Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans -Acting Modifiers

Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation

'A group of totally awesome people who do stuff' - a qualitative descriptive study of a children and young people's patient and public involvement endeavour.

BACKGROUND: In 2013, the Cambridge Clinical Research Facility (CCRF) set up a Children's Non-Executive Research Board to advise on service and facility development and research involving children and young people (CYP). In 2015, the Children's Experiences of Engaging in Research study (CHEER) was conceived to explore the Children's Board as a patient and public involvement initiative. AIM: To explore the views of CYP, staff and parents involved in the Children's Board with the view to describe their experiences of the selected mechanism of involvement (Children's Board) within the context of operation (CCRF). METHODS: A qualitative descriptive methodology involving qualitative content analysis of semi-structured interviews was used to derive descriptive summaries of the interview data. SETTING AND PARTICIPANTS: Interviews were carried out with staff (n = 5), children (n = 2) and parents (n = 2) who participated in the first or second Children's Board meetings. RESULTS: Twelve descriptive summaries emerged: (1) CCRF 'role' perspective (2) purpose, remit and future direction (3) aspirations (4) learning as reciprocation (5) regular meetings, contact and feedback (6) expectation setting and ground rules (7) culture of PPI (8) surprise, underestimation and self-selection (9) reciprocity, incentivisation and participation (10) practicalities, timing and barriers (11) parental roles (12) event structure. These highlighted the importance of selecting the right mechanism of involvement in relation to context for involvement and the reductive biases adults and healthcare providers may unconsciously hold. Both of these aspects may affect the efficacy of PPI endeavours with CYP. DISCUSSION AND CONCLUSIONS: Mechanisms by which CYP are involved in research should be considered from the outset; taking into consideration both the setting and contextual features. Contextual and process factors important in the adult PPI realm were generally observed in this PPI initiative with CYP; however further research is required to explore unconscious biases and reductive perceptions in adult facilitators

Simulated Galactic Cosmic Radiation Exposure Impairs Mouse Vertebral Bone Adaptations to Exercise During Recovery from Partial Weightbearing

Partial weightbearing that simulates Lunar gravity (one-sixth of Earth’s gravitational force) results in a loss of bone volume. High-energy radiation like that found in galactic cosmic radiation exposure also negatively affects the skeleton. Because resistance training is the most effective exercise mode to counteract disuse-induced bone loss, this experiment combined low-dose, high-energy simulated galactic cosmic radiation (GCR) exposure, followed by a period of partial weightbearing (PWB), and then a period of climb training resistance exercise or normal cage activity during recovery. Ex vivo micro-computed tomography (μCT) scans were performed by Matthew Allen, PhD at the Indiana University School of Medicine to quantify cancellous bone microarchitecture in the 4th lumbar vertebral body before biomechanical compression tests were performed at Texas A&M University. Ash weights were calculated on the fifth lumbar vertebrae. Means for cancellous bone volume (%BV/TV), trabecular thickness (Tb.Th.), trabecular number (Tb.N.), ash weight, and maximum stress from Day 42 of the experiment were compared to Day 21 means using unpaired t-tests to determine the changes occurring through the recovery period. These change scores were then analyzed using a two-way ANOVA to determine differences across experimental groups. Exercise had no significant effect on ∆BV/TV or ∆Tb.Th., but ∆BV/TV and ∆Tb.Th. were significantly lower in RAD groups than in SHAM groups (p<0.001). Additionally, Ex SHAM bones showed gains in cancellous bone mass and trabecular thickness during the recovery period. SHAM groups increased in trabecular Tb.Th. during recovery, while the trabeculae of RAD bones became thinner. ∆Tb.N. was significantly higher in exercised groups than non-exercised groups (p<0.05), but no significant differences in ∆Tb.N. were shown between RAD and SHAM groups. Ash weights showed significant differences in bone mineral content between Ex RAD and Ex SHAM groups. While maximum stress data did not show significant changes during recovery, the trends mirror those seen in other tests of bone integrity. These data suggest that GCR exposure diminishes the ability of bone to respond to exercise during recovery form a period of reduced weightbearing

Genomic properties of variably methylated retrotransposons in mouse

Background: Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit interindividual variability in this methylation (VM-IAPs) with implications for genome function. Results: Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis . Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. Conclusion: Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation

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

Constraining the Moho Depth Below Bhutan With Global-Phase Seismic Interferometry

We use a novel technique named global-phase seismic interferometry (GloPSI) to image the lithospheric structure, and in particular the Moho, below two parallel north-south transects belonging to the GANSSER network (2013–2014). The profiles cross the Himalayan orogenic wedge in Bhutan, a tectonically important area within the largest continent-continent collision zone on Earth that is still undergoing crustal thickening and represents a challenging imaging target for the GloPSI approach. GloPSI makes use of direct waves from distant earthquakes and receiver-side reverberations with near vertical incidence. Reflections are isolated from earthquake recordings by solving a correlation integral and are turned into a reflectivity image of the lithosphere below the arrays. Our results compare favorably with first-order features observed from a previous receiver function (RF) study. We show that a combined interpretation of GloPSI and RF results allows for a more in-depth understanding of the lithospheric structure across the orogenic wedge in Bhutan

Genomic properties of variably methylated retrotransposons in mouse

Abstract: Background: Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. Results: Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. Conclusion: Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation

Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade

Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from different conditions are similar and how they impact the longitudinal level of the COVID-19 vaccine response. Single-cell RNA sequencing indicates that ABCs with distinct aetiologies have common transcriptional profiles and can be categorised according to their expression of immune genes, such as the autoimmune regulator (AIRE). Furthermore, higher baseline ABC frequency correlates with decreased levels of antigen-specific memory B cells and reduced neutralising capacity against SARS-CoV-2. ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes, which could contribute to diminish vaccine responses either directly, or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may, therefore, serve as a biomarker identifying individuals at risk of suboptimal responses to vaccination

Combined point of care nucleic acid and antibody testing for SARS-CoV-2 following emergence of D614G Spike Variant

Rapid COVID-19 diagnosis in hospital is essential, though complicated by 30-50% of nose/throat swabs being negative by SARS-CoV-2 nucleic acid amplification testing (NAAT). Furthermore, the D614G spike mutant now dominates the pandemic and it is unclear how serological tests designed to detect anti-Spike antibodies perform against this variant. We assess the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease due to either wild type or the D614G spike mutant SARS-CoV-2. The overall detection rate for COVID-19 is 79.2% (95CI 57.8-92.9%) by rapid NAAT alone. Combined point of care antibody test and rapid NAAT is not impacted by D614G and results in very high sensitivity for COVID-19 diagnosis with very high specificity