Stress

What will it take for childhood trauma research to change paradigms?

gettingwell4 0-1 star Wasted resources, Brain development, Cortisol, Epigenetics, Hippocampus, Hypothalamus, Limbic system, Memory, Neurochemicals, Serotonin, Stress , , ,

This 2018 German human study found:

“DNA methylation in a biologically relevant region of NR3C1-1F [glucocorticoid receptor gene] moderates the specific direction of HPA-axis dysregulation (hypo- vs. hyperreactivity) in adults exposed to moderate-severe CT [childhood trauma].

In contrast, unexposed and mildly-moderately exposed individuals displayed moderately sized cortisol stress responses irrespective of NR3C1-1F DNA methylation. Contrary to some prior work, however, our data provides no evidence for a direct association of CT and NR3C1-1F DNA methylation status.”

The study was an example of why researchers investigating the lasting impacts of human traumatic experiences won’t find causes, effects, and productive therapies until their paradigms change.

1. Limited subject histories

A. Why weren’t the subjects asked for historical information about their parents, grandparents, and great-grandparents?

The researchers had no problem using animal studies to guide the study design, EXCEPT for animal studies of the etiologic bases of intergenerational and transgenerational transmission of biological and behavioral phenotypes. Just the approximate places and dates of three generations of the German subjects’ ancestors’ births, childhoods, adolescences, and early adulthoods may have provided relevant trauma indicators.

B. Why are studies still using the extremely constrained Childhood Trauma Questionnaire? Only one CTQ aspect was acknowledged as a study design limitation:

“Our findings rely on retrospective self-report measures of CT, which could be subject to bias.”

But bias was among the lesser limiting factors of the CTQ.

The study correlated epigenetic changes with what the subjects selectively remembered, beginning when their brains developed sufficient cognitive functionalities to put together the types of memories that could provide CTQ answers – around age four. The basic problem that kept the CTQ from discovering likely most of the subjects’ traumatic experiences causing epigenetic changes was that these experiences predated the CTQ’s developmental starting point:

  1. A human’s conception through prenatal period is when both the largest and the largest number of epigenetic changes occur, and is when our susceptibility and sensitivity to our environment is greatest;
  2. Birth through infancy is the second-largest; and
  3. Early childhood through the age of three is the third largest.

CTQ self-reports were – at best – evidence of experiences after age three, distinct from the  experience-dependent epigenetic changes since conception. If links existed between the subjects’ early-life DNA methylation and later-life conditions, they weren’t necessarily evidenced by CTQ answers about later life that can’t self-report relevant early-life experiences that may have caused DNA methylation.

2. Limited subject selection

The researchers narrowed down the initial 622 potential subjects to the eventual 200 subjects aged 18 to 30. An exclusion criteria that was justified as eliminating confounders led to this limitation statement:

“Our results might be based on a generally more resilient sample as we had explicitly excluded individuals with current or past psychopathology.”

Was it okay for the researchers to assert:

“Exposure to environmental adversity such as childhood trauma (CT) affects over 10% of the Western population and ranges among the best predictors for psychopathology later in life.”

but not develop evidence for the statement by letting people who may have been already affected by age 30 and received treatment participate in the study?

Was the study design so fragile that it couldn’t adjust to the very people who may be helped by the research findings?

3. Limited consequential measurements

The current study design conformed to previous studies’ protocols. The researchers chose cortisol and specific DNA methylation measurements.

A. Here’s what Sex-specific impacts of childhood trauma had to say about cortisol:

“Findings are dependent upon variance in extenuating factors, including but not limited to, different measurements of:

  • early adversity,
  • age of onset,
  • basal cortisol levels, as well as
  • trauma forms and subtypes, and
  • presence and severity of psychopathology symptomology.”

The researchers knew or should have known all of the above since this quotation came from a review.

B. What other consequential evidence for prenatal, infancy, and early childhood experience-dependent epigenetic changes can be measured? One overlooked area was including human emotions as evidence.

There are many animal studies from which to draw inferences about human emotions. There are many animal models of creating measurable behavioral and biological phenotypes of human emotion correlates, with many methods, including manipulating environmental variables during prenatal, infancy, and early childhood periods.

Studies that take detailed histories may arrive at current emotional evidence for human subjects’ earliest experience-dependent changes. Researchers who correlate specific historical environments and events, stress measurements, and lasting human emotions expressed as “I’m all alone” and “No one can help me” will better understand causes and effects.

CTQ answers weren’t sufficiently detailed histories.

4. Limited effective treatments and therapies

The current study only addressed this area in the final sentence:

“Given their potential reversibility, uncovering epigenetic contributions to differential trajectories following childhood adversity may serve the long-term goal of delivering personalized prevention strategies.”

Researchers – if your paradigms demonstrate these characteristics:

  • Why are you spending your working life in efforts that can’t make a difference?
  • Aren’t your working efforts more valuable than that?
  • What else could you investigate that could make a difference in your field?

I hope that researchers will value their professions enough to make a difference with their expertise. And that sponsors won’t thwart researchers’ desires for difference-making science by putting them into endless funding queues.

http://www.psyneuen-journal.com/article/S0306-4530(17)31355-0/pdf “Glucocorticoid receptor gene methylation moderates the association of childhood trauma and cortisol stress reactivity” (not freely available)

Cell senescence and DNA methylation

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This 2018 Baltimore cell study found:

“Based on similarities in overall methylation patterns in replicative senescence and cancers, it is hypothesized that tumor-promoting DNA methylation in cancers derives from cells escaping senescence.

We show that the tumor-associated methylation changes evolve independently of senescence and are pro-survival events with functional implications contrasting that in senescence.

In our analyses, although overall global gains and losses in DNA methylation are similar, at individual genomic regions the methylation patterns are very different for senescence versus transformation.”

https://www.sciencedirect.com/science/article/pii/S1535610818300084 “DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk” (not freely available)

I hesitated to use the study’s main graphic:
because the “Stochastic” labeling of the upper branch didn’t represent the vector’s meaning. The In Brief and the Summary sections contributed to the misrepresentation by stating:

“transformation-associated methylation changes arise stochastically.”

which wasn’t the study’s main finding:

“Our data outlined in the above sections strongly suggest against this senescence bypass hypothesis.”

Although the experimental design and methods evoked randomness:

“Immortalization on the path to malignant transformation involves stochastic epigenetic patterns from which cells contributing to transformation may evolve.”

the graphic’s upper branch vector represented the cells’ evolutionary responses. The Significance section best characterized what the study found:

“Tumor-associated methylation changes evolve independently of senescence and are pro-survival events.”

Would anyone at John Hopkins argue, as the graphic’s upper branch labeling suggested, that cellular aging is a predominantly random process? NO!

1. Epigenetics research and evolution promoted understanding the graphic’s upper branch vector:

“Evolution is an ongoing set of iterative interactions between organisms and the environment. Directionality is introduced by the agency of organisms themselves.”

2. The current study provided another data point about the uselessness of convenient but non-etiologic, inconsequential measurements of global methylation:

“Although overall global gains and losses in DNA methylation are similar, at individual genomic regions the methylation patterns are very different.”

3. The current study was congruent with the below finding of Using an epigenetic clock to distinguish cellular aging from senescence regarding the differentiation of cellular aging from senescence:

“Cellular ageing is distinct from cellular senescence and independent of DNA damage response and telomere length.”

Sex-specific impacts of childhood trauma

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This 2018 Canadian paper reviewed evidence for potential sex-specific differences in the lasting impacts of childhood trauma:

“This paper will provide a contextualized summary of neuroendocrine, neuroimaging, and behavioral epigenetic studies on biological sex differences contributing to internalizing psychopathology, specifically posttraumatic stress disorder and depression, among adults with a history of childhood abuse.

Given the breadth of this review, we limit our definition [of] trauma to intentional and interpersonal experiences (i.e., childhood abuse and neglect) in childhood. Psychopathological outcomes within this review will be limited to commonly explored internalizing disorders, specifically PTSD and depression.

Despite the inconsistent and limited findings in this review, a critical future consideration will be whether the biological effects of early life stress can be reversed in the face of evidence-based behavioral interventions, and furthermore, whether these changes may relate to potentially concurrent reductions in susceptibility to negative mental health outcomes.”

It was refreshing to read a paper where the reviewers often interrupted the reader’s train of thought to interject contradictory evidence, and display the scientific method. For example, immediately after citing a trio of well-respected studies that found:

“Psychobiological research on relationships linking impaired HPA axis functioning and adult internalizing disorders are suggestive of lower basal and afternoon levels of plasma cortisol in PTSD phenotype.”

the reviewers stated:

“However, a recent meta-analysis suggests no association between basal cortisol with PTSD.”

and effectively ended the cortisol discussion with:

“Findings are dependent upon variance in extenuating factors, including but not limited to, different measurements of:

  • early adversity,
  • age of onset,
  • basal cortisol levels, as well as
  • trauma forms and subtypes, and
  • presence and severity of psychopathology symptomology.”

The reviewers also provided good summaries of aspects of the reviewed subject. For example, the “Serotonergic system genetic research, childhood trauma and risk of psychopathology” subsection ended with:

“Going forward, studies must explore the longitudinal effects of early trauma on methylation as well as comparisons of multiple loci methylation patterns and interactions to determine the greatest factors contributing to health outcomes. Only then, can we start to consider the role of sex in moderating risk.”

I didn’t agree with the cause-ignoring approach of the behavior therapy mentioned in the review. Does it make sense to approach one category of symptoms:

“the biological effects of early life stress”

by treating another category of symptoms?

“can be reversed in the face of evidence-based behavioral interventions.”

But addressing symptoms instead of the sometimes-common causes that generate both biological and behavioral effects continues to be the direction.

After receiving short-term symptom relief, wouldn’t people prefer treatments of originating causes so that their various symptoms don’t keep bubbling up? Why wouldn’t research paradigms be aligned accordingly?

I was encouraged by the intergenerational and transgenerational focus of one of the reviewer’s research:

“Dr. Gonzalez’s current research focus is to understand the mechanisms by which early experiences are transmitted across generations and how preventive interventions may affect this transmission.”

This line of hypotheses requires detailed histories, and should uncover causes for many effects that researchers may otherwise shrug off as unexplainable individual differences. Its aims include the preconception through prenatal periods when both the largest and the largest number of epigenetic changes occur, and is when our susceptibility and sensitivity to our environment is greatest. There are fewer opportunities for effective “preventive interventions” in later life compared with these early periods.

Unlike lab rats, women and men can reach some degree of honesty about our early lives’ experiential causes of ongoing adverse effects. Experiential therapies that allow humans to potentially change their responses to these causes deserve more investigation than do therapies that apply external “interventions.”

https://www.sciencedirect.com/science/article/pii/S0272735817302647 “Biological alterations affecting risk of adult psychopathology following childhood trauma: A review of sex differences” (not freely available) Thanks to lead author Dr. Ashwini Tiwari for providing a copy.

Lysine acetylation is gnarly and dynamic

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This 2018 UC San Francisco cell review provided details of lysine acetylation:

“Lysine acetylation has moved from being a specialized mark on histones to a critical modification controlling cell fate, proliferation, and metabolism.

During the lifetime of a protein there are many points at which an acetyl group may be added to influence function. The dynamic interplay between the writers, erasers, and readers of acetylation regulates critical epigenomic and metabolic processes, in addition to other major cellular functions.

Acetylation sites are well conserved, in contrast to methylation, where species-specific differences exist.”

The review included a section on mitochondrial protein acetylation:

“Mitochondria have emerged as organelles in which acetylation is more prominent than phosphorylation and plays a key role in integrating metabolic cues with the bioenergetic equilibrium of the cell.

Increased mitochondrial protein acetylation is associated with physiological conditions that result in higher levels of acetyl-CoA (e.g., fasting, calorie restriction, high-fat diet, and ethanol intoxication).”

https://pubs.acs.org/doi/full/10.1021/acs.chemrev.7b00181 “Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics” (not freely available) Thanks to lead author Ibraheem Ali for providing a full copy.

An emotional center of our brains

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This 2018 McGill/UC San Diego rodent study subject was the dentate gyrus area of the hippocampus:

“Early life experience influences stress reactivity and mental health through effects on cognitive-emotional functions that are, in part, linked to gene expression in the dorsal and ventral hippocampus. The hippocampal dentate gyrus (DG) is a major site for experience-dependent plasticity associated with sustained transcriptional alterations, potentially mediated by epigenetic modifications.

Peripubertal environmental enrichment increases hippocampal volume and enhances dorsal DG-specific differences in gene expression. Overall, our transcriptome and DNA methylation data support a model of regional and environmental effects on the molecular profile of DG neurons.”

The study thoroughly investigated several areas. I’ll quote a few parts with the section heading.

Introduction:

“The dorsal hippocampus, corresponding to the posterior hippocampus in primates, associates closely with cognitive functions and age-related cognitive impairments. In contrast, the ventral hippocampus, (anterior region in primates) is implicated in the regulation of emotional states and vulnerability for affective disorders. This functional specialization is reflected in patterns of gene expression.”

Results subsections:

“Environmental enrichment promotes hippocampal neurogenesis – hippocampal volume is enlarged in mice raised in an enriched environment (EE) compared with standard housing (SH) in both the dorsal and ventral poles. EE also associates with >60% more newborn neurons.

Specialization of gene expression in dorsal and ventral DG – Gene expression was more affected by EE in dorsal than ventral DG, and dorsal DG has twice as many differentially-expressed genes.

DNA methylation differences between dorsal and ventral DG – Each of the three forms of methylation [CpG, non-CpG, and hmC (hydroxymethylation)] exhibited a distinct genomic distribution in dorsal and ventral DG. A key advantage of whole-genome DNA methylation profiling is the ability to identify differentially methylated regions (DMRs), often far from any gene body, that mark tissue-specific gene regulatory elements.

This strong bias, with ~40-fold more hypomethylated regions in the dorsal DG, contrasts with the balanced number of differentially expressed genes in dorsal and ventral DG, suggesting an asymmetric role for DNA methylation in region-specific gene regulation. Despite their small number, ventral hypomethylated DMRs marked key developmental patterning transcription factors..which are linked to the proliferation, maintenance and survival of neural stem cells.

DNA methylation correlates with repression at some genes – CG and non-CG DNA methylation are associated with reduced gene expression, while hmC associates with increased expression. Dorsal DMRs were also enriched at genes that were up- and down-regulated in EE, although over half of dorsal up-regulated genes, and >98.5% of ventral up-regulated genes, contained no DMRs that could explain their region-specific differential expression.”

Discussion:

  • “a The cell stages occurring within the subgranular zone of the dentate gyrus are shown together with a schematic illustration of possible relative proportions consistent with our data. RGL Radial glia-like progenitor, NSC Neural stem cell.
  • b Key genes associated with the RGL stage are up-regulated in ventral DG relative to dorsal DG.
  • c We propose that mCH [non-CpG methylation] accumulates mainly in mature neurons.”

Why do human brain studies that include the hippocampus overwhelmingly ignore its role in our emotions? For example, the researchers of Advance science by including emotion in research could find only 397 suitable studies performed over 22 years from 1990 to 2011. There were tens or hundreds of times more human brain studies done during the same period that intentionally excluded emotional content!

The current rodent study provided physiological bases for dialing back the bias of human brain research focused exclusively on cognitive functions without also investigating attributes of emotional processing. Let’s see human studies designed to correct this recurring deficiency.

https://www.nature.com/articles/s41467-017-02748-x “Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus”

DNA methylation and childhood adversity

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This 2017 Georgia human review covered:

“Recent studies, primarily focused on the findings from human studies, to indicate the role of DNA methylation in the associations between childhood adversity and cardiometabolic disease in adulthood. In particular, we focused on DNA methylation modifications in genes regulating the hypothalamus-pituitary-adrenal axis as well as the immune system.”

Recommendations in the review’s Epigenetics inheritance and preadaptation theory section included:

“Twin studies offer another promising design to explore the mediation effect of DNA methylation between child adversity and cardiometabolic outcomes..which could rule out heterogeneity due to genetic and familia[l]r environmental confounding.”

As it so happened, the below 2018 study provided some evidence.

http://www.sciencedirect.com/science/article/pii/S0167527317352762 “The role of DNA methylation in the association between childhood adversity and cardiometabolic disease” (not freely available) Thanks to lead author Dr. Guang Hao for providing the full study.

This 2018 UK human study:

“Tested the hypothesis that victimization is associated with DNA methylation in the Environmental Risk (E-Risk) Longitudinal Study, a nationally representative 1994-1995 birth cohort of 2,232 twins born in England and Wales and assessed at ages 5, 7, 10, 12, and 18 years. Multiple forms of victimization were ascertained in childhood and adolescence (including physical, sexual, and emotional abuse; neglect; exposure to intimate-partner violence; bullying; cyber-victimization; and crime).

Hypothesis-driven analyses of six candidate genes in the stress response (

  1. NR3C1 [glucocorticoid receptor],
  2. FKBP5 [a regulator of the stress hormone system],
  3. BDNF [brain-derived neurotrophic factor],
  4. AVP [arginine vasopressin],
  5. CRHR1 [corticotropin-releasing hormone receptor 1],
  6. SLC6A4 [serotonin transporter]

) did not reveal predicted associations with DNA methylation.

Epigenetic epidemiology is not yet well matched to experimental, nonhuman models in uncovering the biological embedding of stress.”

One of the sad findings was that as the types of trauma inflicted by other people on the subjects increased, so did the percentage of subjects who hurt themselves by smoking. Two-thirds of teens who reported three or more of the seven adolescent trauma types also smoked by age 18:

Polyvictimization

Self-harming behaviors other than smoking weren’t considered.

Another somber finding was:

“Childhood sexual victimization is associated with stable DNA methylation differences in whole blood in young adulthood. These associations were not observed in relation to sexual victimization in adolescence.”

The researchers guided future studies regarding the proxy measurements of peripheral blood DNA methylation:

“The vast majority of subsequent human studies, including the present one, have relied on peripheral blood. This choice is expedient, but also scientifically reasonable given the aim of detecting effects on stress-related physical health systems that include peripheral circulating processes (immune, neuroendocrine).

But whole blood is heterogeneous, and although cell-type composition can be evaluated and controlled, as in the present study, it does raise the question of whether peripheral blood is a problematic surrogate tissue for research on the epigenetics of stress.

Comparisons of methylomic variation across blood and brain suggest that blood-based EWAS may yield limited information relating to underlying pathological processes for disorders where brain is the primary tissue of interest.”

1. The comment on “epigenetic epidemiology” overstated the study’s findings because the epigenetic analysis, although thorough, was limited to peripheral blood DNA methylation. Other consequential epigenetic effects weren’t investigated, such as histone modifications and microRNA expression.

2. An unstated limitation was that the DNA methylation analyses were constrained by budgets. Studies like The primary causes of individual differences in DNA methylation are environmental factors point out restrictions in the methodology:

“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 [whole-genome bisulfite sequencing] 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.”

I’d expect that in the future, researchers with larger budgets would reanalyze the study samples using other techniques.

3. The researchers started and ended the study presenting their view of human “embedding of stress” as a fact rather than a paradigm. Epigenetic effects of early life stress exposure compared and contrasted this with another substantiated view.

4. The study focused on the children’s intergenerational epigenetic effects. An outstanding opportunity to advance science was missed regarding transgenerational epigenetic inheritance:

  • Wouldn’t the parents’ blood samples and histories – derived from administering the same questionnaires their twins answered at age 18 – likely provide distant causal evidence for some of the children’s observed effects?
  • And lay the groundwork for hypotheses about aspects of future generations’ physiologies and behaviors?

https://ajp.psychiatryonline.org/doi/full/10.1176/appi.ajp.2017.17060693 “Analysis of DNA Methylation in Young People: Limited Evidence for an Association Between Victimization Stress and Epigenetic Variation in Blood” (not freely available) Thanks to coauthor Dr. Helen Fisher for providing the full study.

Make consequential measurements in epigenetic studies

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The subject of this 2017 Spanish review was human placental epigenetic changes:

“39 papers assessing human placental epigenetic signatures in association with either

  • (i) psychosocial stress,
  • (ii) maternal psychopathology,
  • (iii) maternal smoking during pregnancy, and
  • (iv) exposure to environmental pollutants,

were identified.

Their findings revealed placental tissue as a unique source of epigenetic variability that does not correlate with epigenetic patterns observed in maternal or newborn blood.“

Each study’s confounders were summarized by a column in Table 1. Some of the reviewers’ comments included:

“33 out of 39 papers reviewed (85%) reported significant associations between either placental DNA methylation or placental miRNA expression and exposure to any of the risk factors assessed. However, the methodological heterogeneity present throughout the studies reviewed does not allow meta-analytic exploration of reported findings.

Heterogeneity regarding the origin of biological tissues analyzed confounds the replicability and validity of reported findings and their potential synthesis.”

Sponsors and researchers really have to take their work seriously if the developmental origins of health and disease hypothesis can advance to a well-evidenced theory. Study designers should:

  1. Sample consequential dimensions. “There were no studies examining histone modifications.” Why were there no human studies in this important category of epigenetic changes in the placenta, the “barrier protecting the fetus“?
  2. Correct methodological deficiencies in advance. Eliminate insufficiencies like “Once collected, processing and storage of placental samples also differed across studies and was not reported in all of them.”
  3. Stop using convenient but non-etiologic proxy assays such as global methylation. How can a study advance the DOHaD hypothesis if everyone knows ahead of time that its outcome will be yet another finding that epigenetic changes “are associated with” non-causal factors?
  4. Forget about non-biological measurements like educational attainment per Does a societal mandate cause DNA methylation?.

Every human alive today has observable lasting epigenetic effects caused by environmental factors during the earliest parts of our lives, and potentially even before we’re conceived. Isn’t this sufficient rationale to expect serious efforts by research sponsors and designers?

https://www.sciencedirect.com/science/article/pii/S0892036217301769 “The impact of prenatal insults on the human placental epigenome: A systematic review” (click the Download PDF link to read the paper)

Epigenetics research and evolution

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This 2017 UK essay was a longish review of how epigenetics and other research has informed evolutionary theory:

“There are several processes by which directed evolutionary change occurs – targeted mutation, gene transposition, epigenetics, cultural change, niche construction and adaptation.

Evolution is an ongoing set of iterative interactions between organisms and the environment. Directionality is introduced by the agency of organisms themselves.”

A few takeaway items concerned:

“It is of course the functional phenotype that is ‘seen’ by natural selection. DNA sequences are not directly available for selection other than through their functional consequences.

The comparative failure of genome-wide association studies to reveal very much about the genetic origins of health and disease is one of the most important empirical findings arising from genome sequencing.

Environmental epigenetic impacts on biology and disease include:

  • Worldwide differences in regional disease frequencies
  • Low frequency of genetic component of disease as determined with genome wide association studies (GWAS)
  • Dramatic increases in disease frequencies over past decades
  • Identical twins with variable and discordant disease frequency
  • Environmental exposures associated with disease
  • Regional differences and rapid induction events in evolution“

The above list was from the cited 2016 review “Developmental origins of epigenetic transgenerational inheritance” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933018

Further points about behavior’s role in evolution:

“Differential mutation rates are not essential to enable organisms to guide their own evolution.

If organisms have agency and, within obvious limits, can choose their lifestyles, and if these lifestyles result in inheritable epigenetic changes, then it follows that organisms can at least partially make choices that can have long-term evolutionary impact.”

These discussions provided support for the central question of The PRice “equation” for individually evolving: Which equation describes your life?:

“Applying the “How does a phenotype influence its own change?” question to a person:

How can a person remedy their undesirable traits – many of which are from their ancestral phenotype – and acquire desirable traits?”

http://www.mdpi.com/2079-7737/6/4/47/htm “Was the Watchmaker Blind? Or Was She One-Eyed?”

The pain societies instill into children

gettingwell4 2-3 stars Required further work, Beliefs, Cerebrum, Epigenetics, Memory, Primal Therapy, Stress , , , , ,

The human subjects of this 2017 Swiss study had previously been intentionally traumatized by Swiss society:

“Swiss former indentured child laborers (Verdingkinder) were removed as children from their families by the authorities due to different reasons (poverty, being born out of wedlock) and were placed to live and work on farms. This was a practice applied until the 1950s and many of the Verdingkinder were subjected to childhood trauma and neglect during the indentured labor.

DNA methylation modifications indicated experiment-wide significant associations with the following complex posttraumatic symptom domains: dissociation, tension reduction behavior and dysfunctional sexual behavior.”


https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-017-3082-y “A pilot investigation on DNA methylation modifications associated with complex posttraumatic symptoms in elderly traumatized in childhood”

Imagine being taken away from your family during early childhood for no other reason than your parents weren’t married.

Consider just a few of the painful feelings such a child had to deal with then and ever since:

  • I’m unloved.
  • Alone.
  • No one can help me.

Imagine some of the ways a child had to adapt during their formative years because of this undeserved punishment:

  • How fulfilling it would be to believe that they were loved, even by someone they couldn’t see, touch, or hear.
  • How fulfilling it would be to get attention from someone, anyone.
  • How a child became conditioned to do things by themself without asking for help.

The study described a minute set of measurements of the subjects’ traumatic experiences and their consequential symptoms. The researchers tried to group this tiny sample of the subjects’ symptoms into a new invented category.

Another example was provided in Is IQ an adequate measure of the quality of a young man’s life?:

“During this time period [between 1955 and 1990], because private adoptions were prohibited by Swedish law, children were taken into institutional care by the municipalities shortly after birth and adopted at a median age of 6 mo, with very few children adopted after 12 mo of age.”

Swedish society deemed local institutional care the initial destination for disenfranchised infants, regardless of whether suitable families were willing and able to adopt the infants. What happened to infants who weren’t adopted by age 1?

Did Swedish society really need any further research to know that an adoptive family’s care would be better for a child than living in an institution?

It’s hard to recognize when our own thoughts, feelings, and behavior provide evidence of childhood pain that’s still with us.

Let’s not hope and believe that the societies we live in will resolve adverse effects of childhood trauma its members caused. Other people may guide us, but each of us has to individually get our life back:

“What is the point of life if we cannot feel and love others? Without feeling, life becomes empty and sterile.

It, above all, loses its meaning.“

Every society has its horror stories. People who have reached some degree of honesty about their early lives and concomitant empathy for others can document these terrible circumstances and events.

Have traumatic effects on children from societal policies ceased?

Epigenetic study methodologies improved in 2017

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Let’s start out 2018 paying more attention to advancements in science that provide sound empirical data and methodology. Let’s ignore and de-emphasize studies and reviews that aren’t much more than beliefs couched in models and memes, whatever their presumed authority.

Let sponsors direct researchers to focus on ultimate causes of diseases. Let’s put research of treatments affecting causes ahead of those that only address symptoms.

Here are two areas of epigenetic research that improved in 2017.

Improved methodologies enabled DNA methylation studies of adenine, one of the four bases of DNA, to advance, such as this 2017 Wisconsin/Minnesota study N6-methyladenine is an epigenetic marker of mammalian early life stress:

“6 mA is present in the mammalian brain, is altered within the Htr2a gene promoter by early life stress and biological sex, and increased 6 mA is associated with gene repression. These data suggest that methylation of adenosine within mammalian DNA may be used as an additional epigenetic biomarker for investigating the development of stress-induced neuropathology.”

Most DNA methylation research is performed on the cytosine and guanine bases.

Other examples of improved methodologies were discussed in this 2017 Japanese study Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies:

“A strategy focusing on CpG sites with high DNA methylation level variability may attain an improved efficacy..estimated to be 3.7-fold higher than that of the most frequently used strategy.

With ~90% coverage of human CpGs, whole-genome bisulfite sequencing (WGBS) provides the highest coverage among the currently available DNAm [DNA methylation] profiling technologies. However, because of its high cost, it is presently infeasible to apply WGBS to large-scale EWASs [epigenome-wide association studies], which require DNAm profiling of hundreds or thousands of subjects. Therefore, microarrays and targeted bisulfite sequencing are currently practicable for large-scale EWASs and thus, effective strategies to select target regions are essentially needed to improve the efficacy of epigenetic association studies.

DNAm levels measured with microarrays are invariable for most CpG sites in the study populations. As invariable DNAm signatures cannot be associated with exposures, intermediate phenotypes, or diseases, current designs of probe sets are inefficient for blood-based EWASs.”

A review of biological variability

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This 2017 UK/Spanish review subject was biological variability:

“No two cells in a cellular population are the same, and no two individuals of a multi-cellular species are identical-not even if they share the same genetic makeup like monozygotic twins or cloned animals.

Epigenetic and gene expression variability are key contributors to phenotypic differences. There are many possible sources of epigenetic and transcriptional variability, which can be divided into three main categories:

  1. individual-intrinsic factors;
  2. environmental factors; and
  3. random fluctuations, also referred to as stochasticity.”

Most of the review cited cell studies. The reviewers cited their own studies in the Introduction section, for example:

“These studies were among the first to classify disease status or aggressiveness based on variability, where the classical comparison of mean DNA methylation or gene expression levels was not informative.”

to help support a later observation:

“It is critical to obtain a measurement of variability that is independent of the mean to ensure to not confound changes in variability with shifts in mean.”

The review didn’t cover a pertinent aspect of the subject: how standard research approaches miss detecting biological variability.

For example, from Changing an individual’s future behavior even before they’re born that referred to the methodology of genome-wide association studies (GWAS):

“When phenotypic variation results from alleles that modify phenotypic variance rather than the mean, this link between genotype and phenotype will not be detected.”

Another omission was the point made in A study of DNA methylation and age:

“Due to the methods applied in the present study, not all the effects of DNA methylation on gene expression could be detected; this limitation is also true for previously reported results.

The textbook case of DNA methylation regulating gene expression (the methylation of a promoter and silencing of a gene) remains undetected in many cases because in an array analysis, an unexpressed gene shows no signal that can be distinguished from background and is therefore typically omitted from the analysis.”

The reviewers also didn’t cover variability in phenotypic behaviors. I’ll repeat my thoughts from A limited study of parental transmission of anxiety/stress-reactive traits:

“How did parental behavioral transmission of behavioral traits and epigenetic changes become a subject not worth investigating? These traits and effects can be seen everyday in real-life human interactions, and in every human’s physiology.”

Perhaps these omissions reflected the reviewers’ focus on their specialties?

Perhaps it isn’t politically correct to discuss or fund research on aspects of biological variability that would advance science by falsifying preferred previous findings? Or advance science by measuring the extent of parental involvement in shaping their offspring’s behavioral and biological variability?

What do you think?

http://onlinelibrary.wiley.com/doi/10.1002/bies.201700148/full “Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity”

This post has somehow become a target for spammers, and I’ve disabled comments. Readers can comment on other posts and indicate that they want their comment to apply here, and I’ll re-enable comments.

What’s an appropriate exercise recovery time?

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This 2017 New Zealand human research studied the effect of one supplement on recovery from exercise-induced muscle damage:

“Eccentric exercise is known to bring about microstructural damage to muscle, initiating an inflammatory cascade involving various reactive oxygen species. This, in turn, can significantly impair physical performance over subsequent days. Taurine, a powerful endogenous antioxidant, has previously been shown to have a beneficial effect on muscle damage markers and recovery when taken for a few days to several weeks prior to eccentric exercise.

The amount of powder was set at 0.1 g∙kg−1 body weight∙day−1, based on several studies that found no adverse effects at levels of up to 10 g∙day. No participant was at a body weight that resulted in consuming more than 10 g∙day.

Supplementation with taurine twice daily for 72 h following eccentric exercise-induced muscle damage may improve eccentric performance recovery of the biceps brachii in healthy males.”

My main takeaway from the study came from this finding:

“Our results show that neither treatment group fully recovered force output by 72 h.”

I was surprised to see that even three days wasn’t enough time for a muscle to fully recover. And the study’s subjects were young males:

“Age = 26.5 ± 6.5 years, height = 180 ± 9.2 cm, mass = 80 ± 11.5 kg. All participants were recreationally fit, engaging in exercise 2–3 times per week.”

This gave me pause to reflect on how inattention to cumulative strain may have produced repetitive stress injuries. I’ve adjusted my workout routines accordingly.

The study listed a number of limitations. An unstated one was that nobody should take supplements in quantities that are many times greater than normal dosages without being informed by quality human experimental evidence.

http://www.mdpi.com/2076-3921/6/4/79/htm “The Effect of Taurine on the Recovery from Eccentric Exercise-Induced Muscle Damage in Males”

How to cure the ultimate causes of migraines?

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Most of the spam I get on this blog comes in as ersatz comments on The hypothalamus couples with the brainstem to cause migraines. I don’t know what it is about the post that attracts internet bots.

The unwanted attention is too bad because the post represents a good personal illustration of “changes in the neural response to painful stimuli.” Last year I experienced three three-day migraines in one month as did the study’s subject. This led to me cycling through a half-dozen medications in an effort to address the migraine causes.

None of the medications proved to be effective at treating the causes. I found one that interrupted the progress of migraines – sumatriptan, a serotonin receptor agonist. I’ve used it when symptoms start, and the medication has kept me from having a full-blown migraine episode in the past year.

1. It may be argued that migraine headache tendencies are genetically inherited. Supporting personal evidence is that both my mother and younger sister have migraine problems. My father, older sister, and younger brother didn’t have migraine problems. Familial genetic inheritance usually isn’t the whole story of diseases, though.

2. Migraine headaches may be an example of diseases that are results of how humans have evolved. From Genetic imprinting, sleep, and parent-offspring conflict:

“Evolutionary theory predicts: that which evolves is not necessarily that which is healthy.

Why should pregnancy not be more efficient and more robust than other physiological systems, rather than less? Crucial checks, balances and feedback controls are lacking in the shared physiology of the maternal–fetal unit.“

Both migraine causes and effects may be traced back to natural lacks of feedback loops. These lacks demonstrate that such physiological feedback wasn’t evolutionarily necessary in order for humans to survive and reproduce.

3. Examples of other processes occurring during prenatal development that also lack feedback loops, and their subsequent diseases, are:

A. Hypoxic conditions per Lack of oxygen’s epigenetic effects are causes of the fetus later developing:

  • “age-related macular degeneration
  • cancer progression
  • chronic kidney disease
  • cardiomyopathies
  • adipose tissue fibrosis
  • inflammation
  • detrimental effects which are linked to epigenetic changes.”

B. Stressing pregnant dams per Treating prenatal stress-related disorders with an oxytocin receptor agonist caused fetuses to develop a:

and abnormalities:

  • in social behavior,
  • in the HPA response to stress, and
  • in the expression of stress-related genes in the hippocampus and amygdala.”

1. What would be a treatment that could cure genetic causes for migraines?

I don’t know of any gene therapies.

2. What treatments could cure migraines caused by an evolved lack of feedback mechanisms?

We humans are who we have become, unless and until we can change original causes. Can we deal with “changes in the neural response to painful stimuli” without developing hopes for therapies or technologies per Differing approaches to a life wasted on beliefs?

3. What treatments could cure prenatal epigenetic causes for migraines?

The only effective solution I know of that’s been studied in humans is to prevent adverse conditions like hypoxia from taking place during pregnancy. The critical periods of our physical development are over once we’re adults, and we can’t unbake a cake.

Maybe science will offer other possibilities. Maybe researchers could do more than their funding sponsors expect?

Differing approaches to a life wasted on beliefs

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Let’s start by observing that people structure their lives around beliefs. As time goes on, what actions would a person have taken to ward off non-confirming evidence?

One response may be that they would engage in ever-increasing efforts to develop new beliefs that justified how they spent their one precious life’s time so far.

Such was my take on beliefs embedded in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684598/pdf/PSYCHIATRY2017-5491812.pdf “Epigenetic and Neural Circuitry Landscape of Psychotherapeutic Interventions”:

“Animal models have shown the benefits of continued environmental enrichment (EE) on psychopathological phenotypes, which carries exciting translational value.

This paper posits that psychotherapy serves as a positive environmental input (something akin to EE).”

The author conveyed his belief that wonderful interventions were going to happen in the future. However, when scrutinized, most human studies have demonstrated NULL effects of psychotherapeutic interventions on causes. Without sound evidence that treatments affect causes, his belief seemed driven by something else.

The author cited findings of research like A problematic study of oxytocin receptor gene methylation, childhood abuse, and psychiatric symptoms as supporting external interventions to tamp down symptoms of patients’ presenting problems. Did any of the 300+ cited references concern treatments where patients instead therapeutically addressed their problems’ root causes?

For an analogous religious example, a person’s belief caused him to spend years of his life trying to convince men to act so that they could get their own planet after death, and trying to convince women to latch onto men who had this belief. A new and apparently newsworthy belief developed from his underlying causes:

“The founder and CEO of neuroscience company Kernel wants “to expand the bounds of human intelligence.” He is planning to do this with neuroprosthetics; brain augmentations that can improve mental function and treat disorders. Put simply, Kernel hopes to place a chip in your brain.

He was raised as a Mormon in Utah and it was while carrying out two years of missionary work in Ecuador that he was struck by what he describes as an “overwhelming desire to improve the lives of others.”

He suffered from chronic depression from the ages of 24 to 34, and has seen his father and stepfather face huge mental health struggles.”

https://www.theguardian.com/small-business-network/2017/dec/14/humans-20-meet-the-entrepreneur-who-wants-to-put-a-chip-in-your-brain “Humans 2.0: meet the entrepreneur who wants to put a chip in your brain”

The article stated that he had given up Mormonism. There was nothing to suggest, though, that he had therapeutically addressed any underlying causes for his misdirected thoughts, feelings, and behavior.

So he developed other beliefs instead.

What can people do to keep their lives from being wasted on beliefs? As mentioned in What was not, is not, and will never be:

“The problem is that spending our time and efforts on these ideas, beliefs, and behaviors won’t ameliorate their motivating causes. Our efforts only push us further away from our truths, with real consequences: a wasted life.”

The goal of the therapeutic approach advocated by Dr. Arthur Janov’s Primal Therapy is to remove the force of presenting problems’ motivating causes. Success in reaching this goal is realized when patients become better able to live their own lives.

Epigenetic effects of microRNA on fetal heart development

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This 2017 Australian review’s subject was epigenetic impacts involving microRNA in adverse intrauterine environments, and how these affected fetal heart tissue development:

“We describe how an adverse intrauterine environment can influence the expression of miRNAs (a sub-set of non-coding RNAs) and how these changes may impact heart development. Potential consequences of altered miRNA expression in the fetal heart include; Hypoxia inducible factor (HIF) activation, dysregulation of angiogenesis, mitochondrial abnormalities and altered glucose and fatty acid transport/metabolism.

This feedback network between miRNAs and other epigenetic pathways forms an epigenetics–miRNA regulatory circuit that organizes the whole gene expression profile. The human heart encodes over 700 miRNAs.”

A 2016 review Lack of oxygen’s epigenetic effects also provided a details about hypoxia. Those reviewers importantly pointed out the natural lack of a feedback mechanism to the HIF-1α signaling source, and how this evolutionary lack contributed to diseases.

http://www.mdpi.com/1422-0067/18/12/2628/htm “Adverse Intrauterine Environment and Cardiac miRNA Expression”