Excerpt 1) “Among the study’s key findings were some 317 epigenetic modifications significantly more prevalent in people with head and neck cancers and the four most common that were more prevalent in blacks and whites, primarily in a half-dozen biological pathways.”
Excerpt 2) “Researchers also found several related epigenetic alterations – molecular modifications of nuclear DNA—in the PAX pathway, primarily at PAX1 and PAX5, where a chemical process called methylation blocks tumor-suppressing gene activity, silencing the gene.”
My comment: Note how the epigenetic modifications, alterations, and molecular modifications of nuclear DNA are referred to as genetic mutations in the title of this article. Mutations and epigenetic changes then appear to be used interchangeably in the article:
Excerpt 3) ‘For cancers originating at the back of the mouth, or oropharynx, blacks had significantly more NOTCH1 mutations than whites, at 67 percent and 14 percent, respectively. Outside the oropharynx, however, the reverse occurred, with no blacks and 18 percent of whites having a NOTCH1 mutation. PAX1 and PAX5 epigenetic alterations were similarly reversed depending on tumor location, with PAX1 methylation in 52 percent of blacks and in 62 percent of whites…”
My comment: In the agouti mouse, nutrient-dependent parent-of-origin genomic imprinting is a non-Mendelian inherited epigenetic form of gene regulation. It involves changes in DNA methylation and histone alterations, which are heritable during cell division.
In this news article, nutrient-dependent alternative splicings associated with DNA methylation and histone alterations seem to get lost in a confusion of terms. Are the alternative splicings “mutations” or are they epigenetically-effected adaptations? That question can be placed into the context of conserved molecular mechanisms that enable adaptations. However, conserved molecular mechanismst may also contribute to diseases when they are overwhelmed by nutrient stress or social stress.
Stress-induced changes in expression of the single functional allele of an imprinted gene that was parent-of-origin dependent seems likely to contribute to transgenerational epigenetic inheritance of increased susceptibility to developmental and behavioral disorders. These disorders include diabetes and cancer. They may have epigenetic origins that are tractable to sex differences in yeasts, which have been attributed to differences in glucose uptake. In mammals, however, current theory suggests a male vs female parent-of-origin dependent control of the amount of nutrients extracted from the mother by her offspring.
Researchers who are confused about the role conserved molecular mechanisms play in nutrient-dependent alternative splicings that enable the epigenetic landscape to become the physical landscape of DNA with transgenerational effects in species from microbes to man are less likely to grasp the difference between a mutation and an adaptation. Yet here, we have an example: genomic imprinting is portrayed as if it arose in mammals via the evolution of the placenta and advent of viviparity. Get it? The entirety of nutrient-dependent adaptations just became part of the portrayal of mutation-driven evolution, when no experimental evidence has ever indicated that mutations cause anything but diseases and disorders — if they cause anything at all.
Indeed, mutations may be maintained in the genome so long as they do not perturb its functional ability to allow epigenetic effects that are adaptive, as mutations obviously do in cases of diseases and disorders. That fact simply attests to another fact, namely that the effects of nutrition on the epigenome are not limited only to the fetal stage of development, but may also influence early infant and childhood development that is associated with diseases and disorders manifested later in life.
Excerpt 3) “Our research goal is to figure out how all of these ethnically predisposing genetic markers interact; how they turn off and on in response to environmental stimuli such as inflammation and lifestyle factors including smoking and nutrition, and how they trigger cancers of the head and neck,” says Guerrero-Preston.”
I think it would be best if researchers first develop a model-based approach to diseases and disorders that includes differentiating what is typical from what is atypical. Nutrient-dependent epigenetically-effected alternative splicings are typical. Mutations are not.
Indeed, for all we know, mutations that cause diseases and disorders may arise because nutrient-dependent alternative splicings failed to delete them from the genome. But researchers are not going to determine whether that is the case until they can grasp the difference between an adaptation and a mutation.