Josh: Dr. Marth brings up some very good points. Many signaling molecules in cells are not just composted of proteins, but may be molecules that are a combination of protein and sugar (glycoprotein) or protein and fatty acid. Fatty acids alone may be signaling molecules, such as fatty acid derived prostanoids via cyclooxygenase (COX) that play a role in pain signaling. Since these molecules are created by enzymes, studying the genome or proteome alone is not sufficient to understand diseases caused or influenced by defects in them.

Why is it that the origins of many serious diseases remain a mystery? In considering that question, a scientist at the University of California, San Diego School of Medicine has come up with a unified molecular view of the indivisible unit of life, the cell, which may provide an answer.

Reviewing findings from multiple disciplines, Jamey Marth, Ph.D., UC San Diego Professor of Cellular and Molecular Medicine and Investigator with the Howard Hughes Medical Institute, realized that only 68 molecular building blocks are used to construct these four fundamental components of cells: the nucleic acids (DNA and RNA), proteins, glycans and lipids. His work, which illustrates the primary composition of all cells, is published in the September issue of Nature Cell Biology.

Like the periodic table of elements, first published in 1869 by Russian chemist Dmitri Mendeleev, is to chemistry, Marth’s visual metaphor offers a new framework for biologists.

This new illustration defines the basic molecular building blocks of life and currently includes 32 glycans (sugar linkages found throughout the cell) and eight kinds of lipids (which compose cell membranes) along with the more well-known 20 amino acids that are used to make proteins and the eight nucleosides that compose the nucleic acids, DNA and RNA.

“These 68 building blocks provide the structural basis for the molecular choreography that constitutes the entire life of a cell,” said Marth. “And two of the four cellular components are produced by these molecular building blocks in processes that cannot be encoded by the genes. These cellular components – the glycans and lipids – may now hold the keys to uncovering the origins of many grievous diseases that continue to evade understanding.”

Currently, the vast majority of medical research looks to the human genome and proteome for answers, but those answers remain elusive, and perhaps for good reason.

“We have now found instances where the pathogenesis of widespread and chronic diseases can be attributed to a change in the glycome, for example, in the absence of definable changes in the genome or proteome,” Marth said, adding that, as biomedical researchers, “we need to begin to cultivate the integration of disciplines in a holistic and rigorous way in order to perceive and most effectively manipulate the biological mechanisms of health and disease.”

“What is important is that no one has composed it and laid it out so clearly before,” said Ajit Varki, M.D., Distinguished Professor of Medicine and Cellular and Molecular Medicine and founder and co-director of the Glycobiology Research and Training Center at UC San Diego School of Medicine, and chief editor of the major textbook in the field, The Essentials of Glycobiology. “Glycobiology, for example, is a relatively new field of study in which researchers at UC San Diego have much expertise, and Dr. Marth’s work further illustrates the importance of these glycan molecules.”

Marth believes that biology should become more integrative both in academic and research settings. “I’m one who believes that we don’t need to sacrifice breadth of knowledge in order to acquire depth of understanding.”

Source: University of California - San Diego

A unified vision of the building blocks of life. Jamey D. Marth. Nature Cell Biology. September 2008 - Vol 10 No 9. doi:10.1038/ncb0908-1015

Josh: I never would have thought that an autoimmune disease could be triggered by a mutation such as this. I suppose many things in biology and medicine are unexpected and don’t work as you would initially expect. Take, for example, the view of how the heart worked before William Harvey published On the Motion of the Heart and Blood in Animals; Galen’s works stated that blood was a nutritive substance that did not flow in a circuit through the body, and that the purpose of the lungs was to cool the blood. Like Harvey’s discovery, I think unexpected causes such as this will be taken much more seriously in the future and lead to a re-writing of text books. It’s unfortunately a common trend for unexpected results or data to be discarded since it doesn’t fit the accepted theory or view.

A security system wired within every cell to detect the presence of rogue viral DNA can sometimes go awry, triggering an autoimmune response to single-stranded bits of the cell’s own DNA, according to a report in the August 22nd issue of the journal Cell, a Cell Press publication. The source of that single-stranded DNA is so-called endogenous retroelements—genetic elements accounting for a substantial portion of the genome that can move to new locations using a “copy and paste” mechanism, according to the researchers.

The new findings help to explain the cause of a rare autoimmune disorder known as Aicardi-Goutieres Syndrome in which infants appear to suffer from an acute viral infection, despite the fact that no virus had ever been found.

“We and others had demonstrated the existence of a DNA detection pathway within cells, but we are still early in our understanding,” said Daniel Stetson of the Howard Hughes Medical Institute and the University of Washington, Seattle. “Our findings offer an important piece of evidence that this pathway is not only very relevant, but it can be the cause of severe autoimmune disease.”

Detection of foreign nucleic acids is an ancient form of host defense, the researchers explained. In vertebrates, nucleic acid detection activates a program of antiviral defense designed to neutralize the spread of infection. This antiviral program is coordinated by type I interferons (IFNs), which direct a multifaceted response to restrict viral replication within infected cells, alert neighboring cells to the presence of infection, and expand white blood cells to provide long-term and specific protection against the virus.

The defense mechanism includes two systems: one consisting of “Toll-like receptors” on specialized, sentinel immune cells that monitor for infection and another that detects viral nucleic acids within the infected cell itself. That internal system includes one arm for detecting RNA and another for detecting DNA.

The biological relevance of those internal DNA sensors remained somewhat mysterious, according to Stetson, because the “nuts and bolts” of the system hadn’t been worked out.

In a screen for proteins relevant to this pathway they call the interferon-stimulatory DNA (ISD) response, the researchers now identify an enzyme known as 3′ repair exonuclease, aka Trex1. In studies of mice, the researchers showed that single-stranded DNA fragments derived from endogenous retroelements accumulate in Trex1-deficient hearts. Those fragments are produced through a process known as reverse transcription in which specialized enzymes copy RNA back into single-stranded DNA. Trex1 usually breaks down reverse-transcribed DNA of those endogenous retroelements, keeping the ISD response in check.

Mutations in the human Trex1 gene were already known to cause Aicardi-Goutieres Syndrome, although the mechanism remained uncertain. The new findings suggest that the syndrome is triggered by an accumulation of reverse-transcribed DNA. “In a sense, it’s an enemy from within,” Stetson said.

A similar mechanism may underlie other immune disorders as well, he added. In fact, other mutations in Trex1 have been linked to an autoimmune disorder called chilblain lupus and are found more frequently in people with systemic lupus erythematosus than in healthy individuals.

The findings also suggest an unanticipated contribution of endogenous retroelements to autoimmunity.

“Just as commensal bacteria outnumber our own cells by four or five orders of magnitude, endogenous retroelements outnumber our genes by at least 100-fold,” the researchers concluded. “Both have the potential to be detected by the immune system and cause autoimmune disease. Therefore, specific mechanisms evolved to prevent this, and Trex1 represents the first example of a mechanism to prevent autoimmunity caused by endogenous retroelements.”

Source: Cell Press

Trex1 Prevents Cell-Intrinsic Initiation of Autoimmunity. Daniel B. Stetson, Joan S. Ko, Thierry Heidmann, and Ruslan Medzhitov. Cell. August 22, 2008: 134 (4)

Josh: We must remember that not all inherited diseases are genetic in origin. Not only does the “genetic code”, the sequence of A, G, C, and T, matter but so do other modifications to that code. Examples are DNA methylation and histone modification.

A new study in the September issue of the Journal of Lipid Research suggests an unusual form of inheritance may have a role in the rising rate of diabetes, especially in children and young adults, in the United States.

DNA is the primary mechanism of inheritance; kids get half their genes from mom and half from dad. However, scientists are just starting to understand additional kinds of inheritance like metabolic programming, which occurs when an insult during a critical period of development, either in the womb or soon after birth, triggers permanent changes in metabolism.

In this study, the researchers looked at the effects of a diet high in saturated fat on mice and their offspring. As expected, they found that a high-fat diet induced type 2 diabetes in the adult mice and that this effect was reversed by stopping the diet.

However, if female mice continued a high-fat diet during pregnancy and/or suckling, their offspring also had a greater frequency of diabetes development, even though the offspring were given a moderate-fat diet. These mice were then mated with healthy mice, and the next generation offspring (grandchildren of the original high-fat fed generation) could develop diabetes as well.

In effect, exposing a fetal mouse to high levels of saturated fats can cause it and its offspring to acquire diabetes, even if the mouse goes off the high-fat diet and its young are never directly exposed.

The study used mice so it’s not time to warn women to eat differently during pregnancy and breastfeeding but earlier research has shown that this kind of inheritance is at work in humans. For example, there is an increased risk of hypertension and cardiovascular disease in children born of malnourished mothers.

Source: American Society for Biochemistry and Molecular Biology

“Effects of High Fat Diet Exposure During Fetal Life on Type 2 Diabetes Development in the Progeny”. Donatella Gniuli, Alessandra Calcagno, Maria Emiliana Caristo, Alessandra Mancuso, Veronica Macchi, Geltrude Mingrone, and Roberto Vettor. Journal of Lipid Research, Vol. 49, 1936-1945, September 2008

Josh: This is an extremely high penetrance mutation. More doctors and physicians need to be trained to order genetic tests for mutations such as this for their patients, especially those with a family history of colorectal cancer. If someone has this mutation, chances are they are going to get colorectal cancer, so routine screenings may be enough to save their life…preventative medicine at its best.

About one-third of colorectal cancers are inherited, but the genetic cause of most of these cancers is unknown. The genes linked to colorectal cancer account for less than 5 percent of all cases.

Scientists at Northwestern University’s Feinberg School of Medicine and colleagues have discovered a genetic trait that is present in 10 to 20 percent of patients with colorectal cancer. The findings strongly suggest that the trait is a major contributor to colorectal cancer risk and likely the most common cause of colorectal cancer to date.

If a person inherits this trait — which is dominant and clusters in families — the study found the lifetime risk of developing colorectal cancer is 50 percent, compared to 6 percent for the general population. The study will be published August 14 in an advanced on-line report in the journal Science.

“This probably accounts for more colorectal cancers than all other gene mutations discovered thus far,” said Boris Pasche, M.D., a lead author of the paper and director of the Cancer Genetics Program at the Feinberg School and the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. Pasche also is a physician at Northwestern Memorial Hospital.

“The reasonable expectation is this finding will save some lives,” Pasche said. “We will be able to identify a larger number of individuals that are at risk of colorectal cancer and, in the long term, maybe decrease the cases of colorectal cancer and of people dying from it by being able to screen them more frequently.”

Colorectal cancer is the second leading cause of cancer death in the U.S.

The trait, which has been named TGFBR1 ASE, results in decreased production of a key receptor for TGF-beta, the most potent inhibitor of cell growth. With less of this vital protective substance to inhibit cell growth, colon cancer can more easily develop.

In 1998, Pasche and colleagues discovered the first mutation of this gene and in 1999 they showed that it was linked to a higher risk of colorectal cancer.

The results presented in this new study are the first to show that decreased production of this receptor for TGF-beta was present in 10 to 20 percent of patients with colorectal cancer. Decreased production of the same receptor was present in only 1 to 3 percent in healthy control groups.

The findings, which are based on a Caucasian population, need to be confirmed in other studies and may show strong variation between ethnic groups, Pasche said.

Pasche expects that a clinical test will soon be developed that could be offered to families with a history of colorectal cancer and other individuals to determine whether they carry this mutation.

Source: Northwestern University

Germline Allele-specific Expression of TGFBR1 Confers an Increased Risk of Colorectal Cancer. Laura Valle, Tarsicio Serena-Acedo, Sandya Liyanarachchi, Heather Hampel, Ilene Comeras, Zhongyuan Li, Qinghua Zeng, Hong-Tao Zhang, Michael J. Pennison, Maureen Sadim, Boris Pasche, Stephan M. Tanner, and Albert de la Chapelle. Science. Published online August 14 2008; 10.1126/science.1159397 (Science Express Reports)

Josh: This is certainly an interesting study. I suppose the primary question I have is why do cells decrease the expression of the lysosomal receptors with age? Knowing that would be helpful, I think not only for aging and neurodegenerative research, but also for cancer research. Too bad this won’t really be a realistic treatment in its current state…however, perhaps a drug could be used to increase expression.

As people age, their cells become less efficient at getting rid of damaged protein — resulting in a buildup of toxic material that is especially pronounced in Alzheimer’s, Parkinson’s disease, and other neurodegenerative disorders.

Now, for the first time, scientists at the Albert Einstein College of Medicine of Yeshiva University have prevented this age-related decline in an entire organ — the liver — and shown that, as a result, the livers of older animals functioned as well as they did when the animals were much younger. Published in the online edition of Nature Medicine, these findings suggest that therapies for boosting protein clearance might help stave off some of the declines in function that accompany old age. The study’s senior author was Dr. Ana Maria Cuervo, associate professor in the departments of developmental & molecular biology, medicine and anatomy & structural biology at Einstein.

The cells of all organisms have several surveillance systems designed to find, digest and recycle damaged proteins. Many studies have documented that these processes become less efficient with age, allowing protein to gradually accumulate inside cells. But aging researchers continue debating whether this protein buildup actually contributes to the functional losses of aging or instead is merely associated with those losses. The Einstein study was aimed at resolving the controversy.

One of these surveillance systems — responsible for handling 30 percent or more of damaged cellular protein — uses molecules known as chaperones to seek out damaged proteins. After finding such a protein, the chaperone ferries it towards one of the cell’s many lysosomes — membrane-bound sacs filled with enzymes. When the chaperone and its cargo “dock” on a receptor molecule on the lysosome’s surface, the damaged protein is drawn into the lysosome and rapidly digested by its enzymes.

In previous work, Dr. Cuervo found that the chaperone surveillance system, in particular, becomes less efficient as cells become older, resulting in a buildup of undigested proteins within the cells. She also detected the primary cause for this age-related decline: a fall-off in the number of lysosomal receptors capable of binding chaperones and their damaged proteins. Could replenishing lost receptors in older animals maintain the efficiency of this protein-removal system throughout an animal’s lifespan and, perhaps, maintain the function of the animal’s cells and organs as well?

To find out, Dr. Cuervo created a transgenic mouse model equipped with an extra gene — one that codes for the receptor that normally declines in number with increasing age. Another genetic manipulation allowed Dr. Cuervo to turn on this extra gene only in the liver and at a time of her choosing, merely by changing the animals’ diet.

To keep the level of the receptor constant throughout life, Dr. Cuervo waited until mice were six months old (the age that the chaperone system’s efficiency begins to decline) before turning on the added receptor gene. When the mice were examined at 22 to 26 months of age (equivalent to approximately 80 years old in humans), the liver cells of transgenic mice digested and recycled protein far more efficiently than in their normal counterparts of the same age — and, in fact, just as efficiently as in normal six-month old mice.

Does maintaining efficient protein clearance in liver cells of an older animal translate into better functioning for the liver as a whole? Since a key function of the liver is metabolizing chemicals, Dr. Cuervo answered this question by injecting a muscle relaxant into very old transgenic mice and very old normal mice. The very old transgenic mice metabolized the muscle relaxant much more quickly than very old normal mice and at a rate comparable to young normal mice.

“Our study showed that functions can be maintained in older animals so long as damaged proteins continue to be efficiently removed — strongly supporting the idea that protein buildup in cells plays an important role in aging itself,” says Dr. Cuervo. “Even more important, these results show that it’s possible to correct this protein ‘logjam’ that occurs in our cells as we get older, thereby perhaps helping us to enjoy healthier lives well into old age.”

Dr. Cuervo next plans to study animal models of Alzheimer’s, Parkinson’s and other neurodegenerative brain diseases to see whether maintaining efficient protein clearance in the brain might help in treating them. “Most people with these conditions are born with a mutation that gives rise to defective proteins, but they don’t experience symptoms until later in life,” says Dr. Cuervo. “We think that’s because their protein-clearance systems can handle abnormal proteins when the person is younger but get overwhelmed as their efficiency falls with age. By preventing this decline in protein clearance, we may be able to keep these people free of symptoms for a longer time.”

Dr. Cuervo will also investigate whether maintaining efficient protein clearance in all the body’s tissues will influence longevity and prevent the functional losses associated with growing old. “There’s reason to hope that drugs exerting a similar effect throughout the body may help us enjoy healthier lives well into old age,” says Dr. Cuervo. Meanwhile, she notes, evidence is mounting that two dietary interventions —low-fat and calorie-restricted diets — help cells to maintain efficient protein clearance.

Source : Albert Einstein College of Medicine

Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function. Cong Zhang & Ana Maria Cuervo. Nature Medicine. Published online: 10 August 2008; | doi:10.1038/nm.1851

Josh: We must remember that many genetic diseases are not caused by mutations in nuclear DNA, but are the result of mutations in mitochondrial DNA. The press release makes mention that the number of cells with mitochondrial mutations often determines the severity of disease; I assume this refers to the ratio of normal:mutant mitochondria within a cell. Remember, the egg had more than a single mitochondrion, and they may or may not all be genetically identical. When more mitochondria are produced in a cell, they may not all replicate at an even rate.

Researchers at the University of Newcastle, England, and the Virginia Bioinformatics Institute at Virginia Tech in the United States have revealed a large reservoir of mitochondrial DNA mutations present in the general population. Clinical analysis of blood samples from almost 3,000 infants born in north Cumbria, England, showed that at least 1 in 200 individuals in the general public harbor mitochondrial DNA mutations that may lead to disease. The findings, which highlight the need to develop new approaches to prevent the transmission of mitochondrial diseases, were published in The American Journal of Human Genetics.

Mitochondria, the “engines” present in each cell that produce adenosine triphosphate, are passed from mother to offspring. Mutations in mitochondrial DNA inherited from the mother may cause mitochondrial diseases that include muscle weakness, diabetes, stroke, heart failure, or epilepsy. In almost all mitochondrial diseases caused by mutant mitochondrial DNA, the patient’s cells will contain a mixture of mutant and normal mitochondrial DNA. The proportion of mutant mitochondrial DNA in most cases determines the severity of disease.

Previous estimates from epidemiological studies suggested that mitochondrial diseases affect as many as one person in 5,000. However, the incidence of new mitochondrial mutations and the prevalence of those carrying these mutations were never fully established due to limitations in the methods used. Most of the earlier estimates of the frequency of mitochondrial DNA mutations in the general population, for example, have depended on identification of clinically affected patients and subsequent retracing of inheritance on the maternal side of the family. This approach fails to detect the gradual accumulation of mutations in some members of the population, including those individuals who harbor mitochondrial DNA mutations but who otherwise do not show the symptoms of disease.

Dr. David Samuels, Assistant Professor at the Virginia Bioinformatics Institute and an author on this study, commented: “We know from many clinical studies of patients and their families that our cells can tolerate a rather large amount of mutant mitochondrial DNA with no significant loss of function. From that observation we have suspected that there may be a large number of people in the general population who carry pathogenic mitochondrial DNA mutations, but who are not obviously ill with a mitochondrial disease. This study gives us, for the first time, a measurement of the number of these carriers of pathogenic mitochondrial DNA mutations in the general population. One in every 200 individuals is a lot of people – around 1.5 million people in the United States alone. ”

The scientists looked at 10 mitochondrial DNA mutations (arising from single nucleotide replacements) often found in patients with mitochondrial disease. By taking advantage of a high-throughput genotyping system that uses mass spectrometry measurements, the researchers were able to detect mutated mitochondrial DNA at high sensitivity. In each positive case, DNA cloning and sequencing were used to confirm the findings. By looking at differences in tissue samples from mother and child, the researchers were also able to estimate the rate at which new DNA mutations had arisen in the population. The incidence of new mutations was close to 100 for every 100, 000 live births.

Dr. Samuels commented: “These new clinical measurements have given direct evidence for the widespread incidence of pathogenic mitochondrial DNA mutations in the human population. These findings emphasize the pressing need to develop effective ways to interrupt the transmission of these mutations to the next generation.”

Source: Virginia Tech

Hannah R. Elliott, David C. Samuels, James A. Eden, Caroline L. Relton, Patrick F. Chinnery (2008) Pathogenic mitochondrial DNA mutations are common in the general population. American Journal of Human Genetics 83(2): 254-260. doi:10.1016/j.ajhg.2008.07.004

My first paper just got published in this month’s issue of the Journal of Clinical Microbiology. We, primarily researchers at Children’s Hospital of Pittsburgh, developed an assay using a technique called Loop Mediated Isothermal Amplification (LAMP) to identify E. coli in a sample, ranging from blood to urine, without the need to first extract the DNA or to use a PCR machine. Rather, a sample can be added directly to a reaction mixture and heated on a heating block for 30-60 minutes. The sample will change color and fluoresce under UV light, allowing a positive result to be quickly and easily identified. We hope that this technique can be used in out patient clinics and clinics in developing countries to identify E. coli infections such as a UTI (urinary tract infection).

Further research is currently being conducted to develop these rapid tests for other infectious agents and bring them into clinical use.

Hill et al. Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains of Escherichia coli. Journal of Clinical Microbiology. 46 (8): 2800. (2008)

Kevin: Myostatin inhibitors are going to be extremely useful drugs once they reach the marketplace. Other uses include farming animals with more meat and treating muscular dystrophy, plus a very large potential market of people who want more muscle without having to exercise.

Inhibiting a growth factor that keeps muscles from getting too big may optimize recovery of injured soldiers, researchers say.

They are studying two myostatin inhibitors in mice with limb injuries, first to see which works best and then to identify the best delivery mechanism, says Dr. Mark Hamrick, bone biologist in the Medical College of Georgia Schools of Graduate Studies and Medicine.

“Fifty to 60 percent of the injuries occurring in Iraq are to the limbs, and the average injury requires five surgeries,” Dr. Hamrick says. “Myostatin inhibitors are known to improve muscle regeneration and we have evidence that they also increase bone formation. We believe these inhibitors will result in a stronger, more rapid recovery for these soldiers and other victims of traumatic limb injuries.”

A $1.2 million grant from the Office of Naval Research to Dr. Hamrick is enabling laboratory studies of two experimental myostatin inhibitors: a decoy receptor and a binding protein, both developed by MetaMorphix, Inc. of Beltsville, Md. Both inhibitors have been shown effective in muscle regeneration, but this is the first trial that looks at their impact on bone. … Continue Reading »