Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 901 records · Page 50Linked to original sources

bioRxiv2024

CellSexID: Sex-Based Computational Tracking of Cellular Origins in Chimeric Models

Cell tracking in chimeric models is essential yet challenging, particularly in developmental biology, regenerative medicine, and transplantation research. Existing methods such as fluorescent labeling and genetic barcoding are technically demanding, costly, and often impractical for dynamic or heterogeneous tissues. Here, we introduce CellSexID, a computational framework that leverages sex as a surrogate marker for cell origin inference. Using a machine learning model trained on single-cell transcriptomic data, CellSexID accurately predicts the sex of individual cells, enabling in silico distinction between donor and recipient cells in sex-mismatched settings. The model identifies minimal sex-linked gene sets through ensemble feature selection and has been validated using both public datasets and experimental flow sorting, confirming the biological relevance of predicted populations. We further demonstrate CellSexIDs applicability beyond chimeric models, including organ transplantation and multiplexed sample demultiplexing. As a scalable and cost-effective alternative to physical labeling, CellSexID facilitates precise cell tracking and supports diverse biomedical applications involving mixed cellular origins.

bioinformatics↗

bioRxiv2024

Ubiquitin Ligase ITCH Regulates Life Cycle of SARS-CoV-2 Virus

SARS-CoV-2 infection poses a major threat to public health, and understanding the mechanism of viral replication and virion release would help identify therapeutic targets and effective drugs for combating the virus. Herein, we identified E3 ubiquitin-protein ligase Itchy homolog (ITCH) as a central regulator of SARS-CoV-2 at multiple steps and processes. ITCH enhances the ubiquitination of viral envelope and membrane proteins and mutual interactions of structural proteins, thereby aiding in virion assembly. ITCH-mediated ubiquitination also enhances the interaction of viral proteins to the autophagosome receptor p62, promoting their autophagosome-dependent secretion. Additionally, ITCH disrupts the trafficking of the protease furin and the maturation of cathepsin L, thereby suppressing their activities in cleaving and destabilizing the viral spike protein. Furthermore, ITCH exhibits robust activation during the SARS-CoV-2 replication stage, and SARS-CoV-2 replication is significantly decreased by genetic or pharmacological inhibition of ITCH. These findings provide new insights into the mechanisms of the SARS-CoV-2 life cycle and identify a potential target for developing treatments for the virus-related diseases.

molecular biology↗

bioRxiv2024

Oral supplementation with Nicotinamide Riboside treatment protects RGCs in DBA/2J mouse model

PurposeThe aim of this study was to test whether oral administration of nicotinamide riboside (NR), the nicotinamide adenine dinucleotide (NAD+) precursors, protect retina ganglion cells (RGCs) from neurodegeneration in DBA/2J (D2) mice, which is a widely used mouse model of age-related inherited glaucoma. MethodOral NR or NAM administration (NR low dose: 1150mg/kg; NR high dose: 4200mg/kg; NAM low dose group: 500mg/kg; NAM high dose: 2000mg/kg of body weight per day) essentially started when D2 mice were 4 or 9 months old and continued up to 12 months old. Control cohort identically received food/water without NAM or NR. Intraocular pressure (IOP) was measured every month until experiment completion. Pattern electroretinography (PERG) was recorded. Retinas were harvested for whole mount immunofluorescence staining with RGCs marker Brn3a and imaged by fluorescent confocal microscopy. Optic nerves were harvested for axon staining and quantification. Retinal NAD+ levels were enzymatically assayed. ResultsNR oral supplementary treatment started at 4 months old robustly increased retinal NAD+ levels in D2 mice (NRHigh vs. vehicle: 273.7{+/-}23.59% vs. 108.70{+/-}12.10%, p<0.001). In aged vehicle group (12 months old), there was significantly diminution of the P1 and N2 components of PERG response compare with naive group (naive vs. vehicle: P1: 7.82{+/-} 0.70uV vs 1.63{+/-} 0.17uV, p<0.0001; N2: -13.29{+/-} 0.83uV vs. -3.22{+/-} 0.27uV, p<0.0001; Kruskal-Wallis test with Dunn s multiple comparison test). NR treatment preserved aged D2 visual function when mice were 9 and 12 months old. In addition, long-term NR high dose treatment significantly protected against total RGCs loss and optic nerve atrophy (RGC: NRHigh vs. vehicle: 1412{+/-}62.00vs 475.2{+/-}94.68 cells/field, p<0.00001; axon numbers: NRHigh vs. vehicle: 23990{+/-}1159 vs 8573{+/-}1160, n=41-53, p<0.0001). Furthermore, long-term NR supplementation prevent iris depigmentation and delayed IOP elevation. ConclusionNR oral supplementary treatment significantly preserved RGC and axon numbers, potentially preserves retinal function via elevated retinal NAD+ level in aged D2 mice. Interestingly, NR treatment also prevented iris atrophy, delayed IOP elevation associated with this glaucoma model. NR oral supplementation thus treated several aspects of murine pigment dispersion glaucoma. Given parallels between this model and glaucoma in human, out data indicate that NR is worth exploring as a therapeutic candidate in treatment of glaucoma.

neuroscience↗

bioRxiv2024

Structural and functional interrelationship of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis

Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR/Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationship between H2A and its variants H2A.Z and H2A.W. RNA-sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in the mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A is able to substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones derived from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and H2A variants in Arabidopsis.

plant biology↗

bioRxiv2024

CBAM-ResNet34-based classification and evaluation method for developmental processes of greenhouse strawberries

Strawberries, known for their economic significance and rich nutritional value, are cultivated extensively worldwide. However, a host of workers need to be employed every year to identify and categorize the developmental stages of the strawberries in the greenhouses, which is not only time-consuming, inefficient, increasing the cultivation cost, but also difficult to guarantee the classification accuracy. Meanwhile, affected by the complicated background, occlusions, and color interference, the features of strawberries are proven challenging to be extracted via the traditional neural networks due to serious gradient disappearance. Therefore, an improved CBAM-ResNet34- based classification evaluation method for developmental processes of greenhouse strawberries is investigated. The procedure of this method is as follows: firstly, the developmental stages of greenhouse strawberries are classified by experts into four stages: Stage I (initial stage), Stage II (green and white fruit stage), Stage III (early ripening stage), and Stage IV (fully ripe stage). The 627, 640, 604, and 340 strawberry images for these four stages are captured. Subsequently, the images are divided into training, validation, as well as testing sets and then undergo image pre- processing, expansion, and augmentation. Whereafter, the 7x7 convolution kernel in the first layer of the network is replaced by three consecutive 3x3 convolution cores to eliminate the redundant weights and unnecessary model parameters, and the BasicBlocks configuration is adjusted. Finally, the CBAM attention mechanism is added to each BasicBlock so as to pinpoint the spatial position of the strawberries and extract their major features such as shape, size, and color. Comparison experiments with the conventional deep neural networks LeNet5, AlexNet, VGG16, ResNet18, ResNet34, and every improved part of CBAM-ResNet34 demonstrated that when the learning rate is 0.001, the Dropout rate is 0.3, and the Adams weight decay parameter is 0.001, the accuracies for validation and testing sets can reach to 92.36% and 87.56% with F1 scores of 0.92, 0.87, 0.85 and 0.88.

plant biology↗

bioRxiv2024

Single-Cell full-length Isoform Sequencing Unveils Transcriptional Dysregulation in Autism Spectrum Disorder During Cerebral Cortex Development

Regulation of RNA splicing is pivotal in neural development, with established gene isoform expression patterns (1, 2). However, the specific roles of isoform diversity across cell types in both healthy and diseased brains warrant further investigation. Here, we employed a combination of metabolic RNA labeling using 4-thiouridine (4sU) and long-read sequencing based single-cell full-length transcriptome sequencing to capture newly synthesized transcripts within the developing mouse cortices. This approach allowed us to identify predetermined cell states supported by new RNAs and the driving isoforms of transcription factors that regulate the development of deep-and upper-layer neurons. Through detailed single-cell isoform expression analysis, we discovered novel cell type-specific isoforms and uncovered isoform switch events that modulate neuron differentiation. Additionally, we investigated isoform regulation associated with Autism Spectrum Disorder (ASD) during embryonic development of BTBR T+ Itpr3tf (BTBR) mice. Notably, our findings indicate a premature emergence of cortical projection neurons (CPNs) with an immature identity in ASD-affected cortices. These CPNs exhibit the highest degree of differential transcript usage (DTU), significantly overlapping with their cell type markers and being enriched in RNA splicing processes. Exon inclusion was significantly enriched in ASD and the related RNA binding proteins (RBPs) were extracted, nearly 60% of which have been reported as ASD risk genes. Lastly, we revealed a reduction in isoform diversity in ASD, potentially linked to H3K27ac dysregulation in the associated genes. Collectively, our study marks a substantial advancement in understanding the molecular basis of cortical development and function, paving the way for future studies on neurodevelopmental disorders.

developmental biology↗

bioRxiv2024

The DNA Mismatch repair protein, MSH6 is a novel regulator of PD-L1 expression

Immune checkpoint inhibitors (ICIs) are extremely effective in a subgroup of mismatch repair-deficient (MMRd) cancers, but [~]50% remain resistant to treatment. We have shown for the first time that this may be due to the differential regulation of factors linked to response to ICIs upon loss of the different MMR genes. Here, we show that increased PD-L1 expression is observed upon loss of the MMR genes MLH1, MSH2 and PMS2. However, this is not true upon loss of MSH6. Here, we show that this is due to a novel role for MSH6 as a direct regulator of PD-L1 transcription, dependent on recruitment by the histone trimethyltransferase SETD2. Next-generation sequencing of MLH1 and MSH6 knockout (KO) cells revealed that MSH6 KO cells have significantly lower microsatellite instability in comparison to MLH1 KO cells, despite MSH6 KO cells having a higher mutational burden. These findings emphasise the need for gene-specific stratification in the MMRd cohort.

cancer biology↗

bioRxiv2024

Disentangling cell type and state transcriptional programs

Single-cell omics approaches profile molecular constituents of individual cells. Replicated multi-condition experiments in particular aim at studying how the molecular makeup and composition of cell subpopulations changes at the sample-level. Two main approaches have been proposed for these tasks: firstly, cluster-based methods that group cells into (non-overlapping) subpopulations based on their molecular profiles and, secondly, cluster-free but neighborhood-based methods that identify (overlapping) groups of cells in consideration of cross-condition changes. In either approach, discrete cell groups are subjected to differential testing across conditions; and, a low-dimensional cell embedding, which is in turn derived from a subset of selected features, is required to delineate subpopulations or neighborhoods. We hypothesized that decoupling differences in cell type (i.e., between subpopulations) and cell state (i.e., between conditions) for feature selection would yield an embedding space that captures different aspects of cellular heterogeneity. And, that type-not-state embeddings would arrive at differential testing results that are more comparable between cluster- and neighborhood-based differential testing approaches. Our study leverages a simulation framework with competing type and state effects, as well as an experimental dataset, to evaluate a set of feature scoring and selection strategies, and to compare results from downstream differential analyses.

bioinformatics↗

bioRxiv2024

CEACAM1 Targets ABCA1 to Mediate Atrial Fibrillation via Lipophagy-Dependent Ferroptosis

Atrial fibrillation (AF) is one of the most common arrhythmias, imposing a significant burden on individuals due to its association with cerebrovascular events. The mechanisms underlying AF involve cardiac structural remodeling, electrical remodeling, and metabolic remodeling, with oxidative stress playing a crucial role. Our previous studies demonstrated that upregulation of CEACAM1 can increase oxidative stress, inhibit cell proliferation, and potentially contribute to cellular damage, while ferroptosis is closely associated with AF. In this study, we observed a significant increase in CEACAM1 expression in an AF model. Knocking out CEACAM1 revealed changes in mitochondrial membrane potential, reactive oxygen species (ROS) levels, intracellular Ca2+ concentration, channel proteins, and glycolipid metabolic enzymes. This knockout reversed electrical, structural, and metabolic remodeling in AF. Further investigation showed that CEACAM1 knockout inhibited ferroptosis, as evidenced by ferroptosis-related indicators. Using colocalization analyses of lipid droplets, lysosomes, and autophagosomes, we discovered that CEACAM1 knockout suppressed autophagy and lipophagy during AF. Supplementation with free fatty acids (FFAs) in the AF model post-CEACAM1 knockout suggested that the inhibition of ferroptosis was linked to a reduction in FFAs. Transcriptomic and non-targeted metabolomic analyses, along with ABCA1 interference studies, indicated that CEACAM1 knockout mitigates AF by promoting ABCA1 expression. In summary, CEACAM1 targets ABCA1 to alleviate AF through the regulation of lipophagy-dependent ferroptosis, as demonstrated in both cellular and animal models. BackgroundFerroptosis is a regulated form of cell death, but its connection with atrial fibrillation(AF) remains unclear. Since CEACAM1 knockout reduces oxidative stress and protects cells, we investigated the relationship among CEACAM1, ferroptosis, and AF to uncover the regulatory mechanisms of ferroptosis in AF. MethodsWe established AF models using HL-1 cells, human pluripotent stem cells, and rats. CEACAM1 expression levels were assessed in these models, along with changes in mitochondrial membrane potential, ROS levels, intracellular Ca2+ concentration, channel proteins, glycolipid metabolic enzymes, and ferroptosis-related indicators following CEACAM1 knockout. Through transcriptomics, non-target metabolomics, and immunoprecipitation screening, we identified ABCA1 as a downstream gene of CEACAM1 involved in protecting against AF. Subsequently, ABCA1 interference experiments were conducted, and colocalization analyses of lipid droplets, lysosomes, and autophagosomes were performed after the application of ferroptosis activators, lipophagy inhibitors, and lipophagy activators. FFAs were added to the AF model to evaluate changes in lipophagy and ferroptosis following CEACAM1 knockout. ResultsIn the AF model using HL-1 myocytes, CEACAM1 knockout reverse electrical, structural, and metabolic remodeling while inhibiting ferroptosis, with ABCA1 as a downstream gene. In the AF model derived from pluripotent stem cells differentiated into atrial myocytes, CEACAM1 knockout suppressed autophagy and lipophagy during AF, thereby inhibiting ferroptosis, which correlated with reduced FFA release. This process was regulated by ABCA1. In the rat AF model, ABCA1, identified as a downstream gene of CEACAM1, was further confirmed to inhibit ferroptosis by regulating FFA levels. ConclusionThis study reveals that CEACAM1 knockout inhibits ferroptosis in AF models by upregulating ABCA1 and reducing FFA levels, providing a novel regulatory mechanism for ferroptosis in AF. O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/625561v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@809c82org.highwire.dtl.DTLVardef@1a339d6org.highwire.dtl.DTLVardef@12a20d4org.highwire.dtl.DTLVardef@d14927_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Combining Glycosidases and Nanopore Technology for Glycan Sequencing

The efficient characterization of glycan structures remains a critical challenge. Direct glycan sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose a glycan sequencing strategy based on glycosidase -assisted nanopore sensing. We used engineered nanopore -hemolysin (M113R/T115A), which provided high-resolution discrimination of monosaccharide volume differences and sensitivity to variations in glycan chain length. By utilizing the specificity of glycosidases, we sequentially hydrolyzed the terminal residues of the glycan chains and detected the characteristic shifts in electrical signals generated by the translocation of hydrolysis products. The accuracy of recognition of hydrolysis fragments achieved over 90 % using machine learning. This allowed us to efficiently and conveniently determine the sequence of consecutive monosaccharide units in the glycan chains. Based on this principle, we conducted a proof-of-concept demonstration on actual samples and verified the accuracy via HPLC-MS. We achieved the sequencing of consecutive units in glycan chains, confirming the theoretical feasibility of glycosidase -assisted nanopore glycan sequencing. With future optimization, the development of arrayed nanopore glycan sequencing technology based on hydrolysis strategy will provide an innovative approach for rapid decoding of glycans, which could promote the progress of glycomics research and glycobiology.

biochemistry↗

bioRxiv2024

Structural insights into cholesterol sensing by the LYCHOS-mTORC1 pathway

The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cellular metabolism and growth by coordinating nutrient resources, including cholesterol, and its aberrant activation is linked to various age-related diseases. LYCHOS is a cholesterol sensor on the lysosome and bound to the GATOR1 complex, a GTPase-activating protein for the Rag GTPase, at high cholesterol concentrations, thereby activating the protein kinase mTORC1. However, how LYCHOS senses cholesterol and transduces signal to GATOR1 remain largely unknown. Here we report six cryo-electron microscopy structures of human LYCHOS, depicting five distinct states. These are categorized into a contracted state when complexed with a sufficient amount of the cholesterol analogue cholesteryl hemisuccinate (CHS), and an expanded state when CHS is deficient. The structure forms a homodimer, within each monomer the transmembrane region is divided into a permease-like domain (PLD) and a GPCR-like domain (GLD) with two clearly defined adjacent cholesterol binding sites between them. The PLD shares a conserved Na+/H+ antiporter (NhaA) fold, which much resembles plant auxin transporter PINs. Cholesterol locates between PLD and GLD and cholesterol binding induces a translation of GLD towards PLD and exposes the cytosolic extension of transmembrane 15, which mediates the interaction between LYCHOS and GATOR1. Strikingly, structure-guided mutations of Gly702 in GLD of LYCHOS increase its affinity for cholesterol, leading to sustained mTORC1 activation in cells. This indicates that LYCHOSs moderate affinity for cholesterol is crucial as a cholesterol sensor. Our results not only showed a solute carrier mechanistically coordinates a GPCR domain, elucidating the structural mechanism of cholesterol sensing by the mTORC1 pathway on the lysosome; but also provides a structural basis for developing inhibitors that selectively target to mTORC1 pathway to treat age-related diseases by blocking LYCHOS in its expanded state.

biochemistry↗

bioRxiv2024

The Bacteria of a Fig Microcommunity

Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria, Bacteroidota, and Actinobacteriota. Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia, Ochobactrum, and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes. ImportanceUnraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata, a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.

ecology↗

bioRxiv2024

CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models

In recent years, cell segmentation techniques have played a critical role in the analysis of biological images, especially for quantitative studies. Deep learning-based cell segmentation models have demonstrated remarkable performance in segmenting cell and nucleus boundaries, however, they are typically tailored to specific modalities or require manual tuning of hyperparameters, limiting their generalizability to unseen data. Comprehensive datasets that support both the training of universal models and the evaluation of various segmentation techniques are essential for overcoming these limitations and promoting the development of more versatile cell segmentation solutions. Here, we present CellBinDB, a large-scale multimodal annotated dataset established for these purposes. CellBinDB contains more than 1,000 annotated images, each labeled to identify the boundaries of cells or nuclei, including 4,6-Diamidino-2-Phenylindole (DAPI), Single-stranded DNA (ssDNA), Hematoxylin and Eosin (H&E), and Multiplex Immunofluorescence (mIF) staining, covering over 30 normal and diseased tissue types from human and mouse samples. Based on CellBinDB, we benchmarked seven state-of-the-art and widely used cell segmentation technologies/methods, and further analyzed the effects of four cell morphology indicators and image gradient on the segmentation results.

cell biology↗

bioRxiv2024

Cancer-associated DAXX mutations reveal a critical role for ATRX localization in ALT suppression

To maintain genome stability, proliferating cells must enact a program of telomere maintenance. While most tumors maintain telomeres through the action of telomerase, a subset of tumors utilize a DNA-templated process termed Alternative Lengthening of Telomeres or ALT. ALT is associated with mutations in the ATRX/DAXX/H3.3 histone chaperone complex, which is responsible for deposition of non-replicative histone variant H3.3 at heterochromatic regions of the genome including telomeres. We wished to better understand the role DAXX plays in ALT suppression, and to determine which disease-associated DAXX mutations are unable to suppress ALT. To answer this question, we have leveraged the G292 cell line, in which ATRX is wild type but DAXX has undergone a fusion event with the non-canonical kinesin KIFC3. Restoration of wild-type DAXX in G292 localizes ATRX and abrogates ALT. Using this model system, we tested the ability of a panel of disease-associated DAXX missense variants to suppress ALT. Missense mutations in the ATRX binding domain, the histone binding domain, and the C-terminal SUMO interaction motif reduce the ability of DAXX to suppress ALT. Unexpectedly, we find that mutations in the DAXX histone binding domain lead to failure of ATRX localization. We conclude that a key function of DAXX in ALT suppression is the localization of ATRX to nuclear foci.

cancer biology↗

bioRxiv2024

Dual-timescale motor circuit dynamics underlies fast head exploratory behavior and efficient locomotion

Motor systems must balance flexibility and structure to enable efficient and adaptive movements. Traditional hierarchical descending models struggle to explain the intrinsic dynamism in natural behaviors. Here, we investigate the head exploratory behavior of Caenorhabditis elegans, a minimal system capable of intricate motor patterns. Using variational mode decomposition, we identified two distinct motor dynamics: slow rhythmic bends propagating along the body and fast, phase-specific head casts influencing directional bias. Combinatorial ablations of three types of cholinergic motor neurons, in conjunction with dynamical systems analysis, revealed their distinct and overlapping roles: RMD contributes to head casts, SMD sustains bending states, SMB and SMD enable slow rhythmic bending and head-body coupling. Collectively, these neurons form a central pattern generator (CPG) driving forward locomotion. In addition, RMD subgroups displayed unique calcium dynamics correlated with rapid head movements and slow transitions between behavior states. We propose that dual-proprioceptive feedback underlies these multi-timescale dynamics, with slow feedback coordinating rhythmic bending and fast feedback shaping head casts, thereby optimizing roaming efficiency. These findings highlight how intrinsic dynamics and structured composition emerge from highly interactive low-level circuits.

neuroscience↗

bioRxiv2024

SARM1 Activation Promotes Axonal Degeneration Via a Two-Step Liquid-to-Solid Phase Transition

SARM1 protein plays a central role in axonal degeneration, a key process in many neurodegenerative diseases and nerve injuries. It mediates this by depleting axonal NAD+ through its NADase activity, catalyzed by the TIR domain. Normally, this activity is kept in an inactive state and becomes activated in response to various neuronal damage signals. However, the molecular mechanism behind SARM1 activation, particularly how activation is restricted to damaged axons, remains to be fully elucidated. In this study, using a class of pyridine-containing compounds that induce SARM1-dependent cell death and axonal degeneration, we reveal a two-step process of SARM1 activation. The first step involves sub-lethal "priming" activation of SARM1 mediated by the NAD+ precursor NMN, leading to the formation of covalent conjugates between the hydrolyzed product of NAD+, adenosine diphosphate ribose (ADPR), and the compounds catalyzed by the intrinsic base exchange activity of SARM1. In the second step, these ADPR-conjugates act as molecular glues, promoting the formation of self-proliferating superhelical filaments. On these filaments, SARM1s TIR domains adopt an active NADase configuration. As the superhelical filaments rapidly reach their limit of solubility, they precipitate out of the liquid phase as condensates with stable, fully activated NAD hydrolysis activity. Interestingly, we found that a series of reported SARM1 inhibitors currently under clinical development, which target the TIR enzymatic domain, can paradoxically activate SARM1s NADase activity via this mechanism. These findings provide new insights into how SARM1 activation is spatially restricted to damaged axons and offer important implications for the development of therapeutics targeting SARM1.

molecular biology↗

bioRxiv2024

Oncogene-induced senescence and senescence-associated secretory phenotype (SASP) determine the efficacy of palbociclib in PIK3CA mutated colorectal cancer

Palbociclib is an excellent CDK4/6 inhibitor, but its clinical application is mainly limited to the treatment of advanced ER+/HR+ and HER2- breast cancer. Its efficacy in colorectal cancer (CRC) is evaluated in multiple trials and so far remains undetermined. We found that the PIK3CA-mutant CRC cells were insensitive to palbociclib treatment compared with the PIK3CA wild-type counterparts, and they were in an OIS (oncogene-induced senescence) state which was predisposed to a strong senescence-associated secretory phenotype (SASP) upon treatment. These senescent cells excessively secreted various SASP factors LCN2, and ultimately caused palbociclib-resistance via upregulation of EGFR in the non-senescent CRC cells. Importantly, a drug combination screen identified that erlotinib could synergize with palbociclib to overcome the SASP-induced resistance. Overall, we found that PIK3CA mutation-induced senescence compromised the efficacy of palbociclib treatment in CRC but co-targeting EGFR could minimize the OIS-associated side effects while preserving the beneficial effects.

cancer biology↗

bioRxiv2024

Sortilin C-terminal fragment deposition depicts tangle-related nonamyloid neuritic plaque growth in Alzheimers disease

Sortilin C-terminal fragments (sorfra) can co-deposit in {beta}-amyloid (A{beta}) plaques in human brain. However, sorfra plaques develop in the cerebrum with a spatiotemporal trajectory as of tauopathy. Here we examined sorfra pathogenesis relative to neuritic plaque evolution in the human brains with amyloid and tau pathologies converged in the neocortex and hippocampus. Sorfra plaques occurred in correlation with pTau/tangle, but not A{beta}, pathologies across cerebral regions, neighboring cortical/hippocampal areas, and along the sulcal valley to gyral hilltop transition. Sorfra plaques and neuritic plaques were matchable in location, shape and size between consecutive sections, and were colocalized in double-labeling preparations. Microscopical study and tissue clearance three-dimensional imaging revealed sorfra/A{beta} colocalized as well as independent plaques. Among the former, sorfra labeling correlated negatively to A{beta}/amyloid labeling and {beta}-secretase-1 labeling in dystrophic neurites. Sorfra plaques were depleted of microtubule-associated protein 2 (MAP2) labeled neuronal somata and dendrites, whereas normal looking MAP2/sortilin co-labeled profiles occurred nearby. Sorfra deposits were seen in astrocytes but not microglia around the plaques. Taken together, sorfra plaques are anatomically matchable to silver stained neuritic plaques. They develop with tangle-related somatodendritic degeneration, presenting as nonamyloid growth of the A{beta} plaques and formation of A{beta}-independent neuritic plaques during Alzheimers disease pathogenesis.

neuroscience↗