Sunday, August 31, 2014

Red Wine and CVD

Eureka reports on an interesting finding by a Czech researcher. Wine protects only those who also exercise from CVD.

They state:

Evidence suggesting that mild to moderate consumption of wine protects against cardiovascular disease has been accumulating since the early 1990s. In particular, retrospective studies have found that wine increases levels of HDL, the "good" cholesterol. But until now there has been no long-term, prospective, randomised study comparing the effects of red and white wine on HDL cholesterol and other markers of atherosclerosis. The IVV study is the first long-term, prospective randomised trial comparing the effect of red and white wine on markers of atherosclerosis. The study included 146 people with mild to moderate risk of cardiovascular disease according to the HeartScore . Participants were randomised to one year of moderate consumption of red wine (Pinot Noir) or white wine (Chardonnay-Pinot) from the same year and wine region of the Czech Republic....
He added: "The only positive and continuous result was in the subgroup of patients who took more exercise, which means regular exercise at least twice a week, plus the wine consumption. In this group HDL cholesterol increased and LDL and total cholesterol decreased in the red and white wine groups. There may be some synergy between the low dose of ethyl alcohol in wine and exercise which is protective against CVD."

Now this is interesting since having lived in Prague for a while I found the Czechs drink beer and the Slovaks drink wine, usually white. Also there is often a genetic tendency for very low HDL and at the same time low cholesterol, with very low risk of CVD.

Just what this all means I do not know but since it is the middle of Labor Day weekend I thought it would be worth a comment!

Saturday, August 30, 2014

Even the Brits Hate the CATV Companies

The Guardian has a post regarding Comcast and its attempts to block any competition.

They state:

The US cable industry called on the Federal Communications Commission on Friday to block two cities’ plans to expand high-speed internet services to their residents. USTelecom, which represents cable giants Comcast, Time Warner and others, wants the FCC to block expansion of two popular municipally owned high speed internet networks, one in Chattanooga, Tennessee, and the other in Wilson, North Carolina. “The success of public broadband is a mixed record, with numerous examples of failures,” USTelecom said in a blog post. “With state taxpayers on the financial hook when a municipal broadband network goes under, it is entirely reasonable for state legislatures to be cautious in limiting or even prohibiting that activity.” Chattanooga has the largest high-speed internet service in the US, offering customers access to speeds of 1 gigabit per second – about 50 times faster than the US average. The service, provided by municipally owned EPB, has sparked a tech boom in the city and attracted international attention. EPB is now petitioning the FCC to expand its territory. Comcast and others have previously sued unsuccessfully to stop EPB’s fibre optic roll out.

One of my more referenced papers from 2002 on Municipal Broadband detailed what was to happen. No surprises. But what is shocking is that the current Administration appears in my opinion to be in collusion with these characters to further hinder any competition. Pity. But again no surprises.

Friday, August 29, 2014

PSA: Beyond Logic

In a recent Medscape article on the PSA debate the author states:

Cost is another issue. It is estimated that to prevent a single cancer death through screening and treatment costs more than $5 million. Could those dollars be better used to have a greater impact on society? Because although we may prevent a man from dying from prostate cancer, in many cases that doesn't mean that he is going to live a whole lot longer than he would have lived anyway. We have a net dilemma in trying to resolve these controversies. They are not going to be resolved tomorrow. Ultimately, we can hope that 2 things occur. One, going forward, it would be great if the gene tests that are in development turn out to be able to tell us which men need to be diagnosed and treated and which men can be spared. Two, we need to ensure that a similar fiasco does not occur. By that, I mean another screening test for early cancer that is not specific for that cancer being developed, without the right studies being done before it is used. We must avoid approving tests when we don't know for certain that they will be associated with more benefit than harm.

Let me now address each of these assertions:

1. Cost: This calculations makes a set of assumptions which in my opinion as discussed before herein are incorrect. We know the mortality rate of PCa and the costs associated with it. We also know that PSA velocity and % Free are excellent when combined with PSA. What we do not know is when we see a Gleason 6+ cancer whether it is aggressive or indolent. That is a genetic problem. Thus lacking such knowledge it is impossible to make a financial assertion of this type.

2. Genetic Tests: BRCA is a reasonable test for Breast cancer. The problem is that many PCa are not BRCA like, they may be methylation like and thus one needs to sample the actual cancer cells, not just one but many, and many individually to seek a stem cell as well. Not a simple problem.

3. Many tests lack great sp0ecificity. Welcome to testing. We cannot only use tests that  are perfect, medicine is never really like that. We never can give an answer to a patient who says "Doc, how long do I have?". No one patient is the same to all others.

Thus when we see statements like this we should take them with a grain of salt. We use the tools at hand and learn, many of the tools are poor, but they do work, somewhat. Perfection we leave to zealots.

Thursday, August 28, 2014

CATV and Monopolies

I read a piece in Ars Technical alleging that Comcast is taking measures to delimit competition.

The article states:

CenturyLink has accused Comcast of trying to prevent competition in cities and towns by making it difficult for the company to obtain reasonable franchise agreements from local authorities. CenturyLink made the claim yesterday in a filing that asks the Federal Communications Commission to block Comcast’s proposed acquisition of Time Warner Cable (TWC) or impose conditions that prevent Comcast from using its market power to harm competitors. Comcast has a different view on the matter, saying that CenturyLink shouldn’t be able to enter Comcast cities unless CenturyLink promises to build out its network to all residents. Without such conditions, poor people might not be offered service, Comcast argues.

Now that was the same game we saw when we tried to build Hanover, NH.  The incumbent had been Adelphia then bought by Comcast. Then things started, the town demanded almost 100% coverage and more. We wrote a paper discussing this at the time.

It was this added cost that made any entry prohibitive. As we saw it the town just did not comprehend the economics. All we had asked for was a equal and level playing field, the town apparently at the CATV's insistence demanded complete coverage. Frankly no CATV system does that, there are always dead zones due to reasonable economics.

As we have noted before, the merger, politically correct with the current administration, is unacceptable from any reasonable antitrust position in my opinion.

Not a Nice Application of Coase

As I had written yesterday, the poor bemoaning writer from the Times tried to apply Coase to seats on a plane.

Let us use a simple and well used example of Coase.

1. A railroad has a right of way across farm land. Let us assume that as a train goes across the land it sends off sparks.

2. The farmer has given a right of way to allow the tracks to be built but the right of way has no other conditions other then for say $1, and the railroad can then build the tracks and use them.

3. Now the farmer grows acres of corn and wheat. It is harvest time and the crops are dry but well developed and ready to be harvested.

4. A train comes along the tracks spitting out sparks. It sets the fields afire and the farmer looses all his crops.

How can this problem be dealt with.

For Coase there are two options:

1. The State, whatever that is could pass a law mandating how this is to be treated in all cases. The EPA and OSHA are examples of such agencies.

2. Assuming zero litigation costs, whenever such an occurrence happens the parties go to Court and litigate. Let the Courts decide. This is the Common Law approach.

Coase alleges that the second way is always cheaper. That is assuming zero litigation costs.

Now there is a third way in which one could have dealt with this; namely contractual. In the easement or right of way agreement there should be some negotiated and agreed to remedy for direct and indirect harms. A good attorney would have crafted such.

Now in the airline seat case there are, as I had indicated, two levels of rights; "property" right to a seat and a legal right not to be assaulted, which is a criminal issue not a civil one.

Now Mankiw appears to applaud their application to property rights but fails to understand, apparently, the right not to be physically harmed. This I find is common amongst Economists, a certain tunnel vision of self justifying assertions. The real issue here is not a property right, even in the Coasian sense, but the right not to be harmed, assaulted, by another party.

Now let me go back to Coase and the Farmer. Let us assume that the train set off sparks, the corn went afire but this time the farmer was in the field. He get burned to death, a criminal act perhaps, reckless indifference.  Here we have two distinct effects. One is a simple Coase quid pro quo. Sparks and burnt corn. If that were the case then the Farmer could have bought an insurance policy and factored the cost into the right of way. The no matter what both parties would be happy. That is a nice application of Coase. A fried Farmer now is a different story. That now requires, no demands, State intervention.

Let us then return to the airline seat. Yes, I could pay the inconsiderate character in front of me not to swing his seat back, if one were to agree to such an unencumbered property right. Yet there is a second set of issues here, my separated patella, the pain and resulting disability. I could then enter into an agreement with this character in the front seat not to file criminal charges. That is a second Coasian transaction. You see, there are two distinct actions and thus two distinct transactions.

Unfortunately that would not apply in the fried Farmer case, we hope.

Wednesday, August 27, 2014

Whose Rights

I just read a NY Times piece by some individual who apparently in my opinion believes that his right to smash someone's body and thus inflicting pain and harm for his personal comfort is a property right!

Let me pose the issue:

1. Assume that a passenger who is 6'3" is assigned to a seat in which his knees abut against the seat in front of him. Namely the passenger is tall, not obese, and the passenger consumes all of the space allotted to him. Specifically this passenger is using to the fullest his space. No more.

2. Assume we have in front of him a passenger who may or may not fills the space. Yet assume that this passenger desires to recline his seat to the fullest.

3. Now it is a physical impossibility to recline the seat without assaulting the passenger in the seat behind the front passenger. Yet he insists on his property right.

4. If we believe that each has a property right then the assault by the front passenger denies not only the back passenger property right but also inflicts harm. Namely deliberate bodily assault. Let us assume the rear passenger does not employ any means other than his body to inhibit the exercise of the assumed front passenger property right.

5. Then the rear passenger should have a right to file a criminal complaint against the front passenger for deliberate bodily harm, namely depressing the patella and inflicting pain.

Now the Times author in my opinion misrepresents the Coase Theorem. He states:

.... airline seats are an excellent case study for the Coase Theorem. This is an economic theory holding that it doesn’t matter very much who is initially given a property right; so long as you clearly define it and transaction costs are low, people will trade the right so that it ends up in the hands of whoever values it most. That is, I own the right to recline, and if my reclining bothers you, you can pay me to stop. We could (but don’t) have an alternative system in which the passenger sitting behind me owns the reclining rights. In that circumstance, if I really care about being allowed to recline, I could pay him to let me.

That would apply if and only if bodily harm were not inflicted. The act of so inflicting harm may very likely may possibly be criminal and this negates any Coasian solution.

However this piece in my opinion does clearly demonstrate the ego of those people who believe the world owes them and to hell with anyone else. It also perhaps represents the paper in which it was printed!

In fact in the old Salic law there are remedies for this type of assault. On the other hand perhaps we should be glad we no longer apply that law.

The CBO Report

The CBO issued its update on the economy report. What was of most interest was their projections on renormalization of interest rates while keeping inflation at arm's length. Worth a read.

Monday, August 25, 2014

Causes of Obesity

In almost all cases the cause of obesity is over eating. Simple. Now the over eating can be driven by many factors. Family situations are often a driver but that is complex. There are obese family members in the same household as those of normal weight. There is the phenomenon of ethnic groups who have lived for many generations on low caloric diets suddenly being exposed to "regular" diets and becoming obese. Two cases are of merit.

One is the Native American tribes in the Southwest. High obesity and high Type 2 Diabetes. There seems to be a lowered set point in metabolism that when presented with "normal" diets they seem to horde calories. The second is an interesting example, say the Irish after the famine and they come to the US and face a "normal" diet and thus have the same effect, obesity and in turn Type 2 Diabetes.

Now along comes another reason, somewhat suspicious. Namely racial and ethnic subtypes. In Eureka they state:

Many Americans need extraordinary willpower to avoid becoming obese – or to slim down if they already weigh too much. For members of minority groups, maintaining a healthy weight can be that much harder according to new research led by Luis Rivera, an experimental social psychologist at Rutgers University-Newark. Rivera says it is common for minorities in the United States to endure negative stereotypes, pervasive messages that suggest those groups are inferior, and that these attitudes can prevent people from doing what is needed to care for their health. "When you are exposed to negative stereotypes, you may gravitate more toward unhealthy foods as opposed to healthy foods," explains Rivera, whose study appears in this summer's edition of the Journal of Social Issues. "You may have a less positive attitude toward watching your carbs or cutting back on fast food, and toward working out and exercising." 

This seems to be based upon shaky ground. The same effects as seen in Native Americans and Irish Famine immigrants seem to be a better explanation. Immigrants from Hispanic lands in Central and South America come from low caloric diets and heavy manual labor. When the come here they face higher caloric intakes socially. Thus like the other cases one can see a set point difference, one lasting a few generations.

One may ask if this is akin to the methylation arguments seen in the Dutch Famine cases. It most likely is not attitude but a new set point. 

Sunday, August 24, 2014

de Tocqueville and Driving Schools

I read in the NY Times today and interesting piece about the excess regulation in France. They state:

Partly because they are young business school graduates and partly because getting a driver’s license here is so difficult and expensive that it has inspired books on the subject, Mr. Chartier and Mr. Gaignault have become minor celebrities. Various experts say their struggle highlights how the myriad rules governing driving schools — and 36 other highly regulated professions — stifle competition and inflate prices in France.

One need read no farther than de Tocqueville's "Ancient Regime" to see that this is not only new but as he notes was a primary cause of the French Revolution. Paris controlled everything, from the size of milk bottles to the size of sewer caps.  People just got fed up.

I suggest that anyone who wants to understand where we seem to be going in the US today read just one page of The Ancien Régime and the French Revolution and then think how it applies to what we are seeing today with the heavy hand of a centralized Government. Then look at France and see how absurd it can become!

Thursday, August 14, 2014

Just a Reminder

Today is the 69th anniversary of VJ Day. It was on this day in 1944 that Japan formally agreed to a surrender.

Delay is the Deadliest Form of Denial

In a Guardian piece they recount the fact that due to delays in the NHS approach to dealing with cancer patients that the mortality is excessively higher in some areas than others.

They state:

Thousands of people are dying early of cancer every year because of an "inexcusable postcode lottery" in how quickly the NHS diagnoses and treats the disease, a leading charity warns. Delays mean that cancer patients in some areas of England have up to a 61% higher risk of dying within a year of their diagnosis than those in other places, simply because of where they live. While one in four (24%) of newly diagnosed cancer sufferers in north-east Hampshire and Farnham in Surrey die within a year, 38% of those in the London borough of Barking and Dagenham do so, according to a new Macmillan analysis of data from the Office for National Statistics. The same proportion (38%) of patients also die within a year in five other places – Crawley, Sussex; Newham, east London; Swale, Kent; Vale Royal, Cheshire; and Thanet, Kent.

As we look at the massive complexity under the ACA one expects that we will be seeing the same effects here in the US.

It is not that the care is better or worse it is that there is an overwhelming number of patients and too few physicians.

Layoffs in China

In a recent piece by China Daily they report on the layoffs amongst high tech companies. They state:

Labor unrest is expected to spread following massive layoffs at several IT giants, with experts calling on multinationals to take the issue seriously. Cisco Systems has announced a plan for global job cuts, while thousands of Microsoft employees in China are trying to negotiate a deal for better compensation following layoffs. "Labor disputes involving overseas information technology companies are set to grow for the next two years at least as the Chinese economy slows," Zhang Zhiru, a labor rights expert at Shenzhen Chunfeng Labor Disputes Services Center, said on Thursday.

Thus China is starting to see the contraction that can occurs as salaries rise and labor can be outsourced elsewhere.

Obesity, Diabetes and Healthcare Costs

In a recent CDC study they predict a 40% incidence of Type 2 Diabetes in men as BMI continues to increase and as we continue to "treat" the disease instead of eliminating it.

In the Lancet study they state:

On the basis of 2000—11 data, lifetime risk of diagnosed diabetes from age 20 years was 40·2% for men and 39·6%  for women, representing increases of 20 percentage points and 13 percentage points, respectively, since 1985—89. The highest lifetime risks were in Hispanic men and women, and non-Hispanic black women, for whom lifetime risk now exceeds 50%. The number of life-years lost to diabetes when diagnosed at age 40 years decreased from 7·7 years in 1990—99 to 5·8 years  in 2000—11 in men, and from 8·7 years to 6·8 years in women over the same period. Because of the increasing diabetes prevalence, the average number of years lost due to diabetes for the population as a whole increased by 46% in men and 44% in women. Years spent with diabetes increased by 156% in men and 70% in women.

In a WebMD article they state:

The ongoing diabetes and obesity epidemics have combined with ever-increasing human lifespans to increase lifetime risk of type 2 diabetes to about 40 percent for both men and women, said lead study author Edward Gregg, chief of the epidemiology and statistics branch in the division of diabetes translation at the U.S. Centers for Disease Control and Prevention (CDC). "We weren't necessarily surprised that it increased, but we didn't expect it to increase this much," Gregg said. "Forty percent is a humbling number." The odds are even worse for certain minority groups. Half of black women and Hispanic men and women are predicted to develop type 2 diabetes during their lifetime, the researchers reported.

In another Lancet study they comprised data on BMI and cancers. We summarize the Hazard Ratios below:

 Thus BMI has such a broad impact that it is becoming the number one health hazard with no way to stop it.

Saturday, August 9, 2014

The Start of the End

From the notes of the men of the DD 649 USS Albert W Grant, on August 9th 1945:

On the 6th of August, 1945, Ensign Hartung reported to me that he had heard a news broadcast over the wardroom short wave radio saying that a new powerful bomb had been exploded over the Japanese city of Hiroshima and that President Truman had issued an ultimatum to the Japanese to surrender or experience “a rain of destruction such as the world has never known.”  Ensign Hartung literally lived by the wardroom radio during the next few days and kept me advised of the bombing of Nagasaki and the Japanese surrender. On the day of the surrender I ordered that two cans of beer per man be served in the mess hall and opened a bottle of medicinal whiskey in the wardroom to drink a toast to victory.  Normally the beer was kept under lock and key and taken ashore for picnics on atolls.  Drinking on board ship was forbidden by Navy regulations, but I felt that the occasion warranted bending the rules.

Then a personal note regarding my Father and his best fried:

From the crew perspective the end was a bit more enthusiastically received. Carlson recalls:“THE WAR WAS OVER! Terry McGarty, a fire control man and myself were sitting together on deck when we heard the news and both of us cried like babies. So what, we, before long, would be with our loved ones. We had been planning to invade the islands of the Japanese because we had now became a part of the 12th Fleet.

 More than likely the second bomb saved his and many other lives. One always looks back in history and tries to understand how best to handle the slaughter of the innocents in today's world.

Thursday, August 7, 2014

This Makes Organic More Logical

Organic Chemistry synthesis was always a bear. Frankly you just memorized what you needed and forgot it later. You needed the concepts but the details were alchemy to most. I realize that authors try to make it logical but it often falls on deaf ears especially for those of us who are never going to be chemists. Pathways, epigenetics, reaction rates, even phys chem, they all make sense, but synthesis?

I recall asking years ago if one could use a computer to do synthesis and of course the Organic Chemist looked at me as if I was asking to talk with God.

But Nature has a nice piece that seems to she light on this area. They state:

But a growing band of chemists is now trying to free the field from its artisanal roots by creating a device with the ability to fabricate any organic molecule automatically. “I would consider it entirely feasible to build a synthesis machine which could make any one of a billion defined small molecules on demand,” declares Richard Whitby, a chemist at the University of Southampton, UK. True, even a menu of one billion compounds would encompass just an infinitesimal fraction of the estimated 1060 moderately sized carbon-based molecules that could possibly exist. But it would still be at least ten times the number of organic molecules that have ever been synthesized by humans. Such a device could thus offer an astonishing diversity of compounds for investigation by researchers developing drugs, agrochemicals or materials.

Seems logical, given what we do with genes why not! Good luck to these folks!

Tuesday, August 5, 2014

CRISPR and Gene Correction

There is a report in Genome Research of CRISPR being used to correct β-Thalessemia. They state:

β-thalassemia, one of the most common genetic diseases worldwide, is caused by mutations in the human hemoglobin beta (HBB) gene. Creation of human induced pluripotent stem cells (iPSCs) from β-thalassemia patients could offer an approach to cure this disease. Correction of the disease-causing mutations in iPSCs could restore normal function and provide a rich source of cells for transplantation. In this study, we used the latest gene-editing tool, CRISPR/Cas9 technology, combined with the piggyBac transposon to efficiently correct the HBB mutations in patient-derived iPSCs without leaving any residual footprint. No off-target effects were detected in the corrected iPSCs, and the cells retain full pluripotency and exhibit normal karyotypes. When differentiated into erythroblasts using a monolayer culture, gene-corrected iPSCs restored expression of HBB compared to the parental iPSCs line. Our study provides an effective approach to correct HBB mutations without leaving any genetic footprint in patient-derived iPSCs, thereby demonstrating a critical step toward the future application of stem cell-based gene therapy to monogenic diseases. 

This is a real major breakthrough. Wait for more!

Monday, August 4, 2014

The HealthCare Web Site

The GAO issued a scathing report on the HHS development of the web site which was in the news last Fall. They state:

CMS did not develop a required acquisition strategy to identify risks and document mitigation strategies and did not use available information, such as quality assurance plans, to monitor performance and inform oversight. CMS incurred significant cost increases, schedule slips, and delayed system functionality for the FFM and data hub systems due primarily to changing requirements that were exacerbated by oversight gaps. From September 2011 to February 2014, FFM obligations increased from $56 million to more than $209 million. Similarly, data hub obligations increased from $30 million to nearly $85 million. Because of unclear guidance and inconsistent oversight, there was confusion about who had the authority to approve contractor requests to expend funds for additional work. New requirements and changing CMS decisions also led to delays and wasted contractor efforts. Moreover, CMS delayed key governance reviews, moving an assessment of FFM readiness from March to September 2013—just weeks before the launch—and did not receive required approvals. As a result, CMS launched without verification that it met performance requirements.

Anyone thinking that the Government can do a better job ought review this Report. Always remember that morbidly obese GS 9 with an attitude sitting there denying you and your family coverage from some life threatening problem. They already exist in the VA.

Saturday, August 2, 2014

Civil Discourse

In a recent link, Mankiw noted an excellent piece in Forbes regarding Civil Discourse. The Forbes article comments on the loss of civil discourse amongst Economists, and also amongst many others, when it comes to opining on the Internet.

The author states:

But what I’m writing about is not Paul Ryan. I’m writing about the level of national discourse. No one, and I mean no one, deserves to be called stupid. It’s a nasty, demeaning, and incredibly elitist term. Paul, you should know better than to use your very special position to insult people. But this is a longstanding pattern with you. You go after people personally and in so doing you go after yourself. Paul, as someone who knows you, respects you, shares your values, and appreciates your marvelous academic work, knock it off. Stop calling people names. You will feel better about yourself and get people like me to take your views much more seriously.

 Indeed there are many Economists at prestige institutions who act rather childishly when it comes to commenting on their foes, foes in ideas, not in fundamentals or facts. Indeed Economists are all too often at odds and thus one really questions their advice. It is an opinion and not clarity into economic reality. Keynes understood that but many of the current band do not.

Perhaps listening to mother could help. After all, one never saw Einstein rant at his colleagues calling them dumb. But one guesses that few if any were.

And oh by the way, just read one of the snarkiest yet. QED.

Friday, August 1, 2014

Prostate Cancer, Methylation, and Prognostics

There seems to be a continuous flow of genes, miRNAs, epigenetic factors including methylation, SNPs and the like all both diagnostic and prognostic for various cancers. A decade ago one looked for a gene, some gene that somehow got broken, changed, deleted, or the like. The paradigm was the Philadelphia chromosome of a cut and paste example. With the understanding we now have of methylation we see the same occur here, and methylation can be acquired and/or genetically inherited (see imprinting examples). However methylation is still somewhat poorly understood; what causes it, why does it work positively in some cases and negatively in others?

Methylation is but one of the many facets of what we now see as causes of Cancer. We depict a short summary below.

We examine the work of Wojno et al which has received recent interest. They examine the impacts of methylation upon 3 genes and see their presence as prognostic of potential aggressive prostate cancer. Specifically they conclude:

The diagnosis of prostate cancer is dependent on histologic confirmation in biopsy core tissues. The biopsy procedure is invasive, puts the patient at risk for complications, and is subject to significant sampling errors.

An epigenetic test that uses methylation-specific polymerase chain reaction to determine the epigenetic status of the prostate cancer–associated genes GSTP1, APC, and RASSF1 has been clinically validated and is used in clinical practice to increase the negative predictive value in men with no history of prostate cancer compared with standard histopathology. Such information can help to avoid unnecessary repeat biopsies.

The repeat biopsy rate may provide preliminary clinical utility evidence in relation to this assay’s potential impact on the number of unnecessary repeat prostate biopsies performed in US urology practices.

DNA methylation normally can result in the silencing of genes by interrupting the normal process of promoters. CpG islands are often hypermethylated and thus the gene which may regulate cell proliferation is silenced. This may result in uncontrolled cell growth. For example genes controlling MYC are not produced and MYC may then result in excess cell cycle proliferation. Methylation is hypermethylated in the regions of intergenic regions and in repetitive elements and this hypermethylation silences these regions and facilitates normal cell DNA transcription of the gene. Disruption of DNA, namely hypomethylation, in the intergenic and repetitive regions may result in possible loss of imprinting. This hypomethylation is also related to the production of lncRNAs which may in turn interfere with normal gene transcription.

Decitabine is a DNMT inhibitor. Namely, it inhibits the DNA methyltrasferases that facilitate methylation (such as DNMT3 which are de novo and DNMT1 which is maintenance). Decitabine thus has then tendency on the specific hematologic cell lines in MDS to remove methylations which have caused the aberrant cell line proliferations and allow for the return of homeostasis. MDS is a quasi-malignant condition originating in the bone marrow which may in many cases result in Acute Myelogenous Leukemia. With the use of decitabine or a similar DNMTI azacitidine, demethylation of these rapidly reproducing cells may be achieved and possible a normal state of homeostasis achieved.

The use of pharmaceuticals that alter the methylation patterns of DNA can have lasting effects because those patterns may last through subsequent mitotic changes. On the one hand that may be beneficial as is the case with MDS but such broad demethylation may also alter other segments of the DNA altering essential control elements and pathways. In cell development there are two sensitive periods; germ cell development and early embryonic development. It is during these periods that methylation is cleared and reset and that a drug-like a DNMTI would pose a serious risk to the proper resetting of the marks and could result in substantial DNA expression damage.

In summary we will examine the three gene methylation proposition with this test. We summarize this below:

Let us examine what the study presents in a bit more detail. Basically it does the following:

1. It examines three gene products; GSTP1, APC, and RASSF1

2. It determines if the genes are methylated so that the gene products are suppressed.

3. If that is the case after a first biopsy which is deemed normal, then a second biopsy is mandated due to the high incidence of a positive result on the second biopsy for PCa.

Specifically from the paper by Partin et al on the same topic the authors’ state:

The DOCUMENT multicenter trial in the United States validated the performance of an epigenetic test as an independent predictor of prostate cancer risk to guide decision making for repeat biopsy. Confirming an increased negative predictive value could help avoid unnecessary repeat biopsies. We evaluated the archived, cancer negative prostate biopsy core tissue samples of 350 subjects from a total of 5 urological centers in the United States. All subjects underwent repeat biopsy within 24 months with a negative (controls) or positive (cases) histopathological result. Centralized blinded pathology evaluation of the 2 biopsy series was performed in all available subjects from each site.

Biopsies were epigenetically profiled for GSTP1, APC and RASSF1 relative to the ACTB reference gene using quantitative methylation specific polymerase chain reaction. Predetermined analytical marker cutoffs were used to determine assay performance. Multivariate logistic regression was used to evaluate all risk factors.

The epigenetic assay resulted in a negative predictive value of 88% (95% CI 85-91). In multivariate models correcting for age, prostate specific antigen, digital rectal examination, first biopsy histopathological characteristics and race the test proved to be the most significant independent predictor of patient outcome.

The DOCUMENT study validated that the epigenetic assay was a significant, independent predictor of prostate cancer detection in a repeat biopsy collected an average of 13 months after an initial negative result. Due to its 88% negative predictive value adding this epigenetic assay to other known risk factors may help decrease unnecessary repeat prostate biopsies.

Recall that the negative predictive value or NPV is defined as:


Thus an NPV of 88% for the sample size used implies that it is fairly high in predicting True Negatives a priori but may still miss a percentage. There of course is the issue of the pathologist missing the PCa as well. This could be done by a sampling deficiency or confusion on a reading. It is not clear if for example a HGPIN is read.

Thus focusing on methylated genes, specifically just 3 of them, GSTP1, APC and RASSF1, they were able in a small sample to ascertain that there would be no need of a second biopsy if they were found to be unmethylated in the first.

Recall the effects of methylation as we show below:

From an article in Medical Express[1] as well as from an article in Eureka[2] as well as from an article in Science Codex[3] we have the following summary:

More than one million prostate biopsies are performed each year in the U.S. alone, including many repeat biopsies for fear of cancer missed. Therefore there is a need to develop diagnostic tests that will help avoid unnecessary repeat biopsies. Two independent trials have now validated the performance of an epigenetic test that could provide physicians with a better tool to help eliminate unnecessary repeat prostate biopsies, report investigators in The Journal of Urology.

In the previously reported independent MATLOC (Methylation Analysis To Locate Occult Cancer) trial, a multiplex epigenetic assay (ConfirmMDx for Prostate Cancer) profiling the APC, GSTP1 and RASSF1 genes demonstrated a negative predictive value of 90%. GSTP1 methylation is a specific biomarker for (prostate) cancer and this gene is methylated in up to 90% of prostate cancer cases. Additionally, APC and RASSF1 are important field effect markers and increase the diagnostic sensitivity of the assay.

A second multicenter study, DOCUMENT (Detection Of Cancer Using Methylated Events in Negative Tissue), has validated the performance of the epigenetic assay used in the MATLOC trial as an independent predictor of prostate cancer risk to guide decision making for repeat biopsy. In the DOCUMENT study patients with a negative biopsy were evaluated to identify those at low risk for harboring cancer missed, through biopsy sampling error, who could forego an unnecessary repeat biopsy. The validation study resulted in a negative predictive value of 88%.

"This epigenetic assay is a significant, independent predictor and has been shown to be the most valuable diagnostic aid of all evaluated risk factors in two independent trials," comments Alan W. Partin, MD, PhD, of the James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland. "Negative findings of this assay could be used to reduce concern over unsampled cancer and effectively avoid unnecessary repeat biopsies."

A total of 350 patients were enrolled in the DOCUMENT trial from five geographically dispersed medical centers: Cleveland Clinic, Eastern Virginia Medical School, Lahey Hospital & Medical Center, Johns Hopkins University, and University of California Los Angeles. Patients were grouped into those with two consecutive negative biopsies (controls) and those with a negative biopsy followed by a positive biopsy within 24 months. The initial archived, negative for cancer, prostate biopsy core tissue samples were evaluated. All of the men underwent a repeat biopsy on average one year after the initial biopsy.

Only biopsies with a minimum of eight cores per biopsy, collected no earlier than 2007, were included in the study, while initial biopsies with atypical cells suspicious for cancer, i.e. atypical small acinar proliferation by the sites' pathologists, were excluded, since this would have triggered a repeat biopsy based upon histopathology alone.

After correcting for age, prostate specific antigen (PSA), digital rectal exam, histopathological characteristics of the first biopsy, and race, this epigenetic test proved to be the most significant, independent, and strongest predictor of patient outcome with an odds ratio of 2.69 as well as the most valuable diagnostic aid of all evaluated risk factors. The slightly decreased sensitivity of the DOCUMENT trial compared to the MATLOC trial is most likely associated with a higher PSA screening prevalence in the DOCUMENT cohort.

It is important to note the following:

1. The genes selected have been studied for over two decades and especially as regards to their hypermethylation status.

2. The test is an early prognostic test which when combined with prostate biopsy data, especially a benign reading on the prostate biopsy.

3. The test has reasonable statistics given its small sample size but as we shall see there is substantial variability in these tests.

Methylation is but one of the very many changes we see in cancers. Whether they are cause or effect is yet to be determined. We know, for example, that methylation is causal in MDS, myelo-dysplasia syndrome, a precursor often of ALL. However, the cause of this methylation is still problematic. Drugs like DNMT inhibitors, azacitidine and decitabine are methylation inhibitors that seem to work for a while in this disorder. However what they do to other cells is uncertain.

In this study which we examine, there is a multiplicity of questions.

1. What causes the methylation?

There is still a lack of clear process as to how methylation occurs. As we will note shortly there are hypothesis that it is a result from inflammatory states and others that there may be secondary effects of autoimmune conditions. The elements of the process are understood to some degree but no true full causal chain is established.

2. Why are these gene sites methylated?

Why specific CpG islands at specific genes are methylated is still unknown. Are these initial locations or are the related to other as yet to be determined sites. Are certain CpG site more susceptible? Is there some histone issue wherein the histones are demethylated opening the DNA and thus allowing CpG methylation?

3. Why not try the DNMT inhibitors if these methylations are causal for PCa?

DNMT inhibitors are used for MDS with some short term success. Can they be used here as a step towards reversal? The problem is that we do not know what DNMTI sequellae are. The unintended consequences could be significant. Can we develop cell specific DNMTIs or are they even too potent?

4. Are many cancers caused by methylation or demethylation? If so which ones and why?

We have examined several different cancers and there is a large putative collection of genes, translocations, miRNAs, SNPs, methylations, and the like. Almost weekly and perhaps soon daily we will be seeing alleged markers for every element of a cancer development. Two decades ago we saw just gene issues. Today we have a problem of ascertaining the chicken or the egg. This is both a challenge and an opportunity. The problem, however, is that each time one of these has been developed, we see a Press release frenzy as it be a sine qua non.

5. Are the observations made by the researchers causal or coincidental?

This is always a critical question. Is this specific methylation of genes the cause of ultimate PCa or the coincidental effect of some other factor?

6. Are the methylation observations drivers or therapeutic approaches?

This question is a follow on to our question regarding DNMTIs.

7. Should we be examining more cancers from an epigenetic point of view rather than a genetic mutation perspective?

We have examined a few cancers for methylation as drivers for malignancy and metastatic behavior.

8. If as we have seen anecdotally, patients determined to have widespread HGPIN on a first 24 core biopsy and then none on a second 24 core biopsy, is this possibly a demethylation result, a stem cell result, or some other factor.

We have examined HGPIN in previous analyses. Although not considered a true PCa it has been considered as a natural pre-cursor. Namely many assume that HGPIN will always turn into PCa. However we have anecdotally seen patients where the HGPIN actually regresses, to the level of being unidentifiable at on a high density core biopsy. Thus we have asked if the first biopsy actually precipitated the remission, if so how and why, or was there some other factor. Unfortunately there is inadequate data for this study.

9. What of the stem cell factor in PCa?

PCa stem cells are always a concern. We have discussed them at length and basically research continues into these cells in PCa. Yet it does beg the question; what cells need be methylated and are certain cells more likely than others? Furthermore we can ask; how do we segregate prostate cells so as to ascertain the severity of methylation?

10. PTEN mutations have been proposed as a major causal effect of PCa. How does this relate to epigenetic factors?

We have shown that PTEN is controlled in the process of p53 and in turn the MDM2 and its RAS precursor control. Thus the focus on RAS derivatives is consistent with the PTEN argument.

11. Are epigenetic factors the results of inflammatory states? Namely in a patient with for example Type 2 Diabetes and elevated inflammatory status, does this become an initiating factor for methylation?

Hartnett and Egan have recently written:

Recently, epigenetic alterations, in particular alterations in DNA methylation, have been observed during inflammation and inflammation-associated carcinogenesis. The mediators of this, the significance of these changes in DNA methylation and the effect this has on gene expression and the malignant transformation of the epithelial cells during IBD and CAC are discussed in this review. The recent advances in technologies to study genomewide DNA methylation and the therapeutic potential of understanding these molecular mechanisms are also highlighted.

Dayeh et al focus on these types of methylation induced by Type 2 Diabetes in a recent paper as well.

Also it is worth examining the summary by Kundu and Surh on inflammation and cancer. They state:

DNA methylation, the covalent addition of a methyl group to the 5-position of cytosine base in the DNA, represents a critical epigenetic control of gene expression. The perturbation of methylation patterns as either aberrant loss of cytosine methylation in transforming genes or inappropriate gain of cytosine methylation in tumor suppressor genes has been involved in various human malignancies.

The most predominant aberrant DNA methylation is hypermethylation that typically occurs at the CpG islands located in the promoter regions of tumor suppressor genes. Promoter hypermethylation of tumor suppressor genes, such as p16, von-Hippel Lindau (VHL), adenomatous polyposis coli (APC), breast cancer susceptibility gene (BRCA1), retinoblastoma (Rb), E-cadherin (CDH1), p73, p53, and p57, results in transcriptional silencing . By analyzing the methylation status of 11 candidate cancer-related genes in cutaneous squamous cell carcinomas, Murao et al. have demonstrated that the promoter hypermethylation of CDH1, p16, Rb1 and p14 results in the loss of respective protein production.

Therefore, the epigenetic silencing of tumor suppressor genes by promoter CpG island hypermethylation perturbs cell cycle control, apoptosis, DNA repair and cell adhesion, and is recognized as an important mechanism in the tumorigenesis. However, global hypomethylation of certain genes, e.g., insulin-like growth factor-2 (IGF-2), can also result in genomic instability, accelerating malignant transformation.

As Donkena et al state:

“Oxidative stress” is the state of a cell, which is characterized by excess production of reactive oxygen species (ROS) and/or a reduction in antioxidant defenses responsible for metabolism. ROS are formed as a natural byproduct of the normal metabolism of oxygen. Under normal circumstances, the cell is able to maintain an adequate homeostasis between the formation of ROS and its removal through enzymatic pathways or via antioxidants. If, however, this balance is disturbed, then oxidative stress occurs.

This generates an imbalance of production/removal of ROS, which is either directly or indirectly involved in initiation, promotion, and progression phases of carcinogenesis. Oxygen radicals may cause damage to DNA and chromosomes, induce epigenetic alterations, interact with oncogenes or tumor suppressor genes, and impart changes in immunological mechanisms.

The extent of ROS induced oxidative damage can be exacerbated by a decreased efficiency of antioxidant defense mechanisms. …. Hypermethylation of a combination of genes including APC, RASSF1A, PTGS2, PDLIM4, and MDR1 could distinguish cancer from benign prostate tissues with sensitivities of 97.3%–100% and specificities of 92%– 100%. The increase in methylation of these genes with cancer progression indicates that they could be used for biomarkers for both diagnosis and risk assessment  

Furthermore, we showed significant differences in the frequency of methylation at individual CpG sites of PITX2, PDLIM4, KCNMA1, GSTP1, FLNC, EFS, and ECRG4 in recurrent and nonrecurrent subtypes of prostate tumors. Indeed, hypermethylation of a CpG island in PITX2 portended an increased risk of prostate cancer recurrence and was a predictor of distant disease recurrence in tamoxifen-treated, node-negative breast cancer patients.

12. HGPIN has always been an issue of concern. In some cases it appears to revert to fully benign states and in others it progresses to PCa. The question is: How useful would such a test be in HGPIN conditions?

The concern always is the HGPIN cells are confined to the glandular portions of luminal and basal cells. Is it necessary to get HGPIN cells to test or can the test be performed on other cells? Specifically how large a sample is necessary to get adequate sensitivity and specificity?

1.     Ahmed, H, Promoter Methylation in Prostate Cancer and its Application for the Early Detection of Prostate Cancer Using Serum and Urine Samples, Biomarkers in Cancer 2010:2.
2.     Armstrong, L., Epigenetics, Garland (New York) 2013.
3.     Brooks, J., et al, CG Island Methylation Changes Near the GSTP1 Gene in Prostatic Intraepithelial Neoplasia, Cancer Epidemiology, Biomarkers & Prevention , Vol. 7, 531-536, June 1998
4.     Chesire, D., W. Isaacs, β-Catenin signaling in prostate cancer: an early perspective, Endocrine-Related Cancer (2003) 10 537–560.
5.     Dayeh, T., et al, Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion, March 2014, Volume 10, Issue 3.
6.     Donkena, K., et al, Oxidative Stress and DNA Methylation in Prostate Cancer, Hindawi Publishing Corporation, Obstetrics and Gynecology International, Volume 2010.
7.     Francis, J., et al, b-Catenin Is Required for Prostate Development and Cooperates with Pten Loss to Drive Invasive Carcinoma, PLOS Genetics, ,  1 January 2013,| Volume 9, Issue 1, e1003180.
8.     Gonzalgo, M., et al, Prostate Cancer Detection by GSTP1 Methylation Analysis of Post biopsy Urine Specimens, Clin Cancer Res 2003; 9,  2673-2677.
9.     Gordon, M., et al, RASSF1 Polymorphisms in Cancer, Molecular Biology International, Volume 2012, Article ID 365213, 12 pages
10.  Hanna, C., G. Kelsey, The specification of imprints in mammals, Heredity (2014) 113, 176–183.
11.  Hartnett, L., L. Egan, Inflammation, DNA methylation and colitis-associated cancer, Carcinogenesis vol.0 no.0 pp.1–9, 2012.
12.  He, T., et al, Identification of c-MYC as a Target of the APC Pathway, Science, 281, 1509 (1998).
13.  Hotchkiss, R., L. Moldawer, Parallels between Cancer and Infectious Disease, NEJM, 371;4, July 24, 2014.
14.  Jaiswal, J., S. Naryan, p53-dependent Transcriptional Regulation of the APC Promoter in Colon Cancer Cells Treated with DNA Alkylating Agents, THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 276, No. 21, Issue of May 25, pp. 18193–18199, 2001
15.  Kundu, J., Y. Surh, Inflammation: Gearing the journey to cancer, Mutation Research 659 (2008) 15–30.
16.  Laborde, E., Glutathione transferases as mediators of signaling pathways involved in cell proliferation and cell death, Cell Death and Differentiation (2010) 17, 1373–1380.
17.  Mancini et al, MDM4 (MDMX) localizes at the mitochondria and facilitates the p53-mediated intrinsic-apoptotic pathway, The EMBO Journal (2009) 28, 1926–1939.
18.  Marks, F., et al, Cellular Signal Processing, Garland (New York) 2008.
19.  Meirs, I., Glutathione S-Transferase pi (GSTP1), Atlas Genet Cytogenet Oncol Haematol. 2010; 14(12).
20.  Morin, P., A. Weeraratna, The APC Tumor Suppressor Pathway, El Deiry (Editor), Tumor Suppressor Genes, Humana (New York) 2003.
21.  Muller et al, p53 and its mutants in tumor cell migration and invasion, J. Cell Biol. Vol. 192 No. 2 209–218.
22.  Partin, A., et al, Clinical Validation of an Epigenetic Assay to Predict Negative Histopathological Results in Repeat Prostate Biopsies, J Urol. 2014 Apr 18.
23.  Patten, M. et al, The evolution of genomic imprinting: theories, predictions and empirical tests, Heredity (2014) 113, 119–128.
24.  Rabiau, N., et al, Methylation Analysis of BRCA1, RASSF1, GSTP1 and EPHB2 Promoters in Prostate Biopsies According to Different Degrees of Malignancy, in vivo 23: 387-392 (2009)
25.  Richter, A., et al,  The RASSF proteins in cancer; from epigenetic silencing to functional characterization, Biochimica et Biophysica Acta xxx (2009) xxx–xxx.
26.  Wan, X., et al, Activation of β-Catenin Signaling in Androgen Receptor–Negative Prostate Cancer Cells, Clin Cancer Res, 2012.
27.  Wang, T., et al, Glutathione S-transferase P1–1 (GSTP1–1) Inhibits c-Jun N-terminal Kinase (JNK1) Signaling through Interaction with the C Terminus, THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 276, No. 24, Issue of June 15, pp. 20999–21003, 2001.
28.  Wantanabe, M., et al, APC Gene Mutations in Human Prostate Cancer, (Jpn J Clin Oncol 26: 77-81, 1996.
29.  Wojno et al, Reduced Rate of Repeated Prostate Biopsies Observed in ConfirmMDx Clinical Utility Field Study, Am Health Drug Benefits. 2014;7(3):129-134,