Genomic Imprinting and Physiological Processes in Mammals.

Complex multicellular organisms, such as mammals, express two complete sets of chromosomes per nucleus, combining the genetic material of both parents. However, epigenetic studies have demonstrated violations to this rule that are necessary for mammalian physiology; the most notable parental allele expression phenomenon is genomic imprinting. With the identification of endogenous imprinted genes, genomic imprinting became well-established as an epigenetic mechanism in which the expression pattern of a parental allele influences phenotypic expression. The expanding study of genomic imprinting is revealing a significant impact on brain functions and associated diseases. Here, we review key milestones in the field of imprinting and discuss mechanisms and systems in which imprinted genes exert a significant role.

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance.

Generally repressed by epigenetic mechanisms, retrotransposons represent around 40% of the murine genome. At the Agouti viable yellow (Avy) locus, an endogenous retrovirus (ERV) of the intracisternal A particle (IAP) class retrotransposed upstream of the agouti coat-color locus, providing an alternative promoter that is variably DNA methylated in genetically identical individuals. This results in variable expressivity of coat color that is inherited transgenerationally. Here, a systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties. Each exhibits a stable methylation state within an individual but varies between individuals. Only in rare instances do they act as promoters controlling adjacent gene expression. Their methylation state is locus-specific within an individual, and their flanking regions are enriched for CTCF. Variably methylated IAPs are reprogrammed after fertilization and re-established as variable loci in the next generation, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.

Corticoamygdala Transfer of Socially Derived Information Gates Observational Learning.

Observational learning is a powerful survival tool allowing individuals to learn about threat-predictive stimuli without directly experiencing the pairing of the predictive cue and punishment. This ability has been linked to the anterior cingulate cortex (ACC) and the basolateral amygdala (BLA). To investigate how information is encoded and transmitted through this circuit, we performed electrophysiological recordings in mice observing a demonstrator mouse undergo associative fear conditioning and found that BLA-projecting ACC (ACC→BLA) neurons preferentially encode socially derived aversive cue information. Inhibition of ACC→BLA alters real-time amygdala representation of the aversive cue during observational conditioning. Selective inhibition of the ACC→BLA projection impaired acquisition, but not expression, of observational fear conditioning. We show that information derived from observation about the aversive value of the cue is transmitted from the ACC to the BLA and that this routing of information is critically instructive for observational fear conditioning. VIDEO ABSTRACT.

Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity.

More than one-half billion people are obese, and despite progress in genetic research, much of the heritability of obesity remains enigmatic. Here, we identify a Trim28-dependent network capable of triggering obesity in a non-Mendelian, "on/off" manner. Trim28(+/D9) mutant mice exhibit a bi-modal body-weight distribution, with isogenic animals randomly emerging as either normal or obese and few intermediates. We find that the obese-"on" state is characterized by reduced expression of an imprinted gene network including Nnat, Peg3, Cdkn1c, and Plagl1 and that independent targeting of these alleles recapitulates the stochastic bi-stable disease phenotype. Adipose tissue transcriptome analyses in children indicate that humans too cluster into distinct sub-populations, stratifying according to Trim28 expression, transcriptome organization, and obesity-associated imprinted gene dysregulation. These data provide evidence of discrete polyphenism in mouse and man and thus carry important implications for complex trait genetics, evolution, and medicine.

Mutation in folate metabolism causes epigenetic instability and transgenerational effects on development.

The importance of maternal folate consumption for normal development is well established, yet the molecular mechanism linking folate metabolism to development remains poorly understood. The enzyme methionine synthase reductase (Mtrr) is necessary for utilization of methyl groups from the folate cycle. We found that a hypomorphic mutation of the mouse Mtrr gene results in intrauterine growth restriction, developmental delay, and congenital malformations, including neural tube, heart, and placental defects. Importantly, these defects were dependent upon the Mtrr genotypes of the maternal grandparents. Furthermore, we observed widespread epigenetic instability associated with altered gene expression in the placentas of wild-type grandprogeny of Mtrr-deficient maternal grandparents. Embryo transfer experiments revealed that Mtrr deficiency in mice lead to two distinct, separable phenotypes: adverse effects on their wild-type daughters' uterine environment, leading to growth defects in wild-type grandprogeny, and the appearance of congenital malformations independent of maternal environment that persist for five generations, likely through transgenerational epigenetic inheritance.

ZNF445 is a primary regulator of genomic imprinting.

Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation, causing parental origin-specific monoallelic gene expression. Zinc finger protein 57 (ZFP57) is critical for maintenance of this epigenetic memory during post-fertilization reprogramming, yet incomplete penetrance of ZFP57 mutations in humans and mice suggests additional effectors. We reveal that ZNF445/ZFP445, which we trace to the origins of imprinting, binds imprinting control regions (ICRs) in mice and humans. In mice, ZFP445 and ZFP57 act together, maintaining all but one ICR in vivo, whereas earlier embryonic expression of ZNF445 and its intolerance to loss-of-function mutations indicate greater importance in the maintenance of human imprints.

People with more extreme attitudes towards science have self-confidence in their understanding of science, even if this is not justified.

People differ greatly in their attitudes towards well-evidenced science. What characterises this variation? Here, we consider this issue in the context of genetics and allied sciences. While most prior research has focused on the relationship between attitude to science and what people know about it, recent evidence suggests that individuals with strongly negative attitudes towards specific genetic technologies (genetic modification (GM) technology and vaccines) commonly do not objectively understand the science, but, importantly, believe that they do. Here, using data from a probability survey of United Kingdom adults, we extend this prior work in 2 regards. First, we ask whether people with more extreme attitudes, be they positive or negative, are more likely to believe that they understand the science. Second, as negativity to genetics is commonly framed around issues particular to specific technologies, we ask whether attitudinal trends are contingent on specification of technology. We find (1) that individuals with strongly positive or negative attitudes towards genetics more strongly believe that they well understand the science; but (2) only for those most positive to the science is this self-confidence warranted; and (3) these effects are not contingent on specification of any particular technologies. These results suggest a potentially general model to explain why people differ in their degree of acceptance or rejection of science, this being that the more someone believes they understand the science, the more confident they will be in their acceptance or rejection of it. While there are more technology nonspecific opponents who also oppose GM technology than expected by chance, most GM opponents fit a different demographic. For the most part, opposition to GM appears not to reflect a smokescreen concealing a broader underlying negativity.

Subnuclear localisation is associated with gene expression more than parental origin at the imprinted Dlk1-Dio3 locus.

At interphase, de-condensed chromosomes have a non-random three-dimensional architecture within the nucleus, however, little is known about the extent to which nuclear organisation might influence expression or vice versa. Here, using imprinting as a model, we use 3D RNA- and DNA-fluorescence-in-situ-hybridisation in normal and mutant mouse embryonic stem cell lines to assess the relationship between imprinting control, gene expression and allelic distance from the nuclear periphery. We compared the two parentally inherited imprinted domains at the Dlk1-Dio3 domain and find a small but reproducible trend for the maternally inherited domain to be further away from the periphery however we did not observe an enrichment of inactive alleles in the immediate vicinity of the nuclear envelope. Using Zfp57KO ES cells, which harbour a paternal to maternal epigenotype switch, we observe that expressed alleles are significantly further away from the nuclear periphery. However, within individual nuclei, alleles closer to the periphery are equally likely to be expressed as those further away. In other words, absolute position does not predict expression. Taken together, this suggests that whilst stochastic activation can cause subtle shifts in localisation for this locus, there is no dramatic relocation of alleles upon gene activation. Our results suggest that transcriptional activity, rather than the parent-of-origin, defines subnuclear localisation at an endogenous imprinted domain.

Cognitive functional therapy with or without movement sensor biofeedback versus usual care for chronic, disabling low back pain (RESTORE): a randomised, controlled, three-arm, parallel group, phase 3, clinical trial.

BACKGROUND: Low back pain is the leading cause of years lived with disability globally, but most interventions have only short-lasting, small to moderate effects. Cognitive functional therapy (CFT) is an individualised approach that targets unhelpful pain-related cognitions, emotions, and behaviours that contribute to pain and disability. Movement sensor biofeedback might enhance treatment effects. We aimed to compare the effectiveness and economic efficiency of CFT, delivered with or without movement sensor biofeedback, with usual care for patients with chronic, disabling low back pain. METHODS: RESTORE was a randomised, controlled, three-arm, parallel group, phase 3 trial, done in 20 primary care physiotherapy clinics in Australia. We recruited adults (aged ≥18 years) with low back pain lasting more than 3 months with at least moderate pain-related physical activity limitation. Exclusion criteria were serious spinal pathology (eg, fracture, infection, or cancer), any medical condition that prevented being physically active, being pregnant or having given birth within the previous 3 months, inadequate English literacy for the study's questionnaires and instructions, a skin allergy to hypoallergenic tape adhesives, surgery scheduled within 3 months, or an unwillingness to travel to trial sites. Participants were randomly assigned (1:1:1) via a centralised adaptive schedule to usual care, CFT only, or CFT plus biofeedback. The primary clinical outcome was activity limitation at 13 weeks, self-reported by participants using the 24-point Roland Morris Disability Questionnaire. The primary economic outcome was quality-adjusted life-years (QALYs). Participants in both interventions received up to seven treatment sessions over 12 weeks plus a booster session at 26 weeks. Physiotherapists and patients were not masked. This trial is registered with the Australian New Zealand Clinical Trials Registry, ACTRN12618001396213. FINDINGS: Between Oct 23, 2018 and Aug 3, 2020, we assessed 1011 patients for eligibility. After excluding 519 (51·3%) ineligible patients, we randomly assigned 492 (48·7%) participants; 164 (33%) to CFT only, 163 (33%) to CFT plus biofeedback, and 165 (34%) to usual care. Both interventions were more effective than usual care (CFT only mean difference -4·6 [95% CI -5·9 to -3·4] and CFT plus biofeedback mean difference -4·6 [-5·8 to -3·3]) for activity limitation at 13 weeks (primary endpoint). Effect sizes were similar at 52 weeks. Both interventions were also more effective than usual care for QALYs, and much less costly in terms of societal costs (direct and indirect costs and productivity losses; -AU$5276 [-10 529 to -24) and -8211 (-12 923 to -3500). INTERPRETATION: CFT can produce large and sustained improvements for people with chronic disabling low back pain at considerably lower societal cost than that of usual care. FUNDING: Australian National Health and Medical Research Council and Curtin University.

Dlk1 dosage regulates hippocampal neurogenesis and cognition.

Neurogenesis in the adult brain gives rise to functional neurons, which integrate into neuronal circuits and modulate neural plasticity. Sustained neurogenesis throughout life occurs in the subgranular zone (SGZ) of the dentate gyrus in the hippocampus and is hypothesized to be involved in behavioral/cognitive processes such as memory and in diseases. Genomic imprinting is of critical importance to brain development and normal behavior, and exemplifies how epigenetic states regulate genome function and gene dosage. While most genes are expressed from both alleles, imprinted genes are usually expressed from either the maternally or the paternally inherited chromosome. Here, we show that in contrast to its canonical imprinting in nonneurogenic regions, Delta-like homolog 1 (Dlk1) is expressed biallelically in the SGZ, and both parental alleles are required for stem cell behavior and normal adult neurogenesis in the hippocampus. To evaluate the effects of maternally, paternally, and biallelically inherited mutations within the Dlk1 gene in specific behavioral domains, we subjected Dlk1-mutant mice to a battery of tests that dissociate and evaluate the effects of Dlk1 dosage on spatial learning ability and on anxiety traits. Importantly, reduction in Dlk1 levels triggers specific cognitive abnormalities that affect aspects of discriminating differences in environmental stimuli, emphasizing the importance of selective absence of imprinting in this neurogenic niche.

Position Statement: Range Orders in the Management of Pain.

American Society for Pain Management Nursing (ASPMN) supports safe medication practices and the appropriate use of pro re nata (PRN) range orders for analgesics in the management of pain within the scope of nursing practice. Although range orders may apply to many medications prescribed as PRN, the focus of this ASPMN position statement is on PRN analgesic medication. PRN range orders are commonly used to provide flexibility in dosing to meet the analgesic requirements of an individual patient. There are many patient-specific factors that require professional clinical assessment when administering medications to patients. Unfortunately, several myths persist regarding The Joint Commission's (TJC) standard around the implementation of range orders leading many to assume that range orders are not supported or safe. On the contrary, if utilized in a consistent and appropriate manner, PRN range orders can allow nurses to provide optimal pain management while still providing safe administration (Paquette et al., 2022).

Neuromuscular adaptations of swallowing and speech in unilateral cerebral palsy: shared and distinctive traits.

Our aims were to 1) examine the neuromuscular control of swallowing and speech in children with unilateral cerebral palsy (UCP) compared with typically developing children (TDC), 2) determine shared and separate neuromuscular underpinnings of the two functions, and 3) explore the relationship between this control and behavioral outcomes in UCP. Surface electromyography (sEMG) was used to record muscle activity from the submental and superior and inferior orbicularis oris muscles during standardized swallowing and speech tasks. The variables examined were normalized mean amplitude, time to peak amplitude, and bilateral synchrony. Swallowing and speech were evaluated using standard clinical measures. Sixteen children with UCP and 16 TDC participated (7-12 yr). Children with UCP demonstrated higher normalized mean amplitude and longer time to peak amplitude across tasks than TDC (P < 0.01; and P < 0.02) and decreased bilateral synchrony than TDC for swallows (P < 0.01). Both shared and distinctive neuromuscular patterns were observed between swallowing and speech. In UCP, higher upper lip amplitude during swallows was associated with shorter normalized mealtime durations, whereas higher submental bilateral synchrony was related to longer mealtime durations. Children with UCP demonstrate neuromuscular adaptations for swallowing and speech, which should be further evaluated for potential treatment targets. Furthermore, both shared and distinctive neuromuscular underpinnings between the two functions are documented.NEW & NOTEWORTHY Systematically studying the swallowing and speech of children with UCP is new and noteworthy. We found that they demonstrate neuromuscular adaptations for swallowing and speech compared with typically developing peers. We examined swallowing and speech using carefully designed tasks, similar in motor complexity, which allowed us to directly compare patterns. We found shared and distinctive neuromuscular patterns between swallowing and speech.

Preimplantation genetic testing for a chr14q32 microdeletion in a family with Kagami-Ogata syndrome and Temple syndrome.

INTRODUCTION: Kagami-Ogata syndrome (KOS14) and Temple syndrome (TS14) are two disorders associated with reciprocal alterations within the chr14q32 imprinted domain. Here, we present a work-up strategy for preimplantation genetic testing (PGT) to avoid the transmission of a causative micro-deletion. METHODS: We analysed DNA from the KOS14 index case and parents using methylation-sensitive ligation-mediated probe amplification and methylation pyrosequencing. The extent of the deletion was mapped using SNP arrays. PGT was performed in trophectoderm samples in order to identify unaffected embryos. Samples were amplified using multiple displacement amplification, followed by genome-wide SNP genotyping to determine the at-risk haplotype and next-generation sequencing to determine aneuploidies. RESULTS: A fully methylated pattern at the normally paternally methylated IG-DMR and MEG3 DMR in the KOS14 proband, accompanied by an unmethylated profile in the TS14 mother was consistent with maternal and paternal transmission of a deletion, respectively. Further analysis revealed a 108 kb deletion in both cases. The inheritance of the deletion on different parental alleles was consistent with the opposing phenotypes. In vitro fertilisation with intracytoplasmatic sperm injection and PGT were used to screen for deletion status and to transfer an unaffected embryo in this couple. A single euploid-unaffected embryo was identified resulting in a healthy baby born. DISCUSSION: We identify a microdeletion responsible for multigeneration KOS14 and TS14 within a single family where carriers have a 50% risk of transmitting the deletion to their offspring. We show that PGT can successfully be offered to couples with IDs caused by genetic anomalies.

KRAB zinc finger protein diversification drives mammalian interindividual methylation variability.

Most transposable elements (TEs) in the mouse genome are heavily modified by DNA methylation and repressive histone modifications. However, a subset of TEs exhibit variable methylation levels in genetically identical individuals, and this is associated with epigenetically conferred phenotypic differences, environmental adaptability, and transgenerational epigenetic inheritance. The evolutionary origins and molecular mechanisms underlying interindividual epigenetic variability remain unknown. Using a repertoire of murine variably methylated intracisternal A-particle (VM-IAP) epialleles as a model, we demonstrate that variable DNA methylation states at TEs are highly susceptible to genetic background effects. Taking a classical genetics approach coupled with genome-wide analysis, we harness these effects and identify a cluster of KRAB zinc finger protein (KZFP) genes that modifies VM-IAPs in trans in a sequence-specific manner. Deletion of the cluster results in decreased DNA methylation levels and altered histone modifications at the targeted VM-IAPs. In some cases, these effects are accompanied by dysregulation of neighboring genes. We find that VM-IAPs cluster together phylogenetically and that this is linked to differential KZFP binding, suggestive of an ongoing evolutionary arms race between TEs and this large family of epigenetic regulators. These findings indicate that KZFP divergence and concomitant evolution of DNA binding capabilities are mechanistically linked to methylation variability in mammals, with implications for phenotypic variation and putative paradigms of mammalian epigenetic inheritance.

Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity.

Some imprinted genes exhibit parental origin specific expression bias rather than being transcribed exclusively from one copy. The physiological relevance of this remains poorly understood. In an analysis of brain-specific allele-biased expression, we identified that Trappc9, a cellular trafficking factor, was expressed predominantly (~70%) from the maternally inherited allele. Loss-of-function mutations in human TRAPPC9 cause a rare neurodevelopmental syndrome characterized by microcephaly and obesity. By studying Trappc9 null mice we discovered that homozygous mutant mice showed a reduction in brain size, exploratory activity and social memory, as well as a marked increase in body weight. A role for Trappc9 in energy balance was further supported by increased ad libitum food intake in a child with TRAPPC9 deficiency. Strikingly, heterozygous mice lacking the maternal allele (70% reduced expression) had pathology similar to homozygous mutants, whereas mice lacking the paternal allele (30% reduction) were phenotypically normal. Taken together, we conclude that Trappc9 deficient mice recapitulate key pathological features of TRAPPC9 mutations in humans and identify a role for Trappc9 and its imprinting in controlling brain development and metabolism.

Exploring the Efficacy of an Online Training Programme to Introduce Mental Health Recovery to Carers.

Family carers often support people with mental ill-health, however, there is a dearth of research on the importance of recovery to mental health carers. This article describes the delivery and qualitative evaluation of an online training programme on recovery to a group of eleven carers. The participants considered their understanding of the meaning of recovery, differentiating between its personal and clinical nature. They highlighted the importance of carer involvement in the service users' professional support, alongside the need for carers to participate more widely in service development. Finally, the participants found the training useful in enabling them to recognise their own needs in a caring journey, particularly valuing its delivery by a service user and carer trainer. This study is limited by the small number of participants in this programme; however, this series of connected studies suggests its potential to be rolled out more widely, possibly embedded in Recovery Colleges.

Metastable epialleles and their contribution to epigenetic inheritance in mammals.

Many epigenetic differences between individuals are driven by genetic variation. Mammalian metastable epialleles are unusual in that they show variable DNA methylation states between genetically identical individuals. The occurrence of such states across generations has resulted in their consideration by many as strong evidence for epigenetic inheritance in mammals, with the classic Avy and AxinFu mouse models - each products of repeat element insertions - being the most widely accepted examples. Equally, there has been interest in exploring their use as epigenetic biosensors given their susceptibility to environmental compromise. Here we review the classic murine metastable epialleles as well as more recently identified candidates, with the aim of providing a more holistic understanding of their biology. We consider the extent to which epigenetic inheritance occurs at metastable epialleles and explore the limited mechanistic insights into the establishment of their variable epigenetic states. We discuss their environmental modulation and their potential relevance in genome regulation. In light of recent whole-genome screens for novel metastable epialleles, we point out the need to reassess their biological relevance in multi-generational studies and we highlight their value as a model to study repeat element silencing as well as the mechanisms and consequences of mammalian epigenetic stochasticity.

Targeting Huntingtin Expression in Patients with Huntington's Disease.

BACKGROUND: Huntington's disease is an autosomal-dominant neurodegenerative disease caused by CAG trinucleotide repeat expansion in HTT, resulting in a mutant huntingtin protein. IONIS-HTTRx (hereafter, HTTRx) is an antisense oligonucleotide designed to inhibit HTT messenger RNA and thereby reduce concentrations of mutant huntingtin. METHODS: We conducted a randomized, double-blind, multiple-ascending-dose, phase 1-2a trial involving adults with early Huntington's disease. Patients were randomly assigned in a 3:1 ratio to receive HTTRx or placebo as a bolus intrathecal administration every 4 weeks for four doses. Dose selection was guided by a preclinical model in mice and nonhuman primates that related dose level to reduction in the concentration of huntingtin. The primary end point was safety. The secondary end point was HTTRx pharmacokinetics in cerebrospinal fluid (CSF). Prespecified exploratory end points included the concentration of mutant huntingtin in CSF. RESULTS: Of the 46 patients who were enrolled in the trial, 34 were randomly assigned to receive HTTRx (at ascending dose levels of 10 to 120 mg) and 12 were randomly assigned to receive placebo. Each patient received all four doses and completed the trial. Adverse events, all of grade 1 or 2, were reported in 98% of the patients. No serious adverse events were seen in HTTRx-treated patients. There were no clinically relevant adverse changes in laboratory variables. Predose (trough) concentrations of HTTRx in CSF showed dose dependence up to doses of 60 mg. HTTRx treatment resulted in a dose-dependent reduction in the concentration of mutant huntingtin in CSF (mean percentage change from baseline, 10% in the placebo group and -20%, -25%, -28%, -42%, and -38% in the HTTRx 10-mg, 30-mg, 60-mg, 90-mg, and 120-mg dose groups, respectively). CONCLUSIONS: Intrathecal administration of HTTRx to patients with early Huntington's disease was not accompanied by serious adverse events. We observed dose-dependent reductions in concentrations of mutant huntingtin. (Funded by Ionis Pharmaceuticals and F. Hoffmann-La Roche; ClinicalTrials.gov number, NCT02519036.).