Decoding the "Dark Matter" Within

One of the big surprises to come out of the Human Genome Project was the fact that only about 1.5% of our genomes is actually made up of genes – that is, stretches of DNA that codes for proteins. The remainder, once colloquially referred to as “junk DNA” but more recently re-named “non-coding DNA”, has been a bit of a mystery. Scientists knew that at least some of it played a role in regulating when the genes are actually used, but they weren’t entirely sure how much non-coding DNA was used, and in what fashion.


On September 5th, scientists published the results of a multi-year, international study attempting to answer these questions. This project, dubbed ENCODE for Encyclopedia of DNA Coding Elements, made great strides towards dissecting the role of this non-coding DNA. Twelve years ago, scientists were surprised to find that so little of the genome actually codes for proteins; this time around, scientist were surprised to find that so much of the non-coding region seems active in some way. As much as 80% of this DNA now appears to be in play, either in regulating the use of the protein coding regions, or in producing RNA molecules which do not directly make proteins but play some other role – in some cases, an as yet to be determined role.

This finding has direct implications for drug discovery research. Over the past decade, scientists have identified a number of small changes in the genome sequence – dubbed single nucleotide polymorphisms (SNPS) – between people who suffer from certain diseases such as Crohn’s disease, asthma, rheumatoid arthritis, type 1 diabetes, type 2 diabetes, bipolar disorder, and coronary artery disease, amongst others. Certainly some of these differences were identified in genes; however, many also exist in the non-coding regions. This opens up a whole new arena for drug discovery – the possibility of targeting not just the disease protein itself, but also how it is regulated. This may prove to be an invaluable approach in those cases where the disease protein is not amenable to therapeutic intervention.

There is still much to be learned. How do the regulatory regions interact with each other? How many different genes does each regulate? And what are all of those RNA molecules doing? Answering even some of these questions will revolutionize our understanding of human genomics and human disease.

New Gene Therapy Treatment Approved by EMA

Last month (July 20th) the European Medicines Association (EMA) made medical history by recommending regulatory approval for Glybera, the first commercial gene therapy treatment in Europe or the U.S. Gene therapy – delivering a correct version of a gene to replace a patient’s own malfunctioning copy – is a seemingly straightforward idea. However, demonstrating both safety and efficacy has proven to be a significant challenge over the past 20 years.

Recent innovations in gene delivery technology enabled the Dutch company uniQure to develop Glybera for treatment of the rare inherited condition lipoprotein lipase deficiency (LPLD). Patients suffering from LPLD are unable to break down fat globules in the bloodstream, resulting in fat-clogged blood vessels in the pancreas and gut, often leading to debilitating pancreatitis attacks. Glybera consists of a non-harmful virus – a viral vector - that has been genetically modified to contain a correct copy of the gene that codes for lipoprotein lipase. Glybera targets muscle cells, where lipoprotein lipase is normally made.

Previous iterations of genetic therapy also involved the use of viral vectors. However, the vectors used in earlier attempts either did not deliver a stable copy of the therapeutic gene, or were not able to do so in a reliably safe manner. Glybera has proven successful on both counts – it only needs to be administered every few years, and appears to be safe. uniQure expects to file for FDA approval later this year.

 LPLD is a very rare disease, affecting only a few individuals per million. Thus even this new approval does not yet make gene therapy mainstream. The fact that the target protein is normally produced in muscle cells also cautions against extrapolating these results to other genetic diseases – muscle tissues are known to be highly efficient at taking up the viral vectors being developed for gene therapy, something that is not necessarily true for all tissues. Nonetheless, the EMA announcement is an exciting one, and hopefully will herald a new era of investment – both financial and intellectual – in this emerging therapeutic area.

Epigenetics and Cancer: The Rest of The Story

In the 1980s, cancer researchers made great strides towards understanding cancer with the realization that essentially all cancers have genetic roots – a mutation, or a change in DNA sequence, either inherited or acquired, in a gene that is important for regulating cell growth and division, results in out of control cell division – cancer. In the past few years, researchers have been learning more and more that so-called epigenetic changes – changes to gene expression resulting from factors other than mutation – may play a profound role in regulating cellular proliferation. What, exactly, are epigenetic modifications? They are direct chemical modification of either a gene sequence, or the protein that it forms a complex with (histone protein) to make up a structured chromosome. The chemical modifications take the form of attaching small groups of atoms know as methyl groups (three carbon atoms and one hydrogen) or acetyl (two carbons, three hydrogens and one oxygen) groups. Methylation or acetylation, as it is known, results in “silencing” a gene – its protein produjavascript:void(0);ct is no longer made. If a gene responsible for “turning off” cell division – a tumor suppressor gene – is silenced, cancer may result. Overactive methylation of these tumor suppressor proteins is known to be associated with various types of lymphomas, and is likely to also play a role in other types of cancers. This understanding opens up the possibility of a new approach to treating cancer, especially lymphomas. At this year’s American Association for Cancer Research annual meeting, researchers from GlaxoSmithKline reported positive results in preclinical studies of an inhibitor of the methylating-enzyme EZH2. Inhibiting EZH2 reduced the proliferation of lymphoma cells both in tissue culture and in lab animals. Other epigenetic-modifying drugs are already on the market: Vidaza (Celgene) and Dacogen (Eisai) are treatments for myelodysplastic syndrome (precursor of acute myelogenous leukemia) that work by demethylating DNA. And results from trials currently underway (Johns Hopkins Medicine) suggest that drugs inhibiting the removal of acetyl groups may be effective in the treatment of lung cancer - an intriguing finding due to the fact that solid tumors are typically harder to treat than blood cancers. This latest chapter in cancer research drives home the point that understanding the cellular mechanisms behind any disease is the key for discovering new treatments.

Why Grapefruit Juice and Certain Medications Don't Mix

Ever notice a warning label on certain prescription medications advising the patient to avoid eating grapefruits or drinking grapefruit juice, and wondered how such a healthful treat could be ill-advised? In February 2012 the FDA issued a consumer report explaining the connection.

Although generally healthy, grapefruits contain certain chemicals that can inhibit key proteins involved in drug metabolism. Depending on which protein is inhibited, the result will either be an increase in blood concentrations of the drug to potentially toxic levels, or a decrease in the amount of medication reaching target tissues.

How can one fruit have such seemingly opposite affects? The first scenario – toxic levels of the drug accumulating in the bloodstream – occurs when metabolism of a particular drug depends on enzymes known as CYP3A4. These enzymes are found in both the small intestine and the liver. Normally, this means that drug metabolism starts even as it is being absorbed through the intestine and into the bloodstream. Grapefruit inhibits the activity of CYP3A4 – resulting in a too-high concentration of the drug entering the patient’s bloodstream. These higher concentrations may result in direct toxicity, or, over time, may result on liver damage, as it forces the liver to work harder to metabolize the drug. Not all drugs rely on these CYP3A4 enzymes for metabolism, which is why not all medications are affected. Scientists have known for some time that the cholesterol-lowering statin drugs such as Zocor and Lipitor are affected by CYP3A4 inhibition; more recent studies indicate grapefruit consumption can affect a longer list of medicines, including those prescribed to treat high blood pressure (Nifediac and Afeditab), depression or anxiey (Zoloft and BuSpar) and erectile dysfunction (Viagara and Cialis).

The second scenario – needed medication not reaching the target cells – results from grapefruit’s inhibition of a type of protein known as a transporter protein – a protein on cellular surfaces which helps molecules to enter cells. Allergy medicine such as Benadryl and Allegra rely in part on these transporter proteins to enter cells; their inhibition results in lower intercellular drug concentrations with a corresponding loss of effectiveness.

So continue to enjoy what remains a healthy treat – but just be sure to read your medication labels first.

Electricity from Bacteria

Each year, wastewater treatment plants use enormous amounts of energy to rid water from our homes and businesses of waste products. Much of this waste is actually organic matter which itself is a form of energy. What if this stored energy could be harnessed as a useful source of power?

Enter the bacterial strain known as Geobacter sulfurreducens. First discovered along the muddy banks of the Potamic River in 1987, Geobacter is capable of producing electricity as a part of its normal metabolism. Since its discovery, it has been modified in the lab to become even more efficient at electricity production. The challenge now at hand is to harness this ability for industrial applications.

One such potential application is wastewater treatment. Because Geobacter works best under anaerobic – no oxygen – environments, it grows well in large sewage-treatment plants – and can actually use the organic matter that makes up sewage waste as an energy source, converting it to carbon dioxide, clean water, and electricity.

Several different research groups, academic and commercial, are working on this problem. The Israeli company Emefcy (the name derives from the initials MFC - microbial fuel cell) reports the ability to produce 1 kilowatt/hour of electricity from 1 kilogram of organic waste. If scaled up successfully, this translates to megawatts of electricity/hour – with clean water produced as a byproduct.

The biotechnology revolution took off in the 1970s when scientists learned how to engineer bacteria to produce human insulin. In the intervening forty years, dozens of lifesaving therapeutics have been produced using these humble organisms. The next forty years may see bacteria play a pivotal role in another revolution – clean energy.

New Imaging Technology Shows Potential As Cancer Diagnostic

New imaging technologies promise the chance for even earlier detection of cellular abnormalities linked to cancer, according to a study recently published in the journal Cancer Research by Vadim Backman of Northwestern University.

Light microscopy traditionally used to detect changes in cell or tissue structure associated with cancer is limited by the wavelength of light – structures that are smaller than the 400 nanometers (one billionth of a meter) cannot be resolved. Partial wave spectroscopic (PWS) microscopy, in contrast, enables this level of resolution. Instead of directly visualizing cell structures as in traditional microscopy, PWS microscopy looks at how light beams interact within a cell – as beams travel through a cell they interact with different structures within the cell. Light beams are reflected off of or absorbed by these structures differently according to differences in the structures’ density. These patterns of light reflection are reconstructed via computer software in order to distinguish the cell’s nanoscale architecture.

This highly sensitive visualization may prove invaluable in detecting subtle changes that may occur in cancer cells long before a tumor is visible. One subtle change that PWS can detect is changes to the structure of chromatin – the complex of DNA and proteins that make up chromosomes. Changes in how tightly the protein portion of chromatin binds to the DNA portion can influence what genes are used, and how often – so it’s not surprising that preliminary research from the Backman lab using PWS to examine seemingly healthy cells from patients with lung cancer show changes in the chromatin structure.

Studies are ongoing to determine if similar changes are detected in other types of cancer cells. PWS is still years away from use as a routine clinical diagnostic, but it may one day offer clinicians an additional cancer screening tool in at-risk patients.

Obesity, Inflammation, and Diabetes

Diabetes is, in the most basic sense, an inability to properly regulate blood glucose levels. The consequences of having chronically high blood glucose can be severe – ranging from circulatory problems to glaucoma, blindness, coma, and death. The diabetic population has rapidly increased over the past few decades, largely due to an increase in the number of Type 2 diabetics. Type 2 diabetes is also known as non-insulin dependent diabetes – their tissues are no longer sensitive to insulin’s cues to absorb blood glucose. Type 1 diabetes is an autoimmune disorder in which the patient’s own immune system destroys the insulin-producing pancreatic beta cells, with symptoms typically appearing in childhood or adolescence. Type 2 diabetes, in contrast, most often occurs in individuals over forty. The exact causes of type 2 diabetes is not known, but it is now well-established within the medical community that obesity significantly increases one’s risk for Type 2 diabetes. But what exactly is the connection?

Various key research studies over the past several years have pointed to one factor: inflammation. In susceptible individuals, the presence of excess fat deposits – obesity – triggers an infiltration of the immune responder cells known as macrophages. In a healthy person, macrophages play a critical role in defending against foreign invaders such as a cold virus. They work by recognizing the foreign invader – for example, a virus-infected cell – and engulfing it, resulting in the pathogen’s destruction. Macrophages also release chemical signals known as cytokines, which serve to activate other immune cells, which in turn release additional cytokines. This sort of immune response is known as the inflammatory response – and under normal circumstances, is a highly efficient and effective mechanism for ridding the body of foreign pathogens, and which dissipates once those pathogens are cleared. However, if this inflammatory response is initiated by fat deposits within an individual’s body, it will not dissipate as long as those fat deposits remain – setting the stage for chronic inflammation.

Why is chronic inflammation problematic? Think back to the last time that you had the flu, or scraped or bumped your knee. In the case of the flu, you probably felt pretty miserable for a week or so, and most likely experienced a fever. A scraped or bumped knee may result in swelling and heat at the site of injury. These symptoms are actually the result of cytokine production and subsequent inflammatory response – necessary to aid in healing, but damaging and uncomfortable if chronic. In the case of diabetes, it is thought that chronic inflammation plays a role in insulin resistance by interfering with insulin’s signaling mechanisms and by damaging the pancreatic beta cells that produce insulin. Some studies also suggest that chronic inflammation may interfere with the actions of the hormone leptin – a key factor in appetite control, thus interfering with the ability to lose excess fat, setting up a vicious cycle.

Several unanswered questions remain, however. Not all obese individuals suffer from chronic inflammation and diabetes. This suggests that there are genetic factors at work as well – some people are predisposed to having an inflammatory response to the systemic stress caused by excess fat. A related observation is that not all type 2 diabetics are obese or even overweight – about twenty percent are normal weight individuals. These normal weight individuals, however, most often also exhibit chronic inflammation.

Current diabetes treatments focus on insulin support therapy for type 1 diabetics, and attempts at increasing insulin sensitivity or modulating the rate at which glucose enters the blood for those with type 2. The next generation of type 2 diabetes will likely target inflammatory pathways. Physicians have known for some time that patients with rheumatoid arthritis (RA) – an inflammatory disease in which the patient’s immune system attacks the body’s flexible joints, resulting in pain, swelling, and restricted movement – were more likely to get type 2 diabetes. A recently published study in the Journal of the American Medical Association reports that RA patients being treated with inhibitors of inflammatory cytokines such as Enbrel, Humira, and Remicade had lower diabetes risk than those using other means to control the disease. Clinical trials are currently underway to directly test the efficacy of Anakira, another ant-inflammatory RA drug, in diabetes management.

Combined with diet and exercise, these new anti-inflammatory
approaches to diabetes management may provide better health to millions of sufferers.