Posts Tagged ‘National Institutes of Health’

Two Mutations, in the PCSK9 Gene: Eliminates a Protein involved in Controlling LDL Cholesterol

Posted in Biomarkers & Medical Diagnostics, Chemical Biology and its relations to Metabolic Disease, Genome Biology, Genomic Testing: Methodology for Diagnosis, PCSK9 Inhibitor Therapy, Personalized and Precision Medicine & Genomic Research, tagged African American, Cardiovascular disease, Elias Zerhouni, Food and Drug Administration, LDL, Low-density lipoprotein, National Institutes of Health, Sanofi, Texas Medical Center, World Health Organization on April 15, 2013| 2 Comments »

Two Mutations, in the PCSK9 Gene: Eliminates a Protein involved in Controlling LDL Cholesterol

Reporter: Aviva Lev-Ari, PhD, RN

UPDATED on 11/15/2013

Relax, PCSK9ers: FDA won’t roadblock blockbusters from Sanofi, Amgen

By Damian Garde

On the heels of new guidelines casting doubts on a much-hyped new class of cholesterol drugs, the FDA said it would not demand long and costly outcomes trials before approving PCSK9 treatments from the likes of Amgen ($AMGN), Sanofi ($SNY) and Regeneron ($REGN), clearing the way for treatments expected to rake in up to $3 billion a year.

As Bloomberg reports, the FDA plans to stick to its guns in vetting cardiovascular drugs, looking at reductions in LDL cholesterol and blood pressure as surrogate endpoints for long-term health benefits. That’s a relief for the developers of PCSK9-targeting drugs, who have faced mounting uncertainty about what they’ll need to do to get their would-be blockbusters to market. Partners Sanofi and Regeneron lead the pack with the promising alirocumab, followed by Amgen, Pfizer ($PFE) and numerous others.

Earlier this week, the American College of Cardiology and the American Heart Association put out new guidelines for prescribing cholesterol treatments, recommending tried-and-true statins over more novel therapies because the old drugs’ down-the-line cardiovascular benefits are well-told. That stirred up long-running concerns that the FDA would toughen up its requirements for the coming crop of PCSK9 treatments, asking drug developers to dump millions into long-term studies that demonstrate hard outcomes

But while PCSK9 developers may not have to worry about new regulatory hurdles, what’s good enough for the FDA won’t necessarily sway payers, and the billion-dollar sales estimates tied to PCSK9 drugs are contingent on widespread adoption. With that in mind, Pfizer is plotting a massive, 22,000-patient outcomes trial, looking to demonstrate the PCSK9-targeting RN-316’s ability to improve cardiovascular health in the long run, a move that may spur its competitors to follow suit.

And the FDA’s conventional wisdom on cardiovascular endpoints may not stand pat. Eric Colman, a deputy director at CDER, told Bloomberg the agency is keeping a close eye on a post-market study of Merck’s ($MRK) Vytorin, and if the drug’s LDL-lowering ability doesn’t translate to lower rates of cardiovascular events, it may well rethink its requirements.

Related Articles:

AstraZeneca wins, Merck and AbbVie lose with new statin-use guidelines

Sanofi, Regeneron take the lead in blockbuster PhIII race of PCSK9 drugs

Pfizer bets big on PCSK9 with ‘massive’ Phase III outcomes study

 SOURCE

From: FierceBiotech <editors@fiercebiotech.com>
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Date: Fri, 15 Nov 2013 17:56:42 +0000 (GMT)
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Subject: | 11.15.13 | Sanofi, Amgen dodge PCSK9 hurdles

 

http://www.nature.com/news/genetics-a-gene-of-rare-effect-1.12773?goback=%2Egde_96118_member_230797138

Genetics: A Gene of Rare Effect

A mutation that gives people rock-bottom cholesterol levels has led geneticists to what could be the next blockbuster heart drug.

Stephen S. Hall

09 April 2013

ADAPTED FROM: PETER DAZELEY/GETTY

Indeed, Tracy’s well-being has been inspiring to doctors, geneticists and now pharmaceutical companies precisely because she is so normal. Using every tool in the modern diagnostic arsenal — from brain scans and kidney sonograms to 24-hour blood-pressure monitors and cognitive tests — researchers at the Texas medical centre have diagnostically sliced and diced Tracy to make sure that the two highly unusual genetic mutations she has carried for her entire life have produced nothing more startling than an incredibly low level of cholesterol in her blood. At a time when the target for low-density lipoprotein (LDL) cholesterol, more commonly called ‘bad cholesterol’, in Americans’ blood is less than 100 milligrams per decilitre (a level many people fail to achieve), Tracy’s level is just 14.

Related stories

• Cholesterol limits lose their lustre
• ENCODE: The human encyclopaedia
• Humans riddled with rare genetic variants

More related stories

A compact woman with wide-eyed energy, Tracy (not her real name) is one of a handful of African Americans whose genetics have enabled scientists to uncover one of the most promising compounds for controlling cholesterol since the first statin drug was approved by the US Food and Drug Administration in 1987. Seven years ago, researchers Helen Hobbs and Jonathan Cohen at UT-Southwestern reported¹ that Tracy had inherited two mutations, one from her father and the other from her mother, in a gene called PCSK9, effectively eliminating a protein in the blood that has a fundamental role in controlling the levels of LDL cholesterol. African Americans with similar mutations have a nearly 90% reduced risk of heart disease. “She’s our girl, our main girl,” says Barbara Gilbert, a nurse who has drawn some 8,000 blood samples as part of Cohen and Hobbs’ project to find genes important to cholesterol metabolism.

Of all the intriguing DNA sequences spat out by the Human Genome Project and its ancillary studies, perhaps none is a more promising candidate to have a rapid, large-scale impact on human health than PCSK9. Elias Zerhouni, former director of the US National Institutes of Health (NIH) in Bethesda, Maryland, calls PCSK9 an “iconic example” of translational medicine in the genomics era. Preliminary clinical trials have already shown that drugs that inhibit the PCSK9 protein — used with or without statins — produce dramatic reductions in LDL cholesterol (more than 70% in some patients). Half-a-dozen pharmaceutical companies — all aiming for a share of the global market for cholesterol-reducing drugs that could reach US$25 billion in the next five years according to some estimates — are racing to the market with drugs that mimic the effect of Tracy’s paired mutations.

Free interview

Stephen Hall talks about Sharlayne’s unusual condition and whether similar cases might lead to a new line of drugs.

Zerhouni, now an in-house champion of this class of drug as an executive at drug firm Sanofi, headquartered in Paris, calls the discovery and development of PCSK9 a “beautiful story” in which researchers combined detailed physical information about patients with shrewd genetics to identify a medically important gene that has made “super-fast” progress to the clinic. “Once you have it, boy, everything just lines up,” he says. And although the end of the PCSK9 story has yet to be written — the advanced clinical trials now under way could still be derailed by unexpected side effects — it holds a valuable lesson for genomic research. The key discovery about PCSK9‘s medical potential was made by researchers working not only apart from the prevailing scientific strategy of genome research over the past decade, but with an almost entirely different approach.

As for Tracy, who lives in the southern part of Dallas County, the implications of her special genetic status have become clear. “I really didn’t understand at first,” she admits. “But now I’m watching ads on TV [for cholesterol-lowering drugs], and it’s like, ‘Wow, I don’t have that problem’.”

A heart problem

Cardiovascular disease is — and will be for the foreseeable future, according to the World Health Organization — the leading cause of death in the world, and its development is intimately linked to elevated levels of cholesterol in the blood. Since their introduction, statin drugs have been widely used to lower cholesterol levels. But Jan Breslow, a physician and geneticist at Rockefeller University in New York, points out that up to 20% of patients cannot tolerate statins’ side effects, which include muscle pain and even forgetfulness. And in many others, the drugs simply don’t control cholesterol levels well enough.

The search for better treatments for heart disease gained fresh impetus after scientists published the draft sequence of the human genome in 2001. In an effort to identify the genetic basis of common ailments such as heart disease and diabetes, geneticists settled on a strategy based on the ‘common variant hypothesis’. The idea was that a handful of disease-related versions (or variants) of genes for each disease would be common enough — at a frequency of roughly 5% or so — to be detected by powerful analyses of the whole genome. Massive surveys known as genome-wide association studies compared the genomes of thousands of people with heart disease, for example, with those of healthy controls. By 2009, however, many scientists were lamenting the fact that although the strategy had identified many common variants, each made only a small contribution to the disease. The results for cardiovascular disease have been “pretty disappointing”, says Daniel Steinberg, a lipoprotein expert at the University of California, San Diego.

Single-minded: Helen Hobbs and Jonathan Cohen’s approach to heart-disease genetics yielded a target for drugs that could compete with statins.MISTY KEASLER/REDUX/EYEVINE

More than a decade earlier, in Texas, Hobbs and Cohen had taken the opposite tack. They had backgrounds in Mendelian, or single-gene, disorders, in which an extremely rare variant can have a big — often fatal — effect. They also knew that people with a particular Mendelian disorder didn’t share a single common mutation in the affected gene, but rather had a lot of different, rare mutations. They hypothesized that in complex disorders, many different rare variants were also likely to have a big effect, whereas common variants would have relatively minor effects (otherwise natural selection would have weeded them out). “Jonathan and I did not see any reason why it couldn’t be that rare variants cumulatively contribute to disease,” Hobbs says. To find these rare variants, the pair needed to compile detailed physiological profiles, or phenotypes, of a large general population. Cohen spoke of the need to “Mendelize” people — to compartmentalize them by physiological traits, such as extremely high or low cholesterol levels, and then look in the extreme groups for variations in candidate genes known to be related to the trait.

The pair make a scientific odd couple. Hobbs, who trained as an MD, is gregarious, voluble and driven. Cohen, a soft-spoken geneticist from South Africa, has a laid-back, droll manner and a knack for quantitative thinking. In 1999, they set out to design a population-based study that focused on physical measurements related to heart disease. Organized with Ronald Victor, an expert on high blood pressure also at UT Southwestern, and funded by the Donald W. Reynolds Foundation in Las Vegas, Nevada, the Dallas Heart Study assembled exquisitely detailed physiological profiles on a population of roughly 3,500 Dallas residents². Crucially, around half of the participants in the study were African Americans, because the researchers wanted to probe racial differences in heart disease and high blood pressure. The team measured blood pressure, body mass index, heart physiology and body-fat distribution, along with a battery of blood factors related to cholesterol metabolism — triglycerides, high-density lipoprotein (HDL) cholesterol and LDL cholesterol. In the samples of blood, of course, they also had DNA from each and every participant.

As soon as the database was completed in 2002, Hobbs and Cohen tested their rare-variant theory by looking at levels of HDL cholesterol. They identified the people with the highest (95th percentile) and lowest (5th percentile) levels, and then sequenced the DNA of three genes known to be key to metabolism of HDL cholesterol. What they found, both in Dallas and in an independent population of Canadians, was that the number of mutations was five times higher in the low HDL group than in the high group³. This made sense, Cohen says, because most human mutations interfere with the function of genes, which would lead to the low HDL numbers. Published in 2004, the results confirmed that rare, medically important mutations could be found in a population subdivided into extreme phenotypes.

Armed with their extensive database of cardiovascular traits, Hobbs and Cohen could now dive back into the Dallas Heart Study whenever they had a new hypothesis about heart disease and, as Cohen put it, “interrogate the DNA”. It wasn’t long before they had an especially intriguing piece of DNA at which to look.

The missing link

In February 2003, Nabil Seidah, a biochemist at the Clinical Research Institute of Montreal in Canada, and his colleagues reported the discovery of an enigmatic protein⁴. Seidah had been working on a class of enzymes known collectively as proprotein convertases, and the researchers had identified what looked like a new member of the family, called NARC-1: neural apoptosis-regulated convertase 1.

“We didn’t know what it was doing, of course,” Seidah says. But the group established that the gene coding the enzyme showed activity in the liver, kidney and intestines as well as in the developing brain. The team also knew that in humans the gene mapped to a precise genetic neighbourhood on the short arm of chromosome 1.

That last bit of geographical information pointed Seidah to a group led by Catherine Boileau at the Necker Hospital in Paris. Her team had been following families with a genetic form of extremely high levels of LDL cholesterol known as familial hypercholesterolaemia, which leads to severe coronary artery disease and, often, premature death. Group member Marianne Abifadel had spent five fruitless years searching a region on the short arm of chromosome 1 for a gene linked to the condition. When Seidah contacted Boileau and told her that he thought NARC-1 might be the gene she was looking for, she told him, “You’re crazy”, Seidah recalls. Seidah bet her a bottle of champagne that he was correct; within two weeks, Boileau called back, saying: “I owe you three bottles.”

“The PCSK9 story is a terrific example of an up-and-coming pattern of translational research.”

In 2003, the Paris and Montreal groups reported that the French families with hypercholesterolaemia had one of two mutations in this newly discovered gene, and speculated that this might cause increased production of the enzyme⁵. Despite Seidah’s protests, the journal editors gave both the gene and its protein product a new name that fit with standard nomenclature: proprotein convertase subtilisin/kexin type 9, or PCSK9. At around the same time, Kara Maxwell in Breslow’s group at Rockefeller University⁶ and Jay Horton, a gastroenterologist at UT-Southwestern⁷ also independently identified the PCSK9 gene in mice and revealed its role in a previously unknown pathway regulating cholesterol⁸.

The dramatic phenotype of the French families told Hobbs that “this is an important gene”. She also realized that in genetics, mutations that knock out a function are much more common than ones that amplify function, as seemed to be the case with the French families. “So immediately I’m thinking, a loss-of-function mutation should manifest as a low LDL level,” she says. “Let’s go and see if that’s true.”

Going to extremes

Hobbs and Cohen had no further to look than in the extreme margins of people in the Dallas Heart Study. In quick order, they identified the highest and lowest LDL readings in four groups: black women, black men, white women and white men. They then resequenced the PCSK9 gene in the low-cholesterol groups, looking for mutations that changed the make-up of the protein.

They found seven African Americans with one of two distinct ‘nonsense’ mutations in PCSK9 — mutations that essentially aborted production of the protein. Then they went back and looked for the same mutations in the entire population. Just 2% of all black people in the Dallas study had either of the two PCSK9 mutations — and those mutations were each associated with a 40% reduction of LDL cholesterol in the blood⁹. (The team later detected a ‘missense mutation’ in 3% of white people, which impaired but did not entirely block production of the protein.) The frequency of the mutations was so low, Hobbs says, that they would never have shown up in a search for common variants.

When Hobbs and Cohen published their findings in 2005, they suggested that PCSK9 played a crucial part in regulating bad cholesterol, but said nothing about whether the mutations had any effect on heart disease. That evidence came later that year, when they teamed up with Eric Boerwinkle, a geneticist at the University of Texas Health Science Center in Houston, to look forPCSK9 mutations in the Atherosclerosis Risk in Communities (ARIC) study, a large prospective study of heart disease that had been running since 1987. To experts such as Steinberg, the results¹⁰ — published in early 2006 — were “mind-blowing”. African Americans in ARIC who had mutations in PCSK9 had 28% less LDL cholesterol and an 88% lower risk of developing heart disease than people without the mutations. White people with the less severe mutation in the gene had a 15% reduction in LDL and a 47% reduced risk of heart disease.

How did the gene exert such profound effects on LDL cholesterol levels? As researchers went on to determine¹¹, the PCSK9 protein normally circulates in the bloodstream and binds to the LDL receptor, a protein on the surface of liver cells that captures LDL cholesterol and removes it from the blood. After binding with the receptor, PCSK9 escorts it into the interior of the cell, where it is eventually degraded. When there is a lot of PCSK9 (as in the French families), there are fewer LDL receptors remaining to trap and remove bad cholesterol from the blood. When there is little or no PCSK9 (as in the black people with mutations), there are more free LDL receptors, which in turn remove more LDL cholesterol.

“We didn’t understand why everybody wasn’t doing what we were doing.”

The UT-Southwestern group, meanwhile, went back into the community looking for family members who might carry additional PCSK9 mutations. In September 2004, Gilbert, the nurse known as ‘the cholesterol lady’ in south Dallas because of her frequent visits, knocked on the door of Sharlayne Tracy’s mother, an original member of the Dallas Heart Study. Gilbert tested Tracy, as well as her sister, brother and father. “They tested all of us, and I was the lowest,” Tracy says. Zahid Ahmad, a doctor working with Hobbs at UT-Southwestern, was one of the first to look at Tracy’s lab results. “Dr Zahid was in awe,” Tracy recalled. “He said, ‘You’re not supposed to be so healthy!’.”

It wasn’t just that her LDL cholesterol measured 14. As a person with two dysfunctional copies of the gene — including a new type of mutation — Tracy was effectively a human version of a knockout mouse. The gene had been functionally erased from her genome, and PCSK9 was undetectable in her blood without any obvious untoward effects. The genomics community might have been a little slow to understand the significance, Hobbs says, “but the pharmaceutical companies got it right away”.

The next statin?

This being biology, however, the road to the clinic was not completely smooth. The particular biology of PCSK9 has so far thwarted efforts to find a small molecule that would interrupt its interaction with the LDL receptor and that could be packaged in a pill. But the fact that the molecule operates outside cells means that it is vulnerable to attack by monoclonal antibodies — one of the most successful (albeit most expensive) forms of biological medicine.

The results of early clinical trials have caused a stir. Regeneron Pharmaceuticals of Tarrytown, New York, collaborating with Sanofi, published phase II clinical-trial results¹² last October showing that patients with high LDL cholesterol levels who had injections every two weeks of an anti-PCSK9 monoclonal antibody paired with a high-dose statin saw their LDL cholesterol levels fall by 73%; by comparison, patients taking high-dose statins alone had a decrease of just 17%. Last November, Regeneron and Sanofi began to recruit 18,000 patients for phase III trials that will test the ability of their therapy to cut cardiovascular events, including heart attacks and stroke. Amgen of Thousand Oaks, California, has also launched several phase III trials of its own monoclonal antibody after it reported similarly promising results¹³. Among other companies working on PCSK9-based therapies are Pfizer headquartered in New York, Roche based in Basel, Switzerland, and Alnylam Pharmaceuticals of Cambridge, Massachusetts. (Hobbs previously consulted for Regeneron and Pfizer, and now sits on the corporate board of Pfizer.)

Not everyone is convinced that a huge market awaits this class of cholesterol-lowering drugs. Tony Butler, a financial analyst at Barclays Capital in New York, acknowledges the “beautiful biology” of the PCSK9 story, but wonders if the expense of monoclonal drugs — and a natural reluctance of both patients and doctors to use injectable medicines — will constrain potential sales. “I have no idea what the size of the market may be,” he says.

“Everything hinges on the phase III side effects,” says Steinberg. So far, the main side effects reported have been minor, such as reactions at the injection site, diarrhoea and headaches. But animal experiments have raised potential red flags: the Montreal lab reported in 2006 that knocking out the gene in zebrafish is lethal to embryos¹⁴. That is why the case of Tracy was “very, very helpful” to drug companies, says Hobbs. Although her twin mutations have essentially deprived her of PCSK9 throughout her life, doctors have found nothing abnormal about her.

That last point may revive a debate in the cardiology community: should drug therapy to lower cholesterol levels, including statins and the anti-PCSK9 medicines, if they pan out, be started much earlier in patients than their 40s or 50s? That was the message Steinberg took from the people withPCSK9 mutations in the ARIC study — once he got over his shock at the remarkable health effects. “My first reaction was, ‘This must be wrong. How could that be?’And then it hit me — these people had low LDL from the day they were born, and that makes all the difference.” Steinberg argues that cardiologists “should get off our bums” and reach a consensus about beginning people on cholesterol-lowering therapy in their early thirties. But Breslow, a former president of the American Heart Association, cautions against being too aggressive too soon. “Let’s start out with the high-risk individuals and see how they do,” he says.

Not long after Hobbs and Cohen published their paper in 2006, they began to get invited to give keynote talks at major cardiology meetings. Soon after, the genetics community began to acknowledge the strength of their approach. In autumn 2007, then-NIH director Zerhouni organized a discussion at the annual meeting of the institutes’ directors to raise the profile of the rare-variant approach and contrast it with genome-wide studies. “Obviously, the two approaches are opposed to each other, and the question was, what was the relative value of each?” says Zerhouni. “I thought the PCSK9 story was a terrific example of an up-and-coming pattern of translational research” — indeed, he adds, “a harbinger of things to come”.

Hobbs and Cohen might not have found their gene if they had not had a hunch about where to look, but improved sequencing technology and decreasing costs now allow genomicists to incorporate the rare variant approach and to mount large-scale sweeps in search of such variants. “Gene sequencing is getting cheap enough that if there’s another gene like PCSK9 out there, you could probably find it genome-wide,” says Jonathan Pritchard, a population biologist at the University of Chicago, Illinois.

“What was amazing to us,” says Hobbs, “was that the genome project was spending all this time, energy, effort sequencing people, and they weren’t phenotyped, so there was no potential for discovery. We didn’t understand, and couldn’t understand, why everybody wasn’t doing what we were doing. Particularly when we started making discoveries.”

SOURCE:

Nature 496, 152–155 (11 April 2013) doi:10.1038/496152a

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Related stories and links

From nature.com

• Cholesterol limits lose their lustre

  26 February 2013

• ENCODE: The human encyclopaedia

  05 September 2012

• Humans riddled with rare genetic variants

  17 May 2012

• Human genome at ten: Life is complicated

  31 March 2010

• Hiding place for missing heritability uncovered

  25 January 2010

• Personal genomes: The case of the missing heritability

  05 November 2008

• Nature speical: ENCODE

• Nature special: Human genome at 10

• Nature human genome issue, 2001

From elsewhere

• Hobbs-Cohen lab

Author information

Affiliations

1. Stephen S. Hall is a science writer in New York who also teaches public communication to graduate students in science at New York University.

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Paralysis by Sequestration and the Medical Revolution

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Cell Biology, Signaling & Cell Circuits, Genome Biology, Genomic Testing: Methodology for Diagnosis, International Global Work in Pharmaceutical, Interviews with Scientific Leaders, Medical and Population Genetics, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Technology Transfer: Biotech and Pharmaceutical, tagged DNA, Hood, Human Genome Project, Larry H. Bernstein, medicine, National Institutes of Health, Personalized medicine, White House on April 3, 2013| 1 Comment »

Paralysis by Sequestration and the Medical Revolution

Reporter: Larry H Bernstein, MD, FACP

WordCloud Image Produced by Adam Tubman

http://pharmaceuticalintelligence.com/2013/04/03/paralysis-by-s…cal-revolution/

Dysfunction and the Medical Revolution

http://www.genomeweb.com/blog/dysfunction-and-medical-revolution
April 02, 2013
The federal sequestration is cutting back or halting grants that fund “potentially groundbreaking” personalized medicine research funded by the National Institutes of Health, Institute for Systems Biology President Lee Hood opines. Taking his pen to the pages of The Hill, Hood writes that political three-way fisticuffs between lawmakers in both houses and the White House that led to the sequester — an across-the-board five percent whack to all agency budgets — could imperil advances in personalized medicine research that ISB is pursuing.
Hood praises the promise of what he calls P4 medicine, the convergence of new big data and genomic technologies to develop “medicine that is predictive, personalized, preventive, and participatory.”
The forward march of P4 will bring about a new type of medicine, Hood writes, that will improve care through diagnoses and targeted therapies. It also will save money in the long run because new and better treatments and predictive medicine will “reduce the skyrocketing costs of healthcare” and help create new “wellness sector” markets and companies that don’t yet exist, he says.
“In 1986, the automated DNA sequencer I invented was first brought to market, paving the way for the Human Genome Project completed in 2003. In 2010 alone, human genome sequencing activities generated $67 billion in US economic output and created 310,000 US jobs,” he says.
Hood doesn’t want to see a dysfunctional political culture on Capitol Hill hinder the advance of these technologies, markets, and medical innovations.
“On the 10th anniversary of the completion of the Human Genome Project, we can’t let the ongoing tug-of-war in Congress over spending priorities threaten the revolutionary work that is taking place in medical science,” he writes.
Submitted by Scott_K on Tue, 04/02/2013
Couldn’t agree more. I was just up on the Hill meeting with Representatives, and they are sadly bogged down in the sequester. Meanwhile, Medicare has suspended reimbursements for molecular diagnostic testing. Congress is missing an entire paradigm change where the art of patient care has led to the rapid emergence of Personalized Medicine. Without appropriate funding, we will not be able to educate patients, clinicians, reimbursement directors, and Congress themselves on the astounding advancements that have been made in personalized medicine. We can perform whole genome sequencing to identify clinically relevant mutations in individual patient’s tumors- morally, this technology could and should be available to all late stage cancer patients immediately. Frustratingly, we lack the political leadership and vision. In an environment where jobs for many experienced, bright scientists are so desperately needed, the failure of governmental leadership has led to the siphoning off of technological development and jobs to other more perceptive countries. This is a mess that can be corrected in no time with appropriate leadership from the three branches that Dr. Hood mentions. Here’s hoping that Dr. Hood’s communication will open some eyes.

Related articles

• Cloud-based genome sequencing exchange could make personalized medicine easier for physicians (medcitynews.com)
• What is the future for genomics in clinical medicine? (pharmaceuticalintelligence.com)
• Attitudes of Patients about Personalized Medicine (pharmaceuticalintelligence.com)
• Understanding the Role of Personalized Medicine (pharmaceuticalintelligence.com)
• President Barack Obama Announces BRAIN Initiative (eyewire.org)
• President BRAIN Initiative Has San Diego Ties. (bowlersdesk.com)
• Data driven Personalized Medicine Metamed when you cannot afford misdiagnosis (nextbigfuture.com)
• Beyond the Genome (rdmag.com)
• Questions raised in White House BRAIN initiative Twitter Q&A focus on patient benefits, sequestration (medcitynews.com)

Personalized Medicine (Photo credit: Wikipedia)

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

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biomarkers & Medical Diagnostics, BioSimilars, Computational Biology/Systems and Bioinformatics, Drug Delivery Platform Technology, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Population Health Management, Genetics & Pharmaceutical, Technology Transfer: Biotech and Pharmaceutical, tagged Harvard Medical School, national cancer institute, National Institutes of Health, Stanford University School of Medicine, systems biology, Thomson Reuters on March 21, 2013| 12 Comments »

Reporter: Aviva Lev-Ari, PhD, RN

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

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi Data Systems

» 4:15 PLENARY KEYNOTE

Do Network Pharmacologists Need Robot Chemists?

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
Welcome Reception Introduction, Sponsored by Okta

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

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

» 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

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

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 Two-Edged Sword Role of the Mammalian DNA Methyltransferases: New Implication to Cancer Therapy Targeting the Epigenetic Pathway

Che-Kun James Shen, Ph.D., Distinguished Research Fellow, Institute of Molecular Biology, Academia Sinica

Methylation at the 5-position of cytosine (C) to generate 5-methylcytosine (5-mC) on the vertebrate genomes is an essential epigenetic modification that regulates different biological processes including carcinogenesis. This modification has been known to be accomplished by the combined catalytic actions of three DNA methyltransferases (DNMTs), the de novo enzymes DNMT3A/ DNMT3B and the maintenance enzyme DNMT1. This property of DNMTs and the imbalance of CpG methylation in cancer cells have led to the development of cancer therapeutic drugs/ chemicals targeting the DNA methylation activities of DNMTs. However, we have recently discovered that the mammalian DNMTs could also act as active DNA 5-mC demethylases in a Ca++ion-and redox state-dependent manner. This suggests new directions for re-investigation of the structures of DNMTs and their functions in the genome wide and/or local DNA methylation in the mammalian cells. In particular, the concept and strategies for drug therapy targeting the DNMTs may need to be re-evaluated.

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

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

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 Leveraging Mathematical Models to Understand Population Variability in Response to Cardiac Drugs

Eric Sobie, Ph.D., Associate Professor, Pharmacology & Systems Therapeutics, Icahn School of Medicine, Mount Sinai School of Medicine

Mathematical models of heart cells and tissues are sufficiently advanced that the models can predict mechanisms underlying pro-arrhythmic or anti-arrhythmic effects of drugs. At present, however, these models are not adequate for understanding variability across a population, i.e., why a drug may be effective in one patient but ineffective in another patient. I will describe novel computational approaches my laboratory has developed to quantify and predict differences between individuals in response to cardiac drugs.

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 (Guna) Rajagopal, Ph.D., VP & CIO – R&D IT, Research, Bioinformatics & External Innovation, Janssen Pharmaceuticals
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

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

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.

4:00 Conference Adjourns

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CONCURRENT TRACKS
	Track 1: IT Infrastructure – Hardware Big Data Solutions and End-User Perspectives		Track 7: eClinical Trials Solutions Innovative Management in Clinical Trials
	Track 2: Software Development Technologies and Applications for Managing and Sharing Data		NEW THIS YEAR! Track 8: Data Visualization and Exploration Tools From Discovery to the Clinic
	Track 3: Cloud Computing Riding the Cloud to Next-Generation Computing		Track 9: Drug Discovery Informatics Thinking of Drugs Outside of the Box
	Track 4: Bioinformatics Understanding Massive Quantities of -omic Information across Research Initiatives		NEW THIS YEAR! Track 10: Clinical OmicsTools for Integrating and Interrogating Multiple ‘Omic Data Sets
	Track 5: Next-Generation Sequencing Informatics NGS, Genome-Scale Screening and HTP Proteomics		Track 11: Collaborations and Open Access Innovations Collaborative and Open Access Models for Advancing Research, Discovery and Personalized Medicine
	Track 6: Systems Pharmacology Pathways to Patient Response		Track 12: Cancer Informatics Applying Computational Biology to Cancer Research/Care

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WORKSHOPS – VIEW DETAILS

Morning Workshops Integrated Research Data Management Quality Practices for R&D Informatics Beyond the Cloud IT & Informatics in Support of Collaboration and Externalization The Repurposing Challenge

Afternoon Workshops Avoiding Intellectual Property Problems in Research Collaborations Using Information Technology Avoiding Cloud Gotchas Advancing the Use of EHR/EMR for Clinical Research and Drug Development Cloud Computing in Hospital Data Management and Integration Data Visualization in Biology: From the Basics to Big Data Software for Clinical Genomics IT Project Planning and Implementation

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SPONSOR & EXHIBITOR INFORMATION

2013 Prospectus is now available.

Reserve your space early and SAVE!

EVENT FEATURES

• Access All 12 Tracks for One Price
• Network with 2,500+ Global Attendees
• Hear 150+ Technology and Scientific Presentations
• Attend Bio-IT World’s Best Practices Awards
• Connect with Attendees Using CHI’s Intro-Net
• Participate in the Poster Competition
• Choose from 16 Pre-Conference Workshops
• See the Winners of the following 2013 Awards:
  Benjamin Franklin
  Best of Show
  Best Practices
• View Novel Technologies and Solutions in the Expansive Exhibit Hall
• And Much More!

KEYNOTE PRESENTERS:

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

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

PLENARY SESSION:

The Life Sciences CIO Panel

From managing big data and cloud computing capabilities to building virtual communities and optimizing drug development, the life sciences CIO has to be a firefighter, evangelist, visionary. In this special plenary roundtable, Bio-IT World invites a select group of CIOs from big pharma, academia and government to discuss the major issues facing today’s biosciences organization and the prospects for future growth and organizational success.

Special guests:
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 CIO, NIH
Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO – R&D IT, Research, Bioinformatics & External Innovation, Janssen Pharmaceuticals
Cris Ross – CIO, Mayo Clinic

FEATURED SESSIONS:

Managing Big Data: The Genome Center Perspective

Panelists Include: Matthew Trunnell (Broad Institute)
Alexander (Sasha) Wait Zaranek, (Harvard Medical School/Clinical Future, Inc.)
Guy Coates (The Wellcome Trust Sanger Institute)

Building the IT Architecture of the New York Genome Center

Chris Dwan, Acting Senior Vice President, Information Technology and Research Computing, New York Genome Center
Kevin Shianna, Senior Vice President, Sequencing Operations, New York Genome Center
Jim Harding, CTO, Sabey Corporation
Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division

Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York Genome Center

Additional Speakers to be Announced

  

3/4

VIDEO CHANNEL

Cancer Trends Plenary Session (part II) – Bio-IT World Expo 2012

Bio-IT World Expo 2012 – 10th Anniversary Celebration

ClearTrial wins Best of Show 2012

CERF wins Best of Show 2012

OpsCode wins Best of Show 2012

Cambridge Semantics wins Best of Show 2012

Stephen Wolfram, Ph.D., part 1 – Keynote Presentation

BlueArc at 2011 Bio-IT World Conference & Expo

Roche innovative multi-touch environment for scientific decision

Praxeon DocumentLens

Yury Rozenman – Bio-IT World Expo 2011 Keynote Panel

Mark Boguski – Bio-IT World Expo 2011 Keynote Panel

Ken Buetow – Bio-IT World Expo 2011 Keynote Panel

Benjamin Heywood – Bio-IT World Expo 2011 Keynote Panel

Debora Goldfarb – Bio-IT World Expo 2011 Keynote Panel

Martin Leach – Bio-IT World Expo 2011 Keynote Panel

Jonathan Eisen – Ben Franklin Award 2011

Bryn Roberts part 1- Keynote Presentation

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