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Calcium (Ca) supplementation (>1400 mg/day): Higher Death Rates from all Causes and Cardiovascular Disease in Women

Posted in Atherogenic Processes & Pathology, Biomarkers & Medical Diagnostics, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Disease Biology, Small Molecules in Development of Therapeutic Drugs, HTN, Nutrition, Nutritional Supplements: Atherogenesis, lipid metabolism, Origins of Cardiovascular Disease, Pharmacotherapy of Cardiovascular Disease, Systemic Inflammatory Response Related Disorders, tagged BMJ, Calcium, Cardiovascular disease, Heart disease, Potassium, Sodium, Uppsala University on February 19, 2013| 2 Comments »

Curator: Aviva Lev-Ari, PhD. RN

UPDATED on 11/2/2013

Medscape Update on Calcium and Cardiovascular Risk

Curator and Reporter: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/10/11/new-data-dispute-calcium-cardiovascular-risk-in-both-sexes/

Minerals and Cardiovascular Risk

Modern diet contains high sodium to potassium ratio, low omega-3-polyunsaturated acid. (PUFAs) increased omega-6-polyunstaureted, saturated fat and Trans fatty acids these have lead to higher incidence of cardiovascular disease, diabetes mellitus and hyperlipidemia.

Nutrient	Paleolithic diet	Modern diet
Potassium	More than 10,000 mEq/day (256 Grm)	150mEq/day (6gram)
Sodium	Less than 50 mmol/day 1.2 Grm	175 mmol/day (4Gram)
Na/K ratio	Less than 0.13 /day	More than 0.67/day
Fiber	More than 100gram/day	Less than 9 gram/day
Protein	37%	20%
Carbohydrate	41%	40-50%
Fat	22%	30-40%
Poly saturated to saturated ratio	1.4	0.4

Sodium

Increased intake of sodium is associated with hypertension and reduction of salt intake is associated with decrease in BP by 4-6/2-3mmhg in salt sensitive patients. Daily allowance of sodium is not more than 500mg/day.

Cardiovascular events are more common in salt sensitive patients than salt resistance patients, independent of BP reduction. Reduction of BP by salt restriction has benefit apart from BP reduction.

A balance of sodium with other nutrients is important not only for reduction of BP but also for reduction cardiovascular events.

Potassium

Increased intake of potassium is associated with BP reduction. Recommended daily intake of potassium is 650mEq/day with Na/k ratio of 5:1.

Supplements of 120 mEq/day of potassium reduce BP by 4.4/2.5mmhg in hypertensive patients.

Higher Na/K ratio reduces not only BP but also cardiovascular events.

Magnesium

Intake of 500mg/day to 1000mg/day reduces BP by 5.6/2.8mmhg. Reducing intracellular sodium and calcium and increasing intracellular magnesium and potassium improves BP response.

Insulin sensitivity, LVH and dyslipidemia can be improved with magnesium supplementation.

Oral magnesium acts like natural calcium channel blocker, increases nitric oxide, and improves endothelial dysfunction, and induces vasodilatation.

Calcium

Studies show link between calcium and hypertension. But trials supplementing calcium do not show benefit. Below we present results of a recent study on Calcium supplementation citing >1400 mg/day been associated with increased cardiovascular risk and mortality.

Zinc

Low serum zinc levels are associated with hypertension.

http://www.learnonly.com/2013/02/human-evolution-minerals-and.html

Authors of the BMJ of 2/13/2013 article reported, below offer the following Possible Explanations and Implications

Calcium levels in serum are under tight homeostatic control, and calcium intake is not normally correlated with calcium serum levels.

Diets that are low or very high in calcium can, however, override normal homeostatic control causing changes in blood levels of calcium or calciotropic hormones.52
Calcium enriched meals can reduce calcitriol, the active vitamin D metabolite, by inhibition of 1α hydroxylase53and also increase serum levels of fibroblast growth factor 23.54
Higher levels of circulating fibroblast growth factor 23 are associated with an increased risk of cardiovascular events and all cause mortality.55 56 57 In addition,
fibroblast growth factor 23 downregulates calcitriol levels.58
Vitamin D suppression leads to an upregulation of the renin-angiotensin-aldosterone system and hypertension, higher levels of proinflammatory cytokines involved in the pathogenesis of atherosclerosis:

– increased carotid artery intima medial thickness,

– decreased endothelial function,

– hypertrophy of cardiac and vascular muscle cells, and a

– possible increase in serum triglycerides.59 Finally,

high serum calcium levels can increase the risk of cardiovascular mortality60 by induction of a hypercoagulable state.61

Vascular calcification and plaque rupture

There are two types of vascular calcification, intimal calcification of atherosclerosis and medial calcification. Both are associated with increased incidence of ischemic heart disease. Plaque rupture is manly restricted to intimal plaques fibrous cap calcification. Calcification of this fibrous cap is associated with increased incidence of ischemic heart disease. Below discussion is about controversy associated with fibrous cap calcification.

Whether intimal calcification stabilizes the plaque or makes it prone for rupture is a matter debate. Calcified and fibrotic lesions are more hypo-cellular, they are stiffer than cellular lesions, and further more biomechanical data suggest calcification reduces the “stresses” in a plaque does not cause rupture. Plaques with heavily calcified are 5 times stiffer that non-calcified lesions.

Calcium crystal have shown to aggravate inflammation

Above observation are contradictory to each other. If calcium induces inflammation than plaque should get destabilize?

Under mechanical stress produced by balloon angioplasty, calcified plaque is more likely to rupture than non-calcified plaque, and the rupture occurs along the interface between the calcium deposit and soft tissue. So this suggest that plaque rupture may occur at these week points

Conclusion

It has been stated that when entire plaque is calcified it protects against rupture unlike focal calcification

The ratio of surface area to volume in calcium deposits may determine whether they are harmful or protective

http://www.learnonly.com/2013/02/vascular-calcification-and-plaque.html

Lipoprotein a (Lp(a)) genetic variant doubles the causal risk of Aortic valvular calcification.

In the last 15 to 20 years our understanding of aortic valve calcification has changed from just simple degenerative disease to disease secondary to an active process involving endothelial dysfunction, lipid accumulation, an inflammatory infiltrate. With this understanding many potential therapeutic approach have been considered. Statins showed promise in prevention of calcification in retrospective trials but prospective trials did not show benfit. Rennin angiotensin inhibitors have given discordant results in retrospective trials and no randomized control trial is there to prove their efficacy.

Aortic Valvular Calcification

new potential therapeutic target for prevention aortic valve calcification i.e. Lp(a).Article published in NEJM Feb 7 2013 from Johns Hopkins, Harvard University, McGill University, the University of Iceland and the National Institutes of Health says, there is variant of Lp(a) which is associated with aortic valve calcification. In this publication genomewide association was evaluated for 6942 participants of aortic valvular calcification and 3795 participants of mitral valve calcification, detected by CT scanning.

Previous studies showed association of Lp(a) with calcification of aortic valve. Causal or just marker of calcification was not confirmed, present study shows causal relationship of Lp(a) and aortic valve calcification.

From this causal relationship one may think of targeting Lp(a) for preventing aortic valve calcification. Niacin reduces Lp(a) levels. Although HPS-2 THRIVE trial (with niacin/laropiprant) which was done for coronary artery disease did not show clinical benfit, still one may keep hope for prevention of aortic valve calcification. Time may tell about us this in future.

http://www.learnonly.com/2013/02/lipoprotein-lpa-genetic-variant-doubles.html

Types of Vascular Calcification

Artery Medial Calcification (AMC) – Concentric Vessel – Stiffening
Atherosclerotic Intimal Calcification (AIC)

Long term calcium intake and rates of all cause and cardiovascular mortality: community based prospective longitudinal cohort study

BMJ 2013; 346 doi: http://dx.doi.org/10.1136/bmj.f228 (Published 13 February 2013)

Cite this as: BMJ 2013;346:f228

Karl Michaëlsson, professor1,
Håkan Melhus, professor2,
Eva Warensjö Lemming, researcher1,
Alicja Wolk, professor3,
Liisa Byberg, associate professor1

Author Affiliations

¹Department of Surgical Sciences, Section of Orthopedics, Uppsala University, SE-751 85 Uppsala, Sweden
²Department of Medical Sciences, Section of Clinical Pharmacology, Uppsala University, Uppsala, Sweden
³Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden

Correspondence to: K Michaëlsson karl.michaelsson@surgsci.uu.se

Accepted 28 December 2012

Abstract

Objective To investigate the association between long term intake of dietary and supplemental calcium and death from all causes and cardiovascular disease.

Design Prospective longitudinal cohort study.

Setting Swedish mammography cohort, a population based cohort established in 1987-90.

Participants 61 433 women (born between 1914 and 1948) followed-up for a median of 19 years.

Main outcome measures Primary outcome measures, identified from registry data, were time to death from all causes (n=11 944) and cause specific cardiovascular disease (n=3862), ischaemic heart disease (n=1932), and stroke (n=1100). Diet was assessed by food frequency questionnaires at baseline and in 1997 for 38 984 women, and intakes of calcium were estimated. Total calcium intake was the sum of dietary and supplemental calcium.

Results The risk patterns with dietary calcium intake were non-linear, with higher rates concentrated around the highest intakes (≥1400 mg/day). Compared with intakes between 600 and 1000 mg/day, intakes above 1400 mg/day were associated with higher death rates from all causes (hazard ratio 1.40, 95% confidence interval 1.17 to 1.67), cardiovascular disease (1 49, 1.09 to 2.02), and ischaemic heart disease (2.14, 1.48 to 3.09) but not from stroke (0.73, 0.33 to 1.65). After sensitivity analysis including marginal structural models, the higher death rate with low dietary calcium intake (<600 mg/day) or with low and high total calcium intake was no longer apparent. Use of calcium tablets (6% users; 500 mg calcium per tablet) was not on average associated with all cause or cause specific mortality but among calcium tablet users with a dietary calcium intake above 1400 mg/day the hazard ratio for all cause mortality was 2.57 (95% confidence interval 1.19 to 5.55).

Conclusion High intakes of calcium in women are associated with higher death rates from all causes and cardiovascular disease but not from stroke.

Introduction

Calcium is one of the most abundant minerals in the human body and plays a pivotal role in human physiology. The serum levels of calcium are strictly regulated and an insufficient calcium intake is met by a more efficient intestinal absorption and renal conservation of calcium. Calcium is also mobilised from the skeleton, which can lead to bone loss1 and subsequent risk of fractures. Consequently, to prevent fractures in elderly people previous and existing guidelines2 recommend avoidance of low calcium intake. Fractures are common, especially in women, and are associated with high disability, healthcare costs, and mortality.3 Insufficient calcium intakes might also lead to secondary hyperparathyroidism, which is associated with higher mortality.1 4 5 Supplemental use of calcium has become common, and more than 60% of middle aged and older women in the United States are regular users of calcium supplements.6 7 Worryingly, three recent reanalyses of randomised trials in women have indicated a higher risk of both ischemic heart disease and stroke with calcium supplements,8 9 10 a pattern not observed in a reanalysis of another randomised trial.11 Few cohort studies in women have examined the association between dietary and supplemental intake of calcium with risk of cardiovascular incidence and mortality; instead,12 13 14 15 16 the focus has been on the incidence of stroke, with both contrary and inconsistent findings.12 13 14 16

We hypothesised that long term intake of low or high calcium increases the risk of cardiovascular mortality. We investigated associations between long term dietary and supplemental intake of calcium with all cause mortality as well as with cardiovascular mortality in a large population based prospective study of Swedish women.

Methods

The Swedish mammography cohort

The Swedish mammography cohort was established in 1987-90. All women (n=90 303) residing in two Swedish counties (Uppsala and Västmanland) and born between 1914 and 1948 received a mailed invitation to a routine mammography screening. Enclosed with this invitation was a questionnaire covering diet (food frequency questionnaire) and lifestyle, which was completed by 74% of the women. In 1997, a second, expanded questionnaire was distributed to those who were still living in the study area (response rate 70%). The study sample with exclusions has been described previously.17 18 In all, 61 433 women with baseline data (1987-90) and 38 984 with data from 1997 were available for analysis in the present study (fig 1⇓).

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Fig 1 Study samples in Swedish mammography cohort

Outcomes

Follow-up was through the Swedish cause of death registry. Complete linkage with the register is rendered by the personal identity number provided to all Swedish residents. Since 1952 the National Board of Health and Welfare has collected information on the causes of death for all Swedish residents in the cause of death registry. We used the underlying cause of death in the registry to define the outcomes of death from all causes, cardiovascular disease (international classification of diseases, ninth and 10th revisions; ICD-9 codes 390-459 or ICD-10 codes I00-I99), ischaemic heart disease (ICD-9 codes 410-414 or ICD-10 codes I20-I25), and stroke (ICD-9 codes 430-436 or ICD-10 codes I60-I64).

Dietary assessment

The food frequency questionnaires have been described previously.17 19 20 The participants reported their average frequency of consumption of up to 96 foods and beverages during the past year. For most food items, eight categories for frequency of consumption were provided, ranging from never to three or more times daily. For some commonly consumed foods such as milk, sour milk/yogurt, and cheese, participants could fill in the exact number of servings they consumed daily or weekly. We estimated nutrient intakes by multiplying the consumption frequency of each food item by the nutrient content of age specific portion sizes. Nutrient data were obtained from the Swedish National Food Administration database.21 We adjusted nutrient intakes for total energy intake (7.1 MJ or 1700 kcal, mean in the study population) using the residual method.22 To better account for changes in diet during follow-up and to better represent long term dietary intake we treated calcium intake as cumulative average intake.23 In the second questionnaire the lifetime use of dietary supplements and multivitamins was reported. In Sweden one calcium dose contains 500 mg if from calcium supplements and 120 mg if from multivitamins. Total calcium intake included supplemental calcium from any source. Even if supplement use was absent in the first food frequency questionnaire (baseline questionnaire), the frequency of calcium containing supplement use (with or without vitamin D) within the cohort during the first years of follow-up was low (6%),24 and this proportion was similar across the whole range of dietary calcium intake. Calcium intake in the 1997 food frequency questionnaire correlated well with estimates from 14 repeated 24 hour recalls over one year (r=0.77).25 Furthermore, a second validation of calcium intake was carried out with four seven day food records every third month in 104 of the women (r=0.72). Bland-Altman plots revealed only small systematic errors related to intake level between the methods, and the average difference with 95% confidence interval between the 1997 food frequency questionnaire and seven day food record was 56.4 mg/day (95% confidence interval −4.4 to 108.4 mg/day)—that is, as previously reported,25 a tendency of higher estimates for calcium intake with the food frequency method. Similar estimates were achieved for the baseline questionnaire.24

Comorbidity and other additional information

Lifestyle information was obtained from the questionnaires. This information included the use of postmenopausal oestrogen therapy and menopausal status, parity, weight and height, smoking habits, and leisure time physical activity during the past year, with five predefined levels ranging from one hour weekly to more than five hours weekly. Physical activity, collected in the 1997 questionnaire, is valid compared with activity records and accelerometer data.26 We divided educational level into four categories: up to 9 years, 10-12 years, more than 12 years, and other (such as vocational). Diagnosis codes were collated from the national patient registry (ICD codes 8, 9, and 10) to calculate Charlson comorbidity scores.27 28 The Charlson comorbidity index predicts the 10 year mortality for a patient who may have a range of comorbid conditions (up to 22 diseases). Each condition is assigned a score of 1 to 6 depending on the risk of dying associated with this condition.

Statistical analysis

For each participant, follow-up time was accrued from baseline (1987-90) until the first date of death, date of leaving the study regions, or the end of the study period (31 December 2008), whichever occurred first. In secondary analyses we considered time to incidence of cardiovascular disease, ischaemic heart disease, and stroke. To improve the validity of our exposure estimate, we used a calibrated calcium intake obtained by usage of linear regression coefficients between food records (FR) and the food frequency questionnaire (FFQ): (R_iFR=α_FR+ β_FR* FFQi, (R reported calcium in the food records, i in the individual)).29 Using Cox proportional hazards regression we estimated age adjusted and multivariable adjusted hazard ratios and their 95% confidence intervals for prespecified categories of calcium intake: <600, 600-999, 1000-1399, and ≥1400 mg/day. To facilitate comparisons of the estimates we used the same category cut-offs in the analysis of dietary and total calcium intake. We estimated the risk with use of calcium containing supplements from the date of the second questionnaire survey (from 1 January 1998). The proportional hazard assumptions in the Cox models were confirmed graphically by comparing Nelson-Aalen plots. Non-linear trends of risk were additionally analysed using restricted cubic-spline Cox regression. We used four “knots” placed at centiles 5, 35, 65, and 95 of the cumulative average calcium intake.30 The reference level was set to 800 mg of calcium, which corresponds to the recommended daily intake for Swedish women aged more than 50 years.31

To minimise potential bias we used the directed acyclical graph approach to identify a suitable multivariable model. The model included age, total energy and vitamin D intake, body mass index, height (all continuous), educational level (≤9, 10-12, >12 years, other), living alone (yes or no), use of supplements containing calcium (yes or no), a healthy dietary pattern (fifths), physical activity (five categories), smoking status (never, former, current), and score on the Charlson comorbidity index (continuous, 1-16).27 28 A healthy dietary pattern was defined by using a validated method.32 33 Briefly, we used factor analysis to derive the dietary pattern empirically. Factor analysis reduces dietary data to a few composite factors (one being a healthy dietary pattern) that describe the eating pattern in the population. Other potential covariates (such as menopausal status; hormone replacement therapy; intakes of total fat, retinol, alcohol, potassium, phosphorous, and protein; nulliparity; and previous fracture of any type) in the multivariable models only marginally changed the relations and were therefore not included in the models. We treated covariates as cumulative averages.28 The Markov chain Monte Carlo multiple imputation method was used to impute covariates not assessed in the baseline questionnaire in 1987-90 (for example, smoking habits and physical activity). Restriction to non-missing data did not alter our interpretation of the results (data not shown). Moreover, in an attempt to examine whether calcium supplement use modified the association between dietary calcium intake and mortality, we performed stratified analysis by calcium supplement use (no use, use of any type of calcium containing supplements, and specific use of calcium tablets). Additionally, we estimated the synergy index between dietary calcium intake and calcium tablet use.34 We performed sensitivity analysis, limiting the analysis to baseline data using ordinary Cox’s regression without time updated information. In an attempt to validate the robustness of the Cox’s regression model using information updated over time, we used marginal structural modelling.35 The categorical exposure in the marginal structural models was treated as described previously.36 We calculated an additional inverse probability weight for having time varying data, and we gave a weight of zero to those without time varying data.

In addition to ultraviolet radiation and genes, vitamin D intake is a determinant of vitamin D status,37 38 39 and vitamin D insufficiency is related to cardiovascular disease mortality and incidence.40 We therefore investigated effect measure modification between dietary calcium and vitamin D intake by including a product interaction term in the multivariable models and performing likelihood ratio tests of its contribution in nested models. We further calculated the relative excess risk that is due to interaction.34 When analysing cause specific mortality, we considered the potential competing risk problem from other causes of mortality41 and cumulative incidence curves.42 The subhazard ratios were similar to the hazard ratios from the ordinary Cox regression, suggesting no major effect of competing risks, which is also the conclusion drawn after analysis of cumulative incidence curves (data not shown).

The statistical analyses were performed with STATA 11 and SAS, version 9.2.

Results

Table 1⇓ lists the characteristics of the study participants by categories of calcium intake. The average total cumulative calcium intake in the lowest category was 572 mg/day and in the highest was 2137 mg/day. With increasing categories of energy standardised calcium intake, the reported intake for most other nutrients also increased, although alcohol intake tended to decrease. There were small differences in calcium supplement use, comorbidity, educational level, smoking status, and physical activity level between categories of calcium intake.

Vitamin D intake did not significantly modify the associations between calcium intake and the rate of deaths from all causes, cardiovascular disease, or ischaemic heart disease (results not shown).

Discussion

In this study of women in the Swedish mammography cohort, a high calcium intake (>1400 mg/day) was associated with an increased rate of mortality, including death from cardiovascular disease. The increase was moderate with a high dietary calcium intake without supplement use, but the combination of a high dietary calcium intake and calcium tablet use resulted in a more pronounced increase in mortality. For most women with lower intakes we observed only modest differences in risk.

Strengths and weaknesses of the study

Strengths of our study include the population based prospective design, study size, and repeated measurements of calcium intake, as well as a large number of potential covariates. Date and cause of death were traced through national healthcare registries and deterministic record linkage, permitting complete ascertainment of the outcomes. The accuracy of classification of causes of death in the cause of death registry and diagnoses in the national patient registry are high.43 Furthermore, we adjusted for several important covariates (for example, smoking, socioeconomic status, physical activity, nutrients other than calcium, educational level, and comorbidity), but residual confounding remains a possible limitation. The lower age adjusted rates of death from all causes and cardiovascular disease among women with a high total calcium intake were largely explained by their use of dietary supplements (table 2), a variable considered in the multivariable models. Other health related covariates, including a healthy diet and level of physical activity contributed to a lesser degree. People who use dietary supplements have, on average, a healthier lifestyle and a lower risk factor profile for cardiovascular disease44 and not considering this might distort the risk estimates. Moreover, the low proportion of women who took prescription calcium tablets (6%), containing a four times higher dose of calcium than in regular multivitamin dietary supplements, made it difficult to detect modestly strong associations with calcium tablet use specifically. Dietary assessment methods are prone to several limitations, affecting both the precision and accuracy of the measurement. In larger studies, a food frequency questionnaire is used to assess the habitual intake of diet, and a recent review concluded that it was a valid method for assessing dietary mineral intake, particularly for calcium.45 The food frequency questionnaire may, to some extent, overestimate calcium intake,25 which was also indicated by our validation. A further limitation in our study is the use of age standardised portion sizes and not actual individual portion sizes. By use of our calibrated analysis of calcium intake, we none the less tried to avoid some misclassification of study participants. By using repeated measurements on dietary intake we increased the accuracy of the measurement but may also have introduced bias using time dependent Cox regression models. Indeed, after using only baseline data and also after performing the marginal structural model analyses, we no longer observed an increased mortality for women with low calcium intakes or a high total calcium intake. Without being causally linked to death, a low calcium intake could therefore be viewed as a marker of frailty or a less healthy behaviour associated with a higher mortality. There are, however, also theoretical drawbacks of our causal inference model. It is sensitive to correct model specifications and indeed renders estimates with lower precision than ordinary Cox’s regression.46 47 It is worth emphasising that traditionally obtained estimates, such as those from Cox’s regression, would not generally agree with estimates from marginal structural models even when there is no confounding.48 Irrespective of analytical approach, the observational study design precludes conclusions about causality, and cautious interpretations of the results are therefore recommended. The results for women with a high calcium intake are, however, compatible with results from previous randomised studies,8 9 10 and by fitting the marginal structural model we obtained similar risk estimates although with wider confidence intervals. Our results might also not apply to people of different ethnic origins or to men.

Strengths and weaknesses in relation to other studies

Calcium intake in adulthood and all cause mortality in women has not been previously investigated. In an analysis including 387 deaths within the Iowa Women’s Health Study cohort15 a total calcium intake below 700 mg/day but not above 1400 mg/day was associated with higher mortality from ischaemic heart disease. Furthermore, a recent reanalysis of the same cohort showed that use of calcium supplements was inversely related to the total and cardiovascular mortality rate, although the benefit was lost at the highest doses of dietary calcium intake.49In contrast, use of calcium supplements in a Finnish cohort increased the risk of cardiovascular disease.50 Intriguingly, three reanalyses of randomised trials have consistently shown a higher rate of both myocardial infarction and stroke by 25% to 30% and by 15% to 20%, respectively, with calcium supplementation.8 9 10These results were not confirmed in a reanalysis of another randomised trial using a broad composite endpoint of different cardiovascular events.11 Interestingly, the higher risk of cardiovascular events with calcium supplements in a meta-analysis8was only observed in women with a dietary calcium intake higher than 800 mg/day and not in women with lower intake levels.

The results from the few prospective cohort studies that have examined the relation between calcium intake and incidence of cardiovascular disease in women are contradictory or not conclusive. In the Nurses’ Health Study cohort there was a higher risk of stroke in women with a calcium intake below 600 mg/day.12 Similarly, in a Japanese setting with a comparably low average calcium intake, women with an intake below about 500 mg/day had a higher rate of stroke but not of coronary heart disease.13 14 None the less, calcium intake was not related to stroke incidence in a previous analysis in our cohort,16 concordant with the results of the present investigation. We have recently shown that calcium intakes above 700 mg/day do not further reduce the risk of fracture and osteoporosis.18

Vitamin D enhances, directly or indirectly, renal conservation and intestinal absorption of calcium.51 Our results suggest that vitamin D intake did not modify the association of calcium intake and mortality rate. In comparison with exposure to ultraviolet radiation and genetic constitution, vitamin D intake contributes only modestly to vitamin D status,37 38 39 which is determined by serum calcidiol levels, a metabolite not measured in the present investigation.

Possible explanations and implications

Calcium levels in serum are under tight homeostatic control, and calcium intake is not normally correlated with calcium serum levels. Diets that are low or very high in calcium can, however, override normal homeostatic control causing changes in blood levels of calcium or calciotropic hormones.52 Calcium enriched meals can reduce calcitriol, the active vitamin D metabolite, by inhibition of 1α hydroxylase53and also increase serum levels of fibroblast growth factor 23.54 Higher levels of circulating fibroblast growth factor 23 are associated with an increased risk of cardiovascular events and all cause mortality.55 56 57 In addition, fibroblast growth factor 23 downregulates calcitriol levels.58 Vitamin D suppression leads to an upregulation of the renin-angiotensin-aldosterone system and hypertension, higher levels of proinflammatory cytokines involved in the pathogenesis of atherosclerosis, increased carotid artery intima medial thickness, decreased endothelial function, hypertrophy of cardiac and vascular muscle cells, and a possible increase in serum triglycerides.59 Finally, high serum calcium levels can increase the risk of cardiovascular mortality60 by induction of a hypercoagulable state.61

Our present data together with previous observations suggest that for the prevention of fractures in elderly people18 and simultaneous avoidance of possible serious adverse events related to a high calcium intake (such as higher risk of hip fracture,18 62 cardiovascular disease,63 renal stones,64 and, as observed in the current study, mortality) emphasis should be placed on people with a low intake of calcium rather than increasing the intake of those already consuming satisfactory amounts.

Conclusion

When looking at the totality of our data, high calcium intakes were associated with higher rates of death from all causes and cardiovascular disease. Mortality was not increased between 600 and 1400 mg/day of total calcium intake, the most customary levels of intake in this setting. The suggestion of an increased risk of mortality by a low calcium intake in our study seemed to be biased by time varying confounding factors.

What is already known on this topic

A low calcium intake is associated with higher fracture rates in elderly people and a higher risk of stroke and fatal ischaemic heart disease
Meta-analyses of some randomised studies have, however, shown a higher risk of incident ischaemic heart disease and stroke with calcium supplement use
In observational studies, use of calcium supplements has been associated with both lower overall and cardiovascular mortality rate, as well as higher incidence of cardiovascular disease

What this study adds

In this Swedish cohort study of women, high intakes of calcium (>1400 mg/day) were associated with higher mortality
The increase was moderate with a high dietary calcium intake without supplement use, but more pronounced with a high dietary calcium intake with calcium tablet use
For most women with lower calcium intakes only modest differences in risk were observed

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Biomarkers & Diagnostics, World Congress 2013, May 6-8, 2013 Loews Philadelphia Hotel, Philadelphia, PA

Posted in Biomarkers & Medical Diagnostics, tagged biomarker, Clinical Development Oncology on February 19, 2013| Leave a Comment »

Reporter: Aviva Lev-Ari, PhD, RN

http://www.biomarkerworldcongress.com/

DOWNLOADS

http://www.biomarkerworldcongress.com/bmc_content.aspx?id=95326

Conference Programs

May 6 – 7, 2013

Track 1: Translational Biomarkers in Drug Development

Track 2: Clinical Assay Development

Track 3: Cancer Tissue Diagnostics

May 6 – 8, 2013

Track 4: Executive Summit: Companion Diagnostics

May 7 – 8, 2013

Track 5: Biomarkers for Patient Selection

Track 6: Cancer Drug Resistance

Track 7: Exosomes and Microvesicles as Biomarkers

and Diagnostics

SPEAKERS

Jason M. Aliotta, M.D., Assistant Professor, Medicine, Warren Alpert Medical School, Brown University

John L. Allinson, FIBMS, Vice President, Biomarker Laboratory Services, ICON Development Solutions

Maria E. Arcila, M.D., Department of Pathology, Memorial Sloan-Kettering Cancer Center

Khusru Asadullah, M.D., Vice President and Head, Global Biomarkers, Bayer Pharma

Jiri Aubrecht, Pharm.D., Ph.D., Senior Director, Safety Biomarker Group Lead, Drug Safety Research & Development, Pfizer

M.J. Finley Austin, Ph.D., Personalized Healthcare & Biomarker Strategy Director, AstraZeneca

Nazneen Aziz, Ph.D., Director, Molecular Medicine, Transformation Program Office, College of American Pathologists

Geoffrey Stuart Baird, M.D., Ph.D., Assistant Professor, Laboratory Medicine, University of Washington

Robert A. Beckman, M.D., External Faculty, Center for Evolution and Cancer, Helen Diller Family Cancer Center, UCSF; Executive Director, Clinical Development Oncology, Daiichi Sankyo Pharma Development

Darrell R. Borger, Ph.D., Co-Director, Translational Research Laboratory, Massachusetts General Hospital Cancer Center

Mark Broenstrup, Ph.D., Director, Biomarker and Diagnostics, R&D Diabetes Division, Sanofi

Michael Burczynski, Ph.D., Executive Director, Biomarker Technologies, Discovery Medicine and Clinical Pharmacology, Bristol-Myers Squibb

Claudio Carini, M.D., Global Clinical Immunology and Biomarkers Lead, Bioenhancement Development Unit, Pfizer

Luigi Catanzariti, Ph.D., Executive Director and Global Program Director, Diagnostics, Novartis

David Chen, Ph.D., Senior Director, Correlative Sciences, Oncology Clinical Development, Novartis Pharmaceuticals

Carol Cheung, M.D., Ph.D., Department of Pathology, University Health Network

Atish Choudhury, M.D., Instructor in Medicine, Medical Oncology, Dana-Farber Cancer Institute

Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

Mark E. Curran, Ph.D., Vice President, Immunology Biomarkers, Janssen Research & Development

Stephen P. Day, Ph.D., Director, Medical Affairs, Hologic

Viswanath Devanarayan, Ph.D., Global Head, Exploratory Statistics, AbbVie, Inc.

Luis Alberto Diaz, M.D., Associate Professor of Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

Max Diem, Ph.D., Professor, Chemistry and Chemical Biology, Northeastern University

Nicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson & Johnson

Crislyn D’Souza-Schorey, Ph.D., Professor, Biological Sciences, University of Notre Dame

Dominik Duelli, Ph.D., Assistant Professor, Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine & Science, Chicago Medical School

Daniel Edelman, Ph.D., Facility Head, Clinical Molecular Profiling Core, National Cancer Institute, NIH

Reyna Favis, Ph.D., Scientific Director, Clinical Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson

Andrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of Molecular Diagnostics; Director, Molecular Diagnostics Laboratory, Department of Pathology, Virginia Commonwealth University

Andrew Fish, Executive Director, AdvaMedDx

Herbert A. Fritsche, Ph.D., Senior Vice President and CSO, Health Discovery Corporation

Felix Frueh, Entrepreneur-in-Residence, Third Rock Ventures

Steve Furlong, Ph.D., Safety Science Lead, AstraZeneca Clinical Development

George A. Green IV, Ph.D., Director, Pharmacodiagnostics, Bristol-Myers Squibb

Patrick Groody, Ph.D., Divisional Vice President, Research & Development, Abbott

Steven Gutman, M.D., MBA, Strategic Advisor, Myraqa

Abdel Halim, Pharm.D., Ph.D., DABCC-MDx, DABCC-TOX, DABCC-CC, FACB, Director, Clinical Biomarkers, Daiichi Sankyo Pharma Development

Sam Hanash, M.D., Ph.D., Director, McCombs Institute for Cancer Early Detection and Treatment, MD Anderson Cancer Center

Charles R. Handorf, M.D., Ph.D., Professor and Chair, Pathology and Laboratory Medicine, University of Tennessee

Amir Handzel, Ph.D., Associate Director, Translational and Clinical Sciences, OSI Pharma (Astellas)

Chunhai “Charlie” Hao, M.D., Ph.D., Associate Professor, Neuropathology Attending, Department of Pathology & Laboratory Medicine, Emory University School of Medicine

Madhuri Hegde, Ph.D., Executive Director, Emory Genetics Laboratory; Associate Professor, Human Genetics, Emory University School of Medicine

Philip Hewitt, Ph.D., Head, Early Non-Clinical Safety (Liver and Kidney), Merck Serono

Stephen M. Hewitt, M.D., Ph.D., Clinical Investigator, Laboratory of Pathology, National Cancer Institute, NIH

Holly Hilton, Ph.D., Head, Disease and Translational Genomics, Hoffmann-La Roche; Adjunct Professor, University of Medicine and Dentistry New Jersey

Fred H. Hochberg, M.D., Associate Professor, Neurology, Massachusetts General Hospital

Shidong Jia, Ph.D., Scientist, Oncology Biomarker Development, Genentech

Chris Jowett, General Manager, Commercial Operations, Abbott Molecular

Jingfang Ju, Ph.D., Co-Director of Translational Research, Pathology, Stony Brook University

Peter M. Kazon, General Counsel, American Clinical Laboratory Association

Eric Lai, Ph.D., Senior Vice President and Head, Pharmacogenomics, Takeda Pharmaceuticals International

Ira M. Lubin, Ph.D., Team Lead, Genetics Laboratory Research and Evaluation Branch, CDC

Johan Luthman, D.D.S., Ph.D., Senior Program Leader, Neuroscience & Ophthalmology Research & Development Franchise Integrator, Merck

Elaine Lyon, Ph.D., Medical Director, Molecular Genetics, ARUP Laboratories

Ron Mazumder, Ph.D., MBA, Global Head, Research and Product Development, Janssen Diagnostics, Janssen Pharmaceutical Companies of Johnson & Johnson

Duncan McHale, Ph.D., Vice President, Global Exploratory Development at UCB Pharma

Alan Mertz, President, American Clinical Laboratory Association

Yoshi Oda, Ph.D., President, Biomarkers and Personalized Medicine Core Function Unit, Eisai

Lorraine O’Driscoll, Ph.D., Associate Professor, Pharmacology; Director, Research, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin

Carol S. Palackdharry, M.D., MS, Medical Director, ActiveHealth Management; Clinical Lead, Oncology Condition Analysis, Aetna

Saumya Pant, Ph.D., Research Fellow, Merck

Liron Pantanowitz, M.D., Associate Professor, Pathology and Biomedical Informatics, University of Pittsburgh Medical Center

Scott D. Patterson, Ph.D., Executive Director, Medical Sciences, Amgen

Sonia Pearson-White, Ph.D., Scientific Program Manager, Oncology, The Biomarkers Consortium, Foundation for the National Institutes of Health

Emanuel Petricoin III, Ph.D., Co-Director, The Center for Applied Proteomics and Molecular Medicine, George Mason University

Suso Platero, Ph.D., Director, Oncology Biomarkers, Janssen Pharmaceuticals

Mark Priebe, MT(ASCP)SBB, Managing Director, QualityStar Quality Consortium

Debra Rasmussen, MBA, Senior Director, Regulatory Affairs, Johnson & Johnson

Hallgeir Rui, M.D., Ph.D., Professor, Cancer Biology, Medical Oncology, and Pathology, Thomas Jefferson University

Hakan Sakul, Ph.D., Executive Director and Head, Diagnostics, Worldwide R&D, Clinical Research and Precision Medicine, Pfizer

Kurt A. Schalper, M.D., Ph.D., Associate Research Scientist, Pathology, Yale School of Medicine

Stephen C. Schmechel, M.D., Ph.D., Associate Professor, Pathology, University of Washington School of Medicine

Robert Schupp, Ph.D., Executive Director, Diagnostics Hematology/Oncology, Celgene Corporation

Jason S. Simon, Ph.D., Director, Immuno-Oncology Biomarkers, Discovery Medicine and Clinical Pharmacology, Bristol-Myers Squibb

Sharon Sokolowski, Ph.D., Principal Scientist, Pfizer Global Research & Development

Gyongyi Szabo, M.D., Ph.D., Professor, Gastroenterology, University of Massachusetts Medical School

Douglas D. Taylor, Ph.D., Professor, Obstetrics and Gynecology, University of Louisville School of Medicine

Meghna Das Thakur, Ph.D., Presidential PostDoctoral Fellow, Novartis Institutes for BioMedical Research

Emina Torlakovic, M.D., Ph.D., Associate Professor, Laboratory Medicine and Pathobiology, University of Toronto

Jessie Villanueva, Ph.D., Assistant Professor, Molecular & Cellular Oncogenesis Program, The Wistar Institute

Glen J. Weiss, M.D., Co-Head, Lung Cancer Unit, The Translational Genomics Research Institute (TGen); Director, Clinical Research, Cancer Treatment Centers of America; CMO, CRAB-Clinical Trials Consortium

David Wholley, Director, Biomarkers Consortium, Foundation for the NIH

David T.W. Wong, D.M.D., D.M.Sc., Professor, Associate Dean of Research, UCLA School of Dentistry and Director of Dental Research Institute

Janghee Woo, M.D., Albert Einstein Medical Center

Wen Jin Wu, M.D., Ph.D., Principal Investigator, Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, FDA

Brenda Yanak, Ph.D., Precision Medicine Leader, Clinical Innovation, Pfizer

Tammie Yeh, Ph.D., Molecular Biomarkers, Oncology Lead, Merck

Eunhee S. Yi, M.D., Consultant, Anatomic Pathology, Mayo Clinic; Professor, Pathology, Mayo Clinic College of Medicine

Malcolm York, MPhil, Director and Head, Clinical Pathology and Safety Assessment, GlaxoSmithKline R&D

Theresa Zhang, Ph.D., Associate Director, Exploratory and Translational Sciences, Merck

BIOMARKERS

& DIAGNOSTICS

world congress 2013

MAY 6 – 8, 2013 | LOEWS PHILADELPHIA HOTEL | PHILADELPHIA, PA

Cambridge Healthtech Institute’s Ninth Annual

BiomarkerWorldCongress.com

The Leading Annual Meeting Dedicated to Biomarkers

and Diagnostics Research and Implementation

Dinner Courses:

Fit-for-Purpose Biomarker Assay

Development and Validation

Next-Generation Sequencing as

a Clinical Test

Laboratory-Developed Tests

Conference Programs:

May 6 – 7, 2013

Track 1: Translational

Biomarkers in Drug Development

Track 2: Clinical Assay

Development

Track 3: Cancer Tissue

Diagnostics

May 6 – 8, 2013

Track 4: Executive Summit:

Companion Diagnostics

May 7 – 8, 2013

Track 5: Biomarkers for

Patient Selection

Track 6: Cancer Drug Resistance

Track 7: Exosomes and

Microvesicles as Biomarkers

and Diagnostics

Premier Sponsor

Featured Speakers

Hakan Sakul

Head, Diagnostics

Pfizer

Yoshi Oda

President, Biomarkers & Personalized Medicine

Eisai

David Wholley

Director

Biomarkers Consortium

Khusru Asadullah

VP, Head, Global Biomarkers

Bayer

Nicholas C. Dracopoli

VP, Janssen R&D

Johnson & Johnson

Eric Lai

SVP, Head, Pharmacogenomics

Takeda

2 | Biomarkers & Diagnostics World Congress BiomarkerWorldCongress.com

BIOMARKERS & DIAGNOSTICS

world congress 2013

Track 1: Translational Biomarkers

in Drug Development

Track 2: Clinical

Assay Development

Track 3: Cancer Tissue Diagnostics Track 4: Executive Summit:

Companion Diagnostics*

Sunday, May 5

5:00-6:00 Conference Pre-Registration

Monday, May 6

8:30-10:00 Biomarkers in Translational Medicine From Research Biomarkers to

Clinical Assays

Whole-Slide Imaging and

Digital Pathology

Commercialization of

Companion Diagnostics

10:00-10:30 Networking Coffee Break

10:30-11:50 Biomarkers in Translational Medicine From Research Biomarkers to

Clinical Assays

Whole-Slide Imaging and

Digital Pathology

Commercialization of

Companion Diagnostics

11:50-1:20 Luncheon Presentation

Systems Pharmacology: Pathways to Patient Response @ BioIT World, Boston, MA World Trade Center, April 9-11, 2013

Posted in Computational Biology/Systems and Bioinformatics, Scientist: Career considerations, tagged Cancer - General, Harvard Medical School, national cancer institute, NCI, systems biology, Thomson Reuters on February 18, 2013| Leave a Comment »

Reporter: Aviva Lev-Ari, PhD, RN

Systems Pharmacology: Pathways to Patient Response @ BioIT World, Boston, MA World Trade Center, April 9-11, 2013

Conference Tracks:

IT Infrastructure – Hardware

Software Development

Cloud Computing

Bioinformatics

Next-Gen Sequencing Informatics

Systems Pharmacology

eClinical Trials Solutions

Data Visualization NEW!

Drug Discovery Informatics

Clinical Omics NEW!

Collaborations and Open

Access Innovations

Cancer Informatics

Track 6 focuses on how compounds (drugs) work in the body. How are they influenced by various ‘omics’? How do they vary by tissue? The practical implications of such a compound-centric approach are exciting: new targets, new screens, new markers, new understanding of drug failure mechanisms. The systems computational tool sets including multi-scale modeling, simulation, web-based platforms, etc. will be emphasized.

Final Agenda

Download Brochure | Pre-Conference Workshops

TUESDAY, APRIL 9

7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

*Separate Registration Required

2:00 – 7:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute

4:05 Keynote Introduction

Speaker to be Announced, Hitachi Data Systems

» 4:15 PLENARY KEYNOTE

Do Network Pharmacologists Need Robot Chemists?

Andrew Hopkins Andrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry and Drug Design, College of Life Sciences, University of Dundee

5:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPads® or 1 of 2 Kindle Fires®!*

*Apple ® and Amazon are not sponsors or participants in this program

WEDNESDAY, APRIL 10

7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon

» 8:15 PLENARY KEYNOTE

Atul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital; Co-founder, Personalis and Numedii

8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

PHARMACODYNAMIC MODELS

10:50 Chairperson’s Remarks

» Featured Speaker

11:00 Systems Pharmacology in a Post-Genomic Era

Peter Sorger, Ph.D., Professor, Systems Biology, Harvard Medical School; Co-Chair, Harvard Initiative in Systems Pharmacology

I will describe the emergence of “systems pharmacology” as a means to guide the creation of new molecular matter, study cellular networks and their perturbation by drugs, understand pharmaco-kinetics and pharmaco-dynamics in mouse and man and design and analyze clinical trial data. The approach combines mathematical modeling with empirical measurement as a means to tackle basic and clinical problems in pharmacology. Ultimately we aim for models that describe drug responses at multiple temporal and physical scales from molecular mechanism to whole-organism physiology.

11:30 Using Quantitative Systems Pharmacology for De-Risking Projects in CNS R&D

Hugo Geerts, Ph.D., CSO, Computational Neuropharmacology, In Silico Biosciences

Quantitative Systems Pharmacology is a computer based mechanistic modeling approach combining physiology, the functional imaging of genetics with the pharmacology of drug-receptor interaction and parameterized with clinical data and is a possible powerful tool for improving the success rate of CNS R&D projects. The presentation will include failure analyses of unsuccessful clinical trials, correct prospective identification of clinical problems that halted clinical development and estimation of genotype effects on the pharmacodynamics of candidate drugs.

12:00 pm Systems Pharmacology Approaches to Drug Repositioning

Svetlana Bureeva, Ph.D., Director, Professional Services, Thomson Reuters, IP & Science

Drug repositioning requires advanced computational approaches and comprehensive knowledgebase information to reach success. Thomson Reuters will present on recent advances in drug repositioning approaches, their validation and performance, best practices in using systems biology content, and successful case studies.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

HIGH CONTENT ANALYSIS: CANCER CELL LINES

1:40 Chairperson’s Remarks

1:45 Systems Pharmacology Using CellMiner and the NCI-60 Cancerous Cell Lines

William Reinhold, Manager, Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), National Cancer Institute (NCI)

CellMiner is a web-based application that allows rapid access to and comparison between 20,503 compound activities and the expression levels of 26,065 genes and 360 microRNAs. Included are 102 FDA-approved drugs as well as 53 in clinical trials. The tool is designed for the non-informatisist, and allows the user wide latitude in defining the question of interest. This opens the door to systems pharmacological studies for physicians, molecular biologists and others without bioinformatics expertise.

2:15 Oncology Drug Combinations at Novartis

Joseph Lehár, Ph.D., Associate Director, Bioinformatics, Oncology Translational Research, Novartis; Adjunct Assistant Professor, Bioinformatics, Boston University

Novartis is undertaking a large-scale effort to comprehensively describe cancer through the lens of cell cultures and tissue samples. In collaboration with academic and industrial partners, we have generated mutation status, gene copy number, and gene expression data for a library of 1,000 cancer cell lines, representing most cancer lineages and common genetic backgrounds. Most of these cell lines have been tested for chemosensitivity against ~1,200 cancer-relevant compounds, and we are systematically exploring drug combinations for synergy against ~100 prioritized CCLE lines. We expect this large-scale campaign to enable efficient patient selection for clinical trials on existing cancer drugs, reveal many therapeutically promising drug synergies or anti-resistance combinations, and provide unprecedented detail on functional interactions between cancer signaling pathways. I will discuss early highlights of this work and describe our plans to make use of this resource.

2:45 Sponsored Presentations (Opportunities Available)

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

PHARMACODYNAMIC MODELS FOR ONCOLOGY

3:45 Systems Biology in Cancer Immunotherapy: Applications in the Understanding of Mechanism of Action and Therapeutic Response

Debraj Guha Thakurta, Ph.D., Senior Scientist II & Group Leader, Systems Biology, Dendreon Corporation

We are using high-content platforms (DNA and protein microarrays, RNA-seq) in various stages of the development of cellular immunotherapies for cancer. We will provide examples of genomic applications that can aid in the mechanistic understanding and the discovery of molecular markers associated with the efficacy of a cancer immunotherapy..

4:15 Use of Systems Pharmacology to Aid Cancer Clinical Development

Anna Georgieva Kondic, Ph.D., MBA, Senior Principal Scientist, Modeling and Simulation, Merck Research Labs

The last few years have seen an increased use of physiologically-based pharmacokinetics and pharmacodynamics models in Oncology drug development. This is partially due to an improved mechanistic understanding of disease drivers and the collection of better patient-level quantitative data that lends itself to modeling. In this talk, a suite of studies where systems modeling was successfully used to inform either preclinical to clinical transition or clinical study design will be presented. The talk will complete with a potential systems pharmacology framework that can be used systematically in drug development.

4:45 Sponsored Presentations (Opportunities Available)

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes

Thursday, April 11

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

MODELING AND MINING TARGETS

8:45 Chairperson’s Opening Remarks

8:50 Systems Biology Approach for Identification of New Targets and Biomarkers

I-Ming Wang, Ph.D., Associate Scientific Director, Research Solutions and Bioinformatics, Informatics and Analysis, Merck Research Laboratory

A representative gene signature was identified by an integrated analysis of expression data in twelve rodent inflammatory models/tissues. This “inflammatome” signature is highly enriched in known drug target genes and is significantly overlapped with macrophage-enriched metabolic networks (MEMN) reported previously. A large proportion of genes in this signature are tightly connected in several tissue-specific Bayesian networks built from multiple mouse F2 crosses and human tissue cohorts; furthermore, these tissue networks are very significantly overlapped. This indicates that variable expression in this set of co-regulated genes is the main driver of many disease states. Disease-specific gene sets with the potential of being utilized as biomarkers were also identified with the approach we applied. The identification of this “inflammatome” gene signature extends the coverage of MEMN beyond adipose and liver in the metabolic disease to multiple diseases involving various affected tissues.

9:20 Optimizing Therapeutic Index (TI) by Exploring Co-Dependencies of Target and Therapeutic Properties

Madhu Natarajan, Ph.D., Associate Director, Computational Biology, Discovery Research, Shire HGT

Conventional drug-discovery informatics workflows employ combinations of mechanistic/probabilistic in-silico methods to rank lists of targets; therapeutics are then developed for “optimal” targets. I describe a systems pharmacology approach that instead integrates systematic in-silico therapeutic perturbation with models of target/disease biology to identify conditions for optimal TI; non-intuitively optimal TI is sometimes achieved by pairing sub-optimal targets with therapeutics having appropriate properties.

9:50 Sponsored Presentations (Opportunities Available)

10:20 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

» PLENARY KEYNOTE PANEL

11:05 The Life Sciences CIO Panel

Panelists:
Remy Evard, CIO, Novartis Institutes for BioMedical Research
Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec
Andrea T. Norris, Director, Center for Information Technology (CIT) and Chief Information Officer, NIH
Gunaretnam Rajagopal, Ph.D., Vice President and CIO, Bioinformatics & External Innovation at Janssen Pharmaceutical Companies of Johnson & Johnson
Cris Ross, Chief Information Officer, Mayo Clinic

12:15 pm Luncheon in the Exhibit Hall with Poster Viewing

MODELING MOLECULAR AND PATHOPHYSIOLOGICAL DATA

1:55 Chairperson’s Remarks

2:00 Predicting Adverse Side Effects of Drugs Using Systems Pharmacology

Jake Chen, Ph.D., Associate Professor, Indiana University School of Informatics & Purdue University Department of Computer Science; Director, Indiana Center for Systems Biology and Personalized Medicine

A new way of studying drug toxicity is to incorporate biomolecular annotation and network data with clinical observations of drug targets upon drug perturbations. I will describe the development of a novel computational modeling framework, with which we demonstrated the highest drug toxicity prediction accuracies ever reported by far. Adoption of this framework may have profound practical drug discovery implications.

2:30 Holistic Integration of Molecular and Physiological Data and Its Application in Personalized Healthcare

David de Graaf, Ph.D. President and CEO, Selventa

There are multiple industry-wide challenges in aggregating molecular and pathophysiological data for systems pharmacology to transform the process of drug discovery and development. One of the ways to address these challenges is to utilize a common computable biological expression language (BEL) that can provide a comprehensive knowledge network for new discoveries. An application of BEL and its use in identifying clinically relevant predictive biomarkers for patient stratification will be presented.

3:00 The Role of Informatics in ADME Pharmacogenetics

Boyd Steere, Ph.D., Senior Research Scientist, Lilly Research Laboraories, IT Research Informatics, Eli Lilly

The leveraging of pharmacogenetics to support decisions in early-phase clinical trial design requires informatics methods to integrate, visualize, and analyze heterogeneous data sets from many different discovery platforms. This presentation describes challenges and solutions in making sense of diverse sets of genetic, protein, and metabolic data in support of ADME pharmacology projects.

3:30 A Systems Pharmacology Approach to Understand and Optimize Functional Selectivity for Non-Selective Drugs

Joshua Apgar, Principal Scientist, Systems Biology, Dept. of Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc.

Most commonly the selectivity of a compound is defined in an in vitro or cellular assay, and it is thought of as principally a function of the binding energy of the drug to its on-target and off-target proteins; however, in vivo functional selectivity is much more complicated, and is affected by systems level effects such as multiple feedback processes within and between the various on- and off-target pathways. These systems level processes are often impossible to reconstruct in vitro as they involve many cell types, tissues, and organs systems throughout the body. We show here that through mathematical modeling we were able to identify, in silico, molecular properties that are critical to driving functional selectivity. The models, although simple, capture the key systems pharmacology needed to understand the on- an off- target effects. Surprisingly, in this case, the key driver of functional selectivity is not the affinity of the drugs but rather the pharmacokinetics, with drugs having a short half-life predicted to be the most functionally selective.

SOURCE:

http://www.bio-itworldexpo.com/Systems-Pharmacology/?goback=%2Egde_159027_member_213380734

http://www.bio-itworldexpo.com/IT-Infrastructure-Hardware/

Final Agenda

http://www.bio-itworldexpo.com/uploadedFiles/Bio-IT_World_Expo/13/2013-BIT-Brochure.pdf

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The potential contribution of informatics to healthcare is more than currently estimated

Posted in Health Economics and Outcomes Research, Health Law & Patient Safety, HealthCare IT, Medical Devices R&D Investment, Pharmaceutical Industry Competitive Intelligence, Population Health Management, Genetics & Pharmaceutical, Statistical Methods for Research Evaluation, Technology Transfer: Biotech and Pharmaceutical, tagged "To Err is Human", Artificial intelligence, Bennett, Computational Medical Science, Dashboard, Decision making, Diagnosis, Empirical evidence, geometric clustering analysis, Hauser, Health care in the United States, health economics, Indiana University, Inferential Second Opinion, knowledge-based opinion, Markov decision process, medical decision-making, patient flow, patient outcomes, problem-solving constructs, Triplex Medical Science, University of Edinburgh School of Informatics, workload processing, Yale University on February 18, 2013| 3 Comments »

The potential contribution of informatics to healthcare is more than currently estimated

Reporter: Larry H Bernstein, MD, FCAP

I call attention to an interesting article that just came out. The estimate of improved costsavings in healthcare and diagnostic accuracy is extimated to be substantial. I have written about the unused potential that we have not yet seen. In short, there is justification in substantial investment in resources to this, as has been proposed as a critical goal. Does this mean a reduction in staffing? I wouldn’t look at it that way. The two huge benefits that would accrue are:

workflow efficiency, reducing stress and facilitating decision-making.
scientifically, primary knowledge-based decision-support by well developed algotithms that have been at the heart of computational-genomics.

Can computers save health care? IU research shows lower costs, better outcomes

Cost per unit of outcome was $189, versus $497 for treatment as usual

Last modified: Monday, February 11, 2013

BLOOMINGTON, Ind. — New research from Indiana University has found that machine learning — the same computer science discipline that helped create voice recognition systems, self-driving cars and credit card fraud detection systems — can drastically improve both the cost and quality of health care in the United States.

Physicians using an artificial intelligence framework that predicts future outcomes would have better patient outcomes while significantly lowering health care costs.

Using an artificial intelligence framework combining Markov Decision Processes and Dynamic Decision Networks, IU School of Informatics and Computing researchers Casey Bennett and Kris Hauser show how simulation modeling that understands and predicts the outcomes of treatment could

reduce health care costs by over 50 percent while also
improving patient outcomes by nearly 50 percent.

The work by Hauser, an assistant professor of computer science, and Ph.D. student Bennett improves upon their earlier work that

showed how machine learning could determine the best treatment at a single point in time for an individual patient.

By using a new framework that employs sequential decision-making, the previous single-decision research

can be expanded into models that simulate numerous alternative treatment paths out into the future;
maintain beliefs about patient health status over time even when measurements are unavailable or uncertain; and
continually plan/re-plan as new information becomes available.

In other words, it can “think like a doctor.” (Perhaps better because of the limitation in the amount of information a bright, competent physician can handle without error!)

“The Markov Decision Processes and Dynamic Decision Networks enable the system to deliberate about the future, considering all the different possible sequences of actions and effects in advance, even in cases where we are unsure of the effects,” Bennett said. Moreover, the approach is non-disease-specific — it could work for any diagnosis or disorder, simply by plugging in the relevant information. (This actually raises the question of what the information input is, and the cost of inputting.)

The new work addresses three vexing issues related to health care in the U.S.:

rising costs expected to reach 30 percent of the gross domestic product by 2050;
a quality of care where patients receive correct diagnosis and treatment less than half the time on a first visit;
and a lag time of 13 to 17 years between research and practice in clinical care.

Framework for Simulating Clinical Decision-Making

“We’re using modern computational approaches to learn from clinical data and develop complex plans through the simulation of numerous, alternative sequential decision paths,” Bennett said. “The framework here easily out-performs the current treatment-as-usual, case-rate/fee-for-service models of health care.” (see the above)

Bennett is also a data architect and research fellow with Centerstone Research Institute, the research arm of Centerstone, the nation’s largest not-for-profit provider of community-based behavioral health care. The two researchers had access to clinical data, demographics and other information on over 6,700 patients who had major clinical depression diagnoses, of which about 65 to 70 percent had co-occurring chronic physical disorders like diabetes, hypertension and cardiovascular disease. Using 500 randomly selected patients from that group for simulations, the two

compared actual doctor performance and patient outcomes against
sequential decision-making models

using real patient data.

They found great disparity in the cost per unit of outcome change when the artificial intelligence model’s

cost of $189 was compared to the treatment-as-usual cost of $497.
the AI approach obtained a 30 to 35 percent increase in patient outcomes

Bennett said that “tweaking certain model parameters could enhance the outcome advantage to about 50 percent more improvement at about half the cost.”

While most medical decisions are based on case-by-case, experience-based approaches, there is a growing body of evidence that complex treatment decisions might be effectively improved by AI modeling. Hauser said “Modeling lets us see more possibilities out to a further point – because they just don’t have all of that information available to them.” (Even then, the other issue is the processing of the information presented.)

Using the growing availability of electronic health records, health information exchanges, large public biomedical databases and machine learning algorithms, the researchers believe the approach could serve as the basis for personalized treatment through integration of diverse, large-scale data passed along to clinicians at the time of decision-making for each patient. Centerstone alone, Bennett noted, has access to health information on over 1 million patients each year. “Even with the development of new AI techniques that can approximate or even surpass human decision-making performance, we believe that the most effective long-term path could be combining artificial intelligence with human clinicians,” Bennett said. “Let humans do what they do well, and let machines do what they do well. In the end, we may maximize the potential of both.”

“Artificial Intelligence Framework for Simulating Clinical Decision-Making: A Markov Decision Process Approach” was published recently in Artificial Intelligence in Medicine. The research was funded by the Ayers Foundation, the Joe C. Davis Foundation and Indiana University.

For more information or to speak with Hauser or Bennett, please contact Steve Chaplin, IU Communications, at 812-856-1896 or stjchap@iu.edu.

IBM Watson Finally Graduates Medical School

It’s been more than a year since IBM’s Watson computer appeared on Jeopardy and defeated several of the game show’s top champions. Since then the supercomputer has been furiously “studying” the healthcare literature in the hope that it can beat a far more hideous enemy: the 400-plus biomolecular puzzles we collectively refer to as cancer.

Anomaly Based Interpretation of Clinical and Laboratory Syndromic Classes

Larry H Bernstein, MD, Gil David, PhD, Ronald R Coifman, PhD. Program in Applied Mathematics, Yale University, Triplex Medical Science.

Statement of Inferential Second Opinion

Realtime Clinical Expert Support and Validation System

Gil David and Larry Bernstein have developed, in consultation with Prof. Ronald Coifman, in the Yale University Applied Mathematics Program, a software system that is the equivalent of an intelligent Electronic Health Records Dashboard that provides

empirical medical reference and suggests quantitative diagnostics options.

Background

The current design of the Electronic Medical Record (EMR) is a linear presentation of portions of the record by

services, by
diagnostic method, and by
date, to cite examples.

This allows perusal through a graphical user interface (GUI) that partitions the information or necessary reports in a workstation entered by keying to icons. This requires that the medical practitioner finds

the history,
medications,
laboratory reports,
cardiac imaging and EKGs, and
radiology

in different workspaces. The introduction of a DASHBOARD has allowed a presentation of

drug reactions,
allergies,
primary and secondary diagnoses, and
critical information about any patient the care giver needing access to the record.

The advantage of this innovation is obvious. The startup problem is what information is presented and how it is displayed, which is a source of variability and a key to its success.

Proposal

We are proposing an innovation that supercedes the main design elements of a DASHBOARD and

utilizes the conjoined syndromic features of the disparate data elements.

So the important determinant of the success of this endeavor is that it facilitates both

the workflow and
the decision-making process

with a reduction of medical error.

This has become extremely important and urgent in the 10 years since the publication “To Err is Human”, and the newly published finding that reduction of error is as elusive as reduction in cost. Whether they are counterproductive when approached in the wrong way may be subject to debate.

We initially confine our approach to laboratory data because it is collected on all patients, ambulatory and acutely ill, because the data is objective and quality controlled, and because

laboratory combinatorial patterns emerge with the development and course of disease. Continuing work is in progress in extending the capabilities with model data-sets, and sufficient data.

It is true that the extraction of data from disparate sources will, in the long run, further improve this process. For instance, the finding of both ST depression on EKG coincident with an increase of a cardiac biomarker (troponin) above a level determined by a receiver operator curve (ROC) analysis, particularly in the absence of substantially reduced renal function.

The conversion of hematology based data into useful clinical information requires the establishment of problem-solving constructs based on the measured data. Traditionally this has been accomplished by an intuitive interpretation of the data by the individual clinician. Through the application of geometric clustering analysis the data may interpreted in a more sophisticated fashion in order to create a more reliable and valid knowledge-based opinion.

The most commonly ordered test used for managing patients worldwide is the hemogram that often incorporates the review of a peripheral smear. While the hemogram has undergone progressive modification of the measured features over time the subsequent expansion of the panel of tests has provided a window into the cellular changes in the production, release or suppression of the formed elements from the blood-forming organ to the circulation. In the hemogram one can view data reflecting the characteristics of a broad spectrum of medical conditions.

Progressive modification of the measured features of the hemogram has delineated characteristics expressed as measurements of

size,
density, and
concentration,

resulting in more than a dozen composite variables, including the

mean corpuscular volume (MCV),
mean corpuscular hemoglobin concentration (MCHC),
mean corpuscular hemoglobin (MCH),
total white cell count (WBC),
total lymphocyte count,
neutrophil count (mature granulocyte count and bands),
monocytes,
eosinophils,
basophils,
platelet count, and
mean platelet volume (MPV),
blasts,
reticulocytes and
platelet clumps,
perhaps the percent immature neutrophils (not bands)
as well as other features of classification.

The use of such variables combined with additional clinical information including serum chemistry analysis (such as the Comprehensive Metabolic Profile (CMP)) in conjunction with the clinical history and examination complete the traditional problem-solving construct. The intuitive approach applied by the individual clinician is limited, however,

by experience,
memory and
cognition.

The application of rules-based, automated problem solving may provide a more reliable and valid approach to the classification and interpretation of the data used to determine a knowledge-based clinical opinion.

The classification of the available hematologic data in order to formulate a predictive model may be accomplished through mathematical models that offer a more reliable and valid approach than the intuitive knowledge-based opinion of the individual clinician. The exponential growth of knowledge since the mapping of the human genome has been enabled by parallel advances in applied mathematics that have not been a part of traditional clinical problem solving. In a univariate universe the individual has significant control in visualizing data because unlike data may be identified by methods that rely on distributional assumptions. As the complexity of statistical models has increased, involving the use of several predictors for different clinical classifications, the dependencies have become less clear to the individual. The powerful statistical tools now available are not dependent on distributional assumptions, and allow classification and prediction in a way that cannot be achieved by the individual clinician intuitively. Contemporary statistical modeling has a primary goal of finding an underlying structure in studied data sets.

In the diagnosis of anemia the variables MCV,MCHC and MCH classify the disease process into microcytic, normocytic and macrocytic categories. Further consideration of

proliferation of marrow precursors,

the domination of a cell line, and
features of suppression of hematopoiesis

provide a two dimensional model. Several other possible dimensions are created by consideration of

the maturity of the circulating cells.

The development of an evidence-based inference engine that can substantially interpret the data at hand and convert it in real time to a “knowledge-based opinion” may improve clinical problem solving by incorporating multiple complex clinical features as well as duration of onset into the model.

An example of a difficult area for clinical problem solving is found in the diagnosis of SIRS and associated sepsis. SIRS (and associated sepsis) is a costly diagnosis in hospitalized patients. Failure to diagnose sepsis in a timely manner creates a potential financial and safety hazard. The early diagnosis of SIRS/sepsis is made by the application of defined criteria (temperature, heart rate, respiratory rate and WBC count) by the clinician. The application of those clinical criteria, however, defines the condition after it has developed and has not provided a reliable method for the early diagnosis of SIRS. The early diagnosis of SIRS may possibly be enhanced by the measurement of proteomic biomarkers, including transthyretin, C-reactive protein and procalcitonin. Immature granulocyte (IG) measurement has been proposed as a more readily available indicator of the presence of

granulocyte precursors (left shift).

The use of such markers, obtained by automated systems in conjunction with innovative statistical modeling, may provide a mechanism to enhance workflow and decision making.

An accurate classification based on the multiplicity of available data can be provided by an innovative system that utilizes the conjoined syndromic features of disparate data elements. Such a system has the potential to facilitate both the workflow and the decision-making process with an anticipated reduction of medical error.

This study is only an extension of our approach to repairing a longstanding problem in the construction of the many-sided electronic medical record (EMR). On the one hand, past history combined with the development of Diagnosis Related Groups (DRGs) in the 1980s have driven the technology development in the direction of “billing capture”, which has been a focus of epidemiological studies in health services research using data mining.

In a classic study carried out at Bell Laboratories, Didner found that information technologies reflect the view of the creators, not the users, and Front-to-Back Design (R Didner) is needed. He expresses the view:

“Pre-printed forms are much more amenable to computer-based storage and processing, and would improve the efficiency with which the insurance carriers process this information. However, pre-printed forms can have a rather severe downside. By providing pre-printed forms that a physician completes

to record the diagnostic questions asked,

as well as tests, and results,
the sequence of tests and questions,

might be altered from that which a physician would ordinarily follow. This sequence change could improve outcomes in rare cases, but it is more likely to worsen outcomes. “

Decision Making in the Clinical Setting. Robert S. Didner

A well-documented problem in the medical profession is the level of effort dedicated to administration and paperwork necessitated by health insurers, HMOs and other parties (ref). This effort is currently estimated at 50% of a typical physician’s practice activity. Obviously this contributes to the high cost of medical care. A key element in the cost/effort composition is the retranscription of clinical data after the point at which it is collected. Costs would be reduced, and accuracy improved, if the clinical data could be captured directly at the point it is generated, in a form suitable for transmission to insurers, or machine transformable into other formats. Such data capture, could also be used to improve the form and structure of how this information is viewed by physicians, and form a basis of a more comprehensive database linking clinical protocols to outcomes, that could improve the knowledge of this relationship, hence clinical outcomes.

How we frame our expectations is so important that

it determines the data we collect to examine the process.

In the absence of data to support an assumed benefit, there is no proof of validity at whatever cost. This has meaning for

hospital operations, for
nonhospital laboratory operations, for
companies in the diagnostic business, and
for planning of health systems.

In 1983, a vision for creating the EMR was introduced by Lawrence Weed and others. This is expressed by McGowan and Winstead-Fry.

J J McGowan and P Winstead-Fry. Problem Knowledge Couplers: reengineering evidence-based medicine through interdisciplinary development, decision support, and research.

Bull Med Libr Assoc. 1999 October; 87(4): 462–470. PMCID: PMC226622 Copyright notice

Example of Markov Decision Process (MDP) transition automaton (Photo credit: Wikipedia)

Control loop of a Markov Decision Process (Photo credit: Wikipedia)

English: IBM’s Watson computer, Yorktown Heights, NY (Photo credit: Wikipedia)

English: Increasing decision stakes and systems uncertainties entail new problem solving strategies. Image based on a diagram by Funtowicz, S. and Ravetz, J. (1993) “Science for the post-normal age” Futures 25:735–55 (http://dx.doi.org/10.1016/0016-3287(93)90022-L). (Photo credit: Wikipedia)

Artificial intelligence system diagnoses illnesses better than doctors (sott.net)
Wow of the Week: AI that “thinks like a doctor” shows lower costs, better outcomes in study (medcitynews.com)
AI system diagnoses illnesses better than doctors (rawstory.com)
Artificial Intelligence Smarter than Doctors? (americanlivewire.com)
Can computers save health care? IU research shows lower costs, better outcomes (binaryhealthcare.wordpress.com)
CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics and Computational Genomics (pharmaceuticalintelligence.com)
Where Does Informatics Belong? Part II (himss.org)
Kaiser Health News/Philadelphia Inquirer on MedInformaticsMD: “The flaws of electronic records” (hcrenewal.blogspot.com)

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In focus: Melanoma Genetics

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Genome Biology, Genomic Testing: Methodology for Diagnosis, Molecular Genetics & Pharmaceutical, tagged Akt, Apoptosis, ARF, BRAF, CDK4, CDK6, CDKN2A, cell cycle, CGH array, cutaneous melanoma, genetic heterogeneity, genome, genomics, INK4A, locus, malignant, Melanoma, naevi, nodularity, NRAS, p53, PI3K, pigmentation, Raf, Ras, RB, skin cancer, sunburn, ubiquitination, UV-A, UV-B on February 18, 2013| 4 Comments »

Curator: Ritu Saxena, Ph.D.

Melanoma

Melanoma represents approximately 4% of human skin cancers, yet accounts for approximately 80% of deaths from cutaneous neoplasms. It remains one of the most common types of cancer among young adults. Melanoma is recognized as the most common fatal skin cancer with its incidence rising to 15 fold in the past 40 years in the United States. Melanoma develops from the malignant transformation of melanocytes, the pigment-producing cells that reside in the basal epidermal layer in human skin. (Greenlee RT, et al, Cancer J Clin. Jan-Feb 2001;51(1):15-36 ; Weinstock MA, et al, Med Health R I. Jul 2001;84(7):234-6). Classic clinical signs of melanoma include change in color, recent enlargement, nodularity, irregular borders, and bleeding. Cardinal signs of melanoma are sometimes referred to by the mnemonic ABCDEs (asymmetry, border irregularity, color, diameter, elevation) (Chudnovsky Y, et al. J Clin Invest, 1 April 2005; 115(4): 813–824).

Clinical characteristics

Melanoma primarily affects fair-haired and fair-skinned individuals, and those who burn easily or have a history of severe sunburn are at higher risk than their darkly pigmented, age-matched controls. The exact mechanism and wavelengths of UV light that are the most critical remain controversial, but both UV-A (wavelength 320–400 nm) and UV-B (290–320 nm) have been implicated (Jhappan C, et al, Oncogene, 19 May 2003;22(20):3099-112). Case-control studies have identified several risk factors in populations susceptible to developing melanoma. MacKie RM et al (1989) stated that the relative risk of cutaneous melanoma is estimated from the four strongest risk factors identified by conditional logistic regression. These factors are

total number of benign pigmented naevi above 2 mm diameter;
freckling tendency;
number of clinically atypical naevi (over 5 mm diameter and having an irregular edge, irregular pigmentation, or inflammation); and
a history of severe sunburn at any time in life.

Use of this risk-factor chart should enable preventive advice for and surveillance of those at greatest risk (MacKie RM, et al, Lancet 26 Aug1989;2(8661):487-90).

Cutaneous melanoma can be subdivided into several subtypes, primarily based on anatomic location and patterns of growth (Table 1).

Table 1: Clinical Classification of Melanoma (Chudnovsky Y, et al, 2005)

The genetics of melanoma

As in many cancers, both genetic predisposition and exposure to environmental agents are risk factors for melanoma development. Many studies conducted over several decades on benign and malignant melanocytic lesions as well as melanoma cell lines have implicated numerous genes in melanoma development and progression.

Table 2: Genes involved in Melanoma (Chudnovsky Y, et al, 2005)

Apart from the risk factors such as skin pigmentation, freckling, and so on, another significant risk factor is ‘strong family history of melanoma’. Older case-control studies of patients with familial atypical mole-melanoma (FAMM) syndrome suggested an elevated risk of ∼434-to 1000-fold over the general population (Greene MH, et al, Ann Intern Med, Apr 1985;102(4):458-65). A more recent meta-analysis of family history found that the presence of at least one first-degree relative with melanoma increases the risk by 2.24-fold (Gandini S, et al, Eur J Cancer, Sep 2005;41(14):2040-59). Genetic studies of melanoma-prone families have given important clues regarding melanoma susceptibility loci.

CDKN2A, the familial melanoma locus

CDKN2A is located at chromosome 9p21 and is composed of 4 exons (E) – 1α, 1β, 2, and 3. LOH or mutations at this locus cosegregated with melanoma susceptibility in familial melanoma kindred and 9p21 mutations have been observed in different cancer cell lines. The locus encodes two tumor suppressors via alternate reading frames, INK4 (p16^INK4a) and ARF (p14^ARF). INK4A and ARF encode alternative first exons, 1α and 1β respectively and different promoters. INK4A is translated from the splice product of E1α, E2, and E3, while ARF is translated from the splice product of E1β, E2, and E3. Second exons of the two proteins are shared and two translated proteins share no amino acid homology.

INK4A is the founding member of the INK4 (Inhibitor of cyclin-dependent kinase 4) family of proteins and inhibits the G1 cyclin-dependent kinases (CDKs) 4/6, which phosphorylate and inactivate the retinoblastoma protein (RB), thereby allowing for S-phase entry. Thus, loss of INK4K function promotes RB inactivation through hyperphosphorylation, resulting in unconstrained cell cycle progression.

ARF (Alternative Reading Frame) protein of the locus inhibits HDM2-mediated ubiquitination and subsequent degradation of p53. Thus, loss of ARF inactivates another tumor suppressor, p53. The loss of p53 impairs mechanisms that normally target genetically damaged cells for cell cycle arrest and/or apoptosis, which leads to proliferation of damaged cells. Loss of CDKN2A therefore contributes to tumorigenesis by disruption of both the pRB and p53 pathways.

Figure 1: Genetic encoding and mechanism of action of INK4A and ARF.

(Chudnovsky Y, et al, 2005)

RAF and RAS pathways

A genetic hallmark of melanoma is the presence of activating mutations in the oncogenes BRAF and NRAS, which are present in 70% and 15% of melanomas, respectively, and lead to constitutive activation of mitogen-activated protein kinase (MAPK) pathway signaling. However, molecules that inhibit MAPK pathway–associated kinases, like BRAF and MEK, have shown only limited efficacy in the treatment of metastatic melanoma. Thus, a deeper understanding of the cross talk between signaling networks and the complexity of melanoma progression should lead to more effective therapy.

NRAS mutations activate both effector pathways, Raf-MEK-ERK and PI3K-Akt in melanoma. The Raf-MEK-ERK pathway may also be activated via mutations in the BRAF gene. In a subset of melanomas, the ERK kinases have been shown to be constitutively active even in the absence of NRAS or BRAF mutations. The PI3K-Akt pathway may be activated through loss or mutation of the tumor suppressor gene PTEN, occurring in 30–50% of melanomas, or through gene amplification of the AKT3 isoform. Activation of ERK and/or Akt3 promotes the development of melanoma by various mechanisms, including stimulation of cell proliferation and enhanced resistance to apoptosis.

Figure 2: Schematic of the canonical Ras effector pathways Raf-MEK-ERK and PI3K-Akt in melanoma.

Curtin et al (2005) compared genome-wide alterations in the number of copies of DNA and mutational status of BRAF and NRAS in 126 melanomas from four groups in which the degree of exposure to ultraviolet light differs: 30 melanomas from skin with chronic sun-induced damage and 40 melanomas from skin without such damage; 36 melanomas from palms, soles, and subungual (acral) sites; and 20 mucosal melanomas. Significant differences were observed in number of copies of DNA and mutation frequencies in BRAF among the four groups of melanomas. Eighty-one percent of the melanomas on skin without sun-induced damaged had mutations in BRAF or NRAS. Melanomas with wild-type BRAF or NRAS frequently had increases in the number of copies of the genes for cyclin-dependent kinase 4 (CDK4) and cyclin D1 (CCND1), downstream components of the RAS-BRAF pathway. Thus, the genetic alterations identified in melanomas at different sites and with different levels of sun exposure indicate that there are distinct genetic pathways in the development of melanoma and implicate CDK4 and CCND1 as independent oncogenes in melanomas without mutations in BRAF or NRAS. (Curtin JA, et al, N Engl J Med, 17 Nov 2005;353(20):2135-47).

Genetic Heterogeneity of Melanoma

Melanoma exhibits molecular heterogeneity with markedly distinct biological and clinical behaviors. Lentigo maligna melanomas, for example, are indolent tumors that develop over decades on chronically sun-exposed area such as the face. Acral lentigenous melanoma, or the other hand, develops on sun-protected regions, tend to be more aggressive. Also, transcription profiling has provided distinct molecular subclasses of melanoma. It is also speculated that alterations at the DNA and RNA and the non-random nature of chromosomal aberrations may segregate melanoma tumors into subtypes with distinct clinical behaviors.

The melanoma gene atlas

Whole-genome screening technologies such as spectral karyotype analysis and array-CGH have identified many recurrent nonrandom chromosomal structural alterations, particularly in chromosomes 1, 6, 7, 9, 10, and 11 (Curtin JA, et al, N Engl J Med, 17 Nov 2005;353(20):2135-47); however, in most cases, no known or validated targets have been linked to these alterations.

In A systematic high-resolution genomic analysis of melanocytic genomes, array-CGH profiles of 120 melanocytic lesions, including 32 melanoma cell lines, 10 benign melanocytic nevi, and 78 melanomas (primary and metastatic) by Chin et al (2006) revealed a level of genomic complexity not previously appreciated. In total, 435 distinct copy number aberrations (CNAs) were defined among the metastatic lesions, including 163 recurrent, high-amplitude events. These include all previously described large and focal events (e.g., 1q gain, 6p gain/6q loss, 7 gain, 9p loss, and 10 loss). Genomic complexity observed in primary and benign nevi melanoma is significantly less than that observed in metastatic melanoma (Figure 3) (Chin L, et al, Genes Dev. 15 Aug 2006;20 (16):2149-2182).

Figure 3: Genome comparisons of melanocyte lesions (Chin L, et al, 2006)

Thus, genomic profiling of various melanoma progression types could reveal important information regarding genetic events those likely drive as metastasis and possibly, reveal provide cues regarding therapy targeted against melanoma.

Reference:

Sex determination vs. Sex differentiation

Posted in Chemical Genetics, Genome Biology, Genomic Testing: Methodology for Diagnosis, Medical and Population Genetics, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Biology & Bio Instrumentation, tagged chromosome, genitalia, sex determination, sex differentiation, X-linked, XY, Y-linked on February 17, 2013| 1 Comment »

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Human sex refers to the processes by which an individual becomes either a male or female during development. Complex mechanisms are responsible for male sex determination and differentiation. The steps of formation of the testes are dependent on a series of Y-linked, X-linked and autosomal genes actions and interactions. After formation of testes the gonads secrete hormones, which are essential for the formation of the male genitalia. Hormones are transcription regulators, which function by specific receptors. Ambiguous genitalia are result of disruption of genetic interaction. This review describes the mechanisms, which lead to differentiation of male sex and ways by which the determination and differentiation may be interrupted by naturally occurring mutations, causing different syndromes and diseases.

Sex determination: Initial event that determines whether the gonads will develop as testes or ovaries. Sex is determined by “the heat of the male partner during intercourse” –Aristotle (335 B.C.). Today: both environmental and internal mechanisms of sex determination can operate in different species.

Sex differentiation: Subsequent events that ultimately produce either the male or female sexual phenotype. Sexual differentiation is conformed in the human during four successive steps: the constitution of the genetic sex, the differentiation of the gonads, the differentiation of the internal and the external genital tractus and the differentiation of the brain and the hypothalamus.

Sex determination, which depends on the sex-chromosome complement of the embryo, is established by multiple molecular events that direct the development of germ cells, their migration to the urogenital ridge, and the formation of either a testis, in the presence of the Y chromosome (46, XY), or an ovary in the absence of the Y chromosome and the presence of a second X chromosome (46, XX). Sex determination sets the stage for sex differentiation, the sex-specific response of tissues to hormones produced by the gonads after they have differentiated in a male or female pattern. A number of genes have been discovered that contribute both early and late to the process of sex determination and differentiation. In many cases our knowledge has derived from studies of either spontaneous or engineered mouse mutations that cause phenotypes similar to those in humans. How mutations in these genes cause important clinical syndromes and the clinical entities that continue to elude classification at the molecular level have to be tested. Knowledge of the molecular basis of disorders of sex determination and differentiation pathways will continue to have a strong influence on the diagnosis and management of these conditions.

Source References:

http://www.nejm.org/doi/full/10.1056/NEJMra022784

http://en.wikipedia.org/wiki/Sex_determination_and_differentiation_(human)

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A tough after-beginning with the Affordable Care Act

Posted in Health Economics and Outcomes Research, Health Law & Patient Safety, HealthCare IT, tagged Barack Obama, Congress, Independent Advisory Payment Board, IPAB, Medicare, Patient Protection and Affordable Care Act, Republican, Senate on February 17, 2013| Leave a Comment »

New York Methodist Hospital in Park Slope, Brooklyn (Photo credit: Wikipedia)

Larry H Bernstein, MD, FCAP, Triplex Medical Science

New York Methodist Hospital-WeillCornell, an 850+ bed tertiary care hospital in Park Slope, Brooklyn. one of 5 prominent hospitals in NY state has an annual Memorial Lecture in recognition of the former Chief of Orthopedic Surgery. The brother of the deceased is the democratic State Senate leader, Sheldon Silver, from the lower east side of Manhattan. He tells the joke about his brother, the doctor, keeping him focused on the health needs of the community. There is the old Yiddish joke about the mother who recieves a call ferom Washington informing her that her son is elected President (of course this Prez must go to bed every night asking, who needs this! The mother responds, “That’s wonderful, but you know his brother is a DOCTOR!” We have something like that with the Chicago Emanuel brothers.

If you asked her today, she would say, OY! My son the doctor. We are somehow adapting at the same time we are reacting.

This article just appeared in Medscape online.

Official photographic portrait of US President Barack Obama (born 4 August 1961; assumed office 20 January 2009) (Photo credit: Wikipedia)

IPAB Repeal Reintroduced in Senate
Robert Lowes
Feb 15, 2013

Editors’ Recommendations
Imaging Fees for Physicians Get Pushed Over Fiscal Cliff
Presidential Election: Healthcare Game Changer or Time-out?
House Repeals IPAB, Passes Malpractice Damages Cap

English: This is an image of Donald Berwick, who is the Administrator for the US Federal Center for Medicare and Medicaid Services (CMS). CMS is part of the US Department of Health and Human Services. The source website is federally managed by the Department of Health and Human Services. (Photo credit: Wikipedia)

English: Barack Obama signing the Patient Protection and Affordable Care Act at the White House Español: Barack Obama firmando la Ley de Protección al Paciente y Cuidado de Salud Asequible en la Casa Blanca (Photo credit: Wikipedia)

Sticking to their party’s game plan to dismantle the Affordable Care Act (ACA) piece by piece, Sen. John Cornyn (R-TX) and Sen. Orrin Hatch (R-UT) Thursday reintroduced a bill to repeal a controversial Medicare cost control mechanism in the law that is widely opposed by organized medicine.

The cost control mechanism is the Independent Advisory Payment Board (IPAB). The 15-member board must include physicians, but healthcare providers of any stripe must not constitute the majority of the board. Its mission is to advise Congress on how to curb the per capita growth of Medicare spending if it exceeds growth rate targets set by the law. If Congress does not implement IPAB recommendations, it must either enact legislation that saves just as much or let the Department of Health and Human Services make the cuts.

The IPAB, which a reintroduced GOP bill in the House also seeks to repeal, has come under fire from political conservatives and medical societies for offering too much power to a collection of “bureaucrats” who are largely unaccountable to Congress. Critics also warn that it will end up rationing care and subjecting physicians to unfair pay cuts just as Medicare’s sustainable growth rate formula has done.

The ACA explicitly prohibits the IPAB from rationing care or recommending any measures that would reduce Medicare eligibility and benefits or increase costs borne by beneficiaries. Supporters say that the IPAB would perform a salutary end-run around a Congress that is under the sway of healthcare industry lobbyists who protect provider reimbursement to the detriment of the public good.

The Senate bill to repeal the IPAB has 31 sponsors, all Republican. Even if the bill passed in the Senate with Democratic support and sailed through the Republican-controlled House, President Barack Obama is poised to veto it, according to a previous White House pronouncement.

The president has yet to nominate anyone to serve on the IPAB. His appointments under the law require the advice and consent of the Senate. Given that Republicans command enough votes to filibuster any nomination, the IPAB could remain 15 empty chairs, although the president could temporarily fill them through appointments made while the Senate is in recess.

In another new attack on the ACA, Rep. Charles Boustany Jr (R-LA) and Rep. Jim Matheson (D-UT) reintroduced a bill today to repeal an excise tax on health insurers in the law that will raise roughly $100 billion in revenue over 10 years. In addition, earlier this month, a bipartisan group of senators introduced legislation to eliminate an ACA tax on medical devices, which some physicians say will boost the price of diagnostic imaging and other medical equipment during a time of declining reimbursement. The Congressional Budget Office estimates that the device tax will bring $30 billion into the federal treasury.

Any repeal of tax provisions in the ACA presents a Congress committed to deficit reduction with the thorny problem of offsetting revenue losses with either spending cuts or revenue increases elsewhere in the federal budget.

The Four Ways That Obamacare Could Still Be Destroyed (businessinsider.com)
Why don’t House Republicans replace IPAB with Paul Ryan’s proposed boards? (samefacts.com)
Republicans can’t stop IPAB. But they might slow it down. (washingtonpost.com)
Who wants the hardest job in health care? (washingtonpost.com)
What will happen to hospitals when ACA is instituted? (insureyes.com)

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What is the Future for Genomics in Clinical Medicine?

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Infectious Disease & New Antibiotic Targets, International Global Work in Pharmaceutical, Interviews with Scientific Leaders, Medical and Population Genetics, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Industry Competitive Intelligence, Population Health Management, Genetics & Pharmaceutical, Scientist: Career considerations, Stem Cells for Regenerative Medicine, Systemic Inflammatory Response Related Disorders, Technology Transfer: Biotech and Pharmaceutical, tagged biopharmaceutical research, Cell potency, Cellular differentiation, Code of Human Life, designer drugs, DNA, drug targets, Embryonic stem cell, gene expression, Genome Research, genomics to bedside, Human Genome Project, Human subject research, Max Planck Institute for Molecular Biomedicine, Medical research, microbiome, National Human Genome Research Institute, oligomers, oligonucleotide, Personalized medicine, pioneer transcription factros, polynucleotides, post translational modifications, reproductive research, Research Methodology, Scripps Research Institute, Scripps Translational Science Institute, SNPs, Stem cell, Stress, synthetic nucleotides, Technology Transfer, telomerase, telomere, transcription factor identification, transcription factors, Transcriptomics, Translational Medicine, University of Cambridge on February 17, 2013| 5 Comments »

What is the Future for Genomics in Clinical Medicine?

Author and Curator: Larry H Bernstein, MD, FCAP

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WordCloud Image Produced by Adam Tubman

Introduction

This is the last in a series of articles looking at the past and future of the genome revolution. It is a revolution indeed that has had a beginning with the first phase discovery leading to the Watson-Crick model, the second phase leading to the completion of the Human Genome Project, a third phase in elaboration of ENCODE. But we are entering a fourth phase, not so designated, except that it leads to designing a path to the patient clinical experience.
What is most remarkable on this journey, which has little to show in treatment results at this time, is that the boundary between metabolism and genomics is breaking down. The reality is that we are a magnificent “magical” experience in evolutionary time, functioning in a bioenvironment, put rogether like a truly complex machine, and with interacting parts. What are those parts – organelles, a genetic message that may be constrained and it may be modified based on chemical structure, feedback, crosstalk, and signaling pathways. This brings in diet as a source of essential nutrients, exercise as a method for delay of structural loss (not in excess), stress oxidation, repair mechanisms, and an entirely unexpected impact of this knowledge on pharmacotherapy. I illustrate this with some very new observations.

Gutenberg Redone

The first is a recent talk on how genomic medicine has constructed a novel version of the “printing press”, that led us out of the dark ages.

In our series The Creative Destruction of Medicine, I’m trying to get into critical aspects of how we can Schumpeter or reboot the future of healthcare by leveraging the big innovations that are occurring in the digital world, including digital medicine.

We have this big thing about evidence-based medicine and, of course, the sanctimonious randomized, placebo-controlled clinical trial. Well, that’s great if one can do that, but often we’re talking about needing thousands, if not tens of thousands, of patients for these types of clinical trials. And things are changing so fast with respect to medicine and, for example, genomically guided interventions that it’s going to become increasingly difficult to justify these very large clinical trials.

For example, there was a drug trial for melanoma and the mutation of BRAF, which is the gene that is found in about 60% of people with malignant melanoma. When that trial was done, there was a placebo control, and there was a big ethical charge asking whether it is justifiable to have a body count. This was a matched drug for the biology underpinning metastatic melanoma, which is essentially a fatal condition within 1 year, and researchers were giving some individuals a placebo.

The next observation is a progression of what he have already learned. The genome has a role is cellular regulation that we could not have dreamed of 25 years ago, or less. The role is far more than just the translation of a message from DNA to RNA to construction of proteins, lipoproteins, cellular and organelle structures, and more than a regulation of glycosidic and glycolytic pathways, and under the influence of endocrine and apocrine interactions. Despite what we have learned, the strength of inter-molecular interactions, strong and weak chemical bonds, essential for 3-D folding, we know little about the importance of trace metals that have key roles in catalysis and because of their orbital structures, are essential for organic-inorganic interplay. This will not be coming soon because we know almost nothing about the intracellular, interstitial, and intrvesicular distributions and how they affect the metabolic – truly metabolic events.

I shall however, use some new information that gives real cause for joy.

Reprogramming Alters Cells’ Fate

Kathy Liszewski

Gordon Conference Report: June 21, 2012;32(11)

New and emerging strategies were showcased at Gordon Conference’s recent “Reprogramming Cell Fate” meeting. For example, cutting-edge studies described how only a handful of key transcription factors were needed to entirely reprogram cells.

M. Azim Surani, Ph.D., Marshall-Walton professor at the Gurdon Institute, University of Cambridge, U.K., is examining cellular reprogramming in a mouse model. Epiblast stem cells are derived from the early-stage embryonic stage after implantation of blastocysts, about six days into development, and retain the potential to undergo reversion to embryonic stem cells (ESCs) or to PGCs.” They report two critical steps both of which are needed for exploring epigenetic reprogramming. “Although there are two X chromosomes in females, the inactivation of one is necessary for cell differentiation. Only after epigenetic reprogramming of the X chromosome can pluripotency be acquired. Pluripotent stem cells can generate any fetal or adult cell type but are not capable of developing into a complete organism.”

The second read-out is the activation of Oct4, a key transcription factor involved in ESC development. The expression of Oct4 in epiSCs requires its proximal enhancer. Dr. Surani said that their cell-based system demonstrates how a systematic analysis can be performed to analyze how other key genes contribute to the many-faceted events involved in reprogramming the germline.

Reprogramming Expressway

A number of other recent studies have shown the importance of Oct4 for self-renewal of undifferentiated ESCs. It is sufficient to induce pluripotency in neural tissues and somatic cells, among others. The expression of Oct4 must be tightly regulated to control cellular differentiation. But, Oct4 is much more than a simple regulator of pluripotency, according to Hans R. Schöler, Ph.D., professor in the department of cell and developmental biology at the Max Planck Institute for Molecular Biomedicine.

Oct4 has a critical role in committing pluripotent cells into the somatic cellular pathway. When embryonic stem cells overexpress Oct4, they undergo rapid differentiation and then lose their ability for pluripotency. Other studies have shown that Oct4 expression in somatic cells reprograms them for transformation into a particular germ cell layer and also gives rise to induced pluripotent stem cells (iPSCs) under specific culture conditions.

Oct4 is the gatekeeper into and out of the reprogramming expressway. By modifying experimental conditions, Oct4 plus additional factors can induce formation of iPSCs, epiblast stem cells, neural cells, or cardiac cells. Dr. Schöler suggests that Oct4 a potentially key factor not only for inducing iPSCs but also for transdifferention. “Therapeutic applications might eventually focus less on pluripotency and more on multipotency, especially if one can dedifferentiate cells within the same lineage. Although fibroblasts are from a different germ layer, we recently showed that adding a cocktail of transcription factors induces mouse fibroblasts to directly acquire a neural stem cell identity.

Stem cell diagram illustrates a human fetus stem cell and possible uses on the circulatory, nervous, and immune systems. (Photo credit: Wikipedia)

English: Embryonic Stem Cells. (A) shows hESCs. (B) shows neurons derived from hESCs. (Photo credit: Wikipedia)

Transforming growth factor beta (TGF-β) is a secreted protein that controls proliferation, cellular differentiation, and other functions in most cells. http://en.wikipedia.org/wiki/TGFbeta (Photo credit: Wikipedia)

Pioneer Transcription Factors

Pioneer transcription factors take the lead in facilitating cellular reprogramming and responses to environmental cues. Multicellular organisms consist of functionally distinct cellular types produced by differential activation of gene expression. They seek out and bind specific regulatory sequences in DNA. Even though DNA is coated with and condensed into a thick fiber of chromatin. The pioneer factor, discovered by Prof. KS Zaret at UPenn SOM in 1996, he says, endows the competence for gene activity, being among the first transcription factors to engage and pry open the target sites in chromatin.

FoxA factors, expressed in the foregut endoderm of the mouse,are necessary for induction of the liver program. They found that nearly one-third of the DNA sites bound by FoxA in the adult liver occur near silent genes

A Nontranscriptional Role for HIF-1α as a Direct Inhibitor of DNA Replication

ME Hubbi, K Shitiz, DM Gilkes, S Rey,….GL Semenza. Johns Hopkins University SOM
Sci. Signal 2013; 6(262) 10pgs. [DOI: 10.1126/scisignal.2003417] http:dx.doi.org/10.1126/scisignal.2003417

http://SciSignal.com/A Nontranscriptional Role for HIF-1α as a Direct Inhibitor of DNA Replication/

Many of the cellular responses to reduced O2 availability are mediated through the transcriptional activity of hypoxia-inducible factor 1 (HIF-1). We report a role for the isolated HIF-1α subunit as an inhibitor of DNA replication, and this role was independent of HIF-1β and transcriptional regulation. In response to hypoxia, HIF-1α bound to Cdc6, a protein that is essential for loading of the mini-chromosome maintenance (MCM) complex (which has DNA helicase activity) onto DNA, and promoted the interaction between Cdc6 and the MCM complex. The binding of HIF-1α to the complex decreased phosphorylation and activation of the MCM complex by the kinase Cdc7. As a result, HIF-1α inhibited firing of replication origins, decreased DNA replication, and induced cell cycle arrest in various cell types. To whom correspondence should be addressed. E-mail: gsemenza@jhmi.edu
Citation: M. E. Hubbi, Kshitiz, D. M. Gilkes, S. Rey, C. C. Wong, W. Luo, D.-H. Kim, C. V. Dang, A. Levchenko, G. L. Semenza, A Nontranscriptional Role for HIF-1α as a Direct Inhibitor of DNA Replication. Sci. Signal. 6, ra10 (2013).

Identification of a Candidate Therapeutic Autophagy-inducing Peptide

Nature 2013;494(7436). http://nature.com/Identification_of_a_candidate_therapeutic_autophagy-inducing_peptide/ http://www.ncbi.nlm.nih.gov/pubmed/23364696
http://www.readcube.com/articles/10.1038/nature11866

Beth Levine and colleagues have constructed a cell-permeable peptide derived from part of an autophagy protein called beclin 1. This peptide is a potent inducer of autophagy in mammalian cells and in vivo in mice and was effective in the clearance of several viruses including chikungunya virus, West Nile virus and HIV-1.

Could this small autophagy-inducing peptide may be effective in the prevention and treatment of human diseases?

PR-Set7 Is a Nucleosome-Specific Methyltransferase that Modifies Lysine 20 of

Histone H4 and Is Associated with Silent Chromatin

K Nishioka, JC Rice, K Sarma, H Erdjument-Bromage, …, D Reinberg. Molecular Cell, Vol. 9, 1201–1213, June, 2002, Copyright 2002 by Cell Press http://www.cell.com/molecular-cell/abstract/S1097-2765(02)00548-8

http://www.sciencedirect.com/science/article/pii/S1097276502005488 http://www.ncbi.nlm.nih.gov/pubmed/12086618
http://www.cienciavida.cl/publications/b46e8d324fa4aefa771c4d6ece4d2e27_PR-Set7_Is_a_Nucleosome-Specific.pdf

We have purified a human histone H4 lysine 20methyl-transferase and cloned the encoding gene, PR/SET07. A mutation in Drosophila pr-set7 is lethal: second in-star larval death coincides with the loss of H4 lysine 20 methylation, indicating a fundamental role for PR-Set7 in development. Transcriptionally competent regions lack H4 lysine 20 methylation, but the modification coincided with condensed chromosomal regions polytene chromosomes, including chromocenter euchromatic arms. The Drosophila male X chromosome, which is hyperacetylated at H4 lysine 16, has significantly decreased levels of lysine 20 methylation compared to that of females. In vitro, methylation of lysine 20 and acetylation of lysine 16 on the H4 tail are competitive. Taken together, these results support the hypothesis that methylation of H4 lysine 20 maintains silent chromatin, in part, by precluding neighboring acetylation on the H4 tail.

Next-Generation Sequencing vs. Microarrays

Shawn C. Baker, Ph.D., CSO of BlueSEQ
GEN Feb 2013
With recent advancements and a radical decline in sequencing costs, the popularity of next generation sequencing (NGS) has skyrocketed. As costs become less prohibitive and methods become simpler and more widespread, researchers are choosing NGS over microarrays for more of their genomic applications. The immense number of journal articles citing NGS technologies it looks like NGS is no longer just for the early adopters. Once thought of as cost prohibitive and technically out of reach, NGS has become a mainstream option for many laboratories, allowing researchers to generate more complete and scientifically accurate data than previously possible with microarrays.

Gene Expression

Researchers have been eager to use NGS for gene expression experiments for a detailed look at the transcriptome. Arrays suffer from fundamental ‘design bias’ —they only return results from those regions for which probes have been designed. The various RNA-Seq methods cover all aspects of the transcriptome without any a priori knowledge of it, allowing for the analysis of such things as novel transcripts, splice junctions and noncoding RNAs. Despite NGS advancements, expression arrays are still cheaper and easier when processing large numbers of samples (e.g., hundreds to thousands).
Methylation
While NGS unquestionably provides a more complete picture of the methylome, whole genome methods are still quite expensive. To reduce costs and increase throughput, some researchers are using targeted methods, which only look at a portion of the methylome. Because details of exactly how methylation impacts the genome and transcriptome are still being investigated, many researchers find a combination of NGS for discovery and microarrays for rapid profiling.

Diagnostics

They are interested in ease of use, consistent results, and regulatory approval, which microarrays offer. With NGS, there’s always the possibility of revealing something new and unexpected. Clinicians aren’t prepared for the extra information NGS offers. But the power and potential cost savings of NGS-based diagnostics is alluring, leading to their cautious adoption for certain tests such as non-invasive prenatal testing.
Cytogenetics
Perhaps the application that has made the least progress in transitioning to NGS is cytogenetics. Researchers and clinicians, who are used to using older technologies such as karyotyping, are just now starting to embrace microarrays. NGS has the potential to offer even higher resolution and a more comprehensive view of the genome, but it currently comes at a substantially higher price due to the greater sequencing depth. While dropping prices and maturing technology are causing NGS to make headway in becoming the technology of choice for a wide range of applications, the transition away from microarrays is a long and varied one. Different applications have different requirements, so researchers need to carefully weigh their options when making the choice to switch to a new technology or platform. Regardless of which technology they choose, genomic researchers have never had more options.

Sequencing Hones In on Targets

Greg Crowther, Ph.D.

GEN Feb 2013

Cliff Han, PhD, team leader at the Joint Genome Institute in the Los Alamo National Lab, was one of a number of scientists who made presentations regarding target enrichment at the “Sequencing, Finishing, and Analysis in the Future” (SFAF) conference in Santa Fe, which was co-sponsored by the Los Alamos National Laboratory and DOE Joint Genome Institute. One of the main challenges is that of target enrichment: the selective sequencing of genomic or transcriptomic regions. The polymerase chain reaction (PCR) can be considered the original target-enrichment technique and continues to be useful in contexts such as genome finishing. “One target set is the unique gaps—the gaps in the unique sequence regions. Another is to enrich the repetitive sequences…ribosomal RNA regions, which together are about 5 kb or 6 kb.” The unique-sequence gaps targeted for PCR with 40-nucleotide primers complementary to sequences adjacent to the gaps, did not yield the several-hundred-fold enrichment expected based on previously published work. “We got a maximum of 70-fold enrichment and generally in the dozens of fold of enrichment,” noted Dr. Han.

“We enrich the genome, put the enriched fragments onto the Pacific Biosciences sequencer, and sequence the repeats,” continued Dr. Han. “In many parts of the sequence there will be a unique sequence anchored at one or both ends of it, and that will help us to link these scaffolds together.” This work, while promising, will remain unpublished for now, as the Joint Genome Institute has shifted its resources to other projects.
At the SFAF conference Dr. Jones focused on going beyond basic target enrichment and described new tools for more efficient NGS research. “Hybridization methods are flexible and have multiple stop-start sites, and you can capture very large sizes, but they require library prep,” said Jennifer Carter Jones, Ph.D., a genomics field applications scientist at Agilent. “With PCR-based methods, you have to design PCR primers and you’re doing multiplexed PCR, so it’s limited in the size that you can target. But the workflow is quick because there’s no library preparation; you’re just doing PCR.” She discussed Agilent’s recently acquired HaloPlex technology, a hybrid system that includes both a hybridization step and a PCR step. Because no library preparation is required, sequencing results can be obtained in about six hours, making it suitable for clinical uses. However, the hybridization step allows capture of targets of up to 5 megabases—longer than purely PCR-based methods can deliver. The Agilent talk also provided details on the applications of SureSelect, the company’s hybridization technology, to Methyl-Seq and RNA-Seq research. With this technology, 120-mer baits hybridize to targets, then are pulled down with streptavidin-coated magnetic beads.
These are selections from the SFAF conference, which is expected to be a boost to work on the microbiome, and lead to infectious disease therapeutic approaches.

Summary

We have finished a breathtaking ride through the genomic universe in several sessions. This has been a thorough review of genomic structure and function in cellular regulation. The items that have been discussed and can be studied in detail include:

the classical model of the DNA structure
the role of ubiquitinylation in managing cellular function and in autophagy, mitophagy, macrophagy, and protein degradation
the nature of the tight folding of the chromatin in the nucleus
intramolecular bonds and short distance hydrophobic and hydrophilic interactions
trace metals in molecular structure
nuclear to membrane interactions
the importance of the Human Genome Project followed by Encode
the Fractal nature of chromosome structure
the oligomeric formation of short sequences and single nucletide polymorphisms (SNPs)and the potential to identify drug targets
Enzymatic components of gene regulation (ligase, kinases, phosphatases)
Methods of computational analysis in genomics
Methods of sequencing that have become more accurate and are dropping in cost
Chromatin remodeling
Triplex and quadruplex models not possible to construct at the time of Watson-Crick
sequencing errors
propagation of errors
oxidative stress and its expected and unintended effects
origins of cardiovascular disease
starvation and effect on protein loss
ribosomal damage and repair
mitochondrial damage and repair
miscoding and mutational changes
personalized medicine
Genomics to the clinics
Pharmacotherapy horizons
driver mutations
induced pluripotential embryonic stem cell (iPSCs)
The association of key targets with disease
The real possibility of moving genomic information to the bedside
Requirements for the next generation of electronic health record to enable item 29

Retrovirus in the human genome is active in pluripotent stem cells (sciencedaily.com)
Learning from the linker: New study sheds light on cellular reprogramming (phys.org)
A Quantitative System for Discriminating Induced Pluripotent Stem Cells, Embryonic Stem Cells and Somatic Cells (plosone.org)
Stem Cell Therapies May Improve Following Finding That Retrovirus In The Human Genome Is Active In Pluripotent Stem Cells (medicalnewstoday.com)
Leprosy spreads by reprogramming nerve cells into migratory stem cells (guardian.co.uk)
Harvard Researchers: Embryonic Cells Can Cause Cancer (salem-news.com)

DNA Structure and Oligonucleotides

Posted in Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, International Global Work in Pharmaceutical, Metabolomics, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Industry Competitive Intelligence, Pharmacogenomics, Population Health Management, Genetics & Pharmaceutical, Technology Transfer: Biotech and Pharmaceutical, tagged Base pair, Cambridge, DNA, Forensic Science, Nucleic acid double helix, Nucleic acid structure, Science in Society, Watson-Crick on February 15, 2013| 2 Comments »

DNA Structure and Oligonucleotides

Curator: Larry H Bernstein, MD, FCAP

Triplex Medical Science
Expert, Author, Writer, Leaders in Pharmaceutical Business Intelligence
http:/pharmaceuticalintelligence.com/DNA_structure_ and_ Oligonucleotides

A section of DNA; the sequence of the plate-like units (nucleotides) in the center carries information. (Photo credit: Wikipedia)

DNA (Photo credit: Allen Gathman)

Triplex DNA

1. A Third Strand for DNA

The DNA double helix can under certain conditions accommodate a third strand in its major groove. Researchers in the UK have now presented a complete set of

four variant nucleotides that makes it possible to use this phenomenon in gene regulation and mutagenesis.

Natural DNA only forms a triplex if the targeted strand is rich in purines – guanine (G) and adenine (A) – which in addition to the bonds of the Watson-Crick base pairing can form two further hydrogen bonds, and

the ‘third strand’ oligonucleotide has the matching sequence of pyrimidines – cytosine (C) and thymine (T).

Any Cs or Ts in the target strand of the duplex will only bind very weakly, as they contribute just one hydrogen bond. Moreover, the recognition of G requires the C in the probe strand to be protonated, so triplex formation will only work at low pH.

To overcome all these problems, the groups of Tom Brown and Keith Fox at the University of Southampton have developed modified building blocks, and have now completed a set of

four new nucleotides, each of which will bind to one DNA nucleotide from the major groove of the double helix.1

They tested the binding of a 19-mer of these designer nucleotides to a double helix target sequence in comparison with the corresponding triplex-forming oligonucleotide made from natural DNA bases. Using fluorescence-monitored thermal melting and DNase I footprinting, the researchers showed that their construct forms stable triplex even at neutral pH. Tests with mutated versions of the target sequence showed that

three of the novel nucleotides are highly selective for their target base pair,
while the ‘S’ nucleotide, designed to bind to T, also tolerates C.

In principle, triplex formation has already been demonstrated as a way of inducing mutations in cell cultures and animal experiments.2

Michael Gross

References

1 DA Rusling et al, Nucleic Acids Res. 2005, 33, 3025 http://NucleicAcidsRes.com/Rusling_DA
2 KM Vasquez et al, Science 2000, 290, 530 http://Science.org/Vazquez_KM

2. Triplex DNA Structures

Triplex DNA Structures. Frank-Kamenetskii, Mirkin SM. Annual Rev Biochem 1995; 64:69-95./www.annualreviews.org/aronline

Since the pioneering work of Felsenfeld, Davies, & Rich (1), double-stranded polynucleotides containing

purines in one strand
and pydmidines in the other strand [such as poly(A)/poly(U), poly(dA)/poly(dT), or poly(dAG)/poly(dCT)]

have been known to be able to undergo a stoichiometric transition forming a triple-stranded structure containing one polypurine and two polypyrimidine strands. Early on, it was assumed that the third

strand was located in the major groove and associated with the duplex via non-Watson-Crick interactions now known as Hoogsteen pairing.

Triple helices consisting of one pyrimidine and two purine strands were also proposed. However, notwithstanding the fact that single-base triads in tRNAs tructures were well-documented, triple-helical DNA escaped wide attention before the mid-1980s.

The considerable modern interest in DNA triplexes arose due to two partially independent developments.

First, homopurine-homopyrimidine stretches in supercoiled plasmids were found

to adopt an unusual DNA structure, called
H-DNA which includes a triplex as the major structural element.

Secondly, several groups demonstrated that homopyrimidine and some

purine-rich oligonucleotidescan form stable and sequence-specific complexes with
corresponding homopurine-homopyrimidine sites on duplex DNA. These

complexes were shown to be triplex structures rather than D-loops, where the

oligonucleotide invades the double helix and displaces one strand.

A characteristic feature of all these triplexes is that the two chemically homologous strands (both pyrimidine or both purine) are antiparallel. These findings led explosive growth in triplex studies.

One can easily imagine numerous “geometrical” ways to form a triplex, and those that have been studied experimentally. The canonical intermolecular triplex consists of either

three independent oligonucleotide chains or
of a long DNA duplex carrying homopurine-homopyrimidine insert
and the corresponding oligonucleotide.

Triplex formation strongly depends on the oligonucleotide(s) concentration. A single DNA chain may also fold into a triplex connected by two loops. To comply with the sequence and

polarity requirements for triplex formation, such a DNA strand must have a peculiar sequence: It contains
a mirror repeat (homopyrimidine for YR*Y triplexes and homopurine for YR*R triplexes)
flanked by a sequence complementary to one half of this repeat.

Such DNA sequences fold into triplex configuration much more readily than do the corresponding intermolecular triplexes, because all triplex forming segments are brought together within the same molecule.

It has become clear recently, however, that both sequence requirements and chain polarity rules for triplex formation can be met by DNA target sequences built

of clusters of purines and pyrimidines. The third strand consists of

adjacent homopurine and homopyrimidine blocks forming Hoogsteen hydrogen bonds with purines
on alternate strands of the target duplex, and this strand switch preserves the proper chain polarity.
These structures, called alternate-strand triplexes, have been

experimentally observed as both intra- and intermolecular triplexes. These results increase the number of potential targets for triplex formation in natural DNAs somewhat by

adding sequences composed of purine and pyrimidine clusters, although
arbitrary sequences are still not targetable because strand switching is energetically unfavorable.

REFERENCES

Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. J. Biomol. Stract. Dyn. 1986; 3:667-69.  http://JbiomolStractDyn.com/Lyamichev_VI/
Mirkin SM, Lyamichev VI, Drushlyak KN, Dobrynin VN0 Filippov SA, Frank-Kamenetskii MD. Nature 1987; 330:495-97.    http://Nature.com/
Demidov V, Frank-Kamenetskii MD, Egholm M, Buchardt O, Nielsen PE. Nucleic Acids Res. 1993; 21:2103-7.    http://NucleicAcidsResearch.com/
Mirkin SMo Frank-Kamenetskii MD. Anna. Rev. Biophys. Biomol. Struct. 1994; 23:541-76. http://AnnRevBiophysBiomolecStructure.com/
Hoogsteen K. Acta Crystallogr. 1963; 16:907-16   http://ActaCrystallogr.com/
Malkov VA, Voloshin ON, Veselkov AG, Rostapshov VM, Jansen I, et al. Nucleic Acids Res. 1993; 21:105-11.  http://NucleicAcidsResearch.com/
Malkov VA, Voloshin ON, Soyfer VN, Frank-Kamenetskii MD. Nucleic Acids Res. 1993; 21:585-91
Chemy DY, Belotserkovskii BP, Frank-Kamenetskii MD, Egholm M, Buchardt O, et al. Proc. Natl. Acad. Sci. USA 1993; 90:1667-70   http://PNAS.org/

3. Triplex forming Oligonucleotides

Triplex forming oligonucleotides: sequence-specific tools for genetic targeting. Knauert MP, Glazer PM. Human Molec Genetics 2001; 10(20):2243-2251.

http://HumanMolecGenetics.com/Triplex_forming_oligonucleotides: sequence-specific_tools_for _genetic_targeting.

Triplex forming oligonucleotides (TFOs) bind in the major groove of duplex DNA with a high specificity and affinity. Because of these characteristics, TFOs have been proposed as homing devices for genetic manipulation in vivo.

These investigators review work demonstrating the ability of TFOs and related molecules to

alter gene expression and
mediate gene modification in mammalian cells.
TFOs can mediate targeted gene knock out in mice,

providing a foundation for potential application of these molecules in human gene therapy.

4. Novagon DNA

John Allen Berger, founder of Novagon DNA and The Triplex Genetic Code
Over the past 12+ years, Novagon DNA has amassed a vast array of empirical findings which challenge the “validity” of the “central dogma theory”, especially the current five nucleotide Watson-Crick DNA and RNA genetic codes. DNA = A1T1G1C1, RNA =A2U1G2C2.
We propose that our new Novagon DNA 6 nucleotide Triplex Genetic Code has more validity than the existing 5 nucleotide (A1T1U1G1C1) Watson-Crick genetic codes. Our goal is to conduct a “world class” validation study to replicate and extend our findings.

Triplex DNA Structures

Maxim D. Frank-Kamenetskii, Sergei M. Mirkin

A DNA triplex is formed when pyrimidine or purine bases occupyt he major groove of the DNA double Helix forming Hoogsteen pairs with purines of the Watson-Crick basepairs. Intermolecular triplexes are formed

between triplex forming oligonucleotides (TFO) and target sequences on duplex DNAI.ntramolecular triplexes are the major elements of H-DNA usnusual DNA structures, which are formed in homopurine-homopyrimidine regions of supercoiled DNAs. TFOs are promising gene-drugs, which can be used in an anti-gene strategy, that attempt to modulate gene activity in vivo. Numerous chemical modifications of TFO are known. In peptide nucleic acid (PNA), the sugarphosphate backbone is replaced with a protein-like backbone. PNAs form P-loops while interacting with duplex DNA forming triplex with one of DNA strands leaving the other strand displaced. Very unusual recombination or parallel triplexes, or R-DNA have been assumed to form under RecA protein in the course of homologous recombination.

Perspectives and Summary

Since the pioneering work of Felsenfeld, Davies, & Rich (1), double-stranded polynucleotides containing purines in one strand and pydmidines in the other strand [such as poly(A)/poly(U), poly(dA)/poly(dT), or poly(dAG)/poly(dCT)] have been known to be able to undergo a stoichiometric transition forming a triple-stranded structure containing one polypurine and two polypyrimidine strands (2-4). Early on, it was assumedth at the third strand was located in the major groove and associated with the duplex via non-Watson-Crick interactions now known as Hoogsteenp airing. Triple helices consisting of one pyrimidine and two purine strands were also proposed( 5, 6). However notwithstanding the fact that single-base triads in tRNAs tructures were well-documented (reviewed in 7), triple-helical DNA escaped wide attention before the mid-1980s.

The considerable modem interest in DNA triplexes arose due to two partially independent developments. First, homopurine-homopyrimidine stretches in supercoiled plasmids were found to adopt an unusual DNA structure, called H-DNA which includes a triplex as the major structural element (8, 9). Secondly, several groups demonstrated that homopyrimidine and some purine-rich oligonucleotides can form stable and sequence-specific complexes with corresponding homopurine-homopyrimidine sites on duplex DNA(1 0-12). These complexes were shown to be triplex structures rather than D-loops, where the oligonucleotide invades the double helix and displaces one strand. A characteristic feature of all these triplexes is that the two chemically homologous strands (both pyrimidine or both purine) are antiparallel. These findings led explosive growth in triplex studies.

During the study of intermolecular triplexes, it became clear that triplex-forming oligonucleotides (TFOs) might be universal drugs that exhibit sequence-specific recognition of duplex DNA. This is an exciting possibility because, in contrast to other DNA-binding drugs, the recognition principle of TFOs is very simple: Hoogsteen pairing rules between a purine strand of the DNA duplex and the TFO bases. However this mode of recognition is limited in that homopurinehomopyrimidine sites are preferentially recognized. Though significant efforts have been directed toward overcoming this limitation, the problem is still unsolved in general. Nevertheless, the high specificity of TFO-DNA recognition has led to the development of an “antigene” strategy, the goal of which is to modulate gene activity in vivo using TFOs (reviewed in 13).

Although numerous obstacles must be overcome to reach the goal, none are likely to be fatal for the strategy. Even if DNA TFOs proved to be unsuitable as gene-drugs, there are already many synthetic analogs that also exhibit triplex-type recognition. Among them are oligonucleotides with non-natural bases capable of binding the duplex more strongly than can natural TFOs.

Another promising modification replaces the sugar-phosphate backbone of ordinary TFO with an uncharged peptidelike backbone, called a peptide nucleic acid (PNA) (reviewed in 14). Homopyrimidine PNAs form remarkably strong and sequence-specific complexes with the DNA duplex via an unusual strand displacement reaction: Two PNA molecules form a triplex with one of the DNA strands, leaving the other DNA strand displaced (a “P-loop”) (15, 16). The ease and sequence specificity with which duplex DNA and TFOs formed triplexes seemed to support the idea (17) that the homology search preceding homologous recombination might occur via a triplex between a single DNA strand and the DNA duplex without recourse to strand separation in the duplex.

However, these proposed recombination triplexes are dramatically different from the orthodox triplexes observed experimentally. First, the recombination triplexes must be formed for arbitrary sequences and, second, the two identical strands in this triplex are parallel rather than antiparallel. Some data supported the existence of a special class of recombination triplexes, at least within the complex among duplex DNA, RecA protein, and single-stranded DNA (reviewed in Ref. 18), called R-DNA. A stereochemical model of R-DNA was published (19). However the structure of the recombinationi ntermediate is far from being understood, and some recent data strongly favor the traditional model of homology search via local strand separation of the duplex and D-loop formation mediated by RecA protein. Intramolecular triplexes (H-DNA) are formed in vitro under superhelical stress in homopurine-homopyrimidinem irror repeats. The average negative supercoiling in the cell is not sufficient to induce H-DNA formation in most cases.

Annu.Rev.Biochem 1995. 64:65-95

Doubling down: four-stranded, ‘quadruple helix’ DNA discovered

Published January 21, 2013

Quadruplex DNA strands are seen at left, while fluorescent stains at right reveal their presence in human cell nuclei and chromosomes. (Jean-Paul Rodriguez and Giulia Biffi)

60 years after scientists first described the “double helix” shape of human DNA, the chemical code of life, scientists have discovered the first quadruple helix — and it may help them prevent the runaway cell proliferation at the root of cancer.

“It’s been sixty years since its structure was solved but work like this shows us that the story of DNA continues to twist and turn,” said Julie Sharp, senior science information manager at Cancer Research UK.

‘The story of DNA continues to twist and turn.’

– Julie Sharp, senior science information manager at Cancer Research UK

The research, published Monday in the science journal Nature Chemistry, shows clearly a four-stranded DNA structure that the scientists dubbed a “G-quadruplex.” The name comes from the building block guanine, one of the chemical bases that form DNA, along with adenine, cytosine, and thymine (usually abbreviated to their first letter).

By targeting these DNA oddities with synthetic molecules that trap and contain them — preventing cells from replicating their DNA and consequently blocking cell division — it may be possible to halt the spread of cancer, the researchers said.

“We are seeing links between trapping the quadruplexes with molecules and the ability to stop cells dividing, which is hugely exciting,” said professor Shankar Balasubramanian from the University of Cambridge’s Department of Chemistry and Cambridge Research Institute, whose group produced the research.

“We’ve come a long way in 10 years, from simple ideas to really seeing some substance in the existence and tractability of targeting these funny structures,” he told the BBC.

“I’m hoping now that the pharmaceutical companies will bring this on to their radar and we can perhaps take a more serious look at whether quadruplexes are indeed therapeutically viable targets.”

Read more: http://www.foxnews.com/science/2013/01/21/doubling-down-four-stranded-quadruple-helix-dna-discovered/?goback=%2Egde_35214_member_209377206#ixzz2KzGbItnp

Electrochemical Determination of Triple Helices: Electrocatalytic Oxidation of Guanine in an IntramolecularTriplex

Rebecca C. Holmberg and H. Holden Thorp

http://InorganicChemistry.com/Electrochemical Determination_of_Triple_Helices_ Electrocatalytic_Oxidation_of_Guanine_in_an_Intramolecular Triplex/

Inorganic Chemistry 2004 43 (16), 5080-5085

Probing the Solvent Accessibility and Electron Density of Adenine: Oxidation of 7-Deazaadenine in Bent DNA and Purine Doublets

Jennifer D. Tibodeau and H. Holden Thorp

Inorganic Chemistry 2004 43 (2), 408-410

Triplex DNA: fundamentals, advances, and potential applications for gene therapy

Phillip P. Chan, P. M. Glazer

Journal of Molecular Medicine April 1997; 75( 4): 267-282
http://JMolecMed.com/Triplex DNA: fundamentals, advances, and potential applications for gene therapy/

The ability to target specific sequences of DNA through oligonucleotide-based triple-helix formation provides a powerful tool for genetic manipulation. Under experimental conditions, triplex DNA can inhibit DNA transcription and replication, generate site-specific mutations, cleave DNA, and induce homologous recombination. This review describes the binding requirements for triplex formation, surveys recent advancements in the chemistry and biology of triple helices, and considers several potential applications of triplex DNA for use in genetic therapy.

A Gold Nanoparticle Based Approach for Screening Triplex DNA Binders

Min Su Han, Abigail K. R. Lytton-Jean, and Chad A. Mirkin*

The publisher’s final edited version of this article is available at J Am Chem Soc

http://JACS.org/A Gold Nanoparticle Based Approach for Screening Triplex DNA Binders

Nanoparticle assemblies interconnected with DNA triple helixes can be used to colorimetrically screen for triplex DNA binding molecules and simultaneously determine their relative binding affinities based on melting temperatures. Nanoparticles assemble only when DNA triple helixes form between DNA from two different particles and a third strand of free DNA. In addition, the triple helix structure is unstable at room temperature and only forms in the presence of triplex DNA binding molecules which stabilize the triple helix. The resulting melting transition of the nanoparticle assembly is much sharper and at a significantly higher Tm than the analogous triplex structure without nanoparticles. Upon nanoparticle assembly, a concomitant red-to-blue color change occurs. The assembly process and color change does not occur in the presence of duplex DNA binders and therefore provides a significantly better screening process for triplex DNA binding molecules compared to standard methods.

Regulating gene expression by controlling nucleic acid transcription is a potential strategy for the treatment of genetic-based diseases. A promising approach involves the use of triplex forming oligonucleotides (TFOs).1 Triple helix nucleic acids, or triplex structures, are formed through sequence specific Hoogsteen, or reverse Hoogsteen, hydrogen bond formation between a single-stranded TFO and purine bases in the major groove of a target duplex.2 Because TFOs can achieve sequence-specific recognition of genomic DNA, they can, in principle, be used to modulate gene expression by interfering with transcription factors that bind to DNA. However, at present, only purine-rich sequences can be targeted and the resultant triplex structure is less stable than the analogous duplex. This inherent instability has prompted research efforts to develop molecules that selectively bind to such triplex structures to stabilize the TFO-duplex complex. Potentially, triplex specific binding molecules could be used in conjunction with TFOs to achieve control of gene expression.3 Molecules identified as triplex binders include benzoindoloquinoline, benzopyridoquinoxaline, naphthyquinoline, acridine, and anthraquinone derivatives.4 In the past, typical screening processes for identifying triplex binders have included competitive dialysis, mass spectroscopy, electrophoresis and UV/Vis melting experiments, most of which are not applicable to high-throughput screening processes.5 However, with the development of combinatorial libraries which can produce large numbers of potential drug candidates, high-throughput screening strategies have become a necessary part of drug development.6

Systems Integrated Biomedical Research

Cutting a SWATH through Personalized Medicine

The Institute for Systems Biology (ISB) signed a multi-year agreement with AB Sciex to collaborate on the development of methods and technology in proteomics mass spectrometry with the goal of redefining biomarker research and complement genomics through quantitative proteomics analysis. The aim is to help advance the development of a new approach to medical care.

Led by ISB president and co-founder Leroy Hood, M.D., Ph.D., ISB’s research is being accelerated by SWATH™ Acquisition, a data-independent acquisition (DIA) mass spectrometry workflow that reportedly can quantify virtually all detectable peptides and proteins in a sample from a single analysis. ISB will be using the AB Sciex TripleTOF® 5600+ System and an Eksigent ekspert™ nano-LC 400 System as the instrument platforms on which to conduct the protein identification and quantitation. The TripleTOF 5600+ System can reportedly provide the high speed necessary for SWATH Acquisition. ISB also plans to use SelexION™ technology, a recent advancement in differential ion mobility, in the future to advance its research.

“SWATH is a game-changing technique that essentially acts as a protein microarray and is the most reproducible way to generate comprehensive quantitation of the entire proteome,” says Dr. Hood, “It generates a digital record of the entire proteome that can be mined retrospectively for years to come.”

ISB shall support the development of SWATH libraries similar to its SRMAtlas project for the human proteome, pioneered by Rob Moritz, Ph.D., and his collaborators, and the proteomes of other clinically relevant organisms. “With complete proteome-wide libraries, ISB provides the basis to support comprehensive SWATH analysis,” said Dr. Moritz, who is ISB’s proteomics research director.

ISB aims to make the SWATH libraries available to the global scientific community to accelerate the use of SWATH for other biological research. ISB will develop new SWATH technologies and tools to enable the community to adopt comprehensive quantitative proteome analysis.

“Having the proteomics data standardized across laboratories and across samples really enables us to quantitate entire proteomes at a level that hasn’t been done before,” said Dr. Moritz. “We aim to define markers that can predict whether a patient will respond to a certain treatment or not, and applying SWATH will play a big part in taking our advancements to another level. Not only can we now complement the breadth of genomics, but we will have the much-needed libraries and software development going forward to make data-sharing quite easier and standardized.”

AB Sciex forged this alliance with ISB through the AB Sciex Academic Partnership Program to help broaden the availability of new technologies to researchers delving into OMICS research around the world.

“What ISB does with SWATH will set a new benchmark in proteomics research,” said Rainer Blair, president of AB Sciex. “Our collaboration with ISB will help drive SWATH into the mainstream of analytical science and make comprehensive, reproducible and simplified omics data more accessible to biologists around the world.”

SWATH Acquisition was first made available to the worldwide scientific community back in April through a collaboration between AB Sciex and ETH Zurich.

Genetics and Biophysics for Large Volumes of Data

Rresearchers used an interdisciplinary approach combining genetics and biophysics. “It is the first analysis to combine all known protein structures and genomes with folding rates as a physical parameter,” says Dr. Gräter.

The analysis of 92,000 proteins and 989 genomes can only be tackled with computational methods. The group of Gustavo Caetano-Anolles, head of the Evolutionary Bioinformatics Laboratory at Urbana-Champaign, had originally classified most structurally known proteins from the Protein Database (PDB) according to age. For this study, Minglei Wang in his laboratory identified protein sequences in the genomes, which had the same folding structure as the known proteins. He then applied an algorithm to compare them to each other on a time scale. In this way, it is possible to determine which proteins became part of which organism and when. After that, Cedric Debes, a member of Dr. Gräter’s group, applied a mathematical model to predict the folding rate of proteins. The individual folding steps differ in speed and can take from nanoseconds to minutes. No microscope or laser would be able to capture these different time scales for so many proteins. A computer simulation calculating all folding structures in all proteins would take centuries to run on a mainframe computer. This is why the researchers worked with a less data-intensive method. They calculated the folding speed of the single proteins using structures that have been previously determined in experiments: A protein always folds at the same points. If these points are far apart from each other, it takes longer to fold than if they lie close to each other. With the so-called Size-Modified Contact Order (SMCO), it is possible to predict how fast these points will meet and thus how fast the protein will fold, regardless of its length.

“Our results show that in the beginning there were proteins which could not fold very well,” Dr. Gräter summarizes. “Over time, nature improved protein folding so that eventually, more complex structures such as the many specialized proteins of humans were able to develop.”

Researchers develop Compilation of Protein Interaction Data

Posted on January 2, 2013 by grathbone

Researchers have created a platform detailing all atomic data on protein structures and protein interactions for eight organisms. Applying a singular homology-based modelling procedure they have brought together the information previously stored in diverse databases. Interactome3D has been compiled by scientists Roberto Mosca, Arnaud Ceol and Patrick Aloy as an open-access, free web platform as part of their work at the Institute for Research in Biomedicine.

For the first time the platform offers anonymous access to molecular details of protein interaction and 3D models. It means that researchers can easily find the atomic level detail that is fundamental to new discoveries in biology and pharmaceuticals.

Information on more than 12,000 protein interactions for eight model organisms – the plant Arabidopsis thaliana, the worm Caenorhabditis elegans, the fly Drosophila melanogaster, the bacteria Escherichia coli and Helicobacter pylori, the brewer’s yeast Saccharomyces cerevisiae, the mouse Mus musculus, and Homo sapiens – is included. These eight models are the most relevant for biomedical and genetic research.

Patrick Aloy, ICREA researcher at IRB Barcelona, said: “We have designed Interactome3D for molecular and cellular biologists. It is a well organised non-technical interface that presents the results in a simple manner.

With only a few clicks of the mouse, you can get the information you are looking for and you don’t have to be a bioinformatician to navigate around the platform, to look things up or to interpret the results.”

The platform is the result of more than four years of lab experience and collaboration, and the information it contains will be updated every six months, with up to 16,000 protein interaction details expected to be available soon.

Dual coding in alternative reading frames correlates with intrinsic protein disorder

Erika Kovacs, Peter Tompa, Karoly Liliom, and Lajos Kalmar1

Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29, H-1113 Budapest, Hungary

Edited* by Ada Yonath, Weizmann Institue, Rehovot, Israel, and approved January 29, 2010 (received for review July 14, 2009)

http://PNAS.org/Dual_coding_in_alternative_reading_frames_correlates_with_intrinsic_protein_disorder/

Numerous human genes display dual coding within alternatively spliced regions, which give rise to distinct protein products that include segments translated in more than one reading frame. To resolve the ensuing protein structural puzzle, we identified 67 human genes with alternative splice variants comprising a dualcoding region at least 75 nucleotides in length and analyzed the structural status of the protein segments they encode. The inspection of their amino acid composition and predictions by the IUPred and PONDR® VSL2 algorithms suggest a high propensity for structural disorder in dual-coding regions. In the case of þ1 frameshifts, the average level of disorder in the two frames is similarly high (47.2% in the ancestral frame, 58.2% in the derived frame, with the average level of disorder in human proteins being approximately 30%), whereas in the case of −1 frameshifts, there is a significant tendency to become more disordered upon shifting the frame (16.7% in the ancestral frame, 56.3% in the derived frame).

The regions encoded by the derived frame are mostly disordered (disorder percentage >50%) in 39 out of 62 cases, which strongly suggests that structural disorder enables these protein products to exist and function without the need of a highly evolved 3D fold.

The potential advantages are also demonstrated by the appearance of novel functions and the high incidence of transcripts escaping nonsense-mediated decay. By discussing several examples, we demonstrate that dual coding may be an effective mechanism for the evolutionary appearance of novel intrinsically disordered regions with new functions.

Alternative splicing ∣ nonsense-mediated decay ∣ unstructured protein

The process of alternative splicing (AS), in which different combinations of exons are joined together in mRNA maturation, enables several protein isoforms to be encoded by a single gene (1, 2). It is estimated that more than 75% of mammalian genes are alternatively spliced (1, 3) and in about 50% of all AS events the reading frame is altered (4), i.e., a certain stretch of DNA has the potential to be translated in different reading frames. The use of such alternative reading frames (ARFs), however, is often suppressed by a premature termination codon (PTC) that results in nonsense-mediated decay (NMD) of the mRNA product (5, 6). In mammals, a stop codon followed by an exon–exon junction more than 50–55 nucleotides downstream is recognized as a PTC (7) that regulates gene expression and/or acts as a surveillance mechanism against potentially harmful protein products.

A major concern with dual-coding in ARFs is that it gives rise to two intertwined polypeptide sequences which are highly unlikely to both result in two properly folded functional proteins. Thus, dual-coding has long been thought to be prevalent only in viruses and prokaryotes that are under pressure to maintain a compact genome (8, 9). Only relatively recently, results on functional pairs of proteins derived from ARFs (10–16) and bioinformatic studies of conserved overlapping open reading frames (ORFs) (16–19) have pointed to the likely importance of the use of ARFs in eukaryotes.

An enigmatic issue largely overlooked thus far is the protein structural impact of this phenomenon. Because folding of a polypeptide chain to a unique 3D state is a highly evolved feature www.pnas.org/cgi/doi/10.1073/pnas.0907841107 PNAS Early Edition ∣ 1 of 6

This article contains supporting information online at www.pnas.org/cgi/content/full/0907841107/DCSupplemental

Nucleosides

Functionalized Nucleoside 5′-triphosphates for In Vitro Selection of New Catalytic Ribonucleic Acids

JMatulic-Adamic, AT Daniher, A Karpeisky, P Haeberli, D Sweedler and L Beigelman*
http://BioorgMedChemLet.com/Functionalized Nucleoside 5′-triphosphates for In Vitro Selection of New Catalytic Ribonucleic Acids/
Bioorganic & Medicinal Chemistry Letters 10 (2000) 1299±1302

A series of novel 20-modiifed nucleoside 50-triphosphates was synthesized. The amino, imidazole, and carboxylate functionalities were attached to the 5-position of pyrimidine base of these molecules through alkynyl and alkyl spacers, respectively. Two different phosphorylation methods were used to optimize the yields of these highly modified triphosphates.

Recently, much attention has been focused on the development of functionalized nucleotides suitable for in vitro selection with the hope of increasing the potential of nucleic acids for binding and catalysis. For RNA in vitro selections modifications should be at the nucleotide level so that they can be incorporated simply and efficiently using RNA polymerase without problematic side reactions associated with synthetic posttranscriptional modification.

English: The structure of DNA showing with detail showing the structure of the four bases, adenine, cytosine, guanine and thymine, and the location of the major and minor groove. (Photo credit: Wikipedia)

English: A model of a DNA tetrahedron. Each edge of the tetrahedron is a 20bp DNA duplex, and each vertex is a three-arm junction. In this model each basepair is represented by five pseudo-atoms, representing the two sugars, the two phosphates, and the major groove. The scale bar is 1 nm. (Photo credit: Wikipedia)

From left to right, the structures of A-, B- and Z-DNA. The structure a DNA molecule depends on its environment. In aqueous enviromnents, including the majority of DNA in a cell, B-DNA is the most common structure. The A-DNA structure is dominates in dehydrated samples and is similar to the double-stranded RNA and DNA/RNA hybrids. Z-DNA is a rarer structure found in DNA bound to certain proteins. (Photo credit: Wikipedia)

‘Quadruple helix’ DNA discovered in human cells (sciencedaily.com)
Scientists successfully store data in DNA (earthsky.org)
‘Quadruple helix’ DNA discovered in human cells (phys.org)
‘Quadruple helix’ DNA discovered in human cells (esciencenews.com)

Read Full Post »

On the road to improve prostate biopsy

Posted in Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Health Economics and Outcomes Research, HealthCare IT, Imaging-based Cancer Patient Management, Medical Devices R&D Investment, Medical Imaging Technology, Image Processing/Computing, MRI, CT, Nuclear Medicine, Ultra Sound, Personalized and Precision Medicine & Genomic Research, tagged Cancer - General, characterization technology, gleason score, health, histoscanning, medicine, Prostate biopsy, Prostate cancer, prostate guided biopsies, Prostate-specific antigen, psa level, psa screening, systematic prostate biopsies, tissue characterization on February 15, 2013| 3 Comments »

On the road to improve prostate biopsy

Author and Curator: Dror Nir, PhD

Urologists are in constant search for a method that will improve the outcome of prostate biopsy, particularly when it comes to ruling-in and ruling-out clinically significant prostate cancer. As stated in my recent post – State of the art in oncologic imaging of Prostate; “The disease’s staging and related prognosis are determined during diagnosis based on PSA level and the Gleason score of biopsy’s samples. Although prostate-specific antigen (PSA) screening resulted in the diagnosis of prostate cancer at earlier stages and with lower Gleason scores, it has also contributed to concerns about over-diagnosis, overtreatment of clinically insignificant disease, associated treatment-related toxicity, and escalating costs”. I already reported in the past on research conduc ted in this area; New clinical results supports Imaging-guidance for targeted prostate biopsy and Knowing the tumor’s size and location, could we target treatment to THE ROI by applying imaging-guided intervention? Today I report on recent publication presenting the advantage of using targeted trans-perineal biopsy following HistoScanning imaging instead of systematic TRUS biopsies: Computer-aided (HistoScanning) Biopsies Versus Conventional Transrectal Ultrasound-guided Prostate Biopsies: Do Targeted Biopsy Schemes Improve the Cancer Detection Rate? (Moritz F. Hamann, Claudius Hamann, Eckhard Schenk, Amr Al-Najar, Carsten M. Naumann, and Klaus-Peter Jünemann, Urology, Volume 81, Issue 2, February 2013, Pages 370-375

I have mentioned HistoScanning (ultrasound-based tissue characterization technology which I have invented and developed to a medical device) in many of my previous posts. HistoScanning for prostate is a specific HistoScanning application that is applied to the ultrasound’s raw signal (not the image) following a comprehensive scan of the prostate capturing its entire volume. The whole process takes about ten minutes and the output is a digital 3D map of the prostate gland where locations suspicious of presenting with prostate cancer are indicated.

HistoScanning report with 2, bilateral, basal lesions.

The urologist translates such map into a “prostate regional biopsy scheme” when planning his biopsies and direct the needle, under ultrasound guidance, to these predefined suspicious locations.

The systematic biopsy patterns targeted 7 sectors bilaterally: transition zone, apex, center, and base, each medially and laterally.

In that sense, the workflow is similar to using MRI for tumor detection and creating a tumor map for targeting the biopsy.

As reasoning for conducting the study the investigators argue that: “Exact staging of prostate cancer before treatment is essential for relevant therapeutic decision making. Current procedures, such as nerve-sparing prostatectomy and brachytherapy, as well as active surveillance and future focal treatment options, depend on the reliable identification of cancerous lesions within the prostate. Systematic prostate biopsies with at least 10 to 12 cores are the current standard method to detect and locate significant prostate cancer, as scientific evidence during the last decades has shown. Nevertheless, there are no homogeneous data concerning the required number of cores and the technical approach of prostate biopsy procedures. The unstable histologic results on active surveillance and the well-known discrepancy between transrectal diagnostics and radical prostatectomy specimens underline the necessity to develop reliable diagnostic tools for precise detection and localization of prostate cancer. Recent data on HistoScanning computer-aided ultra-sonography have shown favorable results. To generate a greater diagnostic yield than systematic needle biopsies, we integrated HistoScanning-guided targeted biopsies in our general prostate biopsy regimen. We report the cancer detection rate in a prospective series of 80 patients.”

The study’s objective was: “To define potential improvement in prostate cancer detection by application of a computer-aided, targeted, biopsy regimen using HistoScanning.”

Materials and Methods: “The data were collected prospectively from 80 men who consecutively underwent a systematic 14-core prostate biopsy supplemented by targeted transrectal and perineal ultrasound-guided biopsies. All biopsies were performed between March 2011 and September 2011. Indications for prostate biopsy were suspicious findings at the digital rectal examination (DRE), or serum prostate-specific antigen (PSA) level >10 ng/mL, or both. In case of elevated serum PSA levels >4 ng/mL a PSA-velocity of >0.75 ng/mL p.a. and free-to-total PSA ratio <15% were seen as the indication for prostate biopsies. Thirty-six patients had undergone a previous transrectal prostate biopsy. All patients were informed of the mode of the extended prostate biopsy scheme and its potential complications. All patients provided written informed consent for the procedure.After indication and before starting the biopsy procedure, all patients underwent a standardized 3-dimensional (3D) transrectal ultrasound (TRUS) with an end-fire array of a BK 8818 probe. Computer-aided analysis of the raw (radio-frequency) back-scatter data was performed by using the Conformite Europeene-marked and commercially available HistoScanning device, admitted for medical use in the European Union (software version 2.1, Advanced Medical Diagnostics, Belgium).”

“Each patient was diagnosed preoperatively by HistoScanning, defining a maximum of 3 suspicious areas. These areas were biopsied, both transrectally and via the perineum, with a maximum of 3 cores per location.”

Results: “We detected prostatitis in 30 patients (37.5%), premalignant lesions in 10 (12.5%), and prostate cancer in 28 (35%). The transrectal technique was used to detect 78.6% of all cancers using 14 cores by systematic biopsy. With a maximum of 9 targeted cores, 82.1% of all cancers were detected with the targeted perineal approach and 53.6% were detected with the targeted transrectal approach. Although our data did not show significant difference in the performance of targeted transperineal compared with systematic transrectal biopsies, the detection rate of targeted transrectal biopsies was significantly lower.”

Conclusion: “The presented targeted biopsy scheme achieved an overall detection rate of 85% of prostate-specific antigen–relevant pathologic lesions within the prostate. Thus, the presented procedure shows an improved detection rate compared with standard systematic prostate biopsies, and the number of cores required is reduced. Furthermore, the perineal HistoScanning-aided approach seems to be superior to the transrectal approach with respect to the prostate cancer detection rate. The presented procedure might be a step toward reliable ultrasound-based tissue characterization and toward fulfilling the requirements of novel therapeutic strategies.”

The authors’ included an elaborated discussion on the background to their study and its results. This discussion is important for understanding the limitation of the study results and for putting the authors conclusion into balanced context: “When other solid-organ cancer guidelines are compared with prostate cancer guidelines, the common methods of prostate cancer detection are unmasked as an outmoded concept because cancer detection is based on chance as a result of a blinded, subjective examination. A systematic biopsy with at least 10 to 12 cores is considered the standard procedure in prostate cancer diagnostics to date. 1,2 The continuous increase in the number of biopsy cores taken over the last years has predictably improved the detection rate, but several studies report detection rates of only 30% to 40% even in repeated biopsies. 5,9 It is noteworthy that the recommendations must be seen as a compromise bbetween the cancer detection rate and the invasiveness of the surgical procedure. Modern diagnostic procedures, including magnetic resonance imaging, elastography, computerized analysis of TRUS/artiﬁcial neuronal network analysis, and HistoScanning, try to overcome this principle of approach.7,10,11 The current therapeutic concepts and further currently evolving therapy strategies depend on sophisticated prostate cancer diagnostics. It is more important than ever to look for ways to detect and locate the cancer before subjecting patients to more or less invasive procedures as the indication for surgical treatment or prostate-preserving (focal) tumor therapy. The results of magnetic resonance imaging for prostate cancer detection are very promising so far and show a sensitivity of up to 80%. Elastography has also shown promising capabilities for cancer detection, with a recent review article reporting that several studies show 74% to 75% sensitivity.11 HistoScanning has shown 93% sensitivity in detecting and locating prostate cancer. 12 As a matter of principle, our study is unable to report on the accuracy or sensitivity of prostate cancer detection because the exact number of cancer lesions in our patients collective remains incomputable. Integration of HistoScanning for guided, targeted biopsies helped us achieve a prostate cancer detection rate of 35%. These data are lower than results from current publications on initial prostate biopsies but higher than those of repeated biopsy protocols.4,5,13 Given that tumors looked for during initial biopsies are usually large and easy to detect, we believe that this ﬁnding is caused by the smaller overall risk of cancer in a repeated biopsy setting, as was the case in 37.5% of our patients (0.61 biopsies per patient). Overall, HistoScanning seems to improve selective targeting of suspicious prostate lesions. Taking into account all malignant, premalignant, and atypical histologic ﬁndings, including prostate cancer, atypical small acinar proliferations, and high-grade prostatic intraepithelial eoplasia, the detection rate of relevant prostatic lesions by specimens from perineal-targeted biopsies rises to 47.5% and 85%, including prostatitis, respectively. Apart from the high quality of the HistoScanning tissue analysis, we believe in a signiﬁcant effect of the technical approach used to perform the biopsy. As our data show, prostate cancer detection rates from specimens obtained from perineal-targeted biopsies differed signiﬁcantly from the transrectal-targeted biopsy regimen, a difference that occurred independently from previous tissue analysis because both targeted approaches are aligned to the same scanning process. Compared with the transrectal approach, the perineal biopsy technique might reduce variables that can inﬂuence the needle placement. Furthermore, longitudinal biopsy punches following the axis of the prostate seem to allow more accurate sampling of the anterior part. Theoretically, because previous studies reported inhomogeneous results comparing transrectal and transperineal prostate biopsies.3,4,13 The use of a 14-gauge needle in perineal biopsies might be responsible for a systematic bias because it possibly yields more tissue than transrectal cores. Despite this potential advantage, systematic transrectal biopsies do not reﬂect a signiﬁcant difference in the detection rate. Nevertheless, due to the individual setting, our study is unable to report standardized results on the accuracy of comparing transrectal and transperineal needle placement. Template-guided mapping biopsies have recently attracted attention because of the high rate of cancer detection as initial (75%) and even repeat biopsy procedures (46%). 14 It notably increases the ability to locate and differentiate cancer foci within the prostatic gland, implicating mapping biopsies for active surveillance or focal treatment purposes regardless of the considerable surgical trauma generated by the use of extended biopsy protocols. A reduction of tissue trauma by generating a greater diagnostic yield would be a favorable methodologic aspect as initiated by our study. Regarding cancer detection, the presented data show no signiﬁcant differences between the perineal-targeted and transrectal-targeted systematic biopsy regimen, but even though considerably fewer tissue samples (14 vs 9 cores; -35%) were taken from selected prostate areas, we detected no signiﬁcant limitations by the perineal approach. These data are even more encouraging when bearing in mind that the number of samples represents a crucial factor in prostate cancer detection rates, as recently reported. A critical issue in the present study is in the implementation of the modiﬁed biopsy procedures. Although the surgeons at our center are experienced in using TRUS, our data show a learning curve during the ﬁrst 80 procedures. In addition, the overlaying of the HistoScanning image analysis to the B-mode grey-scale live ultrasound picture is done by the surgeon performing the biopsy. This process implies a bias in individual interpretation of the TRUS picture and manual needle guidance. The online fusion of HistoScanning with the ultrasound image presumably would increase the handling accuracy. Further methodologic limitations lie in the heterogeneous and small collective of patients that were included in the study. With regard to the reasonably high number of previous negative biopsy specimens, patient selection can affect the hit rate of positive biopsy specimens. This circumstance might make the cancer detection frequency with HistoScanning look relatively small in this particular study compared with other diagnostic methods in patients undergoing an initial biopsy, but this is due to the daily routine in an academic referral center.

For completeness of this reporting and before stating my own conclusion I bring here below two comments that were made, one by Dr. Stephen Jones of Glickman Urological and Kidney Institute, Cleveland, Ohio and the reply by the first author:

COMMENT

The promise of image-guided diagnosis and management of prostate cancer has been frustratingly elusive. Early pioneers of prostate ultrasound imaging reported that hyperechoic lesionswere indicative of malignancy, but it rapidly became clear that the opposite was actually more realistic. Even so, these hypoechoic lesions were soon shown to be poor indicators of prostate cancer. Thus, the value of visual abnormalities on grey-scale prostate ultrasound imaging remains essentially negligible with current technology. As a result, a number of alternative imaging modalities have been developed and introduced with great excitement. Typically, images in the publications showcase an apparently obvious cancer standing out in contrast to adjacent benign tissues. Unfortunately, the data still reveal minimal value from most of these technologies, and those reported in this article are similarly disappointing. HistoScanning demonstrated interesting color images, but coupled with a transperineal-targeted biopsy found exactly one more case of prostate cancer than did the current standard of care—the 14-core extended transrectal biopsy. This “difference” is actually statistically identical (P >.99). Exactly the same number of patients (n¼ 4) was found exclusively by both transperineal HistoScan-targeted biopsy as with standard transrectal biopsy, and when targeted using the transrectal approach, the technology actually missed almost half of the cancers that were identiﬁed overall. Furthermore, these data do not support the suggestion that 9 cores are less morbid or traumatic than 14 cores, and the literature is replete with reports demonstrating this is simply not true. This is especially misleading when those 9 cores come at the cost, morbidity, time, and complexity of an operation such as this performed under general anesthesia. So the real question remains whether HistoScanning or any emerging technology to image the prostate—improves visualization of prostate cancer. Although magnetic resonance imaging is beginning to show notable promise, the clinical value of most other modalities remains mostly anecdotal. As one whose desire for a solution remains frustratingly unfulﬁlled, I hope that some imaging technique will demonstrate clinical value during my career. J. Stephen Jones, M.D., Department of Regional Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, Ohio

REPLY

In accordance with your comprehensive notes, we have to search for diagnostic improvement and underline the need further investigations in the ﬁeld of prostate cancer diagnostics and staging. Minimally invasive techniques, focal and targeted therapy modalities, and low-risk cancer surveillance probably are future treatment modalities for prostate malignancies that progressively challenge common diagnostic pathways. Sophisticated therapy strategies will require reliable staging results. The constant increase of cores taken during systematic prostate biopsy apparently will not overcome the well-known diagnostic uncertainties. Consequently, imaging techniques and methods of biopsy targeting will gain in importance. Clearly, the presented data do not show signiﬁcant improvement in the overall detection rate of prostate cancer in our patient cohort. Further, the maximum number of 9 biopsy cores must be attributed to the initial study design and will undergo further investigation; however, the results rather support the study approach than reduce its validity. Considering the indeterminate number of cancers, the proof of superiority remains incomputable. Compared with the current standard of care of 12 to 14 cores, we detected no signiﬁcant limitations, although perineal-targeted biopsies took signiﬁcantly fewer cores (3-9 cores [35%]). Maintaining the detection rate unchanged and focusing on 1 to 3 preselected suspicious index lesions display a proof of principle rather than disappointing results. In line with future treatment options mentioned above, any less invasive, focused diagnostic procedure represents an encouraging advance compared with the common and recommended practice of a nonselective, systematic biopsy of the prostate to harbor cancerous tissue. Moritz F. Hamann, M.D., Department of Urology and Pediatric Urology, University of SchleswigeHolstein, Campus Kiel, Kiel, Germany

As mentioned by the authors, further improvement of the outcome of HistoScanning-based targeted biopsies of prostate is expected when an implementation of image-fusion application between the “off-line” generated 3D tumor map and the real-time ultrasound guiding the needle will be available; similar to the results presented already when using ultrasound-MRI image fusion applications for prostate biopsy. Of course, the ultimate biopsy workflow (which I am currently engaged in developing) that urologist are asking for is the one comprised of real-time ultrasound-based tissue characterization and real-time ultrasound guidance of the needle to the lesion.

References

1. Heidenreich A, Bellmunt J, Bolla M, et al. EAU guidelines on prostate cancer. Part 1: screening, diagnosis, and treatment of clinically localised disease. Eur Urol. 2011;59:61-71.

2. National Comprehensive Cancer Network. Clinical Practice Guidelines in Oncology: Prostate Cancer Early Detection. Available at http://www.nccn.org 2011 Accessed May 2011.

3. Abdollah F, Novara G, Briganti A, et al. Trans-rectal versus transperineal saturation re-biopsy of the prostate: is there a difference in cancer detection rate? Urology. 2011;77:921-925.

4. Hara R, Yoshimasa J, Tomohiro F, et al. Optimal approach for prostate cancer detection as initial biopsy: prospective randomized study comparing transperineal versus transrectal systematic 12-core biopsy. Urology. 2008;71:191-195.

5. Patel AR, Jones JS. Optimal biopsy strategies for the diagnosis and staging of prostate cancer. Curr Opin Urol. 2009;19:232-237.

6. Al Otaibi M, Ross P, Fahmy N, et al. Role of repeated biopsy of the prostate in predicting disease progression in patients with prostate cancer on active surveillance. Cancer. 2008;113:286-292.

7. Braeckman J, Autier P, Garbar C, et al. Computer-aided ultrasonography (HistoScanning): a novel technology for locating and characterizing prostate cancer. BJU Int. 2008;101:293-298.

8. Braeckman J, Autier P, Soviany C, et al. The accuracy of transrectal ultrasonography supplemented with computer-aided ultrasonography for detecting small prostate cancers. BJU Int. 2008;102:1560-1565.

9. Presti JC Jr, O’Dowd G, Miller C, et al. Extended peripheral zone biopsy schemes increase cancer detection rates and minimize variance in prostate speciﬁc antigen and age related cancer rates: results of a community multi-practice study. J Urol. 2003;169:125-129.

10. Turkbey B, Mani H, Shah V, et al. Multiparametric 3T prostate magnetic resonance imaging to detect cancer: histopathological correlation using prostatectomy specimens processed in customized magnetic resonance imaging based molds. J Urol. 2011;186: 1818-1824.

11. Trabulsi EJ, Sackett D, Gomella L, et al. Enhanced transrectal ultrasound modalities in the diagnosis of prostate cancer. Urology. 2010;76:1025-1033.

12. Simmons LA, Autier P, Zat_ura F, et al. Detection, localisation and characterisation of prostate cancer by Prostate HistoScanning. BJU Int. 2012;110:28-35.

13. Emiliozzi P, Corsetti A, Tassi B, et al. Best approach for prostate cancer detection: a prospective study on transperineal versus transrectal six-core prostate biopsy. Urology. 2003;61:961-966.

14. Taira AV, Merrick GS, Galbreath RW, et al. Performance of transperineal template-guided mapping biopsy in detecting prostate cancer in the initial and repeat biopsy setting. Prostate Cancer Prostatic Dis. 2010;13:71-77.

Other research papers related to the management of Prostate cancer were published on this Scientific Web site:

Prostate Cancer: Androgen-driven “Pathomechanism” in Early-onset Forms of the Disease

Prostate Cancer and Nanotecnology

Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Imaging agent to detect Prostate cancer-now a reality

Scientists use natural agents for prostate cancer bone metastasis treatment

ROLE OF VIRAL INFECTION IN PROSTATE CANCER

Prostate Cancers Plunged After USPSTF Guidance, Will It Happen Again?

Imaging agent to detect Prostate cancer-now a reality

Scientists use natural agents for prostate cancer bone metastasis treatment

Today’s fundamental challenge in Prostate cancer screening

ROLE OF VIRAL INFECTION IN PROSTATE CANCER

Men With Prostate Cancer More Likely to Die from Other Causes

New Prostate Cancer Screening Guidelines Face a Tough Sell, Study Suggests

New clinical results supports Imaging-guidance for targeted prostate biopsy

Read Full Post »

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Archive for February, 2013

Medscape Update on Calcium and Cardiovascular Risk

Minerals and Cardiovascular Risk

Vascular calcification and plaque rupture

Lipoprotein a (Lp(a)) genetic variant doubles the causal risk of Aortic valvular calcification.

Long term calcium intake and rates of all cause and cardiovascular mortality: community based prospective longitudinal cohort study

Abstract

Introduction

Methods

The Swedish mammography cohort

Outcomes

Dietary assessment

Comorbidity and other additional information

Statistical analysis

Results

Discussion

Strengths and weaknesses of the study

Strengths and weaknesses in relation to other studies

Possible explanations and implications

Conclusion

What is already known on this topic

What this study adds

Other related articles published on this Open Access Online Scientific Journal include the following:

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Systems Pharmacology: Pathways to Patient Response @ BioIT World, Boston, MA World Trade Center, April 9-11, 2013

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The potential contribution of informatics to healthcare is more than currently estimated

Can computers save health care? IU research shows lower costs, better outcomes

Framework for Simulating Clinical Decision-Making

IBM Watson Finally Graduates Medical School

Anomaly Based Interpretation of Clinical and Laboratory Syndromic Classes

Statement of Inferential Second Opinion

Realtime Clinical Expert Support and Validation System

Background

Proposal

Decision Making in the Clinical Setting. Robert S. Didner

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Related articles on Melanoma on this Open Access Online Scientific Journal, include the following:

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What is the Future for Genomics in Clinical Medicine?

Introduction

Gutenberg Redone

Reprogramming Alters Cells’ Fate

Pioneer Transcription Factors

A Nontranscriptional Role for HIF-1α as a Direct Inhibitor of DNA Replication

Identification of a Candidate Therapeutic Autophagy-inducing Peptide

PR-Set7 Is a Nucleosome-Specific Methyltransferase that Modifies Lysine 20 of

Histone H4 and Is Associated with Silent Chromatin

Next-Generation Sequencing vs. Microarrays

Gene Expression

Diagnostics

Sequencing Hones In on Targets

Greg Crowther, Ph.D.

Summary

We have finished a breathtaking ride through the genomic universe in several sessions. This has been a thorough review of genomic structure and function in cellular regulation. The items that have been discussed and can be studied in detail include:

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DNA Structure and Oligonucleotides

Triplex DNA

1. A Third Strand for DNA

2. Triplex DNA Structures

3. Triplex forming Oligonucleotides

4. Novagon DNA

Triplex DNA Structures

Perspectives and Summary

Doubling down: four-stranded, ‘quadruple helix’ DNA discovered