Genomic imprinting and growth

This 2018 UK paper reviewed genomic imprinting:

“Since their discovery nearly 30 years ago, imprinted genes have been a paradigm for exploring the epigenetic control of gene expression. Moreover, their roles in early life growth and placentation are undisputed.

However, it is becoming increasingly clear that imprinted gene function has a wider role in maternal physiology during reproduction – both by modulating fetal and placental endocrine products that signal to alter maternal energy homeostasis, and by altering maternal energetic set points, thus producing downstream actions on nutrient provisioning.”

“Imprinted genes in the conceptus produce products that alter maternal resource allocation by:

  1. altering the transport capacity of the placenta;
  2. increasing fetal demand for resources by their action on the intrinsic growth rate; and
  3. signalling to the mother by the production of fetal/placental hormones that modify maternal metabolism.”

Other studies/reviews I’ve curated that covered genomic imprinting are: “Genomic imprinting, growth and maternal-fetal interactions”


This dietary supplement is better for depression symptoms than placebo

This 2018 Italy/UK meta-analysis subject was the use of dietary supplement acetyl-L-carnitine to treat depression symptoms:

“Deficiency of acetyl-L-carnitine (ALC) appears to play a role in the risk of developing depression, indicating dysregulation of fatty acids transport across the inner membrane of mitochondria. However, the data regarding ALC supplementation in humans are limited. We thus conducted a systematic review and meta-analysis investigating the effect of ALC on depressive symptoms across randomized controlled trials (RCTs).

Pooled data across nine RCTs (231 treated with ALC versus 216 treated with placebo and 20 no intervention) showed that ALC significantly reduced depressive symptoms.

In three RCTs comparing ALC versus antidepressants (162 for each group), ALC demonstrated similar effectiveness compared with established antidepressants [fluoxetine (Prozac), duloxetine (Cymbalta), amisulpride (Solian) respectively below] in reducing depressive symptoms. In these latter RCTs, the incidence of adverse effects was significantly lower in the ALC group [79%] than in the antidepressant group.

Subgroup analyses suggested that ALC was most efficacious in older adults..Future large scale trials are required to confirm/refute these findings.”

From the Study selection subsection:

“Studies were excluded if:

  1. did not include humans;
  2. did not include a control group;
  3. did not use validated scales for assessing depression;
  4. did not report data at follow-up evaluation regarding tests assessing depression;
  5. included the use of ALC with another agent vs. placebo/no intervention.”

The Discussion section was informative regarding possible mechanisms of ALC affecting depression, pain, and linked symptoms. Several citations were of a review rather than of the original studies, however.

Research needs to proceed on to investigate therapies that address ultimate causes for depression and pain. Researchers and sponsors shouldn’t stop at just symptoms and symptom relief, notwithstanding the requirement from a statistical point of view for “future large scale trials.”

Here are other acetyl-L-carnitine topics I’ve curated: “Acetyl-L-Carnitine Supplementation and the Treatment of Depressive Symptoms: A Systematic Review and Meta-Analysis” (not freely available)

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

This 2018 German human study found:

“DNA methylation in a biologically relevant region of NR3C1-1F [the 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 enough to put together the types of memories that could provide CTQ answers, around age four. The basic problem prohibiting the CTQ from discovering likely most of the subjects’ historical traumatic experiences that caused epigenetic changes is 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 earlier experience-dependent epigenetic changes. 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 was very conformant 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 is 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. It’s not too big a leap to correlate specific historical environments and events, stress measurements, and lasting human emotions expressed as “I’m all alone” and “No one can help me” to better understand causes and effects.

CTQ answers aren’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.”

So, researchers, if your paradigms demonstrate these characteristics, why are you spending your working life in efforts that can’t make a difference? Isn’t your working life more valuable than that? What else could you investigate that could make a difference in your field?

I hope that the researchers 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. “Glucocorticoid receptor gene methylation moderates the association of childhood trauma and cortisol stress reactivity” (not freely available)

Sex-specific impacts of childhood trauma

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 don’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 where the largest epigenetic effects on an individual are found. 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. The potential of experiential therapies to allow an individual to change their responses to these causes deserves as much investigation as do therapies that apply external “interventions.” “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.

Using an epigenetic clock to assess liver disease

This 2018 UC San Diego human study investigated the capability of the epigenetic clock methodology to detect biological aging with nonalcoholic steatohepatitis (NASH) patients:

“The ability to measure a surrogate marker of liver aging from a peripheral blood sample has broad implications for assessing clinically “silent” chronic diseases, such as NASH, and, potentially, their response to interventions.

In the current study, we validate the utility of the Horvath clock in measuring age acceleration in a defined cohort of NASH patients with moderate to severe liver fibrosis.”

The study demonstrated several aspects of age acceleration and disease conditions, including:

– Use of clinical trial data.

“This study, however, included patients who were part of a clinical trial in which protocol-obtained biopsies were read by a central pathologist (ZG) and morphometric quantification of collagen standardized.”

– Continuous measures were more relevant than “Stage X” measures.

“The findings in the current work are in contrast to an earlier study that found no association of DNAm with the NAFLD activity score or stage of liver fibrosis in patients with NASH. Importantly, that study assessed liver fibrosis based on conventional histological staging only, using the ordinal METAVIR classification. Similarly, we also found no difference in age acceleration between patients with stage 2 and 3 fibrosis according to the NASH Clinical Research Network (CRN) classification.

On the contrary, by evaluating two continuous measures of fibrosis (hepatic collagen content by morphometry and the serum ELF test), which have a greater dynamic range than traditional histological staging, we found that patients with higher age acceleration have increased hepatic fibrosis.”

– Causalities may not necessarily be ascribed.

“Although these reports establish a potential relationship between fibrosis and specific epigenetic modifications, targeted individual CpG sites may not accurately reflect the complex interaction between causal and compensatory measures in chronic diseases such as NASH.” “DNA methylation signatures reflect aging in patients with nonalcoholic steatohepatitis”

DNA methylation and childhood adversity

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. “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. 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 DNA methylation 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. An outstanding opportunity to advance science was missed regarding intergenerational and 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 grandchildren’s physiologies and behaviors? “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.

Can researchers make a difference in their fields?

The purpose and finding of this 2017 UK meta-analysis of human epigenetics and cognitive abilities was:

“A meta-analysis of the relationship between blood-based DNA methylation and cognitive function.

We identified [two] methylation sites that are linked to an aspect of executive function and global cognitive ability. The latter finding relied on a relatively crude cognitive test..which is commonly used to identify individuals at risk of dementia.

One of the two CpG sites identified was under modest genetic control..there are relatively modest methylation signatures for cognitive function.”

The review’s stated limitations included:

“It is, of course, possible that a reliable blood-based epigenetic marker of cognitive function may be several degrees of separation away from the biological processes that drive cognitive skills.

There are additional limitations of this study:

  • A varying number of participants with cognitive data available for each test;
  • Heterogeneity in relation to the ethnicity and geographical location of the participants across cohorts; and
  • Relating a blood-based methylation signature to a brain-based outcome.

A 6-year window [between ages 70 and 76] is possibly too narrow to observe substantial changes in the CpG levels.”

All of these limitations were known before the meta-analysis was planned and performed. Other “possible” limitations already known by the 47 coauthors include those from Genetic statistics don’t necessarily predict the effects of an individual’s genes.

The paper referenced studies to justify the efforts, such as one (cited twice) coauthored by the lead author of A problematic study of DNA methylation in frontal cortex development and schizophrenia:

“Epigenome-wide studies of other brain-related outcomes, such as schizophrenia, have identified putative blood-based methylation signatures.”

Was this weak-sauce meta-analysis done just to plump up 47 CVs? Why can’t researchers investigate conditions that could make a difference in their fields?

Was this meta-analysis done mainly because the funding was available? I’ve heard that the primary reason there are papers like the doubly-cited one above is that the US NIMH funds few other types of research outside of their biomarker dogma.

The opportunity costs of this genre of research are staggering. Were there no more productive topics that these 47 scientists could have investigated?

Here are a few more-promising research areas where epigenetic effects can be observed in human behavior and physiology:

I hope that the researchers value their professions enough to make a difference with these or other areas of their expertise. And that sponsors won’t thwart researchers’ desires for difference-making science by putting them into endless funding queues. “Meta-analysis of epigenome-wide association studies of cognitive abilities”