Reprogramming to recover youthful epigenetic information and restore vision.

Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity1-3. Changes to DNA methylation patterns over time form the basis of ageing clocks4, but whether older individuals retain the information needed to restore these patterns-and, if so, whether this could improve tissue function-is not known. Over time, the central nervous system (CNS) loses function and regenerative capacity5-7. Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2. These data indicate that mammalian tissues retain a record of youthful epigenetic information-encoded in part by DNA methylation-that can be accessed to improve tissue function and promote regeneration in vivo.

Proximity labeling of endogenous RICTOR identifies mTOR complex 2 regulation by ADP ribosylation factor ARF1.

Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) regulates metabolism, cell proliferation, and cell survival. mTORC2 activity is stimulated by growth factors, and it phosphorylates the hydrophobic motif site of the AGC kinases AKT, SGK, and PKC. However, the proteins that interact with mTORC2 to control its activity and localization remain poorly defined. To identify mTORC2-interacting proteins in living cells, we tagged endogenous RICTOR, an essential mTORC2 subunit, with the modified BirA biotin ligase BioID2 and performed live-cell proximity labeling. We identified 215 RICTOR-proximal proteins, including proteins with known mTORC2 pathway interactions, and 135 proteins (63%) not previously linked to mTORC2 signaling, including nuclear and cytoplasmic proteins. Our imaging and cell fractionation experiments suggest nearly 30% of RICTOR is in the nucleus, hinting at potential nuclear functions. We also identified 29 interactors containing RICTOR-dependent, insulin-stimulated phosphorylation sites, thus providing insight into mTORC2-dependent insulin signaling dynamics. Finally, we identify the endogenous ADP ribosylation factor 1 (ARF1) GTPase as an mTORC2-interacting protein. Through gain-of-function and loss-of-function studies, we provide functional evidence that ARF1 may negatively regulate mTORC2. In summary, we present a new method of studying endogenous mTORC2, a resource of RICTOR/mTORC2 protein interactions in living cells, and a potential mechanism of mTORC2 regulation by the ARF1 GTPase.

Microglia inhibit photoreceptor cell death and regulate immune cell infiltration in response to retinal detachment.

Retinal detachment (RD) is a sight-threatening complication common in many highly prevalent retinal disorders. RD rapidly leads to photoreceptor cell death beginning within 12 h following detachment. In patients with sustained RD, progressive visual decline due to photoreceptor cell death is common, leading to significant and permanent loss of vision. Microglia are the resident immune cells of the central nervous system, including the retina, and function in the homeostatic maintenance of the neuro-retinal microenvironment. It is known that microglia become activated and change their morphology in retinal diseases. However, the function of activated microglia in RD is incompletely understood, in part because of the lack of microglia-specific markers. Here, using the newly identified microglia marker P2ry12 and microglial depletion strategies, we demonstrate that retinal microglia are rapidly activated in response to RD and migrate into the injured area within 24 h post-RD, where they closely associate with infiltrating macrophages, a population distinct from microglia. Once in the injured photoreceptor layer, activated microglia can be observed to contain autofluorescence within their cell bodies, suggesting they function to phagocytose injured or dying photoreceptors. Depletion of retinal microglia results in increased disease severity and inhibition of macrophage infiltration, suggesting that microglia are involved in regulating neuroinflammation in the retina. Our work identifies that microglia mediate photoreceptor survival in RD and suggests that this effect may be due to microglial regulation of immune cells and photoreceptor phagocytosis.

Reciprocal Dysregulation of MiR-146b and MiR-451 Contributes in Malignant Phenotype of Follicular Thyroid Tumor.

Over the last few years, incidental thyroid nodules are being diagnosed with increasing frequency with the use of highly sensitive imaging techniques. The ultrasound thyroid gland examination, followed by the fine-needle aspiration cytology is the standard diagnostic approach. However, in cases of the follicular nature of nodules, cytological diagnosis is not enough. Analysis of miRNAs in the biopsy presents a promising approach. Increasing our knowledge of miRNA's role in follicular carcinogenesis, and development of the appropriate the miRNA analytical technologies are required to implement miRNA-based tests in clinical practice. We used material from follicular thyroid nodes (n.84), grouped in accordance with their invasive properties. The invasion-associated miRNAs expression alterations were assayed. Expression data were confirmed by highly sensitive two-tailed RT-qPCR. Reciprocally dysregulated miRNAs pair concentration ratios were explored as a diagnostic parameter using receiver operation curve (ROC) analysis. A new bioinformatics method (MiRImpact) was applied to evaluate the biological significance of the observed expression alterations. Coupled experimental and computational approaches identified reciprocal dysregulation of miR-146b and miR-451 as important attributes of follicular cell malignant transformation and follicular thyroid cancer progression. Thus, evaluation of combined dysregulation of miRNAs relevant to invasion and metastasis can help to distinguish truly malignant follicular thyroid cancer from indolent follicular adenoma.

Effect of Nanodiamond Sizes on the Efficiency of the Quasi-Specular Reflection of Cold Neutrons.

Nanomaterials can intensively scatter and/or reflect radiation. Such processes and materials are of theoretical and practical interest. Here, we study the quasi-specular reflections (QSRs) of cold neutrons (CNs) and the reflections of very cold neutrons (VCNs) from nanodiamond (ND) powders. The fluorination of ND increased its efficiency by removing/replacing hydrogen, which is otherwise the dominant cause of neutron loss due to incoherent scattering. The probability of the diffuse reflection of VCNs increased for certain neutron wavelengths by using appropriate ND sizes. Based on model concepts of the interaction of CNs with ND, and in reference to our previous work, we assume that the angular distribution of quasi-specularly reflected CNs is narrower, and that the probability of QSRs of longer wavelength neutrons increases if we increase the characteristic sizes of NDs compared to standard detonation nanodiamonds (DNDs). However, the probability of QSRs of CNs with wavelengths below the cutoff of ~4.12 Å decreases due to diffraction scattering on the ND crystal lattice. We experimentally compared the QSRs of CNs from ~4.3 nm and ~15.0 nm ND. Our qualitative conclusions and numerical estimates can help optimize the parameters of ND for specific practical applications based on the QSRs of CNs.

Quantitative analysis of metabolic fluxes in brown fat and skeletal muscle during thermogenesis.

Adaptive thermogenesis by brown adipose tissue (BAT) dissipates calories as heat, making it an attractive anti-obesity target. Yet how BAT contributes to circulating metabolite exchange remains unclear. Here, we quantified metabolite exchange in BAT and skeletal muscle by arteriovenous metabolomics during cold exposure in fed male mice. This identified unexpected metabolites consumed, released and shared between organs. Quantitative analysis of tissue fluxes showed that glucose and lactate provide ~85% of carbon for adaptive thermogenesis and that cold and CL316,243 trigger markedly divergent fuel utilization profiles. In cold adaptation, BAT also dramatically increases nitrogen uptake by net consuming amino acids, except glutamine. Isotope tracing and functional studies suggest glutamine catabolism concurrent with synthesis via glutamine synthetase, which avoids ammonia buildup and boosts fuel oxidation. These data underscore the ability of BAT to function as a glucose and amino acid sink and provide a quantitative and comprehensive landscape of BAT fuel utilization to guide translational studies.

Effect of Particle Sizes on the Efficiency of Fluorinated Nanodiamond Neutron Reflectors.

Over a decade ago, it was confirmed that detonation nanodiamond (DND) powders reflect very cold neutrons (VCNs) diffusively at any incidence angle and that they reflect cold neutrons quasi-specularly at small incidence angles. In the present publication, we report the results of a study on the effect of particle sizes on the overall efficiency of neutron reflectors made of DNDs. To perform this study, we separated, by centrifugation, the fraction of finer DND nanoparticles (which are referred to as S-DNDs here) from a broad initial size distribution and experimentally and theoretically compared the performance of such a neutron reflector with that from deagglomerated fluorinated DNDs (DF-DNDs). Typical commercially available DNDs with the size of ~4.3 nm are close to the optimum for VCNs with a typical velocity of ~50 m/s, while smaller and larger DNDs are more efficient for faster and slower VCN velocities, respectively. Simulations show that, for a realistic reflector geometry, the replacement of DF-DNDs (a reflector with the best achieved performance) by S-DNDs (with smaller size DNDs) increases the neutron albedo in the velocity range above ~60 m/s. This increase in the albedo results in an increase in the density of faster VCNs in such a reflector cavity of up to ~25% as well as an increase in the upper boundary of the velocities of efficient VCN reflection.

Clustering of Diamond Nanoparticles, Fluorination and Efficiency of Slow Neutron Reflectors.

Neutrons can be an instrument or an object in many fields of research. Major efforts all over the world are devoted to improving the intensity of neutron sources and the efficiency of neutron delivery for experimental installations. In this context, neutron reflectors play a key role because they allow significant improvement of both economy and efficiency. For slow neutrons, Detonation NanoDiamond (DND) powders provide exceptionally good reflecting performance due to the combination of enhanced coherent scattering and low neutron absorption. The enhancement is at maximum when the nanoparticle diameter is close to the neutron wavelength. Therefore, the mean nanoparticle diameter and the diameter distribution are important. In addition, DNDs show clustering, which increases their effective diameters. Here, we report on how breaking agglomerates affects clustering of DNDs and the overall reflector performance. We characterize DNDs using small-angle neutron scattering, X-ray diffraction, scanning and transmission electron microscopy, neutron activation analysis, dynamical light scattering, infra-red light spectroscopy, and others. Based on the results of these tests, we discuss the calculated size distribution of DNDs, the absolute cross-section of neutron scattering, the neutron albedo, and the neutron intensity gain for neutron traps with DND walls.