Cancer Initiation

Friday, February 10, 2017

Extending our G6 Model for neuro-developmental abnormalaties


  We previously discussed how toxic components such as mercury could be entered into our 6th Generation model of medical science. In that case, mercury is considered as an additional non-independent variable on the input to the model. Now, we want to extend the same model to neuro-development, a process that is known to be very dependent upon epigenetics, that is, gene regulation by DNA promoter methylation.
   If DNA methylation capacity is limited by reduced function of the single carbon metabolism cycle ( production of glutathione, SAM ) then consequently, neuro-development will be impacted.


Identification of methylation deficiency in impaired children

   It has previously been recognized that impairment at the single carbon metabolism level is a significant factor in autism [1]. A nutritional supplement targeting methylation deficiency was successful in returning the system to it's normal range of function.

 This metabolic profile is consistent with impaired capacity for methylation (significantly lower ratio of SAM to SAH) and increased oxidative stress (significantly lower redox ratio of reduced glutathione to oxidized glutathione) in children with autism. The intervention trial was effective in normalizing the metabolic imbalance in the autistic children.
                                              James (2004) [1]
This study was successful in returning glutathione and SAM to normal ranges, but what is not clear from this study,  or further studies by this group, is whether the neurological symptoms are reversible.

Cognitive Ability 

Education is the study of cognitive ability. Educators are really more interested in the bottom line than with blood levels of chemical intermediaries. For the final chapter of this post, we have to go to China, particularly the Harbin Medical University in Harbin China. A group led by Sun et. al. [2] tested related dietary supplements and their effect on in-class performance of afflicted students.
The results illustrated folic acid intervention improved autism symptoms towards sociability, cognitive verbal/preverbal, receptive language, and affective expression and communication. Furthermore, this treatment also improved the concentrations of folic acid, homocysteine, and normalized glutathione redox metabolism. Folic acid supplementation may have a certain role in the treatment of children with autism.
                                          Sun (2016) [2] 


 Many types of autism are due to failures at the level of glutathione and SAM production. These processes may be dependent upon multiple interacting ( non-independent ) factors that include nutrient availability and toxic load. It has been shown that nutrition supplements can:
  • Restore function of single carbon metabolism cycle
  • improve neurologic performance as measured in a structured teaching mode


[1] S Jill James, Paul Cutler, Stepan Melnyk, Stefanie Jernigan,  Laurette Janak, David W Gaylor, and James A Neubrander Metabolic biomarkers of increased oxidative stress and  impaired methylation capacity in children with autism1,2 [Full Text]

[2] Sun C, Zou M, Zhao D, Xia W, Wu L. Efficacy of Folic Acid Supplementation in Autistic Children Participating in Structured Teaching: An Open-Label Trial. Nutrients. 2016 Jun 7;8(6). pii: E337. [PubMed]

Thursday, February 9, 2017

Extending our 6th Generation Science model for Methyl Mercury Toxicology


 In previous posts, we discussed how biotechnology was changing the nature of medical science and somewhat arbitrarily assigned generations to each mode of scientific research, as they were introduced . We noted that in our model, a 6th generation study was one that took into account many, possibly interacting variables, that is, non-independent variables as inputs, and processed their impact on core systems related to genetic, epigenetic and immunological outputs. We went on to note that this type of thinking was already happening. In one relatively recent paper that we discussed, the authors uses single nucleotide polymorphisms ( SNPs ) related to single carbon metabolism as an input, and related their impact to four disease conditions that included cancer, Parkinsons and others.

The mathematics of non-independent variables

   While most of our traditional statistical models assume "independent" variables as inputs, in our models, we are using "non-independent" variables as inputs. In fact, we do not want to ignore or filter out interactions between variables, we want to find them. For example, what is the interaction between two SNPs, between a SNP and a toxin like methyl mercury, or an interaction between a SNP and a nutrient deficiency, for example in folate or b12.  As we discussed, the model that we use for this is called Dimension Reduction Analysis, were we wish to find interacting non-independent variables and combine them, producing a "dimension reduction" in our resulting model. A package for this is now supported and is available on the web.

Glutathione Detoxification of Mercury

  In our previous discussions, we discussed the Single Carbon Metabolism pathway and its evaluation using glutathione as a biomarker. We once again find that glutathione is an appropriate marker with respect to mercury toxicity. Here is a quote from our reference for the day, Andreoli (2017)[1]. What what we note is that our glutathione biomarker is a primary driver in the subjects attempt to detoxify mercury. Excuse, the length of this quote, but they are saying about what I would like to say.

Reduced glutathione (GSH-γ-glutamyl-cysteinyl-glycine), an essential tripeptide present in large quantities in all mammal cells, is the main agent of the glutathione detoxification system (GSHs). This system, which neutralizes the free radicals producing reactive oxygen species (ROS), protects cells against damage resulting from exposure to many external agents and oxidative stress. GSH, therefore, fosters a positive body’s response to the negative Hg actions towards natural detoxification process, and it is essential to heal the damage within the cells.
Various epidemiological studies have suggested that the response to Hg may be influenced by molecular variants in several regulatory GSHs genes, involved in absorption, distribution, metabolism and excretion process, better known as the Hg toxicokinetics, as reflected in Table 2. Consequently, the genetic component of human Hg susceptibility has now become another aspect not to be underestimated in this context
                                 Andreoli and Sprovieri ( 2017) [1]

At the risk of providing too much from our reference, I am going to add a brief comment from their discussion, which makes part of this articles point:
With the advances in genetics and high-quality information on Hg pollution, current research has shown that the interplay between genes and environment is critical to better understand the Hg impact on human health [87]. Despite the great potential, there has, however, been little use of genetic information in Hg risk assessments for both occupational and environmental exposures.
                               Andreoli and Sprovieri ( 2017) [1]

The Neglected Aspects 

   Andreoli goes on to discuss more pathways that are impacted by Methyl and inorganic mercury, but I would like to take a different direction. We know from our model is the Popeye Diet context that epigenetic processes ( that is DNA methylation ) is linked to glutathione and Single Carbon Metabolism. As such, ALL other pathways are potentially impacted by mercury, by the indirect impact of epigenetic mis-regulation. Time and time again, it is the Single carbon Metabolism pathway that is the most sensitive to toxic insult, and othery pathways follow suit,  presumably as a result of epigenetic mis-regulation.


  We know that auto-immune response is a result of mercury toxicity. Since this is my blog, I am going to go ahead and conclude that this is of failure to suppress Wingspans antigens, and their resulting stimulation of the immune system in those locations where cell division and active immune cells overlap ( the digestive system ) .


[1 ] Virginia Andreoli and Francesca Sprovieri Genetic Aspects of Susceptibility to Mercury Toxicity: An Overview Int J Environ Res Public Healthv.14(1); 2017 Jan [PubMed Central]

Tuesday, February 7, 2017

Circumstancial evidence for an epigenetic checkpoint in the cell cycle


   We have introduced the concept of a checkpoint in the cell cycle, which prevents premature progression of the cell cycle, that is, cell division or mitosis before a new copy of DNA has been completed. At the present time, checkpoints have only been considered with respect to DNA sequence completion, not duplication of the appropriate epigenetic marks, alternately referred to as methylation of the CpG islands. This duplication of methylation process is called "maintenance", and is mediated by the primary maintenance DNA methyl-transferase, DNMT1.

The case of vitamin b12 deficiency

   It is now known that the cell cycle can be blocked in prospective blood cells ( megaloblasts) by a deficiency in vitamin b12. The condition is known as megaloblastic anemia and is described below, or in the first reference . [1] 

From the wikipedia entry on megaloblastic anemia :
 Megaloblastic anemia (or megaloblastic anaemia) is an anemia (of macrocytic classification) that results from inhibition of DNA synthesis during red blood cell production.[1] When DNA synthesis is impaired, the cell cycle cannot progress from the G2 growth stage to the mitosis (M) stage. This leads to continuing cell growth without division, which presents as macrocytosis.

Why would b12 deficiency inhibit DNA synthesis?

  Vitamin b12 has two known functions, or pathways in the body. In relation to the citric acid cycle, ( also called the Krebs cycle ), vitamin b12 mediates the conversion malonal CoA to succinal CoA.  Succinal Coenzyme A is an intermediary in the Krebs cycle, and can go on to function in the production of ATP.
   The other function of b12 is in the Single Carbon Metabolism pathway. In relation to this pathway, b12 is necessary for the production of SAM and glutathione.  In turn, glutathione deficiency is known to impact DNA methylation. [2]


Even though we have never heard of b12 being a factor in the production of DNA, it is a factor in methylation of CpG islands, or promoters, associated with a cells differentiation. We now have a connection between a new prospective checkpoint type mechanism and a potential factor in cancer and other diseases, that is b12 deficiency.


   If in fact there is some mechanism that could be called a checkpoint, then loss of this mechanism could be considered a new source of cancer causation. We know that single nucleotide polymorphsms associated with single carbon metabolism may be significant in increasing risk of caner.  Perhaps this epigenetic checkpoint is active in stem cells which are dividing in environments that are immunologically privileged. Such is the case in bone marrow.


   After consideration of some other types of cells, I am going to go out on a limb and say that the epegenetic checkpoint is not a universal feature of cells. In some cells, such as in the hematopoetic ( blood generation ) system, b12 blocks cell cycle progression because of epigenetic failure associated with the function of DNA methyl-transferase,    DNMT1.


[1] Emmanuel Andres, and Khalid Serraj  Optimal management of pernicious anemia J Blood Med. 2012; 3: 97–103.[PubMed Central]

[2]  Lertratanangkoon K, Wu CJ, Savaraj N, Thomas ML.    Alterations of DNA methylation by glutathione depletion. Cancer Lett. 1997 Dec 9;120(2):149-56. [Abstract]

Friday, February 3, 2017

Wingspans Antigens provide potential targets for CAR-T cell therapy


The emergence of new advanced genetic engineering, even "editing" techniques has created new potential for engineered cancer therapies.  One approach that is receiving much attention is that of CAR T-cell therapy[1].  The acronym CAR stands for Chimeric Antigen Receptor, where Chimeric means combination of different genomes, and Antigen Receptor refers to that Receptor that Targets a particular antigen on a target cell. In short, we engineer T-cells, portions of the immune system, to attack specific targets.

This is an enhancement of a natural system that exists between the immune system and cancer cells.  In short, all cells "of the body" or somatic cells, have repressed antigens called (my terminology) Wingspans antigens.I  These markers all have the property is that their sole (apparent) purpose is to attract the attention of the immune system, and  they are always epigenetically suppressed in normal cells. As cancer stage progresses, the cell goes through what is called "hypomethylation", or failure to suppress those antigens which are supposed to be suppressed. As such, these antigens become uniquely expressed on cancer cells. If the immune system has not been previously destroyed, an immune response will build up against the cancer.

Identification of Wingspans Antigens

With the advent of modern methylation oriented DNA sequencing techniques, such as bi-sulfite sequencing, it is possible not only to enumerate antigens that fit the description of "Wingspans Antigens", but specific tumor biopsy samples could be analyzed to find the best potential treatments.
  The logic is simple. As a cancer progresses, see which genes get turned on which should not be there.   Many Wingspans antigens have already been identified so they are easy to fine. Unknown antigens which have no other known function are candidates.

The Point

 These are two ideas that could and should be combined. The sequencing equipment for customized medicine is available, and new gene editing technques such as CRISPR makes designer "chimerics" a relative snap.


   Each time I read about a new high speed biomedical technique I cringe and think about the difficulties I had in the gene cloning/ gene expression laboratory courses I had. It was like having to paint a Da Vinci of a beautiful sunset, when all you really wanted was a cell phone with a camera.


[1] Dach, Jeffrey Steven A Rosenberg and Cancer Immunotherapy [JeffreyDachMD]

Saturday, January 28, 2017

Glyphosate (Roundup) is not approved as a food additive


  Roundup is a common herbacide that is used in the production of many crops. Typically a genetically modified crop that is resistant to Roundup will be planted, and then application of Roundup will reduce the crop to a mono-culture of the desired product.
  Roundup (glyphosate) is a combination of the amino acid glycine with an extra phosphate group. It looks like a nutrient to the plant but cannot be metabolized. The proposed "beauty" of glyphosate is that after application, it decomposes to natural nutrients, phosphate and an amino acid. For that to be the case, Roundup has to be applied early in the plants life cycle. It has now become apparent that this is not always the case.
   It has been recently recognized that Roundup is also popular "off label". By that I mean that in the case of wheat, glyphosate is applied as a "harvest sweetener" to help dry out wheat before harvest. This novel application of glyphosate has the potential and affect of placing a large amount of un-degraded chemical in the food supply, as a component of flower. Even if the wheat itself is a "non-gmo", it may be harvested with the aid of glyphosate as a "sweetener".


Increasing Toxicological Evidence 

 Because  Roundup was never intended to be in the food supply, there is a dearth of toxicological data. The manufacturers maintain that toxicological data is unnecessary becasue it is not for human consumption. Now that it is on the food supply, more detailed toxicological studiesr are becoming available. [1] The results show that Roundup is liver and kidney toxic in environmentally relevant dosages. The following is a quote from Mesnage[1]

  In an effort to address this gap in commercial GBH toxicity evaluation, a 2-year study was conducted where rats were administered with a Roundup GBH via drinking water at a concentration of 0.1 ppb (0.05 μg/L glyphosate; daily intake 4 ng/kg bw/day), which is an admissible concentration within the European Union (0.1 μg/L) and USA (700 μg/L)18. The results showed that Roundup caused an increased incidence in signs of anatomical pathologies, as well as changes in urine and blood biochemical parameters suggestive of liver and kidney functional insufficiency18.

  Oxidative stress and single-carbon metabolism

   The study be Mesnage et. al. goes on to discuss the contribution of Roundup ( glyphosate  ) to single-carbon metabolism disruption ( oxidative stress) . We have previously noted that disruption of this pathway is the foundation for a number of diseases, currently in epidemic mode, As we mentioned, incidence of coronary artery disease, cancer, lupus and Parkinsons are shown to be connected to methylation capacity ( single carbon metabolism). Of course there are others, including intestinal autoimmune and autism. We should also note that these factors are not necessarily independent. Varibles that affect this  pathway are (non) independent, and may interact strongly with each other in otherwise unpredictable ways, partially as a function of a persons particular genetic makeup.


  The significance of this 2017 study is the term "ultra-low dose".   Notice the abbreviation "ppb" is parts per billion. It really does not take much to get in the parts per billion range. Roundup use at harvest time is threatening for many reasons. Of course less time hurts the ability to decompose, but also cooler temperatures of harvest season could hurt biodegradability.


   Glyhphosate( Roundup )  was never intended to be part of the food supply. It was intended to be a biodegradabale portion of early crop development. With uncontrolled usage it has become a key contaminant in the world food supply.


[1]  Mesnage R1, Renney G2, Séralini GE3, Ward M2, Antoniou MN Multiomics reveal non-alcoholic fatty liver disease in rats following chronic exposure to an ultra-low dose of Roundup herbicide  . Sci Rep. 2017 Jan 9;7:39328.[PubMed Central]

An example of a 6th generation medical science study


 In previous posts, I enumerated the history of medical science paradigms from my point of view. I went on to describe a forthcoming sixth generation.
The underlying sixth generation model consists of a single carbon metabolism cycle that produces glutathione, a convenient biomarker for these studies. Glutathione then is the primary support for DNA methylation by the DNA methyl-transferases, DNMTs.  Study of failure at this level is what is known as  epigenetics study.
 Many disease conditions are now known to be epigenetic in nature. A short list is cancer, lupus, Parkinson's and coronary artery disease.
  An example of what a study of various interacting factors relating to single carbon metabolism is given in Naushad [1].

Whats in that Title?

 The title of Naushad[1] will seem a little unusual so I will discuss just the title for a moment. First of all "multifactor dimensionality reduction" is a term that may be unfamiliar to us old timers. Of course, we are much more familiar with terms like multiple regression and principle component analysis. These "old fashioned" approaches assume that all of the incoming variables are "independent". But what of we don't have a problem that consists of independent variables? In biomedical applications, such as gene/gene interactions or gene/environment interactions, we are looking for a case where the incoming variables are NOT independent. When we find a combination of variables that provides some "zing", then we can start building our model. On other words, we are moving from the world of linear models, to the world of nonlinear models. Lets think of a slot machine. Most of the time, we get a combination that produces no outcome. When the same variables come up "three cherries", we get a big pay out, much bigger that just 3X one cherry, which it typically a zero payout.
   The next term we want to look at is "crosstalk between one-carbon and xeniobiotic metabolic pathways". What this means is that we are going to look at a number of genetic anomalies that may occur in genes that are related to the one-carbon pathway, such as the gene MTHFR, a primary component of the pathway cycling glutathione, 
  The final term is "multi-disease models". In this case, this study is not related to a single medical condition, but four medical conditions,  cancer, lupus, Parkinson's and coronary artery disease, all known to be related to the single-carbon metabolic pathway.


This model that the authors made showed good predictability Parkinson's Disease (PD) and Lupus (SLE). and moderate predictability for breast cancer and Coronary Artery Disease (CAD).
These interaction models showed good predictability of risk for PD (The area under the receiver operating characteristic curve (C) = 0.83) and SLE (C = 0.73); and moderate predictability of risk for breast cancer (C = 0.64) and CAD (C = 0.63).
                                                   Naushad [1] 

Telling us what we know!

Health professionals tell us that we must get a good supply  of vitamins and exercise,   all  of which support good single carbon metabolism. Here we say that genetic components that affect single carbon metabolism are also significant. Good call!.

Direction and suggestion. This type of study and model could be easily extended. For example,  the (non) independent variables (model inputs) could be extended to include known toxins, such as mercury and known nutritional supports, such as folate and vitamin b12. Likewise, dependent variables, or model outputs could autism and Alzheimers.

The immune system (Missing)


 So, amid all the excitement about Naushad ( woohoo ), there is an aspect that is missing. All of the clinical conditions enumerated as dependent variables have immunological components. In the case of cancer, the immunological component is thought to be a natural defense. In the others, such as systemic lupus  erythematosus,  the immune response is part of the disease.
A true 6th generation study, as I have defined them, would also quantify the expression of wingspans antigens, as well as the degree of hypomethylation of the patients DNA.


 Biological systems are very different in nature than economic systems, or social science systems. Our system of statistics has grown up around problems where the "independent variables" are um, "independent". In biomedical systems, models have to built that can handle nonlinear interactions between variables. Presumably, a traditional "principle components" analysis would have been insufficient to model this data.

[1]  Shaik Mohammad Naushad Sana Venkata VijayalakshmiYedluri RupasreeNadella
 Kumudini Sampathkumar Sowganthika Janardhanan Venketlakshmi NaiduM. Janaki RamaiahDunna
 Nageswara raoVijay Kumar Kutala   Multifactor dimensionality reduction analysis to elucidate the cross-talk  between one-carbon and xenobiotic metabolic pathways in multi-disease models
Molecular Biology ReportsJuly 2015, Volume 42, Issue 7, pp 1211–1224  [Abstract]

Tuesday, January 24, 2017

Dear PLOS: Why "vaccines dont cause autism" is not a scientific statement


  The following is a critique of  the article The “Why Vaccines Don’t Cause Autism” Papers
hosted on the Public Library of Science (PLOS) Blog page.

The term vaccine is not specific 

 First of all the term "vaccines" is not scientific. The debate has, in fact for many years, even decades, turned away from the antibody and protein contents of vaccines and turned to mercury, colloidal aluminum, and biological impurities that may include viruses or proteins that were not intended to be in the vaccine. As such, the debate in not vaccines, but vaccine safety. Intravenous delivery bypasses a host of defenses against potential toxins.

Autism is not a scientific term

 Autism essentially means "unusual". In includes  a "spectrum" of individuals ranging from those who are completely incapacitated to those who have Ph. D.s, particularly in technical fields.  In fact in previous years a controversy has arisen over the term  "Aspergers" which includes those on the high performing edge of the so called "spectrum". When these people are classified as autistic, it has the function of burying important variables. Autism is a social science term ( not science at all ). The education system (social science) likes people at the middle of the bell curve, and those at both ends are usually classified as problematic,  at least in the eyes of education system socialists.

 Medical Science has already progressed past nonspecific descriptions

 In what is now considered the base of the argument on vaccines and neurological impact, a vaccine associated "syndrome" is described which includes gastrointestinal autoimmunity and distress in single carbon metabolism. (Wakefield [1] ). This paper detailed elevated methyl-malonic acid, which is a marker for b12 deficiency, or other disruption of single carbon metabolism. Methylation disruption is known to be associated with autoimmunity and neurological defects. I dont believe this paper specifically discusses mercury, but mercury is associated with disruption of single carbon metabolism ( methylation pathways). Many factors affect single carbon metabolism, and as a result DNA methylation. An interaction of factors could obviously disrupt normal development.

Correlation and medical science

  In a previous post, expressly for the purpose of evaluation of the scientific validity of specific arguments in "medical science" terms, I enumerated epistemological generations in medical science. Correlation between raw variables, such as "vaccine" and "autism" is what I would classify as a "Generation 1" argument. That means, no longer part of medical science at all. In the case of Wakefield [1], were specific measurements of single carbon metabolism ( methylmalonic acid level) and histological gastrointestinal pathology ( autoimmune ) are described in medical terms, the appropriate follow up is a Generation 6 study, that means evaluation of more single carbon metabolism and the epigenetic basis of observed autoimmunity.

Statistical arguments are useless serious cases

 Arguments based on statistical outputs are not appropriate in medical cases that involve incapacitation for life. Other statement that are inappropriate are "Russian Roulette works out fine in most cases", and  "generally speaking, apples, peaches, pears, plums and hand grenades are not dangerous." I believe that appropriate term is "confounding" for lost variables in scientific arguments. We are now at about 2 decades of confounded science on the issue of vaccine safety.

Mercury has many sources, and impacts are cumulative

 Mercury may come from amalgam in dental fillings, mothers amalgam in dental fillings, fish, fish mother ate, livestock that was produced with fish meal ( chicken ) other environmental exposure including water and broken light bulbs.   Not to mention,  if several vaccinations are given, and all contained mercury, the impact of the "trace" amounts is cumulative. 


[1] Wakefield et. al. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and
pervasive developmental disorder in children
, the Lancet, 1998 [pdf[