Eugenio F. Fornasiero

Our modern environment – with its artificial lighting, irregular work hours, and frequent travel — often disrupts our circadian rhythms, which can lead to health problems, particularly in learning and memory. This is especially concerning given the aging population and the rising prevalence of dementia. Yet, the biological mechanisms linking circadian disruption to cognitive impairment remain poorly understood. At the molecular level, genetic techniques have been used to attenuate or abolish expression of key genes involved in circadian rhythms and these manipulations have detrimental effects on memory function. However, whether environmentally induced circadian disruption, impairs memory via changes in overall gene expression levels in the hippocampus or rather via changes in the coordinated rhythmic patterns of circadian expression across groups of genes is less known. Here, we examined how environmental circadian disruption affects the expression of genes involved in the circadian clock and memory in the hippocampus of rats using a forced desynchrony model. Circadian disruption changed the rhythmic properties of gene expression in most genes assessed but had no measurable effect on average expression levels across the day. These findings suggest that the inability to maintain circadian synchrony rather than overall expression may underlie the cognitive deficits observed in circadian-related disorders.

MNeonGreen (mNG) is among the brightest and most photostable monomeric green fluorescent proteins and is widely used for protein tagging. Here, we present sdAb(mNG), a high-affinity single-domain antibody (sdAb) that enables biochemical capture, imaging, and manipulation of mNG-tagged proteins. A 1.26 Å crystal structure reveals an extensive interaction surface between mNG and sdAb(mNG), accounting for its high affinity (K _D = 0.39 nM) and robust target recognition across diverse experimental conditions. This allows a single sdAb to support applications that typically require multiple specialized tools. We demonstrate the utility of sdAb(mNG) in several example applications including highly specific immunoprecipitation, direct immunofluorescence, and super-resolution imaging. Importantly, sdAb(mNG) retains high-performance target recognition even in intracellular environments. When expressed as an intrabody in living mammalian cells, sdAb(mNG) enables relocalization of mNG-tagged proteins to defined compartments or visualization of synaptic vesicle transport in primary neurons. In zebrafish, fusion of sdAb(mNG) to an F-box degradation domain induces cell-autonomous depletion of an endogenous mNG-tagged transcription factor and produces a clear developmental phenotype. These findings establish sdAb(mNG) as a versatile and robust affinity reagent that converts mNG from a passive fluorescent reporter into a multifunctional handle for imaging, proteomics, and programmable manipulation of endogenous and engineered proteins.

Synaptic neurotransmission is a critical hallmark of brain activity and one of the first processes affected in neural diseases. Monitoring this process, particularly synaptic vesicle recycling, in living cells has been instrumental in revealing the mechanisms responsible for neurotransmitter release. However, currently available reporters suffer from limitations, such as large probe sizes or limited compatibility for human neurons, hampering the quantitative analysis of synaptic pathophysiology. Here, we describe the NbLumSyt1 toolkit, a panel of nanobody-based affinity probes that target the luminal domain of the synaptic vesicle protein Synaptotagmin 1 (Syt1). These new tools enable quantitative, noninvasive imaging and functional interrogation of Syt1 exo-endocytosis and trafficking in human neurons, with unprecedented precision, versatility and cost efficiency, in technologies ranging from fixed- and live-cell super-resolution imaging to electron microscopy and mass spectrometry. Overall, NbLumSyt1 nanobinders provide a valuable platform for studying synaptic physiology and pathophysiology, benefiting fundamental neuroscience and translational efforts to study and develop treatments for brain-related disorders. Graphical Abstract

Post‐transcriptional regulation of gene expression is orchestrated by RNA‐binding proteins (RBPs), which regulate key aspects of the RNA life cycle including splicing, localization, translation, and decay. Although RBPs have been initially considered as isolated regulators, it is becoming clear that RNA molecules are commonly bound by several RBPs whose coordination directs their fate. These combinatorial interactions produce complex, context‐dependent post‐transcriptional regulatory networks (PTRNs) whose outcomes are difficult to predict. RBPs may also switch function depending on cell state, subcellular localization, or post‐translational modification, adding further complexity to RNA regulation. This review focuses on recent technological advances expanding our ability to map and interpret PTRNs. Multiplexed methods allow profiling of the RNA‐binding patterns of several RBPs in parallel, whereas deeper interaction proteomics studies reveal protein–protein connections and changes in distinct biological settings. Complementary RNA‐targeting pulldown and single‐molecule imaging strategies enable real‐time and single‐cell‐resolution visualization of ribonucleoprotein assembly and dynamics, while functional high‐throughput screens allow assignment of first order functions for these RBPs. Overall, these approaches set the stage for comprehensive decoding of the spatiotemporal structure of PTRNs and reveal how RBP interactions coordinate sets of RNAs to collectively regulate them in response to physiological demands. In addition to describing these systems‐level approaches, we outline key future analytical and experimental innovations that could transform our understanding of RBP function. We believe that a systems‐level understanding of RBPs as dynamic, integrated components of multiscale regulatory regimes is required to fully understand the complexity of gene expression control and its disruption in disease.

Cell identity is traditionally viewed as a product of biochemical signalling, yet cells are exposed to defined physical landscapes, whose role in fate control remains unclear. In particular, how pluripotent stem cells integrate nanoscale extracellular cues into gene regulatory programs remains poorly understood. Here, we show that biomimetic substrate nanotopography acts as a potent regulator of naïve pluripotency in mouse embryonic stem cells (mESCs). Using supersonic cluster beam deposition, we generate substrates with defined nanotopography that recapitulate native features of extracellular matrix. We demonstrate that nanotopography induces a mechanically relaxed cell state characterised by reduced adhesion, cellular and nuclear softening, and altered nuclear architecture. These mechanical changes are coupled with chromatin remodelling, including reduced H3K27me3 and H3K9me2, redistribution of H3K9me3, and increased H3K4me3. Transcriptomic analyses reveal suppression of adhesion- and cytoskeleton-associated programs together with the activation of a naïve pluripotency transcriptional signature, including upregulation of Nanog. Mechanistically, we identify the H3K9 demethylase KDM3A as a mechanosensitive epigenetic regulator required for nanotopography-induced Nanog expression. Together, our findings uncover a novel mechanotransductive pathway directly linking extracellular nanotopography to chromatin state and pluripotency control.

Amyloid-β (Aβ) peptides are a defining feature of Alzheimer’s disease (AD). These peptides are produced by the proteolytic processing of the amyloid precursor protein (APP), which can occur through the synaptic vesicle (SV) cycle. However, how amyloidogenic APP processing alters SV composition and presynaptic function is poorly understood. Using App knock-in mouse models of amyloid pathology, we found that proteins with impaired degradation accumulate at presynaptic sites together with Aβ ₄₂ in the SV lumen. Levetiracetam (Lev) is a US Food and Drug Administration–approved antiepileptic that targets SVs and has shown therapeutic potential to reduce AD phenotypes through an undefined mechanism. We found that Lev lowers Aβ ₄₂ levels by reducing amyloidogenic APP processing in an SV2a-dependent manner. Lev modified SV cycling and increased APP cell surface expression, which promoted its preferential processing through the nonamyloidogenic pathway. Stable isotope labeling combined with mass spectrometry confirmed that Lev prevents Aβ ₄₂ production in vivo. In transgenic mice with aggressive amyloid pathology, electrophysiology and immunofluorescence confirmed that Lev restores SV cycling abnormalities and reduces synapse loss. Last, early Aβ pathology in brains from donors with Down syndrome was characterized by elevated presynaptic proteins. Together, these findings highlight the potential to prevent Aβ pathology before irreversible damage occurs.

An important hallmark of aging is the loss of proteostasis, which can lead to the formation of protein aggregates and mitochondrial dysfunction in neurons. Although it is well known that protein synthesis is finely regulated in the brain, especially at synapses, where mRNAs are locally translated in an activity‐dependent manner, little is known as to the changes in the synaptic proteome and transcriptome during aging. Therefore, this work aims to elucidate the relationship between the transcriptome and proteome at the soma and synaptic levels during aging. Proteomic and transcriptomic data analysis reveal that, in young animals, proteins and transcripts are correlated and synaptic regulation is driven by changes in the soma. During aging, there is a decoupling between transcripts and proteins and between somatic and synaptic compartments. Furthermore, the soma‐synapse gradient of ribosomal genes changes upon aging, that is, ribosomal transcripts are less abundant and ribosomal proteins are more abundant in the synaptic compartment of old mice with respect to younglings. Additionally, transcriptomics data highlight a difference in the splicing of certain synaptic mRNA with aging. Taken together, our data provide a valuable resource for the study of the aging synapse.

Multiplexed super-resolution microscopy enables spatial proteomics at single-protein resolution, but current methods often depend on secondary labels, complicating implementation and limiting throughput. We introduce a streamlined approach that combines speed-optimized DNA-PAINT sequences with their mirror-image analogs (left-handed DNA), enabling rapid and efficient 12-plex imaging. Validated on synthetic and cellular benchmarks, our method maps dense neuronal interactomes in 3D with 15 nm spatial resolution across a 200 × 200 µm² field of view.

Brain aging is a major risk for neurodegeneration, yet the underlying molecular mechanisms remain poorly understood. Here we performed an integrative proteo-transcriptomic analysis of the aging mouse brain, uncovering molecular signatures of aging through the assessment of protein aggregation, mRNA relocalization, and comparative proteomics across eight models of premature aging and neurodegeneration. We identified dynamic changes in physiological aging highlighting differences in synaptic maintenance and energy-allocation. These were linked to changes associated with fundamental protein biochemical properties such as size and net charge. Network analysis highlighted a decrease in mitochondrial complex I proteins not compensated at the mRNA level. Aggregation of 60S ribosome subunits indicated deteriorating translation efficiency and was accompanied by mitochondrial and proteasomal imbalance. The analysis of the nine models revealed key similarities and differences between physiological aging and pathology. Overall, our study provides an extensive resource on molecular aging, and offers insights into mechanisms predisposing to neurodegeneration, easily accessible at our Brain Aging and Molecular Atlas Project (BrainAging-MAP) website.

Aging is a major risk factor for neurodegeneration and is characterized by diverse cellular and molecular hallmarks. To understand the origin of these hallmarks, we studied the effects of aging on the transcriptome, translatome, and proteome in the brain of short-lived killifish. We identified a cascade of events in which aberrant translation pausing led to altered abundance of proteins independently of transcriptional regulation. In particular, aging caused increased ribosome stalling and widespread depletion of proteins enriched in basic amino acids. These findings uncover a potential vulnerable point in the aging brain’s biology—the biogenesis of basic DNA and RNA binding proteins. This vulnerability may represent a unifying principle that connects various aging hallmarks, encompassing genome integrity, proteostasis, and the biosynthesis of macromolecules.