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Endothelial Function and Cardiovascular Disease

Pathologist and AuthorLarry H Bernstein, MD, FCAP 

 

This discussion is a continuation of a series on Nitric Oxide, vascular relaxation, vascular integrity, and systemic organ dysfunctions related to inflammatory and circulatory disorders. In some of these, the relationships are more clear than others, and in other cases the vascular disorders are aligned with serious metabolic disturbances. This article, in particular centers on the regulation of NO production, NO synthase, and elaborates more on the assymetrical dimethylarginine (ADMA) inhibition brought up in a previous comment, and cardiovascular disease, including:

Recall, though, that in SIRS leading to septic shock, that there is a difference between the pulmonary circulation, the systemic circulation and the portal circulation in these events. The comment calls attention to:
Böger RH. Asymmetric dimethylarginine, an endogenous inhibitor of nitric oxide synthase, explains the ‘L-arginine paradox’ and acts as a novel cardiovascular risk factor. J Nutr 2004; 134: 2842S–7S.

This observer points out that ADMA inhibits vascular NO production at concentrations found in pathophysiological conditions (i.e., 3–15 μmol/l); ADMA also causes local vasoconstriction when it is infused intra-arterially. ADMA is increased in the plasma of humans with hypercholesterolemia, atherosclerosis, hypertension, chronic renal failure, and chronic heart failure.

Increased ADMA levels are associated with reduced NO synthesis as assessed by impaired endothelium-dependent vasodilation. We’ll go into that more with respect to therapeutic targets – including exercise, sauna, and possibly diet, as well as medical drugs.

It is remarkable how far we have come since the epic discovery of 17th century physician, William Harvey, by observing the action of the heart in small animals and fishes, proved that heart receives and expels blood during each cycle, and argued for the circulation in man. This was a huge lead into renaissance medicine. What would he think now?

Key Words: eNOS, NO, endothelin, ROS, oxidative stress, blood flow, vascular resistance, cardiovascular disease, chronic renal disease, hypertension, diabetes, atherosclerosis, MI, exercise, nutrition, traditional chinese medicine, statistical modeling for targeted therapy.

Endothelial Function
The endothelium plays a crucial role in the maintenance of vascular tone and structure by means of eNOS, producing the endothelium-derived vasoactive mediator nitric oxide (NO), an endogenous messenger molecule formed in healthy vascular endothelium from the amino acid precursor L-arginine. Nitric oxide synthases (NOS) are the enzymes responsible for nitric oxide (NO) generation. The generation and actions of NO under physiological and pathophysiological conditions are exquisitely regulated and extend to almost every cell type and function within the circulation. While the molecule mediates many physiological functions, an excessive presence of NO is toxic to cells.

The enzyme NOS, constitutively or inductively, catalyses the production of NO in several biological systems. NO is derived not only from NOS isoforms but also from NOS-independent sources. In mammals, to date, three distinct NOS isoforms have been identified:

  1. neuronal NOS (nNOS),
  2. inducible NOS (iNOS), and
  3. endothelial NOS (eNOS).

The molecular structure, enzymology and pharmacology of these enzymes have been well defined, and reveal critical roles for the NOS system in a variety of important physiological processes. The role of NO and NOS in regulating vascular physiology, through neuro-hormonal, renal and other non-vascular pathways, as well as direct effects on arterial smooth muscle, appear to be more intricate than was originally thought.

Vallance et al. described the presence of asymmetric dimethylarginine (ADMA) as an endogenous inhibitor of eNOS in 1992. Since then, the role of this molecule in the regulation of eNOS has attracted increasing attention.
Endothelins are 21-amino acid peptides, which are active in almost all tissues in the body. They are potent vasoconstrictors, mediators of cardiac, renal, endocrine and immune functions and play a role in bronchoconstriction, neurotransmitter regulation, activation of inflammatory cells, cell proliferation and differentiation.

Endothelins were first characterised by Yanagisawa et al. (1988). The three known endothelins ET-1, -2 and -3 are structurally similar to sarafotoxins from snake venoms. ET-1 is the major isoform generated in blood vessels and appears to be the isoform of most importance in the cardiovascular system with a major role in the maintenance of vascular tone.

The systemic vascular response to hypoxia is vasodilation. However, reports suggest that the potent vasoconstrictor endothelin-1 (ET-1) is released from the vasculature during hypoxia. ET-1 is reported to augment superoxide anion generation and may counteract nitric oxide (NO) vasodilation. Moreover, ET-1 was proposed to contribute to increased vascular resistance in heart failure by increasing the production of asymmetric dimethylarginine (ADMA).

A study investigated the role of ET-1, the NO pathway, the potassium channels and radical oxygen species in hypoxia-induced vasodilation of large coronary arteries and found NO contributes to hypoxic vasodilation, probably through K channel opening, which is reversed by addition of ET-1 and enhanced by endothelin receptor antagonism. These latter findings suggest that endothelin receptor activation counteracts hypoxic vasodilation.

Endothelial dysfunction
Patients with Raynaud’s Phemonenon had abnormal vasoconstrictor responses to cold pressor tests (CPT) that were similar in primary and secondary RP. There were no differences in median flow-mediated and nitroglycerin mediated dilation or CPT of the brachial artery in the 2 populations. Patients with secondary RP were characterized by abnormalities in microvascular responses to reactive hyperemia, with a reduction in area under the curve adjusted for baseline perfusion, but not in time to peak response or peak perfusion ratio.

Plasma ET-1, ADMA, VCAM-1, and MCP-1 levels were significantly elevated in secondary RP compared with primary RP. There was a significant negative correlation between ET-1 and ADMA values and measures of microvascular perfusion but not macrovascular endothelial function. Secondary RP is characterized by elevations in plasma ET-1 and ADMA levels that may contribute to alterations in cutaneous microvascular function.

ADMA inhibits vascular NO production within the concentration range found in patients with vascular disease. ADMA also causes local vasoconstriction when infused intra-arterially, and increases systemic vascular resistance and impairs renal function when infused systemically. Several recent studies have supplied evidence to support a pathophysiological role of ADMA in the pathogenesis of vascular dysfunction and cardiovascular disease. High ADMA levels were found to be associated with carotid artery intima-media-thickness in a study with 116 clinically healthy human subjects. Taking this observation further, another study performed with hemodialysis patients reported that ADMA prospectively predicted the progression of intimal thickening during one year of follow-up.

In a nested, case-control study involving 150 middle-aged, non-smoking men, high ADMA levels were associated with a 3.9-fold elevated risk for acute coronary events. Clinical and experimental evidence suggests elevation of ADMA can cause a relative L-arginine deficiency, even in the presence of “normal” L-arginine levels. As ADMA is a competitive inhibitor of eNOS, its inhibitory action can be overcome by increasing the concentration of the substrate, L-arginine. Elevated ADMA concentration is one possible explanation for endothelial dysfunction and decreased NO production in these diseases.
Metabolic Regulation of L-arginine and NO Synthesis 
Methylation of arginine residues within proteins or polypeptides occurs through N-methyltransferases, which utilize S-adenosylmethionine as a methyl donor. After proteolysis of these proteins or polypeptides, free ADMA is present in the cytoplasm. ADMA can also be detected in circulating blood plasma. ADMA acts as an inhibitor of eNOS by competing with the substrate of this enzyme, L-arginine. The ensuing reduction in nitric oxide synthesis causes vascular endothelial dysfunction and, subsequently, atherosclerosis. ADMA is eliminated from the body via urinary excretion and via metabolism by the enzyme DDAH to citrulline and dimethylamine.
Supplementation with L-arginine in animals with experimentally-induced vascular dysfunction atherosclerosis improves endothelium-dependent vasodilation. Moreover, L-arginine supplementation results in enhanced endothelium-dependent inhibition of platelet aggregation, inhibition of monocyte adhesion, and reduced vascular smooth muscle proliferation. One mechanism that explains the occurrence of endothelial dysfunction is the presence of elevated blood levels of asymmetric dimethylarginine (ADMA) – an L-arginine analogue that inhibits NO formation and thereby can impair vascular function. Supplementation with L-arginine has been shown to restore vascular function and to improve the clinical symptoms of various diseases associated with vascular dysfunction.

Beneficial Effects of L-Arginine

  • Angina
  • Congestive Heart Failure
  • Hypertension
  • Erectile dysfunction
  • Sickle Cell Disease and Pulmonary Hypertension

The ratio of L-arginine to ADMA is considered to be the most accurate measure of eNOS substrate availability. This ratio will increase during L-arginine supplementation, regardless of initial ADMA concentration. Due to the pharmacokinetics of oral L-arginine and the positive results from preliminary studies, it appears supplementation with a sustained-release L-arginine preparation will achieve positive therapeutic results at lower dosing levels.

Many prospective clinical trials have shown that the association between elevated ADMA levels and major cardiovascular events and total mortality is robust and extends to diverse patient populations. However, we need to define more clearly in the future who will profit from ADMA determination, in order to use this novel risk marker as a more specific diagnostic tool.
Elimination of ADMA by way of DDAH
Asymmetric dimethylarginine (ADMA) and monomethyl arginine (L-NMMA) are endogenously produced amino acids that inhibit all three isoforms of nitric oxide synthase (NOS). ADMA accumulates in various disease states, including renal failure, diabetes and pulmonary hypertension, and its concentration in plasma is strongly predictive of premature cardiovascular disease and death. Both LNMMA and ADMA are eliminated largely through active metabolism by dimethylarginine dimethylaminohydrolase (DDAH) and thus DDAH dysfunction may be a crucial unifying feature of increased cardiovascular risk. These investigators ask whether ADMA is the underlying issue related to the pathogenesis of the vascular disorder.
They identified the structure of human DDAH-1 and probed the function of DDAH-1 both by deleting the Ddah1 gene in mice and by using DDAH-specific inhibitors that is shown by crystallography, bind to the active site of human DDAH-1. The loss of DDAH-1 activity leads to accumulation of ADMA and reduction in NO signaling. This in turn causes vascular pathophysiology, including endothelial dysfunction, increased systemic vascular resistance and elevated systemic and pulmonary blood pressure. The results suggest that DDAH inhibition could be harnessed therapeutically to reduce the vascular collapse associated with sepsis.
Methylarginines are formed when arginine residues in proteins are methylated by the action of protein arginine methyltransferases (PRMTs), and free methylarginines are liberated following proteolysis. Clear demonstration of an effect of endogenous ADMA and L-NMMA on cardiovascular physiology would be of importance, not only because of the implications for disease, but also because it would expose a link between post-translational modification of proteins and signaling through a proteolytic product of these modified proteins.
Which is it? ADMA or DDHA: Intrusion of a Genetic alteration.
The study showed that loss of DDAH expression or activity causes endothelial dysfunction, we believe that DDAH inhibition could potentially be used therapeutically to limit excessive NO production, which can have pathological effects. They then showed treated cultured isolated blood vessels with lipopolysaccharide (LPS) induced expression of the inducible isoform of NO synthase (iNOS) and generated high levels of NO, which were blocked by the iNOS-selective inhibitor 1400W and by DDAH inhibitors. Treatment of isolated blood vessels with DDAH inhibitors significantly increased ADMA accumulation in the culture medium. Treatment of isolated blood vessels with bacterial LPS led to the expected hyporeactivity to the contractile effects of phenylephrine, which was reversed by treatment with a DDAH inhibitor. The effect of the DDAH inhibitor was large and stereospecific, and was reversed by the addition of L-arginine.
In conclusion, genetic and chemical-biology approaches provide compelling evidence that loss of DDAH-1 function results in increased ADMA concentrations and thereby disrupts vascular NO signaling. A broader implication of this study is that post-translational methylation of arginine residues in proteins may have downstream effects by affecting NO signaling upon hydrolysis and release of the free methylated amino acid. This signaling pathway seems to have been highly conserved through evolution.

The crucial role of nitric oxide (NO) for normal endothelial function is well known. In many conditions associated with increased risk of cardiovascular diseases such as hypercholesterolemia, hypertension, abdominal obesity, diabetes and smoking, NO biosynthesis is dysregulated, leading to endothelial dysfunction. The growing evidence from animal and human studies indicates that endogenous inhibitors of endothelial NO synthase such as asymmetric dimethylarginine (ADMA) and NG-monomethyl-L-arginine (L-NMMA) are associated with the endothelial dysfunction and potentially regulate NO synthase.

Nitric Oxide Synthase

Asymmetric dimethylarginine (ADMA) is one of three known endogenously produced circulating methylarginines (i.e. ADMA, NG-monomethyl-L-arginine (L-NMMA) and symmetrically methylated NG, NG-dimethyl-L-arginine). ADMA is formed by the action of protein arginine methyltransferases that methylate arginine residues in proteins and after which free ADMA is released. ADMA and L-NMMA can competitively inhibit NO elaboration by displacing L-arginine from NO synthase (NOS). The amount of methylarginines is related to overall metabolic activity and the protein turnover rate of cells. Although methylarginines are excreted partly by the kidneys, the major route of elimination of ADMA in humans is metabolism by the dimethylarginine dimethylaminohydrolase enzymes[ dimethylarginine dimethylaminohydrolase-1 and -2 (DDAH)] enzymes. Inhibition of DDAH leads to the accumulation of ADMA and consequently to inhibition of NO-mediated endothelium dependent relaxation of blood vessels.
The potential role of ADMA in angina pectoris has been evaluated by Piatti and co-workers, who reported ADMA levels to be higher in patients with cardiac syndrome X (angina pectoris with normal coronary arteriograms) than in controls. According to preliminary results from the CARDIAC (Coronary Artery Risk Determination investigating the influence of ADMA Concentration) study, patients with coronary heart disease (n 816) had a higher median ADMA plasma concentration than age and sex matched controls (median 0.91 vs. 0.70 mol/l; p 0.0001). Further, in a prospective Chinese study, a high plasma ADMA level independently predicted subsequent cardiovascular adverse events (cardiovascular death, myocardial infarction, and repeated revascularization of a target vessel).

Protein detoxification pathway.

Protein detoxification pathway. (Photo credit: Wikipedia)

There are only few published findings concerning variations in human DDAH. However, polymorphisms in other genes potentially related to risk factors for endothelial dysfunction and cardiovascular events have been studied. Reduced NO synthesis has been implicated in the development of atherosclerosis. For example, there are some functionally important variants of the NOS that could affect individual vulnerability to atherosclerosis by changing the amount of NO generated by the endothelium.
There are probably several functional variations in genes coding DDAH enzymes in different populations. Some of them could confer protection against the harmful effects of elevated ADMA and others impair enzyme function causing accumulation of ADMA in cytosol and/or blood.
In a study of 16 men with either low or high plasma ADMA concentrations were screened to identify DDAH polymorphisms that could potentially be associated with increased susceptibility to cardiovascular diseases. In that study a novel functional mutation of DDAH-1 was identified; the mutation carriers had a significantly elevated risk for cardiovascular disease and a tendency to develop hypertension. These results confirmed the clinical role of DDAH enzymes in ADMA metabolism. Furthermore, it is possible that more common variants of DDAH genes contribute more widely to increased cardiovascular risk.
We found a rare variation in the DDAH-1 gene, which is associated with elevated plasma concentrations of ADMA in heterozygous mutation carriers. There was also an increased prevalence of CHD and a tendency to hypertension among individuals with this DDAH-1 mutation. These observations highlight the importance of ADMA as a possible risk factor and emphasize the essential role of DDAH in regulating ADMA levels.

ADMA Elevation and Coronary Artery Disease
Endothelial dysfunction may be considered as a systemic disorder and involves different vascular beds. Coronary endothelial dysfunction (CED) precedes the development of coronary. Endothelial dysfunction is characterized by a reduction in endogenous nitric oxide (NO) activity, which may be accompanied by elevated plasma asymmetric dimethylarginine (ADMA) levels. ADMA is a novel endogenous competitive inhibitor of NO synthase (NOS), an independent marker for cardiovascular risk.

English: Structure of asymmetric dimethylargin...

English: Structure of asymmetric dimethylarginine; ADMA; N,N-Dimethylarginine Deutsch: Asymmetrisches Dimethylarginin; N,N-Dimethyl-L-arginin; Guanidin-N,N-dimethylarginin (Photo credit: Wikipedia)

In a small study fifty-six men without obstructive coronary artery disease (CAD) who underwent coronary endothelial function testing were studied. Men with CED had significant impairment of erectile function (P ¼ 0.008) and significantly higher ADMA levels (0.50+0.06 vs. 0.45+0.07 ng/mL, P ¼ 0.017) compared with men with normal endothelial function. Erectile function positively correlated with coronary endothelial function. This correlation was independent of age, body mass index, high-density lipoprotein, C-reactive protein, homeostasis model assessment of insulin resistance index, and smoking status, suggesting that CED is independently associated with ED and plasma ADMA concentration in men with early coronary atherosclerosis.

ADMA and Chronic Renal Failure in Hepatorenal Syndrome
The concentration of SDMA was significantly higher in the patients with HRS compared to the patients without HRS and it was also higher than the values obtained from the healthy participants (1.76 ± 0.3 μmol/L; 1.01 ± 0.32 and 0.520 ± 0.18 μmol/L, respectively; p < 0.01). The concentrations of ADMA were higher in the cirrhotic patients with HRS than in those without this serious complication of cirrhosis. The concentration of ADMA in all the examined cirrhotic patients was higher than those obtained from healthy volunteers (1.35 ± 0.27 μmol/L, 1.05 ± 0.35 μmol/L and 0.76 ± 0.21 μmol/L, respectively). In the patients with terminal alcoholic liver cirrhosis, the concentrations
of ADMA and SDMA correlated with the progress of cirrhosis as well as with the development of cirrhosis complications. In the patients with HRS there was a positive correlation between creatinine and SDMA in plasma (r2 = 0.0756, p < 0.001) which was not found between creatinine and ADMA. The results demonstrate that the increase in SDMA concentration is proportionate to the progression of chronic damage of the liver and kidneys. Increased ADMA concentration can be a causative agent of renal insufficiency in patients with cirrhosis.

In patients with cirrhosis, ADMA, as well as SDMA could be markers for kidney insufficiency development. Accumulation of ADMA in plasma causes kidney
vasoconstriction and thereby retention of SDMA. Considering that ADMA has several damaging effects, it can be concluded that modulation of the activity of enzyme which participates in ADMA catabolism may represent a new therapeutic goal which is intended to reduce the progress of liver and kidney damage and thus the development of HRS.

ADMA Therapeutic Targets
Elevated plasma concentrations of the endogenous nitric oxide synthase
inhibitor asymmetric dimethylarginine (ADMA) are found in various clinical settings, including

  • renal failure,
  • coronary heart disease,
  • hypertension,
  • diabetes and
  • preeclampsia.

In healthy people acute infusion of ADMA promotes vascular dysfunction,
and in mice chronic infusion of ADMA promotes progression of atherosclerosis.
Thus, ADMA may not only be a marker but also an active player in cardiovascular disease, which makes it a potential target for therapeutic interventions.

This review provides a summary and critical discussion of the presently available data concerning the effects on plasma ADMA levels of cardiovascular drugs, hypoglycemic agents, hormone replacement therapy, antioxidants, and vitamin supplementation.
We assess the evidence that the beneficial effects of drug therapies on vascular function can be attributed to modification of ADMA levels. To develop more specific ADMA-lowering therapies, mechanisms leading to elevation of plasma ADMA concentrations in cardiovascular disease need to be better understood.

ADMA is formed endogenously by degradation of proteins containing arginine residues that have been methylated by S-adenosylmethionine-dependent methyltransferases (PRMTs). There are two major routes of elimination: renal excretion and enzymatic degradation by the dimethylarginine dimethylaminohydrolases (DDAH-1 and -2).

Oxidative stress causing upregulation of PRMT expression and/or attenuation of DDAH activity has been suggested as a mechanism and possible drug target in clinical conditions associated with elevation of ADMA. As impairment of DDAH activity or capacity is associated with substantial increases in plasma ADMA concentrations, DDAH is likely to emerge as a prime target for specific therapeutic interventions.

Cardiovascular diseases (CVD) in diabetic patients have endothelial dysfunction as a key pathogenetic event. Asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase (NOS), plays a pivotal role in endothelial dysfunction. Different natural polyphenols have been shown to preserve endothelial function and prevent CVD. Another study assessed the effect of silibinin, a widely used flavonolignan from milk thistle, on ADMA levels and endothelial dysfunction in db/db mice.

Plasma and aorta ADMA levels were higher in db/db than in control lean mice. Silibinin administration markedly decreased plasma ADMA; consistently, aorta ADMA was reduced in silibinin-treated animals. Plasma and aorta ADMA levels exhibited a positive correlation, whereas liver ADMA was inversely correlated with both plasma and aorta ADMA concentrations. Endothelium-(NO)-dependent vasodilatation to ACh was impaired in db/db mice and was restored in the silibinin group, in accordance with the observed reduction of plasma and vascular levels of ADMA. Endothelium-independent vasodilatation to SNP was not modified by silibinin administration.

Endothelin Inhibitors
Endothelins are potent vasoconstrictors and pressor peptides and are important mediators of cardiac, renal andendocrine functions. Increased ET-1 levels in disease states such as congestive heart failure, pulmonary hypertension, acute myocardial infarction, and renal failure suggest the endothelin system as an attractive target for pharmacotherapy. A non-peptidic, selective, competitive endothelin receptor antagonist with an affinity for the ETA receptor in the subnanomolar range was administered by continuous intravenous infusion to beagle dogs, rats, and Goettingen minipigs. It caused mild arteriopathy characterised by segmental degeneration in the media of mid- to large-size coronary arteries in the heart of dog, but not rat or minipig.

The lesions only occurred in the atrium and ventricle. Frequency and severity of the vascular lesions was not sex or dose related. No effects were noted in blood vessels in other organs or tissue. Plasma concentrations at steady state, and overall exposure in terms of AUC(0–24h) were higher in minipig and rat than the dog but did not cause cardiac arteriopathy. These findings concur with those caused by other endothelin anatagonists, vasodilators and positive inotropic: vasodilating drugs such as potassium channel openers, phosphodiesterase inhibitors and peripheral vasodilators.

Results by echocardiography indicate treatment-related local vasodilatation in the coronary arteries. These data suggest that the coronary arteriopathy may be the result of exaggerated pharmacology. Sustained vasodilatation in the coronary vascular bed may alter flow dynamics and lead to increased shear stress and tension on the coronary wall with subsequent microscopic trauma. In our experience with a number of endothelin receptor antagonists, the cardiac arteriopathy was only noted in studies with multiple daily or continuous intravenous infusion inviting speculation that sustained high plasma levels are needed for development of the lesions.

Up-regulation of vascular endothelin type B (ETB) receptors is implicated in the
pathogenesis of cardiovascular disease. Culture of intact arteries has been shown to induce similar receptor alterations and has therefore been suggested as a suitable method for, ex vivo, in detail delineation of the regulation of endothelin receptors. We hypothesize that mitogen-activated kinases (MAPK) and protein kinase C (PKC) are involved in the regulation of endothelin ETB receptors in human internal mammary arteries.

The endothelin-1-induced contraction (after endothelin ETB receptor desensitization) and the endothelin ETA receptor mRNA expression levels were not altered by culture. The sarafotoxin 6c contraction, endothelin ETB receptor protein and mRNA expression levels were increased. This increase was antagonized by;

PKC inhibitors (10 μM bisindolylmaleimide I and 10 μM Ro-32-0432), and
inhibitors of the p38, extracellular signal related kinases 1 and 2 (ERK1/2) and C-jun terminal kinase (JNK) MAPK pathways
Endothelin Receptor Antagonist Tezosentan
The effects of changes in the mean (Sm) and pulsatile (Sp) components of arterial wall shear stress on arterial dilatation of the iliac artery of the anaesthetized dog were examined in the absence and presence of the endothelin receptor antagonist tezosentan (10 mg kg_1 I.V.; Ro 61-0612; [5-isopropylpyridine-2-sulphonic acid 6-(2-hydroxy-ethoxy)-5-(2-methoxy-phenoxy)-2-(2-1H-tetrazol-5-ylpyridin-4-yl)-pyrimidin-4-ylamide]).

Changes in shear stress were brought about by varying local peripheral resistance and stroke volume using a distal infusion of acetylcholine and stimulation of the left ansa subclavia. An increase in Sm from 1.81 ± 0.3 to 7.29 ± 0.7 N m_2 (means ± S.E.M.) before tezosentan caused an endothelium-dependent arterial dilatation which was unaffected by administration of tezosentan for a similar increase in Sm from 1.34 ± 0.6 to 5.76 ± 1.4 N m_2 (means ± S.E.M.).

In contrast, increasing the Sp from 7.1 ± 0.8 to a maximum of 11.5 ± 1.1 N m_2 (means ± S.E.M.) before tezosentan reduced arterial diameter significantly. Importantly, after administration of tezosentan subsequent increases in Sp caused arterial dilatation for the same increase in Sp achieved prior to tezosentan, increasing from a baseline of 4.23 ± 0.4 to a maximum of 9.03 ± 0.9 N m_2 (means ± S.E.M.; P < 0.001). The results of this study provide the first in vivo evidence that pulsatile shear stress is a stimulus for the release of endothelin from the vascular endothelium.

Exercise and Diet
Vascular endotheliumis affected by plasma asymmetric dimethylarginine (ADMA), and it is induced by inflammatory cytokines of tumour necrosis factor (TNF)-a in vitro. Would a tight glycemic control restore endothelial function in patients with type-2 diabetes mellitus (DM) with modulation of TNF-a and/or reduction of ADMA level? In 24 patients with type-2 DM, the flow-mediated, endothelium-dependent dilation (FMD: %) of brachial arteries during reactive hyperaemia was determined by a high-resolution ultrasound method. Blood samples for glucose, cholesterol, TNF-a, and ADMA analyses were also collected from these patients after fasting. No significant glycemic or FMD changes were observed in 10 patients receiving the conventional therapy.

In 14 patients who were hospitalized and intensively treated, there was a significant decrease in glucose level after the treatment [from 190+55 to 117+21 (mean+SD) mg/dL, P , 0.01]. After the intensive control of glucose level, FMD increased significantly (from 2.5+0.9 to 7.2+3.0%), accompanied by a significant (P , 0.01) decrease in TNF-a (from 29+16 to 11+9 pg/dL) and ADMA (from 4.8+1.5 to 3.5+1.1 mM/L) levels. The changes in FMD after treatment correlated inversely with those in TNF-a (R ¼ 20.711, P , 0.01) and ADMA (R ¼ 20.717, P , 0.01) levels.
The exaggerated blood pressure response to exercise (EBPR) is an independent predictor of hypertension. Asymmetric dimethylarginine (ADMA) is an endogenous nitric oxide inhibitor and higher plasma levels of ADMA are related to increased cardiovascular risk. The aim of this study is to identify the relationship between ADMA and EBPR.

A total of 66 patients (36 with EBPR and 30 as controls) were enrolled in the study. EBPR is defined as blood pressure (BP) measurements ≥200/100 mmHg during the treadmill test. All the subjects underwent 24-h ambulatory BP monitoring. L-arginine and ADMA levels were measured using a high performance lipid chromatography technique.

The serum ADMA levels were increased in the EBPR group compared to the healthy controls (4.0±1.4 vs 2.6±1.1 μmol/L respectively, P=0.001), but L-arginine levels were similar in the 2 groups (P=0.19). The serum ADMA levels were detected as an independent predictor of EBPR (odds ratio 2.28; 95% confidence interval 1.22–4.24; P=0.002). Serum ADMA levels might play a role in EBPR to exercise.

Endothelial dysfunction occurs early in atherosclerosis in response to cardiovascular risk factors. The occurrence of endothelial dysfunction is primarily the result of reduced nitric oxide (NO) bioavailabilty. It represents an independent predictor of cardiovascular events and predicts the prognosis of the patient. Therefore, endothelial function has been identified as a target for therapeutic intervention. Regular exercise training is a nonpharmacological option to improve endothelial dysfunction in patients with cardiovascular disease by increasing NO bioavailability.

Peripheral Arterial Disease (PAD) is a cause of significant morbidity and mortality in the Western world. risk factor modification and endovascular and surgical revascularisation are the main treatment options at present. However, a significant number of patients still require major amputation. There is evidence that nitric oxide (NO) and its endogenous inhibitor asymmetric dimethylarginine (ADMA) play significant roles in the pathophysiology of PAD.

This paper reviews experimental work implicating the ADMA-DDAH-NO pathway in PAD, focusing on both the vascular dysfunction and both the vascular dysfunction and effects within the ischaemic muscle, and examines the potential of manipulating this pathway as a novel adjunct therapy in PAD.

In patients with CHF, the peripheral vascular resistance is increased via activation of the neurohormonal system, namely by autonomous sympathetic nervous system, rennin -angiotensin- aldosterone system (RAAS), and endothelin system. The vascular endothelial function in patients with CHF, mainly represented by the endothelium-dependent vasodilation, is altered.

Such alteration leads to increased vascular tone and remodeling of the blood vessels, reducing the peripheral blood flow. Hence, the amount of oxygen for the skeletal muscles is compromised, with progressive exercise intolerance. The vascular endothelial dysfunction in the CHF is mainly due to the decrease of the nitric oxide production induced by the reduced gene expression of eNOS and increased oxidative stress.

The endothelium-dependent vasodilation alteration has been virtually reported in all cardiovascular diseases. Using sauna bath as therapeutic option for CHF is not very recent, since in the 1950’s the first studies with CHF patients were conducted and the potential beneficial effect of sauna was suggested. However, some time later the studies emphasized especially its risks and recommended caution in its use for cardiac patients.

Frequently, sports medicine physicians are invited to evaluate the impact of the sauna on diseases and on health in general. Sauna can be beneficial or dangerous depending on its use. In the past few years the sauna is considered beneficial for the cardiovascular diseases’ patients, as the heart failure and lifestyle-related diseases, mainly by improving the peripheral endothelial function through the increase in cardiac output and peripheral vasodilation.

It is widely known that the vasodilators, such as angiotensin converting enzyme inhibitors, improve the CHF and increase the peripheral perfusion. Since the endothelial function is altered in CHF, the endothelium is considered as a new therapeutic target in heart failure. Hence, the angiotensin converting enzyme inhibitors and physical training improve the endothelial function in CHF patients. One of the proposed mechanisms for the alteration of the endothelium-dependent vasodilation would be through the decrease of the NO production in the peripheral vessels in CHF patients. The decrease of peripheral perfusion would decrease the shear stress. The shear stress is an important stimulus for NO production and eNOS expression. On the other hand, the heat increases the cardiac output and improves the peripheral perfusion in CHF patients. Consequently, with the cardiac output improvement in CHF patients, an increase of the shear stress, NO production and eNOS expression are expected.

Sauna bath
The sauna bath represents a heat load of 300-600 W/m2 of body surface area. The skin temperature rapidly increases to ± 40o-41oC and the thermoregulatory mechanisms are triggered. Evaporative heat transfer by sweating is the only effective body heat loss channel in dry sauna. The sweating begins rapidly and reaches its maximum level in ± 15 min. The total sweat secretion represents a heat loss of about 200 W/m2 of the body surface area. The body cannot compensate for the heat load and causing elevation of internal temperature. The skin circulation increases substantially. The skin blood flow, in the thermo-neutral condition (± 20oC) and in rest corresponding to ± 5-10% of the cardiac output, can reach ± 50-70% of the cardiac output.

Thermal therapy in 60oC produced systemic arterial, pulmonary arterial and venous vasodilation, reduced the preload and afterload and improved the cardiac output and the peripheral perfusion, clinical symptoms, life quality, and cardiac arrhythmias in CHF patients. In infants with severe CHF secondary to ventricular septal defect, the sauna therapy decreased the systemic vascular resistance and increased the cardiac output. The sauna benefits in CHF patients are possibly caused by the improvement of the vascular endothelial function and normalization of the neurohormonal system .

Ikeda et al. discovered that the observed improvements in the sauna therapy are due to the eNOS expression increase in the arterial endothelium. They later showed that the thermal therapy with sauna improves the survival of the TO-2 cardiomyopathic hamsters with CHF and, more recently, showed that the repetitive therapy with sauna increases the eNOS expression and the nitric oxide production in artery endothelium of TO-2 cardiomyopathic hamsters with CHF.
Whether n-3 polyunsaturated fatty acid (PUFA) supplementation and/or diet intervention might have beneficial influence on endothelial function was assessed using plasma levels of ADMA and L-arginine. A male population (n = 563, age 70 ± 6 yrs) with long-standing hyperlipidemia, characterized as high risk individuals in 1970–72, was included, randomly allocated to receive placebo n-3 PUFA capsules (corn oil) and no dietary advice (control group), dietary advice (Mediterranean type), n-3 PUFA capsules, or dietary advice and n-3 PUFA combined and followed for 3 years. Fasting blood samples were drawn at baseline and the end of the study.

Compliance with both intervention regimens were demonstrated by changes in serum fatty acids and by recordings from a food frequency questionnaire. No influence of either regimens on ADMA levels were obtained. However, n-3 PUFA supplementation was accompanied by a significant increase in L-arginine levels, different from the decrease observed in the placebo group (p < 0.05). In individuals with low body mass index (<26 kg/m2), the decrease in L-arginine on placebo was strengthened (p = 0.01), and the L-arginine/ADMA ratio was also significantly reduced (p = 0.04). In this rather large randomized intervention study, ADMA levels were not influenced by n-3 PUFA supplementation or dietary counselling. n-3 PUFA did, however, counteract the age related reduction in L-arginine seen on placebo, especially in lean individuals, which might be considered as an improvement of endothelial function.

Traditional Chinese Medicine

Traditional Chinese Medicine (TCM) involves a broad range of empirical testing and refinement and plays an important role in the health maintenance for people all over the world. However, due to the complexity of Chinese herbs, a full understanding of TCM’s action mechanisms is still unavailable despite plenty of successful applications of TCM in the treatment of various diseases, including especially cardiovascular diseases (CVD), one of the leading causes of death.

An integrated system of TCM has been constructed to uncover the underlying action mechanisms of TCM by incorporating the chemical predictors, target predictors and network construction approaches from three representative Chinese herbs, i.e., Ligusticum chuanxiong Hort., Dalbergia odorifera T. Chen and Corydalis yanhusuo WT Wang widely used in CVD treatment, by combined use of drug absorption, distribution, metabolism and excretion (ADME) screening and network pharmacology techniques. These studies have generated 64 bioactive ingredients and identified 54 protein targets closely associated with CVD, to clarify some of the common conceptions in TCM, and provide clues to modernize such specific herbal medicines.

Ligusticum chuanxiong Hort., Dalbergia odorifera T. Chen and Corydalis yanhusuo WT Wang
Twenty-two of 194 ingredients in Ligusticum chuanxiong demonstrate good bioavailability (60%) after oral administration. Interestingly, as the most abundant bioactive compound of Chuanxiong, Ligustilide (M120) only has an adequate OB of 50.10%, although it significantly inhibits the vasoconstrictions induced by norepinephrine bitartrate (NE) and calcium chloride (CaCl2). Indeed, this compound can be metabolized to butylidenephthalide, senkyunolide I (M156), and senkyunolide H (M155) in vivo.

The three natural ingredients produce various pharmacological activities in cerebral blood vessels, the general circulatory system and immune system including spasmolysis contraction effects, inhibitory effects of platelet aggregation and anti-proliferative activity, and thus improve the therapeutic effect on patients. Cnidilide (M93, OB = 77.55%) and spathulenol (M169, OB = 82.37%) also closely correlate with the smooth muscle relaxant action, and thereby have the strongest spasmolytic activity. Carotol (M8) and Ferulic acid (M105) with an OB of 149.03% and 86.56%, respectively, demonstrate better bioavailability compared with cnidilide and spathulenol, which show strong antifungal, antioxidant and anti-inflammatory activity.

The pharmacological activity of ferulic acid results in the improvement of blood fluidity and the inhibition of platelet aggregation, which may offer beneficial effects against cancer, CVD, diabetes and Alzheimer’s disease. As for 3-n-butylphthalide (M85, OB = 71.28%), this compound is not only able to inhibit platelet aggregation, but also decreases the brain infarct volume and enhances microcirculation, thus benefiting patients with ischemic stroke. Platelet aggregation represents a multistep adhesion process involving distinct receptors and adhesive ligands, with the contribution of individual receptor-ligand interactions to the aggregation process depending on the prevailing blood flow conditions, implying that the rheological (blood flow) conditions are an important impact factor for platelet aggregation. Moreover, thrombosis, the pathological formation of platelet aggregates and one of the biggest risk factors for CVD, occludes blood flow causing stroke and heart attack. This explains why the traditional Chinese herb Ligusticum chuanxiong that inhibits platelet aggregates forming and promotes blood circulation can be used in treatment of CVD.

Twenty-six percent (24 of 93) of the ingredients in Dalbergia odorifera meet the OB > 60% criterion irrespective of the pharmacological activity. Relatively high bioavailability values were predicted for the mainly basic compounds odoriflavene (M275, OB = 84.49%), dalbergin (M247, OB = 78.57%), sativanone (M281, OB = 73.01%), liquiritigenin (M262, OB = 67.19%), isoliquiritigenin (M259, OB = 61.38%) and butein (M241, OB = 78.38%). Interestingly, all of the six ingredients show obvious anti-inflammatory property. Butein, liquiritigenin and isoliquiritigenin inhibit cell inflammatory responses by suppressing the NF-κB activation induced by various inflammatory agents and carcinogens, and by decreasing the NF-κB reporter activity. Inflammation occurs with CVD, and Dalbergia odorifera, one of the most potent anti-cardiovascular and anti-cerebrovascular agents, exerts great anti-inflammatory activity.

Corydalis yanhusuo has gained ever-increasing popularity in today’s world because of its therapeutic effects for the treatment of cardiac arrhythmia disease, gastric and duodenal ulcer and menorrhalgia. In our work, 21% (15 of 73) of chemicals in this Chinese herb display good OB (60% or even high), and the four main effective ingredients are natural alkaloid agents.

Dehydrocorydaline blocks the release of noradrenaline from the adrenergic nerve terminals in both the Taenia caecum and pulmonary artery, and thereby inhibits the relaxation or contraction of adrenergic neurons. As for dehydrocavidine with an OB of 47.59%, this alkaloid exhibits a significant spasmolytic effect, which acts via relaxing smooth muscle.

In recent years, CVD has been at the top list of the most serious health problems. Many different types of therapeutic targets have already been identified for the management and prevention of CVD, such as endothelin and others. The key question asked is

  • what the interactions of the active ingredients of the Chinese herbs are with their protein targets in a systematic manner and
  • how do the corresponding targets change under differential perturbation of the chemicals?

The study used an unbiased approach to probe the proteins that bind to the small molecules of interest in CVD on the basis of the Random Forest (RF) and Support Vector Machine (SVM) methods combining the chemical, genomic and pharmacological information for drug targeting and discovery on a large scale. Applied to 64 ingredients derived from the three traditional Chinese medicines Dalbergia odorifera, Ligusticum chuanxiong and Corydalis yanhusuo, which show good OB, 261 ligand-target interactions have been constructed, 221 of which are enzymes, receptors, and ion channels. This indicates that chemicals with multiple relative targets are responsible for the high interconnectedness of the ligand-target interactions. The promiscuity of drugs has restrained the advance in recent TCM, because they were thought to be undesirable in favor of more target-specific drugs.

Target Identification and Validation
To validate the reliability of these target proteins, the researchers performed a docking analysis to select the ligand-protein interactions with a binding free energies of ≤−5.0 kcal/mol, which leads to the sharp reduction of the interaction number from 5982 to 760. These drug target candidates were subsequently subject to PharmGkb (available online: http://www.pharmgkb.org; accessed on 1 December 2011), a comprehensive disease-target database, to investigate whether they were related to CVD or not, and finally, 54 proteins were collected and retained.

Fourty-two proteins (76%) were identified as the targets of Ligusticum chuanxiong, such as dihydrofolate reductase (P150), an androgen receptor (P210) and angiotensin-converting enzyme (P209) that were involved in the development of CVD. Of the proteins, seven and two were recognized as those of Dalbergia odorifera and Corydalis yanhusuo, respectively. For Dalbergia odorifera, this Chinese herb has 48 potential protein targets, 13 of which have at least one link to other drugs.

The three herbs share 29 common targets, accounting for 52.7% of the total number. Indeed, as one of the most important doctrines of TCM
abstracted from direct experience and perception, “multiple herbal drugs for one disease” has played an undeniable role. These studies explored the targets of the three Chinese herbs, indicating that these drugs target the same targets simultaneously and exhibit similar pharmacological effects on CVD. This is consistent with the theory of “multiple herbal drugs for one disease”.

The three Chinese herbs possess specific targets. The therapeutic efficacy of a TCM depends on multiple components, targets and pathways. The complexity becomes a huge obstacle for the development and innovation of TCM. For example, the Chinese herb Ligusticum chuanxiong identifies the protein caspase-3 (P184), a cysteinyl aspartate-specific protease, as one of its specific targets, and exhibits inhibitory effects on the activity of this protease. In fact, connective tissue growth factor enables the activation of caspase-3 to induce apoptosis in human aortic vascular smooth muscle cells.

Thus, modulation of the activity of caspase-3 with Ligusticum chuanxiong suggests an efficient therapeutic approach to CVD. The Chinese herb Dalbergia odorifera has the α-2A adrenergic receptor (P216) as its specific target and probably blocks the release of this receptor, and thus influences its action. As for Corydalisyanhusuo, the protein tyrosine-protein kinase JAK2 (P9) is the only specific target of this Chinese herb. The results indicate different specific targets possessed by the three Chinese herbs.

Ligand-Candidate Target and Ligand-Potential Target Networks
Previous studies have already reported the relationships of the small molecules with CVD, which indicates the reliability of our results [45,46]. Regarding the candidate targets, we have found that prostaglandin G/H synthase 2 (P46) and prostaglandin G/H synthase 1 (P47) possess the largest number of connected ingredients. Following are nitric-oxide synthase, endothelial (P66) and tyrosine-protein phosphatase non-receptor type 1 (P8), which have 62 and 61 linked chemicals, respectively.
The 29 targets shared by the three traditional Chinese herbs exhibit a high degree of correlations with CVD, which further verifies their effectiveness for the treatment of CVD. These results provide a clear view of the relationships of the target proteins with CVD and other related diseases, which actually link the Chinese herbs and the diseases via the protein targets. This result further explains the theory of “multiple herbal drugs for one disease” based on molecular pharmacology.

Target-Pathway Network
Cells communicate with each other using a “language” of chemical signals. The cell grows, divides,or dies according to the signals it receives. Signals are generally transferred from the outside of the cell. Specialized proteins are used to pass the signal—a process known as signal transduction. Cells have a number of overlapping pathways to transmit signals to multiple targets. Ligand binding in many of the signaling proteins in the pathway can change the cellular communication and finally affect cell growth and proliferation. The authors extracted nine signal pathways closely associated with CVD in PharmGkb (available online: http://www.pharmgkb.org; accessed on 1 December 2011).

As the main components in the VEGF system, proto-oncogene tyrosine-protein kinase Src, eNOS, and hsp90-α is also recognized as common targets of Dalbergia odorifera, Ligusticum chuanxiong and Corydalis yanhusuo, which are efficient for the treatment of CVD. This implies that the candidate drugs can target different target proteins involved in the same or different signal pathways, and thereby have potential effects on the whole signal system.

Target Prediction
In search of the candidate targets, the model that efficiently integrates the chemical, genomic and pharmacological information for drug targeting and discovery on a large scale is based on the two powerful methods Random Forest (RF) and Support Vector Machine (SVM). The model is supported by a large pharmacological database of 6511 drugs and 3999 targets extracted from the DrugBank database (available online: http://drugbank.ca/; accessed on 1 June 2011), and shows an impressive performance of prediction for drug-target interaction, with a concordance of 85.83%, a sensitivity of 79.62% and a specificity of 92.76%. the candidate targets were selected according to the criteria that the possibility of interacting with potential candidate targets was higher than 0.6 for the RF model and 0.7 for the SVM model. The obtained candidate targets were finally reserved and were further predicted for their targets.

Target Validation
Molecular docking analysis was carried out using the AutoDock software (available online: http://autodock.scripps.edu/; accessed on 1 February 2012). This approach performs the docking of the small, flexible ligand to a set of grids describing the target protein. During the docking process, the protein was considered as rigid and the molecules as flexible. The crystal structures of the candidate targets were downloaded from the RCSB Protein Data Bank (available online: http://www.pdb.org/; accessed on 1 December 2011), and the proteins without crystal structures were performed based on homology modeling using the Swiss-Model Automated Protein Modelling Server (available online: http://swissmodel.expasy.org/; accessed on 1 February 2012).

TCM is a heritage that is thousands of years old and is still used by millions of people all over the world—even after the development of modern scientific medicine. Chinese herbal combinations generally include one or more plants and even animal products.

The study identified 54 protein targets, which are closely associated with CVD for the three Chinese herbs, of which 29 are common targets (52.7%), which clarifies the mechanism of efficiency of the herbs for the treatment of CVD.

Activation of NFkB

Extracellular stimuli for NFkB activation and NFkB regulated genes
Extracellular stimuli                       Regulated genes
TNFa                                         Growth factors (G/M-CSF)
Interleukin 1                            G/M CSF, M CSF, G CSF
ROS                                              Cell adhesion molecules
UV light                            ICAM-1, VCAM, E-Selectin, P-selectin
Ischaemia                                   Cytokines
Lipopolysaccharide               TNFa, IL-1, IL-2, IL-6, interferon
Bacteria                                        Transcription regulators
Viruses                                         P53, IkB, c-rel, c-myc
Amyloid                                      Antiapoptotic proteins
Glutamate                              TRAF-1, TRAF-2, c-IAP1, c-IAP2
Pathophysiology
Reactive oxygen species (ROS) are toxic and in conditions of a dysbalance between their overproduction and the diminished activity of various antioxidant enzymes and other molecules induce cellular injury termed oxidative stress. ROS are often related to a number of diseases like atherosclerosis. However, the mechanism is not clear at all. Latest years of research have brought the idea of connection between ROS and NFkB. And indeed, in vitro studies showed a rapid activation of NFkB after exposure of certain cell types to ROS. Today, no specific receptor for ROS has been found, thus, the details of the ROS induced activation of NFkB are missing.

Natural occurring agents which actions are still a matter of debate in the theory and nouvelle small molecular derivates activate or inhibit the transcriptional factor. Synthetic oligo and polypeptide inhibitors of NFkB can penetrate the cell membrane and directly act on the Rel proteins. The most sophisticated approaches towards inhibiting the activation and translocation of NFkB into the nucleus represent gene deliveries, using plasmids or adenoviruses containing genes for various super repressors—modified IkB proteins, or so called NFkB decoys, which interact with activated NFkB and thus, inhibit the interaction between the transcription factor and nuclear DNA enhancers.

A simplified scheme of the activation of NFkB by the degradation of IkB. IkB is phosphorylated by IKK and ubiquinatated by the ubiquitine ligase system (ULS). IkB is further degradated by the 26S proteasome (26S).Activated NFkB can pass the nuclear membrane and interact with kB binding sequences in enhancers of NFkB regulated genes. LPS, lipopolysaccharide; ROS, reactive oxygen species; FasL, Fas ligand; TRAF, TNFa receptor associated factor; NIK, NFkB inducing kinase; MEKK, mitogen activated protein kinase/extracellular signal regulated kinases kinases.

The medicine of this century is a medicine of molecules, the diagnostic procedure and the therapy moves further from the “clinical picture” to the use of achievements in molecular biology and genetics. However, sober scepticism and awareness are indicated. Especially the role of NFkB in multiple signal transducing pathways and the tissue dependent variability of responses to alternations in NFkB pathway may be the reasons for unwanted side effects of the therapy that are after in vitro or in vivo experiments hardly to expect in the clinical use.

Therapeutic Targets
Modern drug discovery is primarily based on the search and subsequent testing of drug candidates acting on a preselected therapeutic target. Progress in genomics, protein structure, proteomics, and disease mechanisms has led to a growing interest in an effort for finding new targets and more effective exploration of existing targets. The number of reported targets of marketed and investigational drugs has significantly increased in the past 8 years. There are 1535 targets collected in the therapeutic target database.
Knowledge of these targets is helpful for molecular dissection of the mechanism of action of drugs and for predicting features that guide new drug design and the
search for new targets. This article summarizes the progress of target exploration and investigates the characteristics of the currently explored targets to analyze their sequence, structure, family representation, pathway association, tissue distribution, and genome location features for finding clues useful for searching for new targets. Possible “rules” to guide the search for druggable proteins and the feasibility of using a statistical learning method for predicting druggable proteins directly from their sequences are discussed.

Current Trends in Exploration of Therapeutic Targets
There are 395 identifiable targets described in 1606 patents. Of these targets, 264 have been found in more than one patent and 50 appear in more than 10 patents. The number of patents associated with a target can be considered to partly correlate with the level of effort and intensity of interest currently being directed to it. Approximately one third of the patents with an identifiable target were approved in the past year. This suggests that the effort for the exploration of these targets is ongoing, and there has been steady progress in the discovery of new investigational agents directed to these targets.

Various degrees of progress have been made toward discovery and testing of agents directed at these targets. However, for some of these targets, many difficulties remain to be resolved before viable drugs can be derived. The appearance of a high number of patents associated with these targets partly reflects the intensity of efforts for finding effective drug candidates against these targets.

There are 62 targets being explored for the design of subtype-specific drugs, which represents 15.7% of the 395 identifiable targets in U.S. patents approved in 2000 through 2004. Compared with the 11 targets of FDA approved subtype-specific drugs during the same period, a significantly larger number of targets are being explored for the design of subtype-specific drugs.

What Constitutes a Therapeutic Target?
The majority of clinical drugs achieve their effect by binding to a cavity and regulating the activity, of its protein target. Specific structural and physicochemical properties, such as the “rule of five” (Lipinski et al., 2001), are required for these drugs to have sufficient levels of efficacy, bioavailability, and safety, which define target sites to which drug-like molecules can bind. In most cases, these sites exist out of functional necessity, and their structural architectures accommodate target-specific drugs that minimally interact with other functionally important but structurally similar sites.
These constraints limit the types of proteins that can be bound by drug-like molecules, leading to the introduction of the concept of druggable proteins (Hopkins and Groom, 2002; Hardy and Peet, 2004). Druggable proteins do not necessarily become therapeutic targets (Hopkins and Groom, 2002); only those that play key roles in diseases can be explored as potential targets.

 Prediction of Druggable Proteins by a Statistical Learning Method

Currently, the support vector machine (SVM) method seems to be the most accurate statistical learning method for protein predictions. SVM is based on the structural risk minimization principle from statistical learning theory. Known proteins are divided into druggable and nondruggable classes; each of these proteins is represented by their sequence-derived physicochemical features.

These features are then used by the SVM to construct a hyperplane in a higher dimensional hyperspace that maximally separates druggable proteins and nondruggable ones. By projecting the sequence of a new protein onto this hyperspace, it can be determined whether this protein is druggable from its location with respect to the hyperplane. It is a druggable protein if it is located on the side of druggable class.
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Reveals from ENCODE project will invite high synergistic collaborations to discover specific targets

Reporter: Aviva Lev-Ari, PhD, RN

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Word Cloud By Danielle Smolyar

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Nature (2012) 

doi:10.1038/nature11547 Received 09 January 2012  Accepted 04 September 2012 

Published online 24 October 2012

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRASTP53CDKN2A, SMAD4MLL3TGFBR2, ARID1A andSF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2,MAP2K4NALCNSLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

Figures at a glance

Contributions

The research network comprising the Australian Pancreatic Cancer Genome Initiative, the Baylor College of Medicine Cancer Genome Project and the Ontario Institute for Cancer Research Pancreatic Cancer Genome Study (ABO collaboration) contributed collectively to this study as part of the International Cancer Genome Consortium. Biospecimens were collected at affiliated hospitals and processed at each biospecimen core resource centre. Data generation and analyses were performed by the genome sequencing centres, cancer genome characterization centres and genome data analysis centres. Investigator contributions are as follows: S.M.G., A.V.B., J.V.P., R.L.S., R.A.G., D.A.W., M.-C.G., J.D.M., L.D.S and T.J.H. (project leaders); A.V.B., S.M.G. and R.L.S. (writing team); A.L.J., J.V.P., P.J.W., J.L.F., C.L., M.A., O.H., J.G.R., D.T., C.X., S.Wo., F.N., S.So., G.K. and W.K. (bioinformatics/databases); D.K.M., I.H., S.I., C.N., S.M., A.Chr., T.Br., S.Wa., E.N., B.B.G., D.M.M., Y.Q.W., Y.H., L.R.L., H.D., R. E. D., R.S.M. and M.W. (sequencing); N.W., K.S.K., J.V.P., A.-M.P., K.N., N.C., M.G., P.J.W., M.J.C., M.P., J.W., N.K., F.Z., J.D., K.C., C.J.B., L.B.M., D.P., R.E.D., R.D.B., T.Be. and C.K.Y. (mutation, copy number and gene expression analysis); A.L.J., D.K.C., M.D.J., M.P., C.J.S., E.K.C., C.T., A.M.N., E.S.H., V.T.C., L.A.C., E.N., J.S.S., J.L.H., C.T., N.B. and M.Sc. (sample processing and quality control); A.J.G., J.G.K., R.H.H., C.A.I.-D., A.Cho., A.Mai., J.R.E., P.C. and A.S. (pathology assessment); J.W., M.J.C., M.P., C.K.Y. and mutation analysis team (network/pathway analysis and functional data integration); K.M.M., N.A.J., N.G.C., P.A.P.-M., D.J.A., D.A.L., L.F.A.W., A.G.R., D.A.T., R.J.D., I.R., A.V.P., E.A.M., R.L.S., R.H.H. and A.Maw. (functional screens); E.N., A.L.J., J.S.S., A.J.G., J.G.K., N.D.M., A.B., K.E., N.Q.N., N.Z., W.E.F., F.C.B., S.E.H., G.E.A., L.M., L.T., M.Sam., K.B., A.B., D.P., A.P., N.B., R.D.B., R.E.D., C.Y., S.Se., N.O., D.M., M-S.T., P.A.S., G.M.P., S.G., L.D.S., C.A.I.-D., R.D.S., C.L.W., R.A.M., R.T.L., S.B., V.C., M.Sca., C.B., M.A.T., G.T., A.S. and J.R.E. (sample collection and clinical annotation); D.K.C., M.P., C.J.S., E.S.H., J.A.L., R.J.D., A.V.P. and I.R. (preclinical models).

Competing financial interests

The authors declare no competing financial interests.

International Team Reports on Large-Scale Pancreatic Cancer Analysis

October 24, 2012

NEW YORK (GenomeWeb News) – A whole-exome sequencing and copy number variation study of pancreatic cancer published online today in Nature suggests that the disease sometimes involves alterations to genes and pathways best known for their role in axon guidance during embryonic development.

The work was conducted as part of the International Cancer Genome Consortium effort by researchers with the BCM Cancer Genome Project, the Australian Pancreatic Cancer Genome Initiative, and the Ontario Institute for Cancer Research Pancreatic Cancer Genome Study.

As they reported today, the investigators identified thousands of somatic mutations and copy number alterations in pancreatic ductal adenocarcinoma cancer, the most common form of pancreatic cancer. Some of the mutations affected known cancer genes and/or pathways implicated in pancreatic cancer in the past. Other genetic glitches pointed to processes not previously linked to the disease including mutations to axon guidance genes such as SLIT2, ROBO1, and ROBO2.

“This is a category of genes not previously linked to pancreatic cancer,” Baylor College of Medicine researcher William Fisher, a co-author on the new paper, said in a statement. “We are poised to jump on this gene list and do some exciting things.”

Pancreatic cancer is among the deadliest types of cancer, he and his colleagues explained, with a grim five-year survival rate of less than 5 percent. But despite its clinical importance, direct genomic studies of primary tumors had been stymied in the past due to difficulties obtaining large enough samples for such analyses.

“Genomic characterization of pancreatic ductal adenocarcinoma, which accounts for over 90 [percent] of pancreatic cancer, has so far focused on targeted polymerase chain reaction-based exome sequencing of primary and metastatic lesions propagated as xenografts or cell lines,” the study authors noted.

“A deeper understanding of the underlying molecular pathophysiology of the clinical disease is needed to advance the development of effective therapeutic and early detection strategies,” they added.

For the current study, researchers started with a set of tumor-normal samples from 142 individuals with stage I or stage II sporadic pancreatic ductal adenocarcinoma. Following a series of experiments to assess tumor cellularity and other features that can impact tumor analyses, they selected 99 patients whose samples were assessed in detail.

For whole-exome sequencing experiments, the investigators nabbed coding sequences from matched tumor and normal samples using either Agilent SureSelectII or Nimblegen capture kits before sequencing the exomes on SOLiD 4 or Illumina sequencing platforms. They also used Ion Torrent and Roche 454 platforms to validate apparent somatic mutations in the samples.

For its copy number analyses, meanwhile, the team tested the pancreatic cancer and normal tissue samples using Illumina HumanOmni1 Quad genotyping arrays.

When they sifted through data for the 99 most completely characterized pancreatic tumors, researchers uncovered 1,628 CNVs and roughly 2,000 non-silent, somatic coding mutations. More than 1,500 of the non-silent mutations were subsequently verified through additional sequencing experiments.

On average, each of the tumors contained 26 coding mutations. And despite the variability in mutations present from one tumor to the next, researchers identified 16 genes that were mutated in multiple tumor samples.

Some were well-known cancer players such as KRAS, which was mutated in more than 90 percent of the 142 pancreatic tumors considered initially. Several other genes belonged to cell cycle checkpoint, apoptosis, blood vessel formation, and cell signaling pathways, researchers reported, or to pathways involved in chromatin remodeling or DNA damage repair.

For example, some 8 percent of tumors contained mutations to ATM, a gene participating in a DNA damage repair pathway that includes the ovarian/breast cancer risk gene BRCA1.

Genes falling within axon guidance pathways turned up as well. That pattern was supported by the researchers analyses of data from published pancreatic cancer studies — including two studies based on mutagenesis screens in mouse models of the disease — and by their own gene expression experiments in mice.

The team also tracked down a few more pancreatic ductal adenocarcinoma cases involving mutations to axon guidance genes such as ROBO1, ROBO2, and SLIT2 through targeted testing on 30 more pancreatic cancer patients.

The findings are consistent with those found in some other cancer types, according to the study’s authors, who noted that there is evidence indicating that some axon guidance components feed into signaling pathways related to cancer development, such as the WNT signaling pathway. If so, they explained, it’s possible that mutations to axon guidance genes might influence the effectiveness of therapies targeting such downstream pathways or serve as potential treatment targets themselves.

Still, those involved in the study cautioned that more research is needed not only to explore such possibilities but also to distinguish between driver and passenger mutations in pancreatic cancer.

“The potential therapeutic strategies identified will … require testing in appropriate clinical trials that are specifically designed to target subsets of patients stratified according to well-defined molecular markers,” the study’s authors concluded.

Reporter: Aviva Lev-Ari, PhD, RN

Publishing’s Gender Gap

Female scholars are gaining ground in publishing, but cluster in sub-disciplines and tend not to be listed as first or last authors.

By Beth Marie Mole | October 23, 2012

Marie Curie, Wikimedia, UnknownThe percentage of women authors in academic publishing has risen to 30 percent since 1665, but women are still less likely to be first or last author, and tend to cluster in sub-disciplines, according toresearchers at the University of Washington who analyzed two million academic papers published from 1665 to 2010 by 2.7 million scientists, social scientists, and humanities scholars.

“The results show us what a lot of people have been saying and many of my female colleagues have been feeling,” environmental scientist Jennifer Jacquet of New York University, who was involved in the study, told The Chronicle of Higher Education. “Things are getting better for women in academia,” despite the fact that they are still not publishing at the same rate and level as their male counterparts.

Mining JSTOR, a digital archive of scholarly publications, the researchers tagged articles by field and subfield of research, then used data from the Social Security Administration to identify author age. Most importantly, they also tagged authors by gender, assuming that if a name was used 95 percent of the time for one gender it was probably accurate. Publications with androgynous author names were left out of the analysis.

In 2010, when women scholars reached 30 percent of published authors, women made up 42 percent of full-time faculty, 34 percent of which were tenured professors. This suggests that although women are continually gaining ground in publishing—only 27 percent of authors publishing between 1990 and 2010 were women—they are still not publishing at the same rate as men. Moreover, women are under-represented as the coveted first author, the lead author on the research, as well as last author, considered the senior researcher on the study. In molecular and cellular biology, for example, women made up 30 percent of the authors but only 16.5 percent of the last authors. And only about 19 percent of women were first author overall, with the majority falling in the second, third, or fourth author listed.

When the researchers looked at the gender distribution among sub-disciplines, they found additional disparities. For example, although women comprised 30 percent of authors overall, some subfields, such as paleontology, had only 16.6 percent female authors.

Despite the gaps in publishing, the data don’t necessarily provide evidence for gender discrimination. “The international literature show that when women submit work, there is no bias in it being accepted, but the likelihood of women submitting work may be lower,” human development professor Wendy Williams of Cornell University, who studies women’s role in science, told The Chronicle. Still, most believe the results warrant further study.

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The Nutshell

SOURCES:

Reporter: Aviva Lev-Ari, PhD, RN

Educating Physicians on Genomic Medicine

October 2012

Medical schools across the US are busy this fall, preparing students for the impending transformation in healthcare that advances in genomic knowledge promise to bring.

After only eight weeks of medical coursework, students at Ohio State University will be thrown into a real-world learning environment where they will use patients’ genomic and behavioral risk factors to encourage healthier lifestyles. Medical and PhD students at Stanford University, meantime, have the opportunity to get their own DNA tested and learn how genes influence disease risk and drug response in the context of their own health. And at the University of Florida, medical and pharmacy students will soon be able to practice clinical interactions with digital avatars that can mimic patients with various genetic conditions.

Medical schools are developing such innovative curricula as it becomes increasingly clear that physicians are ill-equipped to practice genomically guided personalized medicine — a discipline that requires doctors to consider a patient’s genomic data in the context of other medical and family history and craft a unique treatment plan. A survey of 800 physicians from last year revealed that, although the majority of respondents believes personalized medicine will influence how they care for patients in coming years, only 10 percent of primary care doctors and cardiologists and 30 percent of oncologists feel they are up to speed with the latest advances in the field.

The same survey, conducted by healthcare communications firm CAHG, found that only 20 percent of practicing physicians had received any training on how to administer genomically guided medicine. The outlook improves somewhat for more recently minted doctors, with around 50 percent of those who graduated from medical school in the past five years reporting that they have had some form of training in personalized medicine.

The challenge of keeping doctors up to date on the latest medical advances looms particularly large considering that, by 2021, spending on genetic testing is projected to jump to $25 billion from $5 billion currently. However, physicians’ limited genomics know-how isn’t the only barrier to the adoption of personalized medicine into mainstream care. While many healthcare providers are enthusiastic about using genomic tools to improve their patients’ health, there are a number of systemic challenges — slow turnaround times for test results, insurers’ reluctance to pay for new technologies, and the lack of genomic data in electronic medical records — that keep them from effectively using these tests.

“Personalized medicine is an ecosystem or a value chain,” says Larry Lesko, who left the US Food and Drug Administration last year to head Florida’s new Center for Pharmacometrics and Systems Pharmacology. “In this ecosystem … there is a lot more than physician education.”

Even if medical students leave academia with knowledge of genomic medicine, in the short term very few will get to apply those principles at a community practice or a hospital. “Unless what we’re teaching them is what they see in the clinical environment, wherever they go from here [they will face] substantial barriers,” says Daniel Clinchot, associate dean for medical education at Ohio State’s medical school. “[Unless] we can ensure that, across the US, we are holding physicians accountable for using the most up-to-date information and the way that information is applied, that sort of undoes the … medical education they received.”

Simulated reality

Physicians today have plenty of reasons not to practice genomic medicine. Take the anticoagulant warfarin for example. Although there is evidence that with genetic testing doctors can dose the drug more accurately than with standard methods and avoid hospitalizations due to adverse reactions, most doctors don’t use it because turnaround times for test results are too long to be useful for patients with acute conditions. For the majority of genetic tests, however, doctors find limited evidence backing their validity and utility in improving patients’ health. Even for genetic tests that are well validated, physicians are wary of coverage denials from insurance companies because there is little proof that the test is cost-effective compared to standard interventions. Meanwhile, healthcare providers who are eager to implement genetic testing more broadly in their practices find it difficult to do so with the dearth of genetic counselors and within the average eight-minute physician-patient interaction.

When developing genomic medicine courses, universities are keeping these realities in mind. With Lesko’s leadership, Florida is testing out the theory that physicians will be more likely to use genomic data in patient care if the information is readily available in electronic medical records.

Patients treated at Florida’s catheterization lab will receive a multi-gene test that doctors will use to discern whether the patients are likely to be poor responders to the antiplatelet drug Plavix and are at heightened risk for cardiac events. If, at a later time, a physician prescribes Plavix to a patient deemed to be a poor responder by genetic testing, the doctor will receive a “best practices advisory alert” in the patient’s EMR, recommending a different treatment strategy.

For the time being, only the test results related to Plavix response are included in the EMR. With patient consent, data on 249 other gene variations the test gauges will be stored in a secure database for research use.

Through this effort, doctors will learn how to consider genomic data in the context of a patient’s overall medical history, but they won’t have to worry about some of the procedural headaches, such as lengthy turnaround times for results, that deter the adoption of many tests by primary care physicians. “You have to focus on education of physicians at the right time,” Lesko says. “If you do it too early, when the infrastructure in somebody’s practice isn’t set up, I don’t think physicians will care, and they won’t retain the knowledge. But if you have the test results already available in the EMR, like we’re doing, then that’s the right time to do the training.”

Similarly, Florida plans to teach its medical students how to discuss genomic information with patients, with the help of digital simulations. Lesko envisions that medical and pharmacy students will be “able to practice clinical care” by interacting with avatars that can “realistically imitate patients with different genetic [data].”

For a few hundred dollars, consumers increasingly have access to genetic testing for numerous health conditions from companies such as 23andMe and Decode Genetics. A doctor with limited genomic knowledge could be at a loss for what to do with a patient who brings in a report with a slew of genetic test results. Under the Florida program, students would learn how to discuss genetic test results with an avatar that behaves like a patient with such a report.

“The idea is to get medical and pharmacy students involved in an active learning process,” Lesko says. “Retention of information [through such simulation programs] is usually fairly high.”

At Ohio State, meanwhile, the focus is on teaching medical students not just how to treat patients, but how to inspire them to stay healthy. “The students learn to be health coaches, which is extremely important in the transformation of medicine,” says Ohio State’s Clinchot. Genomics, particularly in the context of oncology, as well as the principles of P4 medicine — short for predictive, preventive, personalized, and participatory medicine — will be a big part of the students’ four-year training.

“We really try to focus on healthy behaviors by teaching students that they not only need to care for patients with disease, but also care for patients who are healthy currently, but have risk factors for certain things — whether they are genetic or behavioral — so they can [learn] how to prevent the development of things like type 2 diabetes,” Clinchot says.

In creating this program, Ohio State ran a pilot effort where students helped type 2 diabetes patients make lifestyle changes. The project showed that the students’ efforts resulted in patients adhering better to their medication regimens and feeling more in control of their diabetes. This pilot didn’t gauge the impact of DNA information on patient behavior, but Clinchot says that when genetic risk data is conveyed in the context of a more in-depth patient-physician interaction, the effect will be similarly positive.

Previous studies, such as one from the Multiplex Initiative by the National Human Genome Research Institute and a behavioral project conducted by the Scripps Translational Research Institute, have reported that genetic data has a limited impact on people’s behavior and that a minority of people share their test reports with genetic counselors or doctors. However, these surveys also found those who shared their test results with their doctors were the most motivated to make lifestyle changes.

“It’s not enough that you tell a patient [their genetic test results], sort of go over their risk factors and let them go and that’s it,” Clinchot says. “It’s [with] long-term follow up and the coaching aspect of it … that you’ll see a big difference.”

Real world data

Back in the real world, insurers get a little nervous every time a university starts implementing forward-thinking genomic testing programs, such as UF’s multiplex testing effort. They fear that if more people find out about these academic programs, it will raise consumer expectations that these tests — most of which insurers currently consider investigational and not ready for broad implementation — will soon be available at community practices and hospitals.

At the 2010 ECRI Institute’s annual conference, which brought together insurers and academics involved in personalized medicine, Barry Straube, then chief medical officer of the Centers for Medicare & Medicaid Services, expressed concern over efforts at Brigham and Women’s Hospital in Boston to conduct genetic testing to personalize cancer treatment and include this data alongside patients’ medical information in an electronic database for research.

“The reality, although all this is very important and absolutely essential to clinical research, is that when the rubber hits the road, and patients … start coming into medical offices and requesting access to various genetic tests and treatments … the enormity of the cost to society is frightening,” Straube said at the time.

It is no surprise, then, that outside of academia, insurance hurdles seem to be the biggest headache for community physicians administering genetic testing. “Over the last few years genetic testing has become more available, but some of the insurance companies haven’t really acquiesced [with coverage], which has been a real problem with providing testing to families with genetic disorders,” says Michael Mirro, a cardiologist and the medical director of the research center at Parkview Health, a non-profit health services provider in northeast Indiana.

“Medical students may be getting more genomics education, but they’re going to be really frustrated when they start practicing,” Mirro adds.

As an example, Mirro had to work for years, appealing a string of coverage denials, to convince insurer Anthem Blue Cross Blue Shield to pay for a $500 genetic test to see if a patient’s seven children had inherited the heart condition hypertrophic cardiomyopathy — the most common cause of sudden cardiac death in athletes and individuals 35 years old and younger. Since the patient, 38-year-old Matt Christman, carries a gene mutation for hereditary HCM, there is a 50 percent chance that his children are also carriers of this mutation. Mirro thought that testing Christman’s children for the mutations would be a better option than the alternatives — a $1,000 annual heart ultrasound or even pricier imaging tests — and would allow the family to more closely monitor the at-risk children carrying the HCM-associated gene mutation.

After patient groups started lobbying on behalf of Christman’s children and their story was recounted in the media, WellPoint’s Anthem Blue Cross Blue Shield unit agreed to pay for genetic testing for three of the oldest children. However, this was an exception, and the insurer’s latest coverage policy for genetic testing for HCM still deems the intervention “investigational and not medically necessary.” While the American Heart Association and the American College of Cardiology recommend genetic testing of HCM patients’ close relatives, Anthem has said it will require evidence from larger, more rigorously conducted studies that show genetic testing is useful in determining whether someone is at risk for the disease.

“Only with extreme lobbying and pressure are most genetic tests covered,” Mirro says. “Right now, it’s one battle at a time. … Even if physicians know the value of a genetic test most won’t order it because coverage of genetic tests requires an incredible sequence of bureaucratic events that chews up not only their time, but their staff’s time, which costs money.”

Mirro’s difficulties getting coverage for HCM genetic testing for the Christman children didn’t deter him, though, from providing genetic testing services at Parkview Research Center. If anything, it was a learning experience that inspired him to make changes at the research facility. He recently hired a genetic counselor to educate patients about diseases and discuss what test results might mean for their health and families.

Additionally, the research unit is in the process of setting up genetic testing to gauge whether patients who have recently undergone a stent procedure harbor mutations that make them more likely to be poor responders to Plavix. Mirro and his colleagues will follow patients who received this testing and collect data on whether the intervention helped avoid costs due to adverse events and if treating patients with other anti-platelet drugs improved their health.

Having learned that the only way to broadly affect payor policies on genetic tests is with evidence of their usefulness and cost effectiveness, Mirro says he has gotten “very involved with trying to look at the clinical outcomes of patients who have undergone testing and their families to see if there is value in providing these tests.”

With insurers’ increasing data demands for genetic tests, universities are also taking on this kind of research. On the one hand, by setting up a genetic testing program for Plavix and inputting the results into EMRs, the University of Florida is enabling academic physicians to practice personalized medicine. On the other hand, the project is also testing the hypothesis that analyzing many gene variations at once — and before certain conditions manifest in patients — is a cheaper and more efficient way to implement genomic testing in mainstream care.

As the cost of developing genomic tools decreases, the diagnostics industry is moving toward multiplex tests that analyze tens or hundreds of genes at once. However, unwilling to pay for the analysis of gene markers that have the potential to affect future healthcare decisions — but have no immediate impact on treatment — insurance firms currently pay for very few genetic tests that gauge multiple genes linked to a variety of conditions.

If the data collected as part of the Florida project show that multiplex testing is cost-effective, that may convince some payors to cover it. The program is “really a test of the information and the theory that having genetic testing information preemptively is good, having the data in the EMR is a good place to put it, and having it ready at the bedside is a way to facilitate adoption,” Lesko says.

Learning moments

For emerging technologies competing for adoption with established standards of care, industry is often in the best position to not only educate end users, but also lower many of the hurdles hindering uptake. As one of the first companies to commercialize gene expression profiling for breast cancer recurrence, molecular diagnostics company Genomic Health has found physician education to be a critical component of its success.

In 2004, when Genomic Health began marketing Oncotype DX — a test that assesses whether a patient’s disease will return and if she would benefit from chemotherapy — oncologists were used to tracking disease progression by examining the features of a tumor under a microscope, and genomic medicine wasn’t on medical schools’ radar screens. So it was up to the company to address the barriers keeping doctors from using its test, including convincing doctors of its value, making it easier for doctors to provide testing, and getting insurers to cover the diagnostic, which costs several thousand dollars.

Over the years, the company has focused not just on increasing the number of doctors who use Oncotype DX, but on teaching them how to use the test in the proper clinical scenario. For example, clinical validation studies for Oncotype DX have shown that the test determines recurrence risk and chemotherapy benefit only in patients whose tumors are driven by estrogen — a fact the company prominently highlights in brochures, in patient reports, through its sales teams, and in scientific publications. However, in the early days when Oncotype DX was a new test for oncologists, for every tumor sample submitted for testing, Genomic Health’s lab technicians looked at the estrogen receptor level in the tumor sample, and, if it seemed more typical for an ER-negative tumor, the company called the doctor to double-check the ER status of the tumor and reemphasize that Oncotype DX is only for ER-positive disease.

“We knew that one of our obligations was to inform physicians who were ordering the test that they should only test tumors that are ER positive,” says Genomic Health Chief Medical Officer Steve Shak. “We did catch some ER-negative samples that way and cancelled the tests. It was a tremendous educational moment for us and for the physicians.”

Moreover, Genomic Health has published studies involving more than 4,000 patient samples showing that by using the Oncotype DX risk score, in addition to traditional risk factors, physicians can better assess which women are at high or low risk of breast cancer recurrence. Those women Oncotype DX deems to be at low risk of recurrence can be treated with hormonal treatment, avoiding the adverse reactions and costs of chemotherapy.

The strength of the available evidence on Oncotype DX has had the most influence on physician adoption of the test and on insurance companies’ coverage policies, the company says. Genomic Health recently reported data from a Canadian study showing that after receiving Oncotype DX results, physicians changed their decision to give patients chemotherapy for 30 percent of women with early stage, localized breast cancer. In the US, 98 percent of women with breast cancer that hasn’t spread to the lymph nodes have coverage from private payors for Oncotype DX. Medicare also pays for the test.

Meanwhile, Genomic Health’s team of 120 so-called regional oncologic liaisons help physicians figure out the logistical issues that might keep them from using the test, such as how to order the diagnostic, what types of samples they need to submit, and how long it will take to get the results back. Genomic Health also operates a customer service call center that fields an average of 10,000 calls per month.

“This is the type of investment in physician education it takes to be a successful molecular diagnostics company,” Shak says. Genomic Health, which reported more than $200 million in revenues last year, wouldn’t disclose how much it spends on physician education efforts for Oncotype DX. The company, though did report spending about $84 million on sales and marketing efforts in 2011. To date Genomic Health’s strategy has swayed 10,000 physicians to order the test for more than 300,000 patients.

While, industry marketing might drive physician adoption, too aggressive marketing that doesn’t conform to treatment guidelines may raise red flags among insurers. Myriad Genetics’ BRACAnalysis dominates the BRCA1/2 mutation testing market for hereditary breast and ovarian cancer, but insurers have said that 20 percent or more of those tests are being performed for women who don’t meet testing guidelines.

Further, industry-driven education efforts are usually centered around specific products and target a particular physician specialty. These piecemeal programs don’t address the overwhelming need to educate doctors across disciplines and in an independent forum about genomic medicine. Cardiologist Eric Topol has said that he wants to develop a free online certification course on genomic medicine for all physicians, but the effort has been hindered by limited funding and the fragmented nature of medical practice today.

According to Topol, chief academic officer of Scripps Health, there isn’t one group or venue where such a broadly targeted genomics course can be housed. WebMD reaches only half of the 700,000 doctors in the US, while the American Medical Association has around 200,000 members.

“If we just set up a website and say, ‘Come to us,’ that’s not going to work,” he says. Introducing the course by specialty would take too long and cost even more, Topol adds. Although organizers of the program, called the College of Genomic Medicine, have already laid out a curriculum, the main roadblock remains: “How do we get to the physicians?”

Turna Ray is the editor of GenomeWeb’s Pharmacogenomics Reporter. She covers pharmacogenomics, personalized medicine, and companion diagnostics. E-mail her here or follow her GenomeWeb Twitter account at @PGxReporter.

 

Biomarker tool development for Early Diagnosis of Pancreatic Cancer: Van Andel Institute and Emory University

Reporter: Aviva Lev-Ari, PhD, RN

Van Andel, Emory to Develop Early Pancreatic Cancer Dx

October 19, 2012
 

NEW YORK (GenomeWeb News) – Van Andel Institute and Emory University researchers will use a $2.3 million grant from the National Cancer Institute to fund an effort to develop new biomarker tools that can aid in the early diagnosis of pancreatic cancer.

The Van Andel and Emory team plan to use gene expression studies and a shotgun glycomics approach to try to develop useful diagnostic tests for a certain carbohydrate structure that is prevalent in most, but not all, pancreatic cancer tumors.

In a shotgun glycomics approach, all of the glycans from a sample are tagged with a fluorescent tag and separated from each other to create a tagged glycolipid library. This library will be developed through gene expression studies on the tumor tissue.

“One of the most common features of pancreatic cancers is the increased abundance of a carbohydrate structure called the CA 19-9 antigen,” Brian Haab, head of Van Andel’s Laboratory of Cancer Immunodiagnostics, said in a statement.

Because CA 19-9 is attached to many different proteins that the tumor secretes into the blood it is used to confirm diagnosis of and to manage disease progression of pancreatic cancer. Tests for this structure have not yet been useful for early detection or diagnosis, however, because around 20 to 30 percent off incipient tumors produce low levels of CA 19-9.

“The low levels are usually due to inherited genetic mutations in the genes responsible for the synthesis of CA 19-9,” Haab explained. “However, patients who produce low CA 19-9 produce alternate carbohydrate structures that are abnormally elevated in cancer.”

This study aims to characterize and identify these glycans to improve the ability to detect cancer in patients with low CA 19-9 levels.

The research will integrate the use affinity reagents, a type of proteins called lectins, as well as shotgun glycomics, to detect these glycan structures and develop a diagnostic test for pancreatic cancer.

Because pancreatic cancer tends to spread before it is diagnosed and because of its resistance to chemotherapy, it has one of the lowest survival rates of any major cancer. It will affect more than 43,000 Americans in 2012 and will kill more than 37,000, according to NCI.

“We anticipate these new approaches advancing pancreatic cancer diagnostics as well as benefiting other glycobiology research in cancer,” Haab said.

Researchers from the Fred Hutchinson Cancer Research Center, Palo Alto Research Center, the University of Georgia, and the University of Pittsburgh Medical Center also are participating in the project.

 

 

 

Reporter: Aviva Lev-Ari, PhD, RN

 

Study Finds Dopamine Gene Variant Predictive of Placebo Response in IBS Patients

October 24, 2012
 

Researchers led by a group at Beth Israel Deaconess Medical Center have identified a genetic marker associated with the placebo effect in patients with irritable bowel syndrome.

According to the group, the finding is the first to show “genetic modulation of true placebo effects,” and supports the possibility of using genomic information to better design placebo-controlled clinical trials.

The researchers described their results in PLOS One this week. The project used genotyping to measure whether a polymorphism in the dopamine pathway‘s COMT gene was associated with differences in placebo response among 104 IBS patients enrolled in a three-arm trial of different placebo treatments.

After studying the distribution of the val158met polymorphism among the trial’s three arms — no treatment (a waitlist), treatment with placebo alone, and placebo treatment with an “augmented” physician-patient interaction involving more support — the group found that the strongest placebo response occurred in met/met homozygotes who received the augmented placebo treatment.

The researchers identified a weaker link between met/met and response in the placebo-only arm. And patients in the waitlist control arm showed no difference in response based on their genotype.

The study’s first author, Kathryn Hall, told PGx Reporter this week that having a genetic predictor of placebo response could allow researchers to stratify future placebo-controlled drug trials by potential responders and non-responders.

IBS is known to have a high placebo response rate. Hall said it’s likely that the use of genetic predictors for placebo response will be most relevant to trials of drugs for conditions that are similarly associated with high placebo response levels, such as depression, headache, allergies, and pain.

“In conditions where there tends to be a high placebo response, oftentimes a drug fails because it can’t prove efficacy above the placebo response. In those cases, the pharmaceutical companies are basically losing quite a bit of money and time and resources,” Hall said.

“So the question is – is this a possibility? Obviously, it hasn’t been done before and probably will need a lot more validation before anyone actually wants to do it,” she said. “But if it does hold true at least for some conditions and treatments, it would allow you to focus in on just the people who are [not going to respond to the placebo] – so it would build your power [and] reduce your cost, since you don’t have this set of people that are inflating the placebo response.”

Hall cited diseases like Parkinsons and schizophrenia, which involve dopamine metabolism, as examples where new treatments might see their efficacy estimation confounded by the placebo effect.

At a minimum, Hall suggested that drug developers might improve the success rates of their products by balancing the number of patients who are predisposed to respond and not respond to the placebo effect in both the treatment and placebo arms of a trial.

In the study, Hall and her colleagues evaluated a subset of patients from an earlier randomized controlled IBS trial.

In the previous trial, the group measured differences in response, based on patient-reported symptoms, after either placebo treatment alone, “augmented” placebo treatment in which patients were given extra physician interaction and support, or no treatment, and placement on a waiting list.

In the genetic follow-up, the researchers genotyped 104 patient samples to look for associations between val158met genotype and placebo-response, based on reported symptoms and quality of life.

The group coded each patient according to the presence of the COMT met allele and found that patients with the met/met genotype had the greatest level of improvement — based on their scores in a measure called the IBS-Symptom Severity Scale — while those with the val/val type had the least. Val/met patients fell in the middle.

While patients homozygous for the COMT val158met allele were the most responsive to placebo overall, the strongest signal was in the augmented treatment arm, with a smaller effect in the placebo-alone arm, and virtually no effect, or even a reverse effect, in the waitlist control arm.

Overall, the group concluded that the results “strongly suggest that COMT val158met, specifically the met/met genotype, is a potential marker for placebo response in IBS.”

The fact that the genotype is associated with a positive outcome only in groups given a placebo, and not in the control group, indicates that it is a true predictor of placebo effect, not just improvement in general, the group wrote.

While previous studies have looked for a genetic link to placebo response, they have not included this control arm, according to the Beth Israel team. Additional studies that hypothesize a COMT involvement and include a no-treatment arm “will be critical to confirm our findings,” the group added.

According to Hall, the field is likely still far away from using genomic information to influence the design of placebo-controlled trials. However, her group’s results suggest a path forward, she said.

The results may also have implications for more personalized treatment strategies, she said.

“On one hand, you could hypothesize that there are situations where people are placebo responders and taking a drug with a lot of side effects … Obviously giving people placebo pills is a long way off, but [perhaps you could] minimize someone’s drug intake if they are having more of a placebo response so they don’t have to have all the side effects,” she said.

At the same time, she said, the trial highlighted the influence of the “warm, caring doctor relationship.”

“Having a mechanistic understanding of what’s going on there, I think, will reinforce the need and the importance of this part of medicine,” she said, at least for some. The fact that val/val subjects, for example, showed the same lack of response in both the placebo-alone and augmented arms of the study may shed some light on why, “despite their best efforts, many a warm and caring physician has had patients that seemed to derive minimum benefit from their empathic attentions,” the study authors wrote.

      Molika Ashford is a GenomeWeb contributing editor and covers personalized medicine and molecular diagnostics. E-mail her here.

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VIEW VIDEO – Short Overview [1:45 minutes]

FAME and FAME 2

VIEW VIDEO –  Clinical Results [44-54 minutes]

Clinical Results

Clinical Summary

Fractional Flow Reserve-Guided PCI versus Medical Therapy in Stable Coronary Disease

(The FAME II Study)

A Multicenter, Randomized Prospective Study in Consecutive Patients.

This study is sponsored by St. Jude Medical.

Coordinating Clinical Investigator: Bernard De Bruyne, OLV Ziekenhuis, Aalst, Belgium

Fractional Flow Reserve–Guided PCI versus Medical Therapy in Stable Coronary Disease

Bernard De Bruyne, M.D., Ph.D., Nico H.J. Pijls, M.D., Ph.D., Bindu Kalesan, M.P.H., Emanuele Barbato, M.D., Ph.D., Pim A.L. Tonino, M.D., Ph.D., Zsolt Piroth, M.D., Nikola Jagic, M.D., Sven Möbius-Winkler, M.D., Gilles Rioufol, M.D., Ph.D., Nils Witt, M.D., Ph.D., Petr Kala, M.D., Philip MacCarthy, M.D., Thomas Engström, M.D., Keith G. Oldroyd, M.D., Kreton Mavromatis, M.D., Ganesh Manoharan, M.D., Peter Verlee, M.D., Ole Frobert, M.D., Nick Curzen, B.M., Ph.D., Jane B. Johnson, R.N., B.S.N., Peter Jüni, M.D., and William F. Fearon, M.D. for the FAME 2 Trial Investigators

N Engl J Med 2012; 367:991-1001   September 13, 2012DOI: 10.1056/NEJMoa1205361

BACKGROUND

The preferred initial treatment for patients with stable coronary artery disease is the best available medical therapy. We hypothesized that in patients with functionally significant stenoses, as determined by measurement of fractional flow reserve (FFR), percutaneous coronary intervention (PCI) plus the best available medical therapy would be superior to the best available medical therapy alone.

METHODS

In patients with stable coronary artery disease for whom PCI was being considered, we assessed all stenoses by measuring FFR. Patients in whom at least one stenosis was functionally significant (FFR, ≤0.80) were randomly assigned to FFR-guided PCI plus the best available medical therapy (PCI group) or the best available medical therapy alone (medical-therapy group). Patients in whom all stenoses had an FFR of more than 0.80 were entered into a registry and received the best available medical therapy. The primary end point was a composite of death, myocardial infarction, or urgent revascularization.

RESULTS

Recruitment was halted prematurely after enrollment of 1220 patients (888 who underwent randomization and 332 enrolled in the registry) because of a significant between-group difference in the percentage of patients who had a primary end-point event: 4.3% in the PCI group and 12.7% in the medical-therapy group (hazard ratio with PCI, 0.32; 95% confidence interval [CI], 0.19 to 0.53; P<0.001). The difference was driven by a lower rate of urgent revascularization in the PCI group than in the medical-therapy group (1.6% vs. 11.1%; hazard ratio, 0.13; 95% CI, 0.06 to 0.30; P<0.001); in particular, in the PCI group, fewer urgent revascularizations were triggered by a myocardial infarction or evidence of ischemia on electrocardiography (hazard ratio, 0.13; 95% CI, 0.04 to 0.43; P<0.001). Among patients in the registry, 3.0% had a primary end-point event.

CONCLUSIONS

In patients with stable coronary artery disease and functionally significant stenoses, FFR-guided PCI plus the best available medical therapy, as compared with the best available medical therapy alone, decreased the need for urgent revascularization. In patients without ischemia, the outcome appeared to be favorable with the best available medical therapy alone. (Funded by St. Jude Medical; ClinicalTrials.gov number, NCT01132495.)

Supported by St. Jude Medical.

Disclosure forms provided by the authors are available with the full text of this article at NEJM.org.

This article was published on August 28, 2012, and updated on October 18, 2012, at NEJM.org.

SOURCE INFORMATION

From the Cardiovascular Center Aalst, Onze-Lieve-Vrouw Clinic, Aalst, Belgium (B.D.B., E.B.); Department of Cardiology, Catharina Hospital, and Department of Biomedical Engineering, Eindhoven University of Technology — both in Eindhoven, the Netherlands (N.H.J.P., P.A.L.T.); Division of Clinical Epidemiology and Biostatistics, Institute of Social and Preventive Medicine and Clinical Trials Unit Bern, University of Bern, Bern, Switzerland (B.K., P.J.); Hungarian Institute of Cardiology, Budapest (Z.P.); Clinical Center Kragujevac, Kragujevac, Serbia (N.J.); Heart Center Leipzig, Leipzig, Germany (S.M.-W.); Cardiovascular Hospital, Lyon, France (G.R.); Södersjukhuset, Stockholm (N.W.), and Karolinska Institutet at Örebro University Hospital, Örebro (O.F.) — both in Sweden; Department of Internal Medicine and Cardiology, University Hospital Brno, Brno, Czech Republic (P.K.); King’s College Hospital, London (P.M.), Golden Jubilee National Hospital, Glasgow (K.G.O.), Royal Victoria Hospital, Belfast (G.M.), and Department of Cardiology, Southampton University Hospital Trust, Southampton (N.C.) — all in the United Kingdom; Department of Cardiology, Rigshospitalet University Hospital, Copenhagen (T.E.); Atlanta Veterans Affairs Medical Center, Atlanta (K.M.); Northeast Cardiology Associates, Bangor, ME (P.V.); St. Jude Medical, Plymouth, MN (J.B.J.); and Stanford University Medical Center, Stanford, CA (W.F.F.).

Address reprint requests to Dr. De Bruyne at the Cardiovascular Centre Aalst, OLV-Clinic, Moorselbaan 164, B-9300 Aalst, Belgium, or atbernard.de.bruyne@olvz-aalst.be.

The investigators in the Fractional Flow Reserve versus Angiography for Multivessel Evaluation 2 (FAME 2) trial are listed in the Supplementary Appendix, available at NEJM.org.

Conclusions

The FAME II study results show that FFR-guided PCI compared to medical management alone significantly reduces patients’ risk for unplanned hospital readmission with urgent revascularization.

The new data support the paradigm of “Functionally Complete Revascularization,” that is, stenting of ischemic lesions and medical treatment of non-ischemic ones.

Routine Use of Ffr Significantly Improves the Outcome of Treatment in Stable CAD Patients. St. Jude Medical is focused on reducing risk by continuously finding ways to put more control into the hands of those who save and enhance lives.

SUMMARY OF KEY FINDINGS

FFR significantly improves outcome of treatment in stable patients. The results of FAME II, a St. Jude Medical sponsored clinical trial, show a significant benefit in using FFR-guided intervention. In patients with stable coronary artery disease undergoing PressureWireTM-guided intervention, PCI plus medical therapy was found to improve outcomes compared to medical therapy alone.

FFR Significantly Reduces Risk of Unplanned Hospital Readmission for Urgent Revascularization

Background

In patients with clinically stable coronary disease, PCI has not been shown to affect clinical outcomes such as death, nonfatal myocardial infarction and the need for urgent revascularization. In previous trials on revascularization, treatment has been guided by the angiographic appearance of the lesions. It is likely that in all previous trials dealing with patients with nonacute coronary artery disease (CAD), a sizable proportion of patients did not have ischemia.

Objectives

The overall purpose of the FAME II study was to compare the clinical outcomes of FFR-guided contemporary PCI plus medical therapy versus medical therapy alone in patients with stable coronary disease.

Methods

The FAME II trial is a prospective, multicenter randomized clinical trial with an all comers design. All consecutive patients with stable clinical condition and angiographically defined one-, two- or three-vessel coronary artery disease and amenable for PCI were screened and considered for participation in the study. Patients with at least one hemodynamically significant lesion were randomized into PCI (drug-eluting stents [DES] were recommended) plus medical therapy or medical therapy alone. It was expected that in approximately 20% of patients no stenoses would be hemodynamically significant.

Patients without hemodynamically significant lesions were enrolled in the registry portion of the study and treated with medical therapy. For prospectively collected data in the randomized study and the registry, an independent clinical events committee (CEC) adjudicated all clinical endpoints.

Key Exclusion Criteria

 Prior coronary artery bypass grafting (CABG)

Left ventricular ejection fraction (LVEF) <30%

 Left main (LM) stenosis

For patients with one or more significant lesions, there was an 86% relative reduction in the risk for unplanned hospital readmission with urgent revascularization for patients who received FFR-guided PCI plus medical therapy.

These findings support FFR-guided PCI compared to medical management alone to improve outcomes in the treatment of stable patients with single-vessel or multivessel coronary artery disease.

Study Endpoints

Original FAME II Study Flow Chart Primary Endpoint Composite of:

 all-cause death

 nonfatal myocardial infarction

 unplanned hospitalization with urgent revascularization

As adjudicated by an independent CEC.

Secondary Endpoints

 Individual components of the primary endpoint*

 Cardiac death*

 Nonurgent revascularization procedures*

 Angina class

*As adjudicated by an independent CEC.

Stable patients scheduled for 1, 2 or 3 vessel DES stenting

RANDOMIZED TRIAL REGISTRY

FFR in all target lesions

Randomization 1:1

PCI + medical therapy medical therapy

Follow-up after 1, 6 months, 1, 2, 3, 4 and 5 years

At least 1 stenosis with FFR ≤ 0.80 When all FFR > 0.80

Medical Therapy

 Aspirin

 Beta blocker

Calcium blocker and/or nitrate as necessary

 Statin

 ACE inhibitor (or ARB)

Diabetes treatment guided by a specialist

FFR-guided PCI

 FFR measured during hyperemia

 PCI only if FFR ≤ 0.80 and randomized to PCI

 2nd generation drug-eluting stents (recommended)

Fractional Flow Reserve Measurements Intracoronary pressure measurements were obtained with a guiding catheter (fluid-filled) and the St. Jude Medical PressureWire CertusTM or AerisTM guidewire.

Results

The independent Data and Safety Monitoring Board recommended halting patient recruitment due to a significantly increased patient risk of major adverse cardiac events among patients randomized to medical therapy alone compared to patients randomized to medical therapy plus PCI.

The enrollment goal in FAME II was approximately 1,800 patients (randomized study and registry combined). The data sample presented here is the same data on which the decision to halt enrollment was based (January 15, 2012).

A total of 888 (73%) patients with ischemic lesions had been successfully randomized, and an additional 332 (27%) patients were enrolled in the registry because no ischemic lesions were detected. In total, 1,220 patients were enrolled in the FAME II trial, including 1,054 who were assigned to follow-up.

Medical Therapy

Actual FAME II Study Flow Chart

* Note that 6 patients had total occlusions supplying akinetic myocardium and were therefore not considered for PCI; 1 patient had 2 FFR negative lesions and was therefore included in the registry, however, a subsequently detected total occlusion was eventually treated with DES.

Randomized (n = 888)

Underwent FFR (n = 1220)

FFR >0.80 in all lesions included in registry

(n = 332)*

Allocated to medical therapy alone (n = 441)

Received allocated intervention (n = 439)

Did not receive allocated intervention (n = 2)

Erroneously received DES (n = 2)

Randomly selected to receive follow-up (n = 166)

Received medical therapy alone (n = 165)

Received DES (n = 1)

Allocated to PCI+medical therapy (n = 447)

Received allocated intervention (n = 435)

Did not receive allocated intervention (n = 12)

Treated with balloon angioplasty (n = 3)

Underwent CABG rather than PCI (n = 4)

Received medical therapy, planned for staged

procedure (n = 3)

Received medical therapy, unsuccessful PCI (n = 1)

Received medical therapy, FFR >0.8 (n = 1)

Follow-up information for primary endpoint

available until Jan 15, 2012 (n = 446)

Followed up and alive (n = 445)

Deceased (n = 1)

Follow-up at Jan 15, 2012 unavailable (n = 1)

Withdrew (n = 1)

Lost to follow-up (n = 0)

Follow-up information for primary endpoint

available until Jan 15, 2012 (n = 439)

Followed up and alive (n = 436)

Deceased (n = 3)

Follow-up at Jan 15, 2012 unavailable (n = 2)

Withdrew (n = 2)

Lost to follow-up (n = 0)

Follow-up information for primary endpoint

available until Jan 15, 2012 (n = 163)

Followed up and alive (n = 163)

Deceased (n = 0)

Follow-up at Jan 15, 2012 unavailable (n = 3)

Withdrew (n = 1)

Lost to follow-up (n = 2)

Analyzed on primary clinical endpoint (n = 166)

Censored at time of lost to follow-up

or withdrawal (n = 3)

Analyzed on primary clinical endpoint (n = 441)

Censored at time of lost to follow-up

or withdrawal (n = 2)

Analyzed on primary clinical endpoint (n = 447)

Censored at time of lost to follow-up

or withdrawal (n = 1)

Patients n = 447 n = 441 n = 166

Age in years, mean±SD 63.52 ± 9.35 63.86 ± 9.62 63.58 ± 9.75 0.90

Men, n (%) 356 (79.6) 338 (76.6) 113 (68.1) 0.005

BMI, mean±SD 28.29 ± 4.27 28.44 ± 4.55 27.83 ± 3.94 0.14

Family history of coronary artery disease, n (%) 216 (48.3) 207 (46.9) 76 (45.8) 0.65

Current smoking, n (%) 89 (19.9) 90 (20.4) 35 (21.1) 0.79

Hypertension, n (%) 347 (77.6) 343 (77.8) 136 (81.9) 0.23

Hypercholesterolemia, n (%) 330 (73.9) 348 (78.9) 118 (71.1) 0.15

Diabetes mellitus, n (%) 123 (27.5) 117 (26.5) 42 (25.3) 0.65

Insulin requiring diabetes, n (%) 39 (8.7) 39 (8.8) 10 (6.0) 0.24

Renal insufficiency (Creatinine > 2.0 mg/dL), n (%) 8 (1.8) 12 (2.7) 7 (4.2) 0.14

Peripheral vascular disease, n (%) 43 (9.6) 47 (10.7) 8 (4.8) 0.065

History of stroke/TIA, n (%) 33 (7.4) 28 (6.3) 10 (6.0) 0.69

History of MI, n (%) 164 (37.2) 165 (37.8) 60 (36.6) 0.83

History of PCI in target vessel, n (%) 80 (17.9) 76 (17.2) 34 (20.5) 0.37

Angina Class, n (%) 0.64

Asymptomatic 53 (11.9) 46 (10.5) 17 (10.2) .

CCS class I 82 (18.3) 98 (22.3) 42 (25.3) .

CCS class II 204 (45.6) 197 (44.8) 74 (44.6) .

CCS class III 80 (17.9) 65 (14.8) 23 (13.9) .

CCS IV, stabilized 28 (6.3) 34 (7.7) 10 (6.0) .

Silent Ischemia, n (%) 73 (16.3) 73 (16.6) 27 (16.3) 0.96

Left ventricular ejection fraction<50%, n (%) 83 (19.6) 56 (13.7) 27 (18.0) 0.69

Classification of patients according to angiography

No. of significant lesions per patient, mean±SD 1.87 ± 1.05 1.73 ± 0.94 1.32 ± 0.59 <0.001

No. of vessels per patient with at least one significant lesion, n (%) <0.001

1 251 (56.2) 261 (59.2) 136 (81.9) .

2 156 (34.9) 146 (33.1) 26 (15.7) .

3 40 (8.9) 34 (7.7) 4 (2.4) .

Proximal or mid LAD stenosis (%) 65.1 62.6 44.6 <0.001

Classification of patients according to FFR

No. of significant lesions per patient according to FFR, mean±SD 1.52 ± 0.78 1.42 ± 0.73 0.03 ± 0.17 <0.001

No. of vessels with significant lesions by FFR, n (%) 1.00

1 331 (74.0) 343 (77.8) 3.0

2 102 (22.8) 85 (19.3) 0 (0)

3 14 (3.1) 13 (2.9) 0 (0)

Proximal or mid LAD stenosis (%) 62.4 59.6 0.6 <0.001

Lesions n = 890 n = 815 n = 241

Classification of lesions according to angiography .

No. of significant lesions (diameter stenosis>50%), n (%) 837 (94.0) 764 (93.7) 219 (90.9) 0.13

Percent diameter stenosis, n (%) <0.001

<50% 53 (6.0) 51 (6.3) 22 (9.1)

50-69% 317 (35.6) 331 (40.6) 176 (73.0)

70-90% 383 (43.0) 331 (40.6) 38 (15.8)

>90% 101 (11.3) 80 (9.8) 0 (0)

Total occlusions 36 (4.0) 22 (2.7) 5 (2.1)

Classification of lesions according to FFR

No. of significant lesions (FFR≤0.80), n (%) 679 (76.3) 625 (76.7) 5* (2.1) <0.001

FFR in significant lesions, mean±SD 0.68 ± 0.10 0.68 ± 0.15 0.50 ± 0.00 0.013

Randomized Trial Registry p-value for

Trial vs. Registry

PCI+medical therapy medical therapy alone

**Differences between the two randomized groups were not significant with the exception of left ventricular ejection fraction<50% (p<0.05). Data are mean±SD or number of patients assessed (%). P-value using chi square test;

when cells are small Fisher’s test is used. Data for ejection fraction were available for 423 in PCI&medical therapy, 410 in medical therapy and 150 in registry. Data for history of MI were available for 442 in PCI&medical therapy,

436 in medical therapy and 295 in registry. CCS=Canadian Cardiovascular Society functional classification of angina pectoris; Data available in 447 in PCI&medical therapy, 440 in medical therapy, and 166 in registry. **5 totally

occluded arteries supplied infarcted areas and therefore not considered for revascularization using PCI. In patient level analysis p-value calculated using chi-square test, in case of cells <15 Fisher’s test. In lesion level analysis,

mixed maximum-likelihood logistic regression models were used for comparisons between groups for dichotomous variables and mixed maximum-likelihood linear regression models for continuous variables to account for the

correlation of multiple lesions within patients.

Conclusions

The FAME II study results show that FFR-guided PCI compared to medical management alone significantly reduces patients’ risk for unplanned hospital readmission with urgent revascularization.

The new data support the paradigm of “Functionally Complete Revascularization,” that is, stenting of ischemic lesions and medical treatment of non-ischemic ones.

Routine Use of Ffr Significantly Improves the Outcome of Treatment in Stable CAD Patients. St. Jude Medical is focused on reducing risk by continuously finding ways to put more control into the hands of those who save and enhance lives.

SJMprofessional.com

SJMknowledgecenter.com

Product referenced is approved for CE Mark.

Rx Only

Please review the Instructions for Use prior to using these devices for a complete listing of indications, contraindications, warnings, precautions,

potential adverse events, and directions for use.

PressureWire Aeris and PressureWire Certus are designed, developed and manufactured by St. Jude Medical Systems AB. PressureWire, Aeris,

Certus, ST. JUDE MEDICAL, the nine-squares symbol and MORE CONTROL. LESS RISK. are registered and unregistered trademarks and service

marks of St. Jude Medical, Inc. and its related companies.

©2012 St. Jude Medical, Inc. All rights reserved.

IPN 2256-12

ATRIAL FIBRILLATION CARDIAC RHYTHM MANAGEMENT CARDIOVASCULAR NEUROMODULATION

The content of this clinical summary is based on:

 De Bruyne, B., et al. Fractional Flow Reserve-Guided Percutaneous Coronary Intervention Versus Medical Treatment in Stable Coronary Disease,

N Engl J Med 2012; published online ahead of print August 28, 2012.

http://www.Clinicaltrials.gov. FAME II Study Identifier: NCT01132495.

 FAME II study protocol (on file, St. Jude Medical).

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SOURCE:

http://www.sjmprofessional.com/fame2?utm_source=fameii&utm_medium=vanity&utm_campaign=fame2

Reporter: Prabodh Kandala, PhD

The most common breast cancer screening method used today is called dual-view digital mammography, but it isn’t always successful in identifying tumors, said Jianwei (John) Miao, a UCLA professor of physics and astronomy and researcher with the California NanoSystems Institute at UCLA.

“While commonly used, the limitation is that it provides only two images of the breast tissue, which can explain why 10 to 20 percent of breast tumors are not detectable on mammograms,” Miao said. “A three-dimensional view of the breast can be generated by a CT scan, but this is not frequently used clinically, as it requires a larger dose of radiation than a mammogram. It is very important to keep the dose low to prevent damage to this sensitive tissue during screening.”

Recognizing these limitations, the scientists went in a new direction. In collaboration with the European Synchrotron Radiation Facility in France and Germany’s Ludwig Maximilians University, Miao’s international colleagues used a special detection method known as phase contrast tomography to X-ray a human breast from multiple angles.

They then applied equally sloped tomography, or EST — a breakthrough computing algorithm developed by Miao’s UCLA team that enables high-quality image-reconstruction — to 512 of these images to produce 3-D images of the breast at a higher resolution than ever before. The process required less radiation than a mammogram.

In a blind evaluation, five independent radiologists from Ludwig Maximilians University ranked these images as having a higher sharpness, contrast and overall image quality than 3-D images of breast tissue created using other standard methods.

“Even small details of the breast tumor can be seen using this technique,” said Maximilian Reiser, director of the radiology department at Ludwig Maximilians University, who contributed his medical expertise to the research.

The technology commonly used today for mammograms or imaging a patient’s bones measures the difference in an X-ray’s intensity before and after it passes through the body. But the phase contrast X-ray tomography used in this study measures the difference in the way an X-ray oscillates through normal tissue rather than through slightly denser tissue like a tumor or bone. While a very small breast tumor might not absorb many X-rays, the way it changes the oscillation of an X-ray can be quite large, Miao said. Phase contrast tomography captures this difference in oscillation, and each image made using this technique contributes to the overall 3-D picture.

Like cleaning the lenses of a foggy pair of glasses, scientists are now able to use a technique developed by UCLA researchers and their European colleagues to produce three-dimensional images of breast tissue that are two to three times sharper than those made using current CT scanners at hospitals. The technique also uses a lower dose of X-ray radiation than a mammogram.

The computational algorithm EST developed by Miao’s UCLA team is a primary driver of this advance. Three-dimensional reconstructions, like the ones created in this research, are produced using sophisticated software and a powerful computer to combine many images into one 3-D image, much like various slices of an orange can be combined to form the whole. By rethinking the mathematic equations of the software in use today, Miao’s group developed a more powerful algorithm that requires fewer “slices” to get a clearer overall 3-D picture.

“The technology used in mammogram screenings has been around for more than 100 years,” said Paola Coan, a professor of X-ray imaging at Ludwig Maximilians University. “We want to see the difference between healthy tissue and the cancer using X-rays, and that difference can be very difficult to see, particularly in the breast, using standard techniques. The idea we used here was to combine phase contrast tomography with EST, and this combination is what gave us much higher quality 3-D images than ever before.”

While this new technology is like a key in a lock, the door will only swing open — bringing high-resolution 3-D imaging from the synchrotron facility to the clinic — with further technological advances, said Alberto Bravin, managing physicist of the biomedical research laboratory at the European Synchrotron Radiation Facility. He added that the technology is still in the research phase and will not be available to patients for some time.

“A high-quality X-ray source is an absolute requirement for this technique,” Bravin said. “While we can demonstrate the power of our technology, the X-ray source must come from a small enough device for it to become commonly used for breast cancer screening. Many research groups are actively working to develop this smaller X-ray source. Once this hurdle is cleared, our research is poised to make a big impact on society.”

These results represent the collaborative efforts of senior authors Miao, Bravin and Coan. Significant contributions were provided by co-first authors Yunzhe Zhao, a recent UCLA doctoral graduate in Miao’s laboratory, and Emmanuel Brun, a scientist working with Bravin and Coan. Other co-authors included Zhifeng Huang of UCLA and Aniko Sztrókay, Paul Claude Diemoz, Susanne Liebhardt, Alberto Mittone and Sergei Gasilov of Ludwig Maximilians University.

The research was funded by UC Discovery/Tomosoft Technologies; the National Institute of General Medical Sciences, a division of the National Institutes of Health; and the Deutsche Forschungsgemeinschaft-Cluster of Excellence Munich-Centre for Advanced Photonics.

Abstract:

Mammography is the primary imaging tool for screening and diagnosis of human breast cancers, but ∼10–20% of palpable tumors are not detectable on mammograms and only about 40% of biopsied lesions are malignant. Here we report a high-resolution, low-dose phase contrast X-ray tomographic method for 3D diagnosis of human breast cancers. By combining phase contrast X-ray imaging with an image reconstruction method known as equally sloped tomography, we imaged a human breast in three dimensions and identified a malignant cancer with a pixel size of 92 μm and a radiation dose less than that of dual-view mammography. According to a blind evaluation by five independent radiologists, our method can reduce the radiation dose and acquisition time by ∼74% relative to conventional phase contrast X-ray tomography, while maintaining high image resolution and image contrast. These results demonstrate that high-resolution 3D diagnostic imaging of human breast cancers can, in principle, be performed at clinical compatible doses.

Ref:

breast tumors in 3-D with great clarity, reduced radiation. ScienceDaily. Retrieved October 23, 2012, from http://www.sciencedaily.com­/releases/2012/10/121022162710.htm

http://www.pnas.org/content/early/2012/10/17/1204460109

 

Reporter: Aviva Lev-Ari, PhD, RN

Australian-led Team Reports on New Nocturnal Epilepsy Gene

October 22, 2012

NEW YORK (GenomeWeb News) – An international team led by investigators in Australia has linked mutations in a sodium-gated potassium channel subunit gene to a subset of severe nocturnal frontal lobe epilepsy cases.

As they reported online yesterday in Nature Genetics, the researchers began by testing a family with autosomal dominant nocturnal frontal lobe epilepsy, or ADNFLE. Affected members of the family often had not only typical ADNFLE symptoms, but also intellectual and/or psychiatric features that don’t usually characterize the disorder.

After narrowing in on a chromosome 9 region via linkage analyses in the family, the team identified ADNFLE-associated missense mutations in the sodium-gated potassium channel subunit gene KCNT1 by whole-exome sequencing in two affected family members. Follow-up testing on more than 100 other unrelated individuals with nocturnal frontal lobe epilepsy indicated that both inherited and de novo mutations in the gene can cause severe forms of the conditions that tend to include other co-morbidities.

“KCNT1 mutations were identified in two additional families and a sporadic case with severe ADNFLE and psychiatric features,” University of South Australia researcher Leanne Dibbens and the University of Melbourne’s Ingrid Scheffer, the study’s co-corresponding authors, and their colleagues wrote.

“These findings implicate the sodium-gated potassium channel complex in ADNFLE, and, more broadly, in the pathogenesis of focal epilepsies,” they added.

As the name suggests, ADNFLE is inherited in an autosomal dominant manner in affected families. Symptoms of the condition — including seizures that occur while individuals are asleep — generally appear in childhood, the researchers explained. And previous studies have implicated mutations to nicotinic acetylcholine receptor subunit genes in a subset of ADNFLE cases.

For the current study, the team focused on a multi-generational family with an especially severe form of ADNFLE that was accompanied by other symptoms such as intellectual disability and psychiatric disorders.

Genome-wide linkage analyses within the family led to a suspicious 2.36 million base stretch of sequence on chromosome 9, which housed almost 100 genes. Among them: two ion channel-coding genes, KCNT1 and GRIN1.

For two of the affected family members, the team turned to whole-exome sequencing to try to track down the most likely cause of ADNFLE. Indeed, missense mutations in KCNT1 that were predicted to be pathogenic turned up in one of the two exome sequences.

The mutation was not initially identified in the other family member’s exome sequence data, owing to low coverage, researchers explained. But it was subsequently shown to be present in both individuals by Sanger sequencing.

Consistent with the notion that this KCNT1 mutation could be related to ADNFLE pathogenesis, the investigators did not find it when they tested 111 unaffected, ancestry-matched individuals. Nor did it turn up in the dbSNP database, they reported, or in data generated for the 1000 Genomes Project or through the National Heart, Lung, and Blood Institute’s Exome Sequencing Project.

On the other hand, the team did find mutations in KCNT1 when it assessed another 108 unrelated individuals who either had ADNFLE or sporadically occurring nocturnal frontal lobe epilepsy.

That analysis helped the investigators track down two more ADNFLE-affected families with KCNT1 mutations that co-segregated with the disease, along with one case of sporadic nocturnal frontal lobe epilepsy including psychiatric features that seemed to stem from de novo mutations to KCNT1.

“[T]he phenotype associated with KNCT1 mutations is both more severe and more penetrant than that typically found with mutations affecting [nicotinic acetylcholine receptors],” the study’s authors noted.

In addition to showing more pronounced ADNFLE symptoms, they explained, the disease appears to manifest itself at a younger age in the cases linked to KCNT1 mutations.

Moreover, several cases that appear to be caused by alterations to KCNT1 also included intellectual disability, psychiatric, and/or behavioral features. The severity of such symptoms varied from one individual to the next — a pattern that the researchers speculated might be due to differences in the nature and extent of the KCNT1 mutation involved.

In addition to providing clues to help classify ADNFLE cases and offer genetic counseling for families affected by it, those involved in the study say the results should also prove useful for understanding — and potentially targeting — the processes that underlie this type of epilepsy.

“[T]his finding should provide new insights into the biological mechanisms underlying the pathogenesis of ADNFLE,” they concluded, “which may lead to targeted therapies addressing the serious co-morbidities as well as the debilitating seizure disorder.”

Reporter: Aviva Lev-Ari, PhD, RN 

Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

Jan Krumsiek1, Karsten Suhre1,2, Anne M. Evans3, Matthew W. Mitchell3, Robert P. Mohney3, Michael V. Milburn3, Brigitte Wägele1,4, Werner Römisch-Margl1, Thomas Illig5,6, Jerzy Adamski7,8, Christian Gieger9, Fabian J. Theis1,10, Gabi Kastenmüller1*

 

1 Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany, 2 Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar, 3 Metabolon, Research Triangle Park, North Carolina, United States of America, 4 Department of Genome-Oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising, Germany, 5 Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany, 6 Biobank of the Hanover Medical School, Hanover Medical School, Hanover, Germany, 7 Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany, 8 Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany, 9 Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany, 10 Department of Mathematics, Technische Universität München, Garching, Germany

Abstract 

Recent genome-wide association studies (GWAS) with metabolomics data linked genetic variation in the human genome to differences in individual metabolite levels. A strong relevance of this metabolic individuality for biomedical and pharmaceutical research has been reported. However, a considerable amount of the molecules currently quantified by modern metabolomics techniques are chemically unidentified. The identification of these unknown metabolites is still a demanding and intricate task, limiting their usability as functional markers of metabolic processes. As a consequence, previous GWAS largely ignored unknown metabolites as metabolic traits for the analysis. Here we present a systems-level approach that combines genome-wide association analysis and Gaussian graphical modeling with metabolomics to predict the identity of the unknown metabolites. We apply our method to original data of 517 metabolic traits, of which 225 are unknowns, and genotyping information on 655,658 genetic variants, measured in 1,768 human blood samples. We report previously undescribed genotype–metabotype associations for six distinct gene loci (SLC22A2, COMT, CYP3A5, CYP2C18, GBA3, UGT3A1) and one locus not related to any known gene (rs12413935). Overlaying the inferred genetic associations, metabolic networks, and knowledge-based pathway information, we derive testable hypotheses on the biochemical identities of 106 unknown metabolites. As a proof of principle, we experimentally confirm nine concrete predictions. We demonstrate the benefit of our method for the functional interpretation of previous metabolomics biomarker studies on liver detoxification, hypertension, and insulin resistance. Our approach is generic in nature and can be directly transferred to metabolomics data from different experimental platforms.

Introduction 

Recently, genome-wide association studies (GWAS) on metabolic quantitative traits have proven valuable tools to uncover the genetically determined metabolic individuality in the general population [1][5]. Interestingly, a great portion of the genetic loci that were found to significantly associate with levels of specific metabolites are within or in close proximity to metabolic enzymes or transporters with known disease or pharmaceutical relevance. Moreover, compared to GWAS with clinical endpoints the effect sizes of the genotypes are exceptionally high.

The number and type of the metabolic features that went into these GWAS was mainly defined by the metabolomics techniques used: Gieger et al. [1] and Illig et al. [2] used a targeted mass spectrometry (MS)-based approach giving access to the concentrations of 363 and 163 metabolites, respectively. Suhre et al. [3] and Nicholson et al. [4] applied untargeted nuclear magnetic resonance (NMR) based metabolomics techniques, yielding 59 metabolites that had been identified in the spectra prior to the GWAS and 579 manually selected peaks from the spectra, respectively. In Suhre et al. [5], 276 metabolites from an untargeted MS-based approach were analyzed.

While these previous GWAS focused on metabolic features with known identity, untargeted metabolomics approaches additionally provide quantifications of so-called “unknown metabolites”. An unknown metabolite is a small molecule that can reproducibly be detected and quantified in a metabolomics experiment, but whose chemical identity has not been elucidated yet. In an experiment using liquid chromatography (LC) coupled to MS, such an unknown would be defined by a specific retention time, one or multiple masses (e.g. from adducts), and a characteristic fragmentation pattern of the primary ion(s). An unknown observed by NMR spectroscopy would correspond to a pattern in the chemical shifts. Unknowns may constitute previously undocumented small molecules, such as rare xenobiotics or secondary products of metabolism, or they may represent molecules from established pathways which could not be assigned using current libraries of MS fragmentation patterns [6], [7] or NMR reference spectra [8].

The impact of unknown metabolites for biomedical research has been shown in recent metabolomics-based discovery studies of novel biomarkers for diseases and various disease-causing conditions. This includes studies investigating altered metabolite levels in blood for insulin resistance [9], type 2 diabetes [10], and heart disorders [11]. A considerable number of high-ranking hits reported in these biomarker studies represent unknown metabolites. As long as their chemical identities are not clarified the usability of unknown metabolites as functional biomarkers for further investigations and clinical applications is rather limited.

In mass-spectrometry-based metabolomics approaches, the assignment of chemical identity usually involves the interpretation and comparison of experiment-specific parameters, such as accurate masses, isotope distributions, fragmentation patterns, and chromatography retention times [12][14]. Various computer-based methods have been developed to automate this process. For example, Rasche and colleagues [15] elucidated structural information of unknown metabolites in a mass-spectrometry setup using a graph-theoretical approach. Their approach attempts to reconstruct the underlying fragmentation tree based on mass-spectra at varying collision energies. Other authors excluded false candidates for a given unknown by comparing observed and predicted chromatography retention times [16], [17], or by the automatic determination of sum formulas from isotope distributions [18]. Furthermore, Gipson et al. [19] and Weber et al. [20] integrated public metabolic pathway information with correlating peak pairs in order to facilitate metabolite identification. However, these methods might not be applicable for high-throughput metabolomics datasets that have been produced in a fee-for-service manner, since the mass spectra as such might not be readily available.

Approaching the problem from a conceptually different perspective, we here present a novel functional metabolomics method to predict the identities of unknown metabolites using a systems biological framework. By combining high-throughput genotyping data, metabolomics data, and literature-derived metabolic pathway information, we generate testable hypotheses on the metabolite identities based solely on the obtained metabolite quantifications (Figure 1). No further experiment-specific data such as retention times, isotope patterns and fragmentation patterns are required for this analysis.

 

Figure 1. Data integration workflow for the systematic classification of unknown metabolites.

We combine high-throughput metabolomics and genotyping data in Gaussian graphical models (GGMs) [21] and in genome-wide association studies (GWAS) [5] in order to produce testable predictions of the unknown metabolites’ identities. These hypotheses are then subject to experimental verification by mass-spectrometry. Six such cases have been fully worked through and are presented in Table 3. doi:10.1371/journal.pgen.1003005.g001

 http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003005?imageURI=info:doi/10.1371/journal.pgen.1003005.g001#pgen-1003005-g001

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Discussion 

We developed and validated a novel integrative approach for the biochemical characterization of “unknown metabolites” from high-throughput metabolomics and genotyping datasets. Our method allows for the functional annotation of previously unidentified metabolites and, as a consequence, enhances the interpretability of metabolomics data in genome-wide association studies and biomarker discovery. For the first time, we systematically evaluated genetic associations of unknown metabolites, thereby discovering seven new loci of metabolic individuality. By classifying a series of unknown metabolites, we gained new insights into the functional interplay between genetic variation and the metabolome both for previously reported and new loci. Furthermore, several of the unknown compounds that we identified as well as their newly associated loci were independently reported in disease-related studies. In the following, we discuss three genetic loci and their associated phenotypes.

COMT and hepatic detoxification

The first example is a recent biomarker study, where Milburn et al. [34] reported an association of X-11593 with hepatic detoxification. In our GWAS, we find a strong association of X-11593 with the COMT locus, which encodes the catechol-O-methyltransferase enzyme. COMT is responsible for the inactivation of catecholamines such as L-dopa and various neuroactive drugs by O-methylation [35]. Following our identification approach, we experimentally confirmed the identity of X-11593 as O-methylascorbate. Notably, O-methylascorbate is a known product of ascorbate (vitamin C) O-methylation by COMT [36], [37]. Thus, our observations establish a link between O-methylascorbate blood levels, common genetic variation in the COMT locus and COMT-mediated liver detoxification processes.

ACE and hypertension

The second example relates to the ACE gene locus, which is a known risk locus for cardiovascular disease, hypertension and kidney failure. The protein encoded by the ACE locus, angiotensin-converting enzyme, is an exopeptidase which cleaves dipeptides from vasoactive oligopeptides, and plays a central role in the blood pressure-controlling renin-angiotensin system [38]. Moreover, the ACE protein is a target for various pharmaceuticals (ACE inhibitors), especially in the treatment of hypertension [39]. In our study, we identified three unknowns as dipeptides (X-14205, X-14208 and X-14478), two of which also associated with the ACE locus. These dipeptides could thus represent novel, interesting biomarkers for the activity of ACE. Moreover, Steffens et al. [11] reported a connection between heart failure and X-11805, which is in close proximity to angiontensin-related peptides in the GGM. This connection might be revisited after a successful identification of X-11805 in a future study.

UGT1A/ACADM and insulin resistance

The third example is an explorative study to detect biomarkers for insulin sensitivity. Gall et al. [9] reported several known metabolites (most prominently α-hydroxybutyrate) as biomarkers for insulin resistance. They also reported a series of unknown metabolites among their top hits. In the present study, we investigated three of these unknowns: X-11793 associates with UGT1A (UDP glucuronosyltransferase 1) and represents a bilirubin-related substance. Moreover, we experimentally validated X-11421 and X-13431, which display a strong association with ACADM (acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain), as acylcarnitines containing 10 and 9 carbon atoms, respectively. The identification of these latter two unknown metabolites as medium-chain length acylcarnitines is coherent with reports by Adams et al. [40]. The authors found elevated blood plasma acylcarnitine levels in women with type 2 diabetes. Functionally, they attributed this finding to incomplete β-oxidation. Thus, our identification of X-11421 and X-13431 now suggests incomplete β-oxidation as an explanation for the associations found by Gall et al. and implies that acylcarnitines containing 10 and 9 carbon atoms are potential biomarkers for insulin resistance.

Conclusion

In summary, we integrated high-throughput metabolomics and genotyping data from a large population cohort for elucidating the biochemical identities of unknown metabolites. To this end, we applied metabolomics genome-wide association studies and Gaussian graphical modeling in order to link these unknown metabolites with known metabolic classes and biological processes. For six specific scenarios, we went from systematic hypothesis generation over detailed investigation and identity prediction to direct experimental confirmation. Similar validations may now be undertaken for the remaining predictions that we report in Table S1. Finally, we demonstrated the benefit of our method by discussing several of these newly identified metabolites in the context of existing biomarker discovery studies on liver detoxification, hypertension and insulin resistance.

It is to be noted that our method does not specifically require genotyping data. Even metabolomics measurements alone, analyzed through the GGMs, may provide sufficient information for the classification and even precise identity prediction. The unknowns with GGM evidence but without GWAS hits in Figure 4 as well as the HETE scenario represent examples for this approach.

One limitation of our approach is the requirement for associations with functionally described loci or known metabolites. Certain metabolite groups might thus systematically not be identifiable. For instance, if the identity of a whole class of biochemically related molecules is unknown (which might be due to experimental reasons), then the GGM associations between those compounds will not aid in identity elucidation. The 118 unknown compounds for which we could not derive any classification might represent such cases. Thus, our functionally oriented method should be regarded as a complementary extension to the existing identity determination methods.

Accordingly, our approach can be extended in several directions. It can be combined with method-specific, automated techniques that further exclude sets of metabolites. Previously mentioned methods relying on mass-spectra [15] or chromatographic properties [17] are suitable candidates here. Moreover, the method can be directly transferred to other types of metabolomics datasets not specifically originating from MS experiments, such as NMR-based metabolomics.

Beyond the application to metabolite identification, our study demonstrates the general potential of functional metabolomics in the context of genome-wide association studies. The comprehensive metabolic picture provided by GGMs in combination with GWAS allows for the detailed analysis of metabolic functions, chemical classes, enzyme-metabolite relationships and metabolic pathways.

Author Contributions 

Conceived and designed the experiments: JK KS FJT GK. Performed the experiments: AME MWM RPM MVM. Analyzed the data: JK GK. Contributed reagents/materials/analysis tools: BW WR-M TI JA CG. Wrote the paper: JK KS FJT GK.

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