the multipotentiality of hESC, but this is inherently limited by the cellular heterogeneity [37]. We therefore chose a simple, robust model that drives a more homogenous differentiation program, specifically using the bone morphogenetic protein BMP4 that induces differentiation of hESCs to trophoblasts, the cells that comprise the placenta [38]. After 6 days of exposure to BMP4, greater than 80% of cells differentiate and MYC mRNA and protein levels dropped several fold (Figures 3B and 3C), allowing us to study the Myc responsive transcriptome in a more uniform cell population. BMP4-treated H9 hESCs acquired a cobblestone appearance characteristic of differentiated trophoblasts (Figure 3A), and expressed high levels of CGA, GATA2 and KRT7 and reduced levels of pluripotency markers. Flow cytometric analyses revealed >90% of cells expressed high KRT7 levels compared to untreated H9 ESCs (Figure 3B).

Bottom Line: Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types.Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes.Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America. hji@jhsph.edu

ABSTRACT
The functions of key oncogenic transcription factors independent of context have not been fully delineated despite our richer understanding of the genetic alterations in human cancers. The MYC oncogene, which produces the Myc transcription factor, is frequently altered in human cancer and is a major regulatory hub for many cancers. In this regard, we sought to unravel the primordial signature of Myc function by using high-throughput genomic approaches to identify the cell-type independent core Myc target gene signature. Using a model of human B lymphoma cells bearing inducible MYC, we identified a stringent set of direct Myc target genes via chromatin immunoprecipitation (ChIP), global nuclear run-on assay, and changes in mRNA levels. We also identified direct Myc targets in human embryonic stem cells (ESCs). We further document that a Myc core signature (MCS) set of target genes is shared in mouse and human ESCs as well as in four other human cancer cell types. Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types. Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes. Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression. Annotation of this gene signature reveals Myc's primordial function in RNA processing, ribosome biogenesis and biomass accumulation as its key roles in cancer and stem cells.

Show MeSH
Related in: MedlinePlus