Biology subjects

Karpova, A.

Publications and source records attributed to Karpova, A..

9 recordsLinked to original sources

bioRxiv2025

Activity-dependent control of axonal amphisome trafficking governs norepinephrine release in vivo

Amphisomes are autophagy-related organelles formed by the fusion of autophagosomes with late endosomes. In neurons, they contribute to both cargo degradation and signaling, yet their physiological roles in vivo remain unclear. Here, we show that axonal amphisome trafficking in highly branched locus coeruleus (LC) neurons is regulated by neuronal activity, novelty-associated behavioral state, and axonal norepinephrine (NE) signaling. Using fiber-mediated in vivo laser photoconversion and two-photon imaging, combined with chemogenetics and a genetically encoded norepinephrine sensor, we tracked amphisome transport in the intact brains. We show that organelles generated within distal LC axons projecting to the prefrontal and motor cortices (PFC/M1) undergo retrograde trafficking across the entire axonal length toward somatic compartments. Amphisome trafficking dynamics are bidirectionally regulated by presynaptic adrenergic signaling through opposing cAMP/PKA-dependent mechanisms. In vivo, elevated local autoreceptor-mediated norepinephrine signaling, involving association of activated {beta}2-adrenergic autoreceptors with SIPA1L2-positive amphisomes, constrains processive retrograde trafficking by promoting transient immobilization and localized, non-directional "jittery" motility states. Conversely, reduced local norepinephrine signaling promotes amphisome mobilization, and chemogenetic engagement of Gi-coupled signaling accelerated transport by reducing transient immobilization events and reinforcing directional processivity, thereby facilitating cargo delivery toward somatic degradative compartments. Together, these findings identify a local neuromodulatory mechanism linking norepinephrine signaling to axonal amphisome trafficking in vivo and suggest that neuromodulatory states, such as novelty- and wakefulness-associated LC activity, as well as sleep-associated silencing of LC activity, regulate neuronal proteostasis through local control of autophagic cargo transport.

neuroscience↗

bioRxiv2025

Amphisome biogenesis couples synaptic autophagy to local protein synthesis

Synaptic neurotransmission imposes high demands on membrane turnover, metabolism, and the remodeling of presynaptic molecular composition. While the impact of autophagy on neurotransmission has been firmly established, evidence for activity-dependent synaptic induction of autophagy remains surprisingly limited. Here, we demonstrate that amphisomes containing BDNF/TrkB are formed at presynaptic boutons following sustained synaptic activation. Activity-dependent bulk endocytosis serves as a membrane source for amphisome biogenesis, while key autophagy proteins are recruited to the active zone, and autophagy initiation is triggered locally by the energy-sensing kinase AMPK. BDNF/TrkB-containing amphisomes contribute to the turnover of key presynaptic cytoskeletal proteins involved in synaptic vesicle clustering. The formation of amphisomes following sustained synaptic activity facilitates both the degradation of these proteins and their replenishment through local translation of their mRNAs at presynaptic boutons. We propose that activity-induced synaptic autophagy largely reflects amphisome formation, which in turn is required for the replacement of proteins within the local presynaptic cytomatrix.

neuroscience↗

bioRxiv2025

Cognitive Graphs of Latent Structure in Rostral Anterior Cingulate Cortex

Mental maps of environmental structure enable the flexibility that defines intelligent behavior. We describe a striking internal representation in rat prefrontal cortex that exhibits hallmarks of a workspace for constructing goal-specific, cognitive graphs for sequences of abstract states that animals must traverse through their actions. As rats uncover -- unguided -- complex sequential patterns, neural ensemble activity in rostral Anterior Cingulate Cortex develops a highly structured yet compact, scalable representation anchored in states at the start and end of self-organized sequences. Graphs are organized to reflect relational similarities across contexts, and individually, permit flexible refinement of component states. The representations crystalline organization permits instantaneous inference of the animals current state within self-generated sequences, offering insights into the algorithmic and representational principles underlying unguided parsing of open-ended problems.

neuroscience↗

bioRxiv2023

Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages

Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like (PRKCA, SOX6, RGS6, KCNQ3) and luminal A/B (FAM155A, LRP1B) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.

cancer biology↗

bioRxiv2022

A Jacob/nsmf gene knockout does not protect against hypoxia- and NMDA-induced neuronal cell death

Jacob is a synapto-nuclear messenger protein that encodes and transduces the origin of synaptic and extrasynaptic NMDA receptor signals to the nucleus. The protein assembles a signalosome that differs in case of synaptic or extrasynaptic NMDAR activation. Following nuclear import Jacob docks these signalosomes to the transcription factor CREB. We have recently shown that amyloid-beta and extrasynaptic NMDAR activation triggers the translocation of a Jacob signalosome that results in inactivation of the transcription factor CREB, a phenomenon termed Jacob-induced CREB shut-off (JaCS). JaCS contributes to early Alzheimers disease pathology and a gene knockout of nsmf, the gene encoding Jacob, protects against amyloid pathology. Given that extrasynaptic activity is also involved in acute excitotoxicity, like in stroke, we asked whether nsmf gene knockout will also protect against acute insults, like oxygen and glucose deprivation and excitotoxic NMDA stimulation. Here we show that organotypic hippocampal slices from wild-type and nsmf-/- mice display similar degrees of degeneration when exposed to either oxygen glucose deprivation or 50 {micro}M NMDA incubation. This lack of neuroprotection indicates that JaCS is mainly relevant in conditions of low level chronic extrasynaptic NMDAR activation that results in cellular degeneration induced by alterations in gene transcription.

neuroscience↗

bioRxiv2022

ACC neural ensemble dynamics are structured by strategy prevalence

Medial frontal cortical areas are thought to play a critical role in the brains ability to flexibly deploy strategies that are effective in complex settings. Still, the specific circuit computations that underpin this foundational aspect of intelligence remain unclear. Here, by examining neural ensemble activity in rats that sample different strategies in a self-guided search for latent task structure, we demonstrate a robust tracking of individual strategy prevalence in the anterior cingulate cortex (ACC), especially in an area homologous to primate area 32D. Prevalence encoding in the ACC is wide-scale, independent of reward delivery, and persists through a substantial ensemble reorganization that tags ACC representations with contextual content. Our findings argue that ACC ensemble dynamics is structured by a summary statistic of recent behavioral choices, raising the possibility that ACC plays a role in estimating - through statistical learning - which actions promote the occurrence of events in the environment.

neuroscience↗

bioRxiv2020

Anterior Cingulate Cortex Directs Exploration of Alternative Strategies

The ability to adjust ones behavioral strategy in complex environments is at the core of cognition. Doing so efficiently requires monitoring the reliability of the ongoing strategy and switching away from it to evaluate alternatives when appropriate. Studies in humans and non-human primates have uncovered signals in the anterior cingulate cortex (ACC) that track the pressure to switch away from the ongoing strategy, and others that relate to the pursuit of alternatives. However, whether these signals underlie computations that actually underpin strategy switching, or merely reflect tracking of related variables remains unclear. Here we provide causal evidence that rodent ACC actively arbitrates between persisting with ongoing behavioral choice and switching away temporarily to re-evaluate alternatives. Furthermore, by individually perturbing distinct output pathways, we establish that the two associated computations - whether to switch away from the current choice, and the pursuit of alternatives - are segregated within ACC micro-circuitry.

neuroscience↗

bioRxiv2020

A molecular mechanism by which amyloid-β induces transcriptional inactivation of CREB in Alzheimer's Disease

Synaptic dysfunction caused by soluble {beta}-Amyloid (A{beta}) is a hallmark of the early stage of Alzheimers disease (AD) and is tightly linked to cognitive decline. A{beta} induces by yet unknown mechanisms disruption of transcriptional activity of cAMP- responsive element-binding protein (CREB), a master regulator of cell survival and plasticity-related gene expression. Here, we report that A{beta} elicits cytonuclear trafficking of Jacob, a protein serves as a mobile signaling hub that docks a signalosome to CREB, which induces transcriptional inactivation and subsequent synapse impairment and eventually loss in AD. The small chemical compound Nitarsone selectively hinders assembly of this signalosome and thereby restores CREB transcriptional activity. Nitarsone prevents impairment of synaptic plasticity as well as cognitive decline in mouse models of AD. Collectively, the data suggest that targeting Jacob induced CREB shutoff is a therapeutic avenue against early synaptic dysfunction in AD.

neuroscience↗

bioRxiv2019

SIPA1L2 controls trafficking and signaling of TrkB-containing amphisomes at presynaptic terminals

Amphisomes are transient organelles that derive from fusion of autophagosomes with late endosomes. They rapidly transform into degradative autolysosomes, whereas non-degradative roles of the autophagic pathway have been barely described. Here we show that in neurons BDNF/TrkB receptor bearing Rab7 / Light chain 3 (LC3) - positive amphisomes signal at presynaptic boutons during retrograde trafficking to the soma. Local signaling and inward transport essentially require the Rap GTPase-activating (RapGAP) protein SIPA1L2, which directly binds to TrkB and Snapin to connect TrkB-containing amphisomes to dynein. Association with LC3 regulates the RapGAP activity of SIPA1L2 and thereby retrograde trafficking. Following induction of presynaptic plasticity amphisomes dissociate from dynein at boutons, and this enables local signaling and promotes transmitter release. Accordingly, sipa1l2 knockout mice show impaired BDNF-dependent presynaptic plasticity. Collectively, the data suggest that TrkB-signaling endosomes are in fact amphisomes that during retrograde transport have local signaling capacity in the context of presynaptic plasticity.

neuroscience↗