Scientists complete first mapping of molecule found in human embryonic stem cells

ScienceDaily (July 21, 2011) — Stem cell researchers at UCLA have generated the first genome-wide mapping of a DNA modification called 5-hydroxymethylcytosine (5hmC) in embryonic stem cells, and discovered that it is predominantly found in genes that are turned on, or active.See Also:Health & MedicineGenesStem CellsHuman BiologyBrain TumorProstate CancerLymphomaReferenceBRCA1Tumor suppressor geneEmbryonic stem cellDNA microarray

The finding by researchers with the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA may prove to be important in controlling diseases like cancer, where the regulation of certain genes plays a role in disease development.

"Any way you can control genes will be hugely important for human disease and cancer," said Steven E. Jacobsen, a professor of molecular, cell and developmental biology in the Life Sciences and a Howard Hughes Medical Institute investigator. "Cancer is generally a problem of genes being inappropriately turned off or mutated, like tumor suppressors genes, or genes that should be off getting switched on."

The study appears in the July issue of the journal Genome Biology.

5hmC is formed from the DNA base cytosine by adding a methyl group and then a hydroxy group. The molecule is important in epigenetics -- the study of changes in gene expression caused by mechanisms other than changes in the DNA sequence -- because the newly formed hydroxymethyl group on the cytosine can potentially switch a gene on and off, Jacobsen said.

The molecule 5hmC was only recently discovered, and its function has not been clearly understood, Jacobsen said. Until now, researchers didn't know where 5hmC was located within the genome.

"That is important to know because it helps you to understand how it is functioning and what it's being used for," said Jacobsen, who also is a researcher with UCLA's Jonsson Comprehensive Cancer Center. "We had known that DNA could be modified by 5hmC, but it wasn't clear where on the genome this was occurring."

Jacobsen, whose lab studies the molecular genetics and genomics of DNA methylation patterning, used genomics to define where in human embryonic stem cells the 5hmC was present. They used human embryonic stem cells because it had been shown previously that the molecule is abundant in those cells, as well as in brain cells, Jacobsen said.

In the study, Jacobsen found that 5hmC was associated with genes and tended to be found on genes that were active. The study also revealed that 5hmC was present on a type of DNA regulatory element, called enhancers, which help control gene expression. In particular, 5hmC was present on enhancers that are crucial for defining the nature of the human embryonic stem cells.

The results suggest that 5hmC plays a role in the activation of genes. This is opposite of the role of the more well studied 5mC (DNA methylation), which is involved in silencing genes. This relationship is in line with the view that 5hmC is created directly from 5mC.

"If we can understand the function of 5hmC, that will lead to greater understanding of how genes are turned on and off and that could lead to the development of methods for controlling gene regulation," Jacobsen said.

Moving forward, Jacobsen and his team will seek to uncover the mechanism by which 5hmC is created from DNA methylation and how it becomes localized to particular areas of the genome, such as the enhancers.

The two-year study was funded by the Howard Hughes Medical Institute, a Fred Eiserling and Judith Lengyel Graduate Doctoral Fellowship, the Leukemia & Lymphoma Society, the National Institutes of Health and by an Innovation Award from the Eli and Edythe Broad Center of Regenerative Medicine & Stem Cell Research at UCLA.

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Signaling molecule identified as essential for maintaining a balanced immune response

ScienceDaily (July 22, 2011) — St. Jude Children's Research Hospital investigators have identified a signaling molecule that functions like a factory supervisor to ensure that the right mix of specialized T cells is available to fight infections and guard against autoimmune disease.See Also:Health & MedicineImmune SystemStem CellsLymphomaNervous SystemBrain TumorCancerReferenceNatural killer cellT cellImmune systemInflammation

The research also showed the molecule, phosphatase MKP-1, is an important regulator of immune balance. Working in laboratory cell lines and mice with specially engineered immune systems, scientists demonstrated that MKP-1 serves as a bridge between the innate immune response that is the body's first line of defense against infection and the more specialized adaptive immune response that follows. The results are published in the July 22 print edition of the scientific journal Immunity.

The results raise hopes that the MKP-1 pathway will lead to new tools for shaping the immune response, said Hongbo Chi, Ph.D., assistant member of the St. Jude Department of Immunology and the study's senior author. The co-first authors are Gonghua Huang, Ph.D., and Yanyan Wang, Ph.D., both postdoctoral fellows in Chi's laboratory.

The findings provide new details about how dendritic cells regulate the fate of naïve or undifferentiated T cells. Dendritic cells are the sentinels of the innate immune response, patrolling the body and ready to respond at the first sign of infection.

Investigators were surprised that a single molecule regulated production of three out of the four major subsets of T cells, which each play different roles. MKP-1 is a negative regulator of the enzyme p38, which is part of the MAP kinase family of enzymes that control pathways involved in cell proliferation, differentiation and death.

Chi and his colleagues demonstrated that MKP-1 works in dendritic cells by altering production of protein messengers known as cytokines. Those cytokines determine which subset of specialized T cells the undifferentiated T cells are fated to become. In this study, scientists showed that MKP1 controls production of the cytokines that yield T helper 1 (Th1), T helper 17 (Th17) and regulatory T (Treg) cells. Th1 cells combat intracellular bacterial and viral infections. Th17 cells fight extracellular bacterial infections and fungi. Treg cells help with immune suppression, protecting against autoimmune diseases.

The study showed that suppression of p38 by MKP-1 promotes production of interleukin 12 (IL-12), which leads to an increase in Th1 cells. Rising IL-12 coincides with a drop in interleukin 6 (IL-6) and a corresponding dip in production of Th17. MKP-1 also inhibited the generation of Treg cells by down-regulating production of a third cytokine, TGF-beta.

Knocking out MKP-1 in mice disrupted production of IL-12 and IL-6 in dendritic cells as well as the anti-bacterial and anti-fungal immune response, researchers reported. MKP-1 deficiency also promoted T-cell driven inflammation in a mouse model of colitis, an inflammatory disease.

"MKP-1 is the first signaling molecule found in dendritic cells to program differentiation of these diverse T- cell subsets," Chi said.

Previous work by other scientists focused on T cell differentiation in response to stimulation by cytokines. "This research fills a gap in our understanding of dendritic cell-mediated control of T-cell lineage choices," Chi said. "T cells do not recognize pathogens directly, but dendritic cells do. T cells need dendritic cells to tell them what to do. In this study, we show that MKP-1 signaling in dendritic cells bridges the innate and adaptive immune responses by regulating cytokine production."

Other authors are Lewis Shi and Thirumala-Devi Kanneganti, both of St. Jude.

The research was supported in part by the National Institutes of Health, the National Multiple Sclerosis Society, the Cancer Research Institute, The Hartwell Foundation and ALSAC.

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