Biology subjects

Ripa, R.

Publications and source records attributed to Ripa, R..

7 recordsLinked to original sources

bioRxiv2025

Resilience and restoration from fasting-refeeding mediated by a nutrient-regulated linker histone

Intermittent fasting and fasting-refeeding regimens can slow biological aging across taxa1. Shifts between fed and fasted states activate ancient nutrient-sensing pathways which alter cellular and epigenetic states to promote longevity2-4. Yet how biological age trajectories progress during fasting-refeeding, and how nutrient-sensing pathways reprogram epigenetic state remain largely unknown. Here we observe increases in predicted biological age of Caenorhabditis elegans during prolonged fasting in adult reproductive diapause, followed by extraordinary reduction of biological age during refeeding. We identify hil-1/H1-0 as an evolutionarily conserved nutrient-regulated linker histone which mediates adaptations to fasting and refeeding downstream of FOXO and TFEB transcription factors. In C. elegans and human cell culture, hil-1/H1-0 upregulation during low-nutrient states promotes long-term survival and subsequent refeeding-induced recovery. Restoration of C. elegans after prolonged fasting is improved by enhancing the natural downregulation of hil-1 specifically during refeeding. Our study identifies HIL-1/H1.0 as part of an ancestral epigenetic switch during fasting-refeeding that reprograms metabolic and cellular states underlying resilience and restoration.

genetics↗

bioRxiv2024

Loss of killifish cGAS/STING function attenuates cellular senescence and age-related signatures but does not extend organismal life span

The cGAS/STING pathway is a central innate immune signaling pathway whose chronic activation has been implicated in numerous age-related pathologies, yet its impact on life span itself is unknown. Here we engineered knockouts of this pathway in the killifish Nothobranchius furzeri, and assessed physiology and aging. In vitro, loss of killifish cGAS or STING mitigated DNA damage-induced senescence in cultured fibroblasts. In vivo, cGAS knockout unexpectedly led to low-grade inflammation. It also attenuated changes in gene expression in response to DNA damage in young animals, and age-related changes in the old, suggesting dampening of senescence and aging. Necroscopy indicated that tissue pathology appeared milder overall in both mutants, though some tissues showed enhanced sterile macrophage infiltration. Despite an attenuated aging signature, however, longevity was not significantly different from wild type. Our findings reveal a potential tradeoff, where inhibiting the cGAS/STING pathway alleviates age-related signatures, but increases sterile inflammation, offsetting beneficial effects on lifespan.

developmental biology↗

bioRxiv2023

A primordial TFEB-TGFβ signaling axis systemically regulates diapause and stem cell longevity

Fasting/refeeding enhances animal health and lifespan across taxa. C. elegans can endure months of fasting in adult reproductive diapause (ARD) and upon refeeding, regenerate and reproduce. hlh-30/TFEB is an ARD master regulator whose mutants live mere days in ARD and dont recover with refeeding. Here we find that downregulation of TGF{beta} signaling bypasses hlh-30 collapse, and restores recovery, germline stem cell proliferation and reproductive competence. Upon fasting, HLH-30/TFEB(+) downregulates TGF{beta} in sensory neurons, to inhibit Notch and promote reproductive quiescence in the germline. Upon refeeding, these pathways are upregulated to activate stem cells and promote reproduction. hlh-30 loss induces a senescent-like DNA damage, immune and growth metabolic signature reversed by inhibiting TGF{beta} signaling. TFEBs role is conserved in mammalian diapause models, including mouse embryonic and human cancer diapause. Thus, TFEB-TGF{beta} axis relays systemic signals matching nutrient supply with growth signaling, to regulate stem cell longevity, senescence and regeneration across species.

cell biology↗

bioRxiv2023

Mitochondrial translocation of TFEB regulates complex I and inflammation

TFEB is a master regulator of autophagy, lysosome biogenesis and mitochondrial metabolism that works, and immunity, primarily through transcription controlled by cytosol-to-nuclear translocation. Emerging data indicate additional regulatory interactions at the surface of organelles such as lysosomes. Here we show that TFEB has a non-transcriptional role in mitochondria, regulating the electron transport chain complex I to down-modulate inflammation. Proteomic analysis revealed extensive TFEB co-precipitation with several mitochondrial proteins, whose interactions are disrupted upon infection with S. Typhimurium. Localization of TFEB in the mitochondrial matrix was confirmed by high resolution confocal microscopy and biochemistry with translocation dependent on a conserved N-terminal TOMM20-binding motif enhanced by mTOR inhibition. Within the mitochondria, TFEB and protease LONP1 antagonistically co-regulate complex I, reactive oxygen species and the inflammatory response. Consequently, during infection, lack of TFEB specifically in the mitochondria exacerbates the expression of pro-inflammatory cytokines, contributing to innate immune pathogenesis.

cell biology↗

bioRxiv2022

Refeeding-associated AMPKγ1 complex activity is a hallmark of health and longevity.

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.

physiology↗

bioRxiv2020

Optimization of cryopreservation and in vitro fertilization techniques for the African turquoise killifish Nothobranchius furzeri

Over the last decade, the African turquoise killifish, Nothobranchius furzeri, has emerged as an important model system for the study of vertebrate biology and ageing. However, rearing this fish in captivity can pose challenges, due to the short window of fertility, inbreeding problems, and the continuous maintenance of different strains and transgenic lines. To date, the main means of long term strain maintenance is to arrest embryos in diapause, a poorly understood and unreliable method. To solve these problems, we developed a robust protocol to cryopreserve sperm and to revive them for in vitro fertilization (IVF), as a better option for long term storage of N. furzeri lines. We tested a variety of extender and activator buffers for sperm in vitro fertilization, as well as cryoprotectants to achieve maximal long term storage and fertilization conditions tailored to this species. Our optimized protocol was able to preserve sperm in a cryogenic condition for months and to revive an average of 40% upon thawing. Thawed sperm were able to fertilize nearly the same number of eggs as natural fertilization, with an average of ~25% and peaks of ~55% fertilization. This technical advance will greatly facilitate the use of N. furzeri as a model organism.

cell biology↗

bioRxiv2019

Cell cycle dynamics during diapause entry and exit in an annual killifish revealed by FUCCI technology

BackgroundAnnual killifishes are adapted to surviving and reproducing over alternating dry and wet seasons. During the dry season, all adults die and desiccation-resistant embryos remain encased in dry mud for months or years in a state of quiescence, delaying hatching until their habitats are flooded again. Embryonic development of annual killifishes deviates from canonical teleost development. Epiblast cells disperse during epiboly, and a \"dispersed phase\" precedes gastrulation. In addition, annual fish have the ability to enter diapause and block embryonic development at the dispersed phase (diapause I), mid-somitogenesis (diapause II) and the final phase of development (diapause III).\n\nDevelopmental transitions associated with diapause entry and exit can be linked with cell cycle events. Here we set to image this transitions in living embryos.\n\nResultsTo visibly explore cell cycle dynamics during killifish development in depth, we created a stable transgenic line in Nothobranchius furzeri that expresses two fluorescent reporters, one for the G1 phase and one for the S/G2 phases of the cell cycle, respectively (fluorescent ubiquitination based cell cycle indicator, FUCCI). Using this tool, we observed that, during epiboly, epiblast cells progressively become quiescent and exit the cell cycle. All embryos transit through a phase where dispersed cells migrate, without showing any mitotic activity, possibly blocked in the M phase (diapause I).\n\nThereafter, exit from diapause I is synchronous and cells enter directly into the S phase without transiting through G1. The developmental trajectories of embryos entering diapause and of those that continue to develop are different. In particular, embryos entering diapause have reduced growth along the medio-lateral axis. Finally, exit from diapause II is synchronous for all cells and is characterized by a burst of mitotic activity and growth along the medio-lateral axis such that, by the end of this phase, the morphology of the embryos is identical to that of direct-developing embryos.\n\nConclusionsOur study reveals surprising levels of coordination of cellular dynamics during diapause and provides a reference framework for further developmental analyses of this remarkable developmental quiescent state.\n\nList of AbbreviationsIn this paper, we will refer to several developmental stages or morphological structures using abbreviations. To make the reading easier, we resume here a list of all the abbreviations, to which the reader can refer at any time.

developmental biology↗