Ecotoxicological studies mainly focus on chemical pollution, however, since past decades, there has been a growing interest for the acoustic pollution. Previous studies on underwater acoustic pollution showed that noise affects vertebrates' behaviour, like fish and marine mammals. However, little is known about other organisms. Consequently, we studied important lacking aspects, well known with chemical pollution: the effect on a key zooplankton species (used as bioindicator) and the effect on fitness (survival and fecundity). We exposed isolated water fleas, Daphnia magna, to chronic boat noise or to a silence broadcasted as control, from birth to death. We measured effects on lifespan and clonal offspring production (e.g., clutch size, number of produced offspring along life). We did not observe any effect of the chronic boat noise exposition on Daphnia's fitness. These results are consistent with results on previous acute noise exposure, but also opposite to other ones found with acute and chronic noise effect. Thus, we discuss how the noise structure and temporal pattern could affect its impacts on aquatic organisms. Our work highlights that noise pollution should be integrated in ecotoxicological studies, but also that some particular aspects of this pollutant should be considered differently than chemical pollutants. | Make paid
After peripheral nerve injuries, successful axonal growth and functional recovery requires the reprogramming of Schwann cells into a reparative phenotype, a process dependent on the activation of the transcription factor c-Jun. Nevertheless, axonal regeneration is greatly impaired in aged organisms or after chronic denervation leading to important clinical problems. This regenerative failure has been associated to a diminished c-Jun expression by Schwann cells, but whether the inability of these cells to maintain a repair state is associated to the transition into a phenotype inhibitory for axonal growth, has not been evaluated so far. We find that repair Schwann cells transitions into a senescent phenotype, characterized by diminished c-Jun expression and secretion of factor inhibitory for axonal regeneration in both aging and chronic denervation. In both conditions, elimination of senescent Schwann cells by systemic senolytic drug treatment or genetic targeting improves nerve regeneration and functional recovery in aging and chronic denervation, associated with an upregulation of c-Jun expression and a decrease in nerve inflammation. This work provides the first characterization of senescent Schwann cells and their impact over axonal regeneration in aging and chronic denervation, opening new avenues for enhancing regeneration, and functional recovery after peripheral nerve injuries. | Make paid
Late-life-initiated dietary interventions negligibly extend longevity or reduce frailty, yet the reason remains unknown. We investigated the age-related changes associated with the fasting response in adipose tissue of the short-lived killifish N. furzeri. Transcriptomic analysis revealed the presence of a fasting-like transcriptional program (FLTP) in old animals that is irrespective of their nutritional status and characterized by widespread suppression of anabolic processes. FLTP is associated with reduced expression of the AMPK {gamma}1 regulatory subunit. Accordingly, refeeding positively regulates {gamma}1 expression in young but not in old animals. Fish having sustained AMPK{gamma}1 activation had no sign of FLTP in old age and exhibited metabolic health and longevity. In humans, we found that {gamma}1 expression declines with age and is associated with multimorbidity and multidimensional frailty risk. Our study highlights the importance of the refeeding arm in promoting health and longevity and identifies the AMPK{gamma}1 complex as a potential target to prevent age-related diseases in humans. | Make paid
Magnetic Resonance Imaging (MRI) has been one of the primary instruments to measure the properties of the human brain non-invasively in vivo. MRI data generally needs to go through a series of processing steps (i.e., a pipeline) before statistical analysis. Currently, the processing pipelines for multi-modal MRI data are still rare, in contrast to single-modal pipelines. Furthermore, the reliability and validity of the output of the pipelines are critical for the MRI studies. However, the reliability and validity measures are not available or adequate for almost all pipelines. Here, we present PhiPipe, a multi-modal MRI processing pipeline. PhiPipe could process T1-weighted, resting-state BOLD, and diffusion-weighted MRI data and generate commonly used brain features in neuroimaging. We evaluated the test-retest reliability of PhiPipe's brain features by computing intra-class correlations (ICC) in four public datasets with repeated scans. We further evaluated the predictive validity by computing the correlation of brain features with chronological age in three public adult lifespan datasets. The multi-variate reliability and predictive validity of the PhiPipe results were also evaluated. The results of PhiPipe were consistent with previous studies, showing comparable or better reliability and validity when compared with two popular single-modality pipelines, namely DPARSF and PANDA. The publicly available PhiPipe provides a simple-to-use solution to multi-modal MRI data processing. The accompanied reliability and validity assessments could help researchers make informed choices in experimental design and statistical analysis. Furthermore, this study provides a framework for evaluating the reliability and validity of image processing pipelines. | Make paid
Genes that drive the proliferation, survival, invasion and metastasis of malignant cells have been identified for many human cancers1-6. Independent studies have identified cell death pathways that eliminate cells for the good of the organism7-10. The coexistence of the cell death pathways with the driver mutations suggest that the cancer driver could be rewired to activate cell death. We have invented a new class of molecules: TCIPs (Transcriptional/Epigenetic Chemical Inducers of Proximity) that recruit the endogenous cancer driver, or a downstream transcription factor, to the promoters of cell death genes thereby activating their expression. To develop this concept, we have focused on diffuse large B cell lymphoma (DLBCL), in which BCL6 is amplified or mutated11. BCL6 binds to the promoters of cell death genes and epigenetically suppresses their expression12. We produced the first TCIPs by chemically linking BCL6 inhibitors to small molecules that bind transcriptional activators. Several of these molecules robustly kill DLBCL at single-digit nanomolar concentrations, including chemotherapy-resistant, TP53-mutant lines. The dominant gain-of-function approach provided by TCIPs captures the combinatorial specificity inherit to transcription and can thereby accesses new therapeutic space. TCIPs are relatively non-toxic to normal cells and mice, apparently reflecting their need for coincident expression of both target proteins for effective killing. The general TCIP concept has applications in elimination of senescent cells, enhancing expression of therapeutic genes, treatment of diseases produced by haploinsufficiency, and activation of immunogens for immunotherapy. | Make paid
In the last 150 years, in many populations life expectancy has more than doubled, the variation in length of life has decreased, and, as result, more individuals enjoy similarly longer lives (even though with important socio-demographic differences). When it comes to healthy longevity, today more and more people reach older ages in better health than what they used to do only a few decades ago, for many individuals the unhealthy years are getting compressed at the end of life and, overall, healthy life expectancy is increasing globally. But we do not know how many individuals are benefiting from this increase. Indicators of average length of life, such as healthy life expectancy, do not capture the spread, while similar levels of healthy life expectancy can be achieved by different populations: one where most individuals share a similar number of years in good health, or one where few individuals enjoy high numbers of years in good health compared to many others who do not. Here we apply demographic techniques for the analysis of variation to the demography of health to study the fundamental question of the distribution of number of healthy years of life among individuals and the relation between healthy lifespan length and healthy lifespan inequality. We use data from the Global Burden of Disease Study, and we produce the first international landscape of healthy lifespan variation over time and by socioeconomic level of the country. | Make paid
Importance The benefit of physical activity (PA) for increasing longevity is well-established, however, the impact of diurnal timing of PA on mortality remains poorly understood. Objective To derive PA patterns and investigate their associations with all-cause mortality. Design, Setting, and Participants This population-based prospective cohort study analyzed UK Biobank baseline data collected between 2006 and 2010 from adults aged 40 to 79 years in England, Scotland, and Wales. Participants were invited by email to participate in an additional accelerometer study from 2013 to 2015, 7 years (median) after baseline. Participants' vital status was assessed via linkage with mortality registries through September 2021 (England/Wales) and October 2021 (Scotland). Data analyses were performed in July 2022. Exposure Loading scores of functional principal components (fPCs) obtained from wrist accelerometer-measured activity metrics. The 'Euclidean norm minus one' was used as a summary metric of bodily acceleration aggregated to 24 hourly averages across seven days. These timeseries were used for functional principal component analysis (fPCA). Main Outcomes and Measures Examination of time-dependent PA patterns obtained using functional principal component analysis in relation to all-cause mortality estimated by multivariable Cox proportional hazard models. Results Among 96,361 participants (56% female), 2,849 deaths occurred during 6.9 (SD 0.9) years of follow-up. Four distinct functional principal components (fPCs) accounted for 96% of the variation of the accelerometry data. The association of fPC1 and mortality was non-linear (p<0.001). Using a loading score of zero as the reference, a fPC1 score of +2 (high overall PA) was associated with lower mortality (0.91; 95% CI: 0.84-0.99), whereas a score of +1 showed no relation (0.94; 95% CI: 0.89-1.00). A fPC1 score of -2 (low overall PA) was associated with higher mortality (1.71; 95% CI: 1.58-1.84), as was a score of -1 (1.20; 95% CI: 1.13-1.26). A 1-unit score increase on fPC2 (high early day PA) was not associated with mortality (0.97; 95% CI: 0.93-1.02). For fPC3, a 1-unit score increase (high midday PA) was associated with decreased mortality (0.88; 95% CI: 0.84-0.94). In contrast, a 1-unit score increase on fPC4 (high midday and nocturnal PA) was associated with higher mortality (1.14; 95% CI: 1.06-1.24). Conclusions and Relevance Higher risks of death were found for patterns denoting lower overall PA and higher late day and nocturnal PA. Conversely, higher levels of PA, distributed continuously, in one, or in two activity peaks during daytime, were inversely associated with lower mortality. Daily timing of PA may have public health implications, as our results suggest that some level of elevated PA during the day and a nighttime rest is associated with longevity. | Make paid
A substrate specificity of the pharmaceutically attractive tumor-promoter SIRT5 was already investigated multiple times by advanced proteomic tools. However, the present bioinformatic analysis brings new highlights to the knowledge about the lysine demalonylation activity of SIRT5, a member of the sirtuin family with multiple roles in aging and age-related diseases. It shows unreported functional aspects of the lysine demalonylated substrates in Eukaryotic translation elongation (ETE), Amino acid and derivative metabolism (AADM), and Selenoamino acid metabolism (SAM). The cluster of the elongation factors (EEF1A1, EEF2, EEF1D, and EEF1G) belonging to ETE participates in the peptide chain elongation and the export of the tRNA-s from the nucleus to the primary sites of the proteosynthesis. SIRT5 regulates the activity of the key enzymes with tumor-promoting functions involved in AADM (GLUD1, SHMT1, ACAT1). In contrast, SIRT5 also lysine demalonylates tumor suppressor substrates as a part of the AADM and SAM interaction networks (ALDH9A1, BHMT, GNMT). It indicates comparable functions like SIRT3, which has dual tumor promoter/oncogene functions. Similar to the roles of the sirtuins, the SAM pathway impacts longevity, protects against cardiovascular diseases, and is associated with hepatic steatosis. The selen supplementation mediates the calorie restriction effect, which increases the NAD+/NADH ratio in the cells and stimulates the expression of SIRT5 and other sirtuins. SIRT5 in turn regulates the selenocysteine synthesis through the lysine demalonylation of the participating ribosomal proteins, SECISBP2 and GNMT, which creates a regulatory loop. | Make paid
The locus coeruleus (LC), a small subcortical structure in the brainstem, is the brain's principal source of norepinephrine. It plays a primary role in regulating stress, the sleep-wake cycle, and attention, and its degradation is associated with aging and neurodegenerative diseases associated with cognitive deficits (e.g., Parkinson's, Alzheimer's). Yet precisely how norepinephrine drives brain networks to support healthy cognitive function remains poorly understood -- partly because LC's small size makes it difficult to study noninvasively in humans. Here, we characterized LC's influence on brain dynamics using a hidden Markov model fitted to functional neuroimaging data from healthy young adults across four attention-related brain networks and LC. We modulated LC activity using a behavioral paradigm and measured individual differences in LC neuromelanin. The model revealed five hidden states, including a stable state dominated by salience-network activity that occurred when subjects actively engaged with the task. LC neuromelanin correlated with this state's stability across experimental manipulations and with subjects' propensity to enter into and remain in this state. These results provide new insight into LC's role in driving spatiotemporal neural patterns associated with attention, and demonstrate that neuromelanin variation can explain individual differences in these patterns even in healthy young adults. | Make paid
Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome-enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity. | Make paid
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics enabling high-resolution analysis of cell states while preserving lineage relationships. However, reliance on transcriptional profiling limits their adaptation to an ever-expanding tool kit of multiomic single-cell assays. With CellTag-multi, we present a novel approach for profiling lineage barcodes with single-cell chromatin accessibility without relying on co-assay of transcriptional state, paving the way for truly multiomic lineage tracing. We validate CellTag-multi in mouse hematopoiesis, characterizing transcriptional and epigenomic lineage priming across progenitor cell populations. In direct reprogramming of fibroblasts to endoderm progenitors, we use CellTag-multi to comprehensively link early cell state with reprogramming outcomes, identifying core regulatory programs underlying on-target and off-target reprogramming. Further, we reveal the Transcription Factor (TF) Zfp281 as a novel regulator of reprogramming outcome, biasing cells towards an off-target mesenchymal fate via its regulation of TGF-{beta} signaling. Together, these results establish CellTag-multi as a novel lineage tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming. | Make paid
Oscillatory power and phase synchronization map neuronal dynamics and are commonly studied to describe the healthy or diseased human brain. Yet, little is known about the course of these features from early adulthood into old age. Leveraging magnetoencephalography (MEG) resting-state data in a cross-sectional adult sample (n = 350), we probed lifespan differences (18-88 years) in connectivity and power and interaction effects with sex. Building upon recent attempts to link brain structure and function, we tested the spatial correspondence of age effects on cortical thickness and those on functional networks and a direct relationship at the level of the study sample. We found MEG frequency-specific patterns for lower- and higher-order brain regions and divergence between sexes in low frequencies. Connectivity and power exhibited distinct linear trajectories with age or turning points at midlife, which in the delta and beta bands corresponded to the age patterns of cortical thickness. Structure-function coupling was frequency-dependent and observed in unimodal or transmodal regions. Altogether, we provide a comprehensive overview of the topographic functional profile of adulthood that can form a basis for neurocognitive and clinical investigations. This study further sheds new light on how the brain's structural architecture relates to fast oscillatory activity. | Make paid
Autosomal dominant polycystic kidney disease (ADPKD) isone of the most prevalent monogenic human diseases. It is mostly caused by pathogenic variants in PKD1 or PKD2 genes that encode interacting transmembrane proteins polycystin-1 (PC1) and polycystin-2 (PC2). Among many pathogenic processes described in ADPKD, those associated with cAMP signaling, inflammation, and metabolic reprogramming appear to regulate the disease manifestations. Tolvaptan, a vasopressin receptor-2 antagonist that regulates cAMP pathway, is the only FDA-approved ADPKD therapeutic. Tolvaptan reduces renal cyst growth and kidney function loss, but it is not tolerated by many patients and is associated with idiosyncratic liver toxicity. Therefore, additional therapeutic options for ADPKD treatment are needed. As drug repurposing of FDA-approved drug candidates can significantly decrease the time and cost associated with traditional drug discovery, we used the computational approach signature reversion to detect inversely related drug response gene expression signatures from the Library of Integrated Network-Based Cellular Signatures (LINCS) database and identified compounds predicted to reverse disease-associated transcriptomic signatures in three publicly available kidney transcriptomic data sets of mouse ADPKD models. We focused on a pre-cystic model for signature reversion, as it was less impacted by confounding secondary disease mechanisms in ADPKD, and then compared the resulting candidates' target differential expression in the two cystic mouse models. We further prioritized these drug candidates based on their known mechanism of action, FDA status, targets, and by functional enrichment analysis. With this approach, we prioritized 29 unique drug targets differentially expressed in ADPKD cystic models and 16 prioritized drug repurposing candidates that target them, including bromocriptine and mirtazapine. Collectively, these indicate drug targets and repurposing candidates that may effectively treat pre-cystic as well as cystic ADPKD. | Make paid
Aging is a consequence of complex molecular changes, but the roles of individual microRNAs (miRNAs) in aging remain unclear. One of the few miRNAs that are upregulated during both normal and premature aging is miR-29. We confirmed this finding in our study in both mouse and monkey models. Follow-up analysis of the transcriptomic changes during normal aging revealed that miR-29 is among the top miRNAs predicted to drive the aging-related gene expression changes. We also showed that partial loss of miR-29 extends the lifespan of Zmpste24-/- mice, an established model of progeria, which indicates that miR-29 is functionally important in this accelerated aging model. To examine whether miR-29 upregulation alone is sufficient to promote aging-related phenotypes in vivo, we generated mice in which miR-29 can be conditionally overexpressed (miR-29TG). We found that miR-29 overexpression in mice is sufficient to drive aging-related phenotypes including alopecia, kyphosis, osteoporosis, senescence, and leads to early lethality. Transcriptomic analysis of both young miR-29TG and old WT mice revealed shared downregulation of genes enriched in extracellular matrix and fatty acid metabolism, and shared upregulation of genes in pathways linked to inflammation. Together, these results highlight the functional importance of miR-29 in controlling a gene expression program that drives aging-related phenotypes. | Make paid
The pathology of aging impacts multiple organ systems including the kidney, skeletal, and cardiac muscle. Long-term treatment with the mitochondrial targeted peptide elamipretide has previously been shown to improve in vivo mitochondrial function in aged mice that is associated with increased fatigue resistance and treadmill performance, improved cardiovascular diastolic function, and glomerular architecture of the kidney. However, elamipretide is a short tetrameric peptide that is not orally bioavailable limiting its routes of administration. This study tested whether twice weekly intermittent injections of elamipretide could recapitulate the same functional improvements as continuous long-term infusion. We found that intermittent treatment with elamipretide for 8 months preserved endurance running in mice, skeletal muscle force production, and left ventricular mass but did not affect heart or kidney function as previously reported using continuous treatment. | Make paid
Listening in everyday life requires attention to be deployed dynamically - when listening is expected to be difficult and when relevant information is expected to occur - to conserve mental resources. Conserving mental resources may be particularly important for older adults who often experience difficulties understanding speech. In the current study, we use electro- and magnetoencephalography to investigate the neural and behavioral mechanics of attention regulation during listening and the effects that aging has on these. We show that neural alpha oscillatory activity indicates when in time attention is deployed (Experiment 1) and that deployment depends on listening difficulty (Experiment 2). Older adults (54-72 years) also show successful attention regulation but appear to utilize timing information differently compared to younger adults (20-33 years). We further show a notable age-group dissociation in recruited brain regions. In younger adults, superior parietal cortex underlies alpha power during attention regulation, whereas, in older adults, alpha power emerges from more ventro-lateral areas (posterior temporal cortex; Experiment 3). This difference in the sources of alpha activity between age groups only occurred during task performance and was absent during rest (Experiment S1). In sum, our study suggests that older adults employ different neural control strategies compared to younger adults to regulate attention in time under listening challenges. | Make paid
Cerebrovascular reactivity (CVR), defined as the cerebral blood flow response to a vasoactive stimulus, is an imaging biomarker with demonstrated utility in a range of diseases and in typical development and aging processes. A robust and widely implemented method to map CVR involves using a breath-hold task during a BOLD fMRI scan. Recording end-tidal CO2 (PETCO2) changes during the breath-hold task is recommended to be used as a reference signal for modeling CVR amplitude in standard units (%BOLD/mmHg) and CVR delay in seconds. However, obtaining reliable PETCO2 recordings requires equipment and task compliance that may not be achievable in all settings. To address this challenge, we investigated two alternative reference signals to map CVR amplitude and delay in a lagged general linear model (lagged-GLM) framework: respiration volume per time (RVT) and average gray matter BOLD response (GM-BOLD). In 8 healthy adults with multiple scan sessions, we compare spatial agreement of CVR maps from RVT and GM-BOLD to those generated with PETCO2. We define a threshold to determine whether a PETCO2 recording has ''sufficient'' quality for CVR mapping and perform these comparisons in 16 datasets with sufficient PETCO2 and in 6 datasets with insufficient PETCO2. When PETCO2 quality is sufficient, both RVT and GM-BOLD produce CVR amplitude maps that are nearly identical to those from PETCO2 (after accounting for differences in scale), with the caveat they are not in standard units to facilitate between-group comparisons. CVR delays are comparable to PETCO2 with an RVT regressor but may be underestimated with the average GM-BOLD regressor. Importantly, when PETCO2 quality is insufficient, RVT and GM-BOLD CVR recover reasonable CVR amplitude and delay maps, provided the participant attempted the breath-hold task. Therefore, our framework offers a solution for achieving high quality CVR maps in both retrospective and prospective studies where sufficient PETCO2 recordings are not available and especially in populations where obtaining reliable measurements is a known challenge (e.g., children). Our results have the potential to improve the accessibility of CVR mapping and to increase the prevalence of this promising metric of vascular health. | Make paid
Age-related decline in episodic memory performance is a well-replicated finding across numerous studies. Recent studies focusing on aging and individual differences found that the Big Five personality trait Openness to Experience is associated with better episodic memory performance in older adults, but the associated neural mechanisms are largely unclear. Here we investigated the relationship between Openness and memory network function in a sample of 352 participants (143 older adults, 50-80 years; 209 young adults, 18-35 years). Participants underwent functional magnetic resonance imaging (fMRI) during a visual memory encoding task. Functional memory brain-network integrity was assessed using the SAME scores (similarity of activations during memory encoding), which reflect the deviation of a participants memory network activity from prototypical fMRI activity patterns of young adults. Openness was assessed using the NEO Five Factor Inventory (NEO-FFI). Older vs. young adults showed lower memory performance and higher deviation of fMRI activity patterns (i.e., lower SAME scores). Specifically in older adults, high Openness was associated with better memory performance, and mediation analysis showed that this relationship was partially mediated by higher SAME scores. Our results suggest that trait Openness may constitute a protective factor in cognitive aging by better preservation of the brains memory network. | Make paid
The ability to use past experience to effectively guide decision making declines in older adulthood. Such declines have been theorized to emerge from either impairments of striatal reinforcement learning systems (RL) or impairments of recurrent networks in prefrontal and parietal cortex that support working memory (WM). Distinguishing between these hypotheses has been challenging because either RL or WM could be used to facilitate successful decision making in typical laboratory tasks. Here we investigated the neurocomputational basis for age-related decision making deficits using an RL-WM task to disentangle these mechanisms, a computational model to quantify them, and magnetic resonance spectroscopy to link them to their molecular bases. Our results reveal that learning declines in older age are largely attributable to working memory deficits, as might be expected if cortical recurrent networks were unable to sustain persistent activity across multiple trials. Consistent with this, we show that older adults had lower levels of prefrontal glutamate, the excitatory neurotransmitter thought to support persistent activity, compared to younger adults. Individuals with the lowest prefrontal glutamate levels displayed the greatest impairments in working memory after controlling for other anatomical and metabolic factors. Together, our results suggest that reductions in prefrontal glutamate across healthy aging may contribute to failures of working memory systems and impaired decision making in older adulthood. | Make paid
Working memory relies critically on the dorsolateral prefrontal cortex (dlPFC). Morphology and function of the dlPFC, and corresponding working memory performance, are affected early in the aging process. However, these effects are heterogeneous, with nearly half of aged individuals spared of working memory deficits. Translationally relevant model systems are critical for investigating the neurobiological drivers of this variability and identifying why some people experience age-related working memory impairment while others do not. The common marmoset (Callithrix jacchus) is advantageous as a model in which to investigate the biological underpinnings of aging because, as a nonhuman primate, marmosets have a clearly defined dlPFC facilitating investigations of prefrontal-dependent cognitive functions, including working memory, and their short (~10 year) lifespan facilitates longitudinal studies of aging. Here, we conduct the first investigation of synaptic ultrastructure in the dlPFC of the marmoset and investigate whether there are changes to synaptic ultrastructure that are unique to aging with and without working memory impairment. To do this, we characterized working memory capacity in a cohort of marmosets that collectively covered their short lifespan, and found age-related working memory impairment. We also found a remarkable degree of heterogeneity in performance, similar to that found in humans. Utilizing three dimensional reconstruction from serial section electron microscopy, we visualized structural correlates of synaptic efficacy including boutons, mitochondria, and synapses in layer III of the dlPFC of three marmosets: one young adult (YA), one aged cognitively unimpaired (AU), and one aged cognitively impaired (AI). We find that aged marmosets have fewer synapses in dlPFC than young, and this is due to selective vulnerability of small synapses. Next, we tested the hypothesis that violation of the ultrastructural size principle underlies age-related working memory impairment. The ultrastructural size principle states that synaptic efficacy relies on coordinated scaling of synaptic components (e.g., synapses, mitochondria) with presynaptic boutons. While synapses and mitochondria scaled proportionally and were strongly correlated with presynaptic boutons in the YA and AU marmosets, the ultrastructural characteristics of the AI marmoset were alarmingly different. We found that age-related working memory impairment was associated with disproportionately large synapses compared to presynaptic boutons, specifically in those with mitochondria. Remarkably, presynaptic mitochondria and these boutons were completely decorrelated. We posit that this decorrelation results in mismatched energy supply and demand, leading to impaired synaptic transmission. This is the first report of age-related synapse loss in the marmoset, and the first demonstration that violation of the ultrastructural size principle underlies age-related working memory impairment. | Make paid
We recently reported that loss of oligodendrocyte metabolic support through the lactate and pyruvate transporter Monocarboxylate Transporter 1 (MCT1) is well tolerated into adulthood. Only with advanced aging did we observe axonal degeneration and hypomyelination due to loss of MCT1 from oligodendroglia lineage cells. MCT1 is also expressed by other glial subtypes, such as astrocytes and endothelial cells where it has been suggested to be essential for learning and memory tasks. However, the importance of MCT1 in these cell types for long-term axonal metabolic support is still unknown. We therefore addressed whether conditional loss of MCT1 from either of these cell types would lead to widespread axonal degeneration with aging. Using a conditional null approach, similar to what was used for oligodendrocyte MCT1 depletion, we observed that conditional knockout of MCT1 from either astrocytes or endothelial cells did not cause neuronal injury. On the other hand, inducible ubiquitous depletion of MCT1 causes late-onset axonal degeneration, comparable with what was observed in our previous study using the oligodendrocyte lineage MCT1 null mice. In summary, we conclude that unlike oligodendrocyte MCT1, astrocyte MCT1 is not an essential driver of astrocyte mediated axonal energy homeostasis with aging. | Make paid
Transcription factors (TFs) have the potential function in regulating gene expression. Transcription factor TFAP2C plays important roles in the regulation of post-implantation embryonic development in mice, the reprogramming process, trophectoderm formation and carcinogenesis, but its role in porcine early embryo development remains unclear. This study was conducted to investigate the role of TFAP2C in porcine early embryo development using siRNA cytoplasmic injection. The RNAseq and immunofluorescence staining were performed to detect gene expression, and ChIP and dual luciferase reporter assays were used to elucidate the mechanism. The results showed that the deficiency of TFAP2C could lead to embryonic development disorder. The percentage of the blastocyst in the TFAP2C knockdown (TFAP2C-KD) group (7.76{+/-}1.86%) was significantly decreased compared to the control group (22.92{+/-}1.97%) (P**<0.01). The RNAseq results showed that 1208 genes were downregulated and 792 genes were upregulated after siRNA injection. The expression of epigenetic modification enzymes KDM5B, SETD2 (P**<0.01) etc. were significantly elevated in TFAP2C-KD group. Meanwhile, the modification levels of H3K4me3, H3K4me2 and H3K9me3 (P*<0.05) were significantly decreased, and the modification levels of H3K36me3 (P**<0.01) and DNA methylation (P**<0.01) were significantly increased in TFAP2C-KD group. DNMT1 was mostly expressed in cytoplasm in the control group, while it was mainly expressed in nuclei in the TFAP2CKD group. In addition, TFAP2C could bind to the promoter region of SETD2, and the mutation of the TFAP2C binding site resulted in increased activity of SETD2 promoter (P**<0.01). The knockdown of TFAP2C affects histone modification and DNA methylation by regulating the expression of SETD2, KDM5B etc. and other genes, thereby inhibiting embryonic development. TFAP2C binds to the promoter region of SETD2 and acts as a hindrance protein. This study fills in the deficiency of TFAP2C in porcine early embryo development and provides theoretical support for animal husbandry production and biomedicine. | Make paid
The volatile phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, it quickly increases to high concentrations due to its low solubility and diffusion rates in water. The passive, quick and consistent accumulation of ethylene in submerged plant tissues makes it a reliable cue for plants to trigger flood-acclimative responses. However, persistent ethylene accumulation can also have negative effects, notably accelerated leaf senescence. Ethylene is a well-established positive regulator of senescence which is a natural element of plant ageing. However stress-induced senescence hampers the photosynthetic capacity and stress recovery of plants. In submerged Arabidopsis shoots, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid an indiscriminate breakdown of leaves despite high systemic accumulation of ethylene. Here we demonstrate in Arabidopsis plants that even though submergence triggers a leaf-age independent activation of ethylene signaling via EIN3, senescence was initiated only in the old leaves. This EIN3 stabilization also led to the overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1). ORE1 protein accumulated in both old and young leaves during submergence. However, leaf age-dependent senescence could be explained by ORE1 activation via phosphorylation only in old leaves. Our results unravel a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses like flooding. Such an age-dependent phosphorylation of ORE1 ensures that older expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues vital to whole plant survival. | Make paid
Mammalian genomes harbor many more enhancers than genes, which greatly complicates the elucidation of cell-state specific regulatory networks. Here, we developed a computational framework for learning enhancer-based gene networks from joint data on enhancer activity and transcript abundance. Dissecting the developmental plasticity of T helper (Th) cells with this approach, we uncovered a highly connected enhancer-gene network that supports graded Th-cell differentiation states, rather than mutual exclusivity of type-1 and type-2 immunity. Machine learning identifies a small number of regulatory enhancer types as network hubs. Hub enhancers in Th1 cells integrate as inputs the expression level of the master regulator transcription factor, T-bet, and STAT signals governed by the cytokine environment. The quantitative balance between cell-intrinsic T-bet, driving phenotypic stability, and environmental cues enabling plasticity explains the heterogeneous reprogramming capacities of individual Th1 cells differentiating during natural infections in vivo. Moreover, we provide a framework for elucidating genome-scale regulatory networks based on enhancer activity. | Make paid
The clearance of insulin from circulation is critical for metabolic homeostasis. Insulin is depleted in the liver by the insulin degrading enzyme (IDE). WDR23 is a substrate receptor of the Cul4-ubiquitin ligase complex and acts as a sophisticated regulator of protein activation and turnover. Here we establish hepatic WDR23 in the regulation of insulin metabolism by regulating IDE. An unbiased proteomic analysis of liver tissue of mice lacking Wdr23 revealed a significant increase in the steady state levels of IDE which accompanied reduced circulating insulin and diminished sensitivity to insulin stimulation. A comparative assessment of the transcriptomic changes in livers from animals with and without WDR23 reveals significant changes in the targets responding to insulin and glucose receptor signaling. Furthermore, phosphorylation of the insulin signaling cascade proteins, IRS-1, AKT, MAPK and mTOR were dysregulated in Wdr23KO mice. These findings are recapitulated in cultured human cell models with genetic ablation of Wdr23 revealing a conserved role for WDR23 from mice to humans. Mechanistically, the cytoprotective transcription factor NRF2, a direct target of WDR23-Cul4 proteostasis, mediates the enhanced transcriptional expression of IDE when WDR23 is ablated. Moreover, an analysis of human genetic variation in WDR23 across a large naturally aging human cohort in the US Health and Retirement Study reveals a significant association of WDR23 with altered hemoglobin A1C (HbA1c) levels in older adults that supports the use of WDR23 as new molecular determinant of metabolic health in humans. | Make paid
Background: Tissues need to regenerate to restore function after injury. Yet, this regenerative capacity varies significantly between organs and between species. For example, in the heart, some species retain full regenerative capacity throughout their lifespan but human cardiac cells display limited ability to repair injury. After a myocardial infarction, the function of cardiomyocytes is impaired and reduces the ability of the heart to pump, causing heart failure. Therefore, there is a need to restore the function of an injured heart post myocardial infarction. We investigate in cell culture the role of the YAP, a transcriptional co-regulator with a pivotal role in growth, in driving repair after injury. Methods: We express optogenetic YAP (optoYAP) in three different cell lines. We characterised the behaviour and function of optoYAP using fluorescence imaging and quantitative real-time PCR of downstream YAP target genes. Mutant constructs were generated using site-directed mutagenesis. Nuclear localised optoYAP was functionally tested using wound healing assay and anchorage-independent colony formation assay. Results: Utilising optoYAP, which enables precise control of pathway activation, we show that YAP induces the expression of downstream genes involved in proliferation and migration. optoYAP can increase the speed of wound healing in H9c2 cardiomyoblasts. Interestingly, this is not driven by an increase in proliferation, but by collective cell migration. We subsequently dissect specific phosphorylation sites in YAP to identify the molecular driver of accelerated healing. Conclusions: This study shows that optogenetic YAP is functional in H9c2 cardiomyoblasts and its controlled activation can potentially enhance wound healing in a range of conditions. | Make paid
Mitochondria in mammalian cells provide ATP through oxidative phosphorylation. The overproduction of reactive oxygen species (ROS) in mitochondrial cells promotes cancer by modifying gene expression or function. Mating introduces competing mitochondrial (mtDNA) and nuclear DNA (nDNA) gene products, leading to biological differences between males and females for diseases and disorders such as cancer. There is a significant sex bias in aging-related conditions. We aimed to investigate whether sex and age affect mitochondrial protein-coding gene expression in cancer and, if so, to determine the prognosis value in survival outcomes, stemness, and immune cell infiltrates. We compared normal versus primary tumor transcriptomes (bulk RNA-Seq) from The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) projects to test these hypotheses. Correlations between gene expression, survival, protective or risk factor, stemness, and immune cell infiltrate were performed in RStudio using UCSC Xena Shiny. Eleven mitochondrial protein-coding genes were altered in brain cancer (MT-ND2, MT-ND1, MT-ATP8, MT-ATP6, MT-CO2, MT-CYB, MT-CO3, MT-ND4L, MT-ND4, MT-ND3, MT-CO1). MT-ND5 and MT-ND6 are disproportionately expressed in female brain tissues. Mitochondrial global polymorphic expression sites of variation were more significant in the 50-59 and 60-79-year-old age groups than in the 20-49-year-old age groups. Pan-cancer survival analysis revealed a 4-component gene signature (MT-CO1, MT-CO2, MT-ND5, and MT-ND6) downregulated in low-grade glioma (LGG). This gene signature increased LGG overall survival, disease-specific survival, and progression-free interval without sex-specific association. However, the correlation with disease-free interval survival was female-specific. The 4-component gene signature was protective in LGG but risky in thymoma cancer and uterine corpus endometrial carcinoma. In LGG, the 4-component gene signature positively correlated with immune monocyte, NK, and B cell infiltrates and negatively correlated with T cell CD4+ Th2, macrophage M1 and M2, myeloid dendritic cell, and neutrophil. We identified a 13-component mitochondrial protein-coding gene signature associated with stemness in kidney chromophobe. A sex-biased effect was observed in mitochondrial protein-coding for brain tissues, with a female bias. However, an aging effect with higher polymorphic site expression was observed in male tissues. We conclude that the differentially expressed mitochondrial protein-coding genes provide new insights into carcinogenesis, helping to identify new prognostic markers. The overexpression of the 4-component gene signature is associated with a better prognosis in LGG, with positive and negative correlations with immune cell infiltrates. | Make paid
Intertissue RNA transport has emerged as a novel signaling mechanism. In C. elegans, this is conferred by the systemic RNAi pathway, in which the limiting step is the cellular import of extracellular RNAs via SID-1. To better understand the physiological role of systemic RNAi in vivo, we modified the function of SID-1 through loss-of-function mutation and tissue-specific overexpression of sid-1 in C. elegans. We observed that sid-1 loss-of-function mutants are as healthy as wild-type worms. Conversely, overexpression of sid-1 in intestine, muscle, or neurons rendered worms short-lived. The effects of intestinal sid-1 overexpression were reversed by silencing the components of the systemic RNAi pathway sid-1, sid-2 and sid-5, thus implicating RNA transport. Moreover, silencing the miRNA biogenesis proteins pash-1 and dcr-1 rendered the lifespan of worms with intestinal sid-1 overexpression similar to controls. Lastly, we observed that the lifespan decrease produced by tissue-specific sid-1 overexpression was dependent on the bacterial food source. Collectively, our data support the notion that systemic RNA signaling is tightly regulated, and unbalancing that process provokes a reduction in lifespan. | Make paid
Spatially-resolved gene expression profiling provides valuable insight into tissue organization and cell-cell crosstalk; however, spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for a rigorous interpretation of cell states and do not utilize associated histology images. Significant sample variation further complicates the integration of ST datasets, which is essential for identifying commonalities across tissues or altered cellular wiring in disease. Here, we present Starfysh, the first comprehensive computational toolbox for joint modeling of ST and histology data, dissection of refined cell states, and systematic integration of multiple ST datasets from complex tissues. Starfysh uses an auxiliary deep generative model that incorporates archetypal analysis and any known cell state markers to avoid the need for a single-cell-resolution reference in characterizing known or novel tissue-specific cell states. Additionally, Starfysh improves the characterization of spatial dynamics in complex tissues by leveraging histology images and enables the comparison of niches as spatial "hubs" across tissues. Integrative analysis of primary estrogen receptor-positive (ER+) breast cancer, triple-negative breast cancer (TNBC), and metaplastic breast cancer (MBC) tumors using Starfysh led to the identification of heterogeneous patient- and disease-specific hubs as well as a shared stromal hub with varying spatial orientation. Our results show the ability to delineate the spatial co-evolution of tumor and immune cell states and their crosstalk underlying intratumoral heterogeneity in TNBC and revealed metabolic reprogramming shaping immunosuppressive hubs in aggressive MBC. Starfysh is publicly available (https://github.com/azizilab/starfysh). | Make paid
Background: An important hallmark of glioblastoma aggressiveness is its altered metabolism of glucose. This metabolic shift wherein the tumor cells employ aerobic glycolysis regardless of oxygen availability via reprogramming of mitochondrial oxidative phosphorylation is known as the Warburg effect. Previous literatures have linked this metabolic reprograming to tumor progression glioblastoma cell proliferation making it a key target for targeted drug therapy. Objective: To evaluate the anti-Warburg efficacies of the triple-drug combination of temozolomide, metformin and epigallocatechin gallate in preclinical glioblastoma models. Methodology: Based on this lacuna, the current study aimed to explore the therapeutic efficacy of the triple-drug combination of temozolomide, metformin and epigallocatechin gallate in attenuating Warburg effect and glucose uptake in glioblastoma both in vitro and in vivo. Results: Our results showed that the triple-drug combination had significantly reduced glucose uptake and reversed the Warburg effect in glioblastoma cells and in the xenograft-induced glioma rat model. Conclusion: Thus, the triple-drug combination would serve as an effective therapeutic regime to hamper glioblastoma progression via altering glucose metabolism and improve the overall prognosis in patient setting. | Make paid