Epigenetic effects of cow’s milk

This 2015 German paper with 342 references described:

“Increasing evidence that milk is not “just food” but represents a sophisticated signaling system of mammals.

This paper highlights the potential role of milk as an epigenetic modifier of the human genome paying special attention to cow milk-mediated overactivation of FTO [a gene associated with fat mass and obesity] and its impact on the transcriptome of the human milk consumer.”

The author declared “no competing interests” and “There are no sources of funding.” He presumably wasn’t pressured into writing this paper.

The paper wasn’t agenda-free, however. The main thesis was:

“Persistent milk-mediated epigenetic FTO signaling may explain the epidemic of age-related diseases of civilization.”

There were separate sections on how milk may promote:

  • Breast cancer
  • Prostate cancer
  • Obesity
  • Metabolic syndrome
  • Coronary heart disease
  • Early menarche
  • Type 2 diabetes
  • Neurodegenerative diseases

I don’t eat or drink dairy products because I’m lactose-intolerant. I coincidentally don’t have any of the diseases mentioned in the paper.

My life experiences haven’t led me to share the author’s sense of alarm, or to attribute other people’s problems to their consumption of milk products. However, more than a few problems I’ve had are things I’ve done to myself through actions or inaction that may have turned out differently if I had better information.

So I curated this article in case we’re insufficiently informed about the harmful epigenetic effects of milk. What do you think?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687119/ “Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases”

Using twins to estimate the extent of epigenetic effects

This 2015 international study of intellectual disability used human twins to estimate the impact of genetic, shared-environment, and non-shared-environment on the study’s subjects:

  1. “Estimate of 0.46 (95% CI: 0.32–0.60) can be ascribed to genetic factors.
  2. Estimate of 0.30 (95% CI: 0.19–0.41) may be due to environmental factors involved in growing up in the same environment.
  3. The remaining 24% (95% CI: 0.18–0.29) of the difference is due to error of measurement and nonshared environmental influences.”

The primary causes of individual differences in DNA methylation are environmental factors used analysis of the study’s twin subjects’ CpG methylation compared to “CpGs displaying differential methylation in a healthy population (pDMCs)” to estimate:

  1. “37 % of the pDMCs genetic effects
  2. 3 % of the pDMCs had shared environment
  3. The remaining proportion of the non-genetic variance was due to non-shared environment and/or stochastic factors.”

Those researchers performed several additional tests to find and confirm:

“Non-shared environmental DMCs account for 64% of all detected DMCs.”

Comparing the two studies, the current study’s 32%-60% estimate of genetic effects encompassed the second study’s 37% estimate. However, the current study’s researchers treated their 18%-29% non-shared environment estimate as a remainder not warranting further investigation, whereas the second study’s researchers validated their 64% non-shared environment estimate.

Bringing in a third study, a relevant citation from Epigenetic consequences of early-life trauma: What are we waiting for? confirmed the second study’s estimates with a 2000 twin study that found:

“Environmental effects specific to the individual (63%), whilst genetic effects accounted for 37%. Subsequent studies have produced similar results.”

The Increased epigenetic brain capacity is an evolved human characteristic study found:

“The human brain is extensively shaped by its environment no matter its genetics.”

The epigenetic effects of each of our unique experiences of our non-shared environment predominately determine our individual physiology.

http://www.pnas.org/content/early/2015/12/23/1508093112.full.pdf “Discontinuity in the genetic and environmental causes of the intellectual disability spectrum”

Epigenetic consequences of early-life trauma: What are we waiting for?

This 2015 UK human review discussed:

“The progress that has been made by studies that have investigated the relationship between depression, early trauma, the HPA axis and the NR3C1 [glucocorticoid receptor] (GR) gene.

Gene linkage studies for depression, as well as for other common complex disorders, have been perceived by some to be of only limited success; hence the focus on GWAS [genome-wide association studies]. However, even for simple traits, genetic variants identified by GWAS are rarely shown to account for more than 20% of the heritability.

Epigenetic changes are potentially reversible and therefore amenable to intervention, as has been seen in cancer, cardiovascular disease and neurological disorders.”

Five of the review’s references included FKBP5 (a gene that produces a protein that dampens glucocorticoid receptor sensitivity) in their titles, but it wasn’t mentioned in the review itself. A search on FKBP5 also showed human studies such as the 2014 Placental FKBP5 Genetic and Epigenetic Variation Is Associated with Infant Neurobehavioral Outcomes in the RICHS Cohort that found:

“Adverse maternal environments can lead to increased fetal exposure to maternal cortisol, which can cause infant neurobehavioral deficits. The placenta regulates fetal cortisol exposure and response, and placental DNA methylation can influence this function.

Placental FKBP5 methylation reduces expression in a genotype specific fashion, and genetic variation supersedes this effect. These genetic and epigenetic differences in expression may alter the placenta’s ability to modulate cortisol response and exposure, leading to altered neurobehavioral outcomes.”

The authors listed seven human studies conducted 2008-2015 “investigating interactions between methylation of NR3C1, depression and early adversity”:

“Newborn offspring exposed to maternal depression in utero had increased methylation at [a GR CpG site] as well as adverse neurobehavioural outcomes.

Unlike the majority of animal studies examining NR3C1 methylation, many types of potential stressors, sometimes at different developmental stages, have been used to represent early human adversity.

Substantial differences can be expected in the nature of stresses prenatally compared with postnatally, as well as their developmental consequences.”

Seven human studies over the past eight years was a very small number considering both the topic’s importance and the number of relevant animal studies during the period.

Is the topic too offensive for human studies? What makes people pretend that adverse prenatal and perinatal environments have no lasting consequences to the child?

“Many more studies will be needed before effects directly attributable to early life trauma can be separated from those relating to tissue type.

Although investigators have amassed a considerable amount of evidence for an association between differential methylation and HPA axis function in humans, a causal relationship still needs to be fully established.”

Factors that disrupt neurodevelopment may be the largest originators of epigenetic changes that are sustained throughout an individual’s entire lifespan.

Are the multitude of agendas that have resources thrown at them more important than ensuring the well-being of a human before and after they are born?

https://www.researchgate.net/publication/282048312_Early_life_trauma_depression_and_the_glucocorticoid_receptor_gene_-_an_epigenetic_perspective “Early life trauma, depression and the glucocorticoid receptor gene–an epigenetic perspective”

The primary causes of individual differences in DNA methylation are environmental factors

This 2015 Canadian human study by McGill researchers found:

“Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific.

The full scope of environmental variation remains underappreciated.”

The researchers developed their findings using adipose and blood samples from monozygotic and dizygotic twins in the UK Adult Twin registry of Caucasian females aged 40 to 87. The goal of their techniques was to develop:

“A guide to design targeted panels for cost-effective and comprehensive evaluation of only variable methylation in investigated tissues.”

The researchers used whole-genome bisulfite sequencing (WGBS) because:

“Most genome-wide methylation studies of inter-individual variation to date have been biased towards promoter and CpG-dense regions.

A main limitation with studies using the Illumina 450 K array is that the platform only covers ~1.5 % of overall genomic CpGs, which are biased towards promoters and strongly underrepresented in distal regulatory elements, i.e., enhancers.

WGBS offers single-site resolution CpG methylation interrogation at full genomic coverage.

Another advantage of WGBS is its ability to access patterns of non-CpG methylation.”

The researchers provided several examples of how environmental exposure impacted CpG methylation. In one, a pair of monozygotic twins who had both smoked for over 40 years was compared with a monozygotic pair who hadn’t smoked for 20 years. Previous studies’ findings were replicated both as to the patterns of methylation and to methylation of a specific CpG site “involved in asthma with interaction of environmental tobacco smoke.”

http://www.genomebiology.com/content/16/1/290 “Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation”

Epigenetic therapies for cancer

This 2015 commentary on human epigenetic combination therapy for cancer noted:

“Epigenetic therapy is progressively growing in importance as a class of therapies for cancer.

Currently seven drugs are approved by the US FDA for the treatment of a variety of cancers, and target two major epigenetic systems..drugs that inhibit DNA methylation and those drugs that inhibit histone deacetylation.

However, conclusive evidence that these drugs function via an epigenetic mechanism does not exist.”

The authors ended the commentary with a nuanced point:

“The rate of complete response (eradication of the disease and normalization of the bone marrow) was higher with intensive chemotherapy, but the clinical outcome was better with low-dose chronic azacitidine [a DNA methyltransferase inhibitor] treatment.

Perhaps contrasting a killing-the-cancer strategy for intensive chemotherapy versus a modification of the phenotype by epigenetic therapy.”

I can appreciate that cancer researchers wouldn’t provide definitive statements. I’d guess that it may be too late for people diagnosed with cancer to effect “a modification of the phenotype” with the few epigenetic therapies the FDA has currently approved.

I wonder what difficulties existed that caused the authors to state “conclusive evidence that these drugs function via an epigenetic mechanism does not exist.” Did animal studies demonstrate whether preventative actions were effective for “a modification of the phenotype” to a non-cancerous phenotype for the human cancers where epigenetic therapies weren’t curative?

See the Individual evolution page for a discussion about “How does a phenotype influence its own change?”

http://www.futuremedicine.com/doi/abs/10.2217/epi.15.94 “The failure of epigenetic combination therapy for cancer and what it might be telling us about DNA methylation inhibitors”

A problematic study of beliefs and dopamine

This 2015 Virginia Tech human study found:

“Dopamine fluctuations encode an integration of RPEs [reward prediction errors, the difference between actual and expected outcomes] with counterfactual prediction errors, the latter defined by how much better or worse the experienced outcome could have been.

How dopamine fluctuations combine the actual and counterfactual is unknown.”

From the study’s news coverage:

“The idea that “what could have been” is part of how people evaluate actual outcomes is not new. But no one expected that dopamine would be doing the job of combining this information in the human brain.”

Some caveats applied:

  • Measurements of dopamine were taken only from basal ganglia areas. These may not act the same as dopamine processes in other brain and nervous system areas.
  • The number of subjects was small (17), they all had Parkinson’s disease, and the experiment’s electrodes accompanied deep brain stimulation implantations.
  • Because there was no control group, findings of a study performed on a sample of people who all had dysfunctional brains and who were all being treated for neurodegenerative disease may not apply to a population of people who weren’t similarly afflicted.

The researchers didn’t provide evidence for the Significance section statement:

“The observed compositional encoding of “actual” and “possible” is consistent with how one should “feel” and may be one example of how the human brain translates computations over experience to embodied states of subjective feeling.”

The subjects weren’t asked for corroborating evidence about their feelings. Evidence for “embodied states of subjective feeling” wasn’t otherwise measured in studied brain areas. The primary argument for “embodied states of subjective feeling” was the second paragraph of the Discussion section where the researchers talked about their model and how they thought it incorporated what people should feel.

The study’s experimental evidence didn’t support the researchers’ assertion – allowed by the reviewer – that the study demonstrated something about “states of subjective feeling.” That the model inferred such “findings” along with the researchers’ statement that it “is consistent with how one should “feel” reminded me of a warning in The function of the dorsal ACC is to monitor pain in survival contexts:

“The more general message you should take away from this is that it’s probably a bad idea to infer any particular process on the basis of observed activity.”

The same researcher who hyped An agenda-driven study on beliefs, smoking and addiction that found nothing of substance was back again with statements such as:

“These precise, real-time measurements of dopamine-encoded events in the living human brain will help us understand the mechanisms of decision-making in health and disease.”

It’s likely that repeated hubris is one way researchers respond to their own history and feelings, such as their need to feel important as mentioned on my Welcome page.

The Parkinson’s patients were willing to become lab rats with extra electrodes that accompanied brain implantations to relieve their symptoms. Findings based on their playing a stock market game didn’t inform us about “mechanisms of decision-making in health and disease” in unafflicted humans. As one counter example, what evidence did the study provide that’s relevant to healthy humans’ decisions to remain healthy by taking actions to prevent disease?

The unwarranted extrapolations revealed a belief that the goal of research should be to explain human actions by explaining the actions of molecules. One problem caused by the preconceptions of this widespread belief is that it leads to study designs and models that omit relevant etiologic evidence embedded in each of the subjects’ historical experiences.

This belief may have factored into why the subjects weren’t asked about their feelings. Why didn’t the study’s design consider as relevant subject-provided evidence for feelings? Because the model already contrived explanations for feelings underlying the subjects’ actions.

http://www.pnas.org/content/113/1/200.full “Subsecond dopamine fluctuations in human striatum encode superposed error signals about actual and counterfactual reward”

Assessing epigenetic origins of allergies and asthma

This 2015 German paper described the study design of a birth cohort that’s being established to:

“Assess potential associations between early-life exposures and onset of childhood asthma and allergies taking into account epigenetics.

The study builds upon an existing cohort which has been recruited [1995] and in the meantime has been followed up twice [2002 and 2007].

This approach provides the unique opportunity to assess the effects of genetic predisposition, epigenetic factors, and environmental factors such as exposure to environmental tobacco smoke, living conditions, and parental occupation in a prospective and cross-generational study.”

The paper had informative references, one of which was the 2013 Epigenetic mechanisms and models in the origins of asthma:

“We need to determine whether epigenetics should be considered as a major integrator of multiple signals, or, alternatively, whether DNA methylation acts differently at various developmental stages conditional on genetic variants and exposures.

In addition, since there is a lack of critical knowledge on which genes are programmed or re-programmed at what time during gestation and in which developmental phase, birth cohort studies need to trace DNA methylation over time, and ideally over generations.

This will provide critical information about which phases in the course of life are most suitable to prevent deviant DNA methylation (preventive epigenomics) or intervene to normalize DNA methylation to prevent disease (pharmaco-epigenomics).”

I was encouraged by the referenced review’s emphasis that researchers start their investigations at the beginning of human life for causes that produce later-life effects. The subsequent emphasis on prevention was commendable.

The review also revealed the prevalent researcher bias, that the causal and curative results of human disease will be found on the molecular level rather than in human experiences. This preconception leads to ignoring human elements that generate epigenetic changes that manifest themselves in symptoms such as asthma and allergies.

I don’t know how including human emotions in studies became viewed as unscientific, but here we are. I didn’t see any indication that the study design of the birth cohort included investigating emotional states other than possibly work-related stress.

The researchers will have to pretend that proven etiologic factors such as the emotional states of a pregnant woman have no affect on the nervous and immune system development of her fetus. These human elements are unjustified exclusions from a study designed in 2015, but they’re easily ignored when they aren’t measured.

Here’s a search of what Dr. Arthur Janov had to say about allergies over the past eight years. A representative sample from earlier this month was:

“Every therapy we try will be temporary, something we need to do over and over again.

It can be nothing else because the imprint has the force of survival, of a lifesaving memory and must endure until the life-endangering imprint is finally fully felt and resolved.

Clearly this applies to many problems, from high blood pressure to asthma and allergies.

That is why it is urgent that we re-focus on the real problem.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670515/ “Establishing a birth cohort to investigate the course and aetiology of asthma and allergies across three generations – rationale, design, and methods of the ACROSSOLAR study”

Fat made rats fat with dysfunctional brains

This 2015 New York rodent study found:

“Early stage [diet-induced] obesity, before the onset of diabetes or metabolic syndrome, produced deficits on cognitive tasks that require the prefrontal cortex.

These results strongly suggest that obesity must be considered as a contributing factor to brain dysfunction.”

The difference in the diets of the adult male subjects was that the control group ate 10% fat (20% protein, 70% carbohydrates) whereas the obese group ate 45% fat (20% protein, 35% carbohydrates). Significant changes in body weight were present after the first two weeks on the diets, but testing didn’t begin until after eight weeks.

I thought the study design prematurely terminated the experiments. The study didn’t justify the ultimate purpose of conducting rodent experiments, which is to find possible human applicability.

One study design possibility would have been to continue through old age to find how the conditions progressed. Another possibility would have been to reverse the high-fat diet to find whether the conditions reversed.

http://www.pnas.org/content/112/51/15731.full “Obesity diminishes synaptic markers, alters microglial morphology, and impairs cognitive function”

Testing the null hypothesis of psychological therapy

What forms of medicine don’t require an etiological approach, other than psychology and psychiatry?

This 2015 UK human study found:

“Supported cCBT [computerised cognitive behaviour therapy] does not substantially improve depression outcomes compared with usual GP [general practitioner] care alone.

In this study, neither a commercially available nor free to use computerised CBT intervention was superior to usual GP care.”

Subjects had concurrent access to most of the relevant UK health system:

“We imposed no constraints on usual GP care in the control or intervention groups, and participants were therefore free during the trial to access any treatment usually available in primary care, including the use of antidepressants, counselling, psychological services (including Improving Access to Psychological Therapy services, which were present in most sites during the course of the trial), or secondary care mental health services.”

The study’s null hypothesis was developed as follows:

“We based our sample size calculation on the usual care arm of primary care depression trials, where the proportion of patients responding to usual care was in the region of 0.6. This proportion is similar to that found in a UK Health Technology Assessment trial of antidepressants in primary care.

We regarded a figure of not more than 0.15 below this proportion as being acceptable, given the additional care options that are available to patients who do not initially respond to cCBT within a stepped care framework. In our original calculation, to detect non-inferiority with the percentage success in both groups as 60% and a non-inferiority margin of 15% with over 80% power and assuming 25% attrition, we required 200 participants in each of the three arms.”

The study’s null hypothesis was: the two cCBT methods wouldn’t improve on the “60%” “success” of both “the usual care arm” and “antidepressants in primary care.”

What outcome does a person desire when they seek out psychological care? I’d guess that their first need would be to stop their current suffering.

From a patient’s short-term perspective, the null hypothesis – any form of psychological therapy in the UK healthcare system wouldn’t improve their short-term condition – is likely to be initially disproved.

So, what accounts for the 40% failure rate? Or, as phrased in Psychological therapy and DNA methylation:

“Although CBT has been established as an efficacious treatment, roughly 40% of children retain their disorder after treatment.”

The treatments’ methods aren’t capable of anything more than temporarily suppressing symptoms. But the symptoms return, and require further interventions in order to stay suppressed.

From a patient’s long-term perspective, what would it take to disprove the null hypothesis – any form of psychological therapy in the UK healthcare system wouldn’t improve their long-term condition?

To effectively treat patients in the long term, and to prevent future suffering, the originating causes need to be addressed. IAW, hold psychological therapy to the same standard of care expected in other medical treatments.

http://www.bmj.com/content/351/bmj.h5627 “Computerised cognitive behaviour therapy (cCBT) as treatment for depression in primary care (REEACT trial): large scale pragmatic randomised controlled trial”

Beliefs about medical treatments affected perceived stress

This 2015 New Zealand human study found:

“Placebo effects can be translated to a real-life setting in the short-term reduction of stress, anxiety and symptoms of depression in a non-patient population.

In treating psychological distress, placebos may be useful addition to the treatment repertoire.

The researchers provided a self-administered 3-day course of fake “anti-stress treatment spray” and told the participants the spray was either “oxytocin” or “serotonin” with these results:

“Both the ‘serotonin’ and ‘oxytocin’ treatment sprays were effective in reducing symptoms of depression; however, only those in the ‘oxytocin’ group reported less stress and anxiety as compared with controls. Overall, the ‘oxytocin’ was perceived as more effective.”

Will this study of non-patients be used to try to justify manipulating patients’ perceptions of their stress, anxiety, and depression?

http://anp.sagepub.com/content/early/2015/12/16/0004867415621390 “A take-home placebo treatment can reduce stress, anxiety and symptoms of depression in a non-patient population”