2-3 stars Required further work

Research needing further work

Telomerase activity outside of telomere maintenance

gettingwell4 2-3 stars Required further work, Immune system, Telomeres

This 2016 Singapore review was on the role of telomerase in cancers. From its background section:

“Telomeres are conserved, repetitive sequences located at the ends of eukaryotic chromosomes which protect the integrity of genomic DNA. DNA polymerase is unable to replicate the 5′ [carbon number] ends of chromosomes, hence, cells require a RNA dependent DNA polymerase called telomerase to synthesize DNA on the lagging strand. Telomerase activity is tightly regulated and seen mainly in germ cells, stem cells and some immune cell types which have high proliferative needs.

In contrast, somatic cells do not display detectable telomerase activity. As a result, the chromosomes of normal somatic cells shorten 50–200 bp [base pair] each replication at the telomeres due to the problem of end replication. Thus, somatic cells are eventually burdened with DNA damage, replication crisis, cellular senescence or apoptosis and can divide only limited number of times, whereas cells that have active telomerase possess unlimited proliferative potential.”

The main section of the review described the details of how:

“Reactivation of telomerase has been considered as a strategy for telomere maintenance and is a major hallmark of cancer. Although the major function of telomerase is thought to be telomere elongation, accumulating evidence has suggested that it can modulate expression of various genes which affect cancer progression and tumorigenesis.”

http://link.springer.com/article/10.1007/s00018-016-2146-9/fulltext.html “Reactivation of telomerase in cancer”

Epigenetics research that was designed to fall one step short of wonderful

gettingwell4 2-3 stars Required further work, Epigenetics

This 2015 Edinburgh rodent study found:

“In utero exposure of rats to the analgesics indomethacin or acetaminophen, both of which target PG [prostaglandin] pathways, alters fetal germ cell number and development in both male and female fetuses. This results in modest but detrimental effects on F1 [children] female, but not F1 male, fertility in adulthood.

Fetal (F1) exposure of rats to either analgesic resulted in an effect in the second generation (F2 grand-daughters) that manifested as reduced ovarian size and markedly reduced follicle number in females but with evidence of increased follicle activation. The impact on F2 fertility (which was not studied) is unclear.

Our analgesic exposure regimen coincided with the period of chromatin/epigenetic remodelling of the (F1) fetal germ cells in both sexes, events which also occur in the human in the first trimester of pregnancy. The analgesic effects on F2 ovaries were transmitted via both paternal and maternal F1 lines.”

The limitations section showed that the rodents’ acetaminophen dosage was equivalent to a human overdose:

“We administered only a single dose of analgesics. The dose of acetaminophen which we used, resulted in blood levels of acetaminophen 2.5- to 8-fold higher than the levels reported in humans after normal therapeutic dosing (~60 mg/kg/day, divided into 4 doses) during pregnancy.”

I’m puzzled that the researchers didn’t take one more step, and design a great study. They knew what the additional effort would be, per statements such as:

“The impact on F2 fertility (which was not studied) is unclear.

The analgesic-induced reduction in fetal ovarian germ cell number was of particular concern, as the lifetime complement of oocytes is formed in utero at/around the time of birth in women and rodents.”

F3 great-grandchildren were needed to demonstrate “the impact on F2 fertility.” Testing of F3 great-grandchildren may have also provided evidence for or against transgenerational epigenetic inheritance, because those subjects’ cells would have had no direct exposure effects from analgesics.

Weren’t the researchers at the MRC Centre for Reproductive Health, The Queen’s Medical Research Institute University of Edinburgh, interested in understanding whether or not a pregnant woman who overdosed during her fetus’ early development on an analgesic available to billions of people, could potentially adversely affect not only her (F0) and her children’s (F1) and grandchildren’s (F2) reproductive health, but also her F3 great-grandchildren?

Weren’t the researchers interested in being a part of a great study, one that may have advanced science, one that may have shown whether or not epigenetic information was transmitted between generations in the absence of continued analgesic exposure?

http://www.nature.com/articles/srep19789 “Analgesic exposure in pregnant rats affects fetal germ cell development with inter-generational reproductive consequences”

Are hormone ratios useful in explaining health? Behavior? Neurobiology? Anything?

gettingwell4 2-3 stars Required further work, Cortisol, Neurochemicals, Stress, Testosterone

This 2015 Zurich human review addressed:

“A remarkable lack of discussion on the meaning and interpretation of frequently used hormone ratios.

The interpretation of hormone ratios is complicated and in many cases not sufficiently supported from a theoretical point of view.

Based on the assumption that the balance between two interdependent hormones determines their eventual effects on brain and other tissues, this index has been commonly interpreted as an indicator of the balance between two endocrine systems.

The ratio is typically calculated by simply dividing the raw value of one hormone by the raw value of a second hormone. However, endocrine parameters may fluctuate considerably within individuals across short periods of time on the basis of circadian rhythms or contextual factors. Nevertheless, the ratio method has so far only rarely been applied in the context of repeated endocrine assessments.”

The researchers made a non-exhaustive list of three dozen studies that used hormone ratios among cortisol, dehydroepiandrosterone sulfate (DHEA-S), estradiol, progesterone, testosterone, triiodothyronine (T3), thyroxine (T4), etc., to explain various outcome measures such as:

  • “Health status
  • Aggressive behavior
  • Psychopathy
  • Marital violence
  • fMRI response to angry and happy faces
  • Early life adversity
  • Depression
  • Chronic stress
  • Alexithymia”

Their 2015 study on “endocrine correlates of pro-environmental behavior” was used as an illustrative example. It had 229 male subjects between ages 19 and 77. Salivary cortisol (C) and testosterone (T) was sampled with these results:

“T/C and C/T ratios produce different means, standard deviations and distributional properties which significantly deviate from normality.

Height is not significantly associated with either T/C or C/T. In fact, looking at the original variables, C correlates positively with height while T shows no association.

When we include age as a covariate (assuming that it is associated with both height and hormone status) the partial correlation between T/C and height then is significant while the association between C/T and height is non-significant, even though both ratios are based on the exact same data.

Looking at the negative association between age and T/C the observed age-related ratio decline is mainly due to the fact that the T value in the numerator decreases with age while the C value in the denominator remains relatively constant. In this case, the analysis of the individual variables therefore offers more information and a more accurate picture of the underlying relationships.

A few previous studies have standardized the two underlying hormone distributions before calculating the ratio in order to account for the fact that two hormones often exhibit very different means and standard deviations. Standardization leads to values that express each subject’s hormone concentration relative to the sample mean.

A ratio calculated on the basis of such standardized hormones takes on a different meaning. In particular, the ratio no longer merely represents the proportion of the two hormones within the individual but also incorporates how high the two hormone concentrations are with respect to the sample distributions.”

Practices to improve the use and interpretation of hormone measurements included:

“Regression techniques employed on the original variables constitute a better suited alternative devoid of the problems associated with the ratio method. Moderation analysis, in particular, is a useful approach, which often provides more detailed insight into the relationships of interest.

Ratios should either be analyzed with non-parametric techniques, or be log-transformed before parametric statistical methods are applied.”

Set points and variations in an individual’s hormone balances are usually effects of underlying causes. Researchers will hopefully pay more attention to effectively dealing with ultimate causes as the preferred methods of managing an individual’s health, behavioral, and neurobiological effects.

https://www.sciencedirect.com/science/article/abs/pii/S0306453015009531 “How to use and interpret hormone ratios” (not freely available)

The cerebellum’s role in human behavior and emotions

gettingwell4 2-3 stars Required further work, Amygdala, Anterior cingulate cortex, Cerebellum, Cerebrum, Hippocampus, Limbic system, Lower brain

This 2016 Italian human review considered the lower brain’s contributions to an individual’s behavior and temperament:

“In evidencing associations between personality factors and neurobiological measures, it seems evident that the cerebellum has not been up to now thought as having a key role in personality.

Cerebellar volumes correlate positively with novelty seeking scores and negatively with harm avoidance scores. Subjects who search for new situations as a novelty seeker does (and a harm avoiding does not do) show a different engagement of their cerebellar circuitries in order to rapidly adapt to changing environments.

Cerebellar abilities in planning, controlling, and putting into action the behavior are associated to normal or abnormal personality constructs. In this framework, it is worth reporting that increased cerebellar volumes are even associated with high scores in alexithymia, construct of personality characterized by impairment in cognitive, emotional, and affective processing.”

The full paper wasn’t freely available, but a list of the 173 references was. 17 references were of alexithymia, also mentioned in the title.

One freely available reference was The embodied emotion in cerebellum: a neuroimaging study of alexithymia, a 2014 study performed by these same authors, which found:

“Alexithymia scores were linked directly with cerebellar areas and inversely with limbic and para-limbic system, proposing a possible functional modality for the cerebellar involvement in emotional processing.

The increased volumes in Crus 1 of subjects with high alexithymic traits may be related to an altered embodiment process leading to not-cognitively interpreted emotions.”

“Alexithymia scores” referred to one of the methods used to characterize alexithymia symptoms, self-reported answers to questionnaires such as this one. Sample questions from the questionnaire used by the referenced study are:

  • “I am often confused about what emotion I am feeling
  • It is difficult for me to reveal my innermost feelings, even to close friends”

The questionnaire mainly engages a person’s cerebrum. The person may recall emotions, and form ideas as framed by each question. Then they’ll describe these ideas in terms of a scaled answer.

Cerebral answers may provide historical contexts for feelings. However, the person’s cerebellum and other brain areas aren’t necessarily engaged by the diagnostic questionnaire.

Without this engagement, the person may not experience feelings when providing answers about feelings. The answers may be more along the lines of “This is what I think I should be feeling” or “This is what I think I should tell the researchers about what I think I should feel.”

  • Can a questionnaire accurately determine associations among engaged and unengaged brain areas?
  • What can be done regarding “impairment in cognitive, emotional, and affective processing?”
  • What’s the lower brain’s “involvement in emotional processing?”
  • How does the lower brain shape a person’s behavior and traits?
  • When and where in an individual’s lifespan does their cerebellum develop?

http://link.springer.com/article/10.1007/s12311-015-0754-9 “Viewing the Personality Traits Through a Cerebellar Lens: a Focus on the Constructs of Novelty Seeking, Harm Avoidance, and Alexithymia”

Epigenetic effects of cow’s milk

gettingwell4 2-3 stars Required further work, Brain development, Cerebrum, Epigenetics, Glutamate, Hypothalamus, Limbic system, Neurochemicals, Stress, Telomeres , , , , ,

This 2015 German paper with 342 references described:

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

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

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

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

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

There were separate sections on how milk may promote:

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

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

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

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

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

Epigenetic therapies for cancer

gettingwell4 2-3 stars Required further work, Epigenetics

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

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

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

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

The authors ended the commentary with a nuanced point:

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

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

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

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

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

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

Assessing epigenetic origins of allergies and asthma

gettingwell4 2-3 stars Required further work, Epigenetics, Immune system, Memory, Primal Therapy, Stress , , , ,

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

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

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

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

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

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

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

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

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

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

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

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

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

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

“Every therapy we try will be temporary, something we need to do over and over again. It can be nothing else because the imprint has the force of survival, of a lifesaving memory and must endure until the life-endangering imprint is finally fully felt and resolved.

Clearly this applies to many problems, from high blood pressure to asthma and allergies. That is why it is urgent that we re-focus on the real problem.”

Fat made rats fat with dysfunctional brains

gettingwell4 2-3 stars Required further work, Anterior cingulate cortex, Cerebrum, Cortisol, Epigenetics, Hippocampus, Limbic system, Neurochemicals, Stress, Testosterone , , ,

This 2015 New York rodent study found:

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

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

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

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

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

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

Testing the null hypothesis of psychological therapy

gettingwell4 2-3 stars Required further work, Primal Therapy , , ,

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

This 2015 UK human study found:

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

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

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

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

The study’s null hypothesis was developed as follows:

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

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

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

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

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

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

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

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

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

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

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

Beliefs about medical treatments affected perceived stress

gettingwell4 2-3 stars Required further work, Beliefs, Cerebrum, Neurochemicals, Oxytocin, Serotonin, Stress

This 2015 New Zealand human study found:

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

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

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

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

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

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

Emotional memories create long-term epigenetic changes

gettingwell4 2-3 stars Required further work, Anterior cingulate cortex, Brain development, Epigenetics, Hippocampus, Limbic system, Memory, Stress , , , , , ,

This 2015 German rodent study found:

“Histone modifications predominantly changed during memory acquisition and correlated surprisingly little with changes in gene expression.

Although long-lasting changes were almost exclusive to neurons, learning-related histone modification and DNA methylation changes also occurred in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning.”

Chromatin modifications in two limbic system brain areas were studied – the hippocampus (CA1 region) for short-term memories and the anterior cingulate cortex for short-and long-term memory formation and maintenance. The memories were induced by context (C) and context shock (CS) exposure:

“Overall, the data provides very strong and robust evidence for the establishment of long-term memory upon CS exposure, whereas C exposure alone did not induce the formation of long-term memory.”

So, without long-term shock/emotional memories, there would be no positive long-term findings for the researchers to report. There would be no lasting:

  • “Histone modifications
  • DNA methylation changes
  • Changes in gene expression”

The subjects were young adults at age 3 months. The CA1 and ACC studied brain areas are fully developed before this age.

It seemed feasible that if the study were performed with younger subjects, the results may have been different. For example:

“Context exposure alone did not induce the formation of long-term memory”

may not have been the finding for early learning situations.

The researchers qualified their results several times with the phrase “changes are limited to actively expressed genes.” A similar qualifier in A study of DNA methylation and age was a reminder that unexpressed genes may have also been important:

“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.”

This general qualifier may not have necessarily applied to the current study, though, because the study’s design included an unexposed control group.

http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4194.html “DNA methylation changes in plasticity genes accompany the formation and maintenance of memory”

A study of stress factors and neuroplasticity during infancy/early childhood

gettingwell4 2-3 stars Required further work, Cerebrum, Cortisol, Epigenetics, Hippocampus, Hypothalamus, Limbic system, Neurochemicals, Stress , , , , ,

This 2015 French rodent study found:

“The coordinated actions of BDNF and glucocorticoids promote neuronal plasticity and that disruption in either pathway could set the stage for the development of stress-induced psychiatric diseases.

Genetic strategies that disrupted GR [glucocorticoid receptor] phosphorylation or TrkB [the BDNF receptor] signaling in vivo impaired the neuroplasticity to chronic stress and the effects of the antidepressant fluoxetine.

We demonstrate that fluoxetine prevented the neuroplasticity of chronic stress by priming GR phosphorylation at BDNF-sensitive sites.”

It wasn’t too difficult to see how many of the stressors had human equivalents during infancy/early childhood:

“To determine the plasticity of GR phosphorylation upon changes in the endogenous levels of BDNF and glucocorticoids, mice were exposed to a chronic unpredictable stress that included one daily random stressor for 10 consecutive days from P21 [immediately after weaning] to 1 mo of age.

Chronic unpredictable stress includes one of the following daily random stressors (wet bedding, no bedding, food deprivation, crowded cage, 2 h or 6 h restraining, forced swim, tail suspension).”

But who would give fluoxetine – Prozac – to a human infant or young child to prevent “the neuroplasticity of chronic stress” from having adverse effects?

http://www.pnas.org/content/112/51/15737.full “Neurotrophic-priming of glucocorticoid receptor signaling is essential for neuronal plasticity to stress and antidepressant treatment”

Improved methodology in studying epigenetic DNA methylation

gettingwell4 2-3 stars Required further work, Brain development, Cerebrum, Epigenetics, Glutamate, Neurochemicals , , , , ,

This 2015 New York human study was of:

“The two major populations of human prefrontal cortex neurons..the excitatory glutamatergic projection neurons and the inhibitory GABAergic interneurons which constitute about 80% and 20% of all cortical neurons, respectively.

Major differences between the neuronal subtypes were revealed in CpG, non-CpG and hydroxymethylation (hCpG).

A dramatically greater number of undermethylated CpG sites in GLU versus GABA neurons were identified. These differences did not directly translate into differences in gene expression and did not stem from the differences in hCpG methylation, as more hCpG methylation was detected in GLU versus GABA neurons.

Notably, a comparable number of undermethylated non-CpG sites were identified in GLU and GABA neurons, and non-CpG methylation was a better predictor of subtype-specific gene expression compared to CpG methylation.”

The researchers performed numerous cross checks to test the results of their methodologies. This was necessary because, for example, studies such as A human study of changes in gene expression point out that current technologies such as the 450K array:

“Queries only 1.6% of all CpGs in the genome and the CpG selection is biased towards CpG islands.”

From the Discussion section:

“The higher abundance of hmCpG sites in GLU versus GABA neurons appears indicative of a difference in transcriptional potential between the neuronal subtypes. The increased hydroxymethylation could enable certain genes (e.g. activity-dependent genes) to be more readily induced in GLU versus GABA neurons.

These findings emphasize the importance of even subtle differences in the promoter CpG methylation for neuron subtype-specific gene expression. They also suggest that differences in CpG methylation within gene bodies and distal regulatory elements are not always directly reflected in differences in gene expression between neuronal subtypes.

The functional relevance of the association between gene expression and distal non-CpG methylation remains to be characterized.

Our data suggest that, compared to GABA interneurons, GLU projection neurons are characterized by more permissive chromatin state that is less constrained by repressive DNA methylation marks and is instead controlled by more dynamic means of transcription inhibition, such as non-coding RNAs and/or histone modifications.”

This study was similar to A problematic study of DNA methylation in frontal cortex development and schizophrenia in examining:

“If common risk variants determined by the recent genome wide associated studies (GWAS) for several neuropsychiatric diseases including schizophrenia (SCZ), autism spectrum disorder (ASD), major depressive disorder (MDD), and Alzheimer’s disease (AD) significantly overlap.

These findings strongly suggest an association between the epigenetic specification of both GABA and GLU neurons and SCZ. Risk variants associates with ASD, MD, or AD were not enriched.

An alternative explanation of our negative results could be the involvement of different developmental stages and/or brain regions in different diseases.”

The current study performed more detailed analyses, but on fewer subjects. The emphasis was on demonstrating an improved methodology.

Both studies’ findings regarding disease were of effects, not causes. That both study designs were limited to the postmortem prefrontal cortex reminded me of the old joke about looking for lost keys under the street light because the light was better there. At least the current study acknowledged the existence of other areas to search.

http://nar.oxfordjournals.org/content/early/2015/11/25/nar.gkv1304.full “Substantial DNA methylation differences between two major neuronal subtypes in human brain”

Epigenetics is gnarly and dynamic

gettingwell4 2-3 stars Required further work, Beliefs, Cerebrum, Epigenetics ,

From one of the articles in a freely-available Genome editing publication:

“Genomic studies frequently point to the important role that the full collection of epigenetic patterns in a cell nucleus has in complex diseases such as diabetes or schizophrenia, notes Tim Reddy, a genomics researcher also at Duke University. “In a lot of these cases, it really seems to be not a DNA mutation that impacts the protein sequence, but a change in how genes are regulated.”

Reddy says that he was surprised at the extent to which the expression of a target gene increased when a histone in an enhancer region was acetylated. “That result started to convince me that the acetylation of histones may be a direct cause of gene activation.”

Because of its simplicity and versatility, CRISPR–Cas9 opens up an opportunity. “If we want to target a region in the genome, we can have that targeting molecule here tomorrow for five dollars,” says Reddy.”

Reading this article and several of the publication’s other articles revealed the widespread belief that the goal of research should be to explain human conditions by explaining the actions of molecules.

One problem caused by this preconception is that it leads to study designs and models that omit relevant etiologic evidence embedded in each of the subjects’ historical experiences.

http://www.nature.com/nature/journal/v528/n7580_supp/full/528S12a.html “Epigenetics: The genome unwrapped”

Mitochondria interface genetic/epigenetic responses to psychological stress

gettingwell4 2-3 stars Required further work, Cortisol, Dopamine, Epigenetics, Glutamate, Hippocampus, Hypothalamus, Limbic system, Neurochemicals, Serotonin, Stress , , ,

This 2015 Pennsylvania rodent study found:

“Mitochondria can regulate complex whole-body physiological responses, impacting stress perception at the cellular and organismal levels.

Mitochondrial dysfunctions altered the

  1. hypothalamic–pituitary–adrenal [HPA] axis, sympathetic adrenal–medullary activation and catecholamine levels,
  2. the inflammatory cytokine IL-6,
  3. circulating metabolites, and
  4. hippocampal gene expression

responses to stress.

Stress-induced

  1. neuroendocrine,
  2. inflammatory,
  3. metabolic, and
  4. transcriptional responses

coalesced into unique signatures that distinguish groups based on their mitochondrial genotype.”

The study’s design was comprehensive for the subject of mitochondrial function and stress response categories. It interrelated elements that had a common cause of stress, such as:

  • Hyperglycemia
  • Increased lipids
  • Corticosterone sensitivity
  • Epigenetic changes within the brain

The study’s Figure 6E was a hierarchical “heat map” of the correlations among the 77 stress-induced changes that were measured. Figure 6G presented these variables per the five mitochondrial genotypes (a control wild-type and four genetic dysfunctions). Many of the lines forming the hierarchy needed careful reading of the study’s interpretations.

I downgraded the study’s rating because the authors inappropriately forced the “allostatic load” buzzword into the Significance statement and otherwise informative Discussion section. The term refers to a hypothetical long-term situation, but the study’s experiments lasted 2 hours at most before the subjects were killed.

www.pnas.org/content/112/48/E6614.full “Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress”