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Long‐lasting vaginal dosage forms could improve the therapeutic efficacy of vaginal microbicides, but achieving long‐term delivery to the vaginal canal has been a significant challenge. To advance understanding of vaginal dosage retention and biodistribution, we describe a method of noninvasive imaging with 89Zr‐labeled bioadhesive nanoparticles (BNPs) in non‐human primates. We additionally examined the safety of repeated BNP application. BNPs administered vaginally to cynomolgus monkeys were still detected after 24 h (1.7% retention) and 120 h (0.1% retention). BNPs did not translocate to the uterus or into systemic circulation. Analysis of inflammatory biomarkers in the vaginal fluid and plasma suggest that BNPs are safe and biocompatible, even after multiple doses. BNPs are a promising delivery vehicle for vaginally administered therapeutics. Further studies using the non‐human primate imaging materials and methods developed here could help advance clinical translation of BNPs and other long‐lasting vaginal dosage forms. [ABSTRACT FROM AUTHOR]

The apolipoprotein E ɛ4 allele (APOE4) is universally acknowledged as the most potent genetic risk factor for Alzheimer's disease (AD). APOE4 promotes the initiation and progression of AD. Although the underlying mechanisms are unclearly understood, differences in lipid‐bound affinity among the three APOE isoforms may constitute the basis. The protein APOE4 isoform has a high affinity with triglycerides and cholesterol. A distinction in lipid metabolism extensively impacts neurons, microglia, and astrocytes. APOE4 carriers exhibit phenotypic differences from non‐carriers in clinical examinations and respond differently to multiple treatments. Therefore, we hypothesized that phenotypic classification of AD patients according to the status of APOE4 carrier will help specify research and promote its use in diagnosing and treating AD. Recent reviews have mainly evaluated the differences between APOE4 allele carriers and non‐carriers from gene to protein structures, clinical features, neuroimaging, pathology, the neural network, and the response to various treatments, and have provided the feasibility of phenotypic group classification based on APOE4 carrier status. This review will facilitate the application of APOE phenomics concept in clinical practice and promote further medical research on AD. [ABSTRACT FROM AUTHOR]

Bromodomain‐containing protein 4 (BRD4) is overexpressed and functionally implicated in various myeloid malignancies. However, the role of BRD4 in normal hematopoiesis remains largely unknown. Here, utilizing an inducible Brd4 knockout mouse model, we find that deletion of Brd4 (Brd4Δ/Δ) in the hematopoietic system impairs hematopoietic stem cell (HSC) self‐renewal and differentiation, which associates with cell cycle arrest and senescence. ATAC‐seq analysis shows increased chromatin accessibility in Brd4Δ/Δ hematopoietic stem/progenitor cells (HSC/HPCs). Genome‐wide mapping with cleavage under target and release using nuclease (CUT&RUN) assays demonstrate that increased global enrichment of H3K122ac and H3K4me3 in Brd4Δ/Δ HSC/HPCs is associated with the upregulation of senescence‐specific genes. Interestingly, Brd4 deletion increases clipped H3 (cH3) which correlates with the upregulation of senescence‐specific genes and results in a higher frequency of senescent HSC/HPCs. Re‐expression of BRD4 reduces cH3 levels and rescues the senescence rate in Brd4Δ/Δ HSC/HPCs. This study unveils an important role of BRD4 in HSC/HPC function by preventing H3 clipping and suppressing senescence gene expression. Synopsis: BRD4 is required for normal HSC functions by suppressing cell senescence and regulating the cell cycle. Mechanistically, BRD4 regulates chromatin accessibility and prevents H3.3 clipping to regulate senescence‐specific gene expression. Loss of Brd4 induces cell senescence and cell cycle arrest, leading to the impairment of HSC function.BRD4 maintains chromatin accessibility and regulates the expression of genes critical for HSC functions.Brd4 deletion induces histone H3 clipping and upregulates senescence‐specific genes.Re‐expression of Brd4 reduces cH3 levels and senescence of Brd4Δ/Δ HSC/HPCs. [ABSTRACT FROM AUTHOR]

Tumor‐initiating cells are major drivers of chemoresistance and attractive targets for cancer therapy, however, their identity in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a cellular subpopulation with partial epithelial‐mesenchymal transition (EMT)‐like signature marked by high expression of receptor tyrosine kinase‐like orphan receptor 1 (ROR1) is the origin of heterogeneous tumor cells in PDAC. We demonstrate that ROR1 depletion suppresses tumor growth, recurrence after chemotherapy, and metastasis. Mechanistically, ROR1 induces the expression of Aurora kinase B (AURKB) by activating E2F through c‐Myc to enhance PDAC proliferation. Furthermore, epigenomic analyses reveal that ROR1 is transcriptionally dependent on YAP/BRD4 binding at the enhancer region, and targeting this pathway reduces ROR1 expression and prevents PDAC growth. Collectively, our findings reveal a critical role for ROR1high cells as tumor‐initiating cells and the functional importance of ROR1 in PDAC progression, thereby highlighting its therapeutic targetability. Synopsis: Cancer cell diversity and contribution of tumor‐initiating cells to pancreatic ductal adenocarcinoma (PDAC) progression remain poorly defined. In this work, single‐cell RNA sequencing and functional analyses uncovered targetable tumor‐initiating cells in PDAC. Heterogeneous tumor cells in PDAC arise from a subpopulation with partial EMT signature characterized by high expression of ROR1.Intratumoral ROR1high cells are tumor‐initiating cells with increased tumorigenic capacity.ROR1 functionally promotes PDAC tumor growth, relapse after chemotherapy, and metastasis.ROR1 induces the expression of AURKB via activation of AKT/c‐Myc/E2F signaling, thereby enhancing PDAC proliferation.ROR1 transcription is dependent on the YAP/BRD4 axis. [ABSTRACT FROM AUTHOR]

Exposure of human cells to interferon‐γ (IFNγ) results in a mitotically heritable yet reversible state called long‐term transcriptional memory. We previously identified the clustered GBP genes as strongly primed by IFNγ. Here, we discovered that in primed cells, both interferon‐responsive transcription factors STAT1 and IRF1 target chromatin with accelerated kinetics upon re‐exposure to IFNγ, specifically at promotors of primed genes. Priming does not alter the degree of IFNγ‐induced STAT1 activation or nuclear import, indicating that memory does not alter upstream JAK–STAT signaling. We found STAT1 to be critical to establish transcriptional memory but in a manner that is independent of mere transcription activation. Interestingly, while Serine 727 phosphorylation of STAT1 was maintained during the primed state, STAT1 is not required for the heritability of GBP gene memory. Our results suggest that the memory of interferon exposure constitutes a STAT1‐mediated, heritable state that is established during priming. This renders GBP genes poised for subsequent STAT1 and IRF1 binding and accelerated gene activation upon a secondary interferon exposure. Synopsis: Gene activation by interferon‐γ results in mitotically heritable priming of clustered GBP genes. This study shows target gene transcription is not sufficient to induce memory but relies on STAT1‐dependent gene activation. Once primed, memory is maintained in the absence of STAT1 function. Transcription of memorized GBP genes is not sufficient to induce the primed state.Interferon‐gamma induction results in accelerated STAT1 and IRF1 recruitment in primed cells.STAT1 is essential to establish the primed state but dispensable for the memory of interferon‐γ exposure.Priming does not alter the rate of JAK–STAT signaling upon reencounter of interferon‐γ.STAT1 S727 phosphorylation is maintained during the primed state and has a role in memory. [ABSTRACT FROM AUTHOR]

High levels of 4‐hydroxynonenal (HNE), arising from lipid peroxidation, and HNE‐modified proteins have been identified in postmortem brains of ageing and Alzheimer's disease (AD) patients. The goal of this study is to understand the effect of HNE modification on the structure and function of recombinant apolipoprotein E3 (apoE3) and apolipoprotein E4 (apoE4), which play a critical role in brain cholesterol homeostasis. The two isoforms differ in a single amino acid at position 112: Cys in apoE3 and Arg in apoE4. Immunoblot with HNE‐specific antibody indicates HNE modification of apoE3 and apoE4 with a major band at ~ 36 kDa, while LC–MS/MS revealed Michael addition at His140 (60–70% abundance) and His299 (3–5% abundance) in apoE3 and apoE4, and Cys112 adduct in apoE3 (75% abundance). Circular dichroism spectroscopy revealed no major differences in the overall secondary structure or helical content between unmodified and HNE‐modified apoE. HNE modification did not affect their ability to promote cholesterol efflux from J774.1 macrophages. However, it led to a 3‐fold decrease in their ability to bind lipids and 25–50% decrease in the ability of cerebral cortex endothelial cells to uptake lipoproteins bearing HNE‐modified HNE‐apoE3 or HNE‐apoE4 as noted by fluorescence microscopy and flow cytometry. Taken together, the data indicate that HNE modification impairs lipid binding and cellular uptake of both isoforms, and that apoE3, bearing a Cys, offers a protective role by sequestering lipid peroxidation products that would otherwise cause indiscriminate damage to biomolecules. ApoE4, lacking Cys, is unable to protect against oxidative damage that is commensurate with ageing. [ABSTRACT FROM AUTHOR]

Aberrant splicing is typically attributed to splice‐factor (SF) mutation and contributes to malignancies including acute myeloid leukemia (AML). Here, we discovered a mutation‐independent means to extensively reprogram alternative splicing (AS). We showed that the dysregulated expression of eukaryotic translation initiation factor eIF4E elevated selective splice‐factor production, thereby impacting multiple spliceosome complexes, including factors mutated in AML such as SF3B1 and U2AF1. These changes generated a splicing landscape that predominantly supported altered splice‐site selection for ~800 transcripts in cell lines and ~4,600 transcripts in specimens from high‐eIF4E AML patients otherwise harboring no known SF mutations. Nuclear RNA immunoprecipitations, export assays, polysome analyses, and mutational studies together revealed that eIF4E primarily increased SF production via its nuclear RNA export activity. By contrast, eIF4E dysregulation did not induce known SF mutations or alter spliceosome number. eIF4E interacted with the spliceosome and some pre‐mRNAs, suggesting its direct involvement in specific splicing events. eIF4E induced simultaneous effects on numerous SF proteins, resulting in a much larger range of splicing alterations than in the case of mutation or dysregulation of individual SFs and providing a novel paradigm for splicing control and dysregulation. Synopsis: Aberrant splicing in diseases such as AML is typically attributed to splice‐factor (SF) mutation or dysregulation of specific splicing factors. Here, eukaryotic translation initiation factor eIF4E is reported to induce broad‐range alternative splicing by simultaneously affecting multiple splicing factors.eIF4E induces the production of several SFs simultaneously by promoting nuclear mRNA export and directly interacting with a subset of pre‐mRNAs.A separation‐of‐function mutant of eIF4E shows that the loss of nuclear export activity severely impairs SF production.eIF4E physically associates with several components of the major spliceosome complexes.eIF4E interaction with RNAs is predominantly mediated by the m7G cap.eIF4E overexpression does not lead to global transcriptomic changes but alters splice‐site selection for thousands of transcripts in cell lines and AML patient specimens.eIF4E‐dependent splicing is dysregulated in primary high‐eIF4E AML patient samples. [ABSTRACT FROM AUTHOR]

Summary: Polymorphonuclear neutrophils are no longer considered as a homogeneous population of terminally differentiated and short‐lived cells that belong to the innate immune system only. In fact, data from the past decades have uncovered that neutrophils exhibit large phenotypic heterogeneity and functional versatility that render them more plastic than previously thought. Hence, their precise role as effector cells in inflammation, in immune response and in other pathophysiological processes, including tumors, needs to be better evaluated. In such a complex scenario, common knowledge of the differentiation of neutrophils in bone marrow refers to lineage precursors, starting from the still poorly defined myeloblasts, and proceeding sequentially to promyelocytes, myelocytes, metamyelocytes, band cells, segmented neutrophils, and mature neutrophils, with each progenitor stage being more mature and better characterized. Thanks to the development and utilization of cutting‐edge technologies, novel information about neutrophil precursors at stages earlier than the promyelocytes, hence closer to the hematopoietic stem cells, is emerging. Accordingly, this review discusses the main findings related to the very early precursors of human neutrophils and provides our perspectives on human neutropoiesis. [ABSTRACT FROM AUTHOR]

Purpose: To implement and test variants of chemical shift imaging (CSI) acquiring both free induction decays (FIDs) showing all dissolved‐phase compartments and spin echoes for specifically assessing 129$$ {}^{129} $$Xe in lipids in order to perform precise lipid‐dissolved 129$$ {}^{129} $$Xe MR thermometry in a rat model of general hypothermia. Methods: Imaging was performed at 2.89 T. T2$$ {T}_2 $$ of 129$$ {}^{129} $$Xe in lipids was determined in one rat by fitting exponentials to decaying signals of global spin‐echo spectra. Four rats (conventional CSI) and six rats (turbo spectroscopic imaging) were scanned at three time points with core body temperature 37/34/37∘$$ {}^{\circ } $$C. Lorentzian functions were fit to spectra from regions of interest to determine the water‐referenced chemical shift of lipid‐dissolved 129$$ {}^{129} $$Xe in the abdomen. Absolute 129$$ {}^{129} $$Xe‐derived temperature was compared to values from a rectal probe. Results: Global T2$$ {T}_2 $$ of 129$$ {}^{129} $$Xe in lipids was determined as 251.3 ms±81.4 ms$$ 251.3\;\mathrm{ms}\pm 81.4\;\mathrm{ms} $$. Friedman tests showed significant changes of chemical shift with time for both sequence variants and both FID and spin‐echo acquisitions. Mean and SD of 129$$ {}^{129} $$Xe and rectal probe temperature differences were found to be −0.15∘C±0.93∘C$$ -0.1{5}^{\circ}\mathrm{C}\pm 0.9{3}^{\circ}\mathrm{C} $$ (FID) and −0.38∘C±0.64∘C$$ -0.3{8}^{\circ}\mathrm{C}\pm 0.6{4}^{\circ}\mathrm{C} $$ (spin echo) for conventional CSI as well as 0.03∘C±0.77∘C$$ 0.0{3}^{\circ}\mathrm{C}\pm 0.7{7}^{\circ}\mathrm{C} $$ (FID) and −0.06∘C±0.76∘C$$ -0.0{6}^{\circ}\mathrm{C}\pm 0.7{6}^{\circ}\mathrm{C} $$ (spin echo) for turbo spectroscopic imaging. Conclusion: 129$$ {}^{129} $$Xe MRI using conventional CSI and turbo spectroscopic imaging of lipid‐dissolved 129$$ {}^{129} $$Xe enables precise temperature measurements in the rat's abdomen using both FID and spin‐echo acquisitions with acquisition of spin echoes enabling most precise temperature measurements. [ABSTRACT FROM AUTHOR]

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As for the Braak's SP stage, one patient of PD was in A, and both patients with DLB were in C (Table 1). The PD stages of patients with PD were two to six, and the two DLB patients both had the neocortical type. Two out of six patients with PD were in Braak's NFT stage II, and patients with DLB were in stages II and III. [Extracted from the article]

Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes in the level of transcriptional regulation. Here, we used a multi‐omics approach and integrated ATAC‐, RNA‐ and NET‐seq to identify age‐related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility, and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase in transcriptional output. Instead, aging is accompanied by a decrease in promoter‐proximal pausing of RNA polymerase II (Pol II), while initiation of transcription is not decreased as assessed by RNA polymerase mapping using CUT&RUN. Based on the data reported, we propose that these age‐related changes in transcriptional regulation are due to a reduced stability of the pausing complex. Synopsis: Profiling the chromatin landscape and nascent transcriptome in murine liver reveals an age‐related increase in chromatin accessibility at promoters and enhancers and a decrease in promoter‐proximal pausing of RNA polymerase II due to decreased pausing complex stability. Chromatin accessibility at promoters and enhancers increases with age in murine liver tissue.This increase in chromatin accessibility is not accompanied by major transcriptional alterations, neither at nascent nor steady‐state level.Promoter‐proximal Pol II pausing strongly decreases with age likely due to a decrease in the stability of the pausing complex. [ABSTRACT FROM AUTHOR]

Aims: Phagocytosis is the cellular digestion of extracellular particles, such as pathogens and dying cells, and is a key element in the evolution of central nervous system (CNS) disorders. Microglia and macrophages are the professional phagocytes of the CNS. By clearing toxic cellular debris and reshaping the extracellular matrix, microglia/macrophages help pilot the brain repair and functional recovery process. However, CNS resident and invading immune cells can also magnify tissue damage by igniting runaway inflammation and phagocytosing stressed—but viable—neurons. Discussion: Microglia/macrophages help mediate intercellular communication and react quickly to the "find‐me" signals expressed by dead/dying neurons. The activated microglia/macrophages then migrate to the injury site to initiate the phagocytic process upon encountering "eat‐me" signals on the surfaces of endangered cells. Thus, healthy cells attempt to avoid inappropriate engulfment by expressing "do not‐eat‐me" signals. Microglia/macrophages also have the capacity to phagocytose immune cells that invade the injured brain (e.g., neutrophils) and to regulate their pro‐inflammatory properties. During brain recovery, microglia/macrophages engulf myelin debris, initiate synaptogenesis and neurogenesis, and sculpt a favorable extracellular matrix to support network rewiring, among other favorable roles. Here, we review the multilayered nature of phagocytotic microglia/macrophages, including the molecular and cellular mechanisms that govern microglia/macrophage‐induced phagocytosis in acute brain injury, and discuss strategies that tap into the therapeutic potential of this engulfment process. Conclusion: Identification of biological targets that can temper neuroinflammation after brain injury without hindering the essential phagocytic functions of microglia/macrophages will expedite better medical management of the stroke recovery stage. [ABSTRACT FROM AUTHOR]

Anterior cruciate ligament (ACL) injuries are common knee ligament injuries. While generally successful, ACL reconstruction that uses a tendon graft to stabilize the knee is still associated with a notable percentage of failures and long‐term morbidities. Preclinical research that uses small laboratory species (i.e., mice, rats, and rabbits) to model ACL reconstruction are important to evaluate factors that can impact graft incorporation or posttraumatic osteoarthritis after ACL reconstruction. Small animal ACL reconstruction models are also used for proof‐of‐concept studies for the development of emerging biological strategies aimed at improving ACL reconstruction healing. The objective of this review is to provide an overview on the use of common small animal laboratory species to model ACL reconstruction. The review includes a discussion on comparative knee anatomy, technical considerations including types of tendon grafts employed amongst the small laboratory species (i.e., mice, rats, and rabbits), and common laboratory evaluative methods used to study healing and outcomes after ACL reconstruction in small laboratory animals. The review will also highlight common research questions addressed with small animal models of ACL reconstruction. [ABSTRACT FROM AUTHOR]

Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in‐depth nucleome analysis of mouse germ‐cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome‐wide DNA de‐methylation, creates broadly open chromatin with abundant enhancer‐like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re‐methylation, the PGCs‐to‐spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina‐associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency. Synopsis: Multi‐omics profiling of an in vitro system for mouse germ‐cell development delineates key principles of nucleome programming, including progressive euchromatization and dynamic insulation, as a basis for nuclear totipotency. 3D genome matures unidirectionally over epigenetic reprogramming and programming.Epigenetic reprogramming creates broadly open chromatin with enhanced insulation.Spermatogonia show minimal, peripherally‐positioned, and pericentromeric LADs.Nucleome mis‐programming leads to impaired spermatogenic potential. [ABSTRACT FROM AUTHOR]

Mortality rates among patients suffering from acute respiratory failure remain perplexingly high despite the maintenance of blood oxygen homeostasis during ventilatory support. The biotrauma hypothesis advocates that mechanical forces from invasive ventilation trigger immunological mediators that spread systemically. Yet, how these forces elicit an immune response remains unclear. Here, a biomimetic in vitro three‐dimensional (3D) upper airways model allows to recapitulate lung injury and immune responses induced during invasive mechanical ventilation in neonates. Under such ventilatory support, flow‐induced stresses injure the bronchial epithelium of the intubated airways model and directly modulate epithelial cell inflammatory cytokine secretion associated with pulmonary injury. Fluorescence microscopy and biochemical analyses reveal site‐specific susceptibility to epithelial erosion in airways from jet‐flow impaction and are linked to increases in cell apoptosis and modulated secretions of cytokines IL‐6, ‐8, and ‐10. In an effort to mitigate the onset of biotrauma, prophylactic pharmacological treatment with Montelukast, a leukotriene receptor antagonist, reduces apoptosis and pro‐inflammatory signaling during invasive ventilation of the in vitro model. This 3D airway platform points to a previously overlooked origin of lung injury and showcases translational opportunities in preclinical pulmonary research toward protective therapies and improved protocols for patient care. [ABSTRACT FROM AUTHOR]

In order to support bone marrow regeneration after myeloablation, hematopoietic stem cells (HSCs) actively divide to provide both stem and progenitor cells. However, the mechanisms regulating HSC function and cell fate choice during hematopoietic recovery remain unclear. We herein provide novel insights into HSC regulation during regeneration by focusing on mitochondrial metabolism and ATP citrate lyase (ACLY). After 5‐fluorouracil‐induced myeloablation, HSCs highly expressing endothelial protein C receptor (EPCRhigh) were enriched within the stem cell fraction at the expense of more proliferative EPCRLow HSCs. These EPCRHigh HSCs were initially more primitive than EPCRLow HSCs and enabled stem cell expansion by enhancing histone acetylation, due to increased activity of ACLY in the early phase of hematopoietic regeneration. In the late phase of recovery, HSCs enhanced differentiation potential by increasing the accessibility of cis‐regulatory elements in progenitor cell‐related genes, such as CD48. In conditions of reduced mitochondrial metabolism and ACLY activity, these HSCs maintained stem cell phenotypes, while ACLY‐dependent histone acetylation promoted differentiation into CD48+ progenitor cells. Collectively, these results indicate that the dynamic control of ACLY‐dependent metabolism and epigenetic alterations is essential for HSC regulation during hematopoietic regeneration. Synopsis: The metabolic mechanisms driving hematopoietic stem cell (HSC) activation and recovery of the blood system after myeloablation remain unclear. This study reports ATP citrate lyase (ACLY)‐dependent histone acetylation and changes in chromatin accessibility as dynamic determinants of HSC function during bone marrow regeneration. HSC gene expression, metabolic status and histone acetylation differ between early and late stages post 5‐FU treatment in mice.Early after 5‐FU treatment, increased mitochondrial membrane potential, ACLY expression and global H3K27ac levels enhance HSC expansion and in vivo engraftment potential.Increased HSC differentiation capacity at late post‐5‐FU stages is associated with increased accessibility of progenitor cell‐related genes.Suppression of ACLY‐mediated metabolism maintains HSC identity during late regeneration. [ABSTRACT FROM AUTHOR]

Background: Type 2 diabetes mellitus (T2DM) is associated with cognitive decline and altered brain structure and function. However, the interhemispheric coordination of T2DM patients is unclear. Purpose To investigate interhemispheric functional and anatomic connectivity in T2DM, and their associations with cognitive performance and endocrine parameters. Study Type: Prospective. Subjects: 38 T2DM patients and 42 matched controls. Field Strength/Sequences: 3.0 T magnetic resonance imaging (MRI) scanner; magnetization‐prepared rapid acquisition gradient echo sequence; fluid‐attenuated inversion recovery sequence; single‐shot, gradient‐recalled echo‐planar imaging sequence (resting‐state functional MRI); and diffusion‐weighted spin‐echo‐based echo‐planar sequence (diffusion tensor imaging). Assessment Voxel‐mirrored homotopic connectivity (VMHC) value was calculated based on the functional images. Fibers passing through the regions with significant VMHC differences were identified using an atlas‐guided track recognition. The mean fractional anisotropy (FA), mean diffusivity (MD), and fiber length were extracted and compared between the two groups. Finally, correlational analyses were performed to examine the relationships between abnormal interhemispheric connectivity, cognitive performances, and endocrine parameters. Statistical Tests: Two‐sample t‐tests were performed controlling for confounding factors, with partial correlation analysis. False discovery rate (FDR) correction was used for multiple comparisons. A P value <0.05 was considered statistically significant. Results: T2DM patients exhibited significantly decreased VMHC between bilateral lingual gyrus and sensorimotor cortex. The fibers connecting lingual gyrus in patients showed significantly lower FA (P = 0.011) and shorter fiber length (P < 0.001), while the differences in sensorimotor fibers were insignificant (P = 0.096 for FA, P = 0.739 for fiber length and P = 0.150 for MD). The FA value in the lingual fibers was negatively correlated with insulin resistance (IR) level in T2DM group after FDR correction (R = −0.635). Data Conclusion: We noted disruptions in interhemispheric coordination in T2DM patients, involving both functional and anatomical connectivities. IR might be a promising therapeutic target in the intervention of T2DM‐related cognitive impairment. Level of Evidence: 2 Technical Efficacy Stage: 2 [ABSTRACT FROM AUTHOR]

Genetically diverse pluripotent stem cells display varied, heritable responses to differentiation cues. Here, we harnessed these disparities through derivation of mouse embryonic stem cells from the BXD genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, to identify loci regulating cell state transitions. Upon transition to formative pluripotency, B6 stem cells quickly dissolved naïve networks adopting gene expression modules indicative of neuroectoderm lineages, whereas D2 retained aspects of naïve pluripotency. Spontaneous formation of embryoid bodies identified divergent differentiation where B6 showed a propensity toward neuroectoderm and D2 toward definitive endoderm. Genetic mapping identified major trans‐acting loci co‐regulating chromatin accessibility and gene expression in both naïve and formative pluripotency. These loci distally modulated occupancy of pluripotency factors at hundreds of regulatory elements. One trans‐acting locus on Chr 12 primarily impacted chromatin accessibility in embryonic stem cells, while in epiblast‐like cells, the same locus subsequently influenced expression of genes enriched for neurogenesis, suggesting early chromatin priming. These results demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome. SYNOPSIS: The molecular basis for phenotypic variation of embryonic stem cells (ESC) from genetically diverse individuals remains largely unknown. This study combines extensive expression profiling and mouse genetics to identify trans‐acting loci differentially regulating the epigenome during ESC differentiation. Genetic background alters ESC fate and position along the pluripotency spectrum.Genetic background determines ESC differentiation propensity through chromatin regulation in naïve pluripotency.Cellular systems genetics identifies six trans‐acting loci regulating gene expression and chromatin organization.KRAB zinc‐finger protein expression is strain‐dependent, and linked to TRIM28 function at trans‐target genes. [ABSTRACT FROM AUTHOR]

H2A.Z is a H2A‐type histone variant essential for many aspects of cell biology, ranging from gene expression to genome stability. From deuterostomes, H2A.Z evolved into two paralogues, H2A.Z.1 and H2A.Z.2, that differ by only three amino acids and are encoded by different genes (H2AFZ and H2AFV, respectively). Despite the importance of this histone variant in development and cellular homeostasis, very little is known about the individual functions of each paralogue in mammals. Here, we have investigated the distinct roles of the two paralogues in cell cycle regulation and unveiled non‐redundant functions for H2A.Z.1 and H2A.Z.2 in cell division. Our findings show that H2A.Z.1 regulates the expression of cell cycle genes such as Myc and Ki‐67 and its depletion leads to a G1 arrest and cellular senescence. On the contrary, H2A.Z.2, in a transcription‐independent manner, is essential for centromere integrity and sister chromatid cohesion regulation, thus playing a key role in chromosome segregation. Synopsis: This study shows that the very similar histone variants H2A.Z.1 and H2A.Z.2 have different functions in chromatin organisation and cell cycle regulation. H2A.Z.2 is essential for chromosome segregation fidelity.H2A.Z.2 regulates sister chromatid cohesion, CPC localisation and kinetochores.H2A.Z.1 is important for the G1/S transition via MYC transcription and p21/p27 suppression.H2A.Z.1 and H2A.Z.2 have distinct role in chromatin organisation and gene expression. [ABSTRACT FROM AUTHOR]

People who have Alzheimer's disease neuropathologic change (ADNC) typically associated with dementia but not the associated cognitive decline can be considered to be "resilient" to the effects of ADNC. We have previously reported lower neocortical levels of hyperphosphorylated tau (pTau) and less limbic‐predominant age‐related TDP‐43 encephalopathy neuropathologic change (LATE‐NC) in the resilient participants compared to those with dementia and similar ADNC as determined by current NIA‐AA recommendations using traditional semi‐quantitative assessments of amyloid β and pathological tau burden. To better understand differences between AD‐dementia and resilient participants, we developed and applied a deep learning approach to analyze the neuropathology of 14 brain donors from the Adult Changes in Thought study, including seven stringently defined resilient participants and seven age‐matched AD‐dementia controls. We created two novel, fully automated deep learning algorithms to quantify the level of phosphorylated TDP‐43 (pTDP‐43) and pTau in whole slide imaging. The models performed better than traditional techniques for quantifying pTDP‐43 and pTau. The second model was able to segment lesions staining for pTau into neurofibrillary tangles (NFTs) and tau neurites (neuronal processes positive for pTau). Both groups had similar quantities of pTau localizing to neurites, but the pTau burden associated with NFTs in the resilient group was significantly lower compared to the group with dementia. These results validate use of deep learning approaches to quantify clinically relevant microscopic characteristics from neuropathology workups. These results also suggest that the burden of NFTs is more strongly associated with cognitive impairment than the more diffuse neuritic tau commonly seen with tangle pathology and suggest that additional factors may underlie resilience mechanisms defined by traditional means. [ABSTRACT FROM AUTHOR]

Mass‐tag cell barcoding has increased the throughput, multiplexing, and robustness of multiple cytometry approaches. Previously, we adapted mass cytometry for cells to analyze synaptosome preparations (mass synaptometry or SynTOF), extending mass cytometry to these smaller, anuclear particles. To improve throughput and individual event resolution, we report here the application of palladium‐based barcoding in human synaptosomes. Up to 20 individual samples, each with a unique combinatorial barcode, were pooled for labeling with an antibody cocktail. Our synaptosome protocol used six palladium‐based barcoding reagents, and in combination with sequential gating increased the identification of presynaptic events approximately fourfold. These same parameters also efficiently resolved two other anuclear particles: human red blood cells and platelets. The addition of palladium‐based mass‐tag barcoding to our approach improves mass cytometry of synaptic particles. [ABSTRACT FROM AUTHOR]

Introduction: Our study analysed previous studies employing positron emission tomography with co‐registered computer tomography (PET/CT) in andrological patient evaluation and assessed the differences in 2‐[18F]F‐fluoro‐2′‐deoxyglucose (FDG) uptake between three groups: healthy testes, benign and malignant testicular pathology. Methods: Medline and Embase were systematically searched for studies involving FDG‐PET/CT imaging of testes with results expressed as mean standardised uptake value (SUVmean). A one‐way ANOVA was used to compare SUVmean between three groups. All papers assessing andrological parameters were pooled to compare fertility data. Results: Seventeen studies, including three relating to fertility diagnosis, with a total of 830 patients, were included in the review. One‐way ANOVA showed a statistical difference between mean values of tracer SUVmean in healthy and malignant testes (Dif. = −2.77, 95% CI = −4.32 to 1.21, p < 0.01) as well as benign and malignant (Dif. = −2.95, 95% CI = −4.33 to −1.21, p < 0.01) but no difference between healthy and benign (Dif. = 0.19, 95% CI = −0.96 to 1.33, p = 0.90). There is some evidence to suggest that FDG uptake and testicular volume are positively correlated to total sperm count, sperm concentration and sperm motility and that germ cells are likely to account for the majority of testicular FDG accumulation. Conclusion: Our findings indicate that malignant testicular lesions demonstrate a significantly higher FDG uptake than benign testicular lesions or healthy testes. Some evidence also suggests that FDG‐PET could visualise metabolic activity and thus spermatogenesis; however more studies are required to determine whether FDG‐PET could also be used to diagnose infertility. Further studies should focus on correlating both sex hormone‐serum levels and semen analysis results with imaging data. [ABSTRACT FROM AUTHOR]

Testis‐specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin lymphoma (HL) samples showed that the ectopic expression of the eutherian testis‐specific histone variant H2A.B is an inherent feature of HL. In experiments using two HL cell lines derived from different subtypes of HL, H2A.B knockdown inhibited cell proliferation. H2A.B was enriched in both nucleoli of these HL cell lines and primary HL samples. We found that H2A.B enhanced ribosomal DNA (rDNA) transcription, was enriched at the rDNA promoter and transcribed regions, and interacted with RNA Pol I. Depletion of H2A.B caused the loss of RNA Pol I from rDNA chromatin. Remarkably, H2A.B was also required for high levels of ribosomal protein gene expression being located at the transcriptional start site and within the gene body. H2A.B knockdown reduced gene body chromatin accessibility of active RNA Pol II genes concurrent with a decrease in transcription. Taken together, our data show that in HL H2A.B has acquired a new function, the ability to increase ribosome biogenesis. SYNOPSIS: The eutherian testis‐specific histone variant H2A.B is aberrantly expressed in Hodgkin Lymphoma and enhances ribosomal biogenesis by stimulating both RNA Pol I transcription and the transcription of ribosomal protein genes. H2A.B is required for the high cell proliferation rate of Hodgkin Lymphoma cell lines.H2A.B is enriched in rDNA chromatin and interacts with RNA Pol I.H2A.B is required for transcription and alternative splicing of genes that are linked to cancer such as ribosomal proteins.The chromatin accessibility of active genes is enhanced by H2A.B. [ABSTRACT FROM AUTHOR]

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Objective: The objective of this study was to identify genetic variants on the X‐chromosome associated with Parkinson disease (PD) risk. Methods: We performed an X‐chromosome–wide association study (XWAS) of PD risk by meta‐analyzing results from sex‐stratified analyses. To avoid spurious associations, we designed a specific harmonization pipeline for the X‐chromosome and focused on a European ancestry sample. We included 11,142 cases, 280,164 controls, and 5,379 proxy cases, based on parental history of PD. Additionally, we tested the association of significant variants with (1) PD risk in an independent replication with 1,561 cases and 2,465 controls and (2) putamen volume in 33,360 individuals from the UK Biobank. Results: In the discovery meta‐analysis, we identified rs7066890 (odds ratio [OR] = 1.10, 95% confidence interval [CI] = 1.06–1.14, p = 2.2 × 10−9), intron of GPM6B, and rs28602900 (OR = 1.10, 95% CI = 1.07–1.14, p = 1.6 × 10−8) in a high gene density region including RPL10, ATP6A1, FAM50A, and PLXNA3. The rs28602900 association with PD was replicated (OR = 1.16, 95% CI = 1.03–1.30, p = 0.016) and shown to colocalize with a significant expression quantitative locus (eQTL) regulating RPL10 expression in the putamen and other brain tissues in the Genotype‐Tissue Expression Project. Additionally, the rs28602900 locus was found to be associated with reduced brain putamen volume. No results reached genome‐wide significance in the sex‐stratified analyses. Interpretation: We report the first XWAS of PD and identify 2 genome‐wide significant loci. The rs28602900 association was replicated in an independent PD dataset and showed concordant effects in its association with putamen volume. Critically, rs26802900 is a significant eQTL of RPL10. These results support a role for ribosomal proteins in PD pathogenesis and show that the X‐chromosome contributes to PD genetic risk. ANN NEUROL 2021;90:22–34 [ABSTRACT FROM AUTHOR]

Many species of animals have stem cells that they maintain throughout their lives, which suggests that stem cells are an ancestral feature of all animals. From this, we take the viewpoint that cells with the biological properties of 'stemness'—self‐renewal and multipotency—may share ancestral genetic circuitry. However, in practice is it very difficult to identify and compare stemness gene signatures across diverse animals and large evolutionary distances? First, it is critical to experimentally demonstrate self‐renewal and potency. Second, genomic methods must be used to determine specific gene expression in stem cell types compared with non‐stem cell types to determine stem cell gene enrichment. Third, gene homology must be mapped between diverse animals across large evolutionary distances. Finally, conserved genes that fulfill these criteria must be tested for role in stem cell function. It is our viewpoint that by comparing stem cell‐specific gene signatures across evolution, ancestral programs of stemness can be uncovered, and ultimately, the dysregulation of stemness programs drives the state of cancer stem cells. [ABSTRACT FROM AUTHOR]

Giemsa staining of metaphase chromosomes results in a characteristic banding useful for identification of chromosomes and its alterations. We have investigated in silico whether Giemsa bands (G bands) correlate with epigenetic and topological features of the interphase genome. Staining of G‐positive bands decreases with GC content; nonetheless, G‐negative bands are GC heterogeneous. High GC bands are enriched in active histone marks, RNA polymerase II, and SINEs and associate with gene richness, gene expression, and early replication. Low GC bands are enriched in repressive marks, lamina‐associated domains, and LINEs. Histone H1 variants distribute heterogeneously among G bands: H1X is enriched at high GC bands and H1.2 is abundant at low GC, compacted bands. According to epigenetic features and H1 content, G bands can be organized in clusters useful to compartmentalize the genome. Indeed, we have obtained Hi‐C chromosome interaction maps and compared topologically associating domains (TADs) and A/B compartments to G banding. TADs with high H1.2/H1X ratio strongly overlap with B compartment, late replicating, and inaccessible chromatin and low GC bands. We propose that GC content is a strong driver of chromatin compaction and 3D genome organization, that Giemsa staining recapitulates this organization denoted by high‐throughput techniques, and that H1 variants distribute at distinct chromatin domains. Databases: Hi‐C data on T47D breast cancer cells have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE147627. [ABSTRACT FROM AUTHOR]

Acute brain ischemia accounts for most of stroke cases and constitutes a leading cause of deaths among adults and permanent disabilities in survivors. Currently, the intravenous thrombolysis is the only available medication for ischemic stroke; mechanical thrombectomy is an emerging alternative treatment for occlusion of large arteries and has shown some promise in selected subsets of patients. However, the overall narrow treatment window and potential risks largely limit the patient eligibility. New druggable targets are needed to innovate the treatment of brain ischemia. As the rate‐limiting enzyme in the biosyntheses of prostanoids, cyclooxygenase (COX), particularly the inducible isoform COX‐2, has long been implicated in mechanisms of acute stroke‐induced brain injury and inflammation. However, the notion of therapeutically targeting COX has been diminished over the past two decades due to significant complications of the cardiovascular and cerebrovascular systems caused by long‐term use of COX‐2 inhibitor drugs. New treatment strategies targeting the downstream prostanoid signaling receptors regulating the deleterious effects of COX cascade have been proposed. As such, a large number of selective small molecules that negatively or positively modulate these important inflammatory regulators have been evaluated for neuroprotection and other beneficial effects in various animal models of brain ischemia. These timely preclinical studies, though not yet led to clinical innovation, provided new insights into the regulation of inflammatory reactions in the ischemic brain and could guide drug discovery efforts aiming for novel adjunctive strategies, along with current reperfusion therapy, to treat acute brain ischemia with higher specificity and longer therapeutic window. [ABSTRACT FROM AUTHOR]

Rhabdoid tumor (RT) is a pediatric cancer characterized by the inactivation of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. Although this deletion is the known oncogenic driver, there are limited effective therapeutic options for these patients. Here we use unbiased screening of cell line panels to identify a heightened sensitivity of rhabdoid tumor to mithramycin and the second‐generation analogue EC8042. The sensitivity of MMA and EC8042 was superior to traditional DNA damaging agents and linked to the causative mutation of the tumor, SMARCB1 deletion. Mithramycin blocks SMARCB1‐deficient SWI/SNF activity and displaces the complex from chromatin to cause an increase in H3K27me3. This triggers chromatin remodeling and enrichment of H3K27ac at chromHMM‐defined promoters to restore cellular differentiation. These effects occurred at concentrations not associated with DNA damage and were not due to global chromatin remodeling or widespread gene expression changes. Importantly, a single 3‐day infusion of EC8042 caused dramatic regressions of RT xenografts, recapitulated the increase in H3K27me3, and cellular differentiation described in vitro to completely cure three out of eight mice. Synopsis: EC8042 is identified as an inhibitor of oncogenic SWI/SNF and a promising therapeutic candidate for rhabdoid tumor. The mechanism of target inhibition is elucidated and used to optimize compound administration, characterize an associated biomarker, and cure mice bearing rhabdoid tumor xenografts. Mithramycin displaced SMARCB1‐deficient SWI/SNF from chromatin.Mithramycin induced epigenetic reprogramming favoring promoters and SWI/SNF bound CTCF sites to induce mesenchymal differentiation.EC8042, a second‐generation mithramycin analogue, induced mesenchymal differentiation to cure three of eight mice bearing rhabdoid tumor xenografts with a single 3‐day infusion of the drug. [ABSTRACT FROM AUTHOR]

Objectives/hypothesis: The objectives of this study were to evaluate laryngeal inflammation and mucosal integrity in a murine model of reflux disease and to assess the protective effects of topical agents including alginate, hyaluronic acid, and cashew gum.Study Design: Animal study.Methods: A surgical murine model of reflux disease was evaluated at 3 or 7 days postsurgery, and laryngeal samples were collected to measure inflammation (wet weight and myeloperoxidase [MPO]) and mucosal integrity (transepithelial resistance [TER] and mucosal permeability to fluorescein). Additional groups of animals were administered one of several topical agents (alginate, hyaluronic acid, or cashew gum) daily, and laryngeal inflammation and mucosal integrity were evaluated at 3 days postsurgery.Results: At 3 days, and not 7 days postsurgery, we observed increased laryngeal wet weight and MPO, decreased laryngeal TER, and increased laryngeal mucosa permeability. Alginate partially decreased laryngeal inflammation (wet weight and not MPO) and dramatically improved laryngeal mucosal integrity. Conversely, hyaluronic acid eliminated the inflammation; however, it had no effect on laryngeal mucosal integrity impairment. Cashew gum eliminated laryngeal inflammation as well as the impairment in laryngeal mucosal integrity.Conclusions: This study shows that a surgical model of reflux disease induced laryngeal inflammation and impairment in laryngeal barrier function. These observed alterations were partially attenuated by alginate and hyaluronic acid and completely reversed by cashew gum.Level Of Evidence: NA Laryngoscope, 2020. [ABSTRACT FROM AUTHOR]

Aims: Most individuals with AD neuropathological changes have co‐morbidities which have an impact on the integrity of the WM. This study analyses oligodendrocyte and myelin markers in the frontal WM in a series of AD cases without clinical or pathological co‐morbidities. Methods: From a consecutive autopsy series, 206 cases had neuropathological changes of AD; among them, only 33 were AD without co‐morbidities. WM alterations were first evaluated in coronal sections of the frontal lobe in every case. Then, RT‐qPCR and immunohistochemistry were carried out in the frontal WM of AD cases without co‐morbidities to analyse the expression of selected oligodendrocyte and myelin markers. Results: WM demyelination was more marked in AD with co‐morbidities when compared with AD cases without co‐morbidities. Regarding the later, mRNA expression levels of MBP, PLP1, CNP, MAG, MAL, MOG and MOBP were preserved at stages I–II/0–A when compared with middle‐aged (MA) individuals, but significantly decreased at stages III–IV/0–C. This was accompanied by reduced expression of NG2 and PDGFRA mRNA, reduced numbers of NG2‐, Olig2‐ and HDAC2‐immunoreactive cells and reduced glucose transporter immunoreactivity. Partial recovery of some of these markers occurred at stages V–VI/B–C. Conclusions: The present observations demonstrate that co‐morbidities have an impact on WM integrity in the elderly and in AD, and that early alterations in oligodendrocytes and transcription of genes linked to myelin proteins in WM occur in AD cases without co‐morbidities. These are followed by partial recovery attempts at advanced stages. These observations suggest that oligodendrocytopathy is part of AD. [ABSTRACT FROM AUTHOR]

When dormant naïve T cells first become activated by antigen‐presenting cells, they express the autocrine growth factor IL‐2 which transforms them into rapidly dividing effector T cells. During this process, hundreds of genes undergo epigenetic reprogramming for efficient activation, and also for potential reactivation after they return to quiescence as memory T cells. However, the relative contributions of IL‐2 and T cell receptor signaling to this process are unknown. Here, we show that IL‐2 signaling is required to maintain open chromatin at hundreds of gene regulatory elements, many of which control subsequent stimulus‐dependent alternative pathways of T cell differentiation. We demonstrate that IL‐2 activates binding of AP‐1 and STAT5 at sites that can subsequently bind lineage‐determining transcription factors, depending upon what other external factors exist in the local T cell environment. Once established, priming can also be maintained by the stroma‐derived homeostatic cytokine IL‐7, and priming diminishes if Il7r is subsequently deleted in vivo. Hence, IL‐2 is not just a growth factor; it lays the foundation for T cell differentiation and immunological memory. Synopsis: TCR plus IL‐2 signaling transforms naïve T cells to undifferentiated effector T cells by reprograming immune response genes. IL‐2‐induced STAT5 binding renders these genes accessible and receptive to subsequent binding of other differentiation‐inducing factors which replace STAT5. T cell receptor and IL‐2 signaling epigenetically reprogram immune response genes.IL‐2 signaling alone can maintain binding of STAT5 and AP‐1 at primed genes.Sites primed by STAT5 in undifferentiated T cells can subsequently bind other lineage‐specific STAT proteins and transcription factors after differentiation.Terminal T cell differentiation is not pioneered by lineage‐determining factors, but is made possible by IL‐2 signaling which makes lineage‐specific genes receptive to these factors. [ABSTRACT FROM AUTHOR]