A self-referencing study of transgenerational epigenetic inheritance

This 2018 Washington rodent study subject was transgenerational epigenetic inheritance of disease caused by a fungicide that’s been phased out or banned for over a decade:

“This study was designed to help understand how three different epigenetic processes in sperm are correlated with vinclozolin-induced epigenetic transgenerational inheritance of disease.

  1. Most DMRs [differential DNA-methylated regions] identified in this study are unique between the F1, F2, and F3 generations.
  2. The number of lncRNA was much higher than the number of sncRNA [small noncoding RNA, including microRNA]. The overlap between each generation was very low or nonexistent.
  3. The F1 and the F2 generation control versus vinclozolin lineage sperm had negligible DHRs [differential histone retention sites]. This observation suggests that the direct vinclozolin exposure does not alter histone retention or trigger any changes. However, the F3 generation control versus vinclozolin lineage sperm DHRs increased considerably.

It appears that the phenomenon is more complex than just a direct exposure triggering the formation of epimutations that are then simply maintained in the subsequent generations.”


There’s something odd about a study where a third of the 87 cited references list one of the study’s coauthors, who also coauthored A review of epigenetic transgenerational inheritance of reproductive disease. I couldn’t find a satisfactory explanation for the study’s over-the-top self-referencing.

What do you think?

I asked the coauthors why a third of the cited references were self-referencing. The lead author replied:

“The field in epigenetic transgenerational inheritance is expanding, however it is still hard for us to find relevant studies in rodents or human that we can cite. Most of the time DNA methylation, ncRNA and histone modifications are investigated from a direct exposure and/or from a purely mechanistic angle (e.g. DNA methylation of specific genes).

In contrast, transgenerational phenotypes and toxicology by definition excludes direct exposure and must be transmitted through multiple generations (the F3 generation is the first transgenerational one). We are not looking at specific genes but using whole genome sequencing technologies which is a broader approach.

Besides, if you do a pubmed search with the keywords “epigenetics” and “transgenerational”, you will probably find that more than 50% of the studies have been done by Dr Michael K. Skinner. He is also one of the first researcher who started to work on the epigenetic transgenerational inheritance phenomenon 15 years ago. Not citing his previous work is challenging.

We hope to see other labs contributing to this particular field and we will be delighted to cite them. In the meantime, our only option is to reference our previous work.”

I replied:

“Thank you for your reply! It must be exasperating to see other researchers stop their studies short of the F3 generation for no apparent or disclosed reason.

Have you seen even one scientifically adequate human study of transgenerational epigenetic inheritance?”

https://academic.oup.com/eep/article/4/2/dvy010/4987173 “Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease”

Immune memory in the brain

This 2018 German rodent study was a proof-of-principle for immune epigenetic memory in the brain:

“Innate immune memory is a vital mechanism of myeloid [bone marrow] cell plasticity that occurs in response to environmental stimuli and alters subsequent immune responses.

Two types of immunological imprinting can be distinguished – training and tolerance. These are epigenetically mediated and enhance or suppress subsequent inflammation, respectively.

Certain immune stimuli train blood monocytes to generate enhanced immune responses to subsequent immune insults. By contrast, other stimuli induce immune tolerance — suppression of inflammatory responses to subsequent stimuli.

Microglia (brain-resident macrophages) are very long-lived cells. This makes them particularly interesting for studying immune memory, as virtually permanent modification of their molecular profile appears possible. Immune memory in the brain is predominantly mediated by microglia.

In a mouse model of Alzheimer’s pathology, immune training exacerbates cerebral β-amyloidosis and immune tolerance alleviates it; similarly, peripheral immune stimulation modifies pathological features after stroke. Our results identify immune memory in the brain as an important modifier of neuropathology.

Immune memory in the brain could conceivably affect the severity of any neurological disease that presents with an inflammatory component, but this will need to be studied for each individual condition.”


The researchers performed multiple experiments to test different hypotheses about how immune-response experiences are remembered. Modifications to histone methylation and acetylation were targeted.

The dosage of the stimulus needed to produce immune tolerance was usually four times the immune training dosage.

https://www.nature.com/articles/s41586-018-0023-4 “Innate immune memory in the brain shapes neurological disease hallmarks” (not freely available)

Resiliency in stress responses

This 2018 US Veterans Administration review subject was resiliency and stress responses:

Neurobiological and behavioral responses to stress are highly variable. Exposure to a similar stressor can lead to heterogeneous outcomes — manifesting psychopathology in one individual, but having minimal effect, or even enhancing resilience, in another.

We highlight aspects of stress response modulation related to early life development and epigenetics, selected neurobiological and neurochemical systems, and a number of emotional, cognitive, psychosocial, and behavioral factors important in resilience.”

The review cited studies I’ve previously curated:


There were two things I didn’t understand about this review. The first was why the paper isn’t freely available. It’s completely paid for by the US taxpayer, and no copyright is claimed. I recommend contacting the authors for a copy.

The second was why the VA hasn’t participated in either animal or human follow-on studies to the 2015 Northwestern University GABAergic mechanisms regulated by miR-33 encode state-dependent fear. That study’s relevance to PTSD, this review’s subject, and the VA’s mission is too important to ignore. For example:

“Fear-inducing memories can be state dependent, meaning that they can best be retrieved if the brain states at encoding and retrieval are similar.

“It’s difficult for therapists to help these patients,” Radulovic said, “because the patients themselves can’t remember their traumatic experiences that are the root cause of their symptoms.”

The findings imply that in response to traumatic stress, some individuals, instead of activating the glutamate system to store memories, activate the extra-synaptic GABA system and form inaccessible traumatic memories.”

I curated the research in A study that provided evidence for basic principles of Primal Therapy. These researchers have published several papers since then. Here are the abstracts from three of them:

Experimental Methods for Functional Studies of microRNAs in Animal Models of Psychiatric Disorders

“Pharmacological treatments for psychiatric illnesses are often unsuccessful. This is largely due to the poor understanding of the molecular mechanisms underlying these disorders. We are particularly interested in elucidating the mechanism of affective disorders rooted in traumatic experiences.

To date, the research of mental disorders in general has focused on the causal role of individual genes and proteins, an approach that is inconsistent with the proposed polygenetic nature of these disorders. We recently took an alternative direction, by establishing the role of miRNAs in the coding of stress-related, fear-provoking memories.

Here we describe in detail our work on the role of miR-33 in state-dependent learning, a process implicated in dissociative amnesia, wherein memories formed in a certain brain state can best be retrieved if the brain is in the same state. We present the specific experimental approaches we apply to study the role of miRNAs in this model and demonstrate that miR-33 regulates the susceptibility to state-dependent learning induced by inhibitory neurotransmission.”

Neurobiological mechanisms of state-dependent learning

“State-dependent learning (SDL) is a phenomenon relating to information storage and retrieval restricted to discrete states. While extensively studied using psychopharmacological approaches, SDL has not been subjected to rigorous neuroscientific study.

Here we present an overview of approaches historically used to induce SDL, and highlight some of the known neurobiological mechanisms, in particular those related to inhibitory neurotransmission and its regulation by microRNAs (miR).

We also propose novel cellular and circuit mechanisms as contributing factors. Lastly, we discuss the implications of advancing our knowledge on SDL, both for most fundamental processes of learning and memory as well as for development and maintenance of psychopathology.”

Neurobiological correlates of state-dependent context fear

“Retrieval of fear memories can be state-dependent, meaning that they are best retrieved if the brain states at encoding and retrieval are similar. Such states can be induced by activating extrasynaptic γ-aminobutyric acid type A receptors (GABAAR) with the broad α-subunit activator gaboxadol. However, the circuit mechanisms and specific subunits underlying gaboxadol’s effects are not well understood.

Here we show that gaboxadol induces profound changes of local and network oscillatory activity, indicative of discoordinated hippocampal-cortical activity, that were accompanied by robust and long-lasting state-dependent conditioned fear. Episodic memories typically are hippocampus-dependent for a limited period after learning, but become cortex-dependent with the passage of time.

In contrast, state-dependent memories continued to rely on hippocampal GABAergic mechanisms for memory retrieval. Pharmacological approaches with α- subunit-specific agonists targeting the hippocampus implicated the prototypic extrasynaptic subunits (α4) as the mediator of state-dependent conditioned fear.

Together, our findings suggest that continued dependence on hippocampal rather than cortical mechanisms could be an important feature of state-dependent memories that contributes to their conditional retrieval.”


Here’s an independent 2017 Netherlands/UC San Diego review that should bring these researchers’ efforts to the VA’s attention:

MicroRNAs in Post-traumatic Stress Disorder

“Post-traumatic stress disorder (PTSD) is a psychiatric disorder that can develop following exposure to or witnessing of a (potentially) threatening event. A critical issue is to pinpoint the (neuro)biological mechanisms underlying the susceptibility to stress-related disorder such as PTSD, which develops in the minority of ~15% of individuals exposed to trauma.

Over the last few years, a first wave of epigenetic studies has been performed in an attempt to identify the molecular underpinnings of the long-lasting behavioral and mental effects of trauma exposure. The potential roles of non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) in moderating or mediating the impact of severe stress and trauma are increasingly gaining attention. To date, most studies focusing on the roles of miRNAs in PTSD have, however, been completed in animals, using cross-sectional study designs and focusing almost exclusively on subjects with susceptible phenotypes.

Therefore, there is a strong need for new research comprising translational and cross-species approaches that use longitudinal designs for studying trajectories of change contrasting susceptible and resilient subjects. The present review offers a comprehensive overview of available studies of miRNAs in PTSD and discusses the current challenges, pitfalls, and future perspectives of this field.”

Here’s a 2017 Netherlands human study that similarly merits the US Veterans Administration’s attention:

Circulating miRNA associated with posttraumatic stress disorder in a cohort of military combat veterans

“Posttraumatic stress disorder (PTSD) affects many returning combat veterans, but underlying biological mechanisms remain unclear. In order to compare circulating micro RNA (miRNA) of combat veterans with and without PTSD, peripheral blood from 24 subjects was collected following deployment, and isolated miRNA was sequenced.

PTSD was associated with 8 differentially expressed miRNA. Pathway analysis shows that PTSD is related to the axon guidance and Wnt signaling pathways, which work together to support neuronal development through regulation of growth cones. PTSD is associated with miRNAs that regulate biological functions including neuronal activities, suggesting that they play a role in PTSD symptomatology.”


See the below comments for reasons why I downgraded this review’s rating.

https://link.springer.com/article/10.1007/s11920-018-0887-x “Stress Response Modulation Underlying the Psychobiology of Resilience” (not freely available)

The truth about complex traits and GWAS

This 2017 Colorado analysis, “No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes,” found:

“A recent analysis of 25 historical candidate gene polymorphisms for schizophrenia in the largest genome-wide association study [GWAS] conducted to date suggested that these commonly studied variants were no more associated with the disorder than would be expected by chance.

However, the same study identified other variants within those candidate genes that demonstrated genome-wide significant associations with schizophrenia. As such, it is possible that variants within historic schizophrenia candidate genes are associated with schizophrenia at levels above those expected by chance, even if the most-studied specific polymorphisms are not.

As a group, variants in the most-studied candidate genes were no more associated with schizophrenia than were variants in control sets of noncandidate genes. While a small subset of candidate genes did appear to be significantly associated with schizophrenia, these genes were not particularly noteworthy given the large number of more strongly associated noncandidate genes.

The history of schizophrenia research should serve as a cautionary tale to candidate gene investigators examining other phenotypes: our findings indicate that the most investigated candidate gene hypotheses of schizophrenia are not well supported by genome-wide association studies, and it is likely that this will be the case for other complex traits as well.”


One reason I admire scientists is that many of them are genuinely interested in advancing science. They eventually expose the storytelling and directed narratives in reviews such as:

They uncover questionable methods and moneygrubbing to fund research with a goal of confirming sponsors’ biases such as:

They impartially examine evidence supporting agendas and personal aggrandizements in studies such as:

Unbiased facts and analyses are eventually reported by these dedicated scientists. The problem is that their works aren’t on page 1 of journals and search results.

https://www.biologicalpsychiatryjournal.com/article/S0006-3223(17)31772-9/fulltext “No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes” (not freely available)

Are there epigenetic causes for sexual orientation and gender identity?

This US 2018 review lead author was a gynecologic oncologist in private practice:

“Sexual orientation is biologically conferred in the first trimester of pregnancy. Gender identity is biologically conferred during the middle trimester of pregnancy.

Since the genitals differentiate in the first trimester, and the brain becomes imprinted in the latter half of gestation, it is possible for the fetal brain to be imprinted differently than the genitals. As children mature, this innate imprinting expresses as genital anatomy, gender identity, sexual orientation and other physiologic capabilities and natural preferences along a continuum, between masculine and feminine.

The evidence shows that both orientation and identity are biologic features that co-vary with a very large number of other biologic sexually dimorphic traits.”


1. A fetus’ development is influenced by survival reactions to their environment. Although fetal and placental responses to environmental stressors are relevant to sexual orientation and gender identity, the reviewers didn’t explore the subject.

2. Epigenetic adaptations to the prenatal environment involving microRNA were mentioned in a small subsection. But the reviewers didn’t cite relevant studies involving DNA methylation, chromatin and histone modifications for epigenetic causes of and effects on sexual orientation and gender identity.

3. The reviewers included a half-dozen anecdotal quotations from personal correspondence that promoted their narrative. These impressed as appeals to authority rather than evidence for scientific understanding of the subject.

It was insufficient for the review to note “a continuum between masculine and feminine” without also exploring evidence for an individual’s placement on the continuum. The question of possible epigenetic causes for sexual orientation and gender identity remains.

https://www.sciencedirect.com/science/article/pii/S009082581731510X “Biological origins of sexual orientation and gender identity: Impact on health” (not freely available)

Faith-tainted epigenetics

This 2018 Loma Linda review subject was epigenetic interventions for aging:

“Epigenomic markers of aging, global DNA hypomethylation and promoter-specific hypermethylation may be engendered by iron and HCys [homocysteine] retention.

MiR-29/p53 axis may reverse age-related methylomic shifts, stabilizing both the genome and the epigenome, therefore removing a major risk factor of neurodegeneration. Lowering iron and HCys overload can be accomplished via chelation, blood donation and maintaining an adequate omega-6/omega-3 ratio.”


Sometimes it’s difficult to detect researchers’ biases. If a reader didn’t know about the funding sponsor’s mission:

“Each day we seek to extend the teaching and healing ministry of Jesus Christ”

they may view this paper as unbiased rather than as a directed narrative.

Consider the sponsor’s influence from the perspective of someone seeking treatment for Alzheimer’s disease. If a doctor in this review sponsor’s hospital system recommended chelation treatment, hope would be generated for the patient. Adopting the doctor’s belief about the treatment, though, would be contrary to other evidence per this review:

“In 2008, the NIH chelation trial stopped enrolling patients, approximately two years early.

There is no indication for exposing patients with dementia to the risks of chelation therapy because current chelators cannot help them.”

After reading another review that had this sponsor – The lack of oxygen’s epigenetic effects on a fetus – which also reflected the influence of the sponsor’s biases, and had a directed narrative that ignored evidence contradicting the narrative, and involved storytelling, I’m done curating any paper sponsored by this institution.

http://www.nrronline.org/downloadpdf.asp?issn=1673-5374;year=2018;volume=13;issue=4;spage=635;epage=636;aulast=Sfera;type=2 “Epigenetic interventions for brain rejuvenation: anchoring age-related transposons” (click the pdf button)