Posted by Rich Van Konynenburg Sat, 16 Apr 2005 22:32:41 -0400 SNPs, enzymes, autism and CFS Sue Bailey asked me, on another list, to enlarge upon the above subject in order to make it easier to understand. I did so, and I'm posting it here as well, in case there are others who are interested: The cells in the body carry out their various functions by means of a large number of different biochemical reactions. The rates of these reactions must be controlled in order to coordinate the overall operation of the cell. This control is most often carried out by enzymes, which serve as catalysts for the reactions. Enzymes are a type of protein, and they are assembled by the cell as strings of amino acids. The particular sequence of amino acids for each enzyme is coded in the gene for that enzyme, made of DNA and located in the nucleus of the cell. DNA consists of a long double-helix molecule that incorporates a sequence of nucleotides, each made up of one of! four bases (thymine, guanine, adenine or cytosine), a sugar ring (deoxyribose) and a phosphate group. A particular sequence of three nucleotides in the DNA molecule codes for each different amino acid to be placed in the enzyme. The rate of an enzyme-controlled biochemical reaction depends on the concentration of the particular enzyme that is present (number of enzyme molecules per unit volume) and the efficiency in promoting the reaction of the particular form of the enzyme that is present. The concentration depends on "gene expression," i.e. the degree to which the gene code for that particular enzyme has been translated into making enzymes. The particular form of the enzyme that is produced depends on whether mutations have occurred in the gene that code for the enzyme. A mutation involves a change in the sequence of nucleotides in the DNA, and it can be caused by a variety of things, including ionizing radiati! on, toxins and viruses. Mutations occur originally in the DNA in th e sperm or ova of a particular person. From there, they are propagated to the descendents of that person, and they become part of the DNA of every nucleated cell in the body, including the germ cells that they pass on to their offspring. We inherit mutations from our father and mother, and we propagate them on to our offspring. If we have inherited a particular mutation from only one of our parents, we are said to be heterozygous for the corresponding allele (version) of the enzyme. If we got the same mutation from both our parents, we are said to be homozygous for that allele. If an allele is of the type that can cause observed effects (phenotype) in a person who is only heterozygous in that allele, it is called a dominant allele. If it is necessary to be homozygous in a particular allele in order to observe phenotypic expression, then it is called a recessive allele. In the case of dominant alleles, if only one parent is het! erozygous in it, half the offspring will show the phenotypic effect. In the case of recessive alleles, if one parent is heterozygous in it, they are called a carrier. In order for offspring to manifest an observable (phenotypic) effect from a recessive allele, both parents must be carriers of that allele, and even then, on the average, only one out of four of their offspring will manifest the observable effect. There are several possible types of mutation. Some mutations render the enzyme completely nonfunctional. If this enzyme is essential for life, such a mutation is fatal. Other mutations cause the affected enzyme to be less efficient than the normal form of the enzyme, in varying degrees, depending on the particular mutation. One class of mutations is called "single nucleotide polymorphisms," or SNPs. In this class, only one nucleotide has been changed in the normal gene for a particular enzyme. This results in a change! of one amino acid in the enzyme that is made from this coded patte rn, out of perhaps hundreds or thousands in the sequence of amino acids making up the enzyme. If a person has a particular SNP, all the copies of the particular enzyme that is coded for by the gene that has this SNP will have this one amino acid changed from the normal enzyme. Depending on where in the sequence this change has been made, it can have a large or a small effect on the enzymes efficiency in promoting its particular biochemical reaction. The entire human genome is currently thought to code for about 25,000 or 30,000 different proteins. Over 1.5 million different SNPs have been found in the entire human genome. We all have some of them. It's just a question of which ones we have. The differences between the set of SNPs that each of us has are important factors that determine biochemical individuality. Among many other things, these differences give us different susceptibilities to various diseases and toxicities. Because of the progress in understanding the human genome and the biotechnology of gene chips, it is now possible to characterize SNPs on a large scale at a relatively low cost. As a result, many studies have been conducted and others are currently underway to study the prevalence of particular SNPs in people who develop various diseases. In choosing which of the many SNPS to study in connection with a particular disease, it is helpful if the pathogenesis is understood, so that the particular reactions that might be important can be known, and hence SNPs in the particular enzymes for these reactions can be sought. Correlations have been found for many diseases, and if the pathogenesis of a particular disease is understood, it is often possible to understand why a particular SNP would make a person more vulnerable to the disease. Conversely, if the pathogenesis is not understood, SNP correlations can provide clues about the part! icular reactions that may be involved in the pathogenesis. In the case of autism, the recently published research by S. Jill James and coworkers showed that there were abnormalities in several of the substances involved with the methionine cycle (also called the methylation cycle) and the transsulfuration pathway in children with autism. These are important in the synthesis of glutathione, which was found to be about 80% depleted in children with autism. Accordingly, Dr. James and coworkers investigated SNPs in these children in various enzymes and other proteins associated with this cycle and pathway, and they found abnormally high prevalences of SNPs in the genes coding for catechol-O-methyltransferase (COMT), transcobalamin II, and glutathione S-transferase M1. The enzyme catechol-O-methyltransferase catalyzes one of the reactions that breaks down epinephrine (adrenaline) and norepinephrine (noradrenaline). A mutation in this enzyme that slows the rate of this reaction would have the e! ffect of allowing epinephrine to rise to higher concentrations and to have a longer lifetime. Since epinephrine has been found in animal experiments to decrease the rate of production of glutathione in the liver as well as to decrease the rate of chemical reduction (recycling) of oxidized glutathione, it seems likely that a COMT SNP would tend to deplete glutathione. Transcobalamin II is the principal protein that binds vitamin B12 after it is absorbed in the small intestine, and carries it in the blood to the various tissues in the body for their use. A mutation in this protein could decrease the transport of vitamin B12, which is used in the methionine cycle to convert homocysteine to methionine. This could also perturb the synthesis of glutathione. The enzyme glutathione S-transferase M1 is one of a family of enzymes that conjugates (links) glutathione to particular toxins to make them more water-soluble, so they can be removed from the body. This is part of Phase II detoxification. T he M1 enzyme has been found in a German study to be more highly mutated in people who are sensitive to thimerosol, which is the mercury-containing preservative used in some vaccines. Thus, a mutation in this enzyme might make it more difficult for a person to use glutathione to remove mercury from their body, and thus make them more susceptible to mercury toxicity. The significance of all this for CFS, in my opinion, is that since glutathione is known to be depleted in many PWCs, and many are found to be elevated in mercury, it is possible that they may have SNPs in one or more of these same proteins. There are several reasons to suspect that there is a genetic susceptibility in many cases of CFS, and such SNPs may account for it. The Great Smokies Diagnostic Lab, in their Genovations testing, currently offers characterization of panels of SNPs in several enzymes and proteins suspected to be important for particular dis! eases. No prescription is required for such characterization. The Great Smokies representative at the recent OHM meeting told me that they are planning to offer tests for individual SNPs, not as panels, in the near future, and this will decrease the cost to people who are interested in only certain ones. They are also planning to add characterizations of more SNPs in different enzymes as the tests for them become commercially available. He told me that they expect that there will be growth in the number of tests of SNPs involving detoxification, because the drug companies are now being required by the FDA to take account of the different responses that different people have to drugs, because of mutations in the enzymes involved with detoxification. I think that there could be a helpful spin-off from this for PWCs, since problems with detox appear to be a feature of many cases of CFS. When particular SNPs are found, it is often possible to compensate for them by increasing the intake of particular vitamins, minerals, or other substances that may support the particular reactions involved as either cofactors for the enzyme, or as substrates for the reaction (Substrates are reactants that are changed into products by the reaction). Dr. Bruce Ames and colleagues at U.C.-- Berkeley have argued that these mutations are the basis for the observed benefits of megadosing particular nutrients by particular people. In the case of the autism work of Dr. James and coworkers, they found that increasing the intake of vitamin B12 (methylcobalamin), folinic acid (the active form of folic acid) and trimethyglycine (also known as betaine) was effective in bringing the glutathione level up to normal in children with autism. Rich Van Konynenburg, Ph.D.