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Below is this month's longevity research from Biorxiv, Medrxiv, and Arxiv.


New | 27 December 2022 | Medrxiv link | Write review

Importance: Dementia represents a significant and increasing public health burden. DNA methylation age acceleration may be associated with dementia and dementia risk factors, such as education, but investigating their impact on dementia is necessary. Objective: To evaluate the association of educational attainment on dementia and cognitive impairment through DNA methylation age acceleration, while accommodating exposure-mediator interaction effects. Design: In the 2016 Health and Retirement Study wave, we evaluated six epigenetic clocks, including GrimAge, with Langa-Weir classified dementia, cognitive impairment non-dementia, and normal cognition. Age acceleration was the residual between chronological age of participants and DNA methylation clock, dichotomized at zero. To understand the joint association of low education ([≤] 12 years) and DNA methylation age acceleration in relation to cognitive impairment, we used weighted logistic regression and calculated interaction on the additive scale adjusting for chronological age, sex, race/ethnicity, and cell type composition. We performed four-way mediation and interaction decomposition analysis to estimate the: 1) controlled direct effect of education on cognition, 2) interaction reference, 3) interaction mediation, and 4) the pure indirect effect of DNA methylation age acceleration on cognition. Setting: Analysis was conducted on a subsample of Health and Retirement Study participants in the 2016 Venous Blood Study (N=3,724). Results: Both GrimAge acceleration (OR=1.6 95%CI 1.3 - 2.1) and low educational attainment (OR= 2.4 95%CI 1.9 - 3.0) were associated with higher odds of cognitive impairment, non-dementia in a mutually adjusted logistic model. We found additive interaction associations between low education and GrimAge acceleration on dementia. We observed that 6-8% of the association of education on dementia was mediated through GrimAge acceleration. While mediation effects were small, the portion of the association of education due to additive interaction with GrimAge acceleration was between 23.6 and 29.2%. Conclusions and Relevance: Accelerated DNA methylation age was associated with increased odds of cognitive impairment and we observed more than additive interaction effects between education and age acceleration on dementia. These results support the interplay of social disadvantage and biological aging processes on impaired cognition. | Make paid

New | 26 December 2022 | Biorxiv link | Write review

Exercise has the ability to rejuvenate stem cells and improve tissue homeostasis and regeneration in aging animals. However, the cellular and molecular changes elicited by exercise have not been systematically studied across a broad range of cell types in stem cell compartments. To gain better insight into the mechanisms by which exercise affects niche and stem cell function, we subjected young and old mice to aerobic exercise and generated a single cell transcriptomic atlas of muscle, neural and hematopoietic stem cells with their niche cells and progeny. Complementarily, we also performed whole transcriptome analysis of single myofibers from these animals. We identified common and unique pathways that are compromised across these tissues and cell types in aged animals. We found that exercise has a rejuvenating effect on subsets of stem cells, and a profound impact in the composition and transcriptomic landscape of both circulating and tissue resident immune cells. Exercise ameliorated the upregulation of a number of inflammatory pathways as well as restored aspects of cell-cell communication within these stem cell compartments. Our study provides a comprehensive view of the coordinated responses of multiple aged stem cells and niche cells to exercise at the transcriptomic level. | Make paid

New | 26 December 2022 | Biorxiv link | Write review

To understand low viability and fecundity associated with perturbed levels of developmentally expressed and stress-inducible hsr{omega} lncRNAs, we examined oogenesis in near-null hsr{omega}66 homozygotes, and following targeted down- or up-regulation of hsr{omega} transcripts in developing egg chambers. Short lifespan and poor fecundity, hsr{omega}66 females showed fewer ovarioles, reduced Vasa and weak fusomes in early cysts, high apoptosis and poor actin nuclear-cage in mid-stage chambers, low Cut levels in late chambers and ovulation block. Effects of co-alterations in levels of hsr{omega} transcripts, and oogenesis regulators like Notch, Cut, Caz/dFus and TBPH/TDP-43 on oogenesis were also examined. While altered hsr{omega} transcript levels did not modulate defects following active Notch overexpression in follicle cells, they varyingly enhanced or suppressed defects due to targeted down- or up-regulation of Cut, Caz/dFus or TBPH/TDP-43. As expected of a gene producing multiple lncRNAs that interact with diverse regulatory molecules, simple linear causal inter-relations between oogenesis regulators and hsr{omega} lncRNA levels were not evident. Ecdysone feeding to hsr{omega}66 females or targeted expression of the hsr{omega}-RH transcripts in hsr{omega}66 egg chamber substantially restored normal oogenesis. Misexpression of hsr{omega} lncRNAs thus adversely affects oogenesis through disruption of intra- and inter-organ signaling. | Make paid

New | 25 December 2022 | Biorxiv link | Write review

Cell state evolution underlies tumor development and response to therapy, but mechanisms specifying cancer cell states and intratumor heterogeneity are incompletely understood. Schwannomas are the most common tumors of the peripheral nervous system and are treated with surgery and ionizing radiation. Schwannomas can oscillate in size for many years after radiotherapy, suggesting treatment may reprogram schwannoma cells or the tumor microenvironment. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas. We find schwannomas are comprised of 2 molecular groups distinguished by reactivation of neural crest development pathways or misactivation of nerve injury mechanisms that specify cancer cell states and the architecture of the tumor immune microenvironment. Schwannoma molecular groups can arise independently, but ionizing radiation is sufficient for epigenetic reprogramming of neural crest to immune-enriched schwannoma by remodeling chromatin accessibility, gene expression, and metabolism to drive schwannoma cell state evolution and immune cell infiltration. To define functional genomic mechanisms underlying epigenetic reprograming of schwannomas, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of cancer evolution and establish a paradigm of epigenetic reprograming of cancer in response to radiotherapy. | Make paid

New | 24 December 2022 | Biorxiv link | Write review

We herein introduce voyAGEr, an online graphical interface to explore age-related gene expression alterations in 48 human tissues. voyAGEr offers a visualization and statistical toolkit for the finding and functional exploration of sex- and tissue-specific transcriptomic changes with age. In its conception, we developed a novel bioinformatics pipeline leveraging RNA sequencing data, from the GTEx project, for more than 700 individuals. voyAGEr reveals transcriptomic signatures of the known asynchronous aging between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, that likely reflect so-called digital aging, associated with alterations in different biological pathways, cellular composition, and disease conditions. voyAGEr therefore supports researchers with no expertise in bioinformatics in elaborating, testing and refining their hypotheses on the molecular nature of human aging and its association with pathologies, thereby also assisting in the discovery of novel therapeutic targets. voyAGEr is freely available at . | Make paid

New | 23 December 2022 | Biorxiv link | Write review

Canine cognitive dysfunction (CCD) syndrome is a well-recognized naturally occurring disease in aged dogs, with a remarkably similar disease course, both in its clinical presentation and neuropathological changes, as humans with Alzheimers disease (AD). Similar to human AD patients this naturally occurring disease is found in the aging canine population however, there is little understanding of how the canine brain ages pathologically. It is well known that in neurodegenerative diseases, there is an increase in inflamed glial cells as well as an accumulation of hyperphosphorylation of tau (P-tau) and amyloid beta (Amyloid beta 1-42). These pathologies increase neurotoxic signaling and eventual neuronal loss. We assessed these brain pathologies in aged canines and found an increase in the number of glial cells, both astrocytes and microglia, and the activation of astrocytes indicative of neuroinflammation. A rise in the aggregated protein Amyloid beta 1-42 and hyperphosphorylated tau, at Threonine 181 and 217, in the cortical brain regions of aging canines is seen. We then asked if any of these aged canines had CCD utilizing the only current diagnostic, owner questionnaires, verifying positive or severe CCD had pathologies of gliosis and accumulation of Amyloid beta1-42 like their aged matched controls. However uniquely the CCD dogs had P-tau at T217. Therefore, this phosphorylation site of tau at threonine 217 may be a predictor for CCD | Make paid

New | 23 December 2022 | Biorxiv link | Write review

Senescence, particularly in the nucleus pulposus (NP) cells, has been implicated in the pathogenesis of disc degeneration, however, the mechanism(s) of annulus fibrosus (AF) cell senescence is still not well understood. Both TNF and H2O2, have been implicated as contributors to the senescence pathways, and their levels are increased in degenerated discs when compared to healthy discs. This the objective of this study is to identify factor(s) that induces inner AF (iAF) cell senescence Under TNF exposure, at a concentration that can induce senescence in NP cells, bovine iAF cells did not undergo senescence, indicated by their ability to continue to proliferate as demonstrated by Ki67 staining and growth curves and lack of expression of the senescent markers, p16 and p21. Unlike iAF cells, NP cells treated with TNF accumulated more intracellular ROS and secreted more H2O2. Following TNF treatment, only iAF cells had increased expression of the superoxide scavengers SOD1 and SOD2 whereas NP cells had increased NOX4 gene expression, an enzyme that can generate H2O2. Treating iAF cells with low dose H2O2 (50 M) induced senescence, however unlike TNF, H2O2 did not induce degenerative-like changes as there was no difference in COL2, ACAN, MMP13, or IL6 gene expression or number of COL2 and ACAN immunopositive cells compared to untreated controls. The latter result suggests that iAF cells have distinct degenerative and senescent phenotypes. To evaluate paracrine signalling, iAF and TNF-treated NP cells were co-cultured. In contact co-culture the NP cells did induce iAF senescence. Thus, senescent NP cells may secrete soluble factors that induce degenerative and senescent changes within the iAF. This may contribute to a positive feedback loop of disc degeneration, and these processes could include H2O2 and cytokines (TNF). Further studies will investigate if human disc cells respond similarly. | Make paid

New | 23 December 2022 | Biorxiv link | Write review

Valosin-containing protein (VCP) binds and extracts ubiquitinated cargo to regulate protein homeostasis. While VCP has been studied primarily in aging and disease contexts, it also affects germline development. However, the precise molecular functions of VCP in the germline, particularly in males, are poorly understood. Using the Drosophila male germline as a model system, we find that VCP translocates from the cytosol to the nucleus as germ cells transition into the meiotic spermatocyte stage. Importantly, nuclear translocation of VCP appears to be one critical event stimulated by testis-specific TBP-associated factors (tTAFs) to drive spermatocyte differentiation. Like tTAF mutants, spermatocyte gene expression fails to properly activate in VCP-RNAi testes, and germ cells arrest in early meiosis. At a molecular level, VCP activity supports spermatocyte gene expression by downregulating a repressive histone modification, mono-ubiquitinated H2A (H2Aub), at this developmental transition. Remarkably, experimentally blocking H2Aub in VCP-RNAi testes is sufficient to overcome the meiotic-arrest phenotype and to promote development through meiosis. Collectively, our data highlight VCP as a novel downstream effector of tTAFs that downregulates H2Aub to facilitate meiotic progression. | Make paid

New | 23 December 2022 | Biorxiv link | Write review

Alzheimer's disease (AD) takes a more aggressive course in women than men, with higher prevalence and faster progression. Amnestic AD specifically targets the default mode network (DMN), which subserves short-term memory; past research shows relative hyperconnectivity in the posterior DMN in aging women. Higher reliance on this network during memory tasks may contribute to women's elevated AD risk. Here, we applied connectome-based predictive modeling (CPM), a robust linear machine-learning approach, to the Lifespan Human Connectome Project-Aging (HCP-A) dataset (n=579). We sought to characterize sex-based predictors of memory performance in aging, with particular attention to the DMN. Models were evaluated using cross-validation both across the whole group and for each sex separately. Whole-group models predicted short-term memory performance with accuracies ranging from rho=0.21-0.45. The best-performing models were derived from an associative memory task-based scan. Sex-specific models revealed significant differences in connectome-based predictors for men and women. DMN activity contributed more to predicted memory scores in women, while within- and between- visual network activity contributed more to predicted memory scores in men. While men showed more segregation of visual networks, women showed more segregation of the DMN. We demonstrate that women and men recruit different circuitry when performing memory tasks, with women relying more on intra-DMN activity and men relying more on visual circuitry. These findings are consistent with the hypothesis that women draw more heavily upon the DMN for recollective memory, potentially contributing to women's elevated risk of AD. | Make paid

New | 22 December 2022 | Biorxiv link | Write review

The molecular mechanism that drives the resistance/susceptibility of common bean to Pseudomonas syringae pv. phaseolicola (Pph) has not been clarified yet. For this purpose, 15-day-old common bean plants, variety rinon, were infected with Pph to analyze the transcriptomic changes at 2 and 9 h. RNA-seq analysis showed an upregulation of defense-related genes at 2h, most of them being downregulated at 9h, suggesting that Pph would inhibit the transcriptomic reprogramming of the plant. This trend was also observed in the modulation of 101 cell wall (CW) related genes. However, the changes in CW composition at early stages of Pph infection were related to homogalacturonan (HG) methylation and the formation of HG egg boxes. A common bean pectin methylesterase inhibitor 3 (PvPMEI3) gene - closely related to AtPMEI3 - was detected. In addition, PMEI3 protein was located in the apoplast and had inhibitory activity. Therefore, PvPMEI3 seems to be a good candidate to play a key role in infection, because Arabidopsis pmei3 mutant showed susceptibility to Pph. All these changes could be an attempt to reinforce the CW structure and thus, hinder the attack of the bacterium. However, these transcriptional and CW-remodeling processes are not deep enough to block the action of the pathogen. | Make paid

New | 22 December 2022 | Biorxiv link | Write review

Novelty influences hippocampal-dependent memory through metaplasticity, i.e., experience-dependent adaptations in synaptic plasticity. In this respect, mismatch novelty is known to activate the hippocampal CA1 area in humans and to enhance rat hippocampal-dependent learning and exploration. Mismatch novelty training (NT) by varying spatial configuration of objects in a known environment, enhances rat hippocampal synaptic plasticity. Prefrontal cortex GABAergic projections targeting hippocampal VIP interneurons promote exploration. Since VIP, acting on VPAC1 receptors, restrains both hippocampal LTP and depotentiation by modulating disinhibition we now investigated the impact of NT on VPAC1 receptor modulation of hippocampal synaptic plasticity. NT enhanced both CA1 hippocampal long-term potentiation (LTP) and depotentiation. Blockade of VIP VPAC1 receptors with PG 97-269 (100nM) enhanced both LTP and depotentiation in naiuml;ve animals but was much less effective in enhancing LTP and depotentiation in NT rats. Altered endogenous VIP modulation of LTP was absent in animals exposed to the empty environment (HT). Modulation of depotentiation by endogenous VIP was absent in animals exposed to a fixed configuration of objects (FT) or in HT animals. HT and FT animals, but not NT; showed mildly enhanced synaptic VPAC1 receptor expression. Altogether this suggests that NT influences hippocampal synaptic plasticity by reshaping brain circuits modulating disinhibition and its control by VIP-expressing hippocampal interneurons. Also, upregulation of VIP VPAC1 receptors maintains VIP control of LTP in FT and HT rats, the absence of this in NT rats leading to enhanced LTP but not influencing depotentiation. This may be relevant to co-adjuvate cognitive recovery therapies in aging or epilepsy, where LTP/LTD imbalance occurs. | Make paid

New | 21 December 2022 | Medrxiv link | Write review

Background: Risk factors associated with sporadic non-amnestic and early-onset Alzheimer's disease remain underexamined. We investigated a large, clinically heterogeneous Alzheimer's disease cohort for frequencies of established Alzheimer's disease risk factors (hypertension, hyperlipidemia, diabetes mellitus, APOE-{epsilon}4 frequency, and years of education), alongside a suite of novel factors with historical theoretical association (non-right-handedness, learning disability, seizures, and autoimmune disease). Methods: In this case-control study, we screened the demographic and health histories of 750 consecutive early-onset and 750 late-onset Alzheimer's disease patients from the University of California San Francisco Memory and Aging Center for the prevalence of conventional risk and novel Alzheimer's disease factors and compared these results with 8,859 Alzheimer's disease individuals from the National Alzheimer's Coordinating Center, Amsterdam University Medical Center, Amsterdam, and Mayo Clinic, Jacksonville. Results: Early-onset Alzheimer's disease was associated with significantly lower frequencies of established risk factors (hypertension, hyperlipidemia, diabetes mellitus, all p<0.001, APOE-{epsilon}4, p=0.03) and significantly higher frequencies of novel factors (non-right-handedness, learning disability, active seizure, all p<0.001, remote seizure, p=0.002, and autoimmune disease, p=0.007). Logistic regressions predicting EOAD vs. LOAD controlling for sex, education, APOE-{epsilon}4 status, typical, and novel risk factors, produced findings consistent with the above. Principal component analysis loaded novel factors into two components, non-right-handedness and learning disability versus seizure and autoimmune disease, and the combination of factors from both components resulted in an exponential decrease in age at onset from any single factor alone. APOE-{epsilon}4 provided no additional contribution to age at onset decreases within the non-amnestic Alzheimer's disease cohort but shifted the age of onset 3 years earlier within amnestic presentations (p=0.013). Conclusions: We identified non-right-handedness, learning disability, seizures, and autoimmune disease as novel factors that affect both the age at onset and phenotypical targeting of Alzheimer's disease. Together these results support a new theoretical framework of neurodegenerative disease susceptibility and that through the collection of detailed developmental and health history, neurodegenerative disease risk in some may be highly predictable, offering new opportunities towards early detection, monitoring, therapeutic intervention, and ultimately disease prevention. | Make paid

New | 21 December 2022 | Biorxiv link | Write review

In mammals, spatial orientation is synaptically-encoded by sensory hair cells of the vestibular labyrinth. Vestibular hair cells (VHCs) harbor synaptic ribbons at their presynaptic active zones (AZs), which play a critical role in molecular scaffolding and facilitate synaptic release and vesicular replenishment. With advancing age, the prevalence of vestibular deficits increases; yet, a direct link to the functional decline of VHC ribbon synapses remains to be demonstrated. To address this issue, we investigated the effects of aging on the ultrastructure of the ribbon-type AZs in murine utricles using various electron microscopic techniques and combined them with confocal and super-resolution light microscopy as well as metabolic imaging up to one year of age. In older animals, we detected predominantly in type I VHCs the formation of floating ribbon clusters. Our findings suggest that VHC ribbon-type AZs undergo dramatic structural alterations upon aging. | Make paid

New | 21 December 2022 | Biorxiv link | Write review

Climatic hazards affecting the main rice producing regions of Indonesia increase the risk of annual production loss and encourage the development of innovative strategies to maintain stable production. Conversion of oil palm monocultures to rice-based intercropping systems is a strategy to be considered, but relies on the existence of suitable planting management that optimizes both palm productivity while providing enough light for undergrowth rice varieties tolerant to shady conditions. This paper proposes to couple a model of light interception on virtual canopies with indoor experiments to evaluate the feasibility of developing rice-oil palm agroforestry systems. We first selected a planting design that optimized the transmitted light available for rice using a functional-structural plant model (FSPM) of oil palm. Secondly, we reproduced the light regime simulated with specific changes in the intensity and the daily fluctuation of light in controlled conditions. Three light treatments were designed to test independently the effect of daily light quantity and the effect of diurnal fluctuation on contrasted rice subpopulations. Light quantity was the main factor driving changes in plant morphology and architecture, while light fluctuation only appeared to explain variations in yield components and phenology. This study highlighted the importance of light fluctuation in the grain filling process and resource reallocation. The conservation of relative change among varieties between treatments suggests that varietal responses to low light are likely to be heritable, and that varietal screening under full light can provide clue on varietal behavior under low light. However, the identification of specific traits such as a limited expansion of leaf area and a conservation of leaf senescence under shade and high light fluctuation paves the way for selecting varieties dedicated to agroforestry systems. Further investigations including light quality and larger genotypic population to screen are discussed. | Make paid

New | 16 December 2022 | Biorxiv link | Write review

Societal Impact Statement Witchweeds, parasitic plants of the genus Striga, are nicknamed cereal killers because of their devasting destruction of most of the African staple cereals, including maize, sorghum, millets, and upland rice. The parasite relies on biomolecules emitted from the host roots to germinate and therefore initiate its infectious lifecycle. Some sorghum varieties have evolved to not produce effective germination stimulants, making them resistant to the parasite. Here, we assess genetic factors that underpin Striga germination. We discuss how such knowledge can be used to develop new Striga management strategies through the disruption of host-parasite communication exchange. Summary Seeds of the parasitic plant Striga are dormant. They only germinate in response to biomolecules emitted from the root exudate of the host, strigolactones. But, it is now emerging that Striga germination is a much more complex process regulated by crosstalk of hormone signaling pathways. To further understand the genetic basis of the communication exchange between Striga and its host sorghum, we performed comparative transcriptomic analysis. We sought to identify major transcriptomic changes that define the germination process in Striga and a set of genes that may contribute to the differences in germination rates. Results showed that germination proceeds immediately after strigoractone perception and is marked by a wave of transcriptional reprogramming to allow for metabolic processes of energy mobilization. Cluster analysis using self-organizing maps revealed a time-phased and genotype-differentiated response to germination stimulation. The variation in germination was also a function of hormonal crosstalk. The early germination stage was associated with significant repression of genes in the abscisic acid (ABA) biosynthesis pathway. Other hormones influenced germination as follows: (i) ABA and auxin repressed germination, (ii) brassinosteroid, ethylene and jasmonic acid promoted germination, and (iii) cytokinin had a more prominent role post-germination rather than during germination. Perception of SL sets the germination programme leading to different rates of germination in sorghum followed by a complex hormonal regulation network that acts to either repress or enhance germination. These results have far-reaching implications for developing Striga management strategies by disrupting hormonal communication exchange. | Make paid

New | 16 December 2022 | Biorxiv link | Write review

Benign Prostatic Hyperplasia (BPH) occurs progressively with aging in men and drives deteriorating symptoms collectively known as Lower Urinary Tract Symptoms (LUTS). Age associated changes in circulating steroid hormones, and prostate inflammation have been postulated in the etiology of BPH/LUTS. The link between hormones and inflammation in the development of BPH/LUTS is conflicting because they may occur independently or as sequential steps in disease pathogenesis. This study aimed to decipher the prostatic immune landscape in a mouse model of lower urinary tract dysfunction (LUTD). Steroid hormone imbalance was generated by the surgical implantation of testosterone (T) and estradiol (E2) pellets to male C57BL/6J mice and gene expression analysis was performed on ventral prostates (VP). These experiments identified an increase in the expression of macrophage markers and Spp1/osteopontin (OPN). Localization studies of OPN pinpointed that OPN+ macrophages travel to the prostate lumen and transition into lipid accumulating foam cells. We also observed a significantly increased number of tissue macrophages in the VP which was prevented in OPN knockout (OPN-KO) mice. In contrast, mast cells, but not macrophages, were significantly elevated in the dorsal prostate of T+E2 treated mice which was diminished in OPN-KO mice. Steroid hormone implantation progressively increased urinary frequency, which was ameliorated in OPN-KO mice. Our study underscores the role of age associated steroid hormone imbalances as a mechanism of expanding the prostatic macrophage population, their luminal translocation and foam cell differentiation. | Make paid

New | 16 December 2022 | Biorxiv link | Write review

Prior research indicates substantial refinements of regional cortical morphology in the transition period from childhood to adolescence. However, whether and how the spatial pattern of cortical maturation is shaped by underlying white matter connectome architecture remains largely unknown. Here, we address this issue by leveraging 521 longitudinal structural and diffusion magnetic resonance imaging scans from 314 typically developing individuals during childhood and adolescence (aged 6-14 years). We demonstrate widespread cortical thinning from childhood to adolescence predominantly distributed in bilateral frontoparietal heteromodal nodes, and this maturation pattern is structurally constrained by the white matter connectome architecture of the brain. Specifically, this constraint is first observed as a direct association of the cortical maturation extents between nodes and their anatomically connected neighbors. Using a network-level diffusion computational model, we further demonstrate that the spatial maturation of cortical thickness can be significantly predicted by using multiscale diffusion profiles of network links. Furthermore, these connectome-based constraints are primarily dominated by several core nodes located in bilateral frontoparietal regions, which exhibit differential gene expression profiles in microstructural neurodevelopment processes compared to non-dominant brain nodes. These findings are highly reproducible when using another independent neuroimaging dataset from the Lifespan Human Connectome Project in Development (aged 5-14 years). Our results highlight the importance of white matter network structure in shaping the coordinated maturation of regional cortical morphology and demonstrate the feasibility of using a network-based diffusion model to reveal the maturational principle of cortical morphology from childhood to adolescence. | Make paid

New | 15 December 2022 | Medrxiv link | Write review

Background Alzheimer's disease is highly heritable and exhibits neuropathological hallmarks of neurofibrillary tau tangles and neuritic amyloid plaques. Previous genome-wide association studies (GWAS) have identified over 70 genomic risk loci of clinically diagnosed Alzheimer's disease. However, upon autopsy, many Alzheimer's disease patients have multiple comorbid neuropathologies that may have independent or pleiotropic genomic risk factors. Autopsy data combined with GWAS provides the opportunity to study the genetic risk factors of individual neuropathologies. Methods We studied the genome-wide risk factors of eleven Alzheimer's disease-related neuropathology endophenotypes. We used four sources of neuropathological data: National Alzheimer's Coordinating Center, Religious Orders Study and Rush Memory and Aging Project, Adult Changes in Thought study, and Alzheimer's Disease Neuroimaging Initiative. We used generalized linear mixed models to identify risk loci, followed by Bayesian colocalization analyses to identify potential functional mechanisms by which genetic loci influence neuropathology risk. Results We identified two novel loci associated with neuropathology: one PIK3R5 locus (lead variant rs72807981) with neurofibrillary pathology, and one COL4A1 locus (lead variant rs2000660) with cerebral atherosclerosis. We also confirmed associations between known Alzheimer's genes and multiple neuropathology endophenotypes, including APOE (neurofibrillary tangles, neuritic plaques, diffuse plaques, cerebral amyloid angiopathy, and TDP-43 pathology); BIN1 (neurofibrillary tangles and neuritic plaques); and TMEM106B (TDP-43 pathology and hippocampal sclerosis). After adjusting for APOE genotype, we identified a locus near APOC2 (lead variant rs4803778) associated with cerebral amyloid angiopathy that influences DNA methylation at nearby CpG sites in the cerebral cortex. Conclusions rs2000660 is in strong linkage disequilibrium with a synonymous coding variant (rs650724) of COL4A1, providing a candidate functional variant. Two CpG sites affected by the cerebral amyloid angiopathy-associated APOC2 locus were previously associated with dementia in an independent cohort, suggesting that the effect of this locus on disease may be mediated by DNA methylation. BIN1 is associated with neurofibrillary tangles and neuritic plaques but not with amyloid pathology. TMEM106B is associated with hippocampal sclerosis and TDP-43 pathology but not the canonical Alzheimer's disease pathologies. These findings provide insights into known Alzheimer's disease risk loci by refining the pathways affected by these risk genes. | Make paid

New | 15 December 2022 | Biorxiv link | Write review

Aging and protein aggregation diseases are inextricably linked. During aging, cellular response to unfolded proteins are believed to decline which results in diminished protein homeostasis (proteostasis). Indeed, in model organisms, such as C. elegans, proteostatic decline with age has even been linked to the onset of aggregation of proteins in wild-type animals. However, this correlation has not been extensively characterized in aging mammals. To reveal the insoluble portion of the proteome, we analyzed the detergent-insoluble fraction of mouse brain tissues after high-speed centrifugation by quantitative mass spectrometry. We identified a cohort of 171 proteins enriched in the pellet fraction of older mice including the alpha crystallin small heat shock protein. We then performed a meta-analysis to compare features among distinct groups of detergent-insoluble proteins reported in the literature. Surprisingly, our analysis revealed that features associated with proteins found in the pellet fraction differ depending on the ages of the mice. In general, insoluble proteins from young models (<15 weeks) were more likely to be RNA-binding, more disordered and more likely to be found in membraneless organelles. These traits become less prominent with age within the combined dataset, as proteins with more structure enter the pellet fraction. This analysis suggests that age-related changes to proteome organization lead a specific group of proteins to enter the pellet fraction as a result of loss of proteostasis. | Make paid

New | 15 December 2022 | Biorxiv link | Write review

Background: The appearance of bilateral vestibular schwannomas (VS) is one of the most characteristic features of NF2-related schwannomatosis (NF2-related SWN), an autosomal dominant syndrome that predisposes to the development of tumours of the nervous system. VS are caused by the bi-allelic inactivation of the NF2 gene in a cell of the Schwann cell lineage. Our current understanding of VS initiation and progression as well as the development of new effective therapies is hampered by the absence of human non-perishable cell-based models. Principal Findings: We generated and characterized induced pluripotent stem cell (iPSC) lines with single or bi-allelic inactivation of NF2 by combining the direct reprogramming of VS cells with the use of CRISPR/Cas9 editing. Despite the difficulty of maintaining merlin-deficient iPSCs, we were able to differentiate them into neural crest (NC) cells. At this stage, these cells showed spontaneous expression of the SC marker S100B and the impossibility of generating Schwann cells in 2D cultures. Nevertheless, by applying a 3D Schwann cell differentiation protocol, we successfully generated NF2(+/-) and NF2(-/-) spheroids homogeneously expressing classical markers of the NC-SC axis. Conclusions: Our results show a critical function of NF2 for both reprograming and maintaining a stable pluripotent state. In addition, merlin-deficient cultures also denoted an altered differentiation capacity of merlin-deficient cells towards the NC-SC axis, in the in vitro conditions used. Finally, the generated NF2(+/-) and NF2(-/-) spheroids show potential as a genuine in vitro model of NF2-related tumours. | Make paid

New | 15 December 2022 | Biorxiv link | Write review

While autophagy is key to maintain cellular homeostasis, tissue-specific roles of individual autophagy genes are less understood. To study neuronal autophagy in vivo, we inhibited autophagy genes specifically in C. elegans neurons, and unexpectedly found that knockdown of early-acting autophagy genes, i.e., involved in formation of the autophagosome, except for atg-16.2, decreased PolyQ aggregates and increased lifespan, albeit independently of the degradation of autophagosomal cargo. Neuronal aggregates can be secreted from neurons via vesicles called exophers, and we found that neuronal inhibition of early-acting autophagy genes atg-7 and lgg-1/Atg8, but not atg-16.2 increased exopher formation. Moreover, atg-16.2 mutants were unable to form exophers, and atg-16.2 was required for the effects of early autophagy gene reduction on neuronal PolyQ aggregation, exopher formation, and lifespan. Notably, neuronal expression of full-length ATG-16.2 but not ATG-16.2 without a functional WD40 domain, important for non-canonical functions of ATG16L1 in mammalian cells, restored these phenotypes. Collectively, we discovered a specific role for C. elegans ATG-16.2 and its WD40 domain in exopher biogenesis, neuronal proteostasis, and lifespan determination, highlighting a possible role for non-canonical autophagy functions in both exopher formation and in aging. | Make paid

New | 15 December 2022 | Biorxiv link | Write review

Background: Testicular aging is known to cause male age-related fertility decline and hypogonadism, but the underlying molecular mechanisms remain unclear. Methods: We survey the single-cell transcriptomic landscape of testes from young and old men and examine age-related changes in germline and somatic niche cells. Results: In-depth evaluation of the gene expression dynamics of germline cells reveals that disturbance of base-excision repair pathway is a major feature of aging spermatogonial stem cells (SSCs), suggesting that defective DNA repair of SSCs may serve as a potential driver for increased de novo germline mutations with age. Further analysis of aging-associated transcriptional changes shows that stress-related changes and apoptotic signaling pathway accumulate in aged somatic cells. We identify age-related impairment of redox homeostasis in aged Leydig cells and find that pharmacological treatment with antioxidants alleviate this cellular dysfunction of Leydig cells and promote testosterone production. Lastly, our results reveal that decreased pleiotrophin (PTN) signaling is a contributing factor for testicular aging. Conclusions: These findings provide a comprehensive understanding of the cell-type-specific mechanisms underlying human testicular aging at a single-cell resolution, and suggest potential therapeutic targets that may be leveraged to address age-related male fertility decline and hypogonadism. Funding: This work was supported by the National Key Research and Development Program of China (2018YFA0107200, 2018YFA0801404), the National Natural Science Foundation of China (32130046, 82171564, 82101669, 81871110, 81971759), the Key Research and Development Program of Guangdong Province (2019B020234001), the Natural Science Foundation of Guangdong Province, China (2022A1515010371), the Major Project of Medical Science and Technology Development Research Center of National Health Planning Commission, China (HDSL202001000), the Open Project of NHC Key Laboratory of Male Reproduction and Genetics (Family Planning Research Institute of Guangdong Province) (KF202001), the Guangdong Province Regional Joint Fund-Youth Fund Project (2021A1515110921), the China Postdoctoral Science Foundation (2021M703736). | Make paid

New | 15 December 2022 | Biorxiv link | Write review

Partial somatic cell reprogramming has been touted as a promising rejuvenation strategy. However, its association with mechanisms of aging and longevity at the molecular level remains unclear. We identified a robust transcriptomic signature of reprogramming in mouse and human cells that revealed co-regulation of genes associated with reprogramming and response to lifespan-extending interventions, including those related to DNA repair and inflammation. We found that age-related gene expression changes were reversed during reprogramming, as confirmed by transcriptomic aging clocks. The longevity and rejuvenation effects induced by reprogramming in the transcriptome were mainly independent of pluripotency gain. Decoupling of these processes allowed predicting interventions mimicking reprogramming-induced rejuvenation (RIR) without affecting somatic cell identity, including an anti-inflammatory compound osthol, \emph{ATG5} overexpression, and \emph{C6ORF223} knockout. Overall, we revealed specific molecular mechanisms associated with RIR at the gene expression level and developed tools for discovering interventions that support the rejuvenation effect of reprogramming without posing the risk of neoplasia. | Make paid

New | 14 December 2022 | Medrxiv link | Write review

RationaleAsthma and Chronic Obstructive Pulmonary Disease (COPD) are the two main chronic airway inflammatory diseases related to aging. Cellular aging is prevented by telomeres and their shortening induces cellular senescence. Human Telomerase Reverse Transcriptase Enzyme (hTERT) can act directly on DNA and prevent telomere shortening. The goal of this study was to assess hTERT expression in the bronchial mucosa of patients suffering from chronic airway obstructive diseases and to relate the hTERT expression to demographics and lung function characteristics. MethodsWe collected bronchial biopsies from 38 patients suffering from chronic airway diseases including 21 severe asthmatics and 17 COPD who underwent bronchoscopy in routine practice. hTERT expression was assessed by immunochemistry and co-immunostaining was performed to identify hTERT positive cells within the different immune cell populations. ResultshTERT expression in airway mucosa was essentially found in structural cells. Among leukocytes, lymphocytes were the principal cells expressing hTERT. On the whole cohort, hTERT expression score was not different between men and women and not influenced by the age nor by the smoking history as reflected by the pack years. Total airway hTERT positive staining score positively correlated with post-bronchodilation (post-BD) FEV1 % predicted and FEV1/FVC. (r=0.38, p<0.05 for both). hTERT+ lymphocytes were also positively correlated to post-BD FEV1/FVC (r=0.37, p<0.05). Consequently, hTERT expression was lower in those patients with fixed airway obstruction (post-BD FEV1/FVC < 70%). There was no difference between asthmatics and COPD. ConclusionsIn patients with chronic airway diseases, total and lymphocyte hTERT expressions inversely correlate with the degree of airway obstruction and are reduced in patients with fixed airway obstruction, which supports a role of hTERT in airway remodeling. | Make paid

New | 14 December 2022 | Biorxiv link | Write review

Seed deterioration during storage results in poor germination, reduced seed vigor, and non-uniform seedling emergence. The rate of aging depends on storage conditions (RH, temperature, and oxygen) and genetic factors. This study aims to identify these genetic factors determining the longevity of rice seeds stored under experimental aging conditions mimicking long-term dry storage. Genetic variation for tolerance to aging was studied in 300 Indica rice accessions and storing dry seeds under elevated partial pressure of oxygen (EPPO) condition, using a genome-wide association study. The association analysis yielded eleven unique regions across the genome for all measured germination parameters after aging. These genomic regions differed from regions previously identified in rice under humid experimental aging conditions. The significant single nucleotide polymorphism in the most prominent region was located within the Rc gene, encoding a bHLH transcription factor. Storage experiments using isogenic rice lines (SD7-1D (Rc) and SD7-1d (rc)) with the same allelic variation confirmed the functional role of the Rc gene, conferring a stronger tolerance to dry EPPO aging. A functional Rc gene results in the accumulation of pro-anthocyanidins in the pericarp of rice seeds, an important sub-class of flavonoids having strong antioxidant activity, which may explain why genotypes with an allelic variation for this gene show variation in seed tolerance to dry EPPO aging. | Make paid

New | 13 December 2022 | Biorxiv link | Write review

The human mRNA most affected by TDP-43 loss-of-function is transcribed from the STMN2 gene and encodes stathmin-2 (also known as SCG10), whose loss is a neurodegenerative disease hallmark. Here using multiple in vivo approaches, including transient antisense oligonucleotide (ASO)-mediated suppression, chronic shRNA-mediated depletion in aging mice, and germline deletion, we establish stathmin-2 to be essential for acquisition and maintenance of neurofilament-dependent structuring of axoplasm critical for maintaining diameter and conduction velocity of large-myelinated axons. Sustained stathmin-2 loss from an otherwise mature adult nervous system is demonstrated over a time course of eight months to initiate and drive motor neuron disease that includes 1) shrinkage in inter-neurofilament spacing that is required to produce a three-dimensional space filling array that defines axonal caliber, 2) collapse of mature axonal caliber with tearing of outer myelin layers, 3) reduced conduction velocity, 4) progressive motor and sensory deficits (including reduction of the pain transducing neuropeptide CGRP), and 5) muscle denervation. Demonstration that chronic stathmin-2 reduction is itself sufficient to trigger motor neuron disease reinforces restoration of stathmin-2 as an attractive therapeutic approach for TDP-43-dependent neurodegeneration, including the fatal adult motor neuron disease ALS. | Make paid

New | 12 December 2022 | Medrxiv link | Write review

Current research on the angiotensin-converting-enzyme (ACE) gene has yielded controversial results on whether different ACE polymorphisms are linked with human longevity. ACE polymorphisms are a risk factor for Alzheimer's disease and age-onset diseases that may contribute to the mortality of older people. Our goal is to consolidate existing studies with assistance from artificial intelligence and machine-learning-assisted software to come to a more precise understanding of the role of the ACE gene in human longevity. The I (insertion) and D (deletion) polymorphisms in the intron are correlated with the levels of circulating ACE; homozygous D (DD) is high and homozygous I (II) is low. Here, we performed a detailed meta-analysis of the I and D polymorphisms using centenarians (100+ years old), long-lived subjects (85+ years old), and control groups. ACE genotype distribution was analyzed across a total of 2,054 centenarians and 12,074 controls, as well as 1,367 long-lived subjects between the ages of 85-99, using the inverse variance and random effects methods. The ACE DD genotype was found to be favored in centenarians (OR: 1.41 [95% CI: 1.19-1.67], P < 0.0001) with a heterogeneity of 32%, and the II genotype slightly favored the control groups (OR: 0.81 [95% CI: 0.66-0.98], P = 0.03) with a heterogeneity of 28%, corroborating results from previous meta-analyses. Novel to our meta-analysis, the ID genotype was found to be favored in control groups (OR: 0.86 [95% CI: 0.76-0.97], P = 0.01) with a heterogeneity of 0%. The long-lived group showed a similar positive association between the DD genotype and longevity (OR: 1.34 [95% CI: 1.21-1.48, P < 0.0001) and a negative association between the II genotype and longevity (OR: 0.79 [95% CI: 0.70-0.88], P < 0.0001). The long-lived ID genotype did not show significant findings (OR: 0.93 [95% CI: 0.84-1.02], P = 0.79). In conclusion, the results suggest a significant positive association of the DD genotype with human longevity. However, despite the previous study, the results do not confirm a positive association of the ID genotype with human longevity. We suggest a few paradoxical observations: (1) inhibition of ACE can increase longevity in model systems from nematodes to mammals, seemingly opposite to the finding in humans; (2) exceptional longevity associated with homozygous DD is also associated age-related diseases with higher mortality risks in homozygous DD. We discuss ACE, longevity, and age-related diseases. | Make paid

New | 11 December 2022 | Biorxiv link | Write review

Most cases of pre-term labor have unknown cause, and the burden of preterm birth is immense. Placental aging has been proposed to promote labor onset, but specific mechanisms remain elusive. We report findings stemming from unbiased transcriptomic analysis of mouse placenta, which revealed that hypoxia-inducible factor 1 (HIF-1) stabilization is a hallmark of advanced gestational timepoints, accompanied by mitochondrial dysregulation and cellular senescence; we detected similar effects in aging human placenta. In parallel in primary mouse trophoblasts and human choriocarcinoma cells, we modeled HIF-1 induction and demonstrated resultant mitochondrial dysfunction and cellular senescence. Transcriptomic analysis revealed that HIF-1 stabilization recapitulated gene signatures observed in aged placenta. Further, conditioned media from trophoblasts following HIF-1 induction promoted contractility in immortalized uterine myocytes, suggesting a mechanism by which the aging placenta may drive the transition from uterine quiescence to contractility at the onset of labor. Finally, pharmacological induction of HIF-1 via intraperitoneal administration of dimethyloxalyl glycine (DMOG) to pregnant mice caused preterm labor. These results provide clear evidence for placental aging in normal pregnancy, and demonstrate how HIF-1 signaling in late gestation may be a causal determinant of the mitochondrial dysfunction and senescence observed within the trophoblast as well as a trigger for uterine contraction. | Make paid

New | 10 December 2022 | Medrxiv link | Write review

Rationale: Asthma and Chronic Obstructive Pulmonary Disease (COPD) are the two main chronic airway inflammatory diseases related to aging. Cellular aging is prevented by telomeres and their shortening induces cellular senescence. Human Telomerase Reverse Transcriptase Enzyme (hTERT) can act directly on DNA and prevent telomere shortening. The goal of this study was to assess hTERT expression in the bronchial mucosa of patients suffering from chronic airway obstructive diseases and to relate the hTERT expression to demographics and lung function characteristics. Methods: We collected bronchial biopsies from 38 patients suffering from chronic airway diseases including 21 severe asthmatics and 17 COPD who underwent bronchoscopy in routine practice. hTERT expression was assessed by immunochemistry and co-immunostaining was performed to identify hTERT positive cells within the different immune cell populations. Results: hTERT expression in airway mucosa was essentially found in structural cells. Among leukocytes, lymphocytes were the principal cells expressing hTERT. On the whole cohort, hTERT expression score was not different between men and women and not influenced by the age nor by the smoking history as reflected by the pack years. Total airway hTERT positive staining score positively correlated with post-bronchodilation (post-BD) FEV1 % predicted and FEV1/FVC. (r=0.38, p<0.05 for both). hTERT+ lymphocytes were also positively correlated to post-BD FEV1/FVC (r=0.37, p<0.05). Consequently, hTERT expression was lower in those patients with fixed airway obstruction (post-BD FEV1/FVC < 70%). There was no difference between asthmatics and COPD. Conclusions: In patients with chronic airway diseases, total and lymphocyte hTERT expressions inversely correlate with the degree of airway obstruction and are reduced in patients with fixed airway obstruction, which supports a role of hTERT in airway remodeling. | Make paid

New | 9 December 2022 | Biorxiv link | Write review

Effects from aging in single cells are unpredictable, whereas aging phenotypes at the organ- and tissue-levels tend to appear as stereotypical changes. The mammary epithelium is a bilayer of two major phenotypically and functionally distinct cell lineages, the luminal epithelial and myoepithelial cells. Mammary epithelia exhibit substantial stereotypical changes with age that merits attention because they are putative breast cancer-cells-of-origin. We hypothesize that effects from aging that impinge upon maintenance of lineage fidelity increases susceptibility to cancer initiation. We identified two models of age-dependent changes in gene expression, directional changes and increased variance, which contributed to genome-wide loss of lineage fidelity. Age-dependent variant responses were common to both lineages, whereas directional changes were almost exclusively detected in luminal epithelia and implicated downregulation of chromatin and genome organizers such as SATB1. Epithelial expression of gap junction protein GJB6 increased with age, and modulation of GJB6 expression in heterochronous co-cultures revealed that it provided a communication conduit from myoepithelial cells that drove directional change in luminal cells. Age-dependent luminal transcriptomes comprised a prominent signal detectable in bulk tissue during aging and transition into cancers. A machine learning classifier based on luminal-specific aging distinguished normal from cancer tissue and was predictive of breast cancer subtype. We speculate that luminal epithelia are the ultimate site of integration of the variant responses to aging in their surrounding tissue and that their emergent aging phenotype both endows cells with the ability to become cancer-cells-of-origin and embodies a biosensor that presages cancer susceptibility. | Make paid