Miracle-dz/UniFAR-FTUs huggingface dataset:
LRP10 as a novel α-synuclein regulator in Lewy body diseases

Autosomal dominant variants in LRP10 have been identified in patients with Lewy body diseases (LBDs), including Parkinson’s disease (PD), Parkinson’s disease-dementia (PDD), and dementia with Lewy bodies (DLB). Nevertheless, there is little mechanistic insight into the role of LRP10 in disease pathogenesis. In the brains of non-demented individuals, LRP10 is typically expressed in non-neuronal cells like astrocytes and neurovasculature, but in idiopathic and genetic cases of PD, PDD, and DLB it is also present in α-synuclein-positive neuronal Lewy bodies. These observations raise the questions of what leads to the accumulation of LRP10 in Lewy bodies and whether a possible interaction between LRP10 and α-synuclein plays a role in disease pathogenesis. Here, we demonstrate that wild-type LRP10 is secreted via extracellular vesicles (EVs) and can be internalised via clathrin-dependent endocytosis. Additionally, we show that LRP10 secretion is highly sensitive to autophagy inhibition, which induces the formation of atypical LRP10 vesicular structures in neurons in human induced pluripotent stem cells (iPSC)-derived midbrain-like organoids (hMLOs). Furthermore, we show that LRP10 overexpression leads to a strong induction of monomeric α-synuclein secretion, together with time-dependent, stress-sensitive changes in intracellular α-synuclein levels. Interestingly, patient-derived astrocytes carrying the c.1424+5G>A LRP10 variant secrete aberrant high-molecular-weight species of LRP10 in EV-free media fractions. Finally, we show that the truncated LRP10splice protein binds to wild-type LRP10, reduces LRP10 wild-type levels, and antagonises the regulatory effect of LRP10 on α-synuclein levels and distribution. Together, this work provides initial evidence for a functional role of LRP10 in LBDs by regulating intra- and extracellular α-synuclein levels, and pathogenic mechanisms linked to the disease-associated c.1424+5G>A LRP10 variant, pointing towards potentially important disease mechanisms in LBDs.
Investigating the developmental onset of regenerative potential in the annelid Capitella teleta

An animal’s ability to regrow lost tissues or structures can vary greatly during its life cycle. The annelid Capitella teleta exhibits posterior, but not anterior, regeneration as juveniles and adults. In contrast, embryos display only limited replacement of specific tissues. To investigate when during development C. teleta becomes capable of regeneration, we assessed the extent to which larvae can regenerate. We hypothesized that larvae exhibit intermediate regeneration potential and demonstrate some features of juvenile regeneration, but do not successfully replace all lost structures. Both anterior and posterior regeneration potential of larvae were evaluated following amputation. Wound sites were analyzed for re-epithelialization, cell proliferation by EdU incorporation, stem cell and differentiation marker expression by in situ hybridization, presence of neurites and muscle fibers by immunohistochemistry and phalloidin staining respectively, and regrowth of structures. Wound healing occurred within 6 hours of amputation for both anterior and posterior amputations. Cell proliferation at both wound sites was observed for up to 7 days following amputation. In addition, the stem cell marker vasa was expressed at anterior and posterior wound sites. However, growth of new tissue was observed only in posterior amputations. Neurites from the ventral nerve cord were also observed at posterior wound sites. De novo ash expression in the ectoderm of anterior wound sites indicated neuronal cell specification, although the absence of elav expression indicated an inability to progress to neuronal differentiation. In rare instances, cilia and eyes reformed. Both amputations induced expanded expression of the myogenesis gene MyoD in pre-existing tissues. Our results indicate that amputated larvae complete early, but not late, stages of regeneration, indicating a gradual acquisition of regenerative ability in C. teleta. Furthermore, amputated larvae can metamorphose into burrowing juveniles, including those missing brain and anterior sensory structures. To our knowledge, this is the first study to assess regenerative potential of annelid larvae.
Modulation of infraslow oscillation in the dentate gyrus during Non-REM sleep

The importance of sleep in memory consolidation is well-established, with the hippocampal CA1 and CA3 subregions playing a crucial role in this process. The current working hypothesis postulates that episodic memory traces captured during waking hours are replayed in the hippocampal CA1-CA3 areas and transferred to the cortex for long-term storage during sleep. While the entorhinal cortex provides sensory and spatial information primarily to the hippocampus via the dentate gyrus (DG), the DG has traditionally been regarded as a “silent partner” in memory consolidation. The transfer of captured memory traces from the DG to downstream hippocampal areas remains largely unknown. To investigate this, we used optical imaging tools to record neural activity in the DG during different sleep stages. Strikingly, we found that many of the DG cells are even more active during sleep than wakefulness and the populational activity in the DG slowly oscillates during non-REM (NREM) sleep. The cycles of this oscillatory activity coincided with microarousals and were tightly locked to brief serotonin (5-HT) bursts during NREM sleep. Pharmacological blockade of 5-HT1a receptors abolished the calcium oscillations in the DG. Furthermore, genetic knockdown of 5-HT1a receptors in the DG lead to memory impairment in spatial and contextual memory tasks. Together, our findings suggest that serotonin-driven infraslow calcium oscillations in the DG during NREM sleep are necessary for memory consolidation.
Decentralized Mixed Effects Modeling in COINSTAC

Performing group analysis on magnetic resonance imaging (MRI) data with linear mixed-effects (LME) models is challenging due to its large dimensionality and inherent multi-level covariance structure. In addition, as large-scale collaborative projects become commonplace in neuroimaging, data must increasingly be stored and analyzed from different locations. In such settings, substantial overhead can occur in terms of data transfer and coordination between participating research groups. In some cases, data cannot be pooled together due to privacy or regulatory concerns. In this work, we propose a decentralized LME model to perform a large-scale analysis of data from different collaborations without data pooling. This method is efficient as it overcomes the hurdles of data sharing and has lower bandwidth and memory requirements for analysis than the centralized modeling approach. We evaluate our model using features extracted from structural magnetic resonance imaging ( s MRI) data. Results highlight gray matter reductions in the temporal lobe/insula and medial frontal regions in schizophrenia, consistent with prior studies. Our analysis also demonstrates that decentralized LME models achieve similar performance compared to the models trained with all the data in one location. We also implement the decentralized LME approach in COINSTAC, an open source, decentralized platform for federating neuroimaging analysis, providing an easy to use tool for dissemination to the neuroimaging community.
Cul3 substrate adaptor SPOP targets Nup153 for degradation

SPOP is a Cul3 substrate adaptor responsible for degradation of many proteins related to cell growth and proliferation. Because mutation or misregulation of SPOP drives cancer progression, understanding the suite of SPOP substrates is important to understanding regulation of cell proliferation. Here, we identify Nup153, a component of the nuclear basket of the nuclear pore complex, as a novel substrate of SPOP. SPOP and Nup153 bind to each other and colocalize at the nuclear envelope and some nuclear foci in cells. The binding interaction between SPOP and Nup153 is complex and multivalent. Nup153 is ubiquitylated and degraded upon expression of SPOPWT but not its substrate binding-deficient mutant SPOPF102C. Depletion of SPOP via RNAi leads to Nup153 stabilization. Upon loss of SPOP, the nuclear envelope localization of spindle assembly checkpoint protein Mad1, which is tethered to the nuclear envelope by Nup153, is stronger. Altogether, our results demonstrate SPOP regulates Nup153 levels and expands our understanding of the role of SPOP in protein and cellular homeostasis.
DeSide: A unified deep learning approach for cellular decomposition of bulk tumors based on limited scRNA-seq data

Cellular decomposition employing bulk RNA-sequencing (RNA-seq) has been consistently under investigation due to its high fidelity, ease of use, and cost-effectiveness compared to single cell RNA-sequencing (scRNA-seq). However, the intricate nature of the tumor microenvironment, and the significant heterogeneity among patients and cells have made it challenging to precisely evaluate the cellular composition of solid tumors using a unified model. In this work, we developed DeSide, a deep learning and single-cell decomposition method for solid tumors, to estimate proportions of cell types presented in tumor samples. Our new deep neural network (DNN) architecture considers only non-cancerous cells during the training process, indirectly calculating the proportion of cancerous cells. This approach avoids directly handling the often more variable heterogeneity of cancerous cells, and instead leverages scRNA-seq data from three different cancer types to empower the DNN model with a robust generalization capability across diverse cancers. Additionally, we used a new sampling method and filtering strategies to simulate the gene expression profiles (GEPs) of solid tumors, creating a carefully controlled training set that could be compared to the bulk RNA-seq data from The Cancer Genome Atlas (TCGA), a database of bulk RNA-seq data collected from cancer patients. Relying on limited yet diverse scRNA-seq data, our approach outperformed current methods in accurately predicting the celluar composition of samples from TCGA and an additional validation set. Furthermore, we demonstrated that the predicted cellular composition can be utilized to stratify cancer patients into different groups with varying overall survival rates. With increased availability of scRNA-seq data for various types of tumors, DeSide holds the potential for a more precise cellular decomposition model using bulk RNA-seq.
Centromere Innovations Within a Mouse Species

Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying CENP-A nucleosomes at the nexus of a satellite repeat that we identified and term π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ∼6 Mbp of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance drives accumulation of microtubule-binding components of the kinetochore, as well as a microtubule-destabilizing kinesin of the inner centromere. The balance of pro and anti-microtubule-binding by the new centromere permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition. Teaser Chromatin and kinetochore alterations arise in response to evolutionarily rapid changes to underlying repetitive centromere DNA.
Chronic exposure of mice to phthalates enhances TGF beta signaling and promotes uterine fibrosis

Phthalates are synthetic chemicals widely used as plasticizers and stabilizers in various consumer products. Because of the extensive production and use of phthalates, humans are exposed to these chemicals daily. While most studies focus on a single phthalate, humans are exposed to a mixture of phthalates on a regular basis. The impact of continuous exposure to phthalate mixture on uterus is largely unknown. Thus, we conducted studies in which adult female mice were exposed for 6 months to 0.15 ppm and 1.5 ppm of a mixture of phthalates containing di(2-ethylhexyl) phthalate, di-iso-nonyl phthalate, benzyl butyl phthalate, di-n-butyl phthalate, diisobutyl phthalate, and diethyl phthalate via chow ad libitum. Our studies revealed that consumption of phthalate mixture at 0.15 ppm and 1.5 ppm for 6 months led to a significant increase in the thickness of the myometrial layer compared to control. Further investigation employing RNA-sequencing revealed an elevated transforming growth factor beta (TGF-β) signaling in the uteri of mice fed with phthalate mixture. TGF-β signaling is associated with the development of fibrosis, a consequence of excessive accumulation of extracellular matrix components, such as collagen fibers in a tissue. Consistent with this observation, we found a higher incidence of collagen deposition in uteri of mice exposed to phthalate mixture compared to unexposed controls. Second Harmonic Generation imaging showed disorganized collagen fibers and an increase in uterine stiffness upon exposure to phthalate mixture. Collectively, our results demonstrate that chronic exposure to phthalate mixture can have adverse effects on uterine homeostasis.
Non-micellar ganglioside GM1 induces an instantaneous conformational change in Aβ42 leading to the modulation of the peptide amyloid-fibril pathway

Alzheimer’s disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies revealed that structural variation in Aβ fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate Aβ aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote Aβ fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on Aβ42amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a spontaneous change in the peptide secondary structure from random-coil to β-turn with subsequent generation of predominantly β-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 interacts with the amyloidogenic Aβ42 primary nucleus leading to a possible formation of GM1-modified Aβ42 fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between Aβ42 fibrils and GM1-tweaked Aβ42 aggregates. Moreover, GM1-modified Aβ42 aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of Aβ, Aβ40, and Aβ42.
A framework for ultra-low input spatial tissue proteomics

Spatial tissue proteomics combining microscopy-based cell phenotyping with ultra-sensitive mass spectrometry (MS)-based proteomics is an emerging and powerful concept for the study of cell function and heterogeneity in health and disease. However, optimized workflows that preserve morphological information for image-based phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected archival tissue, are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low input formalin-fixed, paraffin-embedded (FFPE) material. Benchmarking in the murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions with high quantitative reproducibility. Applied to human tonsil, we profiled 146 microregions including spatially defined T and B lymphocyte niches and quantified cell type specific markers, cytokines, immune cell regulators and transcription factors. These rich data also highlighted proteome dynamics in spatially defined zones of activated germinal centers, illuminating sites undergoing active B-cell proliferation and somatic hypermutation. Our results demonstrate the power of spatially-resolved proteomics for tissue phenotyping by integrating high-content imaging, laser microdissection, and ultra-sensitive mass spectrometry. This approach has broad implications for a wide range of biomedical applications, including early disease profiling, drug target discovery and biomarker research.
RETAD: Vehicle Trajectory Anomaly Detection Based on Reconstruction Error

Due to the rapid advancement of wireless sensor and location technologies, a large amount of mobile agent trajectory data has become available. Intelligent city systems and video surveillance all benefit from trajectory anomaly detection. The authors propose an unsupervised reconstruction error-based trajectory anomaly detection (RETAD) method for vehicles to address the issues of conventional anomaly detection, which include difficulty extracting features, are susceptible to overfitting, and have a poor anomaly detection effect. RETAD reconstructs the original vehicle trajectories through an autoencoder based on recurrent neural networks. The model obtains moving patterns of normal trajectories by eliminating the gap between the reconstruction results and the initial inputs. Anomalous trajectories are defined as those with a reconstruction error larger than anomaly threshold. Experimental results demonstrate that the effectiveness of RETAD in detecting anomalies is superior to traditional distance-based, density-based, and machine learning classification algorithms on multiple metrics.
Longshot: Indexing Growing Databases using MPC and Differential Privacy

In this work, we propose Longshot, a novel design for secure outsourced database systems that supports ad-hoc queries through the use of secure multi-party computation and differential privacy. By combining these two techniques, we build and maintain data structures (i.e., synopses, indexes, and stores) that improve query execution efficiency while maintaining strong privacy and security guarantees. As new data records are uploaded by data owners, these data structures are continually updated by Longshot using novel algorithms that leverage bounded information leakage to minimize the use of expensive cryptographic protocols. Furthermore, Long-shot organizes the data structures as a hierarchical tree based on when the update occurred, allowing for update strategies that provide logarithmic error over time. Through this approach, Longshot introduces a tunable three-way trade-off between privacy, accuracy, and efficiency. Our experimental results confirm that our optimizations are not only asymptotic improvements but also observable in practice. In particular, we see a 5x efficiency improvement to update our data structures even when the number of updates is less than 200. Moreover, the data structures significantly improve query runtimes over time, about ~10 3 x faster compared to the baseline after 20 updates.
New approach methods to improve human health risk assessment of thyroid hormone system disruption–a PARC project

Current test strategies to identify thyroid hormone (TH) system disruptors are inadequate for conducting robust chemical risk assessment required for regulation. The tests rely heavily on histopathological changes in rodent thyroid glands or measuring changes in systemic TH levels, but they lack specific new approach methodologies (NAMs) that can adequately detect TH-mediated effects. Such alternative test methods are needed to infer a causal relationship between molecular initiating events and adverse outcomes such as perturbed brain development. Although some NAMs that are relevant for TH system disruption are available–and are currently in the process of regulatory validation–there is still a need to develop more extensive alternative test batteries to cover the range of potential key events along the causal pathway between initial chemical disruption and adverse outcomes in humans. This project, funded under the Partnership for the Assessment of Risk from Chemicals (PARC) initiative, aims to facilitate the development of NAMs that are specific for TH system disruption by characterizing in vivo mechanisms of action that can be targeted by in embryo/in vitro/in silico/in chemico testing strategies. We will develop and improve human-relevant in vitro test systems to capture effects on important areas of the TH system. Furthermore, we will elaborate on important species differences in TH system disruption by incorporating non-mammalian vertebrate test species alongside classical laboratory rat species and human-derived in vitro assays.
Shifting the balance: soluble ADAM10 as a potential treatment for Alzheimer's disease

Introduction Accumulation of amyloid β in the brain is regarded as a key initiator of Alzheimer's disease pathology. Processing of the amyloid precursor protein (APP) in the amyloidogenic pathway yields neurotoxic amyloid β species. In the non-amyloidogenic pathway, APP is processed by membrane-bound ADAM10, the main α-secretase in the nervous system. Here we present a new enzymatic approach for the potential treatment of Alzheimer's disease using a soluble form of ADAM10. Methods The ability of the soluble ADAM10 to shed overexpressed and endogenous APP was determined with an ADAM10 knockout cell line and a human neuroblastoma cell line, respectively. We further examined its effect on amyloid β aggregation by thioflavin T fluorescence, HPLC, and confocal microscopy. Using N-terminal and C-terminal enrichment proteomic approaches, we identified soluble ADAM10 substrates. Finally, a truncated soluble ADAM10, based on the catalytic domain, was expressed in Escherichia coli for the first time, and its activity was evaluated. Results The soluble enzyme hydrolyzes APP and releases the neuroprotective soluble APPα when exogenously added to cell cultures. The soluble ADAM10 inhibits the formation and aggregation of characteristic amyloid β extracellular neuronal aggregates. The proteomic investigation identified new and verified known substrates, such as VGF and N-cadherin, respectively. The truncated variant also exhibited α-secretase capacity as shown with a specific ADAM10 fluorescent substrate in addition to shedding overexpressed and endogenous APP. Discussion Our in vitro study demonstrates that exogenous treatment with a soluble variant of ADAM10 would shift the balance toward the non-amyloidogenic pathway, thus utilizing its natural neuroprotective effect and inhibiting the main neurotoxic amyloid β species. The potential of such a treatment for Alzheimer's disease needs to be further evaluated in vivo.