Atlas of the aging mouse brain reveals white matter as vulnerable foci.

Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of the mouse brain, profiling 1,076 samples from 15 regions across 7 ages and 2 rejuvenation interventions. Our analysis identified a brain-wide gene signature of aging in glial cells, which exhibited spatially defined changes in magnitude. By integrating spatial and single-nucleus transcriptomics, we found that glial aging was particularly accelerated in white matter compared with cortical regions, whereas specialized neuronal populations showed region-specific expression changes. Rejuvenation interventions, including young plasma injection and dietary restriction, exhibited distinct effects on gene expression in specific brain regions. Furthermore, we discovered differential gene expression patterns associated with three human neurodegenerative diseases, highlighting the importance of regional aging as a potential modulator of disease. Our findings identify molecular foci of brain aging, providing a foundation to target age-related cognitive decline.

Genetic variants of phospholipase C-γ2 alter the phenotype and function of microglia and confer differential risk for Alzheimer's disease.

Genetic association studies have demonstrated the critical involvement of the microglial immune response in Alzheimer's disease (AD) pathogenesis. Phospholipase C-gamma-2 (PLCG2) is selectively expressed by microglia and functions in many immune receptor signaling pathways. In AD, PLCG2 is induced uniquely in plaque-associated microglia. A genetic variant of PLCG2, PLCG2P522R, is a mild hypermorph that attenuates AD risk. Here, we identified a loss-of-function PLCG2 variant, PLCG2M28L, that confers an increased AD risk. PLCG2P522R attenuated disease in an amyloidogenic murine AD model, whereas PLCG2M28L exacerbated the plaque burden associated with altered phagocytosis and Aß clearance. The variants bidirectionally modulated disease pathology by inducing distinct transcriptional programs that identified microglial subpopulations associated with protective or detrimental phenotypes. These findings identify PLCG2M28L as a potential AD risk variant and demonstrate that PLCG2 variants can differentially orchestrate microglial responses in AD pathogenesis that can be therapeutically targeted.

Ageing-associated changes in transcriptional elongation influence longevity.

Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing1-4. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms5 and flies6 increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.

Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17.

Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing1-3. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds4,5. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.

Dysregulation of brain and choroid plexus cell types in severe COVID-19.

Although SARS-CoV-2 primarily targets the respiratory system, patients with and survivors of COVID-19 can suffer neurological symptoms1-3. However, an unbiased understanding of the cellular and molecular processes that are affected in the brains of patients with COVID-19 is missing. Here we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control individuals (including 1 patient with terminal influenza) and 8 patients with COVID-19. Although our systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations indicating that barrier cells of the choroid plexus sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover microglia and astrocyte subpopulations associated with COVID-19 that share features with pathological cell states that have previously been reported in human neurodegenerative disease4-6. Synaptic signalling of upper-layer excitatory neurons-which are evolutionarily expanded in humans7 and linked to cognitive function8-is preferentially affected in COVID-19. Across cell types, perturbations associated with COVID-19 overlap with those found in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia and depression. Our findings and public dataset provide a molecular framework to understand current observations of COVID-19-related neurological disease, and any such disease that may emerge at a later date.

Exercise plasma boosts memory and dampens brain inflammation via clusterin.

Physical exercise is generally beneficial to all aspects of human and animal health, slowing cognitive ageing and neurodegeneration1. The cognitive benefits of physical exercise are tied to an increased plasticity and reduced inflammation within the hippocampus2-4, yet little is known about the factors and mechanisms that mediate these effects. Here we show that 'runner plasma', collected from voluntarily running mice and infused into sedentary mice, reduces baseline neuroinflammatory gene expression and experimentally induced brain inflammation. Plasma proteomic analysis revealed a concerted increase in complement cascade inhibitors including clusterin (CLU). Intravenously injected CLU binds to brain endothelial cells and reduces neuroinflammatory gene expression in a mouse model of acute brain inflammation and a mouse model of Alzheimer's disease. Patients with cognitive impairment who participated in structured exercise for 6 months had higher plasma levels of CLU. These findings demonstrate the existence of anti-inflammatory exercise factors that are transferrable, target the cerebrovasculature and benefit the brain, and are present in humans who engage in exercise.

Ageing hallmarks exhibit organ-specific temporal signatures.

Ageing is the single greatest cause of disease and death worldwide, and understanding the associated processes could vastly improve quality of life. Although major categories of ageing damage have been identified-such as altered intercellular communication, loss of proteostasis and eroded mitochondrial function1-these deleterious processes interact with extraordinary complexity within and between organs, and a comprehensive, whole-organism analysis of ageing dynamics has been lacking. Here we performed bulk RNA sequencing of 17 organs and plasma proteomics at 10 ages across the lifespan of Mus musculus, and integrated these findings with data from the accompanying Tabula Muris Senis2-or 'Mouse Ageing Cell Atlas'-which follows on from the original Tabula Muris3. We reveal linear and nonlinear shifts in gene expression during ageing, with the associated genes clustered in consistent trajectory groups with coherent biological functions-including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Notably, these gene sets show similar expression across tissues, differing only in the amplitude and the age of onset of expression. Widespread activation of immune cells is especially pronounced, and is first detectable in white adipose depots during middle age. Single-cell RNA sequencing confirms the accumulation of T cells and B cells in adipose tissue-including plasma cells that express immunoglobulin J-which also accrue concurrently across diverse organs. Finally, we show how gene expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to the ageing of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of ageing, providing a foundation from which to track systemic sources of declining health at old age.

Starting Cosmological Simulations from the Big Bang.

The cosmic large-scale structure (LSS) provides a unique testing ground for connecting fundamental physics to astronomical observations. Modeling the LSS requires numerical N-body simulations or perturbative techniques that both come with distinct shortcomings. Here we present the first unified numerical approach, enabled by new time integration and discreteness reduction schemes, and demonstrate its convergence at the field level. In particular, we show that our simulations (i) can be initialized directly at time zero, and (ii) can be made to agree with high-order Lagrangian perturbation theory in the fluid limit. This enables fast, self-consistent, and UV-complete forward modeling of LSS observables.

KL1 Domain of Longevity Factor Klotho Mimics the Metabolome of Cognitive Stimulation and Enhances Cognition in Young and Aging Mice.

Cognitive deficits are a major biomedical challenge-and engagement of the brain in stimulating tasks improves cognition in aged individuals (Wilson et al., 2002; Gates et al., 2011) and rodents (Aidil-Carvalho et al., 2017), through unknown mechanisms. Whether cognitive stimulation alters specific metabolic pathways in the brain is unknown. Understanding which metabolic processes are involved in cognitive stimulation is important because it could lead to pharmacologic intervention that promotes biological effects of a beneficial behavior, toward the goal of effective medical treatments for cognitive deficits. Here we show using male mice that cognitive stimulation induced metabolic remodeling of the mouse hippocampus, and that pharmacologic treatment with the longevity hormone α-klotho (KL), mediated by its KL1 domain, partially mimicked this alteration. The shared, metabolic signature shared between cognitive stimulation and treatment with KL or KL1 closely correlated with individual mouse cognitive performance, indicating a link between metabolite levels and learning and memory. Importantly, the treatment of mice with KL1, an endogenous circulating factor that more closely mimicked cognitive stimulation than KL, acutely increased synaptic plasticity, a substrate of cognition. KL1 also improved cognition, itself, in young mice and countered deficits in old mice. Our data show that treatments or interventions mimicking the hippocampal metabolome of cognitive stimulation can enhance brain functions. Further, we identify the specific domain by which klotho promotes brain functions, through KL1, a metabolic mimic of cognitive stimulation.SIGNIFICANCE STATEMENT Cognitive deficits are a major biomedical challenge without truly effective pharmacologic treatments. Engaging the brain through cognitive tasks benefits cognition. Mimicking the effects of such beneficial behaviors through pharmacological treatment represents a highly valuable medical approach to treating cognitive deficits. We demonstrate that brain engagement through cognitive stimulation induces metabolic remodeling of the hippocampus that was acutely recapitulated by the longevity factor klotho, mediated by its KL1 domain. Treatment with KL1, a close mimic of cognitive stimulation, enhanced cognition and countered cognitive aging. Our findings shed light on how cognition metabolically alters the brain and provide a plausible therapeutic intervention for mimicking these alterations that, in turn, improves cognition in the young and aging brain.

Erratum: Quantifying Qubit Magic Resource with Gottesman-Kitaev-Preskill Encoding [Phys. Rev. Lett. 128, 210502 (2022)].

This corrects the article DOI: 10.1103/PhysRevLett.128.210502.

Ageing-associated small RNA cargo of extracellular vesicles.

Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

Quantifying Qubit Magic Resource with Gottesman-Kitaev-Preskill Encoding.

Quantum resource theories are a powerful framework for characterizing and quantifying relevant quantum phenomena and identifying processes that optimize their use for different tasks. Here, we define a resource measure for magic, the sought-after property in most fault-tolerant quantum computers. In contrast to previous literature, our formulation is based on bosonic codes, well-studied tools in continuous-variable quantum computation. Particularly, we use the Gottesman-Kitaev-Preskill code to represent multiqubit states and consider the resource theory for the Wigner negativity. Our techniques are useful in finding resource lower bounds for different applications as state conversion and gate synthesis. The analytical expression of our magic measure allows us to extend current analysis limited to small dimensions, easily addressing systems of up to 12 qubits.

GeneTrail 3: advanced high-throughput enrichment analysis.

We present GeneTrail 3, a major extension of our web service GeneTrail that offers rich functionality for the identification, analysis, and visualization of deregulated biological processes. Our web service provides a comprehensive collection of biological processes and signaling pathways for 12 model organisms that can be analyzed with a powerful framework for enrichment and network analysis of transcriptomic, miRNomic, proteomic, and genomic data sets. Moreover, GeneTrail offers novel workflows for the analysis of epigenetic marks, time series experiments, and single cell data. We demonstrate the capabilities of our web service in two case-studies, which highlight that GeneTrail is well equipped for uncovering complex molecular mechanisms. GeneTrail is freely accessible at: http://genetrail.bioinf.uni-sb.de.

Comparison of First-Line Anti-PD-1-Based Combination Therapies in Metastatic Renal-Cell Carcinoma: Real-World Experiences from a Retrospective, Multi-Institutional Cohort.

INTRODUCTION: The aim of this study was to test for differences in overall (OS) and progression-free survival (PFS) rates and toxicity in first-line immune checkpoint inhibition (IO) combination therapy in metastatic renal-cell carcinoma (mRCC) patients. METHODS: Between November 2017 and April 2021, 104 patients with histologically confirmed mRCC from 6 tertiary referral centers with either IO + IO (nivolumab + ipilimumab, n = 68) or IO + tyrosine kinase inhibitor (TKI) (pembrolizumab + axitinib, n = 36) were included. Kaplan-Meier and Cox regression analyses tested for OS and PFS differences. RESULTS: Of 104 mRCC patients, 68 received IO + IO (65.4%) and 36 IO + TKI (34.6%) therapy, respectively. Median age was 67 years (interquartile range: 57-70.3). Patients receiving IO + TKI were less likely to be poor risk according to the International Metastatic Renal-Cell Carcinoma Database Consortium score (16.7 vs. 30.9%) and presented with lower T-stage, compared to IO + IO treated patients. Median PFS was 9.8 months (CI: 5.3-17.6) versus 12.3 months (CI: 7.7 - not reached) for IO + IO versus IO + TKI treatment, respectively (p = 0.22). Median OS was not reached, survival rates at 12 months being 73.9 versus 90.0% for IO + IO versus IO + TKI patients (p = 0.089). In subgroup analyses of elderly patients (≥70 years, n = 38), IO + TKI treatment resulted in better OS rates at 12 months compared to IO + IO (91.0 vs. 57.0%; p = 0.042). CONCLUSION: IO + IO and IO + TKI as first-line therapies in mRCC patients were both comparable as for the oncological outcome and toxicity.

Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity.

Dietary, pharmacological and genetic interventions can extend health- and lifespan in diverse mammalian species. DNA methylation has been implicated in mediating the beneficial effects of these interventions; methylation patterns deteriorate during ageing, and this is prevented by lifespan-extending interventions. However, whether these interventions also actively shape the epigenome, and whether such epigenetic reprogramming contributes to improved health at old age, remains underexplored. We analysed published, whole-genome, BS-seq data sets from mouse liver to explore DNA methylation patterns in aged mice in response to three lifespan-extending interventions: dietary restriction (DR), reduced TOR signaling (rapamycin), and reduced growth (Ames dwarf mice). Dwarf mice show enhanced DNA hypermethylation in the body of key genes in lipid biosynthesis, cell proliferation and somatotropic signaling, which strongly correlates with the pattern of transcriptional repression. Remarkably, DR causes a similar hypermethylation in lipid biosynthesis genes, while rapamycin treatment increases methylation signatures in genes coding for growth factor and growth hormone receptors. Shared changes of DNA methylation were restricted to hypermethylated regions, and they were not merely a consequence of slowed ageing, thus suggesting an active mechanism driving their formation. By comparing the overlap in ageing-independent hypermethylated patterns between all three interventions, we identified four regions, which, independent of genetic background or gender, may serve as novel biomarkers for longevity-extending interventions. In summary, we identified gene body hypermethylation as a novel and partly conserved signature of lifespan-extending interventions in mouse, highlighting epigenetic reprogramming as a possible intervention to improve health at old age.

Stone-Free Rate after Treating Kidney Stones Exceeding 10 mm via Flexible Ureteroscopy: Can Endoscopic Assessment Replace Low-Dose Computed Tomography Control?

INTRODUCTION: It is unclear whether endoscopic assessment of the stone-free rate after flexible ureteroscopy (fURS) is as effective as assessment with low-dose computed tomography (CT) scan. METHODS: Prospective documentation of patients with kidney stones > 10 mm diameter from 2 different centers (Freiburg, Regensburg), who underwent fURS and were declared to be endoscopically completely stone-free. Low-dose CT control performed 4-8 weeks postoperatively. RESULTS/CONCLUSION: Thirty-eight patients were treated between October 2015 and August 2016 (12 F, 26 M). Average age was 55.9 years (range 19-82, SD 17.24), and body mass index was 29.7 kg/m2 (range 23.5-42.5, SD 4.37). There were 2.0 (range 1-7, SD 1.55) stones with a mean diameter of 15 mm (range 10-40, SD 6.78) per kidney. Mean surgery time was 74 min (range 38-124, SD 24.28), and lithotripsy was necessary in 33 cases. CT was performed 5.4 weeks afterwards (range 4-8, SD 1.43). One patient had a 2 mm residual which was extracted by URS. Strictly speaking, endoluminal stone removal control failed in only that patient, yielding a negative predictive value of 97%. A routine postoperative CT scan would thus appear unnecessary in the case of negative endoscopic control for residual fragments and should be avoided to reduce radiation exposure. Further investigations with larger patient populations are necessary.

Mechanical ventilation during cardiopulmonary resuscitation with intermittent positive-pressure ventilation, bilevel ventilation, or chest compression synchronized ventilation in a pig model.

OBJECTIVE: Mechanical ventilation with an automated ventilator is recommended during cardiopulmonary resuscitation with a secured airway. We investigated the influence of intermittent positive-pressure ventilation, bilevel ventilation, and the novel ventilator mode chest compression synchronized ventilation, a pressure-controlled ventilation triggered by each chest compression, on gas exchange, hemodynamics, and return of spontaneous circulation in a pig model. DESIGN: Animal study. SETTING: University laboratory. SUBJECTS: Twenty-four three-month-old female domestic pigs. INTERVENTIONS: The study was performed on pigs under general anesthesia with endotracheal intubation. Arterial and central venous catheters were inserted and IV rocuronium (1 mg/kg) was injected. After 3 minutes of cardiac arrest (ventricular fibrillation at t = 0 min), animals were randomized into intermittent positive-pressure ventilation (control group), bilevel, or chest compression synchronized ventilation group. Following 10 minute uninterrupted chest compressions and mechanical ventilation, advanced life support was performed (100% O2, up to six defibrillations, vasopressors). MEASUREMENTS AND MAIN RESULTS: Blood gas samples were drawn at 0, 4 and 13 minutes. At 13 minutes, hemodynamics was analyzed beat-to-beat in the end-inspiratory and end-expiratory cycle comparing the IPPV with the bilevel group and the CCSV group. Data were analyzed with the Mann-Whitney U test. Return of spontaneous circulation was achieved in five of eight (intermittent positive-pressure ventilation), six of eight (bilevel), and four of seven (chest compression synchronized ventilation) pigs. The results of arterial blood gas analyses at t = 4 minutes and t = 13 minutes (torr) were as follows: PaO2 intermittent positive-pressure ventilation, 143 (76/256) and 262 (81/340); bilevel, 261 (109/386) (p = 0.195 vs intermittent positive-pressure ventilation) and 236 (86/364) (p = 0.878 vs intermittent positive-pressure ventilation); and chest compression synchronized ventilation, 598 (471/650) (p < 0.001 vs intermittent positive-pressure ventilation) and 634 (115/693) (p = 0.054 vs intermittent positive-pressure ventilation); PaCO2 intermittent positive-pressure ventilation, 40 (38/43) and 45 (36/52); bilevel, 39 (35/41) (p = 0.574 vs intermittent positive-pressure ventilation) and 46 (42/49) (p = 0.798); and chest compression synchronized ventilation, 28 (27/32) (p = 0.001 vs intermittent positive-pressure ventilation) and 26 (18/29) (p = 0.004); mixed venous pH intermittent positive-pressure ventilation, 7.34 (7.31/7.35) and 7.26 (7.25/7.31); bilevel, 7.35 (7.29/7.37) (p = 0.645 vs intermittent positive-pressure ventilation) and 7.27 (7.17/7.31) (p = 0.645 vs intermittent positive-pressure ventilation); and chest compression synchronized ventilation, 7.34 (7.33/7.39) (p = 0.189 vs intermittent positive-pressure ventilation) and 7.35 (7.34/7.36) (p = 0.006 vs intermittent positive-pressure ventilation). Mean end-inspiratory and end-expiratory arterial pressures at t = 13 minutes (mm Hg) were as follows: intermittent positive-pressure ventilation, 28.0 (25.0/29.6) and 27.9 (24.4/30.0); bilevel, 29.1 (25.6/37.1) (p = 0.574 vs intermittent positive-pressure ventilation) and 28.7 (24.2/36.5) (p = 0.721 vs intermittent positive-pressure ventilation); and chest compression synchronized ventilation, 32.7 (30.4/33.4) (p = 0.021 vs intermittent positive-pressure ventilation) and 27.0 (24.5/27.7) (p = 0.779 vs intermittent positive-pressure ventilation). CONCLUSIONS: Both intermittent positive-pressure ventilation and bilevel provided similar oxygenation and ventilation during cardiopulmonary resuscitation. Chest compression synchronized ventilation elicited the highest mean arterial pressure, best oxygenation, and a normal mixed venous pH during cardiopulmonary resuscitation.