Novel platform technologies and key advances in genomics are rapidly driving the development of molecular diagnostics, reports Genetic Engineering and Biotechnology News (GEN).  The payoff for successful molecular diagnostic products can be significant as Kalorama Information predicts that this market currently exceeds $3.2 billion worldwide and will reach $5.4 billion in four years, according to an article in the October 1 issue of GEN.

“Molecular diagnostic products are based on cutting-edge research in two of the most promising biotechnologies, genomics and proteomics.  These novel tests also utilize sophisticated analytical techniques such as microarrays and mass spectrometry,” notes John Sterling, Editor-in-Chief of GEN.  “Molecular diagnostics are particularly applicable to the early detection of cancer.”

Affymetrix and Illumina have both created array-based products that enable high-speed analysis of DNA, RNA, and proteins as tools for disease research, drug development, and molecular tests.  These gene-sequencing tools are being applied at an earlier stage.

Genetic tests can optimize drug therapy, and companion diagnostics are being touted as a method to better define a patient’s need or predict clinical outcome from a specific drug.  The FDA recently approved a HER-2 test from Invitrogen called Spot-Light that can be used to identify breast cancer patients who are candidates for treatment with Herceptin.  In addition, data was recently presented showing the importance of testing for the K-ras gene to assess the clinical benefit of Erbitux for metastatic colorectal cancer.

Of all the larger integrated healthcare companies, Roche has best executed the synergies of molecular diagnostics and biopharmaceuticals and is well positioned for the future with products in oncology and infectious disease.  Its genetic tests include CYP450 for drug metabolism studies and HER-2 for use with tamoxifen therapy.

Researchers in Florida are reporting an advance toward tapping the enormous potential of an emerging new group of antibiotics identical to certain germ-fighting proteins found in the human immune system.  Their study, which may help fight the growing epidemic of drug-resistant infections, is in the current (August) issue of ACS’ Biomacromolecules, a monthly journal.

In the new study, D. Matthew Eby, Glenn Johnson, and Karen Farrington point out that scientists have long eyed the germ-fighting potential of antimicrobial peptides (AMPs).  These small proteins fight a wide range of bacteria and fungi in the body and have the potential to be developed into powerful drugs to overcome infections that are resistant to conventional drugs.  But scientists report difficulty producing effective AMPs because the antibiotics are fragile and easily destroyed in the body.  An effective way to stabilize them is needed, they say.

In laboratory studies, the researchers showed that the coating protected the antibiotics from destruction by other chemicals while allowing the release of a controlled antibiotic dose for an extended period of time.  These features are key to the effective use of AMPs as antibiotics, they say.

Although every cell of our bodies contains the same genetic instructions, specific genes typically act only in specific cells at particular times. Other genes are “silenced” in a variety of ways. One mode of gene silencing depends upon the way DNA, the genetic material, is packed in the nucleus of cells.

When packed very tightly around complexes of proteins called histones, the DNA double helix is rendered physically inaccessible to molecules that mediate gene expression. Now, a research team that includes Michael Q. Zhang, Ph.D., a professor at Cold Spring Harbor Laboratory (CSHL), has published a comprehensive analysis of modification patterns in histones.

Using a new technology called ChIP-Seq, the team identified 39 histone modifications, including a “core set” of 17 modifications that tended to occur together and were associated with genes observed to be active.

Modification Patterns With Different “Personalities”

Scientists have long known that chemical changes at particular locations in histone complexes influence how tightly the DNA is wrapped around the histones. “But it is important to know whether particular modifications occur together in characteristic patterns, or if these patterns can predict gene activities,” Dr. Zhang explained.

At the heart of the team’s efforts to determine this, Keji Zhao, Ph.D., of the National Heart, Blood, and Lung Institute of the National Institutes of Health, and his colleagues developed a method to map modifications in human white blood cells known as CD4+ T cells. First they used an enzyme to cut the DNA into short segments, which remained attached to histone “spools.” For each of 39 distinct histone modifications, the scientists used an antibody to extract matching histone-DNA combinations. Finally, they used the ChIP-Seq DNA-sequencing technology to determine which parts of the genome were bound to each type of modified histone.

The team’s most recent research, published in the July 2008 issue of Nature Genetics, maps the DNA locations that bind to histones containing molecular configurations called acetyl groups at 18 different positions in the “tails” of the histone proteins. The scientists combined this information with earlier maps for 19 different changes called methylation modifications, and for replacement of one of the histone proteins with a well-known variant.

The various modifications showed distinctive “personalities,” each preferentially associating with particular regulatory regions of genes.

Looking for Patterns

Mapping many modifications enabled the researchers to explore whether different types tend to appear together in the same type of DNA regulatory regions. They found that some recurring combinations did occur frequently at “promoter” and “enhancer” regions in DNA, which are known to increase the activity of nearby genes. In particular, the team identified one combination of 17 modifications that was present in more than a quarter of the more than 12,000 promoter regions they examined.

On average, the genes corresponding to this “backbone” set were expressed more actively. That is to say, they were activated, setting the cellular machinery in motion to produce specific proteins, the workhorses of most life processes.

The rich relationships detected by the researchers among the various histone modifications suggests that specific combinations might carry specific meanings. Previous researchers have proposed a “histone code” hypothesis, which posits that a particular combination of modifications may be recognized by a particular protein module. Some scientists believe such histone code may determine the activity of a given gene.

But, cautions Dr. Zhang, while there are patterns, like the backbone, that are highly correlated, “none of them has exact predictive value.” He maintains “there must be something else” that also affects gene activity.

Since genes with higher or lower expression levels may have the same patterns of modification, and not all active genes share a common pattern, the reality is likely more complex than a universal histone code that predicts exact gene expression level. Nonetheless, the new research provides a rich data source for understanding how specific combinations of histone modifications modulate the effects of many genes, in turn helping to modify activity within and among cells. “Critical future research should focus on finding proteins that target histone modifications to genetic regions with particular sequences,” Dr. Zhang emphasized.

A study published July 11th in the open-access journal PloS Pathogens suggests that herpesviruses use multiple strategies to manipulate important components of the host cell nuclear environment during infection.  The study, conducted by researchers at the University of Toronto in collaboration with Affinium Pharmaceuticals Inc., provides novel insights into the potential functions of over 120 previously uncharacterized viral proteins.

Most people are infected with the three human herpesviruses that were the subject of this study; namely herpes simplex virus (type 1), Epstein-Barr virus, and cytomegalovirus.  Herpesviruses have complex life cycles due to their adept manipulation of the host cell environment.  Although often asymptomatic, herpesviruses can cause life-threatening diseases.  In order to provide a more complete understanding of how these viruses alter host cells, the researchers developed a system to examine each viral protein individually in human cells.

The researchers investigated over 230 individual proteins from the three herpesviruses.  They focused on 93 identified viral proteins that localized to the cell nucleus and altered key cellular components that regulate gene expression, cell growth and death, and antiviral responses.

Cells depend on nuclear structures called PML bodies to control cell proliferation and survival, to ensure damaged DNA is repaired, and to inhibit virus replication.  24 of the nuclear viral proteins, several of which had no previously assigned function, were found to disrupt or reorganize PML bodies, suggesting that herpesviruses employ multiple strategies for manipulating this key regulator of essential cellular processes.

Further studies will be needed to determine how the identified viral proteins function in the context of viral infection, but this research provides a starting point for investigating how these proteins affect important processes of the cell nucleus.

Drugs that target members of the EGFR family of proteins have proven effective for the treatment of certain types of cancer, including breast cancer.  However, in a large number of patients for whom the treatment initially works well, the tumor recurs and is resistant to the effects of the drug.  New insight into the mechanisms of tumor resistance to a drug known as gefitinib, which targets EGFR, has now been provided by a team of researchers at Vanderbilt University Medical Center, Nashville, and Massachusetts General Hospital Cancer Center, Charlestown.  As discussed by both the authors and, in an accompanying commentary, Mark Greene and Qiang Wang, at the University of Pennsylvania Medical Center, Philadelphia, these observations help us understand why tumors become resistant to the effects of EGFR-targeted drugs, information that is essential if more effective therapies are to be developed.

The team, led by Carlos Arteaga and Jeffrey Engelman, generated cancer cells resistant to the effects of gefitinib and found that these cells were constantly sending signals from a protein on their surface known as IGF1R.  This meant that two proteins known as IRS-1 and PI3K were always associated.  If this association was disrupted then the cells once again became susceptible to the effects of gefitinib.  Further analysis showed that if mice with a human tumor were treated with gefitinib and a drug inhibiting IGF1R their tumors did not recur, whereas neither drug alone could prevent tumor recurrence.  The authors therefore suggest that drug combinations that target both EGFR and IGF1R might be of benefit to individuals with cancers that are responsive to EGFR-targeted therapies.