Cancer Initiation

Thursday, April 27, 2017

What is a "Generation Zero" Study?

Introduction

  In a previous post, I somewhat arbitrarily ranked scientific epistemological frameworks, or paradigms, based upon the level of technology underlying concept of "proof". In this article, I am going to discuss published studies, that are "level Zero", or do not intend, or incapable of providing any level of "proof" to an underlying natural system. I am going to throw these examples into three categories, case studies, reviews, and pseudo-science.

The "Case Study"

  The case study is important, particularly in medicine because it provides the medical community with an "alert" to a situation which may be in some way novel. A case study does not necessarily state a statistical "proof" of a natural principle, it is merely what we might call "descriptive". Purely descriptive studies have been around since Newton and Galileo, and there is nothing wrong with them, but they do not attempt to use method, control, repetition and statistics to implore the reader as to a causal relationship. A case study may introduce data, but does not necessarily invoke statistics to determine a correlation between factors, or a causal relationship. Non the less, as many factors as possible should be included in the study, in order to hopefully include the correct direction for further study.

A scientific literature "Review"

    A review is an article that typically introduces no new data, but aggregates findings in previous studies into an organized package, typically for educational purposes. A university "Journal Club" may have various literature based groups that meet to discuss current articles. A journal club meeting might typically discuss a topical contribution in the field as well as a "review" article to provide an understanding of the current state of knowledge in a particular field. For example, if researches intend to discuss a paper on treatment of cancer with tumeric, they might first discuss other papers about the medical affects of tumeric, and observations of their known effects on cancer cells.

Pseudo-Science


  Pseudo science in this context  is a published paper which purports to provide additional information on causal  relationships related to a scientific or medical concept, and yet introduces no new data, offers no statistical insight.  This can be thought of an extension to the definition in the field of philosophy that is commonly referenced.  Very often a pseudo-scientific paper may misrepresent known relationships for the purpose of promoting the acceptance of a particular understanding that is beneficial to a related party. This can work many different ways including attempting to provide evidence for a relationship where there is none ( in the case of potential therapeutics ) or providing evidence for NO relationship where a factor is thought to be hazardous.  An interesting quite is from our Stanford philosophy link:
  Some forms of pseudo-science have as their main objective the promotion of a particular theory of their own, whereas others are driven by a desire to fight down some scientific theory or branch of science. The former can be called pseudo-theory promotion and the latter science denial(ism). Pseudo-theory promotion is exemplified by homeopathy, astrology, and ancient astronaut theories. The term “denial” was first used about the pseudo-scientific claim that the Nazi holocaust never took place. The phrase “holocaust denial” was in use already in the early 1980s (Gleberzon 1983). The term “climate change denial” became common around 2005 (e.g. Williams 2005). Other forms of science denial are relativity theory denial, tobacco disease denial, hiv denialism, and vaccination denialism.

Of particular interest in this quote is that "vaccination denialism" is considered a form of pseudo-science by Stanford philosophers. Given that existing framework, it is only interesting to look at current "pro-vaccine" literature using the current epistemological framework of medical science.

  An example of a "Generation Zero" Case study of current interest

 The foundation of current controversy in medical pediatrics is the case study produced by Dr. Andrew Wakefield and a dozen or so colleagues. [1]  Dr. Wakefield is a gastro-interologist, so it is within his field to report on what his group perceives as a group of unusual cases of "Ileal-lymphoid-nodular hyperplasia.  The Ilium is a portion of the intestines or gastro-intestinal tract ( GI ) , which contains lymph nodes ( lymphoid-nodular )  which can become infected or inflamed ( hyperplasia ).
The "pervasive developmental disorder" that Dr. Wakefield was speaking of is more commonly called autism. The findings were presented as follows :
Onset of behavioural symptoms was associated, by the parents, with measles, mumps, and rubella vaccination in eight of the 12 children, with measles infection in one child, and otitis media in another. All 12 children had intestinal abnormalities, ranging from lymphoid nodular hyperplasia to aphthoid ulceration.
The controversy here is the statement "Onset of behavioral symptoms was associated by the parents, with measles, mumps and rubella vaccination in 8 of the 12 children, with measles infection in one child and otitis media in another.". Although Wakefield and associates made no formal statement of correlation or causation,  the words "associated, by the parents" was enough to trigger pseudo-science accusations and retraction retraction.
  A word about probability and statistics here. The probability of throwing a 1 on a 6 face die is 1/6. The probability of throwing two 1's in a row is 1 / ( 6X6 ) or 1/36. At the time ( before 1998 ) autism was fairly rare, it was not the organizing principle of nearly every public schools system. Lets say 1 in 500, Non-specific colitis, or intestinal inflammation at the clinical level was also fairly rare, lets say also 1 in 500. The probability that these two conditions would occur together, by random coincidence would be 0.000004 . The probability that a dozen or so "0.000004" 's would show up to the same GI a the same time is near zero ( assuming one could get much closer to zero ) . Without saying anything else, this is a valid reason for a "case study" or generation zero description of medical observations.

Syndrome Observations

 For obvious statistical reasons then it became  imperative for the pharmaceutical community to shoot down the observation of autism occurring in conjunction with colitis. The observation has held up though. This from the Dan Marino Autism Research Institute

The Marino Autism Research Institute, or MARI, has funded the science behind ViTA DMF, as well as groundbreaking research linking gastrointestinal issues to ASD. MARI also funds the Marino Scholars Program at Vanderbilt University. This program promotes interdisciplinary training in neuroscience for future researchers and clinicians.

The interpretation presented by Wakefield 

The findings, as worded by  Wakefield were :
We identified associated gastrointestinal disease and developmental regression in a group of previously normal children, which was generally associated in time with possible environmental triggers. [1]
The term "environmental triggers here is meant to mean one or more components of the MMR vaccine or a deficiency in vitamin b12. Elevated urinary methyl-malonic acid was noted an a subset of the children, and this is known to be the strongest marker for vitamin b12 deficiency. I should note here, that in other posts related to autism, auto-immunity and related conditions, I note that vitamin b12 and folate are the necessary inputs that the single carbon metabolism system works on. In other words, Dr. Wakefields wording here is consistent with everything we have observed for the past 20 years.

The Emergence of "Data-Free" "evidence-based" findings

This battle is far from over. in 2017, fully 20 years after the original Wakefield case study, industrial psychologists are still battling over the "environment", meaning non-genetic factors as a cause of autism.  For example, lets look at a "molecular Autism" paper presented by Modabbernia [2].

First of all Modabbernia's title contains the phrase "evidence-based review". The title of the paper itself is a mangling of the difference between a "review" paper and an investigation paper.  The obvious intent is to present itself as an investigation without collecting any data.  A "meta-analysis" is a term that has become popular in politics in the context of a "poll of polls". Unless you have a new method of analyzing existing data, which of course might be interesting, there is no such thing outside of a plain old review.

The "evidence-free" summary of Modabbernai's work is as follows:
Current evidence suggests that several environmental factors including vaccination, maternal smoking, thimerosal exposure, and most likely assisted reproductive technologies are unrelated to risk of ASD.
The reason for providing no evidence is also clearly stated. Its because after 20 years, there in no interest in collecting data that might rock the boat. This is how that is stated.
 Compared to genetic studies of ASD, studies of environmental risk factors are in their infancy and have significant methodological limitations. Future studies of ASD risk factors would benefit from a developmental psychopathology approach, prospective design, precise exposure measurement, reliable timing of exposure in relation to critical developmental periods and should take into account the dynamic interplay between gene and environment by using genetically informed designs.

The above conclusion of "unrelated risk" is based upon a rewording of the study as shown here related to mercury and thimerosal:
 In a meta-analysis of nine studies, Yoshimasu et al. [47] found precise and consistent evidence for lack of association between childhood thimerosal exposure and ASD. The lack of association was consistent in pooled analysis of the adjusted estimates, studies of anti-RhD antibody treatment, and studies of direct thimerosal exposure. In a meta-analysis of three case-control studies, the same authors reported a 60% increase in risk of ASD following higher level of inorganic mercury exposure. Based on their findings, the authors suggested that early life exposure to mercury by vaccination did not increase the risk of ASD, whereas exposure to inorganic mercury in the environment might be associated with an increased risk of ASD (Table 1).

Here the authors are saying that mercury was correlated with autism but not "ethyl-mercury" or thimerosal. There is a presumption ( usually considered false ) that ethyl mercury does not dis-associate into inorganic mercury when it is administered as a vaccine preservative.  That is "yes, but the mercury must have come from somewhere else so  no relationship".

There are other studies that are available that have actual data that do show a relationship between heavy metals ( mercury, lead ) and autism. This from Mohamed [3]
 Results. The mean Levels of mercury, lead, and aluminum in hair of the autistic patients were significantly higher than controls. Mercury, lead, and aluminum levels were positively correlated with maternal fish consumptions, living nearby gasoline stations, and the usage of aluminum pans, respectively. Conclusion. Levels of mercury, lead, and aluminum in the hair of autistic children are higher than controls. Environmental exposure to these toxic heavy metals, at key times in development, may play a causal role in autism. [3]

Conclusion

  Reviews and meta-analysis pseud science are currently being used to pad the literature with reports purporting to be investigations. They consist of lack of relevant data relative to their conclusions, omission of relevant data and misrepresentation of relevant data.

References


[1] Dr AJ Wakefield, et. al. : , Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and
pervasive developmental disorder in children 
The Lancet, 1998  [Full Text]

[2]  Modabbernia A, Velthorst E, Reichenberg A Environmental risk factors for autism: an evidence-based review of systematic reviews and meta-analyses.  Mol Autism. 2017 Mar 17;8:13. eCollection 2017.[PubMed Central]

[3] Mohamed Fel B, Zaky EA, El-Sayed AB, Elhossieny RM, Zahra SS, Salah Eldin W,
Youssef WY, Khaled RA, Youssef AM.Assessment of Hair Aluminum, Lead, and Mercury in a Sample of Autistic  Egyptian Children: Environmental Risk Factors of Heavy Metals in Autism. Behav Neurol. 2015;2015:545674. [PubMed Central]


Thursday, March 30, 2017

A wave of cancer has (again) hit the sea turtles of Florida

Introduction


   Today we go on a Spring Break trip to the Gumbo Limbo Nature Center in Boca Raton, Florida. I was pleasantly greeted by the wonderful volunteers there, but all is not well. Getting right to the point, we (I) are informed that about 70 percent of green sea turtles (Chelonia mydas ) that come into the facility arrive with varying degrees of fibropapillomatosis. As the link shows, this is the name given to cancerous growths, or tumors that arise on sea turtles. Within the facility, infected turtles are referred to as "FP" infected.

 Welcome to Gumbo Limbo Nature Center  of Boca Raton!
The  exact cause of the tumors is not yet known. The local research center in Boca Raton is Florida Atlantic University, and they have provided a report on FP as long ago as 2001 [1].  It is now regarded to be at the intersection of a few factors. One of them is a herpes virus that is specific to sea turtles [2]. Although a viral vector is known to be driving tumor growth, that is not the whole story. The virus is thought to be ancient, and like many other members of the herpes virus family, it has co-evolved with the sea turtle, so it is species specific. So then, healthy turtles have immune systems that make them resistant to this virus. On the other hand, when infected turtles are discovered and recovered, during the process of rehabilitation, they have found to be immune-suppressed.[1]. Sea turtles have a family of white blood cells that is much like humans, and cell counts of these leukocytes have found them to be below normal.. For the sake of this article, that is the definition of immune-suppressed.


 A plastic model of FP ( with cotton balls representing neoplasms )  on display

 

The Mystery


  So then, the mystery is what causes the immuno-suppression that leads to the turtles inability to defend itself from the virus? Unfortunately, there are many potential causes, and most likely, it is not a single cause but a combination or summation that may in fact be different for each turtle. Known causes of turtle stress are, abnormal weather, ( reptiles are at the mercy of the environment for their temperature regulation ), nutrient runoff, heavy metal accumulation ( mercury, lead, arsenic ) , and pesticides and herbicides.

 This is Jade. notice that there is a melon sized growth on his port stern. Jade is currently awaiting surgery

Turtles as a model system.


 We have previously discussed the interaction between environmental factors such as nutrition and exposure to toxins and the immune system. Because we have many of the same factors here, the case of the sea turtle cancer epidemic is relevant, at least in a research sense, to cancer epidemics in humans.  As a model system, the exact causes of this epidemic could probably be easily found if the proper resources were applied.  Although, the turtles are merely wild life, the lessons learned from solving this problem would be easily translatable to humans. We are really no better at addressing human cancer epidemics than we are addressing wildlife epidemics.


According to their status chart, Gumbo Limbo currently has 3 turtles that are infected with FP. Jade is labeled in the upper right hand corner.

As a close up of the key shows, red dots mean FP ( fibropapilloma ) positive


A close up view of the melon sized tumor on Jade.

 

Discussion


   The story of the green sea turtles plight is actually very relevant to issues facing humans. Viral vectors are also responsible for some  tumors in humans, and we are in most cases, reliant upon our immune systems to protect us. The study of how these causative factors interact to create cancer would ultimately help our understanding of medical issues facing humans.

 Acknowledgments


  Thanks to the volunteers at the Gumbo Limbo Nature Center for their dedication and the time they spent with me to explain their operation, and even take some close up pictures for me.  The most profoundly affected turtles are off limits to the general public.

 

References


[1]Lutz, P. L.; Cray, C.; Sposato, P. L. . Studies of the association between
immunosuppression and fibropapillomatosis within three habitats of Chelonia mydas

(Report). Southwest Fisheries Science Center. [pdf]

[2]Lackovichl et. al Association of herpesvirus with fibropapillomatosis of the green turtle Chelonia  mydas and the loggerhead turtle Caretta caretta in Florida  Diseases of Aquatic Organisms Vol. 37: 89-97, 1999 l  [pdf]


Friday, March 3, 2017

The "False Flag" hypothesis and cancer defense


Introduction

 In the field of psychological operations, or "psyops", a "false flag" operation is one in which a group of government backed  insurgent actors  mount an operation in order to trigger a larger operation in the opposite direction. It turns out, that "false flag" defenses exist in the molecular world too, and may in fact be as ancient as the origin of the species.
  We have previously discussed carbohydrates, or glycosylation in terms of cell-cell recognition, and argue that these systems of carbohydrate "flags" are in fact fossils from a very early phase in the evolution of life. The term "fossils", to my knowledge as first coined by Hal White in relation to nucleotide type co-enzymes that are involved in cellular respiration [1]. I have included a discussion on that hypothesis, that is "rna world" type stuff, because carbohydrate signalling, regulatory RNA and many other "non canonical" concepts are important to studying and understanding cancer progression.

  We have previously described the rattlesnake hypothesis as a system of cancer defense where by a number of protein cell surface antigens are epigenetically suppressed in somatic cells, but are expressed in cancerous cells. As triggering the immune system to distressed cells seems to be their only function, they are merely referred to in literature as cancer - testis antigens ( CTA ) , where the testis is the only other tissue where they are found in large quantity. Cancer and testis is quite a mouthful, so here we say Wingspans antigens.
  Here we describe yet another apparent cancer defense which we are going to call the "false flag" defense. In biology we usually think of bacterial cells as having large amounts of polysaccarides ( chains of sugar molecules ) on their surface , or cell wall. This is also called endotoxin, as it triggers a possibly deadly  ( sepsis ) reaction in humans and a few other mammals such as rabbits.
  The "false flag" hypothesis states that mammals such has humans also have the capability to place polysaccarides on their surface that "look like" pathogens, but the glycosyl-transferases, or enzymes used to construct these surface structures are epigenetically suppressed ( expression is blocked by DNA methylation )  in somatic cells. When the maintenance duplication of DNA methylation patterns fails, as in the case of a cancerous clone of cells, these glycosyl-transferases become expressed, and the resulting cell surface antigens are impacted.

The Forssman antigen in Streptococcus pneomoniae

  The Forssman antigen is a cell surface carbohydrate structure discovered and named for -- Forssman. It was originally discovered as a ABO type antigen on sheep blood cells. The genes for construction of the antigen are actually closely related to ABO blood type antigens. The genes associated with antigens like the Forssman antigens are called glycosyl-transferases, because they  encode amino acid sequences for enzymes which in turn are used to construct carbohydrates. In this sense, the term "glycosyl" refers to a sugar or carbohydrate molecule and "transferase" means "enzyme that moves or constructs". In the case of the Forssman antigen (Fs), the constructed carbohydrate is on the cell surface, or membrane.

Cancer and the Forssman Antigen 

Recently (2014), the Forssman Antigen has been reported to be expressed in ovarian cancer. [3]  The specific glycosyl transferase is known as GBTG1. In the words from Jacob[3]:
The GBGT1 gene encodes the globoside alpha-1,3-N-acetylgalactosaminyltransferase 1. This enzyme catalyzes the last step in the multi-step biosynthesis of the Forssman (Fs) antigen, a pentaglycosyl ceramide of the globo series glycosphingolipids.
Expression  and construction of Fs is interesting because it was previously known as an antigen that causes a spontaneous immunologic reaction in humans. That is, if shee form an l immunological reaction, or agglutinate.  What we presume here is that in cells of the body ( somatic cells ) the expression of GBTG1 is blocked by methylation of the appropriate promoter on the DNA. Thus, in the title to Jacob [3] we see the term "epigenetically regulated". Presumably then, when a clone of cancer cells looses control of its cell cycle, the appropriate DNA methylation is lost on successive generations of cells. The appropriate cancer biology term for this is "global hypomethylation" which translates to "everywhere not enough DNA methylation".

Streptococcus pneumoniae and bacterial defense

 The next important thing to known about Fs is that it is expressed in the cell wall of infectious bacteria, including streptococcus pneumoniae, the infectious agent associated with pneumococcal pneumonia, and meningitis. Since our blood reacts with this antigen, when our immune system is healthy, we are immune to this pathogen, it is a factor when a person becomes immuno-compromised. For the sake of providing some additional background on the immunological status of pneumococcus, I give you Gisch [4]. This is a pretty technical paper, but lets look at an operational term for the sake of our argument.
We here also describe for the first time that the terminal sugar residues in the pnLTA (Forssman disaccharide; α-D-GalpNAc-(1→3)-β-D-GalpNAc-(1→)), responsible for the cross-reactivity with -Forssman antigen antibodies, can be heterogeneous with respect to its degree of phosphorylcholine substitution in both O-6-positions.
What this is saying is that there is a carbohydrate ( disacharride ) which as a particular structure that  causes a reaction with the "anti-Forssman" components of blood, or antibodies. The purpose of this paper it to refine the exact structure of Fs.

The bigger picture

What we want to do now is to combine these two concepts from different areas of research, cancer research and  immunology/biochemistry and come up with a new concept. We see that the Forssman antigen is normally not expressed ( epigenetically repressed ) in tissues such as the ovary, but becomes expressed when that repression fails due to loss of control of the cell cycle. Thus, for the sake of this article, we say that the cancerous cells raise a "false flag". We call it a false flag because the immune system is already primed to launch a counter attack. The cancerous clone of cells looks like an invading infection of pneumococcus. Thus the cancer defense system is in a sense riding piggy back on the bacterial defense system. Its an economy. We might also guess that antibodies to the Forssman antigen would inhibit cancer. This too has been investigated. [5] .( Desselle, 2012)

Summary and Conclusion

Here we introduced the Forssman antigen as a carbohydrate cellular marker that is found in the prokaryot kingdom on streptococcus pneumoniae and found in human cancer cells as a result of loss of promoter methylation. The innate portion of the immune system contains an immunoglobin portion known as complement which is reactive with the Forssman antigen, and thus renders healthy individuals immune to streptococcus pneumoniae. The Forssman antigen was long thought to be absent or inactive in humans, but more recently has been found to be expressed on cancer cells as a result of loss of suppression by promoter methylation  ( epigenetic suppression ) .  The point here is that loss of suppression, presumably as a result of "global hypomethylation" leads to cancer cells which are reactive with the compliment component of the innate immune system, and as such, the immune system is activated against the cancer cells in what we refer to here as a "false flag" defense.

References


[1] White H.B. (1976). Coenzymes as fossils of an earlier metabolic state. Journal of Molecular Evolution,7, 101-104 [Abstract]

[2] Graf, J Glycosylaton of extra-cellular matrix proteins as fossils of an earlier metabolic state, Cancer Initiation, 2015 [here]

[3] Jacob F, Hitchins MP, Fedier A, Brennan K, Nixdorf S, Hacker NF, Ward R, Heinzelmann-Schwarz VA. Expression of GBGT1 is epigenetically regulated by DNA methylation in ovarian cancer cells. BMC Mol Biol. 2014 Oct 7;15:24. [PubMed Central]

[4]  Nicolas Gisch, Thomas Kohler, Artur J. Ulmer, Johannes Müthing,
Thomas Pribyl, Kathleen Fischer, Buko Lindner, Sven Hammerschmidt and Ulrich Zähringer
Structural Reevaluation of Streptococcus pneumoniae Lipoteichoic Acid and New
 Insights into Its Immunostimulatory Potency
May 31, 2013 The Journal of Biological Chemistry 288, 15654-15667. [JBC]


[5] Desselle A, Chaumette T, Gaugler MH, Cochonneau D, Fleurence J, Dubois N, Hulin P, Aubry J, Birkle S, Paris F. Anti-gb3 monoclonal antibody inhibits angiogenesis and tumor development. PLoS One. 2012;7(11):e45423. [PMC free article] [PubMed] 



Friday, February 10, 2017

Extending our G6 Model for neuro-developmental abnormalaties

Introduction


  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] 


Conclusion

 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

References


[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

Introduction


 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.

Discussion 


  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 ) .

References


[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

Introduction

   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]

Bingo!

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.

Discussion


   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.


Conclusion


   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.

References


[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

Introduction


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.

Conclusion


   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.

References


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