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Biology subjects

Bens, M.

Publications and source records attributed to Bens, M..

11 recordsLinked to original sources

The Rab32 small GTPase is required for efficient cross-priming of CD8+ T cellsagainst cell-associated antigens by XCR1+ type 1 DCs in vivo.

Type 1 conventional dendritic cells (cDC1s) are critical for initiating adaptive immune responses through the cross-priming of CD8 T cells against antigens from tumor or virus-infected cells. This function depends on specialized cross-presentation pathways that allow cDC1s to process phagocytosed cell debris and present peptide-MHC I complexes. In this study, we identify the small GTPase Rab32 as being highly and selectively over-expressed in cDC1s as compared to cDC2s. While cDC1s from Rab32-deficient mice develop normally and can respond to maturation signals, their capacity to activate CD8 T cells in vivo is impaired. Notably, Rab32- deficient cDC1s retain the ability to stimulate TCR transgenic CD8 T cells ex vivo using both cell-associated antigens and MHC I-binding peptides of varying affinity. However, in vivo, Rab32 is essential for effective CD8 T cell responses to cell-associated antigens, independent of Rab32 expression in T cells themselves. Importantly, Rab32-mediated cross-priming is required for the efficient expansion of tumor-specific CD8 T cells into solid tumors. These findings underscore a critical role for Rab32 in cDC1-mediated cross-priming, highlighting the contribution of non-antigen processing vesicular pathways in shaping CD8 T cell responses to cellular antigens.

immunology↗

Amyloid Beta Precursor Protein contributes to brain aging and learning decline in short-lived turquoise killifish (Nothobranchius furzeri)

Brain aging is a key risk factor for many neurodegenerative diseases, yet its molecular and cellular mechanisms remain elusive. Amyloid-beta precursor protein (APP) is among the most studied proteins linked to brain pathology; however, its role in non-pathological brain aging remains poorly characterized. Here, we investigate the natural impact of APP on normal brain aging using the short-lived turquoise killifish (Nothobranchius furzeri), which exhibits rapid and spontaneous age-related decline. We found that a pyroglutamated APP derivative (APPpE11) accumulates intra-neuronally in an age-dependent manner, co-localizing with a marker of cell death. We found that intraneuronal APPpE11 is also present in brains from healthy elderly humans, suggesting deep evolutionary conservation. To determine APPs role in spontaneous brain aging, we knock-out "amyloid precursor protein a" (appa) in killifish via CRISPR/Cas9. The lack of appa mitigated brain aging from a proteome-wide perspective, reduced age-related cell death and inflammation, and improved neuronal activity and learning capacity in aged individuals. Our findings show an ancestral and previously unrecognized role of amyloid-beta precursor protein in non-pathological brain aging, making it an ideal target for anti-aging interventions.

neuroscience↗

The Greenland shark (Somniosus microcephalus) genome provides insights into extremelongevity

The Greenland shark (Somniosus microcephalus) is the longest-lived vertebrate known, with an estimated lifespan of [~] 400 years. Here, we present a chromosome-level assembly of the 6.45 Gb Greenland shark, rendering it one of the largest non-tetrapod genomes sequenced so far. Expansion of the genome is mostly accounted for by a substantial expansion of transposable elements. Using public shark genomes as a comparison, we found that genes specifically duplicated in the Greenland shark form a functionally connected network enriched for DNA repair function. Furthermore, we identified a unique insertion in the conserved C-terminal region of the key tumor suppressor p53. We also provide a public browser to explore its genome.

genomics↗

Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging

Inference of gene regulatory networks (GRNs) can reveal cell state transitions from single-cell genomics data. However, obstacles to temporal inference from snapshot data are difficult to overcome. Single-nuclei multiomics data offer means to bridge this gap and derive temporal information from snapshot data using joint measurements of gene expression and chromatin accessibility in the same single cells. We developed popInfer to infer networks that characterize lineage-specific dynamic cell state transitions from joint gene expression and chromatin accessibility data. Benchmarking against alternative methods for GRN inference, we showed that popInfer achieves higher accuracy in the GRNs inferred. popInfer was applied to study single-cell multiomics data characterizing hematopoietic stem cells (HSCs) and the transition from HSC to a multipotent progenitor cell state during murine hematopoiesis across age and dietary conditions. From networks predicted by popInfer, we discovered gene interactions controlling entry to/exit from HSC quiescence that are perturbed in response to diet or aging.

systems biology↗

Non-aging despite high mutation rate - genomic insights into the evolution of Hydra

Hydra is a genus of freshwater polyps with remarkable regeneration abilities and a non-senescent phenotype under laboratory conditions. Thus, this animal is particularly interesting for aging research. Here, we gained insights into Hydras recent genetic evolution by genome sequencing of single cells and whole individuals. Despite its extreme longevity, Hydra does not show a lower somatic mutation rate than humans or mice. While we identify biological processes that have evolved under positive selection in animals kept in optimal laboratory conditions for decades, we found no signs of strong negative selection during this tiny evolutionary window. Interestingly, we observe the opposite pattern for the preceding evolution in the wild over a longer time period. Moreover, we found evidence that Hydra evolution in captivity was accompanied and potentially accelerated by loss of heterozygosity. Processes under positive selection in captive animals include pathways associated with Hydras simple nervous system, its nucleic acid metabolic process, cell migration, and hydrolase activity. Genes associated with organ regeneration, regulation of mRNA splicing, histone ubiquitination, and mitochondrial fusion were identified as highly conserved in the wild. Remarkably, several of the processes under strongest selection are closely related to those considered essential for the exapted, i. e. not brought about by natural selection, feature: Hydras non-aging.

evolutionary biology↗

Status-dependent aging rates in long-lived, social mole-rats are shaped by HPA stress axis

Sexual activity and/or reproduction doubles life expectancy in the long-lived rodent genus Fukomys. To investigate the molecular mechanisms underlying this phenomenon, we analyzed a total of 636 RNA-seq samples across 15 tissues. This analysis suggests that the differences in life expectancy between reproductive and non-reproductive mole-rats are mainly caused by critical changes in the regulation of the hypothalamic-pituitary-adrenal stress axis, which we further substantiate with a series of independent evidence. In accordance with previous studies, the up-regulation of the proteasome and several so-called "anti-aging molecules", such as DHEA, is also linked with enhanced life expectancy. On the other hand, several our results oppose crucial findings in short-lived model organisms. For example, we found the up-regulation of the IGF1/GH axis and several other anabolic processes to be compatible with a considerable lifespan prolongation. These contradictions question the extent to which findings from short-lived species can be transferred to longer-lived ones.

genomics↗

Clownfishes are a genetic model of exceptional longevity and reveal molecular convergence in the evolution of lifespan

Standard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that provide protection from predation. We performed a survey and identified at least two species with lifespan of over 20 years. Given their small size and ease of captive reproduction, clownfishes lend themselves as experimental models of exceptional longevity.\n\nTo identify genetic correlates of exceptional longevity, we sequenced the transcriptomes of Amphiprion percula and A. clarkii and performed a scan for positively-selected genes (PSGs). These were compared with PSGs detected in long-lived mole rats and short-lived killifishes revealing convergent evolution in processes such as mitochondrial biogenesis. Among individual genes, the Mitochondrial Transcription Termination Factor 1 (MTERF1), was positively-selected in all three clades, whereas the Glutathione S-Transferase Kappa 1 (GSTK1) was under positive selection in two independent clades. For the latter, homology modelling strongly suggested that positive selection targeted enzymatically important residues.\n\nThese results indicate that specific pathways were recruited in independent lineages evolving an exceptionally extended or shortened lifespan and point to mito-nuclear balance as a key factor.

evolutionary biology↗

Higher transcriptome stability during aging in long-lived giant mole-rats compared to short-lived rats

Many aging-associated physiological changes are known to come up in short- and long-lived species with a different trajectory and emerging evidence suggests that large parts of life history trait differences between species are based on inter-species variation in gene expression. Little information is yet available, however, about transcriptome changes during aging when comparing mammals with different lifespans. For this reason, we studied the transcriptomes of five tissues and two age cohorts in two similar sized rodent species with very different lifespans: rat (Rattus norvegicus) and giant mole-rat (Fukomys mechowii) with maximum lifespans of 3.8 and >20 years, respectively. Our results show that giant mole-rats exhibit higher transcriptome stability during aging than the rat. While well-known aging signatures (e.g. up-regulation of pro-inflammatory genes) were detected in all rat tissues, they showed up only in one giant mole-rat tissue. Furthermore, many differentially expressed genes that were found in both species, were regulated in opposite directions during aging. This suggests that expression changes that cause aging in short-lived species are counteracted in long-lived species. Taken together, transcriptome stability may be one key causal factor of the long life- and healthspan of giant mole-rats and maybe of African mole-rats in general.

systems biology↗

Naked mole-rat transcriptome signatures of socially-suppressed sexual maturation and links of reproduction to aging

Naked mole-rats (NMRs) are eusocially organized in colonies. Although breeders carry the additional metabolic load of reproduction, they are extremely long-lived and remain fertile throughout their lifespan. Comparative transcriptome analysis of ten organs from breeders and non-breeders of the eusocial long-lived NMR and the polygynous shorter-lived guinea pig provide comprehensive and unbiased molecular evidence that sexual maturation in NMR is socially suppressed. After transition into breeders, transcriptomes are markedly sex-specific, show pronounced feedback signaling via gonadal steroids and have similarities to reproductive phenotypes in African cichlid fish. Further, NMRs show functional enrichment of status-related expression differences associated with aging. Lipid metabolism and oxidative phosphorylation - molecular networks known to be linked to aging - were identified among most affected gene sets. Further, a transcriptome pattern associated with longevity is reinforced in NMR breeders contradicting the disposable soma theory of aging and potentially contributing to their exceptional long life- and healthspan.

systems biology↗

Species comparison of liver proteomes reveals enhanced lipid metabolism, reduced mitochondrial respiration and enhanced expression of detoxifying enzymes in the long-lived naked mole-rat.

Mammals display wide range of variation in their lifespan. Investigating the molecular networks that distinguish long-from short-lived species has proven useful to identify determinants of longevity. Here, we compared the liver of long-lived naked mole-rats (NMRs) and the phylogenetically closely related, shorter-lived, guinea pigs using an integrated omic approach. We found that NMRs livers display a unique expression pattern of mitochondrial proteins that result in distinct metabolic features of their mitochondria. For instance, we observed a generally reduced respiration rate associated with lower protein levels of respiratory chain components, particularly complex I, and increased capacity to utilize fatty acids. Interestingly, we show that the same molecular networks are affected during aging in both NMR and humans, supporting a direct link to the extraordinary longevity of both species. Finally, we identified a novel longevity pathway and validated it experimentally in the nematode C. elegans.

systems biology↗

Long-lived rodents reveal signatures of positive selection in genes associated with lifespan and eusociality

The genetic mechanisms that determine lifespan are poorly understood. Most research has been done on short lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. We obtained genomic and transcriptomic data from 17 rodent species and systematically scanned eleven lineages associated with the evolution of longevity and eusociality for positively selected genes (PSGs). The set of 319 PSGs contains regulators of mTOR and is enriched in functional terms associated with (i) processes that are regulated by the mTOR pathway, e.g. translation, autophagy and mitochondrial biogenesis, (ii) the immune system and (iii) antioxidant defense. Analyzing gene expression of PSGs during aging in the long-lived naked mole-rat and up-regulation in the short-lived rat, we found a pattern fitting the antagonistic pleiotropy theory of aging.

evolutionary biology↗